CHEMOENZYMATIC PROCESSES FOR PREPARATION OF

LEVETIRACETAM

RELATED APPLICATION

Benefit of priority is claimed to U.S. Provisional Patent Application Serial No. 60/959,209, to John Lloyd Tucker, Lan Xu, Weihong Yu, Robert William Scott and Lishan Zhao, filed on July 11, 2007, entitled "CHEMOENZYMATIC PROCESSES FOR PREPARATION OF LEVETIRACETAM." Where permitted, the subject matter of the- above mentioned application is incorporated by reference in its entirety.

Field Compounds and processes for preparing intermediates in the synthesis of levetiracetam and precursors of levetiracetam and related compounds are provided. Also provided are processes for the preparation of levetiracetam or a pharmaceutically acceptable salt thereof. Background Levetiracetam, is an agent useful in the treatment of epilepsy (see, e.g., U.S.

Patent No. 4,943,639; EP 162036; Gower et al., (1992) Eur. J. Pharmacol. 222:193-203; and Kasteleijn-Nolst Trenite et al., (1996) Epilepsy Res. 25:225-230) and is the biologically active compound (S)-α-ethyl-2-oxo-1-pyrrolidine acetamide. This compound is marketed under the trade name Keppra ^® by UCB Pharmaceuticals, Inc. Levetiracetam is a protective agent for the treatment and prevention of hypoxic and ischemic type aggressions of the central nervous system. It is used for the treatment of bipolar disorders, migraine, chronic or neuropathic pain, and also possesses anxiolytic activity.

Methods for synthesizing levetiracetam are currently categorized into two types of processes: resolution processes and asymmetric processes. Resolution processes involve either chromatographic separation techniques (see, e.g., U.S. 6,107,492; U.S. 6,124,473; and WO 2003/104480) or use stoichiometric amounts of chemical substances such as amine resolving agents (see, U.S. 4,943,639; and WO 2006/053441), acidic resolving agents (see, WO 2004/076416; and CN 1583721), chiral acids (WO 2006/103696), or a pantolactam derivative (Boschi et al., (2005) Tetrahedron Asym. 16:3739-3745). Such processes require excess chemicals and solvent, and result in loss of material.

Asymmetric processes for the synthesis of levetiracetam generate an asymmetric center or employ chiral starting materials. Synthetic processes that generate an asymmetric center include hydrogenation of esters using chiral catalysts (see, U.S. 6,713,635; U.S. 2003/0040631; WO 2001/064637; and WO 2002/26705), asymmetric alkylation (see WO 2003/104480), and asymmetric cyanohydrin formation (see, CN 1651410). Exemplary syntheses that utilize chiral starting materials include desulfurization of a chiral intermediate (see, GB 2225322), use of a chiral amino amide (see, U.S. 4,943,639; U.S. 6,784,197; U.S. 2003/0120080; WO 2001/062726; WO 2004/069796; WO 2005/028435; and Sarma et al., (2006) Eur. J. Org. Chem. 16:3730- 3737), use of a chiral amino acid (see, U.S. 2005/0182262), use of a chiral amino alcohol (WO 2006/095362), use of a chiral carboxylic acid (see, WO 2006/127300), use of a chiral diol (see, Kotkar et al., (2006) Tetrahedron Let., 47:6813-6815), or use of a chiral amino ester (see, WO 2006/090265). Such processes involve expensive starting materials or reagents, or require numerous synthetic steps. Hence, a need exists for an efficient, cost effective and safe method for the large- scale synthesis of levetiracetam. Accordingly, among the objects herein, it is an object to provide methods for synthesis of levetiracetam or a pharmaceutically acceptable salt thereof.

Summary Provided are methods for the preparation of levetiracetam, (S)-α-ethyl-2-oxo-1- pyrrolidine acetamide:

Also provided are methods for synthesis of racemic and enantiomerically enriched intermediates for the synthesis of levetiracetam and related compounds. Provided are methods for the synthesis of levetiracetam and related compounds that employ a nitrile hydratase enzyme. The methods provided herein use nitrile hydratases to catalyze the conversion of a nitrile substrate to an amide product.

Provided are transformants that express nitrile hydratase. Also provided are methods to produce nitrile hydratase enzymes in a recombinant host. Also provided are

methods to convert a nitrile to the corresponding amide using a transformed host cell expressing a nitrile hydratase. Also provided are methods to convert a nitrile to the corresponding amide using cellular lysate of a transformed host cell that expresses a nitrile hydratase.

Provided herein is a process for the preparation of a compound of Formula IV:

and pharmaceutically acceptable salts thereof. The process includes the step of: (a) treating a compound of Formula III:

with an enzyme that converts a nitrile to an amide.

R ¹ is selected from among hydrogen, C ₁ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl, aryl and heteroaryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl and heteroaryl are optionally substituted. R ² is selected from among hydrogen, F, Cl, Br, I, CN, NO ₂ , OR', SR', SOR',

SO ₂ R', CO ₂ R', NR'R", C(=O)NR'R", NR'C(=O)R", C ₁ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl, aryl and heteroaryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl and heteroaryl are optionally substituted. R' and R" each independently is selected from among hydrogen, C ₁ -C ₈ alkyl, C ₂ -

C ₈ alkenyl, C ₂ -C ₈ alkynyl, C ₁ -C ₈ haloalkyl, C ₁ -C ₈ heteroalkyl, heteroaryl and aryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, heteroaryl and aryl are optionally substituted.

A is selected from among oxygen, sulfur and NR'. n is an integer selected from among 1, 2, 3, 4 and 5 and m is an integer selected from among 0, 1 , 2, 3, 4, 5, 6, 7 and 8.

For any and all of the embodiments, substituents can be selected from among a subset of the listed alternatives. For example, in some embodiments R ¹ is selected from among C ₂ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl having 1-5 heteroatoms selected from among O, N, S and P, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl having 1-5 heteroatoms selected from among O, N, S and P, phenyl and benzyl.

R ² is selected from among hydrogen, F, Cl, Br, I, CN, NO ₂ , C ₂ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl having 1-5 heteroatoms selected from among O, N, S and P, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl having 1-5 heteroatoms selected from among O, N, S and P, phenyl and benzyl.

A is oxygen or sulfur. n is an integer selected from among 1 , 2 and 3 and m is an integer selected from among 0, 1, 2, 3, 4, 5 and 6.

In some embodiments, R ¹ is selected from among C ₂ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ - C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl having 1-5 heteroatoms selected from among O, N, S and P, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl having 1 -5 heteroatoms selected from among O, N, S and P, phenyl and benzyl wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, phenyl and benzyl are optionally substituted with a substituent selected from among halo, hydroxy, amino, cyano, nitro, alkylamido, acyl, C ₁ -C ₆ -alkoxy, C ₁ -C ₆ -alkyl, C ₁ -C ₆ -haloalkyl, C ₁ -C ₆ - hydroxy-alkyl, C ₁ -C ₆ -aminoalkyl, C ₁ -C ₆ -alkylamino, alkylsulfenyl, alkylsulfinyl, alkylsulfonyl, sulfamoyl and trifluoromethyl;

R ² is selected from among hydrogen, C ₂ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl having 1-5 heteroatoms selected from among O, N, S and P, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl having 1-5 heteroatoms selected from among O, N, S and P, phenyl and benzyl wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, phenyl and benzyl are optionally substituted with a substituent selected from among halo, hydroxy, amino, cyano, nitro, alkylamido, acyl, C ₁ -C ₆ -alkoxy, C ₁ -C ₆ -alkyl, C ₁ -C ₆ -haloalkyl, C ₁ -C ₆ -hydroxy-alkyl, C ₁ -C ₆ - aminoalkyl, C ₁ -C ₆ -alkylamino, alkylsulfenyl, alkylsulfinyl, alkylsulfonyl, sulfamoyl and trifluoromethyl;

A is oxygen; n is 1 ; and m is 0 or 1.

In some embodiments, R ¹ is C ₂ -C ₆ alkyl; A is oxygen; n is 1; and m is 0. Provided herein are processes for producing compounds of Formula IV, wherein the process includes step (a) as defined above, and the enzyme of step (a) is a nitrile hydratase. Provided herein are processes for producing compounds of Formula IV, wherein the process includes step (a) as defined above, and the enzyme of step (a) is a nitrile hydratase and the nitrile hydratase is from an organism selected from among the genus Achromobacter, Acinetobacter, Aeromonas, Agrobacterium, Arthrobacter, Aurantimonas, Bacillus, Bacteridium, Bradyrhizobium, Brevibacterium, Burkholderia, Citrobacter, Comamonas, Corynebactehum, Enter obacter, Erwinia, Klebsiella, Micrococcus, Mycobacterium, Myrothecium, Nocardia, Pseudomonas, Pseudonocardia, Rhizobium, Rhodococcus, Silicibacter, Streptomyces, thermophilic Bacillus, and Xanthobacter.

Provided herein are processes for producing compounds of Formula IV, where the process includes step (a) as defined above, and the enzyme of step (a) is a nitrile hydratase that includes an α subunit or β subunit whose sequence of amino acid residues is set forth in any of SEQ ID NOS:2, 3, 5-49, 57, 58, 61, 62, 65, 69, 70, 71, 74, 75, 78, 79, 82 and 83. Also provided are processes for producing compounds of Formula IV, where the process includes step (a) as defined above, and the enzyme of step (a) is a modified nitrile hydratase. Any of the nitrile hydratases provided herein that can convert a compound of Formula III to a compound of Formula IV can be used in the methods provided herein.

Also provided are processes for producing compounds of Formula IV, where the process includes step (a) as defined above, and the enzyme of step (a) is a modified nitrile hydratase that contains a modification selected from among an amino acid replacement, an amino acid insertion and an amino acid deletion. The modified NHase polypeptide used in step (a) can have a conversion of 20% or more. The modified NHase polypeptide used in step (a) can have an SIR ratio of 4:1 or greater. The modified NHase polypeptide used in step (a) can have an E value greater than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more. The modified NHase polypeptides used in step (a) can have an E value greater than 4.5. The modified NHase can include a sequence of amino acid residues as set forth in any of SEQ ID NOS: 77-110. In some embodiments, the modified NHase has 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% homology to a nitrile hydratase

comprising a sequence of amino acid residues as set forth in any of SEQ ID NOS:57-59 and 77-110. In some embodiments, the modified NHase has 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% homology to a nitrile hydratase comprising a sequence of amino acid residues as set forth in any of SEQ ID NOS:2-49, 61-63, 65-67, 69-72 and 74-76.

Provided herein are processes for producing compounds of Formula IV, wherein the process includes step (a) as defined above, and the enzyme of step (a) is a nitrile hydratase whose sequence of nucleotide residues is set forth in SEQ ID NO:1. Also provided are processes for producing compounds of Formula IV, wherein the process includes step (a) as defined above, and the enzyme of step (a) is a nitrile hydratase whose sequence of nucleotide residues is set forth in any of SEQ ID NOS:56, 64, 68, 77 and 81. Also provided are processes for producing compounds of Formula IV, where the process includes step (a) as defined above, and the enzyme of step (a) is a nitrile hydratase that includes an α subunit or β subunit whose sequence of amino acid residues is set forth in any of SEQ ID NOS: 57, 58, 65, 66, 69-71, 78, 79, 82, 83 and 85-110.

Provided herein are processes for producing compounds of Formula IV, wherein the process includes step (a) as defined above, and the enzyme of step (a) is contained within a cell. Provided herein are processes for producing compounds of Formula IV, wherein the process includes step (a) as defined above, and the enzyme of step (a) is in a cell lysate.

Provided herein are processes for producing compounds of Formula IV, wherein the process includes step (a) as defined above, and the enzyme of step (a) is suspended or dissolved in an aqueous solvent. In some embodiments, the aqueous solvent comprises a buffer solution. In some embodiments, the buffer solution is selected from among a glutamic acid-glutamate buffer, a phosphoric acid-phosphate buffer, an acetic acid-acetate buffer and a citric acid-citrate buffer.

Provided herein are processes for producing compounds of Formula IV, wherein the process includes step (a) as defined above, and the enzyme of step (a) is suspended or dissolved in one or more organic solvents. Provided herein are processes for producing compounds of Formula IV, wherein the process includes step (a) as defined above, and the enzyme of step (a) is suspended or dissolved in a mixture of aqueous and organic

solvents. In some embodiments, the organic solvent is selected from among DMSO, acetone, THF, t-butanol, t-pentanol, dioxane, MTBE and combinations thereof.

Provided herein are processes for producing compounds of Formula IV, wherein the process includes step (a) as defined above, and the enzyme of step (a) is in solution or is immobilized on a solid support. In some embodiments, the solid support is selected from among glass, plastic, a film, nitrocellulose, a sol-gel polymer, celite and silica. Provided herein are processes for producing compounds of Formula IV, wherein the process includes step (a) as defined above, and the enzyme of step (a) is in a 2-phase system or in an emulsion. Provided herein is a process for producing a compound of Formula IV comprising step (a) as described above and further comprising the step:

(b) reacting a compound of Formula II:

with a nitrogen-containing a heterocycle of the following structure:

to afford a compound of Formula III:

R ¹ is selected from among hydrogen, C ₁ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl, aryl and heteroaryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl and heteroaryl are optionally substituted;

R ² each independently is selected from among hydrogen, F, Cl, Br, I, CN, NO ₂ , OR', SR', SOR', SO ₂ R', CO ₂ R', NR'R", C(=O)NR'R", NR'C(=O)R", C ₁ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈

heterocycloalkyl, aryl and heteroaryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl and heteroaryl are optionally substituted;

R' and R" each independently is selected from among hydrogen, C ₁ -C ₈ alkyl, C ₂ - C ₈ alkenyl, C ₂ -C ₈ alkynyl, C ₁ -C ₈ haloalkyl, C ₁ -C ₈ heteroalkyl, heteroaryl and aryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, heteroaryl and aryl are optionally substituted;

L is a leaving group selected from among OSO ₂ R ^a , I, Br, Cl, F, N ₂ ⁺ , O(R ^a ) ₂ ⁺ , ONO ₂ , OPO(OH) ₂ , OB(OH) ₂ , S(R ^a ) ₂ ⁺ and N(R ^a ) ₃ ⁺ ; each R ^a is independently selected from among hydrogen, C ₁ -C ₈ alkyl, C ₂ -C ₈ alkenyl, C ₂ -C ₈ alkynyl, C ₁ -C ₈ haloalkyl, C ₁ -C ₈ heteroalkyl, heteroaryl and aryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, heteroaryl and aryl are optionally substituted;

A is selected from among oxygen, sulfur and NR';

Y is selected from among hydrogen, lithium, sodium, potassium, cesium, calcium, magnesium and a pair of electrons where the nitrogen atom bears a negative charge; n is selected from among an integer of 1 , 2, 3, 4 and 5; and m is selected from among an integer of 0, 1, 2, 3, 4, 5, 6, 7 and 8.

For any and all of the embodiments, substituents can be selected from among a subset of the listed alternatives. For example, in some embodiments R ¹ is selected from among C ₂ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl having 1-5 heteroatoms selected from among O, N, S and P, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl having 1-5 heteroatoms selected from among O, N, S and P, phenyl and benzyl;

R ² each independently is selected from among hydrogen, F, Cl, Br, I, CN, NO ₂ , C ₂ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl having 1-5 heteroatoms selected from among O, N, S and P, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl having 1-5 heteroatoms selected from among O, N, S and P, phenyl and benzyl;

L is a leaving group selected from among OSO ₂ R ^a , I, Br, Cl and F; each R ^a is independently selected from among hydrogen, C ₁ -C ₈ alkyl, C ₁ -C ₈ haloalkyl, phenyl and benzyl;

A is oxygen or sulfur;

Y is selected from among hydrogen, lithium, sodium, potassium and cesium;

n is selected from among an integer of 1, 2 and 3; and m is selected from among an integer of 0, 1, 2, 3, 4, 5 and 6.

In some embodiments R ¹ is selected from among C ₂ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ - C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl having 1-5 heteroatoms selected from among O, N, S and P, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl having 1-5 heteroatoms selected from among O, N, S and P, phenyl and benzyl wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, phenyl and benzyl are optionally substituted with a substituent selected from among halo, hydroxy, amino, cyano, nitro, alkylamido, acyl, C ₁ -C ₆ -alkoxy, C ₁ -C ₆ -alkyl, C ₁ -C ₆ -haloalkyl, C ₁ -C ₆ - hydroxy- alkyl, C ₁ -C ₆ -aminoalkyl, C ₁ -C ₆ -alkylamino, alkylsulfenyl, alkylsulfinyl, alkylsulfonyl, sulfamoyl and trifluoromethyl;

R ² each independently is selected from among hydrogen, C ₂ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl having 1-5 heteroatoms selected from among O, N, S and P, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl having 1-5 heteroatoms selected from among O, N, S and P, phenyl and benzyl wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, phenyl and benzyl are optionally substituted with a substituent selected from among halo, hydroxy, amino, cyano, nitro, alkylamido, acyl, C ₁ -C ₆ -alkoxy, C ₁ -C ₆ -alkyl, C ₁ -C ₆ -haloalkyl, C ₁ -C ₆ - hydroxy-alkyl, d-C ₆ -aminoalkyl, C ₁ -C ₆ -alkylamino, alkylsulfenyl, alkylsulfinyl, alkylsulfonyl, sulfamoyl and trifluoromethyl;

L is a leaving group selected from among OSO ₂ Me, OSO ₂ C ₇ H ₇ , OSO ₂ C ₆ H ₅ , OSO ₂ CF ₃ , 1, Br, Cl and F;

Y is hydrogen;

A is oxygen; n is 1 ; and m is 0 or 1.

In some embodiments R ¹ is C ₂ -C ₆ alkyl; L is OSO ₂ C ₇ H ₇ or Cl; Y is hydrogen; A is oxygen; n is 1 ; and m is 0.

Provided herein is a process for producing a compound of Formula IV comprising steps (a) and (b) as described above, and further comprising the step:

(c) converting the hydroxyl group from a compound of Formula I:

to a leaving group (L) containing compound of Formula II:

R ¹ is selected from among hydrogen, C ₁ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl, aryl and heteroaryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl and heteroaryl are optionally substituted;

R each independently is selected from among hydrogen, F, Cl, Br, I, CN, NO ₂ , OR', SR', SOR', SO ₂ R', CO ₂ R', NR'R", C(=O)NR'R", NR'C(=O)R", C ,-C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl, aryl and heteroaryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl and heteroaryl are optionally substituted; R' and R" each independently is selected from among hydrogen, C ₁ -C ₈ alkyl, C ₂ - C ₈ alkenyl, C ₂ -C ₈ alkynyl, C ₁ -C ₈ haloalkyl, C ₁ -C ₈ heteroalkyl, heteroaryl and aryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, heteroaryl and aryl are optionally substituted;

L is a leaving group selected from among OSO ₂ R ^a , I, Br, Cl, F, N ₂ ⁺ , O(R ^a ) ₂ ⁺ , ONO ₂ , OPO(OH) ₂ , OB(OH) ₂ , S(R ^a ) ₂ ⁺ and N(R ^a ) ₃ ⁺ ; each R ^a is independently selected from among hydrogen, C ₁ -C ₈ alkyl, C ₂ -C ₈ alkenyl, C ₂ -C ₈ alkynyl, C ₁ -C ₈ haloalkyl, C ₁ -C ₈ heteroalkyl, heteroaryl and aryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, heteroaryl and aryl are optionally substituted;

A is selected from among oxygen, sulfur and NR';

Y is selected from among hydrogen, lithium, sodium, potassium, cesium, calcium, magnesium and a pair of electrons where the nitrogen atom bears a negative charge; n is selected from among an integer of 1, 2, 3, 4 and 5; and m is selected from among an integer of 0, 1 , 2, 3, 4, 5, 6, 7 and 8.

For any and all of the embodiments, substituents can be selected from among a subset of the listed alternatives.

Provided herein are processes for producing a compound of Formula IV, wherein the process includes step (c) as defined above, and the hydroxyl group is converted to a leaving group by reacting the compound of Formula I with toluenesulfonyl chloride, methanesulfonyl chloride, benzenesulfonyl chloride or trifluoromethanesulfonyl chloride to afford a compound of Formula II.

Provided herein is a process for producing a compound of Formula IV comprising step (a) as described above, and further comprising the step: (d) reacting a compound of Formula V:

with a base to afford a compound of Formula III:

R ¹ is selected from among hydrogen, C ₁ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl, aryl and heteroaryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl and heteroaryl are optionally substituted;

R ² each independently is selected from among hydrogen, F, Cl, Br, I, CN, NO ₂ , OR', SR', SOR', SO ₂ R', CO ₂ R', NR'R", C(=O)NR'R", NR'C(=O)R", C ₁ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl, aryl and heteroaryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl and heteroaryl are optionally substituted; R' and R" each independently is selected from among hydrogen, C ₁ -C ₈ alkyl, C ₂ - C ₈ alkenyl, C ₂ -C ₈ alkynyl, C ₁ -C ₈ haloalkyl, C ₁ -C ₈ heteroalkyl, heteroaryl and aryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, heteroaryl and aryl are optionally substituted;

L is a leaving group selected from among OSO ₂ R ^a , I, Br, Cl, F, N ₂ ⁺ , O(R ^a ) ₂ ⁺ , ONO ₂ , OPO(OH) ₂ , OB(OH) ₂ , S(R ^a ) ₂ ⁺ and N(R ^a ) ₃ ⁺ ; each R ^a is independently selected from among hydrogen, C ₁ -C ₈ alkyl, C ₂ -C ₈ alkenyl, C ₂ -C ₈ alkynyl, C ₁ -C ₈ haloalkyl, C ₁ -C ₈ heteroalkyl, heteroaryl and aryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, heteroaryl and aryl are optionally substituted;

A is selected from among oxygen, sulfur and NR';

Y is selected from among hydrogen, lithium, sodium, potassium, cesium, calcium, magnesium and a pair of electrons where the nitrogen atom bears a negative charge; n is selected from among an integer of 1, 2, 3, 4 and 5; and m is selected from among an integer of 0, 1, 2, 3, 4, 5, 6, 7 and 8.

For any and all of the embodiments, substituents can be selected from among a subset of the listed alternatives.

Provided herein are processes for producing a compound of Formula IV, wherein the process includes step (d) as defined above, and the base is selected from among sodium t-butoxide, potassium t-butoxide, lithium diisopropylamide, lithium hexamethyldisilazide, sodium hydride, potassium hydride, sodium methoxide, potassium methoxide, lithium methoxide, lithium t-butoxide, potassium carbonate, sodium carbonate, lithium carbonate, cesium carbonate and sodium ethoxide. Provided herein is a process for producing a compound of Formula IV comprising steps (a), (b), (c) and (d) as described above.

Provided herein is a process for producing Compound 4:

and pharmaceutically acceptable salts thereof. The process includes the step of: (i) treating Compound 3:

with an enzyme that converts a nitrile to an amide.

Provided herein are processes for producing Compound 4, wherein the process includes step (i) as defined above, and the enzyme of step (i) is a nitrile hydratase. Provided herein are processes for producing Compound 4, wherein the process includes step (i) as defined above, and the enzyme of step (i) is a nitrile hydratase and the nitrile hydratase is from an organism selected from among the genus Achromobacter, Acinetobacter, Aeromonas, Agrobacterium, Arthrobacter, Aurantimonas, Bacillus, Bacteridium, Bradyrhizobium, Brevibacterium, Burkholderia, Citrobacter, Comamonas, Corynebacterium, Enterobacter, Erwinia, Klebsiella, Micrococcus, Mycobacterium, Myrothecium, Nocardia, Pseudomonas, Pseudonocardia, Rhizobium, Rhodococcus, Silicibacter, Streptomyces, thermophilic Bacillus, and Xanthobacter.

Provided herein are processes for producing Compound 4, where the process includes step (i) as defined above, and the enzyme of step (i) is a nitrile hydratase that includes an α subunit or β subunit whose sequence of amino acid residues is set forth in any of SEQ ID NOS:2, 3, 5-49, 57, 58, 61, 62, 65, 66, 69, 70, 71, 74, 75, 78, 79, 82, 83 and 85-110. Also provided are processes for producing Compound 4, where the process includes step (i) as defined above, and the enzyme of step (i) is a modified nitrile hydratase. Also provided are processes for producing Compound 4, where the process includes step (i) as defined above, and the enzyme of step (i) is a modified nitrile hydratase that contains a modification selected from among an amino acid replacement, an amino acid insertion and an amino acid deletion. In some embodiments, the modified NHase polypeptide used in step (i) has a conversion of 20% or more. In some embodiments, the modified NHase polypeptide used in step (i) has an S/R ratio of 4:1 or greater. In some embodiments, the modified NHase polypeptide used in step (i) has an E value greater than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more. In some embodiments, the modified NHase polypeptides used in step (i) has an E value greater than 4.5. In some embodiments, the modified NHase includes a sequence of amino acid residues as set forth of SEQ ID NOS:2-49,57-59, 61-63, 65-67, 69-72, 74-76, 78-80 and 82-110. In some embodiments, the modified NHase has 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% homology to a nitrile hydratase comprising a sequence of amino acid residues as set forth in any of SEQ ID NOS:2-49,57-59, 61-63, 65-67, 69-72, 74-76, 78-80 and 82-110.

Provided herein are processes for producing Compound 4, wherein the process includes step (i) as defined above, and the enzyme of step (i) is a nitrile hydratase whose sequence of nucleotide residues is set forth in SEQ ID NO:1. Also provided are processes for producing Compound 4, wherein the process includes step (i) as defined above, and the enzyme of step (i) is a modified nitrile hydratase whose sequence of nucleotide residues is set forth in any of SEQ ID NOS:56, 64, 68, 77 and 81. Also provided are processes for producing Compound 4, where the process includes step (i) as defined above, and the enzyme of step (i) is a modified nitrile hydratase that includes an α subunit or β subunit whose sequence of amino acid residues is set forth in any of SEQ ID NOS: 57, 58, 65, 66, 69-71, 78, 79, 82, 83 and 85-110.

Provided herein are processes for producing Compound 4, wherein the process includes step (i) as defined above, and the enzyme of step (i) is contained within a cell. Provided herein are processes for producing Compound 4, wherein the process includes step (i) as defined above, and the enzyme of step (i) is in a cell lysate. Provided herein are processes for producing Compound 4, wherein the process includes step (i) as defined above, and the enzyme of step (i) is suspended or dissolved in an aqueous solvent. In some embodiments, the aqueous solvent comprises a buffer solution. In some embodiments, the buffer solution is selected from among a glutamic acid-glutamate buffer, a phosphoric acid-phosphate buffer, an acetic acid-acetate buffer and a citric acid-citrate buffer.

Provided herein are processes for producing Compound 4, wherein the process includes step (i) as defined above, and the enzyme of step (i) is suspended or dissolved in one or more organic solvents. Provided herein are processes for producing Compound 4, wherein the process includes step (i) as defined above, and the enzyme of step (i) is suspended or dissolved in a mixture of aqueous and organic solvents. In some embodiments, the organic solvent is selected from among DMSO, acetone, THF, t- butanol, t-pentanol, dioxane, MTBE and combinations thereof.

Provided herein are processes for producing Compound 4, wherein the process includes step (i) as defined above, and the enzyme of step (i) is in solution or is immobilized on a solid support. In some embodiments, the solid support is selected from among glass, plastic, a film, nitrocellulose, a sol-gel polymer, celite and silica. Provided herein are processes for producing Compound 4, wherein the process includes step (i) as

defined above, and the enzyme of step (i) is in a 2-phase system or in an emulsion.

Provided herein is a process for producing Compound 4, the process comprising step (i) as described above, and further comprising the step:

(ii) reacting Compound 2 ^a :

with 2-pyrrolidinone to afford Compound 3:

R ^a is selected from among hydrogen, C ₁ -C ₈ alkyl, C ₂ -C ₈ alkenyl, C ₂ -C ₈ alkynyl, C ₁ -C ₈ haloalkyl, C ₁ -C ₈ heteroalkyl, heteroaryl and aryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, heteroaryl and aryl are optionally substituted.

For any and all of the embodiments, substituents can be selected from among a subset of the listed alternatives.

Provided herein is a process for producing Compound 4, the process comprising step (i) as described above, and further comprising the step: (iii) reacting Compound 2 ^b :

with 2-pyrrolidinone to afford Compound 3:

X is halo. Provided herein is a process for producing Compound 4, the process comprising step (i), (ii) and/or step (iii) as described above, and further comprising the step: (iv) reacting Compound 1 :

with a sulfonyl halide to afford Compound 2 ^a :

R ^a is selected from among hydrogen, C ₁ -C ₈ alkyl, C ₁ -C ₈ haloalkyl and phenyl. For any and all of the embodiments, substituents can be selected from among a subset of the listed alternatives.

Provided herein are processes for producing Compound 4, wherein the process includes step (iv) as defined above, and the hydroxyl group is converted to a leaving group by reacting Compound 1 with toluenesulfonyl chloride, methanesulfonyl chloride, benzenesulfonyl chloride or trifluoromethanesulfonyl chloride to afford Compound 2 ^a . Provided herein is a process for producing Compound 4, the process comprising step (i) and (iii) as described above, and further comprising the step: (v) converting the hydroxyl group of Compound 1 :

to a halide group X of Compound 2 ^b :

where X is halo.

Provided herein are processes for producing Compound 4, wherein the process includes step (v) as defined above, and the hydroxyl group is converted to a leaving group by reacting Compound 1 with HBr, HCl, HI, SOCl ₂ , (COCl) ₂ , PCl ₅ , PCl ₃ , POCl ₃ , POBR ₃ , or PBr ₃ to afford Compound 2 ^b . Provided herein are processes for producing Compound 4, wherein the process includes step (v) as defined above, and the hydroxyl group is converted to a leaving group by reacting Compound 1 with NaX, KX, or NH ₄ X in a polyhydrogen fluoride-pyridine solution, where X is halo to afford Compound 2 ^b .

Provided herein is a process for producing Compound 4, the process comprising step (i) as described above, and further comprising the step: (vi) reacting Compound 5:

with a base to afford Compound 3:

Provided herein are processes for producing Compound 4, wherein the process includes step (vi) as defined above, and the base is selected from among sodium t- butoxide, potassium t-butoxide, lithium diisopropylamide, lithium hexamethyldisilazide, sodium hydride, potassium hydride, sodium methoxide, potassium methoxide, lithium methoxide, lithium t-butoxide, potassium carbonate, sodium carbonate, lithium carbonate, cesium carbonate and sodium ethoxide.

Provided herein is a process for producing Compound 4, the process comprising step (i), (ii), (iii), (iv) and/or (v), and further comprising step (vi) as described above. Also provided are articles of manufacture, containing packaging material, an intermediate compound as described herein or a pharmaceutically acceptable salt thereof, within the packaging material, and a label that indicates that the compound is used for the synthesis of levetiracetam.

Also provided are kits that include a nitrile hydratase and an intermediate compound as described herein, or salts, esters, acids and other derivatives of the intermediate compound.

Provided herein are modified nitrile hydratase (NHase) polypeptides. In some embodiments, the activities of a modified NHase polypeptide are altered compared to an unmodified NHase polypeptide. In particular, provided herein are modified NHase polypeptides that exhibit increased enantioselectivity and/or nitrile hydration activities. For example, modified NHase polypeptides provided herein can exhibit increased enantioselectivity for an S-amide product. In some examples, modified NHase

polypeptides provided herein can exhibit increased enantioselectivity for an R-amide product. In some examples, modified NHase polypeptides provided herein can exhibit increased rates of conversion of a nitrile substrate to the corresponding amide product. In some examples, modified NHase polypeptides provided herein can exhibit increased thermal stability.

The modified NHase polypeptides can include any combination of modifications provided herein, such that one or more activities or properties of the polypeptide are altered compared to an unmodified NHase polypeptide. Typically however, the modified NHase polypeptide retains its activity (hydration of a nitrile substrate to the corresponding amide product). Also provided herein are nucleic acid molecules, vectors and cells that encode or express modified NHase polypeptides. Articles of manufacture and kits including one or more modified NHase polypeptides and methods of using the modified NHase polypeptides also are provided.

Provided herein are NHase polypeptides, including allelic and species variant thereof or active fragments thereof, that contain a modification selected from among an amino acid replacement, an amino acid insertion and an amino acid deletion. Also provided herein are NHase polypeptides, including allelic and species variant thereof or active fragments thereof, that contain a modification that is at a position in an α subunit or in a β subunit, where the modification is an amino acid replacement. In some embodiments, the amino acid replacement is a conservative amino acid substitution. In some embodiments, the amino acid replacement replaces an amino acid in the polypeptide with a modified or unusual amino acid. In some embodiments the amino acid replacement replaces an amino acid of the polypeptide with a hydrophobic or acidic amino acid. The hydrophobic or acidic amino acid can be selected from among Ala (A), VaI (V), Leu (L), Ile (I), Phe (F), Trp (W), Met (M), Tyr (Y), Cys (C), Asp (D) and Glu (E).

In some instances, a modified NHase polypeptide contains two or more modifications in an NHase polypeptide, allelic and species variant thereof or active fragments thereof, wherein the two or more amino acid modifications are selected from among an amino acid replacement, an amino acid insertion, an amino acid deletion and combinations thereof.

In some instances, a modified NHase polypeptide contains two or more modifications in an NHase polypeptide, allelic and species variant thereof or active

fragments thereof, wherein the two or more amino acid modifications can be an amino acid replacement with a hydrophobic or acidic amino acid. The hydrophobic or acidic amino acid can be selected from among Ala (A), VaI (V), Leu (L), Ile (I), Phe (F), Trp (W), Met (M), Tyr (Y), Cys (C), Asp (D) and Glu (E). Also provided are modified NHase polypeptides that include two or more amino acid modifications, including amino acid substitutions where an amino acid residue is substituted with a conservative amino acid. In some embodiments, the two or more amino acid modifications include replacement of an amino acid residue with a modified or unusual amino acid. Such modified NHase polypeptides can contain 2, 3, 4, 5, 6 or 7 or more modifications. In some embodiments, provided is a modified NHase polypeptide wherein the number of amino acid positions replaced in an unmodified nitrile hydratase is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20.

Provided herein are modified nitrile hydratase polypeptides that exhibit increased selectivity, e.g., increased enantioselectivity, and/or increased activity for the hydration of nitriles to amides, compared to an unmodified nitrile hydratase polypeptide. Modified NHase polypeptides provided herein that exhibit increased selectivity, e.g., increased enantioselectivity, and/or increased activity for the hydration of nitriles to amides, include nitrile hydratase polypeptides modified at one or more amino acid positions compared to an unmodified nitrile hydratase polypeptides. Modified loci are identified with reference to a known unmodified nitrile hydratase polypeptides, such as a B. japonicum USDA 110 nitrile hydratase having a sequence of nucleic acids set forth in SEQ ID NO: 1, or any unmodified NHase polypeptide. Exemplary unmodified NHase polypeptides include an α subunit or β subunit whose sequence of amino acid residues is set forth in any of SEQ ID NOS:2-49. Modified nitrile hydratase polypeptides provided herein contain one or more amino acid replacements, deletions and/or insertions compared with the unmodified reference nitrile hydratase polypeptide. Exemplary modified NHase polypeptides have a sequence of nucleotide residues as set forth in any of SEQ ID NOS:56, 64, 68, 77 and 81. Also provided are modified nitrile hydratases that include an α subunit or β subunit whose sequence of amino acid residues is set forth in any of SEQ ID NOS: 57, 58, 65, 66 and 69-71 , 78, 79, 82, 83 and 85-110. Corresponding loci on other nitrile hydratase polypeptides, including truncated variants, species of nitrile hydratase polypeptides and allelic variants, readily can be identified. Furthermore, shortened or lengthened variants

with insertions or deletions of amino acids, particular at either terminus that retain an activity readily can be prepared and the loci for corresponding mutations identified.

Provided herein are modified nitrile hydratase polypeptides containing one or more amino acid replacements in an unmodified nitrile hydratase polypeptide. In one embodiment, the one or more amino acid replacements is in an α subunit. In one embodiment, the one or more amino acid replacements is in an β subunit. In some embodiments, the one or more amino acid replacements is in an α subunit and a β subunit. Such modified NHase polypeptides exhibit increased selectivity compared to the unmodified nitrile hydratase. In some embodiments, modified NHase polypeptides containing one or more amino acid replacements in an unmodified nitrile hydratase polypeptide results in a modified nitrile hydratase that exhibits increased enantioselectivity. In some embodiments, such modified NHase polypeptides exhibit increased selectivity for production of the S-amide product. In some embodiments, the modified NHase polypeptides have an S/R ratio of 4:1 or greater. In some instances, such modified NHase polypeptides also exhibit an increased activity compared to an unmodified nitrile hydratase polypeptide. In some embodiments, the modified NHase polypeptides have a conversion of 20% or more. In some embodiments, the modified NHase polypeptides have an E value greater than 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10 or more. In some embodiments, the modified NHase polypeptides have an E value greater than 4.5. Provided herein is a modified nitrile hydratase polypeptide that is a bacterial, fungal, or yeast nitrile hydratase polypeptide. In one embodiment, the modified NHase polypeptide is a bacterial NHase polypeptide. In another embodiment, the modified NHase is a fungal nitrile hydratase polypeptide. In another embodiment, the modified NHase polypeptide is a yeast nitrile hydratase polypeptide. Provided herein are any of the above modified nitrile hydratase polypeptides, wherein the one or more amino acid replacements are selected from among natural amino acids, non-natural amino acids and a combination of natural and non-natural amino acids. In one example, the polypeptide exhibits increased selectivity and/or activity by modification of only the primary sequence of the polypeptide. In one embodiment, the modified nitrile hydratase polypeptide is a polypeptide complex wherein the nitrile hydratase polypeptide has been pegylated, albuminated, or glycosylated.

Provided herein are a modified nitrile hydratase (NHase) polypeptides that include a modification in its β-subunit to have increase enantiomeric selectivity (E) for a compound of Formula III

compared to the NHase that does not comprise such modification, where the modification is a change in the primary structure of the NHase. The modification can be an amino acid replacement, an amino acid insertion and an amino acid deletion.

Also provided are modified nitrile hydratase (NHase) polypeptides that include a modification in an unmodified NHase polypeptide or active fragment thereof, where the NHase polypeptide contains a β-subunit and optionally an α-subunit; the β-subunit of the unmodified NHase polypeptide has a sequence of amino acids set forth in SEQ ID NO:58 or has at least about or at least 30% sequence identity to the sequence of amino acids set forth in SEQ ID NO: 58; and the modified NHase polypeptide exhibits NHase activity and increased enantioselectivity and/or nitrile hydration activity upon a substrate selected from among an oxopyrrolidinyl-alkylnitrile, oxopiperidinyl-alkylnitrile, thioxopyrrolidinyl-alkylnitrile and thioxopyrrolidinyl-alkylnitrile as compared to an unmodified NHase. In some embodiments, the β-subunit of the unmodified NHase polypeptide has a sequence of amino acids set forth in SEQ ID NO:58 or has 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to the sequence of amino acids set forth in SEQ ID NO: 58.

The modified NHase polypeptide can include a β-subunit that includes a sequence of amino acids set forth in SEQ ID NOS:12-18, 21 , 22, 25, 27-29, 31, 32, 34, 36, 40, 41, 44, 47, 49, 58, 62, 66, 70, 71, 75, 79 and 83. The β-subunit can be modified or unmodified, and can be from any nitrile hydratase that has activity on the desired substrate, such as an Achromobacter nitrile hydratase, Acinetobacter nitrile hydratase, Aeromonas nitrile hydratase, Agrobacterium nitrile hydratase, Arthrobacter nitrile hydratase, Aurantimonas nitrile hydratase. Bacillus nitrile hydratase, Bacteridium nitrile hydratase, Bradyrhizobium nitrile hydratase, Brevibacterium nitrile hydratase, Burkholderia nitrile hydratase, Citrobacter nitrile hydratase, Comamonas nitrile hydratase, Corynebacterium nitrile hydratase, Enterobacter nitrile hydratase, Erwinia

nitrile hydratase, Klebsiella nitrile hydratase, Micrococcus nitrile hydratase, Mycobacterium nitrile hydratase, Myrothecium nitrile hydratase, Nocardia nitrile hydratase, Pseudomonas nitrile hydratase, Pseudonocardia nitrile hydratase, Rhizobium nitrile hydratase, Rhodococcus nitrile hydratase, Silicibacter nitrile hydratase, Streptomyces nitrile hydratase, a thermophilic Bacillus nitrile hydratase, and a Xanthobacter nitrile hydratase.

Also provided are modified NHase polypeptides that exhibit increased enantioselectivity for production of an S-amide product.

Exemplary oxopyridinyl-alkylnitrile substrates include 2-(2-oxopyrrolidin-1- yl)butanenitrile, 2-(3-methyl-2-oxopyrrolidin-1-yl)butanenitrile, 2-(3-ethyl-2-oxo- pyrrolidin-1-yl)butanenitrile, 2-(3-propyl-2-oxopyrrolidin-1-yl)butanenitrile , 2-(3-butyl- 2-oxopyrrolidin-1-yl)butanenitrile, 2-(3 -isobutyl-2-oxopyrrolidin-1-yl)butanenitrile, 2-(4- methyl-2-oxopyrrolidin-1-yl)butanenitrile, 2-(4-ethyl-2-oxopyrrolidin-1-yl)butanenitrile, 2-(4-propyl-2-oxopyrrolidin-1-yl)butanenitrile , 4-(3-butyl-2-oxopyrrolidin-1-yl)butane- nitrile, 2-(4-isobutyl-2-oxopyrrolidin-1-yl)butanenitrile, 2-(2-methyl-5-oxopyrrolidin-1- yl)butanenitrile, 2-(2-ethyl-5-oxopyrrolidin-1-yl)butanenitrile, 2-(2-propyl-5-oxo- pyrrolidin-1-yl)butanenitrile , 2-(2-butyl-5-oxopyrrolidin-1-yl)butanenitrile, 2-(2- isobutyl-5-oxopyrrolidin-1-yl)butanenitrile, 3-methyl-2-(2-oxopyrrolidin-1- yl)butanenitrile, 3-methyl-2-(2-oxopyrrolidin-1-yl)pentanenitrile, 3-ethyl-2-(2- oxopyrrolidin-1-yl)-pentanenitrile, 3-ethyl-2-(2-methyl-5-oxopyrrolidin-1- yl)pentanenitrile, 3-ethyl-2-(4-methyl-2-oxopyrrolidin-1-yl)pentanenitrile, 3-ethyl-2-(3- methyl-2-oxopyrrolidin-1-yl)-pentanenitrile, 2-(2,3-dimethyl-5-oxopyrrolidin-1-yl)- butanenitrile, 2-(3,5-dimethyl-2-oxopyrrolidin-1-yl)butanenitrile, 2-(2-oxopyrrolidin-1- yl)acetonitrile, 2-(2-methyl-5-oxo-pyrrolidin-1-yl)acetonitrile, 2-(2,3-dimethyl-5-oxo- pyrrolidin-1-yl)acetonitrile, 2-(2,3,4-trimethyl-5-oxopyrrolidin-1-yl)acetonitrile, 2-(3,4- dimethyl-2-oxopyrrolidin-1-yl)-acetonitrile, 2-(3,5-dimethyl-2-oxopyrrolidin-1-yl)- acetonitrile, 2-(2,3,4-trimethyl-5-oxo-pyrrolidin-1-yl)butanenitrile, 2-(3,4-dimethyl-2- oxopyrrolidin-1-yl)butanenitrile and 2-(3,5-dimethyl-2-oxopyrrolidin-1-yl)butanenitrile, particularly 2-(2-oxopyrrolidin-1-yl)butanenitrile Exemplary oxopiperidinyl-alkylnitrile substrates include 2-(2-oxopiperidin-1-yl)- butanenitrile, 2-(3-methyl-2-oxopiperidin-1-yl)butanenitrile, 2-(3-ethyl-2- oxopiperidin-1- yl)butanenitrile, 2-(3-propyl-2- oxopiperidin-1-yl)butanenitrile , 2-(3-butyl-2-oxo-

piperidin-1-yl)butanenitrile, 2-(3-isobutyl-2- oxopiperidin-1-yl)butanenitrile, 2-(4-methyl- 2- oxopiperidin-1-yl)butanenitrile, 2-(4-ethyl-2- oxopiperidin-1-yl)butanenitrile, 2-(4- propyl-2-oxopiperidin-1-yl)butanenitrile , 4-(3-butyl-2-oxopiperidin-1-yl)butanenitrile, 2- (4-isobutyl-2-oxopiperidin-1-yl)butanenitrile, 2-(2-methyl-5-oxopiperidin-1-yl)butane- nitrile, 2-(2-ethyl-5-oxopiperidin-1-yl)butanenitrile, 2-(2-propyl-5-oxopiperidin-1-yl)- butanenitrile, 2-(2-butyl-5-oxopiperidin-1-yl)butanenitrile, 2-(2-isobutyl-5-oxopiperidin-1- yl)butanenitrile, 3-methyl-2-(2-oxopiperidin-1-yl)butanenitrile, 3-methyl-2-(2-oxo- piperidin-1-yl)pentanenitrile, 3-ethyl-2-(2-oxopiperidin-1-yl)pentanenitrile, 3-ethyl-2-(2- methyl-5-oxopiperidin-1-yl)pentanenitrile, 3-ethyl-2-(4-methyl-2-oxopiperidin-1-yl)- pentanenitrile, 3 -ethyl-2-(3 -methyl -2-oxopiperidin-1-yl)pentanenitrile, 2-(2,3-dimethyl-5- oxopiperidin-1-yl)butanenitrile, 2-(3,5-dimethyl-2-oxopiperidin-1-yl)butanenitrile, 2-(2- oxopiperidin-1-yl)acetonitrile, 2-(2-methyl-5-oxopiperidin-1-yl)acetonitrile, 2-(2,3- dimethyl-5-oxopiperidin-1-yl)acetonitrile, 2-(2,3,4-trimethyl-5-oxopiperidin-1-yl)- acetonitrile, 2-(3,4-dimethyl-2-oxopiperidin-1-yl)acetonitrile, 2-(3,5-dimethyl-2-oxo- piperidin-1-yl)acetonitrile, 2-(2,3,4-trimethyl-5-oxopiperidin-1-yl)butanenitrile, 2-(3,4- dimethyl-2-oxopiperidin-1-yl)butanenitrile, 2-(3,5-dimethyl-2-oxopiperidin-1-yl)butane- nitrile, 2-(2,3,4,6-tetramethyl-5-oxopiperidin-1-yl)butanenitrile, 2-(2,3,6-trimethyl-5- oxopiperidin-1-yl)butanenitrile, 2-(2,4,5-trimethyl-3-oxopiperidin-1-yl)butanenitrile, 2-(4- ethyl-3-methyl-5-oxopiperidin-1-yl)butanenitrile and 2-(4,5-diethyl-2-methyl-3-oxo- piperidin-1-yl)butanenitrile.

Exemplary thioxopyrrolidinyl-alkylnitrile substrates include 2-(2-thioxo- pyrrolidin-1-yl)butanenitrile, 2-(3-methyl-2-thioxopyrrolidin-1-yl)butanenitrile, 2-(3- ethyl-2-thioxopyrrolidin-1-yl)butanenitrile, 2-(3-propyl-2-thioxopyrrolidin-1-yl)butane- nitrile , 2-(3-butyl-2-thioxopyrrolidin-1-yl)butanenitrile, 2-(3-isobutyl-2-thioxopyrrolidin- 1 -yl)butanenitrile, 2-(4-methyl-2-thioxopyrrolidin-1-yl)butanenitrile, 2-(4-ethyl-2-thioxo- pyrrolidin-1-yl)butanenitrile, 2-(4-propyl-2-thioxopyrrolidin-1-yl)butanenitrile , 4-(3- butyl-2-thioxopyrrolidin-1-yl)butanenitrile, 2-(4-isobutyl-2-thioxopyrrolidin-1-yl)butane- nitrile, 2-(2-methyl-5-thioxopyrrolidin-1-yl)butanenitrile, 2-(2-ethyl-5-thioxopyrrolidin-1- yl)butanenitrile, 2-(2-propyl-5-thioxopyrrolidin-1-yl)butanenitrile , 2-(2-butyl-5-thioxo- pyrrolidin-1-yl)butanenitrile, 2-(2-isobutyl-5-thioxopyrrolidin-1-yl)butanenitrile, 3- methyl-2-(2-thioxopyrrolidin-1-yl)butanenitrile, 3-methyl-2-(2-thioxopyrrolidin-1-yl)- pentanenitrile, 3-ethyl-2-(2-thioxopyrrolidin-1-yl)pentanenitrile, 3-ethyl-2-(2-methyl-5-

thioxopyrrolidin-1-yl)pentanenitrile, 3-ethyl-2-(4-methyl-2-thioxopyrrolidin-1-yl)- pentanenitrile, 3-ethyl-2-(3-methyl-2-thioxopyrrolidin-1-yl)pentanenitrile, 2-(2,3- dimethyl-5-thioxopyrrolidin-1-yl)butanenitrile, 2-(3,5-dimethyl-2-thioxopyrrolidin-1- yl)butanenitrile, 2-(2-thioxopyrrolidin-1-yl)acetonitrile, 2-(2-methyl-5-thioxopyrrolidin- 1-yl)acetonitrile, 2-(2,3-dimethyl-5-thioxopyrrolidin-1-yl)acetonitrile, 2-(2,3,4-trimethyl- 5-thioxopyrrolidin-1-yl)acetonitrile, 2-(3,4-dimethyl-2-thioxopyrrolidin-1-yl)acetonitrile, 2-(3,5-dimethyl-2-thioxopyrrolidin-1-yl)acetonitrile, 2-(2,3,4-trimethyl-5-thioxo- pyrrolidin-1-yl)butanenitrile, 2-(3,4-dimethyl-2-thioxopyrrolidin-1-yl)butanenitrile and 2- (3,5-dimethyl-2-thioxopyrrolidin-1-yl)butanenitrile. Exemplary thioxopiperidinyl-alkylnitrile substrates include 2-(2-thioxopiperidin-

1 -yl)butanenitrile, 2-(3-methyl-2-thioxopiperidin-1-yl)butanenitrile, 2-(3-ethyl-2-thioxo- piperidin-1-yl)butanenitrile, 2-(3 -propyl -2- thioxopiperidin-1-yl)butanenitrile, 2-(3-butyl- 2- thioxopiperidin-1-yl)butanenitrile, 2-(3-isobutyl-2- thioxopiperidin-1-yl)butanenitrile, 2-(4-methyl-2-thioxopiperidin-1-yl)butanenitrile, 2-(4-ethyl-2-thioxopiperidin-1-yl)- butanenitrile, 2-(4-propyl-2-thioxopiperidin-1-yl)butanenitrile , 4-(3-butyl-2-thioxo- piperidin-1-yl)butanenitrile, 2-(4-isobutyl-2-thioxopiperidin-1-yl)butanenitrile, 2-(2- methyl-5-thioxopiperidin-1-yl)butanenitrile, 2-(2-ethyl-5-thioxopiperidin-1-yl)butane- nitrile, 2-(2-propyl-5-thioxopiperidin-1-yl)butanenitrile, 2-(2-butyl-5-thioxopiperidin-1- yl)butanenitrile, 2-(2-isobutyl-5-thioxopiperidin-1-yl)butanenitrile, 3-methyl-2-(2-thioxo- piperidin-1-yl)butanenitrile, 3-methyl-2-(2-thioxopiperidin-1-yl)pentanenitrile, 3-ethyl-2- (2-thioxopiperidin-1-yl)pentanenitrile, 3-ethyl-2-(2-methyl-5-thioxopiperidin-1- yl)pentanenitrile, 3-ethyl-2-(4-methyl-2-thioxopiperidin-l -yl)pentanenitrile, 3-ethyl-2-(3- methyl-2-thioxopiperidin-1-yl)pentanenitrile, 2-(2,3-dimethyl-5-thioxopiperidin-1- yl)butanenitrile, 2-(3,5-dimethyl-2-thioxopiperidin-1-yl)butanenitrile, 2-(2-thioxo- piperidin-1-yl)acetonitrile, 2-(2-methyl-5-thioxopiperidin-1-yl)acetonitrile, 2-(2,3- dimethyl-5-thioxopiperidin-1-yl)acetonitrile, 2-(2,3,4-trimethyl-5-thioxopiperidin-1- yl)acetonitrile, 2-(3,4-dimethyl-2-thioxopiperidin-1-yl)acetonitrile, 2-(3,5-dimethyl-2- thioxopiperidin-1-yl)acetonitrile, 2-(2,3,4-trimethyl-5-thioxopiperidin-1-yl)butanenitrile, 2-(3,4-dimethyl-2-thioxopiperidin-1-yl)butanenitrile, 2-(3,5-dimethyl-2-thioxopiperidin- 1-yl)butanenitrile, 2-(2,3,4,6-tetramethyl-5-thioxopiperidin-1-yl)butanenitrile, 2-(2,3,6- trimethyl-5-thioxopiperidin-1-yl)butanenitrile, 2-(2,4,5-trimethyl-3-thioxopiperidin-1-

yl)butanenitrile, 2-(4-ethyl-3-methyl-5-thioxopiperidin-1-yl)butanenitrile and 2-(4,5- diethyl-2-methyl-3-thioxopiperidin-1-yl)butanenitrile.

Among the modified NHase polypeptides provided herein are those that include an amino acid replacement at a position corresponding to a position selected from among 169, Y73, W143, P149, E191 and R193 of the α-subunit having a sequence of amino acids set forth in SEQ ID NO: 57 or at a corresponding position in an α-subunit that has 30%, 40%, 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to the sequence of amino acids set forth in SEQ ID NO: 57 and exhibits NHase activity. Also provided are modified NHase polypeptides that include an amino acid replacement in the β-subunit at a position corresponding to a position selected from among L34, V37, R38, G41, A42, A43, G44, A45, F46, N47, 148, S51, R55, F73, L74, G75, L76, V113, V116 and M117 of the β-subunit of a NHase having a sequence of amino acids set forth in SEQ ID NO:58. Also provided are modified NHase polypeptides that include an amino acid replacement in the β-subunit at a position corresponding to a position selected from among L34, V37, R38, A42, A43, G44, A45, N47, R55, F73, L74, G75, L76, V116 and M117 of the β-subunit of a NHase having a sequence of amino acids set forth in SEQ ID NO:58. In some embodiments, the modification is an amino acid replacement at a position corresponding to L34 and the replacement is with an acidic amino acid selected from Asp (D) aspartic acid and Glu (E) residue. In some embodiments, the modification is L34E.

Also provided are modified NHase polypeptides that include an amino acid replacement in the β-subunit at a position corresponding to R38 and the replacement is with a polar neutral amino acid selected from Gly (G), Ser (S), Thr (T), Cys (C), Tyr (Y), Asn (N), or Gln (Q). In some embodiments the modification is R38C.

Also provided are modified NHase polypeptides that include an amino acid replacement in the β-subunit at a position corresponding to G41 and the replacement is with a polar neutral amino acid selected from Ser (S), Thr (T), Cys (C), Tyr (Y), Asn (N), or Gln (Q). In some embodiments, the modification is G41 S.

Also provided are modified NHase polypeptides that include an amino acid replacement in the β-subunit at a position corresponding to A42 and the replacement is

with a polar neutral amino acid selected from Gly (G), Ser (S), Thr (T), Cys (C), Tyr (Y), Asn (N), or Gln (Q) or a nonpolar hydrophobic amino acid selected from among Leu (L), He (I), VaI (V), Pro (P), Phe (F), Trp (W) or Met (M). In some embodiments, the modification is selected from among A42T, A42V, A42L and A42M. Also provided are modified NHase polypeptides that include an amino acid replacement in the β-subunit at a position corresponding to A43 and the replacement is with a polar neutral amino acid selected from Gly (G), Ser (S), Thr (T), Cys (C), Tyr (Y), Asn (N), or Gln (Q) or a nonpolar hydrophobic amino acid selected from among Leu (L), He (I), VaI (V), Pro (P), Phe (F), Trp (W) or Met (M). In some embodiments, the modification is selected from among A43N, A43Q, A43S, A43G, A43T and A43M. Also provided are modified NHase polypeptides that include an amino acid replacement in the β-subunit at a position corresponding to L76 and the replacement is with a nonpolar hydrophobic amino acid selected from among Ala (A), Ile (I), VaI (V), Pro (P), Phe (F), Trp (W) or Met (M). In some embodiments, the modification is L76F or L76V.

Also provided are modified NHase polypeptides that include an amino acid replacement in the β-subunit at a position corresponding to V113 and the replacement is with a nonpolar hydrophobic amino acid selected from among Ala (A), Leu (L), Ile (I), Pro (P), Phe (F), Trp (W) or Met (M). In some embodiments, the modification is V113L. Also provided are modified NHase polypeptides that include an amino acid replacement in the β-subunit at a position selected from among L34, V37, R38, G41, A42, A43, G44, A45, F46, N47, 148, S51, R55, F73, L74, G75, L76, V113, V116 and M117 of the β-subunit of a NHase having a sequence of amino acids set forth in SEQ ID NO:58. In some embodiments, the modified NHase includes one or more further modification(s) selected from among L34D, L34E, R38G, R38S, R38T, R38C, R38Y, R38N, R38Q, G41S, G41T, G41C, G41Y, G41N, G41Q, A42G, A42S, A42T, A42C, A42Y, A42N, A42Q, A42L, A42I, A42V, A42P, A42F, A42W, A42M, A43G, A43S, A43T, A43C, A43Y, A43N, A43Q, A43L, A43I, A43V, A43P, A43F, A43W, A43M, L76A, L76I, L76V, L76P, L76F, L76W, L76M, V113L, V113 A, V1131, V113P, V113F, V113W and V113M. In some embodiments, the modified NHase includes one or more further modification(s) selected from among L34E, R38C, G41S, A42T, A42L, A42V, A42M, A43G, A43S, A43T, A43N, A43Q, A43M, L76F, L76V, and V113L.

Also provided are modified NHase polypeptides that include an amino acid modification in the β-subunit selected from among R38C/A42T, R38C/A42V, R38C/A42L, R38C/A42M, R38C/A43N, R38C/A43Q, R38C/A43S, R38C/A43G, R38C/L76F, R38C/L76V, R38C/V113L, R38C/A43T/V113L, R38C/G41S/A43Q/V113L, R38C/A43N/L76F, R38C/A43G/L76F, R38C/A42V/A43S/V113L,

R38C/A42V/A43Q/L76F, R38C/A43G/L76F/V113L, R38C/A42V/A43M/L76F/V113L, R38C/A42V/A43Q/L76F/V113L, R38C/A42L/A43Q/L76F/V113L, R38C/A42V/A43S/L76F/V113L, R38C/A43Q/L76F and R38C/A43M.

Also provided are modified NHase polypeptides that include an amino acid modification in the α-subunit at a position corresponding to a position selected from among 169, Y73, W143, P149, E191 and R193 of the α-subunit of a NHase having a sequence of amino acids set forth in SEQ ID NO:57 or at a corresponding position in an α-subunit that has 30%, 40%, 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to the sequence of amino acids set forth in SEQ ID NO: 57.

Also provided are modified NHase polypeptides that include a β-subunit that comprises a sequence of amino acid residues set forth in any of SEQ ID NOS: 85-110.

The modified NHase polypeptides provided herein can have an S/R ratio of product of 4:1 or greater. Also provided are modified NHase polypeptides that have an E value greater than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more when converting the substrate to an amide. In some embodiments, the E value is greater than 4.5.

Provided herein are any of the above modified nitrile hydratase polypeptides, in which the increased activity is manifested as an increased conversion of nitrile to amide. In one such embodiment, the modified nitrile hydratase has an activity increased by at least 5%, at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, at least 150%, at least 200%, at least 250%, at least 300%, at least 350%, at least 400%, at least 450% and at least 500% or more compared to the activity of unmodified nitrile hydratase. In another such embodiment, the modified nitrile hydratase has an activity increased by at least 1.5 times, 2 times, 3 times, 4 times, 5 times, 6 times, 7 times, 8 times, 9 times, 10 times, 20 times, 30 times, 40 times, 50 times, 60 times, 70 times, 80 times, 90 times, 100 times, 200 times,

300 times, 400 times, 500 times, 600 times, 700 times, 800 times, 900 times and 1000 times, or more times when compared to the activity of unmodified nitrile hydratase.

Activity can be assessed, for example, by measuring the conversion of a nitrile substrate to an amide. In one embodiment, the nitrile substrate is selected from among 2- hydroxypropanenitrile, 2-hydroxybutanenitrile, 2-hydroxypentanenitrile, hydroxy(phenyl)- ethanenitrile, hydroxy(4-methylphenyl)ethanenitrile, hydroxy(4-methoxyphenyl)- ethanenitrile, (4-chlorophenyl)(hydroxy)ethanenitrile and 2-(2-oxopyrrolidin-1- yl)butanenitrile. In one embodiment, the nitrile substrate is 2-(2-oxopyrrolidin-1- yl)butanenitrile. Also provided herein are modified nitrile hydratase polypeptides produced in bacterial cells, yeast cells, fungal cells, Archea, plant cells, insect cells and animal cells.

In some instances, the modified nitrile hydratase polypeptides are produced in E. coli. In other instances, the modified nitrile hydratase polypeptides are produced in Bacillus species. In other instances, the modified nitrile hydratase polypeptides are produced in yeast. In other instances, the modified nitrile hydratase polypeptides are produced in

Pichia species.

Provided herein are libraries (collections) of modified nitrile hydratase polypeptides containing two, three, four, five, six, 10, 50, 100, 200 or more modified nitrile hydratase polypeptides as described herein. Provided herein are nucleic acid molecules containing a sequence of nucleic acids encoding a modified nitrile hydratase polypeptide as described herein. Provided herein are libraries (collections) of nucleic acid molecules comprising a plurality of the molecules as described herein.

Provided herein are vectors comprising the nucleic acid molecules the encode modified NHase polypeptides. In one embodiment, the vectors are in bacterial cells, yeast cells, fungal cells, Archea, plant cells, insect cells and animal cells. Also provided herein are libraries containing a plurality of the vectors.

Provided herein are methods for expressing a modified nitrile hydratase comprising: i) introducing a nucleic acid encoding a modified nitrile hydratase or a vector containing a nucleic acid encoding a modified nitrile hydratase into a cell, and ii) culturing the cell under conditions in which the encoded modified nitrile hydratase is

expressed. In one embodiment, the vectors are in bacterial cells, yeast cells, fungal cells,

Archea, plant cells, insect cells and animal cells.

Brief Description of the Figures

Figure 1 depicts the modeled interaction between nitrile hydratase and the substrate 2-(2-oxopyrrolidin-1-yl)butanenitrile. The identified amino acid residues are those within approximately 10å of the substrate binding site.

Figure 2 depicts the modeled interaction between nitrile hydratase and the substrate 2-(2-oxopyrrolidin-1-yl)butanenitrile. The identified amino acid residues are those within approximately 15å of the substrate binding site. Detailed Description

A. Definitions

Unless specific definitions are provided, the nomenclature used in connection with, and the laboratory procedures and techniques of, analytical chemistry, biochemistry, synthetic organic chemistry, and medicinal and pharmaceutical chemistry described herein are those known in the art. All patents, patent applications and published materials referred to throughout the entire disclosure herein, unless noted otherwise, are incorporated by reference in their entirety for any purpose. In the event that there are a plurality of definitions for terms herein, those in this section prevail. Where reference is made to a URL or other such identifier or address, it understood that such identifiers can change and particular information on the internet can come and go, but equivalent information can be found by searching the internet. Reference thereto evidences the availability and public dissemination of such information.

It is to be understood that the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive of the subject matter claimed.

Standard techniques can be used for chemical syntheses, chemical analyses, pharmaceutical preparation, formulation and delivery, and treatment of subjects.

Standard techniques can be used for recombinant DNA, oligonucleotide synthesis, and tissue culture and transformation (e.g., electroporation, lipofection). Reactions and purification techniques can be performed e.g., using kits according to manufacturer's specifications or as commonly accomplished in the art or as described herein. The foregoing techniques and procedures generally are performed according to conventional

methods well known in the art and as described in various general and more specific references that are cited and discussed throughout the present specification (see, e.g. , Sambrook et al., Molecular Cloning: A Laboratory Manual, 2d ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989)). As used herein, the abbreviations for any protective groups, amino acids and other compounds are, unless indicated otherwise, in accord with their common usage, recognized abbreviations, or the IUPAC-IUB Commission on Biochemical Nomenclature (1972) Biochem., 11 :942-944.

As used herein, use of the singular includes the plural unless specifically stated otherwise.

As used herein, "or" means "and/or" unless stated otherwise. Furthermore, use of the term "including" as well as other forms, such as "includes," and "included," is not limiting.

As used herein, the terms "treating" or "treatment" encompass either or both responsive and prophylaxis measures, e.g., designed to inhibit, slow or delay the onset of a symptom of a disease or disorder, achieve a full or partial reduction of a symptom or disease state, and/or to alleviate, ameliorate, lessen, or cure a disease or disorder and/or its symptoms.

As used herein, amelioration of the symptoms of a particular disorder by administration of a particular compound or pharmaceutical composition refers to any lessening of severity, delay in onset, slowing of progression, or shortening of duration, whether permanent or temporary, lasting or transient that can be attributed to or associated with administration of the compound or composition.

As used herein, C ₁ -C _x includes C ₁ -C ₂ , C ₁ -C ₃ . . . C ₁ -C _x

The term "alkyl" refers to straight or branched chain substituted or unsubstituted hydrocarbon groups, in one embodiment 1 to 40 carbon atoms, in another embodiment, 1 to 20 carbon atoms, in another embodiment, 1 to 10 carbon atoms. The expression "lower alkyl" refers to an alkyl groups of 1 to 6 carbon atoms. An alkyl group can be a "saturated alkyl," meaning that it does not contain any alkene or alkyne groups and in certain embodiments, alkyl groups are optionally substituted. An alkyl group can be an "unsaturated alkyl," meaning that it contains at least one alkene or alkyne group. An alkyl group that includes at least one carbon-carbon double bond (C=C) also is referred to by the term "alkenyl," and in certain embodiments, alkenyl groups are optionally substituted.

An alkyl group that includes at least one carbon-carbon triple bond (C≡ C) also is referred to by the term "alkynyl," and in certain embodiments, alkynyl groups are optionally substituted.

In certain embodiments, an alkyl contains 1 to 20 carbon atoms (whenever it appears herein, a numerical range such as "1 to 20" refers to each integer in the given range; e.g., "1 to 20 carbon atoms" means that an alkyl group can contain only 1 carbon atom, 2 carbon atoms, 3 carbon atoms, etc., up to and including 20 carbon atoms, although the term "alkyl" also includes instances where no numerical range of carbon atoms is designated). An alkyl can be designated as "C ₁ -C ₄ alkyl" or by similar designations. By way of example only, "C ₁ -C ₄ alkyl" indicates an alkyl having one, two, three, or four carbon atoms, i.e., the alkyl is selected from among methyl, ethyl, propyl, iso-propyl, n-butyl, iso-butyl, sec-butyl and t-butyl. Thus "C ₁ - C ₄ " includes C ₁ - C ₂ , C ₁ - C ₃ , C ₂ - C ₃ and C ₂ - C ₄ alkyl. Alkyls include, but are not limited to, methyl, ethyl, propyl, isopropyl, butyl, isobutyl, tertiary butyl, pentyl, hexyl, ethenyl, propenyl, butenyl, hexenyl, ethynyl, propynyl, butynyl and hexynyl.

As used herein, "halogen", "halide", or "halo" refers to F, Cl, Br or I and includes pseudohalides. As used herein, pseudohalides are compounds that behave substantially similar to halides. Such compounds can be used in the same manner and treated in the same manner as halides (X-, in which X is a halogen, such as Cl, F or Br). Pseudohalides include, but are not limited to, cyanide, cyanate, thiocyanate, selenocyanate, trifluoromethoxy, trifluoromethyl and azide.

As used herein, the term "haloalkyl" alone or in combination refers to an alkyl in that at least one hydrogen atom is replaced with a halogen atom. In certain of the embodiments in that two or more hydrogen atom are replaced with halogen atoms, the halogen atoms are all the same as one another. In certain of such embodiments, the halogen atoms are not all the same as one another. Certain haloalkyls are saturated haloalkyls, which do not include any carbon-carbon double bonds or any carbon-carbon triple bonds. Certain haloalkyls are haloalkenes, which include one or more carbon-carbon double bonds. Certain haloalkyls are haloalkynes, which include one or more carbon- carbon triple bonds. In certain embodiments, haloalkyls are optionally substituted.

Where the number of any given substituent is not specified (e.g., "haloalkyl"), there can be one or more substituents present. For example, "haloalkyl" can include one

or more of the same or different halogens. For example, "haloalkyl" includes each of the substituents CF ₃ , CHF ₂ and CH ₂ F.

As used herein, the term "heteroatom" refers to an atom other than carbon or hydrogen. Heteroatoms are typically independently selected from oxygen, sulfur, nitrogen, and phosphorus, but are not limited to those atoms. In embodiments in which two or more heteroatoms are present, the two or more heteroatoms can all be the same as one another, or some or all of the two or more heteroatoms can each be different from the others.

As used herein, the term "heteroalkyl" alone or in combination refers to a group containing an alkyl and one or more heteroatoms. Certain heteroalkyls are saturated heteroalkyls, which do not contain any carbon-carbon double bonds or any carbon-carbon triple bonds. Certain heteroalkyls are heteroalkenes, which include at least one carbon- carbon double bond. Certain heteroalkyls are heteroalkynes, which include at least one carbon-carbon triple bond. Certain heteroalkyls are acylalkyls, in which the one or more heteroatoms are within an alkyl chain. Examples of heteroalkyls include, but are not limited to, CH ₃ C(=O)CH ₂ -, CH ₃ C(=O)CH ₂ CH ₂ -, CH ₃ CH ₂ C(=O)CH ₂ CH ₂ -,

CH ₃ C(=O)CH ₂ CH ₂ CH ₂ -, CH ₃ OCH ₂ CH ₂ -, CH ₃ OC(=O)CH ₂ - and CH ₃ NHCH ₂ -. In certain embodiments, heteroalkyls are optionally substituted.

As used herein, the term "heterohaloalkyl" alone or in combination refers to a heteroalkyl in which at least one hydrogen atom is replaced with a halogen atom. In certain embodiments, heteroalkyls are optionally substituted.

As used herein, the term "non-cyclic alkyl" refers to an alkyl that is not cyclic (i.e., a straight or branched chain containing at least one carbon atom). Non-cyclic alkyls can be fully saturated or can contain non-cyclic alkenes and/or alkynes. Non-cyclic alkyls can be optionally substituted. As used herein, the term "ring" refers to any covalently closed structure. Rings include, for example, carbocycles (e.g., aryls and cycloalkyls), heterocycles (e.g., heteroaryls and non-aromatic heterocycles), aromatics (e.g., aryls and heteroaryls), and non-aromatics (e.g., cycloalkyls and non-aromatic heterocycles). Rings can be optionally substituted. Rings can form part of a ring system. As used herein, the term "ring system" refers to two or more rings, wherein two or more of the rings are fused. The term "fused" refers to structures in which two or more rings share one or more bonds.

As used herein, the term "carbocycle" refers to a ring where each of the atoms forming the ring is a carbon atom. Carbocyclic rings can be formed by three, four, five, six, seven, eight, nine, or more than nine carbon atoms. Carbocycles can be optionally substituted. As used herein, "cycloalkyl" refers to a saturated mono- or multicyclic ring system where each of the atoms forming a ring is a carbon atom. Cycloalkyls can be formed by three, four, five, six, seven, eight, nine, or more than nine carbon atoms. In one embodiment, the ring system includes 3 to 12 carbon atoms. In another embodiment, they ring system includes 3 to 6 carbon atoms. The term "cycloalkyl" includes rings that contain one or more unsaturated bonds. As used herein, the terms "cycloalkenyl" and "cycloalkynyl" are unsaturated cycloalkyl ring system. Cycloalkyls can be optionally substituted. In certain embodiments, a cycloalkyl contains one or more unsaturated bonds. Examples of cycloalkyls include, but are not limited to, cyclopropane, cyclobutane, cyclopentane, cyclopentene, cyclopentadiene, cyclohexane, cyclohexene, 1,3-cyclohexadiene, 1,4-cyclohexadiene, cycloheptane and cycloheptene.

As used herein, the term "cycloalkenyl" refers to mono- or multicyclic ring systems that includes at least one carbon-carbon double bond (C=C).

As used herein, the term "cycloalkynyl" refers to mono- or multicyclic ring systems that includes at least one carbon-carbon triple bond (C≡ C). Cycloalkenyl and cycloalkynyl groups include ring systems that include 3 to 12 carbon atoms. In some embodiments, the cycloalkenyl groups include 4 to 7 carbon atoms. In some embodiment, the cycloalkynyl groups include 8 to 10 carbon atoms. The ring systems of the cycloalkyl, cycloalkenyl and cycloalkynyl groups can be composed of one ring or two or more rings that can be joined together in a fused, bridged or spiro- connected fashion, and can be optionally substituted with one or more alkyl group substituents.

As used herein, the term "heterocycle" refers to a ring wherein at least one atom forming the ring is a carbon atom and at least one atom forming the ring is a heteroatom. Heterocyclic rings can be formed by three, four, five, six, seven, eight, nine, or more than nine atoms. Any number of those atoms can be heteroatoms (i.e., a heterocyclic ring can contain one, two, three, four, five, six, seven, eight, nine, or more than nine heteroatoms, provided that at lease one atom in the ring is a carbon atom). Herein, whenever the number

of carbon atoms in a heterocycle is indicated (e.g., C ₁ -C ₆ heterocycle), at least one other atom (the heteroatom) must be present in the ring. Designations such as "C ₁ -C ₆ heterocycle" refer only to the number of carbon atoms in the ring and do not refer to the total number of atoms in the ring. It is understood that the heterocyclic ring will have additional heteroatoms in the ring. Designations such as "4-6 membered heterocycle" refer to the total number of atoms that comprise the ring (i.e., a four, five, or six membered ring, in which at least one atom is a carbon atom, at least one atom is a heteroatom and the remaining two to four atoms are either carbon atoms or heteroatoms). In heterocycles containing two or more heteroatoms, those two or more heteroatoms can be the same or different from one another. In one embodiment, the heterocycle includes 3-12 members. In other embodiments, the heterocycle includes 4, 5, 6, 7 or 8 members. The heterocycle can be optionally substituted with one or more substituents. In some embodiments, the substituents of the heterocyclic group are selected from among hydroxy, amino, alkoxy containing 1 to 4 carbon atoms, halo lower alkyl, including trihalomethyl, such as trifluoromethyl, and halogen. As used herein, a heterocyclic group can be referred to as a "heterocyclo" group. As used herein, the term heterocycle can include reference to heteroaryl. Binding to a heterocycle can be at a heteroatom or via a carbon atom. Examples of heterocycles include, but are not limited to the following:

where D, E, F and G independently represent a heteroatom. Each of D, E, F and G can be the same or different from one another.

As used herein, the term "bicyclic ring" refers to two rings, wherein the two rings are fused. Bicyclic rings include, for example, decaline, pentalene, naphthalene, azulene, heptalene, isobenzofuran, chromene, indolizine, isoindole, indole, purine, indoline, indene, quinolizine, isoquinoline, quinoline, phthalazine, naphthyrididine, quinoxaline, cinnoline, pteridine, isochroman, chroman and various hydrogenated derivatives thereof. Bicyclic

rings can be optionally substituted. Each ring is independently aromatic or non-aromatic. In certain embodiments, both rings are aromatic. In certain embodiments, both rings are non-aromatic. In certain embodiments, one ring is aromatic and one ring is non-aromatic. As used herein, the term "aromatic" refers to a planar ring having a delocalized π- electron system containing 4n+2 π electrons, where n is an integer. Aromatic rings can be formed by five, six, seven, eight, nine, or more than nine atoms. Aromatics can be optionally substituted. Examples of aromatic groups include, but are not limited to phenyl, naphthalenyl, phenanthrenyl, anthracenyl, tetralinyl, fluorenyl, indenyl and indanyl. The term aromatic includes, for example, benzenoid groups, connected via one of the ring- forming carbon atoms, and optionally carrying one or more substituents selected from an aryl, a heteroaryl, a cycloalkyl, a non-aromatic heterocycle, a halo, a hydroxy, an amino, a cyano, a nitro, an alkylamido, an acyl, a C _1-6 alkoxy, a C _1-6 alkyl, a C _1-6 hydroxyalkyl, a C _1-6 aminoalkyl, a C _1-6 alkylamino, an alkylsulfenyl, an alkylsulfinyl, an alkylsulfonyl, an sulfamoyl, or a trifluoromethyl. In certain embodiments, an aromatic group is substituted at one or more of the para, meta, and/or ortho positions. Examples of aromatic groups containing substitutions include, but are not limited to, phenyl, 3-halophenyl, 4-halophenyl, 3-hydroxyphenyl, 4-hydroxy-phenyl, 3-aminophenyl, 4-aminophenyl, 3-methylphenyl, 4- methylphenyl, 3-methoxyphenyl, 4-methoxyphenyl, 4-trifluoromethoxyphenyl, 3-cyano- phenyl, 4-cyanophenyl, dimethylphenyl, naphthyl, hydroxynaphthyl, hydroxymethyl- phenyl, (trifluoromethyl)phenyl, alkoxyphenyl, 4-morpholin-4-ylphenyl, 4-pyrrolidin-1- ylphenyl, 4-pyrazolylphenyl, 4-triazolylphenyl and 4-(2-oxopyrrolidin-1-yl)phenyl.

As used herein, the term "aryl" refers to a monocyclic, bicyclic or tricyclic aromatic system that contains no ring heteroatoms. Where the systems are not monocyclic, the term aryl includes for each additional ring the saturated form (perhydro form) or the partially unsaturated form (for example the dihydro form or tetrahydro form) or the maximally unsaturated (nonaromatic) form. In some embodiments, the term aryl refers to bicyclic radicals in which the two rings are aromatic and bicyclic radicals in which only one ring is aromatic. Examples of aryl include phenyl, naphthyl, anthracyl, indanyl, 1 ,2-dihydro- naphthyl, 1,4-dihydronaphthyl, indenyl, 1,4-naphthoquinonyl and 1 ,2,3,4-tetrahydronaphthyl. Aryl rings can be formed by three, four, five, six, seven, eight, nine, or more than nine carbon atoms. In some embodiments, aryl refers to a 3-, 4-, 5-, 6-, 7-, 8-, 9-, 10-, 11-, 12-, 13- or 14-membered, aromatic mono-, bi- or tricyclic system. In some embodiments,

aryl refers to an aromatic C ₃ -C ₉ ring. In some embodiments, aryl refers to an aromatic C ₄ - C ₈ ring. Aryl groups can be optionally substituted.

As used herein, the term "heteroaryl" refers to an aromatic ring in which at least one atom forming the aromatic ring is a heteroatom. Heteroaryl rings can be formed by three, four, five, six, seven, eight, nine and more than nine atoms. Heteroaryl groups can be optionally substituted. Examples of heteroaryl groups include, but are not limited to, aromatic C _3-8 heterocyclic groups containing one oxygen or sulfur atom, or two oxygen atoms, or two sulfur atoms or up to four nitrogen atoms, or a combination of one oxygen or sulfur atom and up to two nitrogen atoms, and their substituted as well as benzo- and pyrido-fused derivatives, for example, connected via one of the ring- forming carbon atoms.

In certain embodiments, heteroaryl is selected from among oxazolyl, isoxazolyl, oxadiazolyl, thiazolyl, isothiazolyl, pyridinyl, pyridazinyl, pyrimidinal, pyrazinyl, indolyl, benzimidazolyl, quinolinyl, isoquinolinyl, quinazolinyl or quinoxalinyl.

In some embodiments, a heteroaryl group is selected from among pyrrolyl, furanyl (furyl), thiophenyl (thienyl), imidazolyl, pyrazolyl, 1,2,3-triazolyl, 1,2,4-triazolyl, 1,3- oxazolyl (oxazolyl), 1,2-oxazolyl (isoxazolyl), oxadiazolyl, 1,3-thiazolyl (thiazolyl), 1,2- thiazolyl (isothiazolyl), tetrazolyl, pyridinyl (pyridyl) pyridazinyl, pyrimidinyl, pyrazinyl, 1,2,3-triazinyl, 1,2,4-triazinyl, 1,3,5-triazinyl, 1 ,2,4,5-tetrazinyl, indazolyl, indolyl, benzothiophenyl, benzofuranyl, benzothiazolyl, benzimidazolyl, benzodioxolyl, acridinyl, quinolinyl, isoquinolinyl, quinazolinyl, quinoxalinyl, phthalazinyl, thienothiophenyl, 1 ,8- naphthyridinyl, other naphthyridinyls, pteridinyl or phenothiazinyl. Where the heteroaryl group includes more than one ring, each additional ring is the saturated form (perhydro form) or the partially unsaturated form (for example the dihydro form or tetrahydro form) or the maximally unsaturated (nonaromatic) form. The term heteroaryl thus includes bicyclic radicals in which the two rings are aromatic and bicyclic radicals in which only one ring is aromatic. Such examples of heteroaryl are include 3H-indolinyl, 2(1H)- quinolinonyl, 4-oxo-1,4-dihydroquinolinyl, 2H-1-oxoisoquinolyl, 1,2-dihydroquinolinyl, (2H)quinolinyl N-oxide, 3,4-dihydroquinolinyl, 1,2-dihydroisoquinolinyl, 3,4-dihydro- isoquinolinyl, chromonyl, 3,4-dihydroiso-quinoxalinyl, 4-(3H)quinazolinonyl, 4H- chromenyl, 4-chromanonyl, oxindolyl, 1 ,2,3,4-tetrahydroisoquinolinyl, 1 ,2,3,4-tetrahydro- quinolinyl, 1H-2,3-dihydroisoindolyl, 2,3-dihydrobenzo[f]isoindolyl, 1 ,2,3,4- tetrahydro- benzo[g]isoquinolinyl, 1 ,2,3,4- tetrahydro-benzo[g]isoquinolinyl, chromanyl,

isochromanonyl, 2,3-dihydrochromonyl, 1,4-benzodioxanyl, 1,2,3,4-tetrahydro- quinoxalinyl, 5,6-dihydroquinolyl, 5,6-dihydroiso-quinolyl, 5,6-dihydroquinoxalinyl, 5,6- dihydroquinazolinyl, 4,5-dihydro-1H-benzimidazolyl, 4,5-dihydrobenzoxazolyl, 1,4- naphthoquinolyl, 5,6,7,8-tetrahydro-quinolinyl, 5,6,7,8-tetrahydroisoquinolyl, 5,6,7,8- tetrahydroquinoxalinyl, 5,6,7,8-tetrahydroquinazolyl, 4,5,6,7-tetrahydro-1H- benzimidazolyl, 4,5,6,7-tetrahydro-benzoxazolyl, 1H-4-oxa-l ,5-diazanaphthalen-2-onyl, 1 ,3-dihydroimidizolo-[4,5]-pyridin-2-onyl, 2,3-dihydro-l ,4-dinaphthoquinonyl, 2,3- dihydro-1H-pyrrol[3,4-b]quinolinyl, 1,2,3,4-tetrahydrobenzo[b][1,7]naphthyridinyl, 1,2,3,4-tetrahydrobenz[b][1,6]-naphthyridinyl, 1,2,3,4-tetrahydro-9H-pyrido[3,4-b]indolyl, 1,2,3,4-tetrahydro-9H-pyrido[4,3-b]indolyl, 2,3-dihydro-1H-pyrrolo[3,4-b]indolyl, 1H- 2,3,4,5-tetrahydro-azepino[3,4-b]indolyl, 1H-2,3,4,5-tetrahydroazepino[4,3-b]indolyl, 1H- 2,3,4,5- tetrahydro-azepino[4,5-b]indolyl, 5,6,7, 8-tetrahydro[1,7]napthyridinyl, 1,2,3,4- tetrahydro[2,7]-naphthyridyl, 2,3-dihydro[1,4]dioxino[2,3-b]pyridyl, 2,3-dihydro[1,4]- dioxino[2,3-b]pyridyl, 3,4-dihydro-2H-1-oxa[4,6]diazanaphthalenyl, 4,5,6,7-tetrahydro- 3H-imidazo[4,5-c]pyridyl, 6,7-dihydro[5,8]diazanaphthalenyl, 1,2,3,4-tetrahydro[1,5]- napthyridinyl, 1 ,2,3,4-tetrahydro[ 1 ,6]napthyridinyl, 1 ,2,3,4-tetrahydro[ 1 ,7]napthyridinyl, 1,2,3,4-tetrahydro[1,8]napthyridinyl or 1,2,3,4-tetrahydro[2,6]napthyridinyl.

In certain embodiments, heteroaryl groups are optionally substituted. In one embodiment, the one or more substituents are each independently selected from among halo, hydroxy, amino, cyano, nitro, alkylamido, acyl, C _1-6 -alkoxy, C _1-6 -alkyl, C _1-6 - haloalkyl, C _1-6 -hydroxy-alkyl, C _1-6 -aminoalkyl, C _1-6 -alkylamino, alkylsulfenyl, alkylsulfinyl, alkylsulfonyl, sulfamoyl, or trifluoromethyl. Examples of heteroaryl groups include, but are not limited to, unsubstituted and mono- or di-substituted derivatives of furan, benzofuran, thiophene, benzothiophene, pyrrole, pyridine, indole, oxazole, benzoxazole, isoxazole, benzisoxazole, thiazole, benzothiazole, isothiazole, imidazole, benzimidazole, pyrazole, indazole, tetrazole, quinoline, isoquinoline, pyridazine, pyrimidine, purine and pyrazine, furazan, 1,2,3-oxadiazole, 1,2,3-thiadiazole, 1,2,4- thiadiazole, triazole, benzotriazole, pteridine, phenoxazole, oxadiazole, benzopyrazole, quinolizine, cinnoline, phthalazine, quinazoline and quinoxaline. In some embodiments, the substituents are halo, hydroxy, cyano, O-C _{1 -6} -alkyl, C _1-6 -alkyl, hydroxy-C _1-6 -alkyl and amino-C _1-6 -alkyl.

As used herein, the term "non-aromatic ring" refers to a ring that does not have a delocalized 4n+2 π-electron system.

As used herein, the term "non-aromatic heterocycle" refers to a non-aromatic ring wherein one or more atoms forming the ring is a heteroatom. Non-aromatic heterocyclic rings can be formed by three, four, five, six, seven, eight, nine, or more than nine atoms. Non-aromatic heterocycles can be optionally substituted. In certain embodiments, non- aromatic heterocycles contain one or more carbonyl or thiocarbonyl groups such as, for example, oxo- and thio-containing groups. Examples of non-aromatic heterocycles include, but are not limited to, lactams, lactones, cyclic imides, cyclic thioimides, cyclic carbamates, tetrahydrothiopyran, 4H-pyran, tetrahydropyran, piperidine, 1,3-dioxin, 1,3- dioxane, 1,4-dioxin, 1,4-dioxane, piperazine, 1,3-oxathiane, 1,4-oxathiin, 1,4-oxathiane, tetrahydro-1,4-thiazine, 2H-1,2-oxazine , maleimide, succinimide, barbituric acid, thiobarbituric acid, dioxopiperazine, hydantoin, dihydrouracil, morpholine, trioxane, hexahydro-1,3,5-triazine, tetrahydrothiophene, tetrahydrofuran, pyrroline, pyrrolidine, pyrrolidone, pyrrolidione, pyrazoline, pyrazolidine, imidazoline, imidazolidine, 1,3- dioxole, 1,3-dioxolane, 1,3-dithiole, 1,3-dithiolane, isoxazoline, isoxazolidine, oxazoline, oxazolidine, oxazolidinone, thiazoline, thiazolidine and 1,3-oxathiolane.

As used herein, the term "arylalkyl" alone or in combination, refers to an alkyl substituted with an aryl that can be optionally substituted. As used herein, the term "heteroarylalkyl" alone or in combination, refers to an alkyl substituted with a heteroaryl that can be optionally substituted.

As used herein, the term "amino" refers to a group of -NH ₂ .

As used herein, the term "hydroxy" refers to a group of -OH.

As used herein, the term "nitro" refers to a group of -NO ₂ . As used herein, the term "O-carboxy" refers to a group of formula RC(=O)O-.

As used herein, the term "C-carboxy" refers to a group of formula -C(=O)OR.

As used herein, the term "alkoxy" refers to a group of formula -OR.

As used herein, the term "acetyl" or "acyl" refers to a group of formula -C(=O)CH ₃ .

As used herein, the term "cyano" refers to a group of formula -CN. As used herein, the term "nitrile" refers to a compound having the structure RC≡N.

As used herein, the term "isocyanato" refers to a group of formula -NCO.

As used herein, the term "thiocyanato" refers to a group of formula -CNS.

As used herein, the term "isothiocyanato" refers to a group of formula -NCS. As used herein, the term "C-amido" refers to a group of formula -C(=O)-NR ₂ . As used herein, the term "N-amido" refers to a group of formula RC(=O)NR'-. As used herein, the term "sulfenyl" refers to a group of formula -SR. As used herein, the term "sulfinyl" refers to a group of formula -S(=O)R.

As used herein, the term "sulfonyl" refers to a group of formula -S(=O) ₂ R. As used herein, the term "sulfamoyl" refers to a group of formula -S(=O) ₂ NR ₂ . As used herein, the term "sulfonyl halide" refers to compound of formula X- S(=O) ₂ R, where X is halo. As used herein, the term "polyhydrogen fluoride-pyridine solution" refers to a solution comprising hydrogen fluoride and pyridine.

As used herein, the term "ester" refers to a group of formula RC(=O)OR', where R'

≠ H.

As used herein, the term "amide" refers to a group of formula RC(=O)NR' ₂ . In certain embodiments, an amide can be an amino acid or a peptide.

As used herein, the terms "amine," "hydroxy," and "carboxyl" include such groups that have been esterified or amidified. Procedures and specific groups used to achieve esterification and amidification are known to those of skill in the art and can readily be found in reference sources such as Greene and Wuts, Protective Groups in Organic Synthesis, 3 ^rd Ed., John Wiley & Sons, New York, NY, 1999, which is incorporated herein in its entirety.

As used herein, the term "leaving group" refers to an atom or group that becomes detached from an atom in what is considered to be the residual or main part of the substrate in a specified reaction. The leaving group can be charged or uncharged. As used herein, the term "together form a bond" refers to the instance in which two substituents to neighboring atoms are null the bond between the neighboring atoms becomes a double bond. For example, if A and B below "together form a bond"

the resulting structure is:

Unless otherwise indicated, the term "optionally substituted," refers to a group in which none, one, or more than one of the hydrogen atoms has been replaced with one or

more group(s) individually and independently selected from among alkyl, cycloalkyl, heteroalkyl, aryl, heteroaryl, non-aromatic heterocycle, hydroxy, alkoxy, aryloxy, mercapto, alkylthio, arylthio, cyano, halo, carbonyl, thiocarbonyl, O-carbamyl, N carbamyl, O thiocarbamyl, N thiocarbamyl, C amido, N amido, S-sulfonamido, N sulfonamido, C carboxy, O carboxy, isocyanato, thiocyanato, isothiocyanato, nitro, silyl, trihalomethane- sulfonyl, and amino, including mono- and di-substituted amino groups, and the protected derivatives of amino groups. Such protective derivatives (and protecting groups that can form such protective derivatives) are known to those of skill in the art and can be found in references such as Greene and Wuts, above. In embodiments in which two or more hydrogen atoms have been substituted, the substituent groups can together form a ring. Throughout the specification, groups and substituents thereof can be chosen by one skilled in the field to provide stable moieties and compounds.

It is to be understood that the compounds provided herein can contain chiral centers. Such chiral centers can be of either the (R) or (S) configuration, or can be a mixture thereof. Thus, the compounds provided herein can be enantiomerically pure, or be stereoisomeric or diastereomeric mixtures. It is to be understood that the chiral centers of the compounds provided herein can undergo epimerization in vivo. As such, one of skill in the art will recognize that administration of a compound in its (R) form is equivalent, for compounds that undergo epimerization in vivo, to administration of the compound in its (S) form.

As used herein, "cis" and "trans" are descriptors that show the relationship between two ligands attached to separate atoms that are connected by a double bond or contained in a ring with a double bond. Two ligands are said to be "cis" to each other if they lie on the same side of a plane. If the ligands are on opposite sides, their relative position is described as "trans." The appropriate reference plane of a double bond is perpendicular to that of the relevant sigma bond that passes through the double bond.

As used herein, "enantiomer" refers to one of a pair of molecular entities that are mirror images of each other and non-superimposable. Enantiomeric excess (ee) can be calculated for a mixture of (R) and (S)-enantiomers. The ee is defined as the absolute value of the mole fractions of F _(R) minus the mole fraction of F _(S) . The percent ee is the absolute value of the mole fractions of F _(R) minus the mole fraction of F _(S) multiplied by 100.

As used herein, "enantioselectivity" refers to the preferential formation in a chemical reaction of one enantiomer over another.

As used herein, "optical activity" refers to the ability of a sample material to rotate the plane of polarized light. A specific enantiomer causes rotation of light in either a clockwise or counterclockwise direction. As used herein, "optical purity" refers to the ratio of observed optical rotation of a sample comprising of a mixture of enantiomers to the optical rotation of one pure enantiomer.

As used herein, the term "substantially pure" means sufficiently homogeneous to appear free of readily detectable impurities as determined by standard methods of analysis, such as thin layer chromatography (TLC), gel electrophoresis, high performance liquid chromatography (HPLC) and mass spectrometry (MS), used by those of skill in the art to assess such purity, or sufficiently pure such that further purification would not detectably alter the physical and chemical properties, such as enzymatic and biological activities, of the substance. Thus, substantially pure object species (e.g., compound) is the predominant species present (i.e., on a molar basis it is more abundant than any other individual species in the composition). In certain embodiments, a substantially purified fraction is a composition wherein the object species contains at least about 50 percent (on a molar basis) of all species present. In certain embodiments, a substantially pure composition will contain more than about 50%, 60%, 70%, 80%, 85%, 90%, 95%, or 99% of all species present in the composition. In certain embodiments, a substantially pure composition will contain more than about 80%, 85%, 90%, 95%, or 99% of all species present in the composition. Methods for purification of the compounds to produce substantially chemically pure compounds are known to those of skill in the art. A substantially chemically pure compound can, however, be a mixture of stereoisomers. In such instances, further purification might increase the specific activity of the compound. The instant disclosure is meant to include all such possible isomers, as well as their racemic and optically pure forms. Optically active (+) and (-), (R)- and (S)-, or (D)- and (L)-isomers can be prepared using chiral synthons or chiral reagents, or resolved using conventional techniques, such as reverse phase HPLC. When the compounds described herein contain olefinic double bonds or other centers of geometric asymmetry, and unless specified otherwise, it is intended that the compounds include both E and Z geometric isomers. Likewise, all tautomeric forms are also intended to be included.

As used herein, an "isolated enzyme" is an enzyme that is obtained in a substantially pure state.

As used herein, "acid" generally refers to a molecular entity or chemical species capable of donating a hydron (proton), otherwise considered a Brønsted acid, or capable of accepting an electron pair, otherwise known as a Lewis acid.

As used herein, "base" refers to a chemical species or molecular entity having an available pair of electrons capable of forming a bond with a hydron (proton), otherwise known as a Brønsted base, or capable of donating an electron pair to form a bond with the vacant orbital of some other species, otherwise known as a Lewis base. As used herein, "activation" of a chemical group occurs when some or all of the energy required for a desired transformation is provided by a preceding reaction. For example, in the scheme: some or all of the energy required for the reaction of X to form products Y and Z is provided by the first reaction between A and B.

As used herein, "chemical resolution" occurs when a mixture of stereoisomers is separated into the component diasteriomers and/or enantiomers. Chemical resolution can also be applied to the separation of olefin cis- and trans- isomers.

As used herein, an "aliquot" refers to a fractional part of known quantity taken from a larger solution or mixture. The properties of the aliquot are usually analyzed and such properties are considered to be representative of the properties of the larger solution or mixture.

As used herein, a "reactant" refers to a substance that is consumed in the course of a chemical reaction. A reactant can also be referred to as a reagent.

As used herein, a "condensation" reaction occurs when two or more reactants yield a single main product with accompanying formation of water or of some other small molecule such as ammonia, ethanol, acetic acid, or hydrogen sulfide. A condensation reaction also can occur between two or more reactive sites within the same molecular entity.

As used herein, "transformation" refers to the conversion of a substrate into a particular product irrespective of the reagents or mechanisms involved. Reference to a transformation does not require full description of all reactants or all products necessary to convert the substrate into product.

As used herein, "cyclization" refers to the formation of a covalently closed ring by formation of a new bond.

As used herein, "reduce" and "reduction" refers to the transfer of one or more electrons to a molecular entity. For example, a compound can be reduced by the addition of hydrogen. A reduced species can also be formed through the gain of electrons. The reverse process in which one or more electrons is removed from a molecular entity is known as "oxidation."

As used herein, "salting" refers to the addition of electrolytes to an solution. Salting often alters the distribution ratio of a particular solute or changes the miscibility of two liquids.

As used herein, "emulsion" refers to a fluid colloidal system in which liquid droplets and/or liquid crystals are dispersed in a liquid. A colloidal system refers to a state of subdivision, implying that the molecules or polymolecular particles dispersed in a medium have at least in one direction a dimension roughly between 1 nm and 1 μm, or that in a system discontinuities are found at distances of that order.

As used herein, "lysate" refers to the contents released from a lysed cell.

As used herein, a "derivative" is a compound obtained or produced by modification of another compound of similar structure. Derivatives can be produced by one or more modification steps. As used herein, "quenched" refers to arresting the course of a chemical or enzymatic reaction by chemical or physical means.

To remove potentially complicating reactive functionality of chemical moieties, the usage of "protecting groups" is often employed. That is, a functional group is temporarily converted into an unreactive form to prevent its interference with transformations to be carried out elsewhere in the molecule. Such temporary functional group modification is known as "protecting" the original group. Subsequent to transformation carried out elsewhere in the molecule, the original unit can be regenerated, i.e., "deprotected," under separate conditions. For example, an alcohol can be protected as a 1,1 -dimethyl ethyl ether by an acid catalyzed reaction of the alcohol with 2-methyl-2- propanol. The resulting ether is inert to some basic, oxidizing, or reducing conditions. The alcohol can be deprotected by removal of the ether group in dilute aqueous acid.

As used herein, "desymmetrization" involves the modification of a compound that results in the loss of one or more symmetry elements. Desymmetrization includes the loss of a symmetry element that precludes chirality, such as a mirror plane, center of inversion, or rotational-reflection axis. Desymmetrization can result in the conversion of a prochiral molecular entity into a chiral entity. The term "prochiral" refers to an structure that lacks chirality, but can become chiral by addition, removal, or replacement of a substituent.

As used herein, "hydrolysis" refers to the general rupture of one or more bonds by water molecules. As used herein, "EC" refers to the Enzyme Commission of the International

Union of Biochemistry and Molecular Biology (IUBMB). As used herein, EC numbers, such as EC 3.4.21.62, are associated with a recommended name for the respective enzyme. The first number designates the major class, the second number designates the subclass, and the third number designates the sub-subclass. The fourth number indicates the serial number of the enzyme in its sub-subclass.

As used herein, a "nitrile hydratase," "NHase" "nitrile hydratase polypeptide" and "NHase polypeptide" refer to an enzyme that catalyzes the hydration of a nitrile substrate to a corresponding amide product. The EC number assigned by IUP AC-IUBMB for NHase is EC 4.2.1.84. NHases are metalloenzymes containing iron or cobalt. NHases are composed of two types of subunits, α and β, which are not related in amino acid sequence. NHases exist as α β dimers or as α ₂ β ₂ tetramers. The iron or cobalt metal ion is generally located in a central cavity at the interface between two subunits. Nitrile hydratase polypeptides include NHase polypeptides, allelic variant isoforms, synthetic molecules prepared from nucleic acids that encode NHase polypeptides, and modified forms thereof. Nitrile hydratase includes homologous polypeptides from different species including, but not limited to bacterial, fungal, or yeast. Nitrile hydratase polypeptide also includes heterogenous lengths or fragments or portions of nitrile hydratase polypeptide that are of sufficient length or include appropriate regions to retain at least one activity of full-length mature polypeptide. As used herein, "product" refers to a substance that is formed during a chemical or enzymatic reaction.

As used herein, "reaction medium" refers to the phase in which a chemical or biological reaction or other such transformation takes place. The reaction medium can include solid, liquid, and gaseous phases and mixtures thereof. Chemical and biological reactants and reagents are commonly dissolved or suspended in various liquid compositions to facilitate a reaction or transformation.

As used herein, a "two phase system" or "2-phase system" comprises a solvent and non-volatile components. The solvent is generally an aqueous solution. The nonvolatile component is generally a mixture of a polymer and a kosmotropic salt, or a mixture of two salts (one chaotropic salt and one kosmotropic salt). Exemplary two phase systems include, but are not limited to, agar-starch systems, agar-gelatin systems, polyethylene glycol (PEG)-dextran systems, PEG-sodium carbonate systems, PEG- phosphate systems, PEG-citrate systems, and PEG-sulfate systems.

As used herein, a "catalyst" is a substance that increases the rate of a reaction. A catalytic substance is a substance that increases the rate of a reaction. As used herein, "biocatalyst" refers to a living organism, enzyme, and/or enzyme complex that catalyses a reaction or otherwise facilitates substrate conversion in various chemical reactions.

As used herein, a "buffer solution" is any substance or mixture of compounds in solution that is capable of neutralizing both acids and bases without appreciably changing the original acidity or alkalinity of the solution. Buffer solutions contain mixture(s) of acid and conjugate base at or near the pK _a to minimize pH changes caused by an influx of acid or base. Buffer solutions can also contain additional solutes such as salts and other compounds.

As used herein, enzyme "deactivation" occurs when an enzyme is no longer capable of catalysis.

As used herein, "substrate" refers to the chemical entity involved in a reaction that undergoes conversion to a product or products. Enzymes can catalyze the conversion of substrate(s) to product(s).

As used herein, the term "precipitate" refers to the act of separating, e.g., a compound or product, from solution or suspension, usually via a chemical or physical change, often resulting in an insoluble oil or amorphous or crystalline solid, and the term also refers to a substance separated from a solution or suspension by chemical or physical change.

As used herein, "supernatant" refers to the liquid floating above the surface of a sediment or precipitate.

As used herein, "peak area" refers to the area between the peak and the baseline of a chromatogram. As used herein, "co-solvent" refers to a mixture of liquids. In some embodiments, the co-solvent is a material that is not necessarily an acceptable solvent that is added to a generally small amount of an active solvent to form a mixture that has enhanced solvent power. For example, a polar cosolvent can be added into a mixture of an organic liquid and a compound having pendant ionomeric groups to solubilize the pendant ionomeric groups. Co-solvents can increase solubility of a compound. The use of cosolvents can increase the solubility by several orders of magnitude. Some commonly used cosolvents in pharmaceuticals are propylene glycol, polyethylene glycols, ethanol and sorbitol. The addition of a co-solvent can increase solubility of hydrophobic molecules by reducing the dielectric constant of the solvent. As used herein, "THF" refers to tetrahydrofuran.

As used herein, the term "combination" refers to any association between two or more items or elements.

As used herein, the term "article of manufacture" is a product that is made and sold and that includes a container and packaging, and optionally instructions for use of the product. For purposes herein, articles of manufacture encompass packaged intermediates as disclosed herein. In one embodiment, the articles of manufacture include one or more intermediates as provided herein and a enzyme. In other embodiments, the articles of manufacture include one or more intermediates as provided herein and a nitrile hydratase.

As used herein, a "kit" refers to a combination of an intermediate provided herein and another item for a purpose including, but not limited to, synthesis of levetiracetam or a related compound. Kits also optionally include instructions for use and/or reagents and glassware and other such items for use with the product.

As used herein, "substantially identical to a product" means sufficiently similar so that the property of interest is sufficiently unchanged so that the substantially identical product can be used in place of the product.

As used herein, "homologous" means about greater than 25% nucleic acid sequence identity, generally 25% 40%, 60%, 80%, 90% or 95%. The terms "homology"

and "identity" are often used interchangeably. In general, sequences are aligned so that the highest order match is obtained (see, e.g., Computational Molecular Biology, Lesk, A.M., ed., Oxford University Press, New York, 1988; Biocomputing: Informatics and Genome Projects, Smith, D.W., ed., Academic Press, New York, 1993; Computer Analysis of Sequence Data, Part I, Griffin, A.M., and Griffin, H. G., eds., Humana Press, New Jersey, 1994; Sequence Analysis in Molecular Biology, von Heinje, G., Academic Press, 1987; Sequence Analysis Primer, Gribskov, M. and Devereux, J., eds., M Stockton Press, New York, 1991; and Carillo et al., (1988) SIAM J Applied Math 48:1073).

As used herein, the term "identity" represents a comparison between a test and a reference polypeptide or polynucleotide. For example, a test polypeptide can be defined as any polypeptide that is 90% or more identical to a reference polypeptide. As used herein, the term "90% identical to" refers to percent identities from 90 to 99.99 relative to the reference polypeptides. Identity at a level of 90% or more is indicative of the fact that, assuming for exemplification purposes a test and reference polynucleotide length of 100 amino acids are compared, no more than 10% (i.e., 10 out of 100) amino acids in the test polypeptide differs from that of the reference polypeptides. Similar comparisons can be made between a test polynucleotide and reference polynucleotides. Such differences can be represented as point mutations randomly distributed over the entire length of an amino acid sequence or they can be clustered in one or more locations of varying length up to the maximum allowable, e.g., in the case of approximately 90% identity, 10/100 amino acid difference. Differences are defined as nucleic acid or amino acid addition, substitutions or deletions.

The number of conserved amino acids are determined by standard alignment algorithms programs, and are used with default gap penalties established by each supplier. Substantially homologous nucleic acid molecules would hybridize typically at moderate stringency or at high stringency all along the length of the nucleic acid of interest. Also contemplated are nucleic acid molecules that contain degenerate codons in place of codons in the hybridizing nucleic acid molecule.

Whether any two nucleic acid molecules have nucleotide sequences that are at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% "identical" can be determined using known computer algorithms such as the "FAST A" program, using for example, the default parameters as in Pearson et al., (1988) Proc. Natl. Acad. Sci. USA 85:2444 (other

programs include the GCG program package (Devereux et al., (1984) Nucleic Acids Research 12(I):387), BLASTP, BLASTN, FASTA (Atschul et al., (1990) J. Molec. Biol. 215:403; Guide to Huge Computers, Martin J. Bishop, ed., Academic Press, San Diego, 1994; and Carillo et al., (1988) SIAM J. Applied Math 48:1073). For example, the BLAST function of the National Center for Biotechnology Information database can be used to determine identity. Other commercially or publicly available programs include DNAStar "MegAlign" program (Madison, WI) and the University of Wisconsin Genetics Computer Group (UWG) "Gap" program (Madison WI)). Percent homology or identity of proteins and/or nucleic acid molecules can be determined, for example, by comparing sequence information using a GAP computer program (e.g. , Needleman et al., ( 1970) J. MoI. Biol. 48:443, as revised by Smith and Waterman ((1981), Adv. Appl. Math. 2:482). Briefly, the GAP program defines similarity as the number of aligned symbols (i.e., nucleotides or amino acids) that are similar, divided by the total number of symbols in the shorter of the two sequences. Default parameters for the GAP program can include: (1) a unary comparison matrix (containing a value of 1 for identities and 0 for non-identities) and the weighted comparison matrix of Gribskov et al., (1986) Nucl. Acids Res. 14:6745, as described by Schwartz and Dayhoff, eds., ATLAS OF PROTEIN SEQUENCE AND STRUCTURE, National Biomedical Research Foundation, pp. 353-358 (1979); (2) a penalty of 3.0 for each gap and an additional 0.10 penalty for each symbol in each gap; and (3) no penalty for end gaps. At the level of homologies or identities above about 85- 90%, the result should be independent of the program and gap parameters set; such high levels of identity readily may be assessed, often without relying on software.

Percent homology or identity of proteins and/or nucleic acid molecules can be determined, for example, by comparing sequence information using a GAP computer program (e.g., Needleman et al., (1970) J. MoI. Biol. 48:443, as revised by Smith and

Waterman ((1981) Adv. Appl. Math. 2:482). Briefly, the GAP program defines similarity as the number of aligned symbols (i.e., nucleotides or amino acids) that are similar, divided by the total number of symbols in the shorter of the two sequences. Default parameters for the GAP program can include: (1) a unary comparison matrix (containing a value of 1 for identities and 0 for non-identities) and the weighted comparison matrix of Gribskov et al., (1986) Nucl. Acids Res. 14:6745, as described by Schwartz and Dayhoff, eds., ATLAS OF PROTEIN SEQUENCE AND STRUCTURE, National Biomedical

Research Foundation, pp. 353-358 (1979); (2) a penalty of 3.0 for each gap and an additional 0.10 penalty for each symbol in each gap; and (3) no penalty for end gaps.

As used herein, heterologous or foreign DNA and RNA are used interchangeably and refer to DNA or RNA that does not occur naturally as part of the genome in which it is present or which is found in a location or locations in the genome that differ from that in which it occurs in nature. Heterologous nucleic acid is generally not endogenous to the cell into which it is introduced, but has been obtained from another cell or prepared synthetically. Generally, although not necessarily, such nucleic acid encodes RNA and proteins that are not normally produced by the cell in which it is expressed. Any DNA or RNA that one of skill in the art would recognize or consider as heterologous or foreign to the cell in which it is expressed is herein encompassed by heterologous DNA. Heterologous DNA and RNA can also encode RNA or proteins that mediate or alter expression of endogenous DNA by affecting transcription, translation, or other regulatable biochemical processes. As used herein, an "amino acid" is an organic compound containing an amino group and a carboxylic acid group. A polypeptide includes two or more amino acids. For purposes herein, amino acids include the twenty naturally-occurring amino acids, non- natural amino acids and amino acid analogs (i.e., amino acids wherein the α-carbon has a side chain). As used herein, the abbreviations for any protective groups, amino acids and other compounds are, unless indicated otherwise, in accord with their common usage, recognized abbreviations, or the IUPAC-IUB Commission on Biochemical Nomenclature (1972) Biochem. 11 : 1726). Each naturally occurring L-amino acid is identified by the standard three letter code (or single letter code) or the standard three letter code (or single letter code) with the prefix "L-;" the prefix "D-" indicates that the stereoisomeric form of the amino acid is D.

As used herein, "amino acid residue" refers to an amino acid formed upon chemical digestion (hydrolysis) of a polypeptide at its peptide linkages. The amino acid residues described herein are presumed to be in the "L" isomeric form. Residues in the "D" isomeric form, which are so designated, can be substituted for any L-amino acid residue as long as the desired functional property is retained by the polypeptide. "NH ₂ " refers to the free amino group present at the amino terminus of a polypeptide. "COOH"

refers to the free carboxy group present at the carboxyl terminus of a polypeptide. In keeping with standard polypeptide nomenclature described in J. Biol. Chem., 243: 3552- 3559 (1969), and adopted in 37 C.F.R.. §§ 1.821-1.822, abbreviations for amino acid residues are shown in Table 1.

Table 1 - Table of Correspondence of Amino Acid Symbols

It should be noted that all amino acid residue sequences represented herein by formulae have a left to right orientation in the conventional direction of amino-terminus to carboxyl-terminus. Furthermore, it should be noted that a dash at the beginning or end of an amino acid residue sequence indicates a peptide bond to a further sequence of one or more amino acid residues, to an amino-terminal group such as NH ₂ or to a carboxyl- terminal group such as COOH.

As used herein, "naturally occurring amino acids" refer to the 20 L-amino acids that occur in polypeptides. As used herein, the term "non-natural amino acid" refers to an organic compound that has a structure similar to a natural amino acid but has been modified structurally to

mimic the structure and reactivity of a natural amino acid. Non-naturally occurring amino acids thus include, for example, amino acids or analogs of amino acids other than the 20 naturally occurring amino acids and include, but are not limited to, the D- isostereomers of amino acids. Exemplary non-natural amino acids are described herein and are known to those of skill in the art.

In addition, the phrase "amino acid residue" is broadly defined to include the amino acids listed in the Table of Correspondence (Table 1) and modified and unusual amino acids, such as those referred to in 37 C.F.R. §§ 1.821-1.822, and incorporated herein by reference. These modified amino acids are listed in Table 2. Table 2. List of modified and unusual amino acids.

(See, Modified and Unusual Amino Acids, Section 7.5.4, The DDBJ/EMBL/GenBank Feature Table Definition, Version 7, 2007, available at the website ddbj.nig.ac.jp/FT/full_index.html).

Conservative amino acid substitutions, such as those set forth in Table 3, are those amino acids that do not eliminate activity, such as nitrile hydratase activity, when used to replace one or more amino acids in an unmodified enzyme, such as a nitrile hydratase. Suitable conservative substitutions of amino acids are known to those of skill in this art and can be made generally without altering the biological activity of the resulting molecule. Those of skill in this art recognize that, in general, single amino acid substitutions in nonessential regions of a polypeptide do not substantially alter biological activity (see, e.g., Watson et al., Molecular Biology of the Gene, 4th Edition, 1987, The Benjamin/Cummings Pub. Co., p.224). Conservative amino acid substitutions are made, for example, in accordance with those set forth in Table 3 as follows:

Table 3: Conservative Amino Acid Substitutions

As used in Table 3, Abu = 2-aminobutanoic acid, Nva = norvaline, NIe norleucine and Orn = ornithine.

As used herein, the term "monitoring" refers to observing an effect or absence of any effect. In certain embodiments, one monitors a reaction after addition of a reactant or change in reaction conditions, such as temperature or pressure. Examples of effects that can be monitored include, but are not limited to, changes in evolution of gas, the appearance of a reaction product or a disappearance of a substrate or reactant.

As used herein, the term "contacting" refers to bringing two or more materials into close enough proximity that they can interact. In certain embodiments, contacting can be accomplished in a vessel such as, e.g., a test tube, flask, petri dish or mixing tank. In certain embodiments, contacting can be performed in the presence of additional materials. As used herein, the term "subject" is an animal, typically a mammal, including human.

As used herein, the term "patient" includes human and animal subjects.

As used herein, the term "carrier" refers to a compound that facilitates the incorporation of another compound into cells or tissues. For example, dimethyl sulfoxide (DMSO) is a commonly used carrier for improving incorporation of certain organic compounds into cells or tissues.

As used herein, the term "pharmaceutical composition" refers to a chemical compound or composition capable of inducing a desired therapeutic effect in a subject. In certain embodiments, a pharmaceutical composition contains an active agent, which is the agent that induces the desired therapeutic effect. The pharmaceutical composition can contain a prodrug of the compounds provided herein. In certain embodiments, a pharmaceutical composition contains inactive ingredients, such as, for example, carriers and excipients.

As used herein, the term "therapeutically effective amount" refers to an amount of a pharmaceutical composition sufficient to achieve a desired therapeutic effect.

As used herein, the term "pharmaceutically acceptable" refers to a formulation of a compound that does not significantly abrogate the biological activity, a pharmacological activity and/or other properties of the compound when the formulated compound is administered to a subject. In certain embodiments, a pharmaceutically acceptable formulation does not cause significant irritation to a subject.

As used herein, pharmaceutically acceptable derivatives of a compound include, but are not limited to, salts, esters, enol ethers, enol esters, acetals, ketals, orthoesters,

hemiacetals, hemiketals, acids, bases, solvates, hydrates or prodrugs thereof. Such derivatives can be readily prepared by those of skill in this art using known methods for such derivatization. The compounds produced can be administered to animals or humans without substantial toxic effects and either are pharmaceutically active or are prodrugs. Pharmaceutically acceptable salts include, but are not limited to, amine salts, such as but not limited to chloroprocaine, choline, N,N'-dibenzyl-ethylenediamine, ammonia, diethanolamine and other hydroxyalkylamines, ethylenediamine, N-methylglucamine, procaine, N-benzyl-phenethylamine, 1 -para-chloro-benzyl-2-pyrrolidin-l '-ylmethyl- benzimidazole, diethylamine and other alkylamines, piperazine and tris(hydroxymethyl)- aminomethane; alkali metal salts, such as but not limited to lithium, potassium and sodium; alkali earth metal salts, such as but not limited to barium, calcium and magnesium; transition metal salts, such as but not limited to zinc; and other metal salts, such as but not limited to sodium hydrogen phosphate and disodium phosphate; and also including, but not limited to, salts of mineral acids, such as but not limited to hydrochlorides and sulfates; and salts of organic acids, such as but not limited to acetates, lactates, malates, tartrates, citrates, ascorbates, succinates, butyrates, valerates and fumarates. Pharmaceutically acceptable esters include, but are not limited to, alkyl, alkenyl, alkynyl, aryl, heteroaryl, aralkyl, heteroaralkyl, cycloalkyl and heterocyclyl esters of acidic groups, including, but not limited to, carboxylic acids, phosphoric acids, phosphinic acids, sulfonic acids, sulfinic acids and boronic acids. Pharmaceutically acceptable enol ethers include, but are not limited to, derivatives of formula C=C(OR) where R is hydrogen, alkyl, alkenyl, alkynyl, aryl, heteroaryl, aralkyl, heteroaralkyl, cycloalkyl or heterocyclyl. Pharmaceutically acceptable enol esters include, but are not limited to, derivatives of formula C=C(OC(O)R) where R is hydrogen, alkyl, alkenyl, alkynyl, aryl, heteroaryl, aralkyl, heteroaralkyl, cycloalkyl or heterocyclyl. Pharmaceutically acceptable solvates and hydrates are complexes of a compound with one or more solvent or water molecules, or 1 to about 100, or 1 to about 10, or one to about 2, 3 or 4, solvent or water molecules.

As used herein, the term "membrane reactor" refers to any reaction vessel in which the catalyst, such as an enzyme, is enclosed in a reactor, either in solution or attached to a solid support, while low-molecular substances within the reactor are able to leave the reactor. In one embodiment, the membrane of the reactor can be integrated directly into the reaction chamber. In another embodiment, the membrane is incorporated outside the reactor

chamber in a separate filtration module, with the reaction solution flowing continuously or intermittently through the filtration module, and with the retentate being recirculated into the reactor.

As used herein, "levetiracetam" refers to (S)-α-ethyl-2-oxo-1-pyrrolidine acetamide or a pharmaceutically acceptable salt thereof.

As used herein, an allelic variant or allelic variation references a polypeptide encoded by a gene that differs from a reference form of a gene (i.e. is encoded by an allele) among a population. Typically the reference form of the gene encodes an unmodified form and/or predominant form of a polypeptide from a population or single reference member of a species. Typically, allelic variants, have at least 80%, 90%, 95% or greater amino acid identity with an unmodified and/or predominant form from the same species.

As used herein, species variants refers to variants of the same polypeptide between and among species. Generally, interspecies allelic variants have at least about 50%, 60%, 70%. 80%, 85%, 90% or 95% identity or greater with an unmodified and/or predominant form from another species, including 96%, 97%, 98%, 99% or greater identity with an unmodified and/or predominant form of a polypeptide.

As used herein, "native nitrile hydratase polypeptide" refers to nitrile hydratase polypeptide encoded by a naturally occurring nitrile hydratase gene, i.e. a nitrile hydratase gene that is present in an organism in nature, such as in a bacteria, fungus, or yeast. Included among native nitrile hydratase polypeptides are the encoded precursor polypeptide, fragments thereof, and processed forms thereof, such as any pre- or post- translationally processed or modified form thereof. For example, bacteria express nitrile hydratase. Also included among native nitrile hydratase polypeptides are those that are post-translationally modified, including those that are proteolytically processed at the C- terminus, and those that include other post-translational modifications such as, for example, glycosylation. Other organism, such as fungi and yeast, express native nitrile hydratase. As noted above, in nature, the polypeptides can occur as a heterogeneous mixture that contains polypeptides of varying lengths and epigenetic modification, such as differences in glycosylation patterns.

As used herein, a "portion or fragment of an NHase polypeptide" or "an active portion" refers to any portion of a NHase polypeptide that exhibits one or more activities of the full-length polypeptide.

As used herein, an "activity" of an NHase polypeptide refers to any activity exhibited by an NHase polypeptide. Such activities can be tested in vitro and include, but are not limited to, catalytic activity, nitrile substrate hydration activity (e.g. nitrile hydration to an amide product) and the ability to bind substrate. Activity can be any level of percentage of activity of the polypeptide, including but not limited to, 1% of the activity, 2%, 3%, 4%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more of functional activity compared to the full-length unmodified polypeptide. For example, percentage of activity of the polypeptide also includes 96%, 97%, 98%, 99%, 100%, 200%, 300%, 400%, 500%, or more of functional activity compared to the full- length unmodified polypeptide. Activity can be assessed in vitro or in vivo using recognized assays well known in the art. For example, the formation of an amide product from a nitrile product can be detected by, for example, HPLC (see e.g. Example 8).

As used herein, "exhibits at least one activity" or "retains at least one activity" refers to the activity exhibited by a modified NHase polypeptide as compared to an unmodified NHase polypeptide. Generally, a modified NHase polypeptide that retains an activity of an unmodified NHase polypeptide either improves or maintains the requisite biological activity (e.g. , conversion of a nitrile substrate to a corresponding amide product) of an unmodified NHase polypeptide. In some instances, a modified NHase polypeptide exhibits an activity that is increased compared to an unmodified NHase polypeptide. Activity of a modified polypeptide can be any level of percentage of activity of the unmodified polypeptide, including but not limited to, 1% of the activity, 2%, 3%, 4%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200%, 300%, 400%, 500%, or more of functional activity compared to the unmodified polypeptide. For example, a modified NHase polypeptide retains at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, ... 20%, ... 30%, ... 40%, ... 50%, ... 60%, ... 70%. ...80%, ...90%, ... 95%, 96%, 97%, 98% or at least 99% of the activity of the unmodified NHase polypeptide. In other embodiments, the change in activity is at least about 2 times, 3 times, 4 times, 5 times, 6 times, 7 times, 8 times, 9 times, 10 times, 20 times, 30 times, 40 times, 50 times, 60 times, 70 times, 80 times, 90 times, 100 times, 200

times, 300 times, 400 times, 500 times, 600 times, 700 times, 800 times, 900 times, 1000 times, or more times greater than unmodified NHase polypeptide. Activity can be measured, for example, using assays such as those described in the Examples below.

As used herein, the phrase "structural homology" refers to the degree of coincidence in space between two or more protein backbones. Protein backbones that adopt the same protein structure, fold and show similarity upon three-dimensional structural superposition in space can be considered structurally homologous. Structural homology is not based on sequence homology, but rather on three-dimensional homology. Two amino acids in two different proteins said to be homologous based on structural homology between those proteins do not necessarily need to be in sequence- based homologous regions. For example, protein backbones that have a root mean squared (RMS) deviation of less than 3.5, 3.0, 2.5, 2.0, 1.7 or 1.5 angstroms at a given space position or defined region between each other can be considered to be structurally homologous in that region and are referred to herein as having a "high coincidence" between their backbones. It is contemplated herein that substantially equivalent (e.g., "structurally related") amino acid positions that are located on two or more different protein sequences that share a certain degree of structural homology have comparable functional tasks; also referred to herein as "structurally homologous loci." These two amino acids then can be said to be "structurally similar" or "structurally related" with each other, even if their precise primary linear positions on the sequences of amino acids, when these sequences are aligned, do not match with each other. Amino acids that are "structurally related" can be far away from each other in the primary protein sequences, when these sequences are aligned following the rules of classical sequence homology. As used herein, a "structural homolog" is a protein that is generated by structural homology. As used herein, "unmodified target protein," "unmodified protein" or "unmodified polypeptide," "unmodified NHase," "unmodified nitrile hydratase" or grammatical variations thereof refer to a starting protein that is selected for modification. The starting unmodified target protein includes a naturally-occurring, native wild-type form of a protein, or a recombinantly produced or synthetically produced polypeptide. Included among various forms of unmodified NHase polypeptides that are contemplated for modification herein, are nitrile hydratase polypeptides that include an α subunit or β subunit whose sequence of amino acid residues is set forth in any of SEQ ID NOS:2-49,

or any polymorphic form of nitrile hydratase thereof. Also included are NHase polypeptides containing N- or C- terminal truncations as compared to the sequence of amino acids of an unmodified NHase.

In addition, the starting unmodified target protein can have been altered or mutated, such that it differs from the native unmodified isoform but is nonetheless referred to herein as a starting unmodified target protein relative to the subsequently modified proteins produced herein. Thus, existing proteins known in the art that have previously been modified to have a desired increase or decrease in a particular activity compared to an unmodified reference protein can be selected and used herein as the starting target protein for further modification. For example, a protein that has been modified from its native form by one or more single amino acid changes and possesses either an increase or decrease in a desired activity, such as rate of conversion, can be used with the methods provided herein as the starting unmodified target protein for further modification of either the same or a different activity. Existing proteins known in the art that previously have been modified to have a desired alteration, such as an increase or decrease, in a particular activity compared to an unmodified or reference protein can be selected and used as provided herein for identification of structurally homologous loci on other structurally homologous target proteins. For example, a protein that has been modified by one or more single amino acid changes and possesses either an increase or decrease in a desired activity, such rate of conversion, can be used with the methods provided herein to identify structurally homologous target proteins, corresponding structurally homologous loci that can be replaced with suitable replacing amino acids and tested for either an increase or decrease in the desired activity. As used herein, "variant," "NHase variant," "modified nitrile hydratase polypeptides" and "modified NHase polypeptides" refers to a nitrile hydratase polypeptide that has one or more mutations compared to an unmodified Nitrile hydratase polypeptide. The one or more mutations can be one or amino acid replacements, insertions or deletions and any combination thereof. Typically, a modified Nitrile hydratase polypeptide has one or more modifications in primary sequence compared to an unmodified NHase. For example, a modified NHase polypeptide provided herein can have 1 , 2, 3, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more mutations

compared to an unmodified NHase polypeptide. Modified NHase polypeptides provided herein include the specified or recited modification, but can be produced as heterogeneous mixtures and/or can be produced with a variety of lengths. Any length polypeptide is contemplated as long as the resulting polypeptide exhibits at least one NHase activity associated with a longer form.

As used herein, an "nitrile hydratase polypeptide that has only a single mutation" refers to a modified NHase polypeptide whose sequence, when aligned with the sequence of an unmodified NHase polypeptide (of corresponding length), contains only one amino acid difference in amino acid sequence compared to the sequence of the unmodified NHase polypeptide.

As used herein, an "nitrile hydratase polypeptide that has 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more mutations" refers to a modified NHase polypeptide whose sequence, when aligned with a sequence of an unmodified NHase polypeptide (of corresponding length), contains 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more amino acid differences in amino acid sequence compared to the sequence of the unmodified NHase polypeptide.

As used herein, "corresponding length" with reference to an unmodified polypeptide, means that the modified polypeptide is compared to an unmodified polypeptide of the same number of amino acids. As noted herein, NHase polypeptides can be heterogeneous in length. For determining the number of mutations, polypeptides of the same length are compared.

As used herein, a "single amino acid replacement" refers to the replacement of one amino acid by another amino acid. The replacement can be by a natural amino acid or non-natural amino acids or modified amino acids. When one amino acid is replaced by another amino acid in a protein, the total number of amino acids in the protein is unchanged.

As used herein, "in a position or positions corresponding to an amino acid position" of a protein, refers to amino acid positions that are determined to correspond to one another based on sequence and/or structural alignments with a specified reference protein. For example, in a position corresponding to an amino acid position of NHase set forth as SEQ ID NO: 1 can be determined empirically by aligning the sequence of amino acids set forth in SEQ ID NO: 1 with a particular NHase of interest. Corresponding

positions can be determined by such alignment by one of skill in the art using manual alignments or by using the numerous alignment programs available (for example, BLASTP). Corresponding positions also can be based on structural alignments, for example by using computer simulated alignments of protein structure. Recitation that amino acids of a polypeptide correspond to amino acids in a disclosed sequence refers to amino acids identified upon alignment of the polypeptide with the disclosed sequence to maximize identity or homology (where conserved amino acids are aligned) using a standard alignment algorithm, such as the GAP algorithm. As used herein, "at a position corresponding to" refers to a position of interest (i.e., base number or residue number) in a nucleic acid molecule or protein relative to the position in another reference nucleic acid molecule or protein. The position of interest to the position in another reference protein can be in, for example, a precursor protein, an allelic variant, a heterologous protein, an amino acid sequence from the same protein of another species, etc. Corresponding positions can be determined by comparing and aligning sequences to maximize the number of matching nucleotides or residues, for example, such that identity between the sequences is greater than 95%, preferably greater than 96%, more preferably greater than 97%, even more preferably greater than 98% and most preferably greater than 99%. The position of interest is then given the number assigned in the reference nucleic acid molecule. By aligning the sequences of nitrile hydratase polypeptides, one skilled in the art can identify corresponding residues, using conserved and identical amino acid residues as guides. In other instances, corresponding regions can be identified. One skilled in the art also can employ conserved amino acid residues as guides to find corresponding amino acid residues between and among NHase sequences from different species. As used herein, the terms "homology" and "identity"" are used interchangeably, but homology for proteins can include conservative amino acid changes. In general to identify corresponding positions the sequences of amino acids are aligned so that the highest order match is obtained (see, e.g.: Computational Molecular Biology. Lesk, A.M., ed., Oxford University Press, New York, 1988; Biocomputing: Informatics and Genome Projects, Smith, D. W., ed., Academic Press, New York, 1993; Computer Analysis of

Sequence Data, Part I, Griffin, A.M., and Griffin, H. G., eds., Humana Press, New Jersey, 1994; Sequence Analysis in Molecular Biology, von Heinje, G., Academic Press, 1987;

and Sequence Analysis Primer, Gribskov, M. and Devereux, J., eds., M Stockton Press, New York, 1991; Carillo et al. (1988) SIAM J Applied Math 48:1073).

As use herein, "sequence identity" refers to the number of identical amino acids (or nucleotide bases) in a comparison between a test and a reference polypeptide or polynucleotide. Homologous polypeptides refer to a pre-determined number of identical or homologous amino acid residues. Homology includes conservative amino acid substitutions as well identical residues. Sequence identity can be determined by standard alignment algorithm programs used with default gap penalties established by each supplier. Homologous nucleic acid molecules refer to a pre-determined number of identical or homologous nucleotides. Homology includes substitutions that do not change the encoded amino acid (i.e., "silent substitutions") as well identical residues. Substantially homologous nucleic acid molecules hybridize typically at moderate stringency or at high stringency all along the length of the nucleic acid or along at least about 70%, 80% or 90% of the full-length nucleic acid molecule of interest. Also contemplated are nucleic acid molecules that contain degenerate codons in place of codons in the hybridizing nucleic acid molecule. (For determination of homology of proteins, conservative amino acids can be aligned as well as identical amino acids; in this case, percentage of identity and percentage homology vary). Whether any two nucleic acid molecules have nucleotide sequences (or any two polypeptides have amino acid sequences) that are at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% "identical" can be determined using known computer algorithms such as the "FAST A" program, using for example, the default parameters as in Pearson et al. Proc. Natl. Acad. Sci. USA 85: 2444 (1988) (other programs include the GCG program package (Devereux, J., et al., Nucleic Acids Research 12(1): 387 (1984)), BLASTP, BLASTN, FASTA (Atschul, S.F., et al., J. Molec. Biol. 215:403 (1990); Guide to Huge Computers. Martin J. Bishop, ed., Academic Press, San Diego (1994), and Carillo et al. SIAM J Applied Math 48: 1073 (1988)). For example, the BLAST function of the National Center for Biotechnology Information database can be used to determine identity. Other commercially or publicly available programs include, DNAStar "MegAlign" program (Madison, WI) and the University of Wisconsin Genetics Computer Group (UWG) "Gap" program (Madison WI)). Percent homology or identity of proteins and/or nucleic acid molecules can be determined, for example, by comparing sequence information using a GAP computer

program (e.g., Needleman et al. J. MoI. Biol. 48: 443 (1970), as revised by Smith and Waterman (Adv. Appl. Math. 2: 482 (1981)). Briefly, a GAP program defines similarity as the number of aligned symbols (i.e., nucleotides or amino acids) which are similar, divided by the total number of symbols in the shorter of the two sequences. Default parameters for the GAP program can include: (1) a unary comparison matrix (containing a value of 1 for identities and 0 for non identities) and the weighted comparison matrix of Gribskov et al. Nucl. Acids Res. 14: 6745 (1986), as described by Schwartz and Dayhoff, eds., Atlas of Protein Sequence and Structure. National Biomedical Research Foundation, pp. 353-358 (1979); (2) a penalty of 3.0 for each gap and an additional 0.10 penalty for each symbol in each gap; and (3) no penalty for end gaps. Therefore, as used herein, the term "identity" represents a comparison between a test and a reference polypeptide or polynucleotide. For example, a test polypeptide can be defined as any polypeptide that is 90% or more identical to a reference polypeptide. In one non-limiting example, "at least 90% identical to" refers to percent identities from 90 to 100% relative to the reference polypeptides. Identity at a level of 90% or more is indicative of the fact that, assuming for exemplification purposes a test and reference polynucleotide length of 100 amino acids are compared, no more than 10% (i.e., 10 out of 100) of amino acids in the test polypeptide differs from that of the reference polypeptides. Similar comparisons can be made between a test and reference polynucleotides. Such differences can be represented as point mutations randomly distributed over the entire length of an amino acid sequence or they can be clustered in one or more locations of varying length up to the maximum allowable, e.g., 10/100 amino acid difference (approximately 90% identity). Differences are defined as nucleic acid or amino acid substitutions, insertions or deletions. At the level of homologies or identities above about 85-90%, the result should be independent of the program and gap parameters set; such high levels of identity can be assessed readily, often without relying on software.

As used herein, "corresponding structurally-related" positions on two or more proteins, such as NHase polypeptides, refer to those amino acid positions determined based upon structural homology to maximize tri-dimensional overlapping between proteins.

As used herein, the phrase "sequence-related proteins" refers to proteins that have at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95% amino acid sequence identity or homology with each other.

As used herein, families of non-related proteins or "sequence-non-related proteins" refer to proteins having less than 50%, less than 40%, less than 30%, less than 20% amino acid identity or homology with each other.

As used herein, it also is understood that the terms "substantially identical" or "similar" varies with the context as understood by those skilled in the relevant art.

As used herein, a polypeptide complex includes polypeptides produced by chemical modification or post-translational modification. Such modifications include, but are not limited to, pegylation, albumination, glycosylation, farnysylation, phosphorylation and other polypeptide modifications known in the art.

As used herein, nucleic acids include DNA, RNA and analogs thereof, including protein nucleic acids (PNA) and mixtures thereof. Nucleic acids can be single- or double- stranded. When referring to probes or primers (optionally labeled with a detectable label, e.g., a fluorescent or a radiolabel), single-stranded molecules are contemplated. Such molecules are typically of a length such that they are statistically unique of low copy number (typically less than 5, generally less than 3) for probing or priming a library. Generally a probe or primer contains at least 14, 16 or 30 contiguous of sequence complementary to, or identical to, a gene of interest. Probes and primers can be 10, 14, 16, 20, 30, 50, 100 or more nucleic acid bases long.

As used herein, heterologous or foreign nucleic acid, such as DNA and RNA, are used interchangeably and refer to DNA or RNA that does not occur naturally as part of the genome in which it occurs or is found at a locus or loci in a genome that differs from that in which it occurs in nature. Heterologous nucleic acid includes nucleic acid not endogenous to the cell into which it is introduced, but that has been obtained from another cell or prepared synthetically. Generally, although not necessarily, such nucleic acid encodes RNA and proteins that are not normally produced by the cell in which it is expressed. Heterologous DNA herein encompasses any DNA or RNA that one of skill in the art recognizes or considers as heterologous or foreign to the cell or locus in or at which it is expressed. Heterologous DNA and RNA also can encode RNA or proteins that mediate or alter expression of endogenous DNA by affecting transcription,

translation, or other regulatable biochemical processes. Examples of heterologous nucleic acid include, but are not limited to, nucleic acid that encodes traceable marker proteins (e.g., a protein that confers drug resistance), nucleic acid that encodes therapeutically effective substances (e.g. , anti-cancer agents), enzymes and hormones, and DNA that encodes other types of proteins (e.g., antibodies). Hence, herein heterologous DNA or foreign DNA, includes a DNA molecule not present in the exact orientation and position as the counterpart DNA molecule found in the genome. It also can refer to a DNA molecule from another organism or species (i.e., exogenous).

As used herein, "isolated with reference to a nucleic acid molecule or polypeptide or other biomolecule" means that the nucleic acid or polypeptide has been separated from the genetic environment from which the polypeptide or nucleic acid were obtained. It also can mean altered from the natural state. For example, a polynucleotide or a polypeptide naturally present in a living animal is not "isolated," but the same polynucleotide or polypeptide separated from the coexisting materials of its natural state is "isolated," as the term is employed herein. Thus, a polypeptide or polynucleotide produced and/or contained within a recombinant host cell is considered isolated. Also intended as an "isolated polypeptide" or an "isolated polynucleotide" are polypeptides or polynucleotides that have been partially or substantially purified from a recombinant host cell or from a native source. For example, a recombinantly produced version of a compound can be substantially purified by the one-step method described in Smith et al., Gene, 67:31-40 (1988). The terms isolated and purified can be used interchangeably.

Thus, by "isolated" it is meant that the nucleic acid is free of coding sequences of those genes that, in the naturally-occurring genome of the organism (if any), immediately flank the gene encoding the nucleic acid of interest. Isolated DNA can be single-stranded or double-stranded, and can be genomic DNA, cDNA, recombinant hybrid DNA or synthetic DNA. It can be identical to a starting DNA sequence or can differ from such sequence by the deletion, addition, or substitution of one or more nucleotides.

"Isolated" or "purified" preparations made from biological cells or hosts mean cell extracts containing the indicated DNA or protein including a crude extract of the DNA or protein of interest. For example, in the case of a protein, a purified preparation can be obtained following an individual technique or a series of preparative or biochemical techniques, and the DNA or protein of interest can be present at various degrees of purity

in these preparations. The procedures can include, but are not limited to, ammonium sulfate fractionation, gel filtration, ion exchange chromatography, affinity chromatography, density gradient centrifugation and electrophoresis.

A preparation of DNA or protein that is "substantially pure" or "isolated" should be understood to mean a preparation free from naturally-occurring materials with which such DNA or protein is normally associated in nature. "Essentially pure" should be understood to mean a highly purified preparation that contains at least 95% of the DNA or protein of interest.

A cell extract that contains the DNA or protein of interest should be understood to mean a homogenate preparation or cell-free preparation obtained from cells that express the protein or contain the DNA of interest. The term "cell extract" is intended to include culture media, especially spent culture media from which the cells have been removed.

As used herein, "recombinant" refers to any progeny formed as the result of genetic engineering. As used herein, a "promoter region" refers to the portion of DNA of a gene that controls transcription of the DNA to which it is operatively linked. The promoter region includes specific sequences of DNA sufficient for RNA polymerase recognition, binding and transcription initiation. This portion of the promoter region is referred to as the "promoter". In addition, the promoter region includes sequences that modulate this recognition, binding and transcription initiation activity of the RNA polymerase.

Promoters, depending upon the nature of the regulation, can be constitutive or regulated by cis acting or trans acting factors.

As used herein, the phrase "operatively linked" generally means the sequences or segments have been covalently joined into one piece of DNA, whether in single- or double-stranded form, whereby control or regulatory sequences on one segment control or permit expression or replication or other such control of other segments. The two segments are not necessarily contiguous. For gene expression, a DNA sequence and a regulatory sequence(s) are connected in such a way to control or permit gene expression when the appropriate molecular, e.g., transcriptional activator proteins, are bound to the regulatory sequence(s).

As used herein, "production by recombinant means by using recombinant DNA methods" means the use of the well-known methods of molecular biology for expressing

proteins encoded by cloned DNA, including cloning expression of genes and methods, such as gene shuffling and phage display with screening for desired specificities. As used herein, a splice variant refers to a variant produced by differential processing of a primary transcript of genomic DNA that results in more than one type of mRNA.

As used herein, the term "vector" refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. One type of exemplary vector is an episome, i.e., a nucleic acid capable of extra-chromosomal replication. Exemplary vectors are those capable of autonomous replication and/or expression of nucleic acids to which they are linked; such vectors typically include origins of replication. Vectors also can be designed for integration into host chromosomes. Vectors capable of directing the expression of genes to which they are operatively linked are referred to herein as "expression vectors." Expression vectors are often in the form of "plasmids," which refer generally to circular double-stranded DNA loops which, in their vector form are not bound to the chromosome. "Plasmid" and "vector" are used interchangeably as the plasmid is the most commonly used form of vectors. Other such other forms of expression vectors that serve equivalent functions and that become known in the art subsequently hereto.

As used herein, vector also includes "virus vectors" or "viral vectors." Viral vectors are engineered viruses that are operatively linked to exogenous genes to transfer (as vehicles or shuttles) the exogenous genes into cells.

As used herein, "allele," which is used interchangeably herein with "allelic variant" refers to alternative forms of a gene or portions thereof. Alleles occupy the same locus or position on homologous chromosomes. When a subject has two identical alleles of a gene, the subject is said to be homozygous for that gene or allele. When a subject has two different alleles of a gene, the subject is said to be heterozygous for the gene. Alleles of a specific gene can differ from each other in a single nucleotide or several nucleotides, and can include substitutions, deletions and insertions of nucleotides. An allele of a gene also can be a form of a gene containing a mutation. As used herein, the terms "gene" or "recombinant gene" refer to a nucleic acid molecule containing an open reading frame and including at least one exon and,

optionally, an intron-encoding sequence. A gene can be either RNA or DNA. Genes can include regions preceding and following the coding region (leader and trailer).

As used herein, "intron" refers to a DNA sequence present in a given gene which is spliced out during mRNA maturation. As used herein, "nucleotide sequence complementary to the nucleotide sequence encoding the amino acid sequence set forth in SEQ ID NO:" refers to the nucleotide sequence of the complementary strand of a nucleic acid strand encoding a polypeptide that includes an amino acid sequence having the particular SEQ ID NO:. The term "complementary strand" is used herein interchangeably with the term "complement." The complement of a nucleic acid strand can be the complement of a coding strand or the complement of a non-coding strand. When referring to double-stranded nucleic acids, the complement of a nucleic acid encoding a polypeptide containing amino acid residues having a sequence set forth in a particular SEQ ID NO: refers to the complementary strand of the strand encoding the amino acid sequence set forth in the particular SEQ ID NO: or to any nucleic acid molecule containing the nucleotide sequence of the complementary strand of the particular nucleic acid sequence. When referring to a single- stranded nucleic acid molecule containing a nucleotide sequence, the complement of this nucleic acid is a nucleic acid having a nucleotide sequence which is complementary to that of the particular nucleic acid sequence. As used herein, the term "coding sequence" refers to that portion of a gene that encodes a sequence of amino acids present in a protein.

As used herein, the term "coding sequence" refers to that portion of a gene that encodes a sequence of amino acids present in a protein.

As used herein, the term "sense strand" refers to that strand of a double-stranded nucleic acid molecule that has the sequence of the mRNA that encodes the sequence of amino acids encoded by the double-stranded nucleic acid molecule.

As used herein, the term "antisense strand" refers to that strand of a double- stranded nucleic acid molecule that is the complement of the sequence of the mRNA that encodes the sequence of amino acids encoded by the double-stranded nucleic acid molecule.

As used herein, an "array" refers to a collection of elements, such as nucleic acid molecules, containing three or more members. An addressable array is one in which the

members of the array are identifiable, typically by position on a solid phase support or by virtue of an identifiable or detectable label, such as by color, fluorescence, electronic signal (i.e., RF, microwave or other frequency that does not substantially alter the interaction of the molecules of interest), bar code or other symbology, chemical or other such label. In certain embodiments, the members of the array are immobilized to discrete identifiable loci on the surface of a solid phase or directly or indirectly linked to or otherwise associated with the identifiable label, such as affixed to a microsphere or other particulate support (herein referred to as beads) and suspended in solution or spread out on a surface. As used herein, a "support" (e.g., a matrix support, a matrix, an insoluble support or solid support, etc.) refers to any solid or semisolid or insoluble support to which a molecule of interest (e.g., a biological molecule, organic molecule or biospecific ligand) is linked or contacted. Such materials include any materials that are used as affinity matrices or supports for chemical and biological molecule syntheses and analyses, such as, but are not limited to: polystyrene, polycarbonate, polypropylene, nylon, glass, dextran, chitin, sand, pumice, agarose, polysaccharides, dendrimers, buckyballs, polyacryl-amide, silicon, rubber, and other materials used as supports for solid phase syntheses, affinity separations and purifications, hybridization reactions, immunoassays and other such applications. The matrix herein can be particulate or can be in the form of a continuous surface, such as a microtiter dish or well, a glass slide, a silicon chip, a nitrocellulose sheet, nylon mesh, or other such materials. When particulate, typically the particles have at least one dimension in the 5-10 mm range or smaller. Such particles, referred collectively herein as "beads," are often, but not necessarily, spherical. Such reference, however, does not constrain the geometry of the matrix, which can be any shape, including random shapes, needles, fibers, and elongated. Roughly spherical "beads," particularly microspheres that can be used in the liquid phase, also are contemplated. The "beads" can include additional components, such as magnetic or paramagnetic particles (see, for example, Dynabeads (Dynal, Oslo, Norway)) for separation using magnets as long as the additional components do not interfere with the methods and analyses herein.

As used herein, matrix or support particles refer to matrix materials that are in the form of discrete particles. The particles have any shape and dimensions, but typically

have at least one dimension that is 100 mm or less, 50 mm or less, 10 mm or less, 1 mm or less, 100 μm or less, 50 μm or less and typically have a size that is 100 mm ³ or less, 50 mm ³ or less, 10 mm ³ or less, and 1 mm ³ or less, 100 μm ³ or less and can be order of cubic microns. Such particles are collectively called "beads."

B. Processes for the Production of Intermediates and Levetiracetam

The following synthetic strategies are useful in the preparation of levetiracetam and related compounds. A compound of Formula IV can be prepared from a compound of Formula I, as shown in Scheme I. Scheme I

wherein R ¹ is selected from among hydrogen, C ₁ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl, aryl and heteroaryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl and heteroaryl are optionally substituted;

R ² is selected from among hydrogen, F, Cl, Br, I, CN, NO ₂ , OR', SR', SOR', SO ₂ R', CO ₂ R', NR'R", C(=O)NR'R", NR'C(=O)R", C, -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl, aryl and heteroaryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl and heteroaryl are optionally substituted;

R' and R" each independently is selected from among hydrogen, C ₁ -C ₈ alkyl, C ₂ - C ₈ alkenyl, C ₂ -C ₈ alkynyl, C ₁ -C ₈ haloalkyl, C ₁ -C ₈ heteroalkyl, heteroaryl and aryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, heteroaryl and aryl are optionally substituted; L is a leaving group selected from among OSO ₂ R ³ , 1, Br, Cl, F, N ₂ ⁺ , O(R ^a ) ₂ ⁺ ,

ONO ₂ , OPO(OH) ₂ , OB(OH) ₂ , S(R ^a ) ₂ ⁺ and N(R ^a ) ₃ ⁺ ; each R ^a is independently selected from among hydrogen, C ₁ -C ₈ alkyl, C ₂ -C ₈ alkenyl, C ₂ -C ₈ alkynyl, C ₁ -C ₈ haloalkyl, C ₁ -C ₈ heteroalkyl, heteroaryl and aryl, wherein

the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, heteroaryl and aryl are optionally substituted;

A is selected from among oxygen, sulfur and NR'; n is selected from among an integer of 1 , 2, 3, 4 and 5; and m is selected from among an integer of 0, 1, 2, 3, 4, 5, 6, 7 and 8.

For any and all of the embodiments, substituents can be selected from among a subset of the listed alternatives.

For example, in certain embodiments, R ¹ is selected from among hydrogen, C ₁ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl, aryl and heteroaryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl and heteroaryl are optionally substituted with a substituent selected from among halo, hydroxy, amino, cyano, nitro, alkylamido, acyl, C ₁ -C ₆ -alkoxy, C ₁ -C ₆ -alkyl, C ₁ -C ₆ -haloalkyl, C ₁ -C ₆ -hydroxy-alkyl, C ₁ - C ₆ -aminoalkyl, C ₁ -C ₆ -alkylamino, alkylsulfenyl, alkylsulfinyl, alkylsulfonyl, sulfamoyl and trifluoromethyl.

In certain embodiments, R ¹ is selected from among C ₂ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl having 1-5 heteroatoms selected from among O, N, S and P, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl having 1-5 heteroatoms selected from among O, N, S and P, phenyl and benzyl. In other embodiments, R ¹ is selected from among C ₂ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -

C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl having 1-5 heteroatoms selected from among O, N, S and P, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl having 1 -5 heteroatoms selected from among O, N, S and P, phenyl and benzyl wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, phenyl and benzyl are optionally substituted with a substituent selected from among halo, hydroxy, amino, cyano, nitro, alkylamido, acyl, C ₁ -C ₆ -alkoxy, C ₁ -C ₆ -alkyl, C ₁ -C ₆ -haloalkyl, C ₁ -C ₆ - hydroxy-alkyl, C ₁ -C ₆ -aminoalkyl, C ₁ -C ₆ -alkylamino, alkylsulfenyl, alkylsulfinyl, alkylsulfonyl, sulfamoyl and trifluoromethyl.

In other embodiments, R ¹ is selected from among C ₂ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl having 1-5 heteroatoms selected from among O, N, S and P. In other embodiments, R ¹ is selected from among C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl having 1 -5 heteroatoms selected from among O, N, S and P.

In some embodiments, R ¹ is a mono- or bicyclic C ₃ - C ₁₂ aryl or mono- or bicyclic C ₃ -C ₁₂ heteroaryl having one to ten heteroatoms selected from among O, N, S and P, wherein the aryl and heteroaryl are optionally substituted with a substituent selected from among halo, hydroxy, amino, cyano, nitro, alkylamido, acyl, C _1-6 -alkoxy, C ₁ -C ₆ -alkyl, C ₁ -C ₆ -haloalkyl, C ₁ -C ₆ -hydroxy-alkyl, C ₁ -C ₆ -aminoalkyl, C ₁ -C ₆ -alkylamino, alkylsulfenyl, alkylsulfinyl, alkylsulfonyl, sulfamoyl and trifluoromethyl.

In some embodiments, R ¹ is phenyl or benzyl, wherein phenyl and benzyl are optionally substituted with a substituent selected from among halo, hydroxy, amino, cyano, nitro, alkylamido, acyl, C ₁ -C ₆ -alkoxy, C ₁ -C ₆ -alkyl, C ₁ -C ₆ -haloalkyl, C ₁ -C ₆ - hydroxy-alkyl, C ₁ -C ₆ -aminoalkyl, C ₁ -C ₆ -alkylamino, alkylsulfenyl, alkylsulfinyl, alkylsulfonyl, sulfamoyl and trifluoromethyl.

In some embodiments, R ² is selected from among hydrogen, F, Cl, Br, I, CN, NO ₂ , OR', SR', SOR', SO ₂ R', CO ₂ R', NR'R", C(=O)NR'R", NR'C(=O)R", C ₁ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl, C ₃ -C ₉ aryl and C ₃ -C ₉ heteroaryl, wherein R' and R" each independently is selected from among hydrogen, C ₁ -C ₈ alkyl, C ₂ -C ₈ alkenyl, C ₂ -C ₈ alkynyl, C ₁ -C ₈ haloalkyl, C ₁ -C ₈ heteroalkyl, heteroaryl and aryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, heteroaryl and aryl are optionally substituted with a substituent selected from among halo, hydroxy, amino, cyano, nitro, alkylamido, acyl, C ₁ -C ₆ -alkoxy, C ₁ -C ₆ -alkyl, C ₁ -C ₆ -haloalkyl, C ₁ -C ₆ -hydroxy-alkyl, C ₁ -C ₆ -aminoalkyl, C ₁ -C ₆ -alkylamino, alkylsulfenyl, alkylsulfinyl, alkylsulfonyl, sulfamoyl and trifluoromethyl.

In some embodiments, R ² is selected from among OR', SR', SOR', SO ₂ R', CO ₂ R', NR'R", C(=O)NR'R" and NR'C(=O)R", wherein R' and R" each independently is selected from among hydrogen, C ₁ -C ₈ alkyl, C ₂ -C ₈ alkenyl, C ₂ -C ₈ alkynyl, C ₁ -C ₈ haloalkyl, C ₁ -C ₈ heteroalkyl, heteroaryl and aryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, heteroaryl and aryl are optionally substituted with a substituent selected from among halo, hydroxy, amino, cyano, nitro, alkylamido, acyl, C ₁ -C ₆ -alkoxy, C ₁ -C ₆ -alkyl, C ₁ -C ₆ -haloalkyl, C ₁ -C ₆ -hydroxy-alkyl, C ₁ -C ₆ -aminoalkyl, C ₁ -C ₆ -alkylamino, alkylsulfenyl, alkylsulfinyl, alkylsulfonyl, sulfamoyl and trifluoromethyl. In some embodiments, R ² is selected from among OR', SR', SOR', SO ₂ R', CO ₂ R',

NR'R", C(=O)NR'R" and NR'C(=O)R", wherein R' and R" each independently is selected from among hydrogen, C ₁ -C ₈ alkyl, C ₂ -C ₈ alkenyl, C ₂ -C ₈ alkynyl, C ₁ -C ₈ haloalkyl and

C ₁ -C ₈ heteroalkyl, wherein the alkyl, alkenyl, alkynyl, haloalkyl and heteroalkyl are optionally substituted with a substituent selected from among halo, hydroxy, amino, cyano, nitro, alkylamido, acyl, C ₁ -C ₆ -alkoxy, C ₁ -C ₆ -alkyl, C ₁ -C ₆ -haloalkyl, C ₁ -C ₆ - hydroxy-alkyl, C ₁ -C ₆ -aminoalkyl, C ₁ -C ₆ -alkylamino, alkylsulfenyl, alkylsulfinyl, alkylsulfonyl, sulfamoyl and trifluoromethyl.

In some embodiments, R ² is selected from among SR', SOR' and SO ₂ R', wherein R' is selected from among hydrogen, C ₁ -C ₈ alkyl, C ₂ -C ₈ alkenyl, C ₂ -C ₈ alkynyl, C ₁ -C ₈ haloalkyl and C ₁ -C ₈ heteroalkyl, wherein the alkyl, alkenyl, alkynyl, haloalkyl and heteroalkyl are optionally substituted with a substituent selected from among halo, hydroxy, amino, cyano, nitro, alkylamido, acyl, C ₁ -C ₆ -alkoxy, C ₁ -C ₆ -alkyl, C ₁ -C ₆ - haloalkyl, C ₁ -C ₆ -hydroxy-alkyl, C ₁ -C ₆ -aminoalkyl, C ₁ -C ₆ -alkylamino, alkylsulfenyl, alkylsulfinyl, alkylsulfonyl, sulfamoyl and trifluoromethyl.

In some embodiments, R ² is selected from among NR'R", C(=O)NR'R" and NR'C(=O)R", wherein R' and R" each independently is selected from among hydrogen, C ₁ -C ₈ alkyl, C ₂ -C ₈ alkenyl, C ₂ -C ₈ alkynyl, C ₁ -C ₈ haloalkyl and C ₁ -C ₈ heteroalkyl, wherein the alkyl, alkenyl, alkynyl, haloalkyl and heteroalkyl are optionally substituted with a substituent selected from among halo, hydroxy, amino, cyano, nitro, alkylamido, acyl, C ₁ -C ₆ -alkoxy, C ₁ -C ₆ -alkyl, C ₁ -C ₆ -haloalkyl, C ₁ -C ₆ -hydroxy-alkyl, C ₁ -C ₆ - aminoalkyl, C ₁ -C ₆ -alkylamino, alkylsulfenyl, alkylsulfinyl, alkylsulfonyl, sulfamoyl and trifluoromethyl.

In some embodiments, R is OR' or CO ₂ R', wherein R' is selected from among hydrogen, C ₁ -C ₈ alkyl, C ₂ -C ₈ alkenyl, C ₂ -C ₈ alkynyl, C ₁ -C ₈ haloalkyl and C ₁ -C ₈ heteroalkyl, wherein the alkyl, alkenyl, alkynyl, haloalkyl and heteroalkyl are optionally substituted with a substituent selected from among halo, hydroxy, amino, cyano, nitro, alkylamido, acyl, C ₁ -C ₆ -alkoxy, C ₁ -C ₆ -alkyl, C ₁ -C ₆ -haloalkyl, C ₁ -C ₆ -hydroxy-alkyl, C ₁ - C ₆ -aminoalkyl, C ₁ -C ₆ -alkylamino, alkylsulfenyl, alkylsulfinyl, alkylsulfonyl, sulfamoyl and trifluoromethyl.

In some embodiments, R ² is selected from among hydrogen, F, Cl, Br, I, CN, NO ₂ , C ₂ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl having 1-5 heteroatoms selected from among O, N, S and P, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl having 1 -5 heteroatoms selected from among O, N, S and P, phenyl and benzyl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, cycloalkyl,

heterocycloalkyl, phenyl and benzyl are optionally substituted with a substituent selected from among halo, hydroxy, amino, cyano, nitro, alkylamido, acyl, C ₁ -C ₆ -alkoxy, C ₁ -C ₆ - alkyl, C ₁ -C ₆ -haloalkyl, C ₁ -C ₆ -hydroxy-alkyl, C ₁ -C ₆ -aminoalkyl, C ₁ -C ₆ -alkylamino, alkylsulfenyl, alkylsulfinyl, alkylsulfonyl, sulfamoyl and trifluoromethyl. In some embodiments, R ² is selected from among hydrogen, F, Cl, Br, I, CN and

NO ₂ . In some embodiments, R ² is selected from among C ₂ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl and C ₁ -C ₆ heteroalkyl having 1-5 heteroatoms selected from among O, N, S and P.

In some embodiments, R ² is C ₃ -C ₈ cycloalkyl or C ₃ -C ₈ heterocycloalkyl having 1-5 heteroatoms selected from among O, N, S and P, wherein the cycloalkyl or heterocycloalkyl is optionally substituted with a substituent selected from among halo, hydroxy, amino, cyano, nitro, alkylamido, acyl, C ₁ -C ₆ -alkoxy, C ₁ -C ₆ -alkyl, C ₁ -C ₆ - haloalkyl, C ₁ -C ₆ -hydroxy-alkyl, C ₁ -C ₆ -aminoalkyl, C ₁ -C ₆ -alkylamino, alkylsulfenyl, alkylsulfinyl, alkylsulfonyl, sulfamoyl and trifluoromethyl. In some embodiments, R ² is a mono- or bicyclic C ₃ -C ₁₂ aryl or mono- or bicyclic C ₃ - C ₁₂ heteroaryl having one to ten heteroatoms selected from among O, N, S and P, wherein the aryl and heteroaryl are optionally substituted with a substituent selected from among halo, hydroxy, amino, cyano, nitro, alkylamido, acyl, C ₁ -C ₆ -alkoxy, C ₁ -C ₆ -alkyl, C ₁ -C ₆ - haloalkyl, C ₁ -C ₆ -hydroxy- alkyl, C ₁ -C ₆ -aminoalkyl, C ₁ -C ₆ -alkylamino, alkyl-sulfenyl, alkylsulfinyl, alkylsulfonyl, sulfamoyl and trifluoromethyl. In some embodiments, R ² is a benzyl or phenyl, wherein the benzyl and phenyl are optionally substituted with a substituent selected from among halo, hydroxy, amino, cyano, nitro, alkylamido, acyl, C ₁ -C ₆ -alkoxy, C ₁ - C ₆ -alkyl, C ₁ -C ₆ -haloalkyl, C ₁ -C ₆ -hydroxy-alkyl, C ₁ -C ₆ -aminoalkyl, C ₁ -C ₆ -alkylamino, alkylsulfenyl, alkylsulfinyl, alkylsulfonyl, sulfamoyl and trifluoromethyl. In some embodiments, A is selected from among oxygen, sulfur and NR', wherein

R' is selected from among hydrogen, C ₁ -C ₈ alkyl, C ₂ -C ₈ alkenyl, C ₂ -C ₈ alkynyl, C ₁ -C ₈ haloalkyl and C ₁ -C ₈ heteroalkyl, wherein the alkyl, alkenyl, alkynyl, haloalkyl and heteroalkyl are optionally substituted with a substituent selected from among halo, hydroxy, amino, cyano, nitro, alkylamido, acyl, C ₁ -C ₆ -alkoxy, C ₁ -C ₆ -alkyl, C ₁ -C ₆ - haloalkyl, C ₁ -C ₆ -hydroxy-alkyl, C ₁ -C ₆ -aminoalkyl, C ₁ -C ₆ -alkylamino, alkylsulfenyl, alkylsulfinyl, alkylsulfonyl, sulfamoyl and trifluoromethyl. In some embodiments, A is oxygen or sulfur. In some embodiments, A is oxygen. In some embodiments, A is sulfur.

In some embodiments, n is 1, 2, 3, 4 or 5. In some embodiments, n is 1. In some embodiments, n is 2. In some embodiments, n is 3. In some embodiments, n is 4. In some embodiments, n is 5.

In some embodiments, m is 0, 1, 2, 3, 4, 5, 6, 7 or 8. In some embodiments, m is 1. In some embodiments, m is 2. In some embodiments, m is 3. In some embodiments, m is 4. In some embodiments, m is 5. In some embodiments, m is 6. In some embodiments, m is 7. In some embodiments, m is 8.

In some embodiments, R ¹ is selected from among hydrogen, C ₁ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl, aryl and heteroaryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl and heteroaryl are optionally substituted;

R ² is selected from among hydrogen, F, Cl, Br, I, CN, NO ₂ , OR', SR', SOR', SO ₂ R', CO ₂ R', NR'R", C(=O)NR'R", NR'C(=O)R", C ,-C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl, aryl and heteroaryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl and heteroaryl are optionally substituted;

R' and R" each independently is selected from among hydrogen, C ₁ -C ₈ alkyl, C ₂ - C ₈ alkenyl, C ₂ -C ₈ alkynyl, C ₁ -C ₈ haloalkyl, C ₁ -C ₈ heteroalkyl, heteroaryl and aryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, heteroaryl and aryl are optionally substituted;

A is selected from among oxygen, sulfur and NR'; n is an integer selected from among 1, 2, 3, 4 and 5; and m is an integer selected from among 0, 1, 2, 3, 4, 5, 6, 7 and 8.

In some embodiments, R ¹ is selected from among C ₂ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ - C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl having 1-5 heteroatoms selected from among O, N, S and P, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl having 1 -5 heteroatoms selected from among O, N, S and P, phenyl and benzyl;

R ² is selected from among hydrogen, F, Cl, Br, I, CN, NO ₂ , C ₂ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl having 1-5 heteroatoms selected from among O, N, S and P, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl having 1-5 heteroatoms selected from among O, N, S and P, phenyl and benzyl;

A is oxygen or sulfur;

n is an integer selected from among 1, 2 and 3; and m is an integer selected from among 0, 1, 2, 3, 4, 5 and 6.

In some embodiments, R ¹ is selected from among C ₂ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ - C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl having 1-5 heteroatoms selected from among O, N, S and P, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocyclo alkyl having 1-5 heteroatoms selected from among O, N, S and P, phenyl and benzyl wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, phenyl and benzyl are optionally substituted with a substituent selected from among halo, hydroxy, amino, cyano, nitro, alkylamido, acyl, C ₁ -C ₆ -alkoxy, C ₁ -C ₆ -alkyl, C ₁ -C ₆ -haloalkyl, C ₁ -C ₆ - hydroxy-alkyl, C ₁ -C ₆ -aminoalkyl, C ₁ -C ₆ -alkylamino, alkylsulfenyl, alkylsulfinyl, alkylsulfonyl, sulfamoyl and trifluoromethyl;

R is selected from among hydrogen, C ₂ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl having 1-5 heteroatoms selected from among O, N, S and P, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl having 1-5 heteroatoms selected from among O, N, S and P, phenyl and benzyl wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, phenyl and benzyl are optionally substituted with a substituent selected from among halo, hydroxy, amino, cyano, nitro, alkylamido, acyl, C ₁ -C ₆ -alkoxy, C ₁ -C ₆ -alkyl, C ₁ -C ₆ -haloalkyl, C ₁ -C ₆ -hydroxy-alkyl, C ₁ -C ₆ - aminoalkyl, C ₁ -C ₆ -alkylamino, alkylsulfenyl, alkylsulfinyl, alkylsulfonyl, sulfamoyl and trifluoromethyl;

A is oxygen; n is 1 ; and m is 0 or 1.

In some embodiments, R ¹ is C ₂ -C ₆ alkyl; A is oxygen; n is 1 ; and m is 0. Scheme I. Formula I:

Compounds of Formula I, also known as α-hydroxynitriles or cyanohydrins, are commercially available or are readily prepared by one of skill in the art (see, e.g., U.S.

4,360,479; and U.S. 4,761,494). For example, compounds of Formula I include, but are not limited to, 2-hydroxypropanenitrile (Sigma-Aldrich Co., St. Louis, MO, Cat. No. 69830), 2-hydroxybutanenitrile (Sigma-Aldrich Co., Cat. No. 81880), 2- hydroxypentanenitrile, hydroxy(phenyl)ethanenitrile (Sigma-Aldrich Co., Cat. No.

12023), hydroxy(4-methylphenyl)ethanenitrile (Sigma-Aldrich Co., Cat. No. 469734),

hydroxy(4-methoxyphenyl)ethanenitrile (Sigma-Aldrich Co., Cat. No. 469688), and (4- chlorophenyl)(hydroxy)ethanenitrile (Sigma-Aldrich Co., Cat. No. 469742).

Scheme I, Formula H:

The hydroxyl group of a compound of Formula I is converted to a good leaving group (L) to afford a compound of Formula II. Any method known in the art for converting a hydroxyl group to a good leaving group can be used for this transformation (see, e.g., Smith and March, March's Advanced Organic Chemistry, 6 ^th ed., 2007, Wiley: Hoboken, NJ, p. 496-502). For example, the hydroxyl group can be converted to a halide by reaction with halogen acids, such as HBr, HCl, and HI, or by treatment with inorganic acid halides, such as (COCl) ₂ , SOCl ₂ , PCl ₅ , PCl ₃ , POCl ₃ , POBr ₃ and PBr ₃ (see, e.g.,

Smith and March, March's Advanced Organic Chemistry, 6 ^th ed., 2007, Wiley: Hoboken, NJ, p. 576-580). Other methods include treatment of the hydroxyl with NaX, KX, or NH ₄ X in a polyhydrogen fluoride-pyridine solution, where X is a halide (see, Olah et al., (1979) J. Org. Chem. 44:3872; and Yin et al., (2004) Org. Lett. 6:1465). The hydroxyl group can be converted to a sulfonic ester, such as a tosylate, benzenesulfonate, mesylate or triflate, by treatment with sulfonyl halides, such as toluenesulfonyl chloride, benzenesulfonyl chloride, methanesulfonyl chloride or trifluoromethanesulfonyl chloride, in the presence of a base, such as pyridine or triethylamine (see, e.g., Smith and March, March's Advanced Organic Chemistry, 6 ^th ed., 2007, Wiley: Hoboken, NJ, p. 545-547). The reaction can be performed at various temperatures and over various temperature ranges. The temperature depends upon various parameters such as reactant and solvent selection, and can be empirically determined. For example, the reaction can be performed at room temperature (e.g., 21 °C). The reaction can be performed below room temperature, for example, at temperatures between 5 to 0 °C, between 0 to -10 °C, between 0 to -20 °C, or between 0 to -35 °C (or lower). As reactant and solvent selection allow, the reaction can be performed at temperatures greater than room temperature, for example, at temperatures between 40-250 °C (or higher). The reaction can be performed between 40 to 80 °C, between 80 to 120 °C, between 120 to 180 °C, or between 150 to 250 °C. The reaction can be performed in various solvents and solvent combinations, including organic solutions, aqueous solutions and combinations thereof. A suitable solvent or solvent mixture can be determined empirically by one of skill in the art, taking

into account the properties of the reactants. The solvent can be an organic protic or aprotic solvent including, but not limiting to, an alcohol, such as t-butanol, acetone, ethyl acetate, dithianes, THF, dioxane, acetonitrile, nitromethane, dichloromethane, dichloroethane, chloroform, diethyl ether, dimethylformamide (DMF), dimethylsulfoxide (DMSO), dimethyl-acetamide, N-methylpyrrolidinone, hexanes, benzene, toluene, or any combination thereof.

The reaction can be performed with reactants at dilute or concentrated levels. For example, the reactants can be at concentrations between about 0.1 - 5 nmol/L, 0.01-0.5 mmol/L, 1-10 mmol/L, or 0.1-5 mol/L. The reaction can be performed over any time period. For example, the reaction can be conducted for about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58 or 59 minutes. The reaction can be conducted for about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 or 24 hours. The reaction can be conducted over a period of about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 days. The concentration and time for the reaction depend on various parameters such as temperature, solvent and reactants, and can be empirically determined.

The reaction can be homogeneous or heterogeneous. The reaction can' be a bi- phasic mixture or an emulsion, or the reactants can be immobilized to a solid support. The solid support can be selected from among metal, ceramic or plastic plates, beads, microbeads, membranes, filaments, microtitre trays, and the wall of a reaction chamber. For example, suitable solid supports include semi-permeable membranes, glass capillaries, alumina, alumina supported polymers, silica, chemically bonded hydrocarbons on silica, polyolefins, agarose, polysaccharides such as dextran, or glycoproteins such as fibronectin. One of skill in the art can determine appropriate conditions depending upon the reactant selected for the transformation.

Scheme I, Formula III:

The compound of Formula II is converted to a compound of Formula III by nucleophilic substitution of the leaving group with a nitrogen-containing heterocycle of the following structure:

wherein:

R ² is selected from among hydrogen, F, Cl, Br, I, CN, NO ₂ , OR', SR', SOR', SO ₂ R', CO ₂ R', NR'R", C(=O)NR'R", NR'C(=O)R", C ₁ -C ₆ alkyl, C ₂ -C ₆ alkenyl, C ₂ -C ₆ alkynyl, C ₁ -C ₆ haloalkyl, C ₁ -C ₆ heteroalkyl, C ₃ -C ₈ cycloalkyl, C ₃ -C ₈ heterocycloalkyl, aryl and heteroaryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl and heteroaryl are optionally substituted;

R' and R" each independently is selected from among hydrogen, C ₁ -C ₈ alkyl, C ₂ - C ₈ alkenyl, C ₂ -C ₈ alkynyl, C ₁ -C ₈ haloalkyl, C ₁ -C ₈ heteroalkyl, heteroaryl and aryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, heteroaryl and aryl are optionally substituted;

A is selected from among oxygen, sulfur and NR'; n is selected from among an integer of 1, 2, 3, 4 and 5; m is selected from among an integer of 0, 1, 2, 3, 4, 5, 6, 7 and 8; and Y is selected from among hydrogen, lithium, sodium, potassium, cesium, calcium, magnesium and a pair of electrons such that the nitrogen atom bears a negative charge. Any method known in the art for nucleophilic substitution can be used for this reaction. For example, the compound of Formula II can be reacted with a nitrogen- containing ring including, but not limited to, 2-pyrrolidinone, 2-pyrrolidinthione, 2- pyrrolidinimine, 2-piperidinone, 2-piperidinthione, 2-piperidinimine, 2-azepanone, 2- azepanthione, 2-azepanimine, 2-azocanone, 2-azocanethione or 2-azocanimine in the presence of a base, such as sodium t-butoxide, potassium t-butoxide, lithium t-butoxide or lithium hexamethyldisilazide (LHMDS).

The reaction can be performed at various temperatures and over various temperature ranges. The temperature depends upon various parameters such as reactant and solvent selection, and can be empirically determined. For example, the reaction can be performed at room temperature (e.g., 21 °C). The reaction can be performed below room temperature, for example, at temperatures between 5 to 0 °C, between 0 to -10 °C, between 0 to -20 °C, or between 0 to -35 °C (or lower). As reactant and solvent selection allow, the reaction can be performed at temperatures greater than room temperature, for

example, at temperatures between 40-250 °C (or higher). The reaction can be performed between 40 to 80 °C, between 80 to 120 °C, between 120 to 180 °C, or between 150 to 250 °C.

The reaction can be performed in various solvents and solvent combinations. A suitable solvent or solvent mixture can be determined empirically by one of skill in the art, taking into account the properties of the reactants. The solvent can be an organic solvent including, but not limiting to, acetone, ethyl acetate, dithianes, THF, dioxane, acetonitrile, dichloromethane, dichloroethane, chloroform, diethyl ether, dimethylformamide (DMF), dimethylsulfoxide (DMSO), dimethyl-acetamide, hexanes, benzene, toluene, or any combination thereof.

The reaction can be performed with reactants at dilute or concentrated levels. For example, the reactants can be at concentrations between about 0.1 - 5 nmol/L, 0.01-0.5 mmol/L, 1-10 mmol/L, or 0.1-5 mol/L. The reaction can be performed over any time period. For example, the reaction can be conducted for about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58 or 59 minutes. The reaction can be conducted for about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 or 24 hours. The reaction can be conducted over a period of about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 days. The concentration and time for the reaction depend on various parameters such as temperature, solvent and reactants, and can be empirically determined.

The reaction can be homogeneous or heterogeneous. The reaction can be a bi- phasic mixture or an emulsion, or the reactants can be immobilized to a solid support. The solid support can be selected from among metal, ceramic or plastic plates, beads, microbeads, membranes, filaments, microtitre trays, and the wall of a reaction chamber. For example, suitable solid supports include semi-permeable membranes, glass capillaries, alumina, alumina supported polymers, silica, chemically bonded hydrocarbons on silica, polyolefins, agarose, polysaccharides such as dextran, or glycoproteins such as fibronectin. One of skill in the art can determine appropriate conditions depending upon the reactant selected for the transformation.

Scheme I, Formula IV:

The compound of Formula III is a mixture of two enantiomeric nitriles (R- and S- isomers), and an enzyme can selectively hydrate one of the enantiomers such as the S- enantiomer to an amide, resulting in a compound of Formula IV. Selective conversion of one of the two enantiomeric nitriles to the optically pure, desired amide product is known in the art as enzymatic kinetic resolution. Any enzymatic transformation known in the art for converting a nitrile substrate to an amide product can be used for this process. An exemplary enzyme is a nitrile hydratase (EC 4.2.1.84).

Suitable conditions for the enzymatic preparation of amide products using nitrile hydratases are well known in the art (see, e.g., Martinkova et al., (2002) Biocatal.

Biotransform. 20:73-93; and U.S. 7,153,663). Wild-type microorganisms that have nitrile hydratase activity can be used to convert nitriles to the corresponding amides (see, e.g. Nagasawa et al., (1993) Appl. Microbiol. Biotechnol. 40:189-195; Cowan et al (1998) Extremophiles 2:207-216; and U.S. 7,153,663). For example, the nitrile hydratase of Rhodococcus rhodochrous Jl converts a variety of aromatic and heteroaromatic nitriles to the corresponding amides with 100% molar conversion (see, Mauger et al., (1989) Tetrahedron, 45:1347-1354; and Mauger et al., (1988) J. Biotechnol. 8:87-96).

In addition to the use of wild-type unmodified organisms, recombinant organisms containing heterologous genes for the expression of nitrile hydratase also convert a nitrile group to an amide. For example, nitrile hydratase genes were isolated from C. testosteroni and expressed in E. coli. (see, WO 9504828). The transformed hosts effectively convert nitriles to amides, including substrates comprising one nitrile and one carboxylate group. Other E. coli transformants that express nitrile hydratases have been reported (see, e.g., U.S. 6,316,242; U.S. 5,811,286; EP 5024576; and Wu et al., Appl. Microbiol. Biotechnol. (1997) 48:704-708).

Cell lysates of organisms containing genes for the expression of nitrile hydratase also convert nitriles to the corresponding amides (see, e.g., Kim et al., (2000), Enzyme Microb. Tech. 27:492-501). Also, isolated nitrile hydratase enzymes convert nitriles to the corresponding amides (see, e.g., Nagasawa et al., (1978) Eur. J. Biochem. 162:691- 698; Nagasawa et al., (1991) Eur. J. Biochem. 196:581-589; Payne et al., (1997) Biochemistry 36:5447-5454).

An aqueous reaction mixture containing the nitrile of Formula III is prepared by mixing the nitrile with an aqueous suspension of the nitrile hydratase catalyst. Intact microbial cells can be used as catalyst without any pretreatment, such as permeabilization or heating. Alternatively, the cells can be immobilized in a polymer matrix (e.g., alginate, carrageenan, polyvinyl alcohol, or polyacrylamide gel) or on a soluble or insoluble support (e.g., glass, plastic, a film, nitrocellulose, a sol-gel polymer, celite and silica) to facilitate recovery and reuse of the catalyst. Methods to immobilize cells in a polymer matrix or on a soluble or insoluble support have been widely reported and are well known to those skilled in the art. Lysates of cells that express nitrile hydratase can be used to convert the nitrile to the corresponding amide. The enzyme also can be isolated from the microbial cells and used directly as catalyst, or the enzyme can be immobilized in a polymer matrix or on a soluble or insoluble support. These methods have also been widely reported and are well known to those skilled in the art (Methods in Biotechnology, Vol. 1 : Immobilization of Enzymes and Cells; Gordon F. Bickerstaff, Editor; Humana Press, Totowa, N. J., USA; 1997).

Intact microbial cells, either immobilized or unimmobilized, containing genes that encode a polypeptide having nitrile hydratase activity, or containing genes that encode a combination of polypeptides separately having nitrile hydratase activity, can be used as catalyst without any pretreatment, such as permeabilization, freeze thawing or heating. Alternatively, the microbial cells can be permeabilized by methods familiar to those skilled in the art (e.g., treatment with toluene, detergents, or freeze-thawing) to improve the rate of diffusion of materials into and out of the cells. Methods for permeabilization of microbial cells are well-known to those skilled in the art (Felix, (1982) Anal. Biochem. 120:211-234). Some of the nitriles of Formula III can be moderately water soluble. Their solubility depends on the temperature of the solution and the salt concentration in the aqueous phase. The reaction can be carried out in an organic, aqueous or 2-phase system (including an organic solvent phase that is not miscible with water, such as ethyl acetate, and also an aqueous phase), or in an emulsion. Organic solvents include, but are not limited to, acetone, diisoproyl ether, methyl tert-butyl ether (MTBE), dibutyl ether, and ethyl acetate. Suitable aqueous phases include, but are not limited to, buffers such as

glutamic acid-glutamate, phosphoric acid-phosphate, acetic acid-acetate and citric acid- citrate buffers.

The aqueous phase of a two-phase reaction mixture can contain as much water as is sufficient to result in conversion of the nitrile to the corresponding amide and maintenance of the activity of the enzyme catalyst. The reaction also can be run by adding the nitrile to the reaction mixture at a rate approximately equal to the enzymatic hydration reaction rate, thereby maintaining a single-phase aqueous reaction mixture, thereby avoiding the potential problem of substrate inhibition of the enzyme at high starting material concentrations. The concentration of enzyme catalyst in the reaction mixture depends on the specific catalytic activity of the enzyme catalyst and is chosen to obtain the desired rate of reaction. The wet cell weight of the microbial cells used as catalyst in reactions typically ranges from 0.001 grams to 0.300 grams of wet cells per mL of total reaction volume, generally from 0.002 grams to 0.050 grams of wet cells per mL; the cells can be optionally immobilized as described above. The specific activity of the microbial cells (IU/gram dry cell weight) is determined by measuring the rate of conversion of a 0.10- 0.50 M solution of a nitrile substrate to the desired amide product at 25 °C, using a known weight of microbial cell catalyst. An IU of enzyme activity is defined as the amount of enzyme activity required to convert one micromole of substrate to product per minute. For the methods herein, typically 10 to 10,000 IU of nitrile hydratase is added to the reaction for every gram of nitrile.

The temperature of the reaction is selected to facilitate the reaction rate and the stability of enzyme catalyst. The temperature of the reaction can range from just above the freezing point of the reaction mixture (ca. 0 °C) to 65 °C, with a general range of reaction temperature of from 0 °C to 45 °C. In one embodiment, an ambient temperature is maintained throughout the reaction.

An enzyme catalyst solution or suspension can be prepared by suspending the unimmobilized or immobilized cells in distilled water, or in an aqueous reaction mixture of a buffer or by suspending the immobilized enzyme catalyst in a similar mixture, or by preparing a solution of a cell extract, partially purified or purified enzyme(s), or a soluble form of the immobilized enzymes in a similar mixture. A suitable pH for the reaction can be determined by one of skill in the art, taking into account the activity and stability of the

nitrile hydratase. A pH range from 2 to 11 is contemplated for the methods herein. Typically, however, the pH of the reaction is at or about 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.2, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, or 9.0. The reaction can be run to convert the nitrile with no pH control, or a suitable acid or base can be added over the course of the reaction to maintain the desired pH.

The reaction can be monitored by, for example, gas chromatography (GC), high performance liquid chromatography (HPLC) or thin layer chromatography (TLC) to determine the point of completion. For a kinetic resolution process, the theoretical yield of the desired enantiomeric product is 50%. The optical purity (ee) of product can be monitored by chiral chromatographic methods such as chiral HPLC, GC or EC, as known in the art. The resulting amide of Formula IV can be isolated by extraction, precipitation, evaporation, or other suitable separation methods. Scheme L Formula V: The treatment of a compound of Formula III with an enzyme can afford a mixture of compounds of Formula IV (the desired enantiomeric product) and Formula V (the unreacted enantiomeric nitrile substrate). Any method known in the art can be used to isolate either a compound of Formula IV or Formula V from the mixture of products. Such methods include, but are not limited to, precipitation, distillation, sublimation, extraction, chromatography, and any combination thereof. For example, a solution of Formula IV and Formula V can be azeotropically displaced into a solvent such as diisopropyl ether to precipitate a compound of Formula IV. The compound of Formula V remains dissolved in the solvent. Thus, the compound of Formula V can then be isolated by removing the solvent and purification, if necessary, by methods known in the art. The unreacted nitrile starting material (Formula V of Scheme I) can be racemized back to the corresponding mixture of two enantimers (Formula III of Scheme I). The compound of Formula III obtained by this process can be subjected to the enzyme- catalyzed kinetic resolution described above to afford a compound of Formula IV. Therefore, the unreacted nitrile starting material can be recycled. Thus, the overall process shown in Scheme I can afford a compound of Formula IV in excess of the theoretical yield of 50% for a single kinetic resolution step.

The compound of Formula V can be converted to a compound of Formula III by treatment with a base. Any method known in the art for racemization of a product can be used to afford a compound of Formula III from a compound of Formula V. For example, the compound of Formula V can be treated with sodium t-butoxide, potassium t-butoxide, lithium diisopropylamide, lithium hexamethyldisilazide, sodium hydride, potassium hydride, sodium methoxide, potassium methoxide, lithium methoxide, lithium t-butoxide, potassium carbonate, sodium carbonate, lithium carbonate, cesium carbonate, or sodium ethoxide. The resulting compound of Formula III can then be treated, as outlined above, to afford compounds of Formula IV, such as by treatment with a nitrile hydratase. The reaction can be performed at various temperatures and over various temperature ranges. The temperature depends upon various parameters such as reactant and solvent selection, and can be empirically determined. For example, the reaction can be performed at room temperature (e.g., 21 °C). The reaction can be performed below room temperature, for example, at temperatures between 5 to 0 °C, between 0 to -10 °C, between 0 to -20 °C, or between 0 to -35 °C (or lower). As reactant and solvent selection allow, the reaction can be performed at temperatures greater than room temperature, for example, at temperatures between 40-250 °C (or higher). The reaction can be performed between 40 to 80 °C, between 80 to 120 °C, between 120 to 180 °C, or between 150 to 250 °C. The reaction can be performed in various solvents and solvent combinations, including organic solutions, aqueous solutions and combinations thereof. A suitable solvent or solvent mixture can be determined empirically by one of skill in the art, taking into account the properties of the reactants. The solvent can be an organic protic or aprotic solvent including, but not limiting to, an alcohol, such as methanol, ethanol, isopropanol, butanol, pentanol or hexanol, acetone, ethyl acetate, dithianes, THF, dioxane, acetonitrile, nitromethane, dichloromethane, dichloroethane, chloroform, diethyl ether, dimethylformamide (DMF), dimethylsulfoxide (DMSO), dimethyl-acetamide, hexanes, benzene, toluene, or any combination thereof.

The reaction can be performed with reactants at dilute or concentrated levels. For example, the reactants can be at concentrations between about 0.1 - 5 nmol/L, 0.01-0.5 mmol/L, 1-10 mmol/L, or 0.1-5 mol/L. The reaction can be performed over any time period. For example, the reaction can be conducted for about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,

11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58 or 59 minutes. The reaction can be conducted for about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 or 24 hours. The reaction can be conducted over a period of about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 days. The concentration and time for the reaction depend on various parameters such as temperature, solvent and reactants, and can be empirically determined.

The reaction can be homogeneous or heterogeneous. The reaction can be a bi- phasic mixture or an emulsion, or the reactants can be immobilized to a solid support. The solid support can be selected from among metal, ceramic or plastic plates, beads, microbeads, membranes, filaments, microtitre trays, and the wall of a reaction chamber. For example, suitable solid supports include semi-permeable membranes, glass capillaries, alumina, alumina supported polymers, silica, chemically bonded hydrocarbons on silica, polyolefins, agarose, polysaccharides such as dextran, or glycoproteins such as fibronectin. One of skill in the art can determine appropriate conditions depending upon the reactant selected for the transformation.

A process for the production of levetiracetam, 4, is shown in Scheme II: Scheme II

wherein R ^a is selected from among hydrogen, C ₁ -C ₈ alkyl, C ₂ -C ₈ alkenyl, C ₂ -C ₈ alkynyl, C ₁ -C ₈ haloalkyl, C ₁ -C ₈ heteroalkyl, heteroaryl and aryl, wherein the alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, heteroaryl and aryl are optionally substituted; and

X is halogen. Scheme H, Compound 2 ^a :

In some embodiments, Compound 1, propionaldehyde cyanohydrin (Sigma Aldrich Co., St. Louis, MO, Cat. No. 81880; Young et al., (1990) Organic Syntheses,

7:381) is converted to a sulfonic ester, Compound 2 ^a . Any method known in the art for converting a hydroxyl group to a sulfonic ester, such as a tosylate, benzenesulfonate, mesylate or triflate, can be used for this transformation. For example, treatment of Compound 1 with a sulfonyl halide, such as toluenesulfonyl chloride, benzenesulfonyl chloride, methanesulfonyl chloride or trifluoromethanesulfonyl chloride, in the presence of a base, such as pyridine or triethylamine, affords Compound 2 ^a . (see, e.g., Smith and March, March's Advanced Organic Chemistry, 6 ^th ed., 2007, Wiley: Hoboken, NJ, p. 545-547).

The reaction can be performed at various temperatures and over various temperature ranges. The temperature depends upon various parameters such as reactant and solvent selection, and can be empirically determined. For example, the reaction can be performed at room temperature (e.g., 21 °C). The reaction can be performed below room temperature, for example, at temperatures between 5 to 0 °C, between 0 to -10 °C, between 0 to -20 °C, or between 0 to -35 °C (or lower). As reactant and solvent selection allow, the reaction can be performed at temperatures greater than room temperature, for example, at temperatures between 40-250 °C (or higher). The reaction can be performed between 40 to 80 °C, between 80 to 120 °C, between 120 to 180 °C, or between 150 to 250 °C.

The reaction can be performed in various solvents and solvent combinations, including organic solutions, aqueous solutions and combinations thereof. A suitable solvent or solvent mixture can be determined empirically by one of skill in the art, taking into account the properties of the reactants. The solvent can be an organic protic or aprotic solvent including, but not limiting to, an alcohol, such as t-butanol, acetone, ethyl acetate, dithianes, THF, dioxane, acetonitrile, nitromethane, dichloromethane, dichloroethane, chloroform, diethyl ether, dimethylformamide (DMF), N- methylpyrrolidinone, dimethylsulfoxide (DMSO), dimethyl-acetamide, hexanes, benzene, toluene, or any combination thereof.

The reaction can be performed with reactants at dilute or concentrated levels. For example, the reactants can be at concentrations between about 0.1 - 5 nmol/L, 0.01-0.5 mmol/L, 1-10 mmol/L, or 0.1-5 mol/L. The reaction can be performed over any time period. For example, the reaction can be conducted for about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,

35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58 or 59 minutes. The reaction can be conducted for about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 or 24 hours. The reaction can be conducted over a period of about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 days. The concentration and time for the reaction depend on various parameters such as temperature, solvent and reactants, and can be empirically determined.

The reaction can be homogeneous or heterogeneous. The reaction can be a bi- phasic mixture or an emulsion, or the reactants can be immobilized to a solid support. The solid support can be selected from among metal, ceramic or plastic plates, beads, microbeads, membranes, filaments, microtitre trays, and the wall of a reaction chamber. For example, suitable solid supports include semi-permeable membranes, glass capillaries, alumina, alumina supported polymers, silica, chemically bonded hydrocarbons on silica, polyolefins, agarose, polysaccharides such as dextran, or glycoproteins such as fibronectin. One of skill in the art can determine appropriate conditions depending upon the reactant selected for the transformation. Scheme II, Compound 2 ^b :

In some embodiments, the hydroxyl group of Compound 1, propionaldehyde cyanohydrin (Sigma Aldrich Co., St. Louis, MO, Cat. No. 81880; Young et al., (1990) Organic Syntheses, 7:381) is converted to a halide, Compound 2 ^b . Any method known in the art for converting a hydroxyl group to a halide, such as F, Cl, Br, or I, can be used for this transformation. For example, treatment of Compound 1 with halogen acids, such as HBr, HCl, or HI affords Compound 2 ^b . Compound 1 also can be treated with an inorganic acid halide, such as (COCl) ₂ , SOCl ₂ , PCl ₅ , PCl ₃ , POCl ₃ , POBr ₃ , and PBr ₃ to afford Compound 2 ^b (see, e.g., Smith and March, March's Advanced Organic Chemistry, 6 ^th ed., 2007, Wiley: Hoboken, NJ, p. 576-580). Other methods include treatment of Compound 1 with NaX, KX, or NH ₄ X in a polyhydrogen fluoride-pyridine solution, where X is a halide (see, Olah et al., (1979) J. Org. Chem. 44:3872; and Yin et al., (2004) Org. Lett. 6:1465). The reaction can be performed at various temperatures and over various temperature ranges. The temperature depends upon various parameters such as reactant and solvent selection, and can be empirically determined. For example, the reaction can

be performed at room temperature (e.g., 21 °C). The reaction can be performed below room temperature, for example, at temperatures between 5 to 0 °C, between 0 to -10 °C, between 0 to -20 °C, or between 0 to -35 °C (or lower). As reactant and solvent selection allow, the reaction can be performed at temperatures greater than room temperature, for example, at temperatures between 40-250 °C (or higher). The reaction can be performed between 40 to 80 °C, between 80 to 120 °C, between 120 to 180 °C, or between 150 to 250 °C.

The reaction can be performed in various solvents and solvent combinations, including organic solutions, aqueous solutions and combinations thereof. A suitable solvent or solvent mixture can be determined empirically by one of skill in the art, taking into account the properties of the reactants. The solvent can be an organic protic or aprotic solvent including, but not limiting to, an alcohol, such as methanol, ethanol, isopropanol, butanol, pentanol or hexanol, acetone, ethyl acetate, dithianes, THF, dioxane, acetonitrile, nitromethane, dichloromethane, dichloroethane, chloroform, diethyl ether, dimethylformamide (DMF), dimethylsulfoxide (DMSO), dimethyl-acetamide, hexanes, benzene, toluene, or any combination thereof.

The reaction can be performed with reactants at dilute or concentrated levels. For example, the reactants can be at concentrations between about 0.1 - 5 nmol/L, 0.01-0.5 mmol/L, 1-10 mmol/L, or 0.1-5 mol/L. The reaction can be performed over any time period. For example, the reaction can be conducted for about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58 or 59 minutes. The reaction can be conducted for about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 or 24 hours. The reaction can be conducted over a period of about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29 or 30 days. The concentration and time for the reaction depend on various parameters such as temperature, solvent and reactants, and can be empirically determined.

The reaction can be homogeneous or heterogeneous. The reaction can be a bi- phasic mixture or an emulsion, or the reactants can be immobilized to a solid support. The solid support can be selected from among metal, ceramic or plastic plates, beads, microbeads, membranes, filaments, microtitre trays, and the wall of a reaction chamber.

For example, suitable solid supports include semi-permeable membranes, glass capillaries, alumina, alumina supported polymers, silica, chemically bonded hydrocarbons on silica, polyolefins, agarose, polysaccharides such as dextran, or glycoproteins such as fibronectin. One of skill in the art can determine appropriate conditions depending upon the reactant selected for the transformation. Scheme II, Compound 3:

Compound 2 ^a or 2 ^b is converted to Compound 3 by nucleophilic substitution with a nitrogen-containing heterocycle. Any method known in the art for nucleophilic substitution can be used for this reaction. For example, Compound 2 ^a or 2 ^b is reacted with 2-pyrrolidinone in the presence of a base, such as sodium t-butoxide, potassium t- butoxide, lithium t-butoxide or lithium hexamethyldisilazide (LHMDS).

The reaction can be performed at various temperatures and over various temperature ranges. The temperature depends upon various parameters such as reactant and solvent selection, and can be empirically determined. For example, the reaction can be performed at room temperature (e.g., 21 °C). The reaction can be performed below room temperature, for example, at temperatures between 5 to 0 °C, between 0 to -10 °C, between 0 to -20 °C, or between 0 to -35 °C (or lower). As reactant and solvent selection allow, the reaction can be performed at temperatures greater than room temperature, for example, at temperatures between 40-250 °C (or higher). The reaction can be performed between 40 to 80 °C, between 80 to 120 °C, between 120 to 180 °C, or between 150 to 250 °C.

The reaction can be performed in various solvents and solvent combinations. A suitable solvent or solvent mixture can be determined empirically by one of skill in the art, taking into account the properties of the reactants. The solvent can be an organic solvent including, but not limiting to, acetone, ethyl acetate, dithianes, THF, dioxane, acetonitrile, dichloromethane, dichloroethane, chloroform, diethyl ether, dimethylformamide (DMF), dimethylsulfoxide (DMSO), dimethyl-acetamide, N- methylpyrrolidinone, hexanes, benzene, toluene, or any combination thereof.

The reaction can be performed with reactants at dilute or concentrated levels. For example, the reactants can be at concentrations between about 0.1 - 5 nmol/L, 0.01-0.5 mmol/L, 1 -10 mmol/L, or 0.1-5 mol/L. The reaction can be performed over any time period. For example, the reaction can be conducted for about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,

11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58 or 59 minutes. The reaction can be conducted for about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 or 24 hours. The reaction can be conducted over a period of about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 days. The concentration and time for the reaction depend on various parameters such as temperature, solvent and reactants, and can be empirically determined.

The reaction can be homogeneous or heterogeneous. The reaction can be a bi- phasic mixture or an emulsion, or the reactants can be immobilized to a solid support. The solid support can be selected from among metal, ceramic or plastic plates, beads, microbeads, membranes, filaments, microtitre trays, and the wall of a reaction chamber. For example, suitable solid supports include semi-permeable membranes, glass capillaries, alumina, alumina supported polymers, silica, chemically bonded hydrocarbons on silica, polyolefins, agarose, polysaccharides such as dextran, or glycoproteins such as fibronectin. One of skill in the art can determine appropriate conditions depending upon the reactant selected for the transformation. Scheme II, Compound 4:

Compound 3 is a mixture of two enantiomeric nitriles (R- and S- isomers), and an enzyme can selectively hydrate one of the enantiomers, such as the S-enantiomer, to an amide, resulting in Compound 4. Selective conversion of one of the two enantiomeric nitriles to the optically pure, amide product is known in the art as enzymatic kinetic resolution. Any enzymatic transformation known in the art for converting a nitrile substrate to an amide product can be used for this process. An exemplary enzyme is a nitrile hydratase (EC 4.2.1.84).

Suitable conditions for the enzymatic preparation of amide products using nitrile hydratases are well known in the art (see, e.g., (2002) et al., Biocatal. Biotransform. 20:73- 93; and U.S. 7,153,663). Wild-type microorganisms having nitrile hydratase activity can be used to convert nitriles to the corresponding amides (see, e.g., Nagasawa et al., (1993) Appl. Microbiol. Biotechnol. 40:189-195; Cowan et al. (1998) Extremophiles 2:207-216; and U.S. 7,153,663). For example, nitrile hydratase activity of Rhodococcus rhodochrous Jl converts a variety of aromatic and heteroaromatic nitriles to the corresponding amides

with 100% molar conversion (see, Mauger et al., (1989) Tetrahedron 45:1347-1354; and Mauger et al., (1988) J. Biotechnol. 8:87-96). Several Rhodococcus strains convert of 3- cyanopyridine to nicotinamide (see, U.S. 2004/0142447).

In addition to the use of wild-type organisms, recombinant organisms containing heterologous genes for the expression of nitrile hydratase can be used the conversion of nitriles. For example, E. coli transformants that express nitrile hydratases can be used (see, e.g., U.S. 6,316,242; U.S. 5,811,286; WO 9504828; EP 5024576; and Wu et al., (1997) Appl. Microbiol. Biotechnol. 48:704-708).

Cell lysates of organisms containing genes for the expression of nitrile hydratase can be used for the conversion of nitriles to the corresponding amides (see, e.g., Kim et al, (2000) Enzyme Microb. Tech. 27:492-501). Also, nitrile hydratase enzymes can be isolated and optionally purified and used for the conversion of nitriles to the corresponding amides (see, e.g., Nagasawa et al., (1978) Eur. J. Biochem. 162:691-698; Nagasawa et al., (1991) Eur. J. Biochem. 196:581-589; Payne et al., (1997) Biochemistry 36:5447-5454).

An aqueous reaction mixture containing the nitrile, Compound 3, is prepared by mixing the nitrile with an aqueous suspension of the nitrile hydratase catalyst. Intact microbial cells can be used as catalyst without any pretreatment, such as permeabilization or heating. Alternatively, the cells can be immobilized in a polymer matrix (e.g., alginate, carrageenan, polyvinyl alcohol, or polyacrylamide gel) or on a soluble or insoluble support (e.g., glass, plastic, a film, nitrocellulose, a sol-gel polymer, celite and silica) to facilitate recovery and reuse of the catalyst. Methods to immobilize cells in a polymer matrix or on a soluble or insoluble support have been widely reported and are well known to those skilled in the art. Lysates of cells that express nitrile hydratase can be used to convert the nitrile to the corresponding amide. The enzyme also can be isolated from the microbial cells and used directly as catalyst, or the enzyme can be immobilized in a polymer matrix or on a soluble or insoluble support. Methods for immobilizing cells and enzymes have also been widely reported and are well known to those skilled in the art (Methods in Biotechnology, Vol. 1 : Immobilization of Enzymes and Cells; Gordon F. Bickerstaff, Editor; Humana Press, Totowa, N.J., USA; 1997).

Intact microbial cells, either immobilized or unimmobilized, containing genes that encode a polypeptide having nitrile hydratase activity, or containing genes that encode a

combination of polypeptides separately having nitrile hydratase activity, can be used as catalyst without any pretreatment, such as permeabilization, freeze thawing or heating. Alternatively, the microbial cells can be permeabilized by methods familiar to those skilled in the art (e.g., treatment with toluene, detergents, or freeze-thawing) to improve the rate of diffusion of materials into and out of the cells. Methods for permeabilization of microbial cells are well-known to those skilled in the art (see, Felix, (1982) Anal. Biochem. 120:211-234).

Compound 3 can be moderately water soluble. The solubility depends on the temperature of the solution and the salt concentration in the aqueous phase. The reaction can be carried out in an organic, aqueous or 2-phase system (including an organic solvent phase that is not miscible with water, such as ethyl acetate, and also an aqueous phase), or in an emulsion. Organic solvents can include, but are not limited to, acetone, diisoproyl ether, methyl tert-butyl ether (MTBE), dibutyl ether, and ethyl acetate. Suitable aqueous phases include, but are not limited to, buffers such as glutamic acid-glutamate, phosphoric acid-phosphate, acetic acid-acetate and citric acid-citrate buffers.

The aqueous phase of a two-phase reaction mixture can contain as much water as is sufficient to result in conversion of the nitrile to the corresponding amide and maintenance of the activity of the enzyme catalyst. The reaction can also be run by adding the nitrile to the reaction mixture at a rate approximately equal to the enzymatic hydration reaction rate, thereby maintaining a single-phase aqueous reaction mixture, thereby avoiding the potential problem of substrate inhibition of the enzyme at high starting material concentrations.

The concentration of enzyme catalyst in the reaction mixture depends on the specific catalytic activity of the enzyme catalyst and is chosen to obtain the desired rate of reaction. The wet cell weight of the microbial cells used as catalyst in reactions typically ranges from 0.001 grams to 0.300 grams of wet cells per mL of total reaction volume, generally from 0.002 grams to 0.050 grams of wet cells per mL; the cells can be optionally immobilized as described above. The specific activity of the microbial cells (IU/gram dry cell weight) is determined by measuring the rate of conversion of a 0.10- 0.50 M solution of a nitrile substrate to the desired amide product at 25° C, using a known weight of microbial cell catalyst. An IU of enzyme activity is defined as the amount of enzyme activity required to convert one micromole of substrate to product per minute.

For the methods herein, typically 10 to 10,000 IU of nitrile hydratase is added to the reaction for every gram of nitrile.

The temperature of the reaction is selected to facilitate the reaction rate and the stability of enzyme catalyst. The temperature of the reaction can range from just above the freezing point of the reaction mixture (ca. 0° C) to 65° C, with a general range of reaction temperature of from 0° C to 45° C. In one embodiment, an ambient temperature is maintained throughout the reaction.

An enzyme catalyst solution or suspension can be prepared by suspending the unimmobilized or immobilized cells in distilled water, or in an aqueous reaction mixture of a buffer or by suspending the immobilized enzyme catalyst in a similar mixture, or by preparing a solution of a cell extract, partially purified or purified enzyme(s), or a soluble form of the immobilized enzymes in a similar mixture. A suitable pH for the reaction can be determined by one of skill in the art, taking into account the activity and stability of the nitrile hydratase. A pH range from 2 to 11 is contemplated for the methods herein. Typically, however, the pH of the reaction is at or about 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.2, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, or 9.0. The reaction can be run to convert the nitrile with no pH control, or a suitable acid or base can be added over the course of the reaction to maintain the desired pH. The reaction can be monitored by, for example, gas chromatography (GC), high performance liquid chromatography (HPLC) or thin layer chromatography (TLC) to determine the point of completion. The resulting amide, Compound 4, can be isolated by extraction, precipitation, evaporation, or other suitable separation methods. Scheme II, Compound 5: The treatment Compound 3 with an enzyme affords a mixture of Compound 4 and

Compound 5. Any method known in the art for separating a mixture of products can be used to isolate Compound 4 or 5. Such methods include, but are not limited to, precipitation, distillation, sublimation, extraction, chromatography, and any combination thereof. For example, a solution of Compound 4 and Compound 5 can be azeotropically displaced into a solvent such as diisopropyl ether to precipitate Compound 4. Compound 5 can remain dissolved in the solvent. Thus, Compound 5 can then be isolated by removing the solvent and purification, if necessary, by methods known in the art.

The unreacted nitrile starting material (Compound 5) can be racemized back to the corresponding mixture of two enantimers (Compound 3). Compound 3 obtained by this process can be subjected to the enzyme-catalyzed kinetic resolution described above to afford Compound 4, Scheme II. Therefore, the unreacted nitrile starting material can be recycled. Thus, the overall process shown in Scheme II can afford Compound 4 in excess of the theoretical yield of 50% for a single kinetic resolution step.

Compound 5 can be converted to Compound 3 by treatment with a base. Any method known in the art for racemization of a product can be used to afford Compound 3 from Compound 5. For example, Compound 5 can be treated with sodium t-butoxide, potassium t-butoxide, lithium diisopropylamide, lithium hexamethyldisilazide, sodium hydride, potassium hydride, sodium methoxide, potassium methoxide, lithium methoxide, lithium t-butoxide, potassium carbonate, sodium carbonate, lithium carbonate, cesium carbonate or sodium ethoxide. The resulting Compound 3 can then be treated, as outlined above, to afford Compound 4, such as by treatment with a nitrile hydratase. The reaction can be performed at various temperatures and over various temperature ranges. The temperature depends upon various parameters such as reactant and solvent selection, and can be empirically determined. For example, the reaction can be performed at room temperature (e.g., 21 °C). The reaction can be performed below room temperature, for example, at temperatures between 5 to 0 °C, between 0 to -10 °C, between 0 to -20 °C, or between 0 to -35 °C (or lower). As reactant and solvent selection allow, the reaction can be performed at temperatures greater than room temperature, for example, at temperatures between 40-250 °C (or higher). The reaction can be performed between 40 to 80 °C, between 80 to 120 °C, between 120 to 180 °C, or between 150 to 250 °C.

The reaction can be performed in various solvents and solvent combinations, including organic solutions, aqueous solutions and combinations thereof. A suitable solvent or solvent mixture can be determined empirically by one of skill in the art, taking into account the properties of the reactants. The solvent can be an organic protic or aprotic solvent including, but not limiting to, an alcohol, such as methanol, ethanol, isopropanol, butanol, pentanol or hexanol, acetone, ethyl acetate, dithianes, THF, dioxane, acetonitrile, dichloromethane, dichloroethane, chloroform, diethyl ether, dimethylformamide (DMF), dimethylsulfoxide (DMSO), dimethyl-acetamide, hexanes, benzene, toluene, or any combination thereof.

The reaction can be performed with reactants at dilute or concentrated levels. For example, the reactants can be at concentrations between about 0.1 - 5 nmol/L, 0.01-0.5 mmol/L, 1-10 mmol/L, or 0.1-5 mol/L. The reaction can be performed over any time period. For example, the reaction can be conducted for about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58 or 59 minutes. The reaction can be conducted for about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 or 24 hours. The reaction can be conducted over a period of about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 days. The concentration and time for the reaction depend on various parameters such as temperature, solvent and reactants, and can be empirically determined.

The reaction can be homogeneous or heterogeneous. The reaction can be a bi- phasic mixture or an emulsion, or the reactants can be immobilized to a solid support. The solid support can be selected from among metal, ceramic or plastic plates, beads, microbeads, membranes, filaments, microtitre trays, and the wall of a reaction chamber. For example, suitable solid supports include semi-permeable membranes, glass capillaries, alumina, alumina supported polymers, silica, chemically bonded hydrocarbons on silica, polyolefins, agarose, polysaccharides such as dextran, or glycoproteins such as fibronectin. One of skill in the art can determine appropriate conditions depending upon the reactant selected for the transformation. C. Enzymes

The methods provided herein use enzymes to convert a nitrile group to an amide. An exemplary class of enzymes is nitrile hydratases. Any nitrile hydratase suitable for use therein can be employed. Such nitrile hydratases can be identified, if necessary, by screening, such as screening collections or libraries of nitrile hydratases and/or collections or libraries of modified nitrile hydratases or individually testing nitrile hydratases. Nitrile Hydratase

The methods provided herein use nitrile hydratases to catalyze the formation of an amide product from a nitrile substrate. Nitrile hydratases (EC 4.2.1.84), also called NHases or nitrile hydro-lyases, are catalysts for the hydration or addition of water to nitrile groups. Nitrile hydratases have been isolated and characterized from a number of

bacteria. For example, organisms that produce nitrile hydratases include, but are not limited to, the genus Achromobacter, Acinetobacter, Aeromonas, Agrobacterium, Arthrobacter, Aurantimonas, Bacillus, Bacteridium, Bradyrhizobium, Brevibacterium, Burkholderia, Citrobacter, Comamonas, Corynebacterium, Enter obacter, Erwinia, Klebsiella, Micrococcus, Mycobacterium, Myrothecium, Nocardia, Pseudomonas, Pseudonocardia, Rhizobium, Rhodococcus, Silicibacter, Streptomyces, thermophilic Bacillus, and Xanthobacter (see, e.g., Nishiyama et al., (199Ij J. Bacteriol. 173:2465- 2472; Kobayashi et al., (1991) Biochem. Biophys. Acta 1129:23-33; Mayaux et al., (1990) J. Bacteriol. 172:6764-6773; Ikehata et al., (1989) Eur. J. Biochem. 181 :563-570; Payne et al., (1997) Biochemistry 36:5447-5454; Martinkova, (2002) Biocatal. Biotransfor. 20:73-93; and Cowan et al., (1998) Extremophiles 2:207-216).

Nitrile hydratases generally exhibit broad substrate specificity (see, Payne et al., (1997) Biochemistry 36:5447-5454). The catalytic centers of nitrile hydratases can contain iron (Fe) or cobalt (Co). It has been shown that Fe-type nitrile hydratases can hydrate aliphatic nitriles (see, Nagaswa et al., (1987) Eur. J. Biochem. 162:581-589). Iron-containing nitrile hydratases contain a nonheme iron ion. Cobalt-type nitrile hydratases can hydrate aromatic nitriles (see, Nagasawa et al., (1991) Eur. J. Biochem. 196:581-589) and contain a noncorrin cobalt ion.

The nitrile hydratase enzyme includes α and β subunits (see, Miyanaga et al., (2004) Eur. J. Biochem. 271 :429-438). The amino acid sequences of the α and β subunits do not show homology. However, each subunit shares a relatively high homology with respect to amino acid sequence. For example, the α subunit contains a cysteine cluster region containing three cysteine residues and one serine residue. In particular, the -V-C- (T/S)-L-C-S-C- consensus sequence in the α subunit, which form the metal coordination site, is fully conserved (Payne, M.S., Wu, S., Fallon, R.D., Tudor, G., Stieglitz, B.,

Turner, I.M and Nelson, M.J. (1997), Biochemistry 36, 5447-5454). The cobalt NHases have a threonine (T) in the sequence, whereas the ferric NHases have a serine (S). The β subunit contains two arginine residues and several conserved aromatic residues that form a hydrophobic pocket. Three-dimensional X-ray structures of NHases revealed almost superimposable metal coordination sites, even though they bind different metals. Of the residues

participating in the recognition of the substrate, several conserved aromatic residues in the β subunit form a hydrophobic pocket. This pocket is thought to accommodate the alkyl chain or aromatic ring of a nitrile substrate. The substrate binding pockets in the Co-type NHases are larger and wider than those of the Fe-type NHases. The difference in shape and size of the substrate binding pocket has been suggested to confer the substrate preference among NHases (Miyanaga, A., Fushinobu, S., Ito, K., Shoun, H. and Wakagi, T. (2004) Eur. J. Biochem. 271, 429-438).

Alignment of the amino acid sequences of nitrile hydratases can be accomplished using three cysteine residues and one serine residue in the cysteine cluster region, two conserved arginine residues, and one conserved tyrosine residue, or by aligning residues involved in the formation of the substrate binding pocket (Miyanga, A., Fushinobu, S., Ito, K., Shoun, H. and Wakagi, T., (2003), Eur. J. Biochem., 271, 429-438). Alignment of the amino acid sequences of nitrile hydratases also can be accomplished using the cysteine cluster region, which contains the conserved sequence -VC(S/T)LCSC-. The open reading frames (ORFs) of the α and β subunits reside in the same nitrile hydratase operon, with the α subunit located upstream of the β subunit in most bacterial strains. An ORF downstream of the β subunit can be required for production of an active nitrile hydratase from Rhodococcus sp. N-771 (Nojiri et al., (1999) J. Biochem. 125:696- 704), Comamonas testosteroni 5-MGAM-4D (Petrillo et al., (2005) Appl. Microbiol. Biotechnol. 67:664-670) and Pseudomonas putida 5B (Wu et al., (1997) Appl. Microbl. Biotechnol. 48:704-708). The flanking regions usually encode a small putative protein of about 100 amino acids, such as P7K in Comamonas testosteroni 5-MGAM-4D and P14 K in Pseudomonas putida 5B. However, other studies have shown intact α and β subunits alone produce active protein, such as a nitrile hydratase from Bacillus sp. BR449 (see Kim et al., (2000) Enzyme Microb. Technol. 27:492-50). 1. Exemplary nitrile hydratases

Several nitrile hydratase have been characterized and can be used in the methods herein. For example, the complete genomic sequence of Bradyrhizobium japonicum USDA 110 (ATCC 10324) was determined (see Kaneko et al., (2002) DNA Res. 9:225- 256). The nitrile hydratase nucleotide sequence from B. japonicum USDA 110 was determined (SEQ ID NO:1). The amino acid sequences were also determined for the

alpha (SEQ ID NO:2), beta (SEQ ID NO:3) and flanking activator (SEQ ID NO:4) portions. Additional examples of nitrile hydratases include nitrile hydratases from Brevibacterium sp. A4, P. putida BRT 2034-3, Rhodococcus sp. CM 1008, Rhodococcus sp. HT 40-6, and R. erythropolis FZB 53 (see, Martinkova et al., (2002) Biocatal. Biotransform. 20:73-93). Furthermore, there are hundreds of nucleotide sequences in the GenBank that are tentatively annotated as nitrile hydratase encoding genes based on their sequence similarities to the known, characterized nitrile hydratases. Exemplary subunits of wildtype nitrile hydratases are shown in Table 4. Table 4: Exemplary subunits of wildtype nitrile hydratases.

2. Modified nitrile hydratase polypeptides

Provided herein are variants of nitrile hydratase (also referred to herein as modified nitrile hydratase polypeptides) that display improved selectivity, e.g., improved enantioselectivity. In one embodiment, the modified NHase produce the S-amide product to a greater extent than the R-amide product. Enantioselectivity can be assessed by monitoring the conversion of a selected nitrile substrate to is corresponding amide product. In one embodiment, improved selectivity is assessed by determining the conversion of racemic 2-(2-oxopyrrolidin-1-yl)-butanenitrile to the S-amide product. Measurement of the conversion of the nitrile substrate to the S-amide product can be determined by any method known in the art.

Such variants can have an increased E value. In one embodiment, the modified nitrile hydratase polypeptides provided herein confer increased enantioselectivity. For example, the modified nitrile hydratase polypeptides have E values at least 1.5 times, 2

times, 3 times, 4 times, 5 times, 6 times, 7 times, 8 times, 9 times, 10 times or more times the E value of unmodified nitrile hydratase.

Such variants also can have increased activity, where the increased activity is manifested as an increased conversion of a nitrile substrate to its corresponding amide product. In one such embodiment, the modified nitrile hydratase has an activity increased by at least 5%, at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, at least 150%, at least 200%, at least 250%, at least 300%, at least 350%, at least 400%, at least 450% and at least 500% or more compared to the activity of unmodified nitrile hydratase. In another such embodiment, the modified nitrile hydratase has an activity increased by at least 1.5 times, 2 times, 3 times, 4 times, 5 times, 6 times, 7 times, 8 times, 9 times, 10 times, 20 times, 30 times, 40 times, 50 times, 60 times, 70 times, 80 times, 90 times, 100 times, 200 times, 300 times, 400 times, 500 times, 600 times, 700 times, 800 times, 900 times and 1000 times, or more times when compared to the activity of unmodified nitrile hydratase. Modified nitrile hydratase polypeptides provided herein include modified nitrile hydratase polypeptides that have been modified at one or more than one amino acid as compared to an unmodified nitrile hydratase polypeptide. Such polypeptides contain a single mutation compared to a native polypeptide, or contain 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more mutations compared to an unmodified polypeptide. In some examples, modified nitrile hydratase polypeptides provided herein are variants of native nitrile hydratase. The nitrile hydratase polypeptide can be of any bacterial, fungal or yeast origin. Exemplary unmodified NHase polypeptides include an α subunit or β subunit whose sequence of amino acid residues is set forth in any of SEQ ID NOS:2-49. Modified nitrile hydratase polypeptides provided herein contain one or more amino acid replacements, deletions and/or insertions compared with the unmodified reference nitrile hydratase polypeptide. Exemplary modified NHase polypeptides have a sequence of nucleotide residues as set forth in any of SEQ ID NOS:56, 64, 68, 77 and 81. Also provided are modified nitrile hydratases that include an α subunit or β subunit whose sequence of amino acid residues is set forth in any of SEQ ID NOS: 57, 58, 65, 66, 69-71, 78-80 and 82-110. Corresponding loci on other nitrile hydratase polypeptides, including truncated variants, species of nitrile hydratase polypeptides and allelic variants, readily can be identified. Furthermore, shortened or lengthened variants with insertions or

deletions of amino acids, particular at either terminus that retain an NHase activity readily can be prepared and the loci for corresponding mutations identified.

Modified nitrile hydratase polypeptides also include polypeptides that are hybrids of different nitrile hydratase polypeptides and also synthetic nitrile hydratase polypeptides prepared recombinantly or synthesized or constructed by other methods known in the art based upon known polypeptides.

The modified nitrile hydratase polypeptides provided herein are altered in their amino acid sequence such that variants possess increased enantioselectivity or increased activity. Hence, the nitrile hydratase variants provided herein offer nitrile hydratase polypeptides with advantages including a selective conversion of a racemic nitrile substrate to an S-amide product or an R-amide product. In one embodiment, the modified nitrile hydratase demonstrates a selective conversion of a racemic nitrile substrate to an S- amide product.

Mutations of any one or more than one amino acid residue in a nitrile hydratase polypeptide provided herein confer increased enantioselectivity or increased activity by virtue of a change in the primary sequence of the polypeptide. For example, conservative amino acid substitutions can be made in any of the nitrile hydratases provided that the resulting protein exhibits activity. Conservative amino acid substitutions, such as those set forth in Table 4, are those amino acids that do not eliminate nitrile hydratase activity when used to replace one or more amino acids in an unmodified NHase. Other substitutions also are contemplated and can be determined empirically or in accord with known conservative substitutions. For example, other modifications that are or are not in the primary sequence of the polypeptide also can be included, such as, but not limited to, the addition of a carbohydrate moiety due to glycosylation of the polypeptide, the addition of polyethylene glycol (PEG) moiety to the polypeptide, and other such modifications. Typically, modifications provided herein include those that increase the enantioselectivity of nitrile hydratase while either improving or maintaining the requisite activity (e.g., conversion of a nitrile substrate to its corresponding amide product). These modifications include modification of hydrophobic areas to increase polar interactions and modification of hydrophilic areas to decrease polar interactions.

Structural modifications in nitrile hydratase include combining one, two or more amino acid replacements at different positions within the nitrile hydratase polypeptide to

increase the enantioselectivity and/or activity of the nitrile hydratase polypeptide. For example, two or more modifications in one or more categories can be combined, where the categories are selected from, for example, modification of hydrophobic stretches to increase polar interactions and modifications of any known type that increase thermal tolerance. Thus, also among the variants provided herein are modified nitrile hydratase polypeptide with two or more modifications compared to native or wild-type nitrile hydratase. Modified nitrile hydratase polypeptides include those with 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more modified positions. The two or more modifications can include two or more modifications of the same property, e.g., two modifications that modify nitrile hydratase thermal tolerance or two modifications that increase 5-selectivity.

Among the modified nitrile hydratase polypeptides provided herein are nitrile hydratase variants modified to: 1) increase ^-selectivity; 2) increase conversion rate of the nitrile substrate to the amide product; 3) increase organic solvent tolerance; and 4) that increase thermal tolerance. Particular of modifications of nitrile hydratase polypeptides provided herein are modifications of nitrile hydratase that have increased stability by increasing the tolerance of the modified nitrile hydratase to temperature or other denaturing agent.

In one embodiment, a nitrile hydratase polypeptide is modified to include one or more single amino acid replacements compared with unmodified nitrile hydratase polypeptide. In one embodiment, such modified nitrile hydratase polypeptide includes a single amino acid replacement compared with the unmodified nitrile hydratase. In another embodiment, the positions modified correspond to modification of more than one amino acid position, e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20 or more positions. In one embodiment, such modified nitrile hydratase include two amino acid replacements compared with the unmodified nitrile hydratase. a. Construction of mutant proteins

Modified nitrile hydratase polypeptides can be made by altering the sequence of their nucleic acids or amino acids by substitutions, additions or deletions that yield functional molecules with equivalent or enhanced activity. Due to the degeneracy of nucleotide coding sequences, other nucleic sequences that encode substantially the same amino acid sequence as a nitrile hydratase gene can be used. These include, but are not

limited to, nucleotide sequences comprising all or portions of nitrile hydratase genes that are altered by the substitution of different codons that encode the amino acid residue within the sequence, thus producing a silent change. Likewise, the nitrile hydratase derivatives include, but are not limited to, those containing, as a primary amino acid sequence, all or part of the amino acid sequence of a nitrile hydratase, including altered sequences in which functionally equivalent amino acid residues are substituted for residues within the sequence resulting in a silent change. For example, one or more amino acid residues within the sequence can be substituted by another amino acid of a similar polarity that acts as a functional equivalent, resulting in a silent alteration. Substitutes for an amino acid within the sequence can be selected from other members of the class to which the amino acid belongs. For example, the nonpolar (hydrophobic) amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan and methionine. The polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine. The positively charged (basic) amino acids include arginine, lysine and histidine. The negatively charged (acidic) amino acids include aspartic acid and glutamic acid. Such changes can be systematically introduced and tested for activity in in vitro assays, such as those provided herein.

For example, the enzyme active site or substrate binding site can be targeted for modification. The amino acid residues that make up the active site or the substrate binding pocket can be specifically targeted. In addition to the residues that potentially interact with the substrate, resides that are spatially distant from the substrate binding site also can be targeted because of their potential remote effect on the enzyme activity. In some embodiments, active site amino acid residues that participate in substrate binding and enzyme catalysis are identified, such as by constructing a homology model. A homology model can be constructed using known nitrile hydratase crystal structures as a template (e.g., see Hourai et al., Biochem Biophys Res Commun. 312(2): 340-345 (2003); Miyanaga et al., Biochem Biophys Res Commun. 288(5): 1169-1174 (2001); Huang et al., Structure 5(5): 691-699 (1997); Song et al., Biochem Biophys Res Commun. 362(2): 319-324 (2007); Tastan et al., Biochem Biophys Res Commun. 343(1): 319-325 (2006); Hourai et al., Acta Crystallogr Sect F Struct Biol Cryst Commun. 61(Pt 11): 974-977 (2005); Miyanaga et al., Eur J Biochem. 271(2): 429-438 (2004); Jackson et al, Inorg Chem. 40(7): 1646- 1653 (2001); Nakasako et al., Biochemistry 38(31): 9887-

9898 (1999); and Nagashima et al., Nat Struct Biol. 5(5): 347-351 (1998). The docking of substrates in the enzyme active site allows identification of active site residues that can potentially affect substrate binding and enzyme catalysis. For example, residues that are within a distance of about 10-15å of the substrate binding site and/or the catalytic center can be targeted for modification, such as by mutagenesis, to provide, e.g., increased conversion, decreased reaction time, improved selectivity, improved enantiomeric ratio (E value), increased activity and/or thermal stability and/or stability to organic solvents, increased expression level, and/or increased solubility in aqueous solution, as compared to the unmodified enzyme. Such a method is exemplified in Example 14, below. Once residues that can potentially affect substrate binding and enzyme catalysis have been identified in one nitrile hydratase, the corresponding residues in other nitrile hydratases also can be identified for mutation by alignment of the amino acid sequences using, for example, alignment algorithms well known in the art.

The nitrile hydratase derivatives can be produced by various methods known in the art. For example, once a recombinant cell expressing a nitrile hydratase protein or a derivative thereof, is identified, the individual gene product can be isolated and analyzed. This is achieved by assays based on the physical and/or functional properties of the protein, including, but not limited to, radioactive labeling of the product followed by analysis by gel electrophoresis, immunoassay, or cross-linking to marker-labeled product. The nitrile hydratase protein can be isolated and purified by standard methods known in the art (either from natural sources or recombinant host cells expressing the complexes or proteins), including but not restricted to column chromatography (e.g., ion exchange, affinity, gel exclusion, reversed-phase high pressure, fast protein liquid, etc.), differential centrifugation, differential solubility, or by any other standard technique used for the purification of proteins. Functional properties can be evaluated using any suitable assay known in the art.

Alternatively, once a nitrile hydratase protein or its derivative is identified, the amino acid sequence of the protein can be deduced from the nucleotide sequence of the gene that encodes it. As a result, the protein or its derivative can be synthesized by standard chemical methods known in the art (see, e.g., Hunkapiller et al., (1984) Nature 310:105-111).

Manipulations of nitrile hydratase protein sequences can be made at the protein level. Also contemplated herein are nitrile hydratase proteins, derivatives or analogs or fragments thereof, which are differentially modified during or after translation, e.g., by glycosylation, acetylation, phosphorylation, amidation, derivatization by known protecting/blocking groups, proteolytic cleavage, linkage to an antibody molecule or other cellular ligand, etc. Any of numerous chemical modifications can be carried out by known techniques, including, but not limited to, specific chemical cleavage by cyanogen bromide, trypsin, chymotrypsin, papain, V8 protease, NaBH ₄ , acetylation, formylation, oxidation, reduction, metabolic synthesis in the presence of tunicamycin, etc. In addition, analogs and derivatives of a nitrile hydratase protein can be chemically synthesized. For example, a peptide corresponding to a portion of a nitrile hydratase protein, which includes the desired domain or that mediates the desired activity in vitro, can be synthesized by use of a peptide synthesizer. Furthermore, if desired, non- classical amino acids or chemical amino acid analogs can be introduced as a substitution or addition into the nitrile hydratase protein sequence. Non-classical amino acids include, but are not limited to, the D-isomers of the common amino acids, I-amino isobutyric acid, 4-aminobutyric acid, Abu, 2-aminobutyric acid, ε-Abu, e-Ahx, 6-amino hexanoic acid, Aib, 2-amino isobutyric acid, 3-amino propionic acid, ornithine, norleucine, norvaline, hydroxyproline, sarcosine, citrulline, cysteic acid, t-butylglycine, t-butylalanine, phenylglycine, cyclohexylalanine, β-alanine, fluoro-amino acids, β-methyl amino acids, Ca-methyl amino acids, Na-methyl amino acids, and amino acid analogs in general. Furthermore, the amino acid can be D (dextrorotary) or L (levorotary).

In cases where natural products are suspected of being mutant or are isolated from new species, the amino acid sequence of the nitrile hydratase protein isolated from the natural source, as well as those expressed in vitro, or from synthesized expression vectors in vivo or in vitro, can be determined from analysis of the DNA sequence, or alternatively, by direct sequencing of the isolated protein. Such analysis can be performed by manual sequencing or through use of an automated amino acid sequenator. These procedures also can be used to synthesize peptides in which amino acids other than the 20 naturally occurring, genetically encoded amino acids are substituted at one, two, or more positions of the peptide. For instance, naphthylalanine can be substituted for tryptophan, facilitating synthesis. Other synthetic amino acids that can be

substituted into the peptides include L-hydroxypropyl, L-3, 4-dihydroxy-phenylalanyl, d amino acids such as L-d-hydroxylysyl and D-d-methylalanyl, L-α-methylalanyl, β amino acids, and isoquinolyl. D amino acids and non-naturally occurring synthetic amino acids can also be incorporated into the peptides (see, e.g., Roberts et al., "Unusual amino acids in peptide synthesis," in The Peptides: Analysis, Synthesis, Biology (Gross & Meienhfer (Eds.), 1983, vol. 5, Chap. 6, pp. 341-449)).

The nitrile hydratase peptides also can be modified by phosphorylation (see, e.g., Bannwarth et al., (1996) Bioorganic and Medicinal Chemistry Letters, 6:2141-2146), and other methods for making peptide derivatives (see, e.g., Hruby et al., (1990) Biochem. J., 268(2):249-262).

Those of skill in the art recognize that a variety of techniques are available for constructing nitrile hydratase derivatives with the same or similar desired biological activity as the corresponding nitrile hydratase peptide. Methods for preparing peptide derivatives modified at the N-terminal amino group, the C-terminal carboxyl group, and/or changing one or more of the ami do linkages in the peptide to a non-amido linkage are known to those of skill in the art. Amino terminus modifications include alkylating, acetylating, adding a carbobenzoyl group and forming a succinimide group (see, e.g., Murray et al., (1995) Burger's Medicinal Chemistry and Drug Discovery, 5th ed., Vol. 1, Manfred E. Wolf, ed., John Wiley and Sons, Inc.). C-terminal modifications include replacing the C-terminal carboxyl group by an ester, an amide or modifications to form a cyclic peptide. Methods for derivatizing peptide compounds or for coupling peptides to polymers have been described (see, e.g., Zallipsky, (1995) Bioconjugate Chem. 6:150- 165; Monfardini et al., (1995) Bioconjugate Chem. 6:62-69; Hruby et al., (1990) Biochem. J., 268:249-262; U.S. 4,640,835; U.S. 4,496,689; U.S. 4,301,144; U.S. 4,670,417; U.S. 4,791,192; U.S. 4,179,337; and WO 95/34326, all of which are incorporated by reference in their entirety herein). i. Random Mutagenesis

Any of a variety of general approaches for directed protein evolution based on mutagenesis can be employed. Any of these, alone or in combination can be used to modify a polypeptide such as nitrile hydratase to achieve a desired property. Such methods include random mutagenesis, where the amino acids in the starting protein sequence are replaced by all (or a group) of the 20 natural amino acids (as well as

unnatural amino acids) either in single or multiple replacements at different amino acid positions on the same molecule, at the same time. Another method, restricted random mutagenesis, introduces either all or some of the 20 natural amino acids (as well as unnatural amino acids) or DNA-biased residues. The bias is based on the sequence of the DNA and not on that of the protein in a stochastic or semi-stochastic manner, respectively, within restricted or predefined regions of the protein known in advance to be involved in the biological activity being "evolved." Any method known in the art can be used to modify or alter a polypeptide sequence, such as a nitrile hydrolase polypeptide. Random mutagenesis methods include, for example, use of E. coli XLl red, UV irradiation, chemical modification such as by deamination, alkylation, or base analog mutagens, or PCR methods such as DNA shuffling, cassette mutagenesis or site-directed random mutagenesis. Such examples include, but are not limited to, chemical modification by hydroxylamine (Ruan, H., et al. (1997) Gene 188:35-39), the use of dNTP analogs (Zaccolo, M., et al. (1996) J. MoI. Biol. 255:589-603), or the use of commercially available random mutagenesis kits such as, for example, GeneMorph PCR- based random mutagenesis kits (Stratagene) or Diversify random mutagenesis kits (Clontech). The Diversify random mutagenesis kit allows the selection of a desired mutation rate for a given DNA sequence (from 2 to 8 mutations/ 1000 base pairs) by varying the amounts of manganese (Mn ²⁺ ) or dGTP in the reaction mixture. Raising manganese levels initially increases the mutation rate, with a further mutation rate increase provided by increased concentration of dGTP. Even higher rates of mutation can be achieved by performing additional rounds of PCR. ii. Focused Mutagenesis

Focused mutation can be achieved by making one or more mutation in a pre- determined region of a gene sequence, for example, in the α subunit of the nitrile hydratase, such as in the region flanking the conserved -VC(S/T)LCSC- sequence of the α subunit or the starting codon thereof, in the β subunit, or in regions including residues involved in the formation of the substrate binding pocket.

In one example, any one or more amino acids of a nitrile hydratase polypeptide are mutated using any standard single or multiple site-directed mutagenesis kit such as for example QuikChange (Stratagene). In another example, any one or more amino acids of a protease are mutated by saturation mutagenesis (Zheng et al. (2004) Nucl. Acids. Res.,

32:115). In one exemplary embodiment, a saturation mutagenesis technique is used in which the residue(s) of a region or domain are mutated to each of the 20 possible natural amino acids (as well as unnatural amino acids) (see for example the Kunkle method, Current Protocols in Molecular Biology, John Wiley and Sons, Inc., Media, PA). In such a technique, a degenerate mutagenic oligonucleotide primer can be synthesized which contains a randomization of nucleotides at the desired codon(s) encoding the selected amino acid(s). Exemplary randomization schemes include NNS- or NNK-randomization, where N represents any nucleotide, S represents guanine or cytosine and K represents guanine or thymine. The degenerate mutagenic primer is annealed to the single stranded DNA template and DNA polymerase is added to synthesize the complementary strand of the template. After ligation, the double stranded DNA template is transformed into E. coli for amplification.

In an additional example, focused mutagenesis can be restricted to amino acids that are identified as targets in the initial rounds of screening. For example, following selection of modified nitrile hydratase polypeptides from randomly mutagenized combinatorial libraries, a disproportionate number of mutations can be observed at specific positions or regions. Functional assays, such as those known in the art and described herein, then can be performed on the modified nitrile hydratase polypeptides to determine whether the mutations correlate with the one or more desired property or activity, such as enantioselectivity. If correlation between the mutation(s) and the desired activity or property is verified, focused mutagenesis then can be used to specifically target these regions for further mutagenesis. This strategy allows for a more diverse and deep mutagenesis at particular specified positions, as opposed to the more shallow mutagenesis that occurs following random mutagenesis of a polypeptide sequence. For example, saturation mutagenesis can be used to mutate nitrile hydratase polypeptides such as by using oligos containing NNt/g or NNt/c at these positions.

Once one or more targets are selected as set forth above, replacing amino acids are introduced. Mutant proteins typically are prepared using recombinant DNA methods and assessed in appropriate biological assays for the particular activity (feature) optimized. An exemplary method of preparing the mutant proteins is by mutagenesis of the original, such as native, gene using methods well known in the art. Mutant molecules are generated one-by-one, such as in addressable arrays, such that each individual mutant

generated is the single product of each single and independent mutagenesis reaction. Individual mutagenesis reactions are conducted separately, such as in addressable arrays where they are physically separated from each other. Once a population of sets of nucleic acid molecules encoding the respective mutant proteins is prepared, each is separately introduced one-by-one into appropriate cells for the production of the corresponding mutant proteins. This also can be performed, for example, in addressable arrays where each set of nucleic acid molecules encoding a respective mutant protein is introduced into cells that are confined to a discrete location, such as in a well of a multi-well microtiter plate. Each individual mutant protein is individually phenotypically characterized and performance is quantitatively assessed using assays appropriate for the feature being optimized (e.g., enantioselectivity). Again, this step can be performed in addressable arrays. Those mutants displaying a desired increased enantioselectivity and/or nitrile hydration activity compared to the original, such as native molecules, are identified. From the beginning of the process of generating the mutant DNA molecules up through the readout and analysis of the performance results, each candidate mutant is generated, produced and analyzed individually, such as from its own address in an addressable array. The process is amenable to automation. The specific mutation of the candidate polypeptide can be determined using routine recombinant DNA techniques, such as sequencing. In one embodiment, combinations of targeted mutations can be made to further increase the properties and/or enantioselectivity of the modified nitrile hydratase polypeptide.

Once one or more target amino acids are selected, one of the steps in modifying the polypeptide can include identifying amino acids that will replace the original, such as native, amino acid at each target position to alter the activity level for the particular feature being evolved. The set of replacing amino acids to be used to replace the original, such as native, amino acid at each target position can be different and specific for the particular target position. The choice of the replacing amino acids takes into account the need to preserve the physicochemical properties such as hydrophobicity, charge and polarity of essential (e.g., catalytic, binding, etc.) residues and alter some other property of the protein (e.g., thermal stability and/or enantioselectivity). The number of replacing amino acids of the remaining 19 non-native (or non-original) amino acids that can be used

to replace a particular target position ranges from 1 up to about 19 and anywhere in between depending on the properties for the particular modification.

Numerous methods of selecting replacing amino acids (also referred to herein as "replacement amino acids") are well known in the art. Protein chemists determined that certain amino acid substitutions commonly occur in related proteins from different species. As the protein still functions with these substitutions, the substituted amino acids are compatible with protein structure and function. Often, these substitutions are to a chemically similar amino acid, but other types of changes, although relatively rare, also can occur. Knowing the types of changes that are most and least common in a large number of proteins can assist with predicting alignments and amino acid substitutions for any set of protein sequences. Amino acid substitution matrices are used for this purpose. Such matrices also are known and available in the art. For example, exemplary amino acid substitution matrices, include, but are not limited to, block substitution matrix (BLOSUM) (Henikoff et al., Proc. Natl. Acad. Sci. USA, 89: 10915-10919 (1992)), Jones et al. (Comput. Appl. Biosci., 8: 275-282 (1992)), Gonnet et al. (Science, 256: 1433-1445 (1992)), Fitch (J. MoI Evol., 16(1): 9-16 (1966)), Feng et al. (J. MoI. EvoL, 21 : 112-125 (1985)), McLachlan (J MoI. Biol, 61 : 409-424 (1971)), Grantham (Science, 185: 862- 864 (1974)), Miyata (J MoI. Evol, 12: 219-236 (1979)), Rao (J Pept. Protein Res., 29: 276-281 (1987)), Risler (J MoI. Biol, 204: 1019-1029 (1988)), Johnson et al (J MoI. Biol, 233: 716-738 (1993)), and Point Accepted Mutation (PAM) (Dayhoff et al., Atlas Protein Seq. Struct. 5: 345-352 (1978)).

The outcome of this mutagenesis is that the amino acid positions that are the target for mutagenesis are identified and the replacing amino acids for the original, such as native, amino acids at the target site(s) are identified, to provide a collection of mutant molecules that are expected to perform differently from the native molecule. These are assayed for a desired optimized (or improved or altered) activity, e.g. , enantioselectivity. iii. Exemplary modified nitrile hydratase polypeptides Provided herein are modified nitrile hydratase polypeptides with altered properties, including but not limited to, increased S-selectivity, increased conversion rates of substrate to product, increased organic solvent tolerance and increased thermal tolerance. Exemplary of modified nitrile hydratases for use in the methods herein are

modified nitrile hydratases from Bradyrhizobium japonicum USDA 505. The modified nitrile hydratases contain one or more mutations that are introduced to, for example, alter the enzyme enantioselectivity to a more desired S-selectivity. Thus, when tested using an appropriate in vitro assay, such as those described in Example 13, the modified nitrile hydratases can exhibit improved enantiomeric ratios (E values).

The modified nitrile hydratase polypeptides can be modified at one or more amino acid positions in the α-subunit and/or β-subunit providing that the resulting polypeptide retains activity and exhibits the desired properties, such as the desired enzyme enantioselectivity. In some examples, the nitrile hydratase is modified at one or more amino acid positions in the α-subunit, while in other examples the nitrile hydratase is modified at one or more amino acid positions in the β-subunit. In further examples, both the α-subunit and the β-subunit are modified.

In embodiments where the β-subunit is modified, the polypeptides can be modified at one or more amino acid positions. In some embodiments, one or more than one Ala residue in the β-subunit is replaced with a nonpolar (hydrophobic) amino acid, such as leucine, isoleucine, valine, proline, phenylalanine, tryptophan or methionine. In some embodiments, one or more than one Ala residue in the β-subunit is replaced with a polar neutral amino acid, such as glycine, serine, threonine, cysteine, tyrosine, asparagine or glutamine. In some embodiments, one or more than one Ala residue in the β-subunit is replaced with a non-classical or non-natural amino acid. In some embodiments, one or more than one Ala residue in the β-subunit is replaced with a synthetic amino acid. In some embodiments, one or more than one Ala residue in the β-subunit is replaced with a D amino acid.

In some embodiments, a Leu residue in the β-subunit is replaced with a negatively charged acidic amino acid, such as aspartic acid or glutamic acid. In some embodiments, a Leu residue in the β-subunit is replaced with a with a nonpolar (hydrophobic) amino acid, such as alanine, isoleucine, valine, proline, phenylalanine, tryptophan or methionine. In some embodiments, a Leu residue in the β-subunit is replaced with a synthetic amino acid. In some embodiments, a Leu residue in the β-subunit is replaced with a non- classical or non-natural amino acid. In some embodiments, a Leu residue in the β-subunit is replaced with a D amino acid.

In some embodiments, an Arg residue in the β-subunit is replaced with a polar neutral amino acid, such as glycine, serine, threonine, cysteine, tyrosine, asparagine or glutamine. In some embodiments, an Arg residue in the β-subunit is replaced with a positively charged amino acid, such as lysine or histidine. In some embodiments, an Arg residue in the β-subunit is replaced with a non-classical or non-natural amino acid. In some embodiments, an Arg residue in the β-subunit is replaced with a synthetic amino acid. In some embodiments, an Arg residue in the β-subunit is replaced with a D amino acid.

In some embodiments, a Gly residue in the β-subunit is replaced with a polar neutral amino acid, such as serine, threonine, cysteine, tyrosine, asparagine or glutamine. In some embodiments, a Gly residue in the β-subunit is replaced with a non-classical or non-natural amino acid. In some embodiments, a Gly residue in the β-subunit is replaced with a synthetic amino acid. In some embodiments, a Gly residue in the β-subunit is replaced with a D amino acid. In some embodiments, a VaI residue in the β-subunit is replaced with nonpolar

(hydrophobic) amino acid, such as alanine, leucine, isoleucine, proline, phenylalanine, tryptophan or methionine. In some embodiments, a VaI residue in the β-subunit is replaced with a non-classical or non-natural amino acid. In some embodiments, a VaI residue in the β-subunit is replaced with a synthetic amino acid. In some embodiments, a VaI residue in the β-subunit is replaced with a D amino acid.

Exemplary of modified nitrile hydratases from Bradyrhizobium japonicum USDA 505 are those that are modified at one or more of amino acid positions corresponding to amino acid positions L34, V37, R38, G41, A42, A43, G44, A45, F46, N47, 148, S51, R55, F73, L74, G75, L76, V113, V116 and M117 of the β-subunit set forth in SEQ ID NO:58 and 169, Y73, W143, P149, E191 and R193 of the α-subunit set forth in SEQ ID NO:57. For example, provided herein are modified nitrile hydratases that contain an amino acid substitution whereby the leucine at amino acid position 34 of the β-subunit set forth in SEQ ID NO:58 is replaced with an acidic amino acid, such as an aspartic acid or glutamic acid residue. In another example, the arginine at position 38 is replaced with a polar neutral amino acid, such as a glycine, serine, threonine, cysteine, tyrosine, asparagine, or glutamine. In some embodiments, the glycine at position 41 is be replaced is replaced with a polar neutral amino acid, such as a glycine, serine, threonine, cysteine,

amino acid substitutions set forth in Table 5. For example, a modified nitrile hydratase polypeptide can contain amino acid substitutions at positions 38 and 42 of the β-subunit set forth in SEQ ID NO:58, such as for example, R38C and A42T. In other embodiment, a modified nitrile hydratase polypeptide can contain amino acid substitutions at five amino acid positions. For example, a modified nitrile hydratase polypeptide can contain the amino acid substitutions R38C, A42V, A43S, L76F and V113L. Exemplary modified nitrile hydratase polypeptides that contain single amino acid replacements or that contain two or more amino acid replacements at one or more of the amino acid positions 34, 38, 41, 42, 43, 76 and 113 of the β-subunit set forth in SEQ ID NO:58, are those provided in Table 6. In Table 6 below, the sequence identifier (SEQ ID NO) is identified in which exemplary amino acid sequences of the β-subunits of the modified nitrile hydratase polypeptides are set forth. Table 6. Exemplary modified nitrile hydratase polypeptides

b. Enantiomeric selection

The preparation of chiral amides is of growing importance in the chemical and pharmaceutical industry. Preparation of enantiomerically pure compounds facilitates the production of biologically active substances, including levetiracetam. The addition of water to a nitrile group can result in the production of an enantiomeric mixture of optically active amides. Typically, however, only one of the two enantiomers is biologically active. For example, levetiracetam is the pharmacologically active (S)-enantiomer of α-ethyl-2- oxo-1-pyrrolidine acetamide. Selective production of a substituted chiral aliphatic amide

tyrosine, asparagine, or glutamine. In further examples, the alanine at position 42 or 43 is replaced with a polar neutral or nonpolar (hydrophobic) amino acid, such as for example, glycine, serine, threonine, cysteine, tyrosine, asparagine, alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan or methionine. In further aspects, the leucine at position 76 of the β-subunit set forth in SEQ ID NO:58 is replaced with a nonpolar (hydrophobic) amino acid, such as for example, alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan or methionine. In another example, the valine at position 113 is replaced with a nonpolar (hydrophobic) amino acid, such as an alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan or methionine. Table 5 sets forth non-limiting examples of exemplary amino acid substitutions at amino acid positions 34, 38, 41, 42, 43, 76 and 113 of the β-subunit set forth in SEQ ID NO:58. Table 5. Exemplary β-subunit amino acid substitutions

Exemplary of modified nitrile hydratase polypeptides are those that contain one or more amino acid substitutions at amino acid positions corresponding to amino acid positions 34, 38, 41, 42, 43, 76 and 113 of the β-subunit set forth in SEQ ID NO:58, such as any one or more or the amino acid substitutions set forth in Table 5. In some examples, the modified nitrile hydratase polypeptides contain an amino acid substitution at only one amino acid position. In other examples, combination mutants are generated in which the modified nitrile hydratase polypeptides contain an amino acid substitution at 2, 3, 4, 5, 6 or 7 amino acid positions. Thus, such polypeptides can contain 2, 3, 4, 5, 6 or 7 of the

of either the (S) or (R) configuration such as levetiracetam, precursors of levetiracetam or related compounds is therefore of benefit.

Nitrile hydratases exhibit enantioselectivity, such that particular nitrile hydratases selectively hydrate one enantiomer from a racemic mixture of nitrile substrates. Thus, a particular nitrile hydratase can convert an achiral nitrile substrate into a chiral product or mixture of products of either the (S)- or (R)-configuration. (see, Martinkova et al., (2002) Biocatal. Biotransform. 20:73-93). For example, nitrile hydratases from P. putida 5B, A. tumefaciens d3, R. equi A4, Pseudomonas sp. 2D- 11-5-1c, and Serratia liquefaciens MOB/IM/N3 selectively produce amide products of the (S)-configuration. Nitrile hydratases from Moraxella sp. 3L-A-1-5-1a-1, P. putida 2D-11-5-1b, P. putida 5B-

MNG-2P, and Pseudomonas aureofaciens MOB C2-1 selectively produce amide products of the (R)-configuration. The stereoselectivity of nitrile hydratases can be substrate dependent. The optical purity of the resulting amide compound is measured as enantiomer excess (ee), which is often expressed as a percentage to describe the percentage of the selective enantiomer in the product mixture. Nitrile hydratases can result in 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 92%, 94%, 95%, 96%, 98%, 99%, or more, ee. The more selective the nitrile hydratase, the higher the purity of the desired chiral product, and the higher the optical purity of the final enantiomeric compound. Nitrile hydratases can exhibit different substrate acceptance profiles, and display different selectivity strength for substrates. Typical substrates for nitrile hydratases are aliphatic and aromatic nitriles, including α substituted aliphatic nitriles and α substituted aromatic nitriles (see, e.g., Nagasawa et al., (1991) Eur. J. Biochem. 196:581-589). Exemplary substrates of nitrile hydratases include, but are not limited to, 4-acetyl- benzonitrile, 2-aminobenzonitrile, 3-aminobenzonitrile, 4-aminobenzonitrile, 2-chloro- benzonitrile, 3-chlorobenzonitrile, 4-chlorobenzonitrile, 2-hydroxybenzonitrile, 3-hydroxy- benzonitrile, 4-hydroxybenzonitrile, 2-methoxybenzonitrile, 3-methoxy-benzonitrile, 4- methoxybenzonitrile, 2-methyl-2-butenenitrile, 2-methyl-3-butenenitrile, 2-nitrobenzo- nitrile, 3-nitrobenzonitrile, 2-cyanobenzaldehyde, 3-cyanobenzaldehyde, 4-cyano- benzaldehyde, 2-cyanothiophene, 2-cyanofuran, 4-cyano-1-cyclohexene, 2-pentenenitrile, 3-pentenenitrile, 2-cyanopyridine, 3-cyanopyridine, 4-cyanopyridine, 2-pyridineaceto- nitrile, 3-indoleacetonitrile, 4-cyanopyridine N-oxide, acetonitrile, acrylonitrile,

benzonitrile, benzylcyanide, chloroacetonitrile, cinnamonitrile, crotononitrile, cyano- acetamide, cyanoacetic acid ethylester, cyanoacetic acid, cyclopropyl cyanide, cyano- pyrazine, ethylene cyanhidrine, isobutyronitrile, lactonitrile, methacrylonitrile, methoxy- acetonitrile, n-butyronitrile, n-capronitrile, p-hydroxybenzonitrile, pivalonitrile, potassium cyanide, propionitrile, p-tolunitrile, m-tolunitrile, p-tolunitrile, β-cyano-L-alanine, β- hydroxyacetonitrile, n-valeronitrile, isovaleronitrile, n-capronitrile, and isocapronitrile. In some embodiments, the substrate is selected from among an oxopyrrolidinyl- alkylnitrile, oxopiperidinyl-alkylnitrile, thioxopyrrolidinyl-alkylnitrile and thioxopyrrolidinyl-alkylnitrile. Exemplary oxopyrrolidinyl-alkylnitriles include 2-(2- oxopyrrolidin-1-yl)butanenitrile, 2-(3-methyl-2-oxopyrrolidin-1-yl)butanenitrile, 2-(3- ethyl-2-oxopyrrolidin-1-yl)butanenitrile, 2-(3-propyl-2-oxopyrrolidin-1-yl)butanenitrile , 2-(3-butyl-2-oxopyrrolidin-1-yl)butanenitrile, 2-(3-isobutyl-2-oxopyrrolidin-1-yl)butane- nitrile, 2-(4-methyl-2-oxopyrrolidin-1-yl)butanenitrile, 2-(4-ethyl-2-oxopyrrolidin-1- yl)butanenitrile, 2-(4-propyl-2-oxopyrrolidin-1-yl)butanenitrile , 4-(3-butyl-2-oxo- pyrrolidin-1-yl)butanenitrile, 2-(4-isobutyl-2-oxopyrrolidin-1-yl)butanenitrile, 2-(2- methyl-5-oxopyrrolidin-1-yl)butanenitrile, 2-(2-ethyl-5-oxopyrrolidin-1-yl)butanenitrile, 2-(2-propyl-5-oxopyrrolidin-1-yl)butanenitrile , 2-(2-butyl-5-oxopyrrolidin-1-yl)butane- nitrile, 2-(2-isobutyl-5-oxopyrrolidin-1-yl)butanenitrile, 3-methyl-2-(2-oxopyrrolidin-1- yl)butanenitrile, 3-methyl-2-(2-oxopyrrolidin-1-yl)pentanenitrile, 3-ethyl-2-(2-oxo- pyrrolidin-1-yl)pentanenitrile, 3-ethyl-2-(2-methyl-5-oxopyrrolidin-1-yl)pentanenitrile, 3- ethyl-2-(4-methyl-2-oxopyrrolidin-1-yl)pentanenitrile, 3-ethyl-2-(3-methyl-2-oxo- pyrrolidin-1-yl)pentanenitrile, 2-(2,3-dimethyl-5-oxopyrrolidin-1-yl)butanenitrile, 2-(3,5- dimethyl-2-oxopyrrolidin-1-yl)butanenitrile, 2-(2-oxopyrrolidin-1-yl)acetonitrile, 2-(2- methyl-5-oxopyrrolidin-1-yl)acetonitrile, 2-(2,3-dimethyl-5-oxopyrrolidin-1-yl)aceto- nitrile, 2-(2,3,4-trimethyl-5-oxopyrrolidin-1-yl)acetonitrile, 2-(3,4-dimethyl-2- oxopyrrolidin-1-yl)acetonitrile, 2-(3,5-dimethyl-2-oxopyrrolidin-1-yl)acetonitrile, 2- (2,3,4-trimethyl-5-oxopyrrolidin-1-yl)butanenitrile, 2-(3,4-dimethyl-2-oxopyrrolidin-1- yl)butanenitrile and 2-(3,5-dimethyl-2-oxopyrrolidin-1-yl)butanenitrile.

Exemplary oxopiperidinyl-alkylnitriles include 2-(2-oxopiperidin-1-yl)butane- nitrile, 2-(3-methyl-2-oxopiperidin-1-yl)butanenitrile, 2-(3-ethyl-2- oxopiperidin-1-yl)- butanenitrile, 2-(3-propyl-2- oxopiperidin-1-yl)butanenitrile , 2-(3-butyl-2-oxopiperidin-1- yl)butanenitrile, 2-(3-isobutyl-2- oxopiperidin-1-yl)butanenitrile, 2-(4-methyl-2-oxo-

piperidin-1-yl)butanenitrile, 2-(4-ethyl-2-oxopiperidin-1-yl)butanenitrile, 2-(4-propyl-2- oxopiperidin-1-yl)butanenitrile , 4-(3-butyl-2-oxopiperidin-1-yl)butanenitrile, 2-(4- isobutyl-2-oxopiperidin-1-yl)butanenitrile, 2-(2-methyl-5-oxopiperidin-1-yl)butanenitrile, 2-(2-ethyl-5-oxopiperidin-1-yl)butanenitrile, 2-(2-propyl-5-oxopiperidin-1-yl)butanenitrile, 2-(2-butyl-5-oxopiperidin-1-yl)butanenitrile, 2-(2-isobutyl-5-oxopiperidin-1-yl)butane- nitrile, 3-methyl-2-(2-oxopiperidin-1-yl)butanenitrile, 3-methyl-2-(2-oxopiperidin-1-yl)- pentanenitrile, 3-ethyl-2-(2-oxopiperidin-1-yl)pentanenitrile, 3-ethyl-2-(2-methyl-5-oxo- piperidin-1-yl)pentanenitrile, 3-ethyl-2-(4-methyl-2-oxopiperidin-1-yl)pentanenitrile, 3- ethyl-2-(3-methyl-2-oxopiperidin-1-yl)pentanenitrile, 2-(2,3-dimethyl-5-oxopiperidin-1- yl)butanenitrile, 2-(3,5-dimethyl-2-oxopiperidin-1-yl)butanenitrile, 2-(2-oxopiperidin-1- yl)acetonitrile, 2-(2-methyl-5-oxopiperidin-1-yl)acetonitrile, 2-(2,3-dimethyl-5-oxo- piperidin-1-yl)acetonitrile, 2-(2,3,4-trimethyl-5-oxopiperidin-1-yl)acetonitrile, 2-(3,4- dimethyl-2-oxopiperidin-1-yl)acetonitrile, 2-(3,5-dimethyl-2-oxopiperidin-1-yl)acetonitrile, 2-(2,3,4-trimethyl-5-oxopiperidin-1-yl)butanenitrile, 2-(3,4-dimethyl-2-oxopiperidin-1- yl)butanenitrile, 2-(3,5-dimethyl-2-oxopiperidin-1-yl)butanenitrile, 2-(2,3,4,6-tetramethyl- 5-oxopiperidin-1-yl)butanenitrile, 2-(2,3,6-trimethyl-5-oxopiperidin-1-yl)butanenitrile, 2- (2,4,5-trimethyl-3-oxopiperidin-1-yl)butanenitrile, 2-(4-ethyl-3-methyl-5-oxopiperidin-1- yl)butanenitrile and 2-(4,5-diethyl-2-methyl-3-oxopiperidin-1-yl)butanenitrile.

Exemplary thioxopyrrolidinyl-alkylnitriles include_2-(2-thioxopyrrolidin-1-yl)- butanenitrile, 2-(3-methyl-2-thioxopyrrolidin-1-yl)butanenitrile, 2-(3-ethyl-2-thioxo- pyrrolidin-1-yl)butanenitrile, 2-(3-propyl-2-thioxopyrrolidin-1-yl)butanenitrile , 2-(3- butyl-2-thioxopyrrolidin-1-yl)butanenitrile, 2-(3-isobutyl-2-thioxopyrrolidin-1-yl)- butanenitrile, 2-(4-methyl-2-thioxopyrrolidin-1-yl)butanenitrile, 2-(4-ethyl-2-thioxo- pyrrolidin-1-yl)butanenitrile, 2-(4-propyl-2-thioxopyrrolidin-1-yl)butanenitrile , 4-(3- butyl-2-thioxopyrrolidin-1-yl)butanenitrile, 2-(4-isobutyl-2-thioxopyrrolidin-1-yl)- butanenitrile, 2-(2-methyl-5-thioxopyrrolidin-1-yl)butanenitrile, 2-(2-ethyl-5-thioxo- pyrrolidin-1-yl)butanenitrile, 2-(2-propyl-5-thioxopyrrolidin-1-yl)butanenitrile , 2-(2- butyl-5-thioxopyrrolidin-1-yl)butanenitrile, 2-(2-isobutyl-5-thioxopyrrolidin-1-yl)- butanenitrile, 3-methyl-2-(2-thioxopyrrolidin-1-yl)butanenitrile, 3-methyl-2-(2-thioxo- pyrrolidin-1-yl)pentanenitrile, 3-ethyl-2-(2-thioxopyrrolidin-1-yl)pentanenitrile, 3-ethyl- 2-(2-methyl-5-thioxopyrrolidin-1-yl)pentanenitrile, 3 -ethyl-2-(4-methyl-2-thioxo- pyrrolidin-1-yl)pentanenitrile, 3-ethyl-2-(3-methyl-2-thioxopyrrolidin-1-yl)pentanenitrile,

2-(2,3-dimethyl-5-thioxopyrrolidin-1-yl)butanenitrile, 2-(3,5-dimethyl-2-thioxo- pyrrolidin-1-yl)butanenitrile, 2-(2-thioxopyrrolidin-1-yl)acetonitrile, 2-(2-methyl-5- thioxopyrrolidin-1-yl)acetonitrile, 2-(2,3-dimethyl-5-thioxopyrrolidin-1-yl)acetonitrile, 2- (2,3,4-trimethyl-5-thioxopyrrolidin-1-yl)acetonitrile, 2-(3,4-dimethyl-2-thioxopyrrolidin- 1-yl)acetonitrile, 2-(3,5-dimethyl-2-thioxopyrrolidin-1-yl)acetonitrile, 2-(2,3,4-trimethyl- 5-thioxopyrrolidin-1-yl)butanenitrile, 2-(3 ,4-dimethyl-2-thioxopyrrolidin-1-yl)butane- nitrile and 2-(3,5-dimethyl-2-thioxopyrrolidin-1-yl)butanenitrile.

Exemplary thioxopiperidinyl-alkylnitriles include_2-(2-thioxopiperidin-1-yl)- butanenitrile, 2-(3-methyl-2-thioxopiperidin-1-yl)butanenitrile, 2-(3-ethyl-2- thioxo- piperidin-1-yl)butanenitrile, 2-(3 -propyl -2- thioxopiperidin-1-yl)butanenitrile , 2-(3-butyl- 2- thioxopiperidin-1-yl)butanenitrile, 2-(3-isobutyl-2- thioxopiperidin-1-yl)butanenitrile, 2-(4-methyl-2-thioxopiperidin-1-yl)butanenitrile, 2-(4-ethyl-2-thioxopiperidin-1-yl)- butanenitrile, 2-(4-propyl-2-thioxopiperidin-1-yl)butanenitrile , 4-(3-butyl-2-thioxo- piperidin-1-yl)butanenitrile, 2-(4-isobutyl-2-thioxopiperidin-1-yl)butanenitrile, 2-(2- methyl-5-thioxopiperidin-1-yl)butanenitrile, 2-(2-ethyl-5-thioxopiperidin-1-yl)butane- nitrile, 2-(2-propyl-5-thioxopiperidin-1-yl)butanenitrile, 2-(2-butyl-5-thioxopiperidin-1- yl)butanenitrile, 2-(2-isobutyl-5-thioxopiperidin-1-yl)butanenitrile, 3-methyl-2-(2-thioxo- piperidin-1 -yl)butanenitrile, 3-methyl-2-(2-thioxopiperidin-1-yl)pentanenitrile, 3-ethyl-2- (2-thioxopiperidin-1-yl)pentanenitrile, 3-ethyl-2-(2-methyl-5-thioxopiperidin-1-yl)- pentanenitrile, 3-ethyl-2-(4-methyl-2-thioxopiperidin-1-yl)pentanenitrile, 3-ethyl-2-(3- methyl-2-thioxopiperidin-1-yl)pentanenitrile, 2-(2,3-dimethyl-5-thioxopiperidin-1-yl)- butanenitrile, 2-(3,5-dimethyl-2-thioxopiperidin-1-yl)butanenitrile, 2-(2-thioxopiperidin- 1 -yl)acetonitrile, 2-(2-methyl-5-thioxopiperidin-1-yl)acetonitrile, 2-(2,3-dimethyl-5- thioxopiperidin-1-yl)acetonitrile, 2-(2,3,4-trimethyl-5-thioxopiperidin-1-yl)acetonitrile, 2- (3,4-dimethyl-2-thioxopiperidin-1-yl)acetonitrile, 2-(3,5-dimethyl-2-thioxopiperidin-1- yl)acetonitrile, 2-(2,3,4-trimethyl-5-thioxopiperidin-1-yl)butanenitrile, 2-(3,4-dimethyl-2- thioxopiperidin-1-yl)butanenitrile, 2-(3,5-dimethyl-2-thioxopiperidin-1-yl)butanenitrile, 2-(2,3,4,6-tetramethyl-5-thioxopiperidin-1-yl)butanenitrile, 2-(2,3,6-trimethyl-5-thioxo- piperidin-1-yl)butanenitrile, 2-(2,4,5-trimethyl-3-thioxopiperidin-1-yl)butanenitrile, 2-(4- ethyl-3-methyl-5-thioxopiperidin-1-yl)butanenitrile and 2-(4,5-diethyl-2-methyl-3-thioxo- piperidin-1-yl)butanenitrile.

c. Screening

The modified polypeptides can be tested in screening assays individually, or can be tested as collections such as in libraries. In one example, the nitrile hydratase variant polypeptides are randomly generated by mutagenesis, and cloned individually. Activity assessment is then individually performed on each individual protein mutant molecule, following protein expression and measurement of the appropriate activity. In some examples, the individual clones can be assayed in an addressable array, such that they are physically separated from each other so that the identity of each individual polypeptide is known based on its location in the array. For example, if each one is the single product of an independent mutagenesis reaction, the specific mutation can be easily determined without the need for sequencing. Alternatively, sequencing can be performed on the resulting modified polypeptides to determine those mutations that confer an activity.

In another example, the modified nitrile hydratase polypeptides can be screened as collections or in a library. For example, a library of nitrile hydratase polypeptides can be displayed on a genetic package for screening, including, but not limited to, any replicable vector, such as a phage, virus, or bacterium, that can display a polypeptide moiety. The plurality of displayed polypeptides is displayed by a genetic package in such a way as to allow the polypeptide to bind and/or interact with a target polypeptide. Exemplary genetic packages include, but are not limited to, bacteriophages (see, e.g., Clackson et al. (1991) Making Antibody Fragments Using Phage Display Libraries, Nature, 352:624- 628; Glaser et al. (1992) Antibody Engineering by Condon-Based Mutagenesis in a Filamentous Phage Vector System, J. Immunol., 149:3903 3913; Hoogenboom et al. (1991) Multi-Subunit Proteins on the Surface of Filamentous Phage: Methodologies for Displaying Antibody (Fate) Heavy and 30 Light Chains, Nucleic Acids Res., 19:4133- 41370), baculoviruses (see, e.g., Boublik et al. (1995) Eukaryotic Virus Display:

Engineering the Major Surface Glycoproteins of the Autographa California Nuclear Polyhedrosis Virus (ACNPV) for the Presentation of Foreign Proteins on the Virus Surface, Bio/Technology, 13:1079-1084), bacteria and other suitable vectors for displaying a protein, such as a phage-displayed protease. For example bacteriophages of interest include, but are not limited to, T4 phage, Ml 3 phage and HI phage. Genetic packages are optionally amplified such as in a bacterial host.

Phage display is known to those of skill in the art and is described, for example, in Ladner et al., U.S. Pat. No. 5,223,409; Rodi et al. (2002) Curr. Opin. Chem. Biol. 6:92- 96; Smith (1985) Science 228:1315-1317; WO 92/18619; WO 91/17271; WO 92/20791; WO 92/15679; WO 93/01288; WO 92/01047; WO 92/09690; WO 90/02809; de Haard et al. (1999) J. Biol. Chem 274:18218-30; Hoogenboom et al. (1998) Immunotechnology 4:1-20; Hoogenboom et al. (2000) Immunol Today 2:371-8; Fuchs et al. (1991) Bio/Technology 9:1370-1372; Hay et al. (1992) Hum Antibod Hybridomas 3:81-85; Huse et al. (1989) Science 246:1275-1281; Griffiths et al. (1993) EMBO J 12:725-734; Hawkins et al. (1992) J MoI Biol 226:889-896; Clackson et al. (1991) Nature 352:624- 628; Gram et al. (1992) PNAS 89:3576-3580; Garrard et al. (1991) Bio/Technology 9:1373-1377; Rebar et al. (1996) Methods Enzymol. 267:129-49; Hoogenboom et al. (1991) Nuc Acid Res 19:4133-4137; and Barbas et al. (1991) PNAS 88:7978-7982. Nucleic acids suitable for phage display, e.g., phage vectors, are known in the art (see, e.g., Andris-Widhopf et al. (2000) J Immunol Methods, 28: 159-81, Armstrong et al. (1996) Academic Press, Kay et al., Ed. pp. 35-53; Corey et al. (1993) Gene 128(1):129- 34; Cwirla et al. (1990) Proc Natl Acad Sci USA 87(16):6378-82; Fowlkes et al. (1992) Biotechniques 13(3):422-8; Hoogenboom et al. (1991) Nuc Acid Res 19(15):4133-7; McCafferty et al. (1990) Nature 348(6301):552-4; McConnell et al. (1994) Gene 151(1- 2): 115-8; Scott and Smith (1990) Science 249(4967):386-90). Libraries of variant nitrile hydratase polypeptides for screening also can be expressed on the surfaces of cells, for example, prokaryotic or eukaryotic cells. Exemplary cells for cell surface expression include, but are not limited to, bacteria, yeast, insect cells, avian cells, plant cells, and mammalian cells (Chen and Georgiou (2002) Biotechnol Bioeng 79: 496-503). In one example, the bacterial cells for expression are Escherichia coli.

Variant polypeptides can be expressed as a fusion protein with a protein that is expressed on the surface of the cell, such as a membrane protein or cell surface-associated protein. For example, a variant nitrile hydratase can be expressed in E. coli as a fusion protein with an E. coli outer membrane protein (e.g. OmpA), a genetically engineered hybrid molecule of the major E. coli lipoprotein (Lpp) and the outer membrane protein OmpA or a cell surface-associated protein (e.g. pili and flagellar subunits). Generally, when bacterial outer membrane proteins are used for display of heterologous peptides or

proteins, it is achieved through genetic insertion into permissive sites of the carrier proteins. Expression of a heterologous peptide or protein is dependent on the structural properties of the inserted protein domain, since the peptide or protein is more constrained when inserted into a permissive site as compared to fusion at the N- or C-terminus of a protein. Modifications to the fusion protein can be done to improve the expression of the fusion protein, such as the insertion of flexible peptide linker or spacer sequences or modification of the bacterial protein (e.g. by mutation, insertion, or deletion, in the amino acid sequence). Enzymes, such as β-lacatamase and the Cex exoglucanase of Cellulomonas fimi, have been successfully expressed as Lpp-OmpA fusion proteins on the surface of E. coli (Francisco J. A. and Georgiou G. Ann N Y Acad Sci. 745:372-382 (1994) and Georgiou G. et al. Protein Eng. 9:239-247 (1996)). Other peptides of 15-514 amino acids have been displayed in the second, third, and fourth outer loops on the surface of OmpA (Samuelson et al. J. Biotechnol. 96: 129-154 (2002)). Thus, outer membrane proteins can carry and display heterologous gene products on the outer surface of bacteria.

It is also possible to use other display formats to screen libraries of variant polypeptides. Exemplary other display formats include nucleic acid-protein fusions, ribozyme display (see e.g. Hanes and Pluckthun (1997) Proc. Natl. Acad. Sci. U.S.A. 13:4937-4942), bead display (Lam, K. S. et al. Nature (1991) 354, 82-84; , K. S. et al. (1991) Nature, 354, 82-84; Houghten, R. A. et al. (1991) Nature, 354, 84-86; Furka, A. et al. (1991) Int. J. Peptide Protein Res. 37, 487-493; Lam, K. S., et al. (1997) Chem. Rev., 97, 411-448; U.S. Published Patent Application 2004-0235054) and protein arrays (see e.g. Cahill (2001) J. Immunol. Meth. 250:81-91, WO 01/40803, WO 99/51773, and US2002-0192673-A1) In other cases, it can be advantageous to instead attach the variant polypeptides or phage libraries or cells expressing variant polypeptides to a solid support. For example, in some examples, cells expressing variant nitrile hydratase polypeptides can be naturally adsorbed to a bead, such that a population of beads contains a single cell per bead (Freeman et al. Biotechnol. Bioeng. (2004) 86:196-200). Following immobilization to a glass support, microcolonies can be grown and screened with a chromogenic or fluorogenic substrate. In another example, variant nitrile hydratase polypeptides or phage

libraries or cells expressing variant nitrile hydratase can be arrayed into titer plates and immobilized.

To identify those modified nitrile hydratase polypeptides that exhibit increase enantioselectivity, modified nitrile hydratase polypeptides are screened individually or in a library and tested in functional assays to identify those that display increased enantioselectivity and/or increased activity (hydration of a nitrile substrate). Such assays are described herein or are known to those of skill in the art. In some embodiments, one or more enzymes are first screened for suitability for use as a nitrile hydratase for the methods provided herein. For example, a library of nitrile hydratases that contain enzymes from multiple species and/or contain one or more variants thereof, can be screened for (S)-enantioselectivity. In particular, the one or more enzymes are screened for (S)-enantioselectivity using a compound of Formula III as the substrate. Screening libraries of enzymes facilitates the identification of an optimal nitrile hydratase that exhibits substrate acceptance for a compound of Formula III with good yield and selectivity. Suitable assays are known in the art, and can use, for example, high performance liquid chromatography (HPLC) or gas chromatography (GC) to determine the amounts of (R)- and (S)-enantiomer in the final product. In one embodiment, an enzyme assay is performed to determine the enantiomeric selection and enzyme activity of the candidate nitrile hydratase. In some embodiments, various dilutions of the candidate nitrile hydratase are assayed. Aliquots from the reaction are taken at various times and the product is then assessed by HPLC using an appropriate chiral stationary phase, such as cellulose tris(4-methylbenzoate), which separates the enantiomers and the starting substrate. The molar amounts of the remaining substrate and the (R)- and (S)- products are measured to determine the ee and the enzyme activity (i.e., the amount of enzyme that produced one micromole of product per minute). In other embodiments, chiral gas chromatography can be used to assess the enantiomeric selection and enzymatic activity of the candidate. In some embodiments, high-throughput assays are performed to identify the one or more nitrile hydratase useful for the methods provided herein. In one embodiment, modified nitrile hydratase polypeptides are tested for improved selectivity, e.g., improved enantioselectivity, as assessed by the conversion of racemic 2-(2-oxopyrrolidin-1-yl)butanenitrile to the S-amide product. The conversion of the nitrile substrate to the amide product can be determined by any method known in the

art. For example, the conversion can be determined by HPLC (50% CH ₃ CN / 50% water containing 0.07% perchloric acid on a Kromasil C4 column). The S/R ratio of the products and their enantiomeric excess (ee) are determined , for example, by either a reverse-phase HPLC (70% water / 30% CH ₃ CN on a Chiralpak ^® AD-RH column) or a normal-phase method (85% heptane / 15% ethanol on a Chiralpak AD column). The enantiomeric ratio (E value) is calculated from the conversion (c) and the ee of the amide (ee _p ) as follows:

E = ll[1-c(1+ee _p )] / ln[1-c(1-ee _p )] .

In some embodiments, the modified NHase polypeptides provided herein have a conversion of 20% or more. In some embodiments, the modified NHase polypeptides provided herein have an S/R ratio of 4:1 or greater. In some embodiments, the modified NHase polypeptides provided herein have an E value greater than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more. In some embodiments, the modified NHase polypeptides provided herein have an E value greater than 4.5. In some embodiments, the modified NHase polypeptides provided herein have an E value greater than 5.

Any one or more of the approaches described herein can be selected to identify those candidate nitrile hydratase polypeptides or modified NHase polypeptides that exhibit the desired properties or activities. The selection of variant nitrile hydratase polypeptides is based on testing the variant polypeptide for the specific activity or property being modified (e.g., improved enantioselectivity and/or activity and/or thermal stability and/or stability to organic solvents). Standard assays known in the art or described herein below can be performed in vitro or in vivo in order to perform the assessments. For example, the catalytic activity of nitrile hydratase can be assessed using various methods, including measuring the hydration of various nitrile substrates, or measuring the conversion activity in various solvent systems or at various temperatures (see, e.g. Examples 10 and 11 below). One of skill in the art can assess concomitant changes in catalytic activity, or enantioselectivity, or thermal stability or any other activity or property, to determine whether the modified nitrile hydratase polypeptide would be useful as a biocatalyst, such as, for example, the conversion of a racemic nitrile substrate to its corresponding S-amide product on a commercial scale.

The activities and properties of NHase polypeptides can be assessed in vitro and/or in vivo. Assays for such assessment are known to those of skill in the art. In one example, NHase variants can be assessed in comparison to unmodified and/or wild-type unmodified NHase. In vitro assays include any laboratory assay known to one of skill in the art, such as for example, cell-based assays including binding assays, protein assays, and molecular biology assays.

Exemplary in vitro assays include assays to assess polypeptide activity. Assays for activity include, but are not limited to, measurement of NHase hydration of one or more selected nitrile substrates to the corresponding amide products. Exemplary nitrile substrates include, but are not limited to, 2-hydroxypropanenitrile, 2-hydroxybutanenitrile, 2-hydroxypentanenitrile, hydroxy(phenyl)-ethanenitrile, hydroxy(4-methylphenyl)ethane- nitrile, hydroxy(4-methoxyphenyl)ethanenitrile, (4-chlorophenyl)(hydroxy)ethanenitrile and 2-(2-oxopyrrolidin-1-yl)butanenitrile. In one embodiment, the nitrile substrate for the assay is 2-(2-oxopyrrolidin-1-yl)butanenitrile. Assessment of the products of nitrile hydration catalyzed by NHase polypeptide or modified NHase polypeptide reactions can be performed using methods including, but not limited to, chromogenic substrate cleavage, HPLC, SDS-PAGE analysis, ELISA, Western blotting, immunohistochemistry and immunoprecipitation.

Concentrations of NHase polypeptides and modified NHase polypeptides can be assessed by methods well-known in the art, including, but not limited to, enzyme-linked immunosorbent assays (ELISA), SDS-PAGE; Bradford, Lowry, BCA methods, UV absorbance, and other quantifiable protein labeling methods, such as, but not limited to, immunological, radioactive and fluorescent methods and related methods.

Structural properties of modified NHase polypeptides also can be assessed. For example, X-ray crystallography, nuclear magnetic resonance (NMR), and cryoelectron microscopy (cryo-EM) of modified NHase polypeptides can be performed to assess three- dimensional structure of the NHase polypeptides and/or other properties of NHase polypeptides, such as Co or Fe ion binding.

3. Production of nitrile hydratase polypeptides Nitrile hydratase polypeptides, including modified nitrile hydratase polypeptides, or domains thereof, can be obtained by methods well known in the art for protein

purification and recombinant protein expression. Any method known to those of skill in the art for identification of nucleic acids that encode desired genes can be used. Any method available in the art can be used to obtain a full length (i.e., encompassing the entire coding region) cDNA or genomic DNA clone encoding a nitrile hydratase polypeptide. Modified nitrile hydratase polypeptides can be engineered as described herein, such as by site-directed mutagenesis.

Nitrile hydratase can be cloned or isolated using any available methods known in the art for cloning and isolating nucleic acid molecules. Such methods include PCR amplification of nucleic acids and screening of libraries, including nucleic acid hybridization screening, antibody-based screening and activity-based screening.

Methods for amplification of nucleic acids can be used to isolate nucleic acid molecules encoding a nitrile hydratase polypeptide, including for example, polymerase chain reaction (PCR) methods. A nucleic acid containing material can be used as a starting material from which a nitrile hydratase-encoding nucleic acid molecule can be isolated. For example, DNA and mRNA preparations or cell extracts can be used in amplification methods. Nucleic acid libraries also can be used as a source of starting material. Primers can be designed to amplify a nitrile hydratase-encoding molecule. For example, primers can be designed based on expressed sequences from which a nitrile hydratase is generated. Primers can be designed based on back-translation of a nitrile hydratase amino acid sequence. Nucleic acid molecules generated by amplification can be sequenced and confirmed to encode a nitrile hydratase polypeptide.

Additional nucleotide sequences can be joined to a nitrile hydratase -encoding nucleic acid molecule, including linker sequences containing restriction endonuclease sites for the purpose of cloning the synthetic gene into a vector, for example, a protein expression vector or a vector designed for the amplification of the core protein coding DNA sequences. Furthermore, additional nucleotide sequences specifying functional DNA elements can be operatively linked to a nitrile hydratase-encoding nucleic acid molecule. Examples of such sequences include, but are not limited to, promoter sequences designed to facilitate intracellular protein expression, and secretion sequences designed to facilitate protein secretion. Additional nucleotide sequences such as sequences specifying protein binding regions also can be linked to nitrile hydratase- encoding nucleic acid molecules. Such regions include, but are not limited to, sequences

to facilitate uptake of nitrile hydratase into specific target cells, or otherwise enhance the pharmacokinetics of the synthetic gene.

The identified and isolated nucleic acids then can be inserted into an appropriate cloning vector. A large number of vector-host systems known in the art can be used. Possible vectors include, but are not limited to, plasmids or modified viruses, but the vector system must be compatible with the host cell used. Such vectors include, but are not limited to, bacteriophages such as lambda derivatives, or plasmids, such as pBR322, pUC18, pET21d, pTrcHis2A, pKK223-3, pUB110, pTZ4, pC194, ρ11, φ1, φ105, pHV14, TRp7, YEp7 and pBS7, pUC plasmid derivatives or the Bluescript vector (such as Bluescript II SK(+), Stratagene, La Jolla, CA).

The insertion into a cloning vector can, for example, be accomplished by ligating the DNA fragment into a cloning vector which has complementary cohesive termini. Insertion can be effected using TOPO cloning vectors (Invitrogen, Carlsbad, CA). If the complementary restriction sites used to fragment the DNA are not present in the cloning vector, the ends of the DNA molecules can be enzymatically modified. Alternatively, any site desired can be produced by ligating nucleotide sequences (linkers) onto the DNA termini; these ligated linkers can contain specific chemically synthesized oligonucleotides encoding restriction endonuclease recognition sequences. In an alternative method, the cleaved vector and nitrile hydratase protein gene can be modified by homopolymeric tailing. Recombinant molecules can be introduced into host cells via, for example, transformation, transfection, infection, electroporation and sonoporation, so that many copies of the gene sequence are generated.

A recombinant plasmid can be constructed by inserting the nitrile hydratase gene into a plasmid vector having a control region necessary for the expression of the nitrile hydratase gene and a self-replication region, and this can be introduced into any desired host to make it produce the nitrile hydratase. Any host can be used, including, but not limited to, Escherichia coli, any microorganisms of the genus Bacillus (such as Bacillus subtilis), yeasts and actinomyces. The control region necessary for the expression includes a promoter sequence (including the operator sequence for control of transcription), a ribosome-binding sequence (SD sequence) and a transcription- terminating sequence. The promoter sequence can include a trp promoter of tryptophan operon and a lac promoter of lactose operon, a PL promoter and a PR promoter, such as

those derived from lambda phage, and a glucuronic acid synthetase promoter (gnt), an alkali protease promoter (apr), a neutral protease promoter (npr) and an -amylase promoter (amy), such as those derived from Bacillus subtilis. In addition to these, a tac promoter also can be used. The ribosome-binding sequence can include, for example, a sequence derived from Escherichia coli and/or Bacillus subtilis, as well as the sequence intrinsic to the organism from which the native nitrile hydratase is derived. For example, a consensus sequence comprising a series of 4 or more continuous bases that are complementary to the 3 '-terminal region of 16S ribosome RNA may be prepared through DNA synthesis and used as the ribosome-binding sequence. In some embodiments, the sequence of the control region on the recombinant plasmid is in a particular order. In one embodiment, the promoter sequence, the ribosome-binding sequence, the nitrile hydratase gene, and the transcription-terminating sequence are in that order, starting from the upstream side of the 5'-terminal end of the region.

In specific embodiments, transformation of host cells with recombinant DNA molecules that incorporate the isolated nitrile hydratase protein gene, cDNA, or synthesized DNA sequence enables generation of multiple copies of the gene. Thus, the gene can be obtained in large quantities by growing transformants, isolating the recombinant DNA molecules from the transformants and, when necessary, retrieving the inserted gene from the isolated recombinant DNA. a. Vectors and Cells

For recombinant expression of nitrile hydratase proteins, the nucleic acid containing all or a portion of the nucleotide sequence encoding the NHase protein can be inserted into an appropriate expression vector, i.e., a vector that contains the necessary elements for the transcription and translation of the inserted protein coding sequence. The necessary transcriptional and translational signals also can be supplied by the native promoter for a NHase gene, and/or their flanking regions.

Also provided are vectors that contain nucleic acid encoding the NHase or modified NHase. Cells containing the vectors also are provided. The cells include eukaryotic and prokaryotic cells, and the vectors are any suitable for use therein. Prokaryotic and eukaryotic cells containing the vectors are provided. Such cells include bacterial cells, yeast cells, fungal cells, Archea, plant cells, insect cells and animal cells. The cells are used to produce a NHase polypeptide or modified NHase polypeptide

by growing the above-described cells under conditions whereby the encoded NHase protein is expressed by the cell, and recovering the expressed NHase protein. For purposes herein, the NHase can be secreted into the medium.

In one embodiment, vectors containing a sequence of nucleotides that encodes a polypeptide that has NHase activity and contains all or a portion of the NHase polypeptide, or multiple copies thereof, are provided. The vectors can be selected for expression of the NHase polypeptide or modified NHase polypeptide in the cell or such that the NHase protein is expressed as a secreted protein. When the NHase is expressed the nucleic acid is linked to nucleic acid encoding a secretion signal, such as the Saccharomyces cerevisiae α-mating factor signal sequence or a portion thereof, or the native signal sequence.

A variety of host- vector systems can be used to express the protein coding sequence. These include but are not limited to mammalian cell systems infected with virus (e.g. vaccinia virus, adenovirus and other viruses); insect cell systems infected with virus (e.g. baculovirus); microorganisms such as yeast containing yeast vectors; or bacteria transformed with bacteriophage, DNA, plasmid DNA, or cosmid DNA. The expression elements of vectors vary in their strengths and specificities. Depending on the host- vector system used, any one of a number of suitable transcription and translation elements can be used. Any methods known to those of skill in the art for the insertion of DNA fragments into a vector can be used to construct expression vectors containing a chimeric gene containing appropriate transcriptional/translational control signals and protein coding sequences. These methods can include in vitro recombinant DNA and synthetic techniques and in vivo recombinants (genetic recombination). Expression of nucleic acid sequences encoding a NHase polypeptide or modified NHase polypeptide, or domains, derivatives, fragments or homologs thereof, can be regulated by a second nucleic acid sequence so that the genes or fragments thereof are expressed in a host transformed with the recombinant DNA molecule(s). For example, expression of the proteins can be controlled by any promoter/enhancer known in the art. In a specific embodiment, the promoter is not native to the genes for a NHase protein. Promoters which can be used include but are not limited to the SV40 early promoter (Bernoist and Chambon, Nature 290:304-310 (1981)), the promoter contained in the 3' long terminal repeat of Rous

sarcoma virus (Yamamoto et al. Cell 22:787-797 (1980)), the herpes thymidine kinase promoter (Wagner et al., Proc. Natl. Acad. Sci. USA 78:1441-1445 (1981)), the regulatory sequences of the metallothionein gene (Brinster et al., Nature 296:39-42 (1982)); prokaryotic expression vectors such as the β-lactamase promoter (Jay et al., (1981) Proc. Natl. Acad. Sci. USA 78:5543) or the tac promoter (DeBoer et al., Proc. Natl. Acad. Sci. USA 80:21-25 (1983)); see also "Useful Proteins from Recombinant Bacteria": in Scientific American 242:79-94 (1980)); plant expression vectors containing the nopaline synthetase promoter (Herrar-Estrella et al., Nature 303:209-213 (1984)) or the cauliflower mosaic virus 35S RNA promoter (Garder et al., Nucleic Acids Res. 9:2871 (1981)), and the promoter of the photosynthetic enzyme ribulose bisphosphate carboxylase (Herrera-Estrella et al., Nature 310:115-120 (1984)); promoter elements from yeast and other fungi such as the Gal4 promoter, the alcohol dehydrogenase promoter, the phosphoglycerol kinase promoter and the alkaline phosphatase promoter. In a specific embodiment, a vector is used that contains a promoter operably linked to nucleic acids encoding a NHase polypeptide or modified NHase polypeptide, or a domain, fragment, derivative or homolog, thereof, one or more origins of replication, and optionally, one or more selectable markers (e.g., an antibiotic resistance gene). Vectors and systems for expression of NHase polypeptides include the well known Pichia vectors (available, for example, from Invitrogen, San Diego, CA), particularly those designed for secretion of the encoded proteins. Exemplary plasmid vectors for expression in mammalian cells include, for example, pCMV. Exemplary plasmid vectors for transformation of E. coli cells, include, for example, the pQE expression vectors (available from Qiagen, Valencia, CA; see also literature published by Qiagen describing the system). pQE vectors have a phage T5 promoter (recognized by E. coli RNA polymerase) and a double lac operator repression module to provide tightly regulated, high-level expression of recombinant proteins in E. coli, a synthetic ribosomal binding site (RBS II) for efficient translation, a 6XHis tag coding sequence, t ₀ and T1 transcriptional terminators, CoIE1 origin of replication, and a beta-lactamase gene for conferring ampicillin resistance. The pQE vectors enable placement of a 6xHis tag at either the N- or C-terminus of the recombinant protein. Such plasmids include pQE 32, pQE 30, and pQE 31 which provide multiple cloning sites for all three reading frames and provide for the expression of N-terminally 6xHis-tagged proteins. Other exemplary

plasmid vectors for transformation of E. coli cells, include, for example, the pεT expression vectors (see, U.S. patent 4,952,496; available from NOVAGεN, Madison, WI; see, also literature published by Novagen describing the system). Such plasmids include pεT 11 a, which contains the T71ac promoter, T7 terminator, the inducible E. coli lac operator, and the lac repressor gene; pεT 12a-c, which contains the T7 promoter, T7 terminator, and the E. coli ompT secretion signal; and pεT 15b and pεT19b (NOVAGEN, Madison, WI), which contain a His-Tag™ leader sequence for use in purification with a His column and a thrombin cleavage site that permits cleavage following purification over the column, the T7-lac promoter region and the T7 terminator. b. NHase expression and expression systems

NHase polypeptides (modified and unmodified) can be produced by any methods known in the art for protein production including in vitro and in vivo methods such as, for example, the introduction of nucleic acid molecules encoding NHase into a host cell, host organism and expression from nucleic acid molecules encoding NHase in vitro. NHase and modified NHase polypeptides can be expressed in any organism suitable to produce the required amounts and forms of a NHase polypeptide needed for administration and treatment. Expression hosts include prokaryotic and eukaryotic organisms such as E. coli, yeast, plants and insect cells, mammalian cells, including human cell lines and transgenic animals. Expression hosts can differ in their protein production levels as well as the types of post-translational modifications that are present on the expressed proteins. The choice of expression host can be made based on these and other factors, such as regulatory and safety considerations, production costs and the need and methods for purification.

A number of genes encoding nitrile hydratases have been isolated. For example, a nitrile hydratase gene was isolated and sequenced from Comamonas testosteroni 5- MGAM-4D (see U.S. 2006/0024747). The complete genomic sequence of Bradyrhizobium japonicum USDA 110 was also determined (see, Kaneko et al., (2002) DNA Res. 9:225-256). Furthermore, there are hundreds of nucleotide sequences in the GenBank that are tentatively annotated as nitrile hydratase encoding genes based on their sequence similarities to the known, characterized nitrile hydratases.

The nitrile hydratase genes and gene products can be produced in heterologous host cells. Expression in recombinant microbial hosts can be used for the expression of

various pathway intermediates, for the modulation of pathways already existing in the host, or for the synthesis of new products heretofore not possible using the host.

Heterologous host cells for expression of the nitrile hydratase genes and nucleic acid fragments are microbial hosts that can be found broadly within the fungal or bacterial families and that grow over a wide range of temperature, pH values, and solvent tolerances. For example, any bacteria, yeast, and filamentous fungi is a suitable host expression of the nitrile hydratase nucleic acid fragments. Because the transcription, translation and the protein biosynthetic apparatus is the same irrespective of the cellular feedstock, functional genes are expressed irrespective of carbon feedstock used to generate cellular biomass. Large-scale microbial growth and functional gene expression can utilize a wide range of simple or complex carbohydrates, organic acids and alcohols, saturated hydrocarbons, such as methane, or carbon dioxide in the case of photosynthetic or chemoautotrophic hosts. However, the functional genes can be regulated, repressed or depressed by specific growth conditions, which can include the form and amount of nitrogen, phosphorous, sulfur, oxygen, carbon or any trace micronutrient including small inorganic ions. In addition, the regulation of functional genes can be achieved by the presence or absence of specific regulatory molecules that are added to the culture and are not typically considered nutrient or energy sources.

Examples of host strains include, but are not limited to, bacterial, fungal, or yeast species such as Acinetobacter, Agrobacterium, Alcaligenes, Anabaena, Aspergillus, Aurantimonas, Bacillus, Bradyrhizobium, Brevibacterium, Candida, Chlorobium, Chromatium, Corynebacteria, Cytophaga, Deinococcus, Erwinia, Erythrobacter, Escherichia, Flavobacterium, Hansenula, Klebsiella, Methanobacterium, Methylobacter, Methylobacterium, Methylococcus, Methylocystis, Methylomicrobium, Methylomonas, Methylosinus, Mycobacterium, Myxococcus, Pantoea, Pichia, Pseudomonas,

Rhodobacter, Rhodococcus, Saccharomyces, Salmonella, Sphingomonas, Staphylococcus Streptomyces, Synechococcus, Synechocystis, Thiobacillus, Trichoderma,and Zymomonas. In another embodiment, suitable host strains are selected from the group comprising Bradyrhizobium, Agrobacterium, Aurantimonas, Aspergillus, Saccharomyces, Pichia, Candida, Hansuela, Bacillus, Rhodococcus, Streptomyces, Brevibacterium, Corynebacteria, Escherichia, Pseudomonas, Methylomonas, Synechocystis, and Klebsiella. In a further embodiment, suitable host strains are selected from the group

comprising Bradyrhizobium, Bacillus, Rhodococcus, Escherichia, Pseudomonas, Klebsiella, and Methylomonas.

Microbial expression systems and expression vectors containing regulatory sequences that direct high level expression of foreign proteins are well known to those skilled in the art. Any one of these is selected and used to construct chimeric genes for expression of the nitrile hydratase. These chimeric genes can be introduced into appropriate microorganisms via transformation to provide high-level expression of the enzymes.

Accordingly, introduction of chimeric genes encoding a nitrile hydratase enzyme under the control of the appropriate promoter will demonstrate increased nitrile to amide conversion in the host. It is useful to express the nitrile hydratase genes both in natural host cells as well as in a heterologous host. Introduction of the nitrile hydratase genes into native hosts will result in altered levels of existing nitrile hydratase activity. Additionally, the nitrile hydratase genes can be introduced into non-native host bacteria where an existing nitrile-amide pathway can be manipulated.

Vectors or cassettes useful for the transformation of suitable host cells are well known in the art. Typically the vector or cassette contains sequences directing transcription and translation of the relevant gene, a selectable marker, and sequences allowing autonomous replication or chromosomal integration. Suitable vectors include a region 5' of the gene that harbors transcriptional initiation controls and a region 3' of the DNA fragment controls transcriptional termination. Control regions are often derived from genes homologous to the transformed host cell, although it is to be understood that such control regions need not be derived from the genes native to the specific species chosen as a production host. Initiation control regions or promoters, which are useful to drive expression of the nitrile hydratase open reading frame (ORF) in the desired host cell, are numerous and familiar to those skilled in the art. Virtually any promoter capable of driving these genes is suitable including but not limited to CYC1, HIS3, GAL1, GAL10, ADH1, PGK, PHO5, GAPDH, ADC1 , TRP1, URA3, LEU2, ENO, TPI (useful for expression in Saccharomyces); AOXl (useful for expression in Pichia); and lac, ara, tet, trp, IP _L , IP _R , T7, tac, and trc (useful for expression in Escherichia colϊ) as well as the amy, apr, npr promoters and various phage promoters useful for expression in Bacillus. Additionally, the

deoxy-xylulose phosphate synthase or methanol dehydrogenase operon promoter (Springer et al., (1998) FEMS Microbiol Lett. 160:119-124), the promoter for polyhydroxyalkanoic acid synthesis (Foeliner et al., (1993) Appl. Microbiol. Biotechnol. 40:284-291), promoters identified from native plasmids in methylotrophs (EP 0296484), promoters identified from methanotrophs (WO 0333698), and promoters associated with antibiotic resistance (for example, kanamycin (Springer et al., (1998) FEMS Microbiol Lett. 160:119-124; Ueda et al., (1991) Appl. Environ. Microbiol. 57:924-926) or tetracycline (U.S. 4,824,786)) can be used for expression of nitrile hydratase coding sequences, especially in Cl metabolizers. Termination control regions also can be derived from various genes native to the host. Optionally, a termination site is unnecessary.

Expression in eukaryotic hosts can include expression in yeasts such as Saccharomyces cerevisiae and Pichia pastoria, insect cells such as Drosophila cells and lepidopteran cells, plants and plant cells such as tobacco, corn, rice, algae, and the aquatic plant lemna. Eukaryotic cells for expression also include mammalian cells lines such as Chinese hamster ovary (CHO) cells or baby hamster kidney (BHK) cells.

Many expression vectors are available and known to those of skill in the art for the expression of NHase. The choice of expression vector is influenced by the choice of host expression system. Such selection is well within the level of skill of the skilled artisan. In general, expression vectors can include transcriptional promoters and optionally enhancers, translational signals, and transcriptional and translational termination signals. Expression vectors that are used for stable transformation typically have a selectable marker which allows selection and maintenance of the transformed cells. In some cases, an origin of replication can be used to amplify the copy number of the vectors in the cells. NHase or modified NHase polypeptides also can be used or expressed as a fusion protein. For example, a fusion protein can be generated to add additional functionality to a polypeptide. Examples of fusion proteins include, but are not limited to, fusions of a signal sequence, a tag, such as for localization, e.g. a his ₆ tag or a myc tag, or a tag for purification, for example, a GST fusion, and a sequence for directing protein secretion and/or membrane association.

i. Prokaryotic expression

Prokaryotes, especially E. coli and Bacillus species, provide a system for producing NHase (e.g., see U.S. Pat. No. 5,910,432). Transformation of E. coli is a simple and rapid technique well known to those of skill in the art. Expression vectors for E. coli can contain inducible promoters that are useful for inducing high levels of protein expression and for expressing proteins that exhibit some toxicity to the host cells. Examples of inducible promoters include the lac promoter, the trp promoter, the hybrid tac promoter, the T7 and SP6 RNA promoters and the temperature regulated λP _L promoter. Any media known in the art can be used for incubating the transformant cells.

Exemplary media include, but are not limited to, LB media and M9 media. Because the nitrile hydratase is a metalloenzyme, the media for incubating the transformant cells can be supplemented with Fe ions and/or Co ions. In one embodiment, the Fe ions and/or Co ions are present in the medium in an amount of about 0.05 Tg/ml or more. ii. Yeast

Yeasts such as Saccharomyces cerevisiae, Schizosaccharomyces pombe, Yarrowia lipolytica, Kluyveromyces lactis, and Pichia pastoris can be used as expression hosts for NHase. Yeast can be transformed with episomal replicating vectors or by stable chromosomal integration by homologous recombination. Typically, inducible promoters are used to regulate gene expression. Examples of such promoters include GAL1, GAL7, and GAL5 and metallothionein promoters such as CUP1. Expression vectors often include a selectable marker such as LEU2, TRP1, HIS3, and URA3 for selection and maintenance of the transformed DNA. Proteins expressed in yeast are often soluble and co-expression with chaperonins, such as Bip and protein disulfide isomerase, can improve expression levels and solubility. Additionally, proteins expressed in yeast can be directed for secretion using secretion signal peptide fusions such as the yeast mating type alpha- factor secretion signal from Saccharomyces cerevisiae and fusions with yeast cell surface proteins such as the Aga2p mating adhesion receptor or the Arxula adeninivorans glucoamylase. A protease cleavage site (e.g., the Kex-2 protease) can be engineered to remove the fused sequences from the polypeptides as they exit the secretion pathway.

iii. Insects and insect cells

Insects and insect cells, particularly using a baculovirus expression system, are useful for expressing polypeptides such as NHase or modified forms thereof (see, for example, Muneta et al. (2003) J. Vet. Med. Sci. 65(2):219-23). Insect cells and insect larvae, including expression in the hemolymph, express high levels of protein and are capable of most of the post-translational modifications used by higher eukaryotes. Baculoviruses have a restrictive host range which improves the safety and reduces regulatory concerns of eukaryotic expression. Typically, expression vectors use a promoter such as the polyhedrin promoter of baculovirus for high level expression. Commonly used baculovirus systems include baculoviruses such as Autographa californica nuclear polyhedrosis virus (AcNPV), and the Bombyx mori nuclear polyhedrosis virus (BmNPV) and an insect cell line such as Sf9 derived from Spodoptera frugiperda, Pseudaletia unipuncta (A7S) and Danaus plexippus (DpNl). For high level expression, the nucleotide sequence of the molecule to be expressed is fused immediately downstream of the polyhedrin initiation codon of the virus. Mammalian secretion signals are accurately processed in insect cells and can be used to secrete the expressed protein into the culture medium. In addition, the cell lines Pseudaletia unipuncta (A7S) and Danaus plexippus (DpNl) produce proteins with glycosylation patterns similar to mammalian cell systems. An alternative expression system in insect cells is the use of stably transformed cells. Cell lines such as the Schnieder 2 (S2) and Kc cells (Drosophila melanogaster) and C7 cells (Aedes albopictus) can be used for expression. The Drosophila metallothionein promoter can be used to induce high levels of expression in the presence of heavy metal induction with cadmium or copper. Expression vectors are typically maintained by the use of selectable markers such as neomycin and hygromycin. iv. Mammalian cells

Mammalian expression systems can be used to express NHase polypeptides. Expression constructs can be transferred to mammalian cells by viral infection such as adenovirus or by direct DNA transfer such as liposomes, calcium phosphate, DEAE- dextran and by physical means such as electroporation and microinjection. Expression vectors for mammalian cells typically include an mRNA cap site, a TATA box, a translational initiation sequence (Kozak consensus sequence) and polyadenylation

elements. Such vectors often include transcriptional promoter-enhancers for high level expression, for example the SV40 promoter-enhancer, the human cytomegalovirus (CMV) promoter, and the long terminal repeat of Rous sarcoma virus (RSV). These promoter-enhancers are active in many cell types. Tissue and cell-type promoters and enhancer regions also can be used for expression. Exemplary promoter/enhancer regions include, but are not limited to, those from genes such as elastase I, insulin, immunoglobulin, mouse mammary tumor virus, albumin, alpha- fetoprotein, alpha 1 -antitrypsin, beta-globin, myelin basic protein, myosin light chain-2, and gonadotropic releasing hormone gene control. Selectable markers can be used to select for and maintain cells with the expression construct. Examples of selectable marker genes include, but are not limited to, hygromycin B phosphotransferase, adenosine deaminase, xanthine-guanine phosphoribosyl transferase, aminoglycoside phosphotransferase, dihydrofolate reductase and thymidine kinase. Fusion with cell surface signaling molecules such as TCR-ζ and Fc _ε RI-γ can direct expression of the proteins in an active state on the cell surface.

Many cell lines are available for mammalian expression including mouse, rat human, monkey, and chicken and hamster cells. Exemplary cell lines include, but are not limited to, BHK (i.e., BHK-21 cells), 293-F, CHO, Balb/3T3, HeLa, MT2, mouse NS0 (non-secreting) and other myeloma cell lines, hybridoma and heterohybridoma cell lines, lymphocytes, fibroblasts, Sp2/0, COS, NIH3T3, HEK293, 293S, 293T, 2B8, and HKB cells. Cell lines also are available adapted to serum-free media which facilitates purification of secreted proteins from the cell culture media. One such example is the serum free EBNA-I cell line (Pham et al., (2003) Biotechnol. Bioeng. 84:332-42). v. Plants Transgenic plant cells and plants can be used for the expression of NHase.

Expression constructs are typically transferred to plants using direct DNA transfer such as microprojectile bombardment and PEG-mediated transfer into protoplasts, and with agrobacterium-mediated transformation. Expression vectors can include promoter and enhancer sequences, transcriptional termination elements, and translational control elements. Expression vectors and transformation techniques are usually divided between dicot hosts, such as Arabidopsis and tobacco, and monocot hosts, such as corn and rice. Examples of plant promoters used for expression include the cauliflower mosaic virus

promoter, the nopaline synthase promoter, the ribose bisphosphate carboxylase promoter and the ubiquitin and UBQ3 promoters. Selectable markers such as hygromycin, phosphomannose isomerase and neomycin phosphotransferase are often used to facilitate selection and maintenance of transformed cells. Transformed plant cells can be maintained in culture as cells, aggregates (callus tissue) or regenerated into whole plants. Transgenic plant cells also can include algae engineered to produce proteins (see, for example, Mayfield et al. (2003) PNAS 100:438-442). d. Regulation of nitrile hydratase expression

Methods of manipulating genetic pathways are common and well known in the art. Selected genes in a particular pathway can be up-regulated or down-regulated by a variety of methods. Additionally, competing pathways can be eliminated or sublimated by gene disruption and similar techniques.

Once a key genetic pathway has been identified and sequenced, specific genes can be up-regulated to increase the output of the pathway. For example, additional copies of the targeted genes can be introduced into the host cell on multicopy plasmids such as pBR322. Alternatively the target genes can be modified so as to be under the control of non-native promoters. Where it is desired that a pathway operate at a particular point in a cell cycle or during a fermentation run, regulated or inducible promoters can used to replace the native promoter of the target gene. Similarly, in some cases the native or endogenous promoter can be modified to increase gene expression. For example, endogenous promoters can be altered in vivo by mutation, deletion, and/or substitution (see, e.g., U.S. 5,565,350; and EP 0672159).

Alternatively, it may be necessary to reduce or eliminate the expression of certain genes in a pathway or in competing pathways that can serve as competing sinks for energy or carbon. Methods of down-regulating genes for this purpose have been explored. Where the sequence of the gene to be disrupted is known, an effective method of gene down-regulation is targeted gene disruption, where foreign DNA is inserted into a structural gene so as to disrupt transcription. This can be effected by the creation of genetic cassettes including the DNA to be inserted (often a genetic marker) flanked by sequence having a high degree of homology to a portion of the gene to be disrupted.

Introduction of the cassette into the host cell results in insertion of the foreign DNA into

the structural gene via the native DNA replication mechanisms of the cell (Hamilton et al, (1989) J. Bacteriol. 171 :4617-4622; Balbas et al., (1993) Gene 136:211-213; Gueldener et al., (1996) Nucleic Acids Res. 24:2519-2524; and Smith et al., (1996) Methods MoI. Cell. Biol. 5:270-277). Antisense technology is another method of down-regulating genes where the sequence of the target gene is known. To accomplish this, a nucleic acid segment from the desired gene is cloned and operably linked to a promoter such that the anti-sense strand of RNA will be transcribed. This construct is then introduced into the host cell and the antisense strand of RNA is produced. Antisense RNA inhibits gene expression by preventing the accumulation of mRNA that encodes the protein of interest. The person skilled in the art will know that special considerations are associated with the use of antisense technologies in order to reduce expression of particular genes. For example, the proper level of expression of antisense genes can require the use of different chimeric genes utilizing different regulatory elements known to the skilled artisan. Although targeted gene disruption and antisense technology offer effective means of down-regulating genes where the sequence is known, other less specific methodologies have been developed that are not sequence based. For example, cells can be exposed to UV radiation and then screened for the desired phenotype. Mutagenesis with chemical agents also is effective for generating mutants and commonly used substances include chemicals that affect non-replicating DNA such as HNO ₂ and NH ₂ OH, as well as agents that affect replicating DNA such as acridine dyes, notable for causing frameshift mutations. Specific methods for creating mutants using radiation or chemical agents are well documented in the art (see, e.g., Brock et al., Biotechnology: A Textbook of Industrial Microbiology, Second Edition (1989) Sinauer Associates, Inc., Sunderland, MA; and Deshpande, (1992) Appl. Biochem. Biotechnol. 36:227-234).

Another non-specific method of gene disruption is the use of transposable elements or transposons. Transposons are genetic elements that insert randomly in DNA but can be later retrieved on the basis of sequence to determine where the insertion has occurred. Both in vivo and in vitro transposition methods are known. Both methods involve the use of a transposable element in combination with a transposase enzyme.

When the transposable element or transposon is contacted with a nucleic acid fragment in the presence of the transposase, the transposable element will randomly insert into the

nucleic acid fragment. The technique is useful for random mutagenesis and for gene isolation, since the disrupted gene can be identified on the basis of the sequence of the transposable element. Kits for in vitro transposition are commercially available (see, e.g., The Primer Island Transposition Kit, available from Perkin Elmer Applied Biosystems, Branchburg, NJ, based upon the yeast TyI element; The Genome Priming System, available from New England Biolabs, Beverly, MA; based upon the bacterial transposon Tn7; and the EZ::TN Transposon Insertion Systems, available from Epicentre Technologies, Madison, WI., based upon the Tn5 bacterial transposable element). e. Large-scale nitrile hydratase expression Large-scale production of a nitrile hydratase gene product can be produced by both batch and continuous culture methodologies. A classical batch culturing method is a closed system where the composition of the media is set at the beginning of the culture and not subject to artificial alterations during the culturing process. Thus, at the beginning of the culturing process the media is inoculated with the desired organism or organisms and growth or metabolic activity is permitted to occur adding nothing to the system. Typically, however, a "batch" culture is batch with respect to the addition of carbon source and attempts are often made at controlling factors such as pH and oxygen concentration. In batch systems, the metabolite and biomass compositions of the system change constantly up to the time the culture is terminated. Within batch cultures, cells moderate through a static lag phase to a high growth log phase and finally to a stationary phase where growth rate is diminished or halted. If untreated, cells in the stationary phase will eventually die. Cells in log phase are often responsible for the bulk of production of end product or intermediate in some systems. Stationary or post-exponential phase production can be obtained in other systems. A variation on the standard batch system is the Fed-Batch system. Fed-Batch culture processes also are suitable and comprise a typical batch system with the exception that the substrate is added in increments as the culture progresses. Fed-Batch systems are useful when catabolite repression is apt to inhibit the metabolism of the cells and where it is desirable to have limited amounts of substrate in the media. Measurement of the actual substrate concentration in Fed-Batch systems is difficult and is therefore estimated on the basis of the changes of measurable factors such as pH, dissolved oxygen and the partial pressure of waste gases such as CO ₂ . Batch and Fed-Batch culturing methods are

common and well known in the art and examples can be found in Brock et al., Biotechnology: A Textbook of Industrial Microbiology, Second Edition (1989) Sinauer Associates, Inc., Sunderland, MA; and Deshpande, (1992) Appl. Biochem. Biotechnol. 36:227-234. Large-scale production of biocatalysts also can be accomplished with a continuous culture. Continuous cultures are an open system where a defined culture media is added continuously to a bioreactor and an equal amount of conditioned media is removed simultaneously for processing. Continuous cultures generally maintain the cells at a constant high-liquid-phase density where cells are primarily in log phase growth. Continuous or semi-continuous culture allows for the modulation of one factor or any number of factors that affect cell growth or end product concentration. For example, one method will maintain a limiting nutrient such as the carbon source or nitrogen level at a fixed rate and allow all other parameters to moderate. In other systems a number of factors affecting growth can be altered continuously while the cell concentration, measured by media turbidity, is kept constant. Continuous systems strive to maintain steady state growth conditions and thus the cell loss due to media being drawn off must be balanced against the cell growth rate in the culture. Methods of modulating nutrients and growth factors for continuous culture processes as well as techniques for maximizing the rate of product formation are well known in the art of industrial microbiology and a variety of methods are detailed by Brock et al., Biotechnology: A Textbook of Industrial Microbiology, Second Edition (1989) Sinauer Associates, Inc., Sunderland, MA.

Fermentation media must contain suitable carbon substrates. Suitable substrates can include but are not limited to aliphatic carboxylic acid and dicarboxylic acids (such as lactic acid or succinic acid), glycerol, monosaccharides (such as glucose and fructose), disaccharides (such as lactose or sucrose), oligosaccharides (such as soluble starch), polysaccharides (such as starch or cellulose or mixtures thereof, and unpurified mixtures from renewable feedstocks (such as cheese whey permeate, cornsteep liquor, sugar beet molasses, and barley malt). Additionally the carbon substrate also can be one-carbon substrates such as carbon dioxide, methane, or methanol for which metabolic conversion into key biochemical intermediates has been demonstrated. In addition to one and two carbon substrates, methylotrophic organisms are also known to utilize a number of other carbon-containing compounds such as methylamine, glucosamine, and a variety of amino

acids for metabolic activity. For example, methylotrophic yeast are known to utilize the carbon from methylamine to form trehalose or glycerol (see, Bellion et al., in Microbial Growth on Cl Compounds, Murrel et al., eds., Intercept, Ltd., Andover, Hampshire, UK, (1993), p. 415-32). Similarly, various species of Candida will metabolize alanine or oleic acid (Suiter et al., (1990) Arch. Microbiol. 153:485-489). Therefore, it is contemplated that the source of carbon utilized can encompass a wide variety of carbon-containing substrates and will only be limited by the microorganism employed. f. Purification

Methods for purification of NHase polypeptides from host cells depend on the chosen host cells and expression systems. For secreted molecules, proteins are generally purified from the culture media after removing the cells. For intracellular expression, cells can be lysed and the proteins purified from the extract.

NHase can be purified using standard protein purification techniques known in the art including but not limited to, SDS-PAGE, size fraction and size exclusion chromatography, ammonium sulfate precipitation, chelate chromatography and ionic exchange chromatography. For example, NHase polypeptides can be purified by anion exchange chromatography. Affinity purification techniques also can be used to improve the efficiency and purity of the preparations. For example, antibodies, receptors and other molecules that bind NHase can be used in affinity purification. Expression constructs also can be engineered to add an affinity tag such as a myc epitope, GST fusion or His ₆ and affinity purified with myc antibody, glutathione resin, and Ni-resin, respectively, to a protein. Purity can be assessed by any method known in the art including gel electrophoresis and staining and spectrophotometric techniques. g. Nucleotide sequences Nucleic acid molecules encoding subunits of NHase or subunits of modified

NHase polypeptides are provided herein. Nucleic acid molecules include allelic variants or splice variants of any encoded NHase polypeptide. Exemplary of nucleic acid molecules provided herein are any that encode a subunit of a modified NHase polypeptide provided herein, such as a sequence as set forth in any of SEQ ID NOS: 56, 64, 68, 78, 79, 82, 83 and 85-110. In one embodiment, nucleic acid molecules provided herein have at least 50, 60, 65, 70, 75, 80, 85, 90, 91 , 92, 93, 94, 95, or 99% sequence identity or hybridize under conditions of medium or high stringency along at least 70% of the full-

length of any nucleic acid encoding a NHase polypeptide provided herein. In another embodiment, a nucleic acid molecule can include those with degenerate codon sequences encoding any of the NHase polypeptides provided herein.

4. Conditions for nitrile hydratase catalysis Suitable conditions for the enzymatic preparation of amide products using nitrile hydratases are well known in the art, and can be employed in the methods provided herein and described in the art (see, e.g., Martinkova et al., (2002) Biocatal. Biotransform. 20:73-93; and U.S. 7,153,663). Wild-type microorganisms known to possess nitrile hydratase activity can be used to convert nitriles to the corresponding amides (see, e.g. Nagasawa et al., (1993) Appl. Microbiol. Biotechnol. 40:189-195; Cowan et al. (1998) Extremophiles 2:207-216; and U.S. 7,153,663). For example, nitrile hydratase activity of Rhodococcus rhodochrous Jl converts a variety of aromatic and heteroaromatic nitriles to the corresponding amides with 100% molar conversion (see, Mauger et al., (1989) Tetrahedron 45:1347-1354; and Mauger et al., (1988) J. Biotechnol. 8:87-96). Several Rhodococcus strains convert of 3-cyanopyridine to nicotinamide (see, U.S. 2004/0142447).

In addition to the use of wild-type organisms, recombinant organisms containing heterologous genes for the expression of nitrile hydratase also can be used for the conversion of nitriles. For example, E. coli transformants that express nitrile hydratases can be used (for examples of such transformants, see, e.g., U.S. 6,316,242; U.S. 5,811,286; WO 9504828; EP 5024576; and Wu et al., (1997) Appl. Microbiol. Biotechnol. 48:704- 708).

Cell lysates of organisms containing genes for the expression of nitrile hydratase can be used for the conversion of nitriles to the corresponding amides (see, e.g., Kim et al, (2000) Enzyme Microb. Tech. 27:492-501). Also, isolated nitrile hydratase enzymes can be used for the conversion of nitriles to the corresponding amides (see, e.g., Nagasawa et al., (1978) Eur. J. Biochem. 162:691-698; Nagasawa et al., (1991) Eur. J. Biochem. 196:581-589; and Payne et al., (1997) Biochemistry 36:5447-5454).

An aqueous reaction mixture containing the nitrile of Formula III is prepared by mixing the nitrile with an aqueous suspension of the nitrile hydratase catalyst. Intact microbial cells can be used as catalyst without any pretreatment, such as permeabilization or heating. Alternatively, the cells can be immobilized in a polymer matrix (e.g., alginate,

carrageenan, polyvinyl alcohol, or polyacrylamide gel) or on a soluble or insoluble support (e.g., glass, plastic, a film, nitrocellulose, a sol-gel polymer, celite and silica) to facilitate recovery and reuse of the catalyst. Methods to immobilize cells in a polymer matrix or on a soluble or insoluble support have been widely reported and are well known to those skilled in the art. Lysates of cells that express nitrile hydratase can be used to convert the nitrile to the corresponding amide. The enzyme can also be isolated and used directly for catalysis, or the enzyme can be immobilized in a polymer matrix or on a soluble or insoluble support (see Methods in Biotechnology, Vol. 1 : Immobilization of Enzymes and Cells; Gordon F. Bickerstaff, Editor; Humana Press, Totowa, NJ. , USA; 1997).

Intact microbial cells, either immobilized or unimmobilized, containing genes that encode a polypeptide having nitrile hydratase activity, or containing genes that encode a combination of polypeptides separately having nitrile hydratase activity, can be used as a catalyst without any pretreatment, such as permeabilization, freeze thawing or heating. Alternatively, the microbial cells can be permeabilized by methods familiar to those skilled in the art (e.g., treatment with toluene, detergents, or freeze- thawing) to improve the rate of diffusion of materials into and out of the cells. Methods for permeabilization of microbial cells are well-known to those skilled in the art (see, Felix, (1982) Anal. Biochem. 120:211-234). Some of the nitriles of Formula III can be moderately water soluble. Their solubility also depends on the temperature of the solution and the salt concentration in the aqueous phase. The reaction can be carried out in an organic, aqueous or 2-phase system (including an organic solvent phase that is not miscible with water, such as ethyl acetate, and also an aqueous phase), or in an emulsion. Organic solvents can include, but are not limited to, acetone, diisoproyl ether, methyl tert-butyl ether (MTBE), dibutyl ether, and ethyl acetate. Suitable aqueous phases include, but are not limited to, buffers such as glutamic acid-glutamate, phosphoric acid-phosphate, acetic acid-acetate and citric acid- citrate buffers.

The aqueous phase of a two-phase reaction mixture can contain as much water as is sufficient to result in conversion of the nitrile to the corresponding amide and maintenance of the activity of the enzyme catalyst. The reaction can also be run by adding the nitrile to the reaction mixture at a rate approximately equal to the enzymatic

hydration reaction rate, thereby maintaining a single-phase aqueous reaction mixture, thereby avoiding the potential problem of substrate inhibition of the enzyme at high starting material concentrations.

The concentration of enzyme catalyst in the reaction mixture depends on the specific catalytic activity of the enzyme catalyst and is chosen to obtain the desired rate of reaction. The wet cell weight of the microbial cells used as catalyst in reactions typically ranges from 0.001 grams to 0.300 grams of wet cells per mL of total reaction volume, generally from 0.002 grams to 0.050 grams of wet cells per mL; the cells can be optionally immobilized as described above. The specific activity of the microbial cells (IU/gram dry cell weight) is determined by measuring the rate of conversion of a 0.10-

0.50 M solution of a nitrile substrate to the desired amide product at 25° C, using a known weight of microbial cell catalyst. An IU of enzyme activity is defined as the amount of enzyme activity required to convert one micromole of substrate to product per minute. For the methods herein, typically 10 to 10,000 IU of nitrile hydratase is added to the reaction for every gram of nitrile.

The temperature of the reaction is selected to facilitate the reaction rate and the stability of enzyme catalyst. The temperature of the reaction can range from just above the freezing point of the reaction mixture (ca. 0° C) to 65° C, with a general range of reaction temperature of from 0° C to 45° C. In one embodiment, an ambient temperature is maintained throughout the reaction.

An enzyme catalyst solution or suspension can be prepared by suspending the unimmobilized or immobilized cells in distilled water, or in an aqueous reaction mixture of a buffer or by suspending the immobilized enzyme catalyst in a similar mixture, or by preparing a solution of a cell extract, partially purified or purified enzyme(s), or a soluble form of the immobilized enzymes in a similar mixture. A suitable pH for the reaction can be determined by one of skill in the art, taking into account the activity and stability of the nitrile hydratase. A pH range from 2 to 11 is contemplated for the methods herein. Typically, however, the pH of the reaction is at or about 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.2, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, or 9.0. The reaction can be run to convert the nitrile with no pH control, or a suitable acid or base can be added over the course of the reaction to maintain the desired pH.

The reaction can be monitored by, for example, gas chromatography (GC), high performance liquid chromatography (HPLC) or thin layer chromatography (TLC) to determine the point of completion. The resulting amide can be isolated by extraction, precipitation, evaporation, or other suitable separation methods. Thus, one of skill in the art can readily identify one or more enzymes that can catalyze the conversion of a nitrile to the corresponding amide, as depicted in Schemes I and II.

4. Compounds of Formula III as nitrile hydratase substrates

The methods of producing levetiracetam provided herein involve nitrile hydratase mediated addition of water to a nitrile group to produce a chiral α substituted aliphatic amide. The substrate is an α-(N-azacycloalkyl)-alkylnitrile derivative (see Scheme I,

Formula III), which is converted to an (S)-α-(N-azacycloalkyl)-alkylamide derivative (see Scheme I, Formula IV). Thus, nitrile hydratases particularly useful for the methods herein are nitrile hydratases that selectively enrich for amide products of the S- configuration. Any nitrile hydratase that accepts the nitrile substrate of Formula III can be used in the methods herein. Additionally, a nitrile hydratase that accepts Compound 3 as a substrate and affords Compound 4 is demonstrated by the methods described herein, as shown in Scheme II.

Nitrile hydratases, including wild-type and variant nitrile hydratases, with unknown selectivity and/or substrate acceptance can be screened to determine their suitability for the methods provided herein, using various assays well known in the art. For example, the selectivity and substrate acceptance of a nitrile hydratase can be determined by assessing the enantiomeric mixture produced when the nitrile hydratase catalyzes the addition of water to a nitrile group on one or more substrates. As described in more detail below, the molar amount of (S)- and (R)-α-(N-azacycloalkyl)-alkylamide derivative product can be measured to determine the yield and establish an ee value for the reaction. One of skill in the art can, therefore, readily identify nitrile hydratases that are (S)-selective and accept nitrile substrates of Formula III. Those nitrile hydratases that exhibit (S)-selectivity with good ee, such as 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 92%, 94%, 95%, 96%, 98%, 99%, or more, ee, and good yields, such as 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 92%, 94%, 95%, 96%,

98%, 99%, or more, when catalyzing a reaction using a compound of Formula III as the substrate can be selected for use in the methods described herein.

D. Examples

The following examples, including experiments and results achieved, are provided for illustrative purposes only and are not to be construed as limiting the claimed subject matter.

Example 1

1 -cyanopropyl 4-methylbenzenesulfonate (Formula II, Scheme I, R ¹ = ethyl, L = 4-methylbenzenesulfonate;

Compound 2 ^a , Scheme II, R' = 4-methylphenyl)

Propionaldehyde cyanohydrin (Sigma-Aldrich Co, St. Louis, MO, Cat. No. 81880; Young et al., (1990) Organic Syntheses, 7:381 ; 19.72 g, 231.7 mmol) was dissolved in methylene chloride (296 mL; 15 L/Kg of cyanohydrin) in a 500 mL round bottom flask under nitrogen atmosphere. The solution was cooled to 0-5 °C. Triethylamine (38.75 mL, 278 mmol) was added, and the exotherm increased the temperature to 11 °C. The solution was stirred 13 minutes at which point the temperature had returned to 0-5 °C. To the reaction was added jo-toluenesulfonyl chloride (44.17 g, 231.7 mmol) in a single charge. The temperature first decreased to -2 °C, and then increased to a high point of 8.9 °C. After stirring 20 minutes, a slurry had formed. Cooling was removed and stirring was continued. After 3 hours, the slurry was added to water (296 mL). The mixture was stirred 5 minutes, settled, then separated. The organic layer was successively washed, settled, and separated using 1M NaOH (2 X 200 mL) and water (1 X 200 mL). The organic layer was dried with anhydrous sodium sulfate and concentrated to an oil to provide 53.27 g (96%) of 1 -cyanopropyl 4-methylbenzenesulfonate. ¹ H NMR (CDCl ₃ ): 1.10 (3H, t, J= 7.4), 1.90-2.10 (2H, m), 2.50 (3H, s), 5.02 (1H, t, J= 6.4), 7.41 (2H, d, J = 8.2), 7.84 (2H, d, J= 8.5).

Example 2

2-chlorobutanenitrile

(Formula II, Scheme I, R ¹ = ethyl, L = chloro; Compound 2 ^b , Scheme II, X = chloro)

LiCl was added to 1 -cyanopropyl 4-methylbenzenesulfonate in 2-pyrrolidinone and the reaction was heated. The reaction was monitored by HPLC for disappearance of the starting tosylate and the production of p-toluenesulfonic acid (indicating that exchange was complete). Example 3 2-(2-oxopyrrolidin-1-yl)butanenitrile

(Formula III, Scheme I, R ¹ = ethyl, A = oxygen, n = 1 , m = 0; Compound 3, Scheme H) Method A: 1 -Cyanopropyl 4-methylbenzenesulfonate (1.27 g, 5.3 mmol) was added to a flask under nitrogen atmosphere. 2-Pyrrolidinone (6.35 mL, 5 L/Kg starting material, 15.6 equivalents, 82.8 mmol) was added, resulting in a solution. Sodium tert- butoxide (0.84g, 1.65 equivalents, 8.8 mmol) was added in a single charge. The reaction immediately began to warm due to exotherm, but the temperature was maintained < 50 °C with an ice/water bath. The initial near-solution quickly became a thick slurry. Upon cooling below 40 °C, the temperature was maintained at 40 °C via oil bath heating. After 2 hours, water (15 mL) was added and the mixture extracted with THF (30 mL). Saturated aqueous NaCl solution (5 mL) was added to aid in separation. After settling and separating, the THF layer was washed with saturated aqueous NaCl solution (20 mL) then dried with anhydrous sodium sulfate. Concentration to an oil provided 0.90 g that contained a ratio of approximately 1 :1 desired product to 2-pyrrolidinone. The crude product (0.66 g) was dissolved in 6.5 mL EtOAc and washed with water (2 X 3 mL). The organic layer was dried with anhydrous sodium sulfate and concentrated to provide 0.27 g (45% yield) of 2-(2-oxopyrrolidin-1-yl)butanenitrile.

Method B: To a solution of 2-chlorobutanenitrile in 2-pyrrolidinone, NaOtBu was added to initiate 2-pyrrolidinone displacement of the chloride group. The reaction was allowed to progress at 50 °C for 22 h using a total of 2.4 equivalents of NaOtBu. Water and EtOAc were added and the phases were separated. The aqueous phase was extracted with EtOAc. The organic phases were combined and washed with water, dried and concentrated to an oil. The oil was a mixture of 2-pyrrolidinone and the title compound. Calculation using NMR data reveals 50% yield of the title compound for this exchange reaction.

Method C: (R)-2-(2-oxopyrrolidin-1-yl)butanenitrile (Compound 5) was dissolved in THF. Sodium f-butoxide was added to the reaction mixture to afford 2-(2- oxopyrrolidin-1-yl)butanenitrile (Compound 3).

¹ H NMR (CDCl ₃ ): 1.08 (3H, t, J= 7.4), 1.65-1.85 (1H, m), 1.85-2.05 (1H, m), 2.05-2.25 (2H, m), 2.46 (2H, t, J- 8.0), 3.35-3.65 (2H, m), 5.04 (1H, t, J= 8.1).

Example 4 Cloning of nitrile hydratase DNA

The complete genomic sequence of Brady rhizobium japonicum USDA 110 was determined (see Kaneko et al., (2002) DNA Res. 9:225-256) and one gene was annotated as encoding a nitrile hydratase. A closely related bacterial strain, Bradyrhizobium japonicum USDA 505, was purchased from American Type Culture Collection (ATCC 10324) and cultivated in Nutrient Broth at 26 °C for four days. The genomic DNA was extracted using phenol/chloroform. A DNA fragment encoding the nitrile hydratase α and β subunits as well as a downstream flanking region (126 amino acids) was obtained by PCR: (phosphorylated primer 5'-caacagACCTGCCAGGCATGcagcccatcccatggcccgatg - 3' (SEQ ID NO:50) and primer 5'-GTCGACttacctaaaatcctccggcttcagc - 3' (SEQ ID NO:51) with the underlined regions for BspMI and SalI restriction enzyme sites) and subcloned into PmeI -digested pTrcHis2A vector (SEQ ID NO:52; Invitrogen, Carlsbad, CA). The nitrile hydratase DNA fragment was enriched by PCR: (primer 5'-ctgcagACCTGCCAGGCATGcagcccatcccatggcccgatg-3' (SEQ ID NO:53) and 5'-ggatGTCGACttacctaaaatcctccggcttcagc-3' (SEQ ID NO:54)) by using the resulting pTrcHis2A vector as the template, which was subsequently digested with BspMl and Sail

restriction enzymes and subcloned into pET21d vector (SEQ ID NO:55; Novagen, Madison, WI) under control of the T7 promoter.

Example 5

Nitrile hydratase enzyme expression The plasmid containing the genes encoding the nitrile hydratase was transformed into Rosetta™ 2 (DE3) competent cells (Novagen, Madison, WI). E. coli cells were grown at 30 °C with addition of cobalt chloride and sodium citrate at final concentration of 0.02 mg/ml and 0.2 mg/ml respectively. Induction was typically carried out at 20 °C overnight with addition of 0.6 mM IPTG. The recombinant E. coli cells were harvested by centrifugation, and the pellet was washed with cold phosphate buffer saline (PBS) before being resuspended in PBS. A cell-free lysate was prepared either by French Press cell homogenizer or ultrasonication and the cell debris was removed by centrifugation. Production of alpha (26 kDa) and beta (24 kDa) subunits was confirmed by standard SDS-PAGE analysis. The resulting nitrile hydratase was named NH33. NH33 either in the form of cell-free lysate or lyophilized powder was used for the hydration of nitrile substrate reactions. The NH33 was shown to be active toward acrylonitrile and benzonitrile.

Example 6 Cloning and expression of other nitrile hydratase enzymes Other nitrile hydratase genes were cloned and expressed by methods similar to

Examples 4 and 5. The resulting nitrile hydratases were named NH9, NH35, NH38, NH44, NH50, and NH51. NH9 was cloned from Burkholderia cepacia AAMD (GenBank accession number AAJL01000020). The nucleotide sequence of NH9 α- and β-subunits and the flanking region is set forth as SEO ID NO:77. The amino acid sequence of the NH9 α-subunit is set forth as SEQ ID NO:78. The amino acid sequence of the NH9 β-subunit is set forth as SEQ ID NO:79. The amino acid sequence of the NH9 flanking sequence is set forth as SEQ ID NO:80. NH35 was cloned from Aurantimonas sp. SI85-9A1 (GenBank accession number NZ_AAP J01000002).

NH38 was cloned from Silicibacter sp. TM1040 (GenBank accession number NC 008044). The nucleotide sequence of NH38 α- and β-subunits and the flanking region is set forth as SEQ ID NO:81. The amino acid sequence of the NH38 α-subunit is

set forth as SEQ ID NO:82. The amino acid sequence of the NH38 β-subunit is set forth as SEQ ID NO: 83. The amino acid sequence of the NH38 flanking sequence is set forth as SEQ ID NO:84. NH44 was cloned from Rhodococcus pyridinivorans MW3. NH50 was cloned from Agrobacterium tumefaciens. NH51 cloned from Pseudonocardia thermophila Al 8.

Example 7

(S)-2-(2-oxopyrrolidin-1-yl)butanamide (Formula IV, Scheme I, R ¹ = ethyl, A = oxygen, n = 1, m = 0; Compound 4, Scheme II)

To a 200 mL flask was added cell lysate (Example 5, 28.8 mL at 5mg/mL concentration), 2-(2-oxopyrrolidin-1-yl)butanenitrile (965.6 μL at 10mg/mL), acetone (5.2 mL) and 0.2M potassium phosphate buffer (69.1 mL, pH 7.1). The mixture was stirred at 4 °C and was monitored for conversion by withdrawing 20 μL of the reaction mixture and diluting with 100 μL acetonitrile. The sample was centrifuged to remove solids and analyzed by HPLC (Restek Kromasil C4 column, 150 x 4.6 mm, 50% CH ₃ CN/50% 0.07% aqueous perchloric acid). Enantioselectivity was measured by diluting 20 μL of the reaction mixture with 100 μL isopropanol. The sample was cleared by centrifugation and analyzed by normal phase HPLC (85% Heptane and 15% Ethanol, Chiral Technologies Chiralpak ^® AD column, 250 x 4.6 mm). The reaction mixture was 40.8% complete containing 68.8% ee (S)-2-(2-oxopyrrolidin-1-yl)butanamide.

Acetone (86 mL) was added to a portion of the reaction solution (43 mL, 2.67 mmol theory). The mixture was stirred for 18 minutes, and filtered over celite (2.2g). The celite was washed with acetone (10 mL). The filtrate solution was concentrated to dryness. To the residue was added diisopropyl ether (DIPE, 5 mL) and the solution heated to reflux for 30 minutes and allowed to cool to ambient temperature. After stirring overnight, the solids were filtered and then washed with DIPE (3.5 mL) to provide 333 mg of crude solids. A portion of the crude solid (161 mg) was warmed to 50 °C in absolute ethanol (1.6 mL) and held at this temperature for approximately 5 hours. The

mixture was allowed to cool to ambient temperature and stirred overnight. The mixture was filtered, and the residue was washed with absolute ethanol (0.5 mL). The mother liquor was concentrated to dryness and triturated with DIPE and filtered to provide 63 mg (29% overall yield) of (S)-2-(2-oxopyrrolidin-1-yl)butanamide. ¹ H NMR (CDCl ₃ ): 0.93 (3H, t, J= 7.4), 1.60-1.80 (1H, m), 1.90-2.15 (3H, m), 2.30-2.60 (2H, m), 3.43 (2H, t, J = 7.0), 4.47 (1H, dd, J- 6.9, 6.9), 5.20-5.70 (1H, br s), 6.05-6.40 (1H, br s).

Example 8

Hydration of 2-(2-oxopyrrolidin-1-yl)butanenitrile bv NH33 lysate

levetiracetam

(Formula IV, Scheme L R ¹ = ethyl, A = oxygen, n = 1. m = 0;

Compound 4, Scheme II)

The racemic 2-(2-oxopyrrolidin-1-yl)butanenitrile (1 g/L) was mixed with 0.26 g/L NH33 lysate in 0.2 M phosphate buffer, pH 7.1. The reaction was carried out at 30 °C and monitored by withdrawing samples at different time points. The conversion of the nitrile substrate to the amide product was determined by HPLC (50% CH ₃ CN / 50% water containing 0.07% perchloric acid on a Kromasil C4 column). The enantiomeric excess (ee) of the amide product was determined by either a reverse-phase HPLC (70% water / 30% CH ₃ CN on a Chiralpak ^® AD-RH column) or a normal-phase method (85% heptane / 15% ethanol on a Chiralpak AD column). The enantiomeric ratio (E value) was calculated from the conversion (c) and the ee of the amide (ee _p ) as follows:

E = In[1-c(1+ee _p )] / ln[1-c(1-ee _p )]

At 0.26 g/L NH33 loading, over a reaction time of 4.5 hours, the percent conversion (c) was 21.5 %. For these conditions, the S/R product ratio was 4.18:1, the percent ee of product (ee _p ) was 61.4%, and the E value was 4.9.

Example 9

Hydration of 2-(2-oxopyrrolidin-1-yl)butanenitrile by NH33 whole cells

The recombinant E. coli cells expressing the nitrile hydratase of Example 5 were harvested. The racemic 2-(2-oxopyrrolidin-1-yl)butanenitrile substrate was mixed with the recombinant E. coli cells to afford levetiracetam.

Example 10

Solvent and additive effect on NH33

Different solvents and additives were investigated to enhance the selectivity and/or activity of NH33 -catalyzed hydration of 2-(2-oxopyrrolidin-1-yl)butanenitrile (1 g/L). For example, acetone was used as a co-solvent, while 15-crown-5 and PEG-400 were used as additives. The results are shown in Table 7. Table 7. NH33 -catalyzed reaction with 5% acetone, 5% 15-crown-5 and 5% PEG-400

Acetone increased the enzyme activity and slightly enhanced its enantioselectivity. 15- crown-5 and 5% (v/v) PEG-400 also showed slightly enhanced enantioselectivity.

Example 11

Effect of temperature on the stereoselectivity of NH33

Different temperatures were investigated to enhance the selectivity and/or activity of NH33-catalyzed hydration of 2-(2-oxopyrrolidin-1-yl)butanenitrile. The nitrile hydration reaction of 2-(2-oxopyrrolidin-1-yl)butanenitrile (1 g/L) using NH33 was performed at 22 °C, 15 °C and 4 °C. The results are shown in Table 8. Lower temperature resulted in enhanced enantioselectivity. Table 8. Effect of temperature on the enantioselectivity of NH33.

awith 5 g/L NH33 1ysate.

Example 12

Effect of substrate concentration on NH33 catalyzed conversions Higher substrate concentrations were investigated for the NH33 catalyzed conversion of 2-(2-oxopyrrolidin-1-yl)butanenitrile substrate to levetiracetam product. For example, concentrations of 1 g/L, 10 g/L and 50 g/L were investigated. The reactions were conducted at 4 °C and terminated by adding acetonitrile. The results are shown in Table 9.

Table 9. Conversion and selectivity of the reactions at higher substrate loadings.

Example 13

Hydration of 2-(2-oxopyrrolidin-1-yl)butanenitrile by mutants

NH9, NH35, NH38. NH44, NH50 and NH51

The hydration of 2-(2-oxopyrrolidin-1-yl)butanenitrile by NH9, NH35, NH38, NH44, NH50 and NH51 to afford levetiracetam was determined by methods similar to that described in Example 8 above. The racemic 2-(2-oxopyrrolidin-1-yl)butanenitrile (1 g/L) was mixed with nitrile hydratase lysates in 0.2 M phosphate buffer, pH 7.1. The reaction was carried out at 30 °C and monitored by withdrawing samples at different time points. The conversion of the nitrile substrate to the amide product was determined by HPLC (50% CH ₃ CN / 50% water containing 0.07 % perchloric acid on a Kromasil ^® C4 column). The S/R ratio of the products and their enantiomeric excess (ee) were determined by either a reverse-phase HPLC (70% water / 30% CH ₃ CN on a Chiralpak ^® AD-RH column) or a normal-phase method (85% heptane / 15% ethanol on a Chiralpak ^® AD column). The enantiomeric ratio (E value) was calculated from the conversion (c) and the ee of the amide (ee _p ) as follows:

E = ln[ 1-c(1+ee _p )] / ln[ 1-c(1-ee _p )] The results from these enzyme-catalyzed reactions are listed in Table 7.

Table 7. Conversion and selectivity of NH35, NH44, NH50 and NH51.

Example 14

Identification of NH33 Mutants With Increased Enantioselectivity and/or Reactivity for the Substrate 2-(2-oxopyrrolidin-1-yl)butanenitrile Identification of Candidate Residues for Mutagenesis Computer modeling of the interaction between NH33 and the racemic substrate 2-

(2-oxopyrrolidin-1-yl)butanenitrile was performed to identify residues in NH33 that make up the substrate binding pocket and/or that reside approximately 10 to 15 Angstroms from the substrate binding pocket and catalytic center. The known crystal structure of NH33 was used to perform the homology modeling (Hourai et al. (2003) Biochem.Biophys. Res.Commun., 312:340-345; rcsb.org/pdb/cgi/explore.cgi?pdbld=lv29). The resulting homology models are set forth in Figures 1 and 2. Figure 1 sets forth residues in the Alpha (Trpl43; Prol49; Glul91; and Argl93) and Beta subunit (Leu34; Val37; Arg38; Gly41 ; Asn47; Ile48; Ser51; Arg55) ofNH33 identified by the homology modeling and docking studies that reside within approximately 10 Angstroms distance to the substrate binding site. Figure 2 sets forth residues in the Alpha (Tyr73; Ile69) and Beta subunit (Ala42; Ala43; Gly44; Ala45; Phe46; Phe73; Leu73; Leu74; Gly75; Leu76; VaI113; VaI116; Met117) of NH33 identified by the homology modeling and docking studies that reside within approximately 15 Angstroms distance to the substrate binding site. NH33 mutant library construction The residues identified in the homology and docking studies were considered to be active site residues that potentially affect substrate binding and enzyme catalysis. These included the twelve active site residues that make up the substrate binding pocket (those within 10 Angstroms), as well as the 14 residues that are farther from the proposed substrate binding site but were identified as having a likely effect on the enzyme activity (those within 15 Angstroms). These residues were used in saturation mutagenesis to improve the enzymes enantioselectivity. All 19 possible amino acids at the selected sites were introduced one at a time by saturation mutagenesis. Mutagenesis of NH33 was performed following the protocol described in Stratagene's QuikChange™ Site-Directed Mutagenesis kit. Primers containing degenerate codons on residues to be mutated were used in mutant strand synthesis reactions. After primers annealed to DNA template, high fidelity DNA polymerase was used to extend the primers. After the reaction, the parental DNA (methylated) was digested by Dpnl endonuclease. The mutated molecules

generated by these reactions were each transformed to E. coli competent cells. Colony numbers on each transformation plate were counted to ensure the proper amino acid coverage. Plates with desired colony numbers were washed with media. The washed off colonies were cultured in liquid media until proper density. Plasmid DNA was extracted from each sample and then transformed to Rosetta™ 2 Dε3 for expression. Plates with colony number less than sub-library size were put aside. The corresponding DNA samples were cleaned, concentrated and re-transformed to E. coli competent cells until desired colony numbers were reached. NH33 mutant library screening To hasten the process of protein expression and isolation and thus facilitate the screening of large numbers of mutant enzymes, bacteria were cultured in 96-well plates. Fresh overnight culture (50 μl) was added to each well containing 1.1 mL LB medium with appropriate antibiotic and the plate was incubated at 30 °C for approximately 6-7 hours until the optical density at 600 nm (OD600) was 0.7-1.0. Protein expression was then induced by addition of 0.6 mM IPTG with further incubation at room temperature for 16 hours. The plate then was centrifuged to pellet the cells, and the pellet was washed with cold potassium phosphate buffer once. The cell pellet was resuspended with 100 μL enzyme assay buffer (0.2M potassium phosphate buffer pH 7.1 or 0.02 M potassium phosphate buffer pH 6.5) and then frozen and thawed for four times to ensure cell lysis. The resulting lysed cell suspension was used directly in the enzyme assay.

The enzyme assay was performed by adding to each well the 2-(2-oxopyrrolidin-1- yl)butanenitrile substrate to a final concentration of either lg/L or 10g/L. Appropriate amount of enzyme assay buffer was added to make up 500 μL reaction mixture. The reaction mixture was incubated at 30 °C. At different time points, 20 μL reaction mixture was withdrawn and diluted with 100 μL acetonitrile. The mixture was centrifuged to remove solids and the conversion of each sample was analyzed by an HPLC method (CH ₃ CN / 50% water containing 0.07% perchloric acid on a Kromasil C4 column).

Another 80 μL reaction mixture also was withdrawn at the same time, then diluted with 400 μL acetonitrile and subsequently dried in a Savant SpeedVac to remove water and solvent. The dried sample was resuspended with 100 μl isopropanol. Samples with a conversion between about 10%-60% were subjected to a chiral-HPLC analysis to determine the enantioselectivity (85% heptane / 15% ethanol on a Chiralpak ^® AD

column.). Table 9 below sets forth exemplary results for some of the mutants using 10g/1 substrate in the reaction.

Table 9: Enantioselectivity and Reactivity of Exemplary Mutants

Mutants with improved enantiomeric ratio (E value) were identified. Multiple mutations combining two or more or all of the identified single mutants were made sequentially using a strategy similar to that used to generate the mutant library. Double- mutants were generated by adding one more mutation to an Arg38Cys template. Triple-

mutants were generated by adding one more mutation to double-mutants or by adding two mutations together to single-mutants if these two new mutations are geographically close to each other. Quadruple-mutants were generated by adding one more mutation to triple- mutants or by adding two mutations together to double-mutants if these two new mutations are geographically close to each other. Genes with 5 mutations were generated by adding two geographically close mutations to triple-mutants. The multiple mutants also were tested as above to identify those with an improved enantiomeric ration. The mutation sites and the change in amino acid sequence of exemplary mutants identified to have improved enantioselectivity are summarized in Table 10. The mutated sites of the selected mutants occurred exclusively in the β-subunit. Accordingly, only the sequences of the mutated β- subunit are listed.

Table 10. Mutation sites of the Mutants having increased Enantioselectivity .

Hydration of nitrile-pyrrolidinone to its corresponding amide by improved mutants with increased enantioselectivity

Hydration reactions of nitrile-pyrrolidinone substrate were performed using selected NH33 mutants and combination mutants obtained by site-saturation mutagenesis and identified has having increased enantioselectivity. The reactions were performed at a substrate loading of 10g/L in a total reaction volume of 5 mL at 4 °C. The results are summarized in Tables 10 and 11.

Table 10 . Screenin results for the site-saturation muta enesis

Table 11. Screening results for combination i mutation

pH optimization for nitrile hydration reaction

Buffer pH optimum was determined for βLeu34Glu (SEQ ID NO: 85) and βArg38Cys (SEQ ID NO: 86). The nitrile hydration reaction using either βLeu34Glu (SEQ ID NO: 85) or βArg38Cys (SEQ ID NO: 86) was performed using a substrate loading of 8% (w/w) at a temperature of 4 °C. The results are shown in Table 12. A pH optimum of 6.5 was determined for both mutants. Table 12. pH Optimization of Nitrile Hydratase Mutants βLeu34Glu and βArg38Cys

Buffer effects on catalysis using mutants βLeu34Glu and βArg38Cys In addition to phosphate buffer, the effects of acetate and Tris buffers on enantioselectivity of nitrile hydratase mutants were examined. The nitrile hydration reaction using either βLeu34Glu (SEQ ID NO: 85) or βArg38Cys (SEQ ID NO: 86) was performed using a substrate loading of 8% (w/w) at a temperature of 4 °C and one of sodium phosphate (NaPi), potassium acetate (KOAc) and Tris hydrochloride as a buffer at pH 6.5. Mutant βLeu34Glu (SEQ ID NO: 85) afforded product with higher enantioselectivity in Tris buffer than in acetate or phosphate buffer. Table 13. Effect of Buffer on Enantioselectivity of Nitrile Hydratase Mutants

Effect of CoCl ₂ on enantioselectivity of mutant βArg38Cys (SEO ID NO: 86)

The effect of CoCl ₂ on enantioselectivity was examined. The nitrile hydration reaction using either βLeu34Glu (SEQ ID NO: 85) or βArg38Cys (SEQ ID NO: 86) was

performed using a substrate loading of 8% (w/w) at a temperature of 4 °C and pH of 6.5 and 0, 50 μM, 0.2 raM and 1 mM CoCl ₂ . The results are shown in Table 14. Increasing CoCl ₂ concentration was found to increase hydrolysis rate. Addition of CoCl ₂ to a final concentration of 0.2 mM doubled the hydrolysis rate without negatively impacting the enantiomeric ratio (E value). Further increasing CoCl ₂ to 1 mM resulted in a 25% increase in reaction rate, while the E value is approximately the same. Addition of CoCl ₂ increased the reaction rate without adversely affecting the enzyme's enantioselectivity. Table 14. Effect of CoCl ₂ on enantioselectivity of mutant βArg38Cys (SEQ ID NO: 86)

Gram-scale Hydration of nitrile-pyrrolidinone by NH33 mutant βLeu34Glu

NH33-βLeu34Glu (SEQ ID NO: 85) was used to catalyze the enzymatic hydration reaction of nitrile-pyrrolidinone substrate. Three different batches of gram-scale reactions were preformed at scales of 2 grams, 4 grams and 6 grams. In a typical reaction, nitrile-pyrrolidinone substrate was added to an appropriate sized Erlenmeyer flask to yield a final concentration of 10g/L and mixed with lyophilized cell lysate powder. The reactions were carried out at 4 °C with addition of 5% acetone. The conversion of the reaction was monitored by withdrawing 20 μL of the reaction mixture and diluted with 100 μl acetonitrile. The reaction mixture was cleared by centrifugation and the conversion of the reaction was analyzed by an HPLC method (CH ₃ CN / 50% water containing 0.07% perchloric acid on a Kromasil ^® C4 column). To obtain the enantioselectivity of the reaction, the reaction was quenched by addition of 2 times the volume of acetone and the mixture was stirred to precipitate most of the salt and enzyme. The mixture was filtered and dried using a RotaVac rotary vacuum dryer. The dried reaction mixture was resuspended with 0.5 mL of isoproponal and the enantioselectivity was analyzed using a normal phase HPLC method (85% heptane / 15% ethanol on a Chiralpak AD column). The results are provided in Table 15.

Table 15. Gram scale enzymatic reactions catalyzed by NH33 βLeu34Glu

*50% of the cell lysate lyophilized powder is protein. Of the total protein, 10% is the desired enzyme based on SDS gel analysis. Enzyme loading is calculated based on the ratio between the weight of the desired enzyme loaded and the weight of the substrate loaded in the reactions. Mutant βArg38Cys (SEO ID NO:86) production from 10L fermentation

A 10L fermentation of mutant βArg38Cys (SEQ ID NO: 86) was produced. BL21 (DE3) cells containing βArg38Cys (SEQ ID NO:86) DNA construct were used to express the enzyme. An initial culture of 600 mL was inoculated into the 10L fermentor and incubated at 30°C. The pH was maintained at 7. The glucose level was monitored throughout the fermentation. The culture was incubated until the OD reached 4.2 before inducing protein production by addition of 1 mM IPTG, 0.2 mg/ml sodium citrate and 0.02 mg/ml CoCl ₂ . The induction was carried out 20 °C for 6 hours until the OD reached 67 and the OD did not increased significantly within 2-3 hour period. During the induction, the level of the nitrile hydratase produced in the culture was monitored by a UV assay using acrylonitrile as the substrate. The resulting cells (about 800 g wet weight) were harvested by centrifugation at 6,000 g for 15 minutes and washed once with cold phosphate buffer saline. The cells were resuspended into 3 L 20 mM phosphate buffer (pH 6.5) and were lysed by passing through a microfluidizer for 4 passes at 12,000 psi. The resulting cell lysate was cleared by centrifugation at 12,000 g for 35 minutes. Based on the Bradford assay, the final protein concentration was 36.4 mg/ml. The total protein production from the 10L fermentor was 116.6 mg.

Gram-scale NH33 mutant βArg38Cys -catalyzed hydration reactions

In order to develop the downstream process for the production of the final product, levetiracetam, several gram-scale βArg38Cys (SEQ ID NO:86) catalyzed hydration reactions were performed at an industrial relevant substrate concentration of 100 g/L. βArg38Cys enzyme produced from the 10L fermentor in the previous Example

was used for the biotransformation. All the reactions were conducted at 4 °C with 1 % acetone addition. The results were summarized in Table 16.

These gram scale reaction demonstrated that at 100 g/L substrate loading, mutant βArg38Cys catalyzed the reaction to more than 40% conversion within 24 hours with reasonably good enantioselectivity.

Table 16. Gram scale enzymatic reactions catalyzed by NH33 βArg38Cys (SEQ ID NO:86)

Example 15

Large scale hydration of (S)-2-(2-oxopyrrolidin-1-yl)butanenitrile

(SV2-(2-oxopyrrolidin-1-yl)butanamide (Formula IV, Scheme I, R ¹ = ethyl, A = oxygen, n = 1, m = 0;

Compound 4, Scheme II)

Cell lysate (Example 5, 60 g; 40% w/w; 33 mg/mL concentration), 2-(2- oxopyrrolidin-1-yl)butanenitrile (142.7 mL at 100 mg/mL), acetone (15 mL) and 0.2M potassium phosphate buffer (1423 mL, pH 6.5) were added to a 3 L flask. The mixture was stirred at 5 °C and was monitored for conversion by withdrawing 20 μL of the reaction mixture and diluting with 100 μL acetonitrile. The sample was centrifuged to remove solids and analyzed by HPLC (Restek Kromasil C4 column, 150 x 4.6 mm, 50% CH ₃ CN/50% 0.07% aqueous perchloric acid). Enantioselectivity was measured by diluting 20 μL of the reaction mixture with 100 μL isopropanol. The sample was centrifuged to remove solids ("cleared") and analyzed by normal phase HPLC (85% Heptane and 15% Ethanol, Chiral Technologies Chiralpak AD column, 250 x 4.6 mm).

The reaction mixture was 46.1% complete containing 92% ee (S)-2-(2-oxopyrrolidin-1- yl)butanamide. Total reaction time was 23.5 hours.

Ethanol (1500 mL) was added to the reaction mixture. The mixture was distilled at atmospheric pressure down to 5 volumes (750 mL - head temperature 100 °C). The mixture was cooled to 30 °C and acetone (1.5 L) was added. The mixture was stirred at ambient temperature for 12 hours, filtered over celite (56 g) and rinsed with acetone (450 mL). The resulting filtrate was distilled at atmospheric pressure down to 5 volumes (750 mL) and the water was azeotropically removed by adding isopropanol and continuing distillation. The total amount of isopropanol used was 3000 mL and the final head temperature was 82 °C. The solution was filtered through a lμ membrane filter and rinsed with isopropanol (25 mL). The resulting solution was slowly added to diisopropyl ether (1500 mL) and was stirred at ambient temperature for 15 hr. The mixture was then distilled at atmospheric pressure to displace the isopropanol, adding diisopropyl ether (3000 mL total) as needed to maintain a 1200 mL working volume. When the head temperature was 67.5 °C, the slurry was allowed to cool to ambient temperature. The mixture was filtered and the solids washed with diisopropyl ether (150 mL) to provide 53.9 g (32% overall yield, 94% ee) of (S)-2-(2-oxopyrrolidin-1-yl)butanamide crude solid. ¹ H NMR (CDCl ₃ ): 0.93 (3H, t, J= 7.4), 1.60-1.80 (1H, m), 1.90-2.15 (3H, m), 2.30-2.60 (2H, m), 3.43 (2H, t, J= 7.0), 4.47 (1H, dd, J= 6.9, 6.9), 5.20-5.70 (1H, br s), 6.05-6.40 (1H, br s).

A portion of the crude product (2.59 g) was recrystallized by suspending the solids in hot acetone (8 volumes), filtering through a 0.45 μm teflon filter, rinsing with acetone (1 volume), and distillation to 3 volumes. The solution was cooled to ambient temperature, seeded, and allowed to crystallize. Ice cooling of the slurry followed by filtration and washing with cold acetone (2 volumes) gave purified (S)-2-(2-oxopyrrolidin-1-yl)- butanamide (1.87 g, 72.2% recovery, 99.7% ee).

Example 16 Racemization of 2-(2-oxopyrrolidin-1-yl)butanenitrile

(R,S)-2-(2-oxopyrrolidin-1-yl)butanenitrile

(Formula III, Scheme I, R ¹ = ethyl, A = oxygen, n = 1, m = 0:

Compound 3. Scheme II)

The filtrate from the isolation of (S)-2-(2-oxopyrrolidin-1-yl)butanamide (see e.g., Examples 7 and 14), containing 2-(2-oxopyrrolidin-1-yl)butanenitrile enriched in the R- enantiomer can be racemized by the following procedure.

An aliquot of the diisopropyl ether solution was concentrated to an oil (2.67 g). The oil was dissolved in THF (10 mL) and sodium tert-butoxide (1.1 eq) was added at ambient temperature. After 17 minutes, chiral HPLC (85% Heptane and 15% Ethanol, Chiral Technologies Chiralpak ^® AD column, 250 x 4.6 mm) indicated complete racemization. Water (10 mL) and brine (19 mL) were added and the mixture was extracted with ethyl acetate (10 mL). The organic layer was washed with water (10 mL), dried over magnesium sulfate, filtered and evaporated to an oil (2.14 g). ¹ H NMR (CDCl ₃ ): 1.08 (3H, t, J= 7.4), 1.65-1.85 (1H, m), 1.85-2.05 (1H, m), 2.05-2.25 (2H, m), 2.46 (2H, t, J= 8.0), 3.35-3.65 (2H, m), 5.04 (1H, t, J= 8.1). The isolated racemic nitrile demonstrated comparable reactivity and selectivity in the enzymatic hydration reaction to that produced in Example 3.

Since modifications will be apparent to those of skill in this art, it is intended that this invention be limited only by the scope of the appended claims.