Biosynthesis of Paclitaxel Intermediate

This invention was made with government support under Grant No. RC062544 by the National Science Foundation. The government has certain rights in the invention.

Background of the Invention

Drug shortages in the United States have become an increasing problem. Taxol ^® , otherwise known by the generic name paclitaxel, is a chemotherapeutic agent used to treat breast cancer, as well as ovarian, lung and colon cancers. Shortages of paclitaxel can limit or curtail treatment options for cancer patients. New, more efficient procedures for making paclitaxel may avoid such drug shortages and ensure a reliable pharmaceutical supply chain.

Paclitaxel has been produced by semisynthetic and plant cell fermentation (PCF) techniques. The semisynthetic method of making paclitaxel (shown below) requires over seventeen synthetic steps and involves use of voluminous organic solvents during the production process.

While the simplicity of coupling the necessary phenylisoserine side chain to the diterpene core of the paclitaxel molecule made such semisynthetic methods attractive, the multiple steps and the environmental hazards of the solvents and side products involved make the semisynthetic approach less attractive than the plant cell fermentation methods. However, while the plant cell fermentation procedures do tend to use less toxic materials, the amount of paclitaxel obtained can be low. For example, in cell cultures, the concentration of paclitaxel ranges from 0.04 to 0.2%, depending on cell lines. Large fermentation vats must be used and the isolation and separation of paclitaxel from the milieu of plant cell lysates must be very efficient to obtain useful amounts of paclitaxel.

Summary

The invention relates to more efficient and non-toxic methods for making paclitaxel where not only the production but also the purification of the paclitaxel product is simplified. In particular, the enzymes and methods described herein can generate aminopropanyl-CoA intermediates, such as (^)-β- phenylalanyl-CoA and (2R,35)-phenylisoserinyl CoA, that are useful substrates in an enzymatic pathway for the production of paclitaxel and related anti-cancer drugs.

The methods of making paclitaxel, or analogs or derivatives thereof, include preparing an aminopropanoyl-CoA in a reaction catalyzed by a

Tyrocidine synthetase A (TycA) to thereby make an intermediate for production of paclitaxel or an analog or derivative thereof. The Tyrocidine synthetase A can have a bacterial amino acid sequence. For example, the Tyrocidine synthetase A can have a Bacillus brevis or Brevibacillus parabrevis Tyrocidine synthetase A. In some embodiments, the Tyrocidine synthetase A can have an amino acid sequence of a Tyrocidine synthetase A from bacteria deposited with the

American Type Culture Collection under deposit number ATCC 8185. In other embodiments, a serine in the Tyrocidine synthetase A can be replaced with a substitute amino acid that does not have a hydroxy in its side chain. For example, the substitute amino acid in the Tyrocidine synthetase A can be an alanine, valine, isovaline, leucine, isoleucine, proline, glycine, arginine, lysine, histidine, tryptophan, phenylalanine, methionine or cysteine. In some embodiments, the Tyrocidine synthetase A has an amino acid sequence comprising a sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO: 6, and an amino acid sequence with 85% sequence identity to any of SEQ ID NO: 1, SEQ ID NO:3, SEQ ID NO:5, or SEQ ID N0:6. The Tyrocidine synthetase A can, for example, be encoded by a nucleic acid sequence comprising a sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:7, and an nucleic acid sequence with 85% sequence identity to any of SEQ ID NO:2, SEQ ID NO:4 or SEQ ID NO:7.

The reaction can be performed in vitro. For example, the reaction can be performed in a cell-free reaction such as an enzymatic reaction that can proceed in a mixture of the Tyrocidine synthetase A, the substrate, ATP and a divalent cation. The Tyrocidine synthetase A can be immobilized or attached to a solid surface (e.g., a bead, a column matrix, a reaction wall and the like).

Alternatively, a substrate for the Tyrocidine synthetase A can be immobilized or attached to a solid surface (e.g., a bead, a column matrix, a reaction wall and the like). Such attachment can facilitate isolation of the products of the reaction and removal of unreacted materials, side products, and other materials that are no longer needed. In some embodiments, the reaction can be performed in a cultured cell. In other embodiments, the reaction can be performed in a cultured cell during a plant cell fermentation process.

A variety of substrates can be employed. For example, the

aminopropanoyl-CoA can be prepared from a substrate of the following formula I:

wherein:

X is hydrogen;

Y is hydrogen or OH; and

Ring is an unsubstituted or substituted (C4-C10) aryl, (C4- C9)heteroaryl, (C4-C10)cycloalkyl, or (C4-C9)heterocycloalkyl. Such a substrate can be immobilized or attached to a solid surface (e.g., a bead, a column matrix, a reaction wall and the like). The aminopropanoyl-CoA prepared by the methods described herein can be a compound of formula II:

II

wherein: X, Y and Ring are as described herein. Such an aminopropanoyl-CoA is a useful intermediate for making paclitaxel or paclitaxel analog or derivative. For example, such paclitaxel, paclitaxel analogs or paclitaxel derivatives can have the following structure:

wherein: Ring is an unsubstituted or substituted (C4-C10) aryl, (C4- C9)heteroaryl, (C4-C10)cycloalkyl, or (C4-C9)heterocycloalkyl. In some embodiments, Ring is a single aryl or heteroaryl ring of about 4-8 carbon atoms, and where the heteroatom is oxygen or nitrogen. The Ring can have a variety of substituents. For example, the Ring can be substituted with 1 or 2 alkyl, amino, hydroxy, cyano, carboxy, nitro, thio, alkoxy, and halogen groups.

In some embodiments, the aminopropanoyl-CoA can be prepared from a substrate with formula III or IV:

III IV

wherein: X is hydrogen; Y is hydrogen or OH; Z is CH, CH , oxygen (O) or nitrogen (NH or NH ); and Ri is selected from the group consisting of hydrogen, alkyl, amino, hydroxy, cyano, carboxy, nitro, thio, alkoxy, and halogen.

In other embodiments, the aminopropanoyl-CoA can have formula V or

V VI

wherein:

X is hydrogen;

Y is hydrogen or OH;

Z is CH, CH ₂ , oxygen (O), or nitrogen (NH or NH ₂ ); and

Ri is selected from the group consisting of hydrogen, alkyl, amino, hydroxy, cyano, carboxy, nitro, thio, alkoxy, and halogen.

The aminopropanoyl-CoA substrates and/or intermediates can be immobilized or attached to a solid surface (e.g., a bead, a column matrix, a reaction wall and the like). Such immobilization or attachment can facilitate reaction to generate paclitaxel (or an analog or derivative thereof), as well as purification of intermediates and final products along the synthetic route.

The method can further include reaction B involving combining the aminopropanoyl-CoA with Baccatin III:

Baccatin III

to form N-debenzoyl-2'-deoxypaclitaxel or an analog or derivative thereof. For example, reaction B can be catalyzed by an acyltransferase such as a Taxus acyltransferase. In some embodiments, reaction B can be catalyzed by baccatin III O-phenylpropanoyltransferase (BAPT). When performing reaction B, the reaction can, for example, proceed in a mixture of aminopropanyl-CoA, baccatin III O-phenylpropanoyltransferase (BAPT), and Baccatin III. The

aminopropanoyl-CoA, baccatin III O-phenylpropanoyltransferase (BAPT), or Baccatin III. can be immobilized or attached to a solid surface (e.g., a bead, a column matrix, a reaction wall and the like). Such immobilization or attachment can facilitate reaction to generate paclitaxel (or an analog or derivative thereof), as well as purification of intermediates and final products along the synthetic route. The N-debenzoyl-2'-deoxypaclitaxel or an analog or derivative thereof can have the following structure:

3'-N-Debenzoyltaxol or an analog

or derivative thereof

wherein:

X is hydrogen;

Y is hydrogen or OH; and

Ring is an unsubstituted or substituted (C4-C10) aryl, (C4- C9)heteroaryl, (C4-C10)cycloalkyl, or (C4-C9)heterocycloalkyl.

Reaction B can also be performed in vitro, for example, in a cell-free reaction such as an enzymatic reaction. In other embodiments, Reaction B can be performed in a cultured cell, or in a plant cell fermentation process, for example, in combination with the reaction for preparing an aminopropanoyl-CoA that can be catalyzed by Tyrocidine synthetase A.

The methods provided herein can further include a reaction A that includes transfer of benzoyl group to a free amine of a propanoid side chain of 3'-N-debenzoyl-paclitaxel or an analog or derivative thereof to form paclitaxel or an analog or derivative thereof. The 3'-N-debenzoyl-paclitaxel (or an analog or derivative thereof) or the paclitaxel (or analog or derivative thereof) can be immobilized or attached to a solid surface (e.g., a bead, a column matrix, a reaction wall and the like). Such immobilization or attachment can facilitate reaction to generate paclitaxel (or an analog or derivative thereof), as well as purification of the paclitaxel (or analog or derivative thereof) product. For example, when the paclitaxel or an analog or derivative thereof is attached or immobilized on a solid surface, the solid surface can be washed to remove reactants, enzymes, side products and the like. Upon cleavage from the solid surface, a purified paclitaxel or an analog or derivative thereof can be obtained.

The paclitaxel or an analog or derivative thereof can have the following structure:

wherein: Ring is an unsubstituted or substituted (C4-C10) aryl, (C4- C9)heteroaryl, (C4-C10)cycloalkyl, or (C4-C9)heterocycloalkyl. In some embodiments, the Ring can be a single aryl or heteroaryl ring of about 4-8 carbon atoms, and where the heteroatom is oxygen or nitrogen. For example, the Ring can be substituted with 1 or 2 alkyl, amino, hydroxy, cyano, carboxy, nitro, thio, alkoxy, and halogen groups.

Reaction A can be catalyzed by an acyltransferase, for example, a Taxus acyltransferase. In some embodiments, reaction A can be catalyzed by N - debenzoyl-2'-deoxypaclitaxel: N-benzoyltransferase (NDTBT). For example, reaction A can proceed in a mixture of 3'-N-debenzoyl-paclitaxel, a benzoyl- contributing agent and N -debenzoyl-2'-deoxypaclitaxel: N-benzoyltransferase (NDTBT). Such a reaction A can be performed in vitro, for example, reaction A can be performed in a cell-free reaction. In other embodiments, reaction A can be performed in a cultured cell, or in a plant cell fermentation process, for example, in combination with the reaction for preparing an aminopropanoyl- CoA that can be catalyzed by Tyrocidine synthetase A. The methods provided herein can also include other reaction steps for generating paclitaxel, paclitaxel analogs and paclitaxel derivatives, including those described herein or otherwise available. Description of the Figures

FIG. 1 shows compounds formed during the TycA thioesterification of aminophenylpropanoates and mass to charge (m/z) values for those compounds and fragments thereof.

FIGs. 2A-F illustrates the MS(/MS) ionization profiles of products isolated after separately incubating TycA or TycA-S563A with (S)-a- phenylalanine, (R)- -phenylalanine, or (2R,35)-phenylisoserine under standard assay conditions with CoA. FIG. 2A shows an MS(/MS) ionization profile of pure (5)-a-phenylalanine demonstrating that an [M - H] consistent with phenylalanyl-CoA (m/z 913) is present in the total ion profile (FIG. 2A1); and the types of fragment ions derived by MS/MS of the corresponding m/z 913 ion (FIG. 2A2). FIG. 2B shows an MS(/MS) ionization profile of pure (R)-p- phenylalanine demonstrating that an [M - H] consistent with β-phenylalanyl- CoA (m/z 913) in is present in the total ion profile (FIG. 2B-1); and the types of fragment ions derived by MS/MS of the corresponding m/z 913 ion (FIG. 2B-2). FIG. 2C shows an MS(/MS) ionization profile of pure (2R,35)-phenylisoserine demonstrating that an [M - H] consistent with phenylisoserinyl- CoA (m/z 929) is present in the total ion profile (FIG. 2C-1); and the types of fragment ions derived by MS/MS of the corresponding m/z 929 ion (FIG. 2C-2). The [M - H] ion selected for MS/MS analysis from each sample are identified in bold with an asterisk.

FIG. 3A-C shows representative a liquid chromatography multiple reaction monitoring (LC-ESI-MRM) profiles of purified

aminophenylpropanoyl-CoA compounds (FIG. 3A1, 3B 1, 3C1), LC-ESI-MS total ion profiles (FIG. 3A2, 3B2, 3C2), and fragment ions (FIG. 3A3, 3B3, 3C3) derived by MS/MS of the corresponding [M - H] molecular ion of biosynthetic a-phenylalanyl-CoA (FIG. 3A), β-phenylalanyl-CoA (FIG. 3B), and

phenylisoserinyl-CoA (FIG. 3C) made in reactions containing TycA or TycA- S563A (100 μg), ATP (1 mM), MgCl ₂ (3 mM), CoA (1 mM), and the corresponding aminophenylpropanoate (1 mM).

FIG. 4A-F shows a total ion chromatograms obtained by LC-ESI-MS analysis (scan mode: mlz 100 to 1200) of the compounds in assays incubated for 30 min at 31 °C containing TycA (100 μg), ATP (1 mM, 100 nmol in 0.1 mL), CoA (1 mM), and Mg ²⁺ (3 mM) as well as 1 mM a-phenylalanine (FIG. 4A), or 1 mM β-phenylalanine (FIG. 4B). Control assays contained the same ingredients for a-phenylalanine without ATP (FIG. 4C) or for β-phenylalanine without ATP (FIG. 4D). Other control assays contained the same ingredients for a- phenylalanine without CoA (FIG. 4E) or for β-phenylalanine without CoA (FIG. 4F).

FIG. 5A-D shows total ion chromatograms obtained by LC-ESI-MS analysis (scan mode: mlz 100 to 1200) of the compounds in a (2S,3R)- phenylisoserinyl CoA assay. The assay containing TycA (100 μg), ATP (1 mM, 100 nmol in 0.1 mL), CoA (1 mM), Mg ²⁺ (3 mM) as well as 1 mM (25,3R)- phenylisoserine that was incubated for 30 min at 31 °C (FIG. 5A). Control assays contained the same ingredients but without (25',3R)-phenylisoserine (FIG. 5B) or without ATP (FIG. 5C), or without CoA (FIG. 5D).

FIG. 6A-C shows representative liquid chromatography multiple reaction monitoring (LC-ESI-MRM) profiles of purified phenylalanyl-N- acetylcysteamine or phenylisoserinyl-N-acetylcysteamine compounds (FIG. 6A1, 6B 1, 6C1), LC-ESI-MS analyses of total ion profiles (FIG. 6A2, 6B2, 6B2), and fragment ions derived by MS/MS of the corresponding [M + H] ⁺ molecular ion (FIG. 6A3, 6B3, 6C3) of biosynthetic a-phenylalanyl N- acetylcysteamine (FIG. 6A), β-phenylalanyl N-acetylcysteamine (FIG.6B), and (25',3R)-phenylisoserinyl N-acetylcysteamine (FIG. 6C) made in reactions containing TycA or TycA-S563A (50 μg), ATP (1 mM), MgCl ₂ (3 mM), N- acetylcysteamine (5 mM), and the corresponding aminophenylpropanoate at 1 mM. The [M + H] ⁺ ions selected for MS/MS analysis from each sample are identified in bold and with an asterisk.

FIG. 7A-C illustrates total ion profile of LC-ESI-MS analyses (FIG. 7A1, 7B1, 7C1) and fragment ions derived by MS/MS of the corresponding [M + H] ⁺ molecular ion (FIG. 7A2, 7B2, 7C2) of authentic [^-((^-a-phenylalany^-N- (acetyl)] cysteamine (FIG. 7A), [5'-((R)- -phenylalanyl)-N-(acetyl)]cysteamine (FIG. 7B), and [5 ^, -(2R,35)-phenylisoserinyl-N-(acetyl)]cysteamine (FIG. 7C). The [M + H] ⁺ ion selected for MS/MS analysis from each sample are designated with asterisk and bold.

FIG. 8 illustrates the CoA thioesterification reaction catalyzed by TycA.

In the following detailed description of example embodiments of the invention, reference is made to the accompanying drawings which form a part hereof, and which is shown by way of illustration only, specific embodiments in which the invention may be practiced. It is to be understood that other embodiments may be utilized and structural changes may be made without departing from the scope of the present invention.

Detailed Description

Currently, Taxus plant cell fermentation (PCF) is used for mass- producing the anti-cancer drug paclitaxel (Taxol ^® ) as well as some related drugs. The structure of paclitaxel is shown below.

Plant cell fermentation has replaced a semisynthetic method that employed 1) a synthetic phenylisoserine (Phelso) precursor (as a β-lactam) that was coupled to the C13-hydroxyl group of baccatin III, 2) compulsory protecting group steps, and 3) voluminous hazardous solvents and toxic reagents for the large-scale production of paclitaxel (Mountford, The Taxol® Story - Development of a Green Synthesis via Plant Cell Fermentation. In Green Chemistry in the Pharmaceutical Industry, P.J. Dunn, A.S. Wells, and M.T. Williams, eds. (Wiley-VCH Verlag GmbH & Co. KGaA), pp. 145-160 (2010)). Although plant cell fermentation procedures avoid the use of some of the hazardous solvents and toxic reagents used in the semisynthetic methods, the paclitaxel product must still be extracted and purified from the plant cells. Such extraction and purification can still require several steps to separate the paclitaxel from plant molecules with similar chemical and physical properties. Although the organic solvents employed (e.g., isobutyl acetate, isopropanol, dichloromethane, dimethylformamide and others) are generally less toxic than those employed for the semi-synthetic process of making paclitaxel, a cell-free enzymatic process of making paclitaxel would eliminate many impurities and make isolation of paclitaxel even simpler. Larger quantities of paclitaxel could also be produced without the need to grow up large vats of plant cells.

As described herein, important compounds useful in the synthesis of paclitaxel and its analogs can readily be produced by use of a tyrocidine synthetase enzyme.

Synthesis of Paclitaxel and its analogs and derivatives

As described herein, Tyrocidine synthetases, such as tyrocidine A, can catalyze the synthesis of aminopropanoyl-CoA compounds via the following reactio

Aminopropanoate Aminopropanoyl-CoA wherein:

X is hydrogen;

Y is hydrogen or OH; and

Ring is an unsubstituted or substituted (C4-C10) aryl, (C4-C9)heteroaryl, (C4-C10)cycloalkyl, or (C4-C9)heterocycloalkyl.

The aminopropanoyl-CoA compound is useful for making paclitaxel as well as paclitaxel analogs and derivatives. For example, the aminopropanoyl- CoA compound can be used to make a paclitaxel compound or a paclitaxel analog or derivative w

The Ring on the aminopropanoyl-CoA compound or on the paclitaxel, or analog or derivative thereof, can be an unsubstituted or substituted (C4- C10)cycloalkyl, (C4-C9)heterocycloalkyl, (C4-C10)cycloaryl, (C4- C9)heterocycloaryl. The Ring can be a single aryl, heteroaryl, cycloalkyl, or heterocycloalkyl ring; or a fused ring system with 1-3 aryl, heteroaryl, cycloalkyl, or heterocycloalkyl rings, where fusion can be visualized as replacement of a bond to a hydrogen atom on one ring with a bond to a carbon atom in another ring. Examples of a suitable Ring group include a 5-6 membered aryl, or a 5-6 membered heteroaryl ring, where the heteroatom can be oxygen, nitrogen or sulfur.

The Ring group can be substituted with 1 or 2 alkyl, amino, hydroxy, cyano, carboxy, nitro, thio, alkoxy, and halogen groups. The alkyl group(s) can be lower alkyl group(s) (e.g., C1-C6 alkyl groups).

Cycloalkyl groups are cyclic alkyl groups such as, but not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, and cyclooctyl groups. In some embodiments, the cycloalkyl group can have 3 to about 8-12 ring members, whereas in other embodiments the number of ring carbon atoms range from 4, 5, 6, or 7. Cycloalkyl groups can include cycloalkyl rings having at least one double bond between 2 carbons (i.e., cycloalkenyl rings). Thus for example, the Ring can also be a cycloalkenyl group such as a cyclohexenyl, cyclopentenyl, or cyclohexadienyl group. Cycloalkenyl groups can have from 4 to about 8-12 ring members.

Cycloalkyl groups further include polycyclic cycloalkyl groups such as, but not limited to, norbornyl, adamantyl, bornyl, camphenyl, isocamphenyl, and carenyl groups, and fused rings such as, but not limited to, decalinyl, and the like. Cycloalkyl groups also include rings that are substituted with straight or branched chain alkyl groups as defined above. Representative substituted cycloalkyl groups can be mono-substituted or substituted more than once, such as, but not limited to, 2,2-, 2,3-, 2,4- 2,5- or 2,6-disubstituted cyclohexyl groups or mono-, di- or tri-substituted norbornyl or cycloheptyl groups. The term "cycloalkenyl" alone or in combination denotes a cyclic alkenyl group.

Aryl groups are cyclic aromatic hydrocarbons that do not contain heteroatoms. Thus aryl groups include, but are not limited to, phenyl, azulenyl, heptalenyl, biphenyl, indacenyl, fluorenyl, phenanthrenyl, triphenylenyl, pyrenyl, naphthacenyl, chrysenyl, biphenylenyl, anthracenyl, and naphthyl groups. In some embodiments, aryl groups contain about 6 to about 14 carbons in the ring portions of the groups. Aryl groups can be unsubstituted or substituted, as defined above. Representative substituted aryl groups can be mono-substituted or substituted more than once, such as, but not limited to, 2-, 3-, 4-, 5-, or 6-substituted phenyl or 2-8 substituted naphthyl groups, which can be substituted with carbon or non-carbon groups such as those listed above.

Heterocyclyl groups include aromatic and non-aromatic ring compounds containing 3 or more ring members, of which, one or more is a heteroatom such as, but not limited to, N, O, and S. In some embodiments, heterocyclyl groups include 3 to about 20 ring members, whereas other such groups have 3 to about 15 ring members. A heterocyclyl group designated as a C2-heterocyclyl can be a 5-ring with two carbon atoms and three heteroatoms, a 6-ring with two carbon atoms and four heteroatoms and so forth. Likewise a C4-heterocyclyl can be a 5- ring with one heteroatom, a 6-ring with two heteroatoms, and so forth. The number of carbon atoms plus the number of heteroatoms sums up to equal the total number of ring atoms. A heterocyclyl ring can also include one or more double bonds. A heteroaryl ring is an embodiment of a heterocyclyl group. The phrase "heterocyclyl group" includes fused ring species including those comprising fused aromatic and non-aromatic groups. For example, a dioxolanyl ring and a benzdioxolanyl ring system (methylenedioxyphenyl ring system) are both heterocyclyl groups within the meaning herein. The phrase also includes polycyclic ring systems containing a heteroatom such as, but not limited to, quinuclidyl. Heterocyclyl groups can be unsubstituted, or can be substituted as discussed above. Heterocyclyl groups include, but are not limited to, pyrrolidinyl, piperidinyl, piperazinyl, morpholinyl, pyrrolyl, pyrazolyl, triazolyl, tetrazolyl, oxazolyl, isoxazolyl, thiazolyl, pyridinyl, thiophenyl,

benzothiophenyl, benzofuranyl, dihydrobenzofuranyl, indolyl, dihydroindolyl, azaindolyl, indazolyl, benzimidazolyl, azabenzimidazolyl, benzoxazolyl, benzothiazolyl, benzothiadiazolyl, imidazopyridinyl, isoxazolopyridinyl, thianaphthalenyl, purinyl, xanthinyl, adeninyl, guaninyl, quinolinyl,

isoquinolinyl, tetrahydroquinolinyl, quinoxalinyl, and quinazolinyl groups. Representative substituted heterocyclyl groups can be mono-substituted or substituted more than once, such as, but not limited to, piperidinyl or quinolinyl groups, which are 2-, 3-, 4-, 5-, or 6-substituted, or disubstituted with groups such as those listed above.

Heteroaryl groups are aromatic ring compounds containing 5 or more ring members, of which, one or more is a heteroatom such as, but not limited to, N, O, and S; for instance, heteroaryl rings can have 5 to about 8-12 ring members. A heteroaryl group designated as a C2-heteroaryl can be a 5 -ring with two carbon atoms and three heteroatoms, a 6-ring with two carbon atoms and four heteroatoms and so forth. Likewise a C4-heteroaryl can be a 5 -ring with one heteroatom, a 6-ring with two heteroatoms, and so forth. The number of carbon atoms plus the number of heteroatoms sums up to equal the total number of ring atoms. Heteroaryl groups include, but are not limited to, groups such as pyrrolyl, pyrazolyl, triazolyl, tetrazolyl, oxazolyl, isoxazolyl, thiazolyl, pyridinyl, thiophenyl, benzothiophenyl, benzofuranyl, indolyl, azaindolyl, indazolyl, benzimidazolyl, azabenzimidazolyl, benzoxazolyl, benzothiazolyl, benzothiadiazolyl, imidazopyridinyl, isoxazolopyridinyl, thianaphthalenyl, purinyl, xanthinyl, adeninyl, guaninyl, quinolinyl, isoquinolinyl,

tetrahydroquinolinyl, quinoxalinyl, and quinazolinyl groups. Heteroaryl groups can be unsubstituted, or can be substituted with groups as is discussed above. Representative substituted heteroaryl groups can be substituted one or more times with groups such as those listed above.

Additional examples of aryl and heteroaryl groups include but are not limited to phenyl, biphenyl, indenyl, naphthyl (1-naphthyl, 2-naphthyl), N- hydroxytetrazolyl, N-hydroxytriazolyl, N-hydroxyimidazolyl, anthracenyl (1- anthracenyl, 2-anthracenyl, 3-anthracenyl), thiophenyl (2-thienyl, 3-thienyl), furyl (2-furyl, 3-furyl) , indolyl, oxadiazolyl, isoxazolyl, quinazolinyl, fluorenyl, xanthenyl, isoindanyl, benzhydryl, acridinyl, thiazolyl, pyrrolyl (2-pyrrolyl), pyrazolyl (3-pyrazolyl), imidazolyl (1-imidazolyl, 2-imidazolyl, 4-imidazolyl, 5- imidazolyl), triazolyl (1,2,3-triazol-l-yl, l,2,3-triazol-2-yl l,2,3-triazol-4-yl, l,2,4-triazol-3-yl), oxazolyl (2-oxazolyl, 4-oxazolyl, 5-oxazolyl), thiazolyl (2- thiazolyl, 4-thiazolyl, 5 -thiazolyl), pyridyl (2-pyridyl, 3-pyridyl, 4-pyridyl), pyrimidinyl (2-pyrimidinyl, 4-pyrimidinyl, 5-pyrimidinyl, 6-pyrimidinyl), pyrazinyl, pyridazinyl (3- pyridazinyl, 4-pyridazinyl, 5-pyridazinyl), quinolyl (2- quinolyl, 3-quinolyl, 4-quinolyl, 5-quinolyl, 6-quinolyl, 7-quinolyl, 8-quinolyl), isoquinolyl (1-isoquinolyl, 3-isoquinolyl, 4-isoquinolyl, 5-isoquinolyl, 6- isoquinolyl, 7-isoquinolyl, 8-isoquinolyl), benzo[b]furanyl (2-benzo[b]furanyl, 3-benzo[b]furanyl, 4-benzo[b]furanyl, 5-benzo[b]furanyl, 6-benzo[b]furanyl, 7- benzo[b]furanyl), 2,3-dihydro-benzo[b]furanyl (2-(2,3-dihydro- benzo[b]furanyl), 3-(2,3-dihydro-benzo[b]furanyl), 4-(2,3-dihydro- benzo[b]furanyl), 5-(2,3-dihydro-benzo[b]furanyl), 6-(2,3-dihydro- benzo[b]furanyl), 7-(2,3-dihydro-benzo[b]furanyl), benzo[b]thiophenyl (2- benzo[b] thiophenyl, 3 -benzo[b] thiophenyl, 4-benzo[b]thiophenyl,

5 -benzo [b] thiophenyl, 6-benzo [b] thiophenyl, 7-benzo [b] thiophenyl),

2,3-dihydro-benzo[b]thiophenyl, (2-(2,3-dihydro-benzo[b]thiophenyl), 3-(2,3- dihydro-benzo[b]thiophenyl), 4-(2,3-dihydro-benzo[b]thiophenyl), 5-(2,3- dihydro-benzo[b]thiophenyl), 6-(2,3-dihydro-benzo[b]thiophenyl), 7 -(2,3- dihydro-benzo[b]thiophenyl), indolyl (1-indolyl, 2-indolyl, 3-indolyl, 4-indolyl, 5-indolyl, 6-indolyl, 7-indolyl), indazole (1-indazolyl, 3-indazolyl, 4-indazolyl, 5-indazolyl, 6-indazolyl, 7-indazolyl), benzimidazolyl (1-benzimidazolyl, 2-benzimidazolyl, 4-benzimidazolyl, 5-benzimidazolyl, 6-benzimidazolyl, 7-benzimidazolyl, 8-benzimidazolyl), benzoxazolyl (1-benzoxazolyl, 2- benzoxazolyl), benzothiazolyl (1-benzothiazolyl, 2-benzothiazolyl, 4- benzothiazolyl, 5-benzothiazolyl, 6-benzothiazolyl, 7-benzothiazolyl), carbazolyl (1-carbazolyl, 2-carbazolyl, 3-carbazolyl, 4-carbazolyl),

5H-dibenz[b,f]azepine (5H-dibenz[b,f]azepin-l-yl, 5H-dibenz[b,f]azepine-2-yl, 5H-dibenz[b,f]azepine-3-yl, 5H-dibenz[b,f]azepine-4-yl, 5H-dibenz[b,f]azepine- 5-yl), 10,1 l-dihydro-5H-dibenz[b,f]azepine (10,1 l-dihydro-5H- dibenz[b,f]azepine-l-yl, 10, 1 l-dihydro-5H-dibenz[b,f]azepine-2-yl, 10, 11- dihydro-5H-dibenz[b,f]azepine-3-yl, 10, l l-dihydro-5H-dibenz[b,f]azepine-4-yl, 10,1 l-dihydro-5H-dibenz[b,f]azepine-5-yl), and the like.

In general, the Ring group is preferably a single aryl or heteroaryl ring of about 4-8 carbon atoms, where the heteroatom is oxygen or nitrogen.

The paclitaxel derivatives can be formed by substitution with groups such as succinyl, glutaryl, glutamide and other groups. For example, the paclitaxel analogs and derivatives can include water-soluble paclitaxel derivatives such as those selected from the group consisting of a 2'-succinyl- paclitaxel; 2'-succinyl-paclitaxel triethanolamine; 2'glutaryl-paclitaxel; 2'- glutaryl-paclitaxel triethanolamine salt; 2'-0-ester paclitaxel with N- (dimethylaminoethyl) glutamide; and 2'-0-ester of paclitaxel with N- (dimethylaminoethyl) glutamide hydrochloride salt.

Tyrocidine synthetase A (TycA)

As described herein, Tyrocidine synthetases can catalyze the formation of aminopropanoyl-CoA compounds useful for synthesizing paclitaxel and its analogs and derivatives. Tyrocidine synthetases are bacterial enzymes that join L-amino acids and D-amino acids together to make cyclic decapeptides. Such decapeptides often have antibiotic activity. For example, the peptide tyrocidine A is made by three Bacillus brevis tyrocidine synthetases and has the following sequence:

DPhe-Pro-DPhe-Asn-Gln-Tyr-Val-Orn-Leu.

Tyrocidine peptides with different amino acid sequences are not produced by different enzymes, but instead by the tyrocidine synthetase system that is capable of incorporating different amino acids at different positions. The amino acid sequence of the tyrocidine peptide is determined by the organization of enzymatic modules within a complex of synthetases and not by any R A template.

Three tyrocidine synthetases TycA, TycB, and TycC are involved in the synthesis of tyrocidine peptides, and each tyrocidine synthetase includes modules and domains of activity. All of the ten modules of TycA, TycB, and TycC tyrocidine synthetic activity are encoded in the tyrocidine operon. Each module contains defined domains that catalyze adenylation, thioesterification and peptide bond formation. While TycA has a single module involved in activation of D-phenylalanine for insertion in a tyrocidine peptide, TycB has three modules and TycC has six modules.

TycA has three domains, the adenylation (A), peptidyl carrier protein (PCP), and epimerization (E) domains. In some embodiments, the TycA may not have the condensation domain that is present in other tyrocidine synthetases. In its natural environment, the adenylation domain employs ATP to activate a specific amino acid, which for TycA is (S)-a-phenylalanine. Such activation uses one molecule of ATP for each activated amino acid and yields an aminoacyl adenylate enzyme complex with diphosphate (also called pyrophosphate) as a side product. The adenylation proceeds as follows where / ^' is TycA, ATP, and Mg ²⁺ .

In its natural environment, TycA activates (S)-a-Phenylalanine to an adenylate anhydride and then transfers the amino acyl moiety to a pendent pantetheine of the adjacent thiolation domain (T-domain), which is part of the peptidyl carrier protein.

⁽ ffValpha-Phenylalanine- -phosphopantetheinyl T-domain adduct

As described herein, the adenylation domain of TycA can surprisingly function as an amino phenylpropropanoykCoA ligase, making a-phenylalanyl- CoA, (R)- -phenylalanyl-CoA, and (2R, 35)-phenylisoserinyl-CoA. The latter two are intermediates useful for making paclitaxel. For example, the reaction can proceed as follows.

Aminophenylpropanoate Aminophenylpropanoyl-CoA

When the aminopropropanoate starting material is (R)--Phenylalanine, the X and Y are both hydrogen. However, when the aminopropropanoate starting material is (2R,35)-Phenylisoserine, X is hydrogen, Y is OH.

As described herein, the conversion of an aminophenylpropanoate to an aminophenylpropanoyl-CoA is surprisingly mediated by tyrocidine synthetase A (TycA), which functions as a CoA ligase. A variety of TycA ligases can be employed to catalyze such a reaction. For example, one amino acid sequence for wild type TycA with a histidine tail is provided below as SEQ ID NO: 1.

1 MVANQANLID NKRELEQHAL VPYAQGKSIH QLFEEQAEAF

41 PDRVAIVFEN RRLSYQELNR KANQLARALL EKGVQTDSIV 81 GVMMEKSIEN VIAILAVLKA GGAYVPIDIE YPRDRIQYIL

121 QDSQTKIVLT QKSVSQLVHD VGYSGEVVVL DEEQLDARET

161 ANLHQPSKPT DLAYVIYTSG TTGKPKGTML EHKGIANLQS

201 FFQNSFGVTE QDRIGLFASM SFDASVWEMF MALLSGASLY 241 ILSKQTIHDF AAFEHYLSEN ELTI ITLPPT YLTHLTPERI 281 TSLRIMITAG SASSAPLVNK WKDKLRYINA YGPTETSICA

321 TIWEAPSNQL SVQSVPIGKP IQNTHIYIVN EDLQLLPTGS

361 EGELCIGGVG LARGYWNRPD LTAEKFVDNP FVPGEKMYRT

401 GDLAKWLTDG TIEFLGRIDH QVKIRGHRIE LGEIESVLLA

441 HEHITEAVVI AREDQHAGQY LCAYYISQQE ATPAQLRDYA 481 AQKLPAYMLP SYFVKLDKMP LTPNDKIDRK ALPEPDLTAN

521 QSQAAYHPPR TETESILVSI WQNVLGIEKI GIRDNFYSLG

561 GDSIQAIQW ARLHSYQLKL ETKDLLNYPT IEQVALFVKS 601 TTRKSDQGII AGNVPLTPIQ KWFFGKNFTN TGHWNQSSVL 641 YRPEGFDPKV IQSVMDKIIE HHDALRMVYQ HENGNVVQHN 681 RGLGGQLYDF FSYNLTAQPD VQQAIEAETQ RLHSSMNLQE

721 GPLVKVALFQ TLHGDHLFLA IHHLWDGIS WRILFEDLAT

761 GYAQALAGQA ISLPEKTDSF QSWSQWLQEY ANEADLLSEI

801 PYWESLESQA KNVSLPKDYE VTDCKQKSVR NMRIRLHPEE 841 TEQLLKHANQ AYQTEINDLL LAALGLAFAE WSKLAQIVIH 881 LEGHGREDII EQANVARTVG WFTSQYPVLL DLKQTAPLSD

921 YIKLTKENMR KIPRKGIGYD ILKHVTLPEN RGSLSFRVQP

961 EVTFNYLGQF DADMRTELFT RSPYSGGNTL GADGKNNLSP 1001 ESEVYTALNI TGLIEGGELV LTFSYSSEQY REESIQQLSQ 1041 SYQKHLLAII AHCTEKKEVE RTPSDFSVKG LQMEEMDDIF 1081 ELLANTLRGS RS

Such a TycA protein can have a histidine tag, for example, on its C-terminus. nucleic acid sequence for this wild type, histidine-tagged TycA is provided below as SEQ ID NO:2.

1 ATGGTAGCAA ATCAGGCCAA TCTCATCGAC AACAAGCGGG

41 AACTGGAGCA GCATGCGCTA GTTCCATATG CACAGGGCAA

81 GTCGATCCAT CAATTGTTCG AGGAACAAGC AGAGGCTTTT

121 CCAGACCGCG TTGCCATCGT TTTTGAAAAC AGGCGGCTTT

161 CGTATCAGGA GTTGAACAGG AAAGCCAATC AACTGGCAAG

201 AGCCTTGCTC GAAAAAGGGG TGCAAACAGA CAGCATCGTC

241 GGTGTGATGA TGGAGAAGTC CATCGAAAAT GTCATCGCGA 281 TTCTGGCCGT TCTTAAAGCA GGCGGAGCCT ATGTGCCCAT 321 CGACATCGAA TATCCCCGCG ATCGCATCCA ATATATTTTG 361 CAGGATAGTC AAACGAAAAT CGTGCTTACC CAAAAAAGCG 401 TCAGCCAGCT CGTGCATGAC GTCGGGTACA GCGGAGAGGT 441 AGTTGTACTC GACGAAGAAC AGTTGGACGC TCGCGAGACT 481 GCCAATCTGC ACCAGCCCAG CAAGCCTACG GATCTTGCCT

521 ATGTCATTTA CACCTCAGGC ACGACAGGCA AGCCAAAAGG

561 CACCATGCTT GAACATAAAG GCATCGCCAA TTTGCAATCC

601 TTTTTCCAAA ATTCGTTTGG CGTCACCGAG CAAGACAGGA 641 TCGGGCTTTT TGCCAGCATG TCGTTCGACG CATCCGTTTG 681 GGAAATGTTC ATGGCTTTGC TGTCTGGCGC CAGCCTGTAC 721 ATCCTTTCCA AACAGACGAT CCATGATTTC GCTGCATTTG 761 AACACTATTT GAGTGAAAAT GAATTGACCA TCATCACACT

801 GCCGCCGACT TATTTGACTC ACCTCACCCC AGAGCGCATC 841 ACCTCGCTAC GCATCATGAT TACGGCAGGA TCAGCTTCCT 881 CCGCACCCTT GGTAAACAAA TGGAAAGACA AACTCAGGTA 921 CATAAATGCA TACGGCCCGA CGGAAACGAG CATTTGCGCG 961 ACGATCTGGG AAGCCCCGTC CAATCAGCTC TCCGTGCAAT 1001 CGGTTCCGAT CGGCAAACCG ATTCAAAATA CACATATTTA 1041 TATCGTCAAT GAAGACTTGC AGCTACTGCC GACTGGCAGC 1081 GAAGGCGAAT TGTGCATCGG CGGAGTCGGC TTGGCAAGAG 1121 GCTATTGGAA TCGGCCCGAC TTGACCGCAG AAAAATTCGT 1161 AGACAATCCG TTCGTACCAG GCGAAAAAAT GTACCGCACA 1201 GGTGACTTGG CCAAATGGCT GACGGATGGA ACGATCGAGT 1241 TTCTCGGCAG AATCGACCAT CAGGTGAAAA TCAGAGGTCA 1281 TCGCATCGAG CTTGGCGAAA TCGAGTCTGT TTTGTTGGCA 1321 CATGAACACA TCACAGAGGC CGTGGTCATT GCCAGAGAGG 1361 ATCAACACGC GGGACAGTAT TTGTGCGCCT ATTATATTTC 1401 GCAACAAGAA GCAACTCCTG CGCAGCTCAG AGACTACGCC 1441 GCCCAGAAGC TTCCGGCTTA CATGCTGCCA TCTTATTTCG 1481 TCAAGCTGGA CAAAATGCCG CTTACGCCAA ATGACAAGAT 1521 CGACCGCAAA GCGTTGCCCG AGCCTGATCT TACGGCAAAC 1561 CAAAGCCAGG CTGCCTACCA TCCTCCGAGA ACCGAGACAG 1601 AATCGATTCT CGTCTCCATC TGGCAAAACG TTTTGGGAAT 1641 TGAAAAGATC GGGATTCGCG ATAATTTTTA CTCGCTCGGC

1 6 8 1 GGAGATTCGA TCCAAGCGAT CCAGGTCGTG GCTCGTCTGC

1 7 2 1 ATTCCTATCA ATTGAAGCTA GAGACGAAAG ACTTGCTGAA

1 7 6 1 TTACCCGACG ATCGAGCAGG TTGCTCTTTT TGTCAAGAGC

1 8 0 1 ACGACGAGAA AAAGCGATCA GGGCATCATC GCTGGAAACG

1 8 4 1 TACCGCTTAC ACCCATTCAG AAGTGGTTTT TCGGGAAAAA

1 8 8 1 CTTTACGAAT ACAGGCCATT GGAACCAATC GTCTGTGCTC

1 9 2 1 TATCGCCCGG AAGGCTTTGA TCCTAAAGTC ATCCAAAGTG

1 9 6 1 TCATGGACAA AATCATCGAA CACCACGACG CGCTCCGCAT

2 0 0 1 GGTCTATCAG CACGAAAACG GAAATGTCGT TCAGCACAAC

2 0 4 1 CGCGGCTTGG GTGGACAATT ATACGATTTC TTCTCTTATA

2 0 8 1 ATCTGACCGC GCAACCAGAC GTCCAGCAGG CGATCGAAGC

2 1 2 1 AGAGACGCAA CGTCTGCACA GCAGCATGAA TTTGCAGGAA

2 1 6 1 GGACCTCTGG TGAAGGTTGC CTTATTTCAG ACGTTACATG

2 2 0 1 GCGATCATTT GTTTCTCGCA ATTCATCATT TGGTCGTGGA

2 2 4 1 TGGCATTTCC TGGCGCATTT TGTTTGAAGA TTTGGCAACC

2 2 8 1 GGATACGCGC AGGCACTTGC AGGGCAAGCG ATCAGTCTGC

2 3 2 1 CCGAAAAAAC GGATTCTTTT CAAAGCTGGT CACAATGGTT

2 3 6 1 GCAAGAATAT GCGAACGAGG CGGATTTGCT GAGCGAGATT

2 4 0 1 CCGTACTGGG AGAGTCTCGA ATCGCAAGCA AAAAATGTGT

2 4 4 1 CCCTGCCGAA AGACTATGAA GTGACCGACT GCAAACAAAA

2 4 8 1 GAGCGTGCGA AACATGCGGA TACGGCTGCA CCCGGAAGAG

2 5 2 1 ACCGAGCAGT TGTTGAAGCA CGCCAATCAG GCCTATCAAA

2 5 6 1 CGGAAATCAA CGATCTGTTG TTGGCGGCGC TCGGCTTGGC

2 6 0 1 TTTTGCGGAG TGGAGCAAGC TTGCGCAAAT CGTCATTCAT

2 6 4 1 TTGGAGGGGC ACGGGCGCGA GGACATCATC GAACAGGCAA

2 6 8 1 ACGTGGCCAG AACGGTCGGA TGGTTTACGT CGCAATATCC

2 7 2 1 GGTATTGCTC GACTTGAAGC AAACCGCTCC CTTGTCCGAC

2 7 6 1 TATATCAAGC TCACCAAAGA GAATATGCGG AAGATTCCTC

2 8 0 1 GTAAAGGGAT CGGTTACGAC ATCTTGAAGC ATGTGACACT

2 8 4 1 TCCAGAAAAT CGCGGTTCCT TATCCTTCCG CGTGCAGCCG

2 8 8 1 GAAGTGACGT TCAACTACTT GGGACAGTTT GATGCGGACA

2 9 2 1 TGAGAACGGA ACTGTTTACC CGCTCACCCT ACAGCGGCGG

2 9 6 1 CAACACGTTA GGCGCAGATG GCAAAAACAA TCTGAGTCCT

3 0 0 1 GAGTCAGAGG TGTACACCGC TTTGAATATA ACCGGATTGA

3 0 4 1 TTGAAGGCGG AGAGCTCGTC CTCACATTCT CTTACAGCTC

3 0 8 1 GGAGCAGTAT CGGGAAGAGT CCATCCAGCA ATTGAGCCAA

3 1 2 1 AGTTATCAAA AGCATCTGCT TGCCATCATC GCGCATTGCA

3 1 6 1 CCGAGAAAAA AGAAGTAGAG CGAACGCCCA GCGATTTCAG

3 2 0 1 CGTCAAAGGT CTCCAAATGG AAGAAA GGA CGATATCTTC

3 2 4 1 GAATTGCTTG CAAATACACT GCGCGGATCC AGATCTCATC

3 2 8 1 ACCATCACCA TCACTAAGCT TAA

In some embodiments, the AMP binding domain of the TycA protein resides within amino acid positions from about 54 to about 449, or from about 402 to about 507. The acyl carrier function of the TycA protein can reside within amino acid positions from about 533 to about 599. The phosphopantetheine attachment site can reside within amino acid positions from about 537 to about 598, or at about position 563. The condensation domain can reside within amino acid positions from about 610 to about 913. The non-ribosomal peptide synthase domain can reside within amino acid positions from about 917 to about 1079.

For experiments described herein, this wild-type iycA cDNA encoding the A-, T-, and E-domains was subcloned into a pSU18 vector and

heterologously expressed as a His ₆ -fusion in Escherichia coli BL21(DE3). However, the E. coli BL21 encodes the 4'-Phosphopantetheine transferase enzyme within its genome that can post-translationally couple 4'- phosphopantetheine (Ppant) to certain serine residues of various polypeptides (Jeong, et al, J. Mol. Biol. 394, 644-652 (2009)). Ser563 of TycA was changed to Ala563 (TycA-S563A) to prevent Ppant coupling at Ser563 of the T-domain and thus stall the reaction progress of TycA-S563A at the acyl-adenylate tetrahedral intermediate.

The T-domain mutant TycA-S563A has the following amino acid sequence (SEQ ID NO:3). 1 MVANQANLID NKRELEQHAL VPYAQGKSIH QLFEEQAEAF 41 PDRVAIVFEN RRLSYQELNR KANQLARALL EKGVQTDSIV 81 GVMMEKSIEN VIAILAVLKA GGAYVPIDIE YPRDRIQYIL 121 QDSQTKIVLT QKSVSQLVHD VGYSGEVVVL DEEQLDARET 161 ANLHQPSKPT DLAYVIYTSG TTGKPKGTML EHKGIANLQS 201 FFQNSFGVTE QDRIGLFASM SFDASVWEMF MALLSGASLY 241 ILSKQTIHDF AAFEHYLSEN ELTIITLPPT YLTHLTPERI 281 TSLRIMITAG SASSAPLVNK WKDKLRYINA YGPTETSICA 321 TIWEAPSNQL SVQSVPIGKP IQNTHIYIVN EDLQLLPTGS 361 EGELCIGGVG LARGYWNRPD LTAEKFVDNP FVPGEKMYRT

401 GDLAKWLTDG TIEFLGRIDH QVKIRGHRIE LGEIESVLLA 441 HEHI EAVVI AREDQHAGQY LCAYYISQQE ATPAQLRDYA 481 AQKLPAYMLP SYFVKLDKMP LTPNDKIDRK ALPEPDLTAN 521 QSQAAYHPPR TETESILVSI WQNVLGIEKI GIRDNFYSLG 561 GDAIQAIQVV ARLHSYQLKL ETKDLLNYPT IEQVALFVKS

601 TTRKSDQGII AGNVPLTPIQ KWFFGKNFTN TGHWNQSSVL 641 YRPEGFDPKV IQSVMDKIIE HHDALRMVYQ HENGNVVQHN 681 RGLGGQLYDF FSYNLTAQPD VQQAIEAETQ RLHSSMNLQE 721 GPL KVALFQ TLHGDHLFLA IHHLVVDGIS WRILFEDLAT 761 GYAQALAGQA ISLPEKTDSF QSWSQWLQEY ANEADLLSEI

801 PYWESLESQA KNVSLPKDYE VTDCKQKSVR NMRIRLHPEE 841 TEQLLKHANQ AYQTEINDLL LAALGLAFAE WSKLAQIVIH 881 LEGHGREDII EQAN ARTVG WFTSQYPVLL DLKQTAPLSD 921 YIKLTKENMR KIPRKGIGYD ILKHVTLPEN RGSLSFRVQP 961 EVTFNYLGQF DADMRTELFT RSPYSGGNTL GADGKNNLSP

1001 ESEVYTALNI TGLIEGGELV LTFSYSSEQY REESIQQLSQ 1041 SYQKHLLAII AHCTEKKEVE RTPSDFSVKG LQMEEMDDIF 1081 ELLANTLRGS RSHHHHHH*

The alanine that replaces Ser-563 in the SEQ ID NO: 3 amino acid sequence highlighted in bold and with underlining.

A nucleotide sequence for the mutant TycA S563A protein (SEQ ID NO:3) is provided below as SEQ ID NO:4.

1 ATGGTAGCAA ATCAGGCCAA TCTCATCGAC AACAAGCGGG 41 AACTGGAGCA GCATGCGCTA GTTCCATATG CACAGGGCAA

81 GTCGATCCAT CAATTGTTCG AGGAACAAGC AGAGGCTTTT 121 CCAGACCGCG TTGCCATCGT TTTTGAAAAC AGGCGGCTTT 161 CGTATCAGGA GTTGAACAGG AAAGCCAATC AACTGGCAAG 201 AGCCTTGCTC GAAAAAGGGG TGCAAACAGA CAGCATCGTC

241 GGTGTGATGA TGGAGAAGTC CATCGAAAAT GTCATCGCGA 281 TTCTGGCCGT TCTTAAAGCA GGCGGAGCCT ATGTGCCCAT 321 CGACATCGAA TATCCCCGCG ATCGCATCCA ATATATTTTG 361 CAGGATAGTC AAACGAAAAT CGTGCTTACC CAAAAAAGCG 401 TCAGCCAGCT CGTGCATGAC GTCGGGTACA GCGGAGAGGT 444411 AGTTGTACTC GACGAAGAAC AGTTGGACGC TCGCGAGACT 481 GCCAATCTGC ACCAGCCCAG CAAGCCTACG GATCTTGCCT

521 ATGTCATTTA CACCTCAGGC ACGACAGGCA AGCCAAAAGG 561 CACCATGCTT GAACATAAAG GCATCGCCAA TTTGCAATCC

60 1 TTTTTCCAAA ATTCGTTTGG CGTCACCGAG CAAGACAGGA

64 1 TCGGGCTTTT TGCCAGCATG TCGTTCGACG CATCCGTTTG

68 1 GGAAATGTTC ATGGCTTTGC TGTCTGGCGC CAGCCTGTAC

72 1 ATCCTTTCCA AACAGACGAT CCATGATTTC GCTGCATTTG

76 1 AACACTATTT GAGTGAAAAT GAATTGACCA TCATCACACT

80 1 GCCGCCGACT TATTTGACTC ACCTCACCCC AGAGCGCATC

84 1 ACCTCGCTAC GCATCATGAT TACGGCAGGA TCAGCTTCCT

88 1 CCGCACCCTT GGTAAACAAA TGGAAAGACA AACTCAGGTA

92 1 CATAAATGCA TACGGCCCGA CGGAAACGAG CATTTGCGCG

96 1 ACGATCTGGG AAGCCCCGTC CAATCAGCTC TCCGTGCAAT

100 1 CGGTTCCGAT CGGCAAACCG ATTCAAAATA CACATATTTA

104 1 TATCGTCAAT GAAGACTTGC AGCTACTGCC GACTGGCAGC

108 1 GAAGGCGAAT TGTGCATCGG CGGAGTCGGC TTGGCAAGAG

112 1 GCTATTGGAA TCGGCCCGAC TTGACCGCAG AAAAATTCGT

116 1 AGACAATCCG TTCGTACCAG GCGAAAAAAT GTACCGCACA

120 1 GGTGACTTGG CCAAATGGCT GACGGATGGA ACGATCGAGT

124 1 TTCTCGGCAG AATCGACCAT CAGGTGAAAA TCAGAGGTCA

128 1 TCGCATCGAG CTTGGCGAAA TCGAGTCTGT TTTGTTGGCA

132 1 CATGAACACA TCACAGAGGC CGTGGTCATT GCCAGAGAGG

136 1 ATCAACACGC GGGACAGTAT TTGTGCGCCT ATTATATTTC

140 1 GCAACAAGAA GCAACTCCTG CGCAGCTCAG AGACTACGCC

144 1 GCCCAGAAGC TTCCGGCTTA CATGCTGCCA TCTTATTTCG

148 1 TCAAGCTGGA CAAAATGCCG CTTACGCCAA ATGACAAGAT

152 1 CGACCGCAAA GCGTTGCCCG AGCCTGATCT TACGGCAAAC

156 1 CAAAGCCAGG CTGCCTACCA TCCTCCGAGA ACCGAGACAG

160 1 AATCGATTCT CGTCTCCATC TGGCAAAACG TTTTGGGAAT

164 1 TGAAAAGATC GGGATTCGCG ATAATTTTTA CTCGCTCGGC

168 1 GGAGATGCGA TCCAAGCGAT CCAGGTCGTG GCTCGTCTGC

172 1 ATTCCTATCA ATTGAAGCTA GAGACGAAAG ACTTGCTGAA

176 1 TTACCCGACG ATCGAGCAGG TTGCTCTTTT TGTCAAGAGC

180 1 ACGACGAGAA AAAGCGATCA GGGCATCATC GCTGGAAACG

184 1 TACCGCTTAC ACCCATTCAG AAGTGGTTTT TCGGGAAAAA

188 1 CTTTACGAAT ACAGGCCATT GGAACCAATC GTCTGTGCTC

192 1 TATCGCCCGG AAGGCTTTGA TCCTAAAGTC ATCCAAAGTG

196 1 TCATGGACAA AATCATCGAA CACCACGACG CGCTCCGCAT

200 1 GGTCTATCAG CACGAAAACG GAAATGTCGT TCAGCACAAC

204 1 CGCGGCTTGG GTGGACAATT ATACGATTTC TTCTCTTATA

208 1 ATCTGACCGC GCAACCAGAC GTCCAGCAGG CGATCGAAGC

212 1 AGAGACGCAA CGTCTGCACA GCAGCATGAA TTTGCAGGAA

216 1 GGACCTCTGG TGAAGGTTGC CTTATTTCAG ACGTTACATG

220 1 GCGATCATTT GTTTCTCGCA ATTCATCATT TGGTCGTGGA

224 1 TGGCATTTCC TGGCGCATTT TGTTTGAAGA TTTGGCAACC

228 1 GGATACGCGC AGGCACTTGC AGGGCAAGCG ATCAGTCTGC

232 1 CCGAAAAAAC GGATTCTTTT CAAAGCTGGT CACAATGGTT

236 1 GCAAGAATAT GCGAACGAGG CGGATTTGCT GAGCGAGATT

240 1 CCGTACTGGG AGAGTCTCGA ATCGCAAGCA AAAAATGTGT

244 1 CCCTGCCGAA AGACTATGAA GTGACCGACT GCAAACAAAA

248 1 GAGCGTGCGA AACATGCGGA TACGGCTGCA CCCGGAAGAG

252 1 ACCGAGCAGT TGTTGAAGCA CGCCAATCAG GCCTATCAAA 2561 CGGAAATCAA CGATCTGTTG TTGGCGGCGC TCGGCTTGGC 2601 TTTTGCGGAG TGGAGCAAGC TTGCGCAAAT CGTCATTCAT 2641 TTGGAGGGGC ACGGGCGCGA GGACATCATC GAACAGGCAA 2681 ACGTGGCCAG AACGGTCGGA TGGTTTACGT CGCAATATCC 2721 GGTATTGCTC GACTTGAAGC AAACCGCTCC CTTGTCCGAC 2761 TATATCAAGC TCACCAAAGA GAATATGCGG AAGATTCCTC 2801 GTAAAGGGAT CGGTTACGAC ATCTTGAAGC ATGTGACACT 2841 TCCAGAAAAT CGCGGTTCCT TATCCTTCCG CGTGCAGCCG 2881 GAAGTGACGT TCAACTACTT GGGACAGTTT GATGCGGACA 2921 TGAGAACGGA ACTGTTTACC CGCTCACCCT ACAGCGGCGG 2961 CAACACGTTA GGCGCAGATG GCAAAAACAA TCTGAGTCCT 3001 GAGTCAGAGG TGTACACCGC TTTGAATATA ACCGGATTGA 3041 TTGAAGGCGG AGAGCTCGTC CTCACATTCT CTTACAGCTC 3081 GGAGCAGTAT CGGGAAGAGT CCATCCAGCA ATTGAGCCAA 3121 AGTTATCAAA AGCATCTGCT TGCCATCATC GCGCATTGCA 3161 CCGAGAAAAA AGAAGTAGAG CGAACGCCCA GCGATTTCAG 3201 CGTCAAAGGT CTCCAAATGG AAGAAA GGA CGATATCTTC 3241 GAATTGCTTG CAAATACACT GCGCGGATCC AGATCTCATC 3281 ACCATCACCA TCACTAAGCT TAA

The T-domain mutant TycA-S563A was also subcloned into a pSU18 vector and heterologously expressed as a His6-fusion in Escherichia coli BL21(DE3).

Related TycA enzymes can also be employed to catalyze the formation of an aminopropanyl-CoA. At least some amino acid and nucleic acid sequences for proteins related to the SEQ ID NO: 1 TycA sequence are available from the

National Center for Biotechnology Information (NCBI) database (see, e.g., the website at ncbi.nlm.nih.gov). For example, an amino acid sequence for

Tyrocidine synthase 1 from Brevibacillus parabrevis is available from the NCBI database as accession number P09095.2 (GL6175106) and is provided below as

SEQ ID NO:5.

1 MLANQANLID NKRELEQHAL VPYAQGKSIH QLFEEQAEAF 61 PDRVAIVFEN RRLSYQELNR KANQLARALL EKGVQTDSIV 81 GVMMEKSIEN VIAILAVLKA GGAYVPIDIE YPRDRIQYIL 121 QDSQTKIVLT QKSVSQLVHD VGYSGEVVVL DEEQLDARET 161 ANLHQPSKPT DLAYVIYTSG TTGKPKGTML EHKGIANLQS 201 FFQNSFGVTE QDRIGLFASM SFDASVWEMF MALLSGASLY 241 ILSKQTIHDF AAFEHYLSEN ELTIITLPPT YLTHLTPERI 281 TSLRIMITAG SASSAPLVNK WKDKLRYINA YGPTETSICA 321 TIWEAPSNQL SVQSVPIGKP IQNTHIYIVN EDLQLLPTGS 361 EGELCIGGVG LARGYWNRPD LTAEKFVDNP FVPGEKMYRT 401 GDLAKWLTDG TIEFLGRIDH QVKIRGHRIE LGEIESVLLA 441 HEHITEAVVI AREDQHAGQY LCAYYISQQE ATPAQLRDYA 481 AQKLPAYMLP SYFVKLDKMP LTPNDKIDRK ALPEPDLTAN

521 QSQAAYHPPR TETESILVSI WQNVLGIEKI GIRDNFYSLG

561 GDSIQAIQVV ARLHSYQLKL ETKDLLNYPT IEQVALFVKS

601 TTRKSDQGI I AGNVPLTPIQ KWFFGKNFTN TGHWNQSSVL 641 YRPEGFDPKV IQSVMDKIIE HHDALRMVYQ HENGNVVQHN

681 RGLGGQLYDF FSYNLTAQPD VQQAIEAETQ RLHSSMNLQE

721 GPLVKVALFQ TLHGDHLFLA IHHLWDGIS WRILFEDLAT

761 GYAQALAGQA ISLPEKTDSF QSWSQWLQEY ANEADLLSEI

781 PYWESLESQA KNVSLPKDYE VTDCKQKSVR NMRIRLHPEE 841 TEQLLKHANQ AYQTEINDLL LAALGLAFAE WSKLAQIVIH

881 LEGHGREDI I EQANVARTVG WFTSQYPVLL DLKQTAPLSD

901 YIKLTKENMR KIPRKGIGYD ILKHVTLPEN RGSLSFRVQP

961 EVTFNYLGQF DADMRTELFT RSPYSGGNTL GADGKNNLSP

1001 ESEVYTALNI TGLIEGGELV LTFSYSSEQY REESIQQLSQ 1041 SYQKHLLAI I AHCTEKKEVE RTPSDFSVKG LQMEEMDDIF

1081 ELLANTLR

Another amino acid sequence for a protein related to TycA is available from the NCBI database as accession number CAA31623.1 (GI:39401 ; also from Brevibacillus parabrevis) and is provided below as SEQ ID NO: 6.

1 MLANQANLID NKRELEQHAL VPYAQGKSIH QLFEEQAEAF

41 PDRVAIVFEN RRLSYQELNR KANQLARALL EKGVQTDSIV

81 GVMMEKSIEN VIAILAVLKA GGAYVPIDIE YPRDRIQYIL

121 QDSQTKIVLT QKSVSQLVHD VGYSGEVVVL DEEQLDARET 161 ANLHQPSKPT DLAYVIYTSG TTGKPKGTML EHKGIAICNP

201 FSKIRLASPS KTGSGFLPAC RSTHPFGKCS WLCCLAPRVH

241 PSKQTIHDFA AFEHYLSENE LTIITLPPTY LTHLTPERIT

281 SLRIMITAGS ASSAPLVNKW KDKLRYINAY GPTETSICAT

321 IWEAPSNQLS VQSVPIGKPI QNTHIYIVNE DLQLLPTADE 361 GELCIGGVGL ARGYWNRPDL TAEKFVDNPF VPGEKMYRTG

401 DLAKWLTDGT IEFLGRIDHQ VKIRGHRIEL GEIESVLLAH

441 EHITEAWIA REDQHAGQYL CAYYISQQEA TPAQLRDYAA

481 QKLPAYMLPS YFVKLDKMPL TPNDKIDRKA LPEPDLTANQ

521 SQAAYHPPRT ETESILVSIW QNVLGIEKIG IRDNFYSLGG 561 DSIQAIQWA RLHSYQLKLE TKDLLNYPTI EQVALFVKST

601 TRKSDQGIIA GNVPLTPIQK WFFGKNFTNT GHWNQSSVLY

641 RPEGFDPKVI QSVMDKIIEH HDAVRMVYQH ENGNVVQHNR

681 GLGGQLYDFF SYNLTAQPDV QQAIEAETQR LHSSMNLQEG

721 PLVKVALFQT LHGDHFFLAI HHLWDGISW RILFKIWQPD 761 TRRHLQGKRS VCPKKRILFK AGHNGCKNNA NEADLLSEIP

801 YWESLESQAK NVSLPKDYEV TDCKQKSVRN MRIRLHPEET

841 EQLLKHANQA YQTEINDLLL AALGLAFAEW SKLAKSSFIW

881 RGTGARTSSN RQTVARTVGW FTSQYPVLLD LKQTAPLSDY

921 IKLTKENMRK IPRKGIGYDI LKHVTLPENR GSLSFRVQPE 961 VTFNYLGQFD ADMRTELFTR SPYSGGNTLG ADGKNNLSPE

1001 SEVYTALNIT GLIEGGELVL TFSYSSEQYR EESIQQLSQS

1041 YQKHLLAIIA HCTEKKEVER TPSDFSVKGL QMEEMDDIFE 1081 LLANTLR

A nucleic acid sequence for the SEQ ID NO: 6 protein is available in the NCBI database as accession number X13237.1 (GL39400; Brevibacillus brevis), and is provided below as SEQ ID NO:7.

1 CTGGTGGATC GCAAAGTACA TGCCAAACTG CTGGTGGATT 41 TTCCTTGAAC CAAATTTCGC TGGCAGCCAG CATGGTTCAA

81 ACCTTTTCTC TAAAAAGCTG CGTCACGTCA AAAAAGAGGG

121 GGTAGGAATT GTGCCTTTTT ATCACATGCC TTTTTACGAA

161 AGTCTGCGGA CTGATCAGGA CAATAGCTGC TGATCCAGAT

201 AGGCAGCACA CAGGAAAACA GCCTCTCGTT TTTCCGTAGA 241 AGAAAATTCC TGTTTTCCCA GTATAAAGCA TTATATGGCT

281 TGTGAACATA TAAAAATTTT AATGTTATGA AAATATTTAT

321 CGTCAAAATA TAGCCGTACG CTTTCCTTTT TTATAGACAA

361 GTTGAAAAGG AAAAATGTTG CAGCGCCGAA ACGAGCCAAT

401 CACTGGCTTC ACCAAAGGGA AAAACACGTG TGCCGCTTAT 441 TGATTACGCA AGCGGGAGCA GGTTTGCCAA GCAAAACTTG

481 GATTTACGTA AAAAGGTTGT AAAAAAACTT GTTGAATTTT

521 TTGCAAAATA TCCCTATTTT TTAATCGACT TCCAATTTTT

561 CTCTGCTATA ATGAGTTTCA GCGTCAGTAA CCTAGTGCTT

601 TCAGCCTGTC AGCCGATCGG GGAACTTCCT GTGATTGTTT 641 TCATGCAAAT CAGTTTTCCT TCGTTCGCAG CGTAAGCAGG

681 CGTATCCGGC AGCGGAATAC CAGCACCCAT TTTCCGCTAC

721 AGCATGAGCA AAATATGACT TTAGTATGAA GGGAATTTCC

761 CAGAAACAGG AAATTTTCTT GTTGTTAAAA TTACCCAAAT

801 GATGGAAAAT GGGAAATTGG AATGGAACGT TGACCTTGCC 841 TGTCTCTTGT TGGCAACCAT TTCGTCACAC TTCATGATAA

881 GCAGAAGTAA TTCCATTATC GGAGGGGACA TATGTTAGCA

921 AATCAGGCCA ATCTCATCGA CAACAAGCGG GAACTGGAGC

961 AGCATGCGCT AGTTCCATAT GCACAGGGCA AGTCGATCCA

1001 TCAATTGTTC GAGGAACAAG CAGAGGCTTT TCCAGACCGC 1041 GTTGCCATCG TTTTTGAAAA CAGGCGGCTT TCGTATCAGG

1081 AGTTGAACAG GAAAGCCAAT CAACTGGCAA GAGCCTTGCT

1121 CGAAAAAGGG GTGCAAACAG ACAGCATCGT CGGTGTGATG

1161 ATGGAGAAGT CCATCGAAAA TGTCATCGCG ATTCTGGCCG

1201 TTCTTAAAGC AGGCGGAGCC TATGTGCCCA TCGACATCGA 1241 ATATCCCCGC GATCGCATCC AATATATTTT GCAGGATAGT

1281 CAAACGAAAA TCGTGCTTAC CCAAAAAAGC GTCAGCCAGC

1321 TCGTGCATGA CGTCGGGTAC AGCGGAGAGG TAGTTGTACT

1361 CGACGAAGAA CAGTTGGACG CTCGCGAGAC TGCCAATCTG

1401 CACCAGCCCA GCAAGCCTAC GGATCTTGCC TATGTCATTT 1441 ACACCTCAGG CACGACAGGC AAGCCAAAAG GCACCATGCT

1481 TGAACATAAA GGCATCGCAA TTTGCAATCC TTTTTCCAAA

1521 ATTCGTTTGG CGTCACCGAG CAAGACAGGA TCGGGCTTTT 1561 TGCCAGCATG TCGTTCGACG CATCCGTTTG GGAAATGTTC

16 01 ATGGCTTTGC TGTCTGGCGC CACGTGTACA TCCTTCCAAA

16 41 CAGACGATCC ATGATTTCGC TGCATTTGAA CACTATTTGA

16 81 GTGAAAATGA ATTGACCATC ATCACACTGC CGCCGACTTA

17 21 TTTGACTCAC CTCACCCCAG AGCGCATCAC CTCGCTACGC

17 61 ATCATGATTA CGGCAGGATC AGCTTCCTCC GCACCCTTGG

18 01 TAAACAAATG GAAAGACAAA CTCAGGTACA TAAATGCATA

18 41 CGGCCCGACG GAAACGAGCA TTTGCGCGAC GATCTGGGAA

18 81 GCCCCGTCCA ATCAGCTCTC CGTGCAATCG GTTCCGATCG

19 21 GCAAACCGAT TCAAAATACA CATATTTATA TCGTCAATGA

19 61 AGACTTGCAG CTACTGCCGA CTGCGGACGA AGGCGAATTG

20 01 TGCATCGGCG GAGTCGGCTT GGCAAGAGGC TATTGGAATC

20 41 GGCCCGACTT GACCGCAGAA AAATTCGTAG ACAATCCGTT

20 81 CGTACCAGGC GAAAAAATGT ACCGCACAGG TGACTTGGCC

21 21 AAATGGCTGA CGGATGGAAC GATCGAGTTT CTCGGCAGAA

21 61 TCGACCATCA GGTGAAAATC AGAGGTCATC GCATCGAGCT

22 01 TGGCGAAATC GAGTCTGTTT TGTTGGCACA TGAACACATC

22 41 ACAGAGGCCG TGGTCATTGC CAGAGAGGAT CAACACGCGG

22 81 GACAGTATTT GTGCGCCTAT TATATTTCGC AACAAGAAGC

23 21 AACTCCTGCG CAGCTCAGAG ACTACGCCGC CCAGAAGCTT

23 61 CCGGCTTACA TGCTGCCATC TTATTTCGTC AAGCTGGACA

24 01 AAATGCCGCT TACGCCAAAT GACAAGATCG ACCGCAAAGC

24 41 GTTGCCCGAG CCTGATCTTA CGGCAAACCA AAGCCAGGCT

24 81 GCCTACCATC CTCCGAGAAC CGAGACAGAA TCGATTCTCG

25 21 TCTCCATCTG GCAAAACGTT TTGGGAATTG AAAAGATCGG

25 61 GATTCGCGAT AATTTTTACT CGCTCGGCGG AGATTCGATC

26 01 CAAGCGATCC AGGTCGTGGC TCGTCTGCAT TCCTATCAAT

26 41 TGAAGCTAGA GACGAAAGAC TTGCTGAATT ACCCGACGAT

26 81 CGAGCAGGTT GCTCTTTTTG TCAAGAGCAC GACGAGAAAA

27 21 AGCGATCAGG GCATCATCGC TGGAAACGTA CCGCTTACAC

27 61 CCATTCAGAA GTGGTTTTTC GGGAAAAACT TTACGAATAC

28 01 AGGCCATTGG AACCAATCGT CTGTGCTCTA TCGCCCGGAA

28 41 GGCTTTGATC CTAAAGTCAT CCAAAGTGTC ATGGACAAAA

28 81 TCATCGAACA CCACGACGCC GTCCGCATGG TCTATCAGCA

29 21 CGAAAACGGA AATGTCGTTC AGCACAACCG CGGCTTGGGT

29 61 GGACAATTAT ACGATTTCTT CTCTTATAAT CTGACCGCGC

30 01 AACCAGACGT CCAGCAGGCG ATCGAAGCAG AGACGCAACG

30 41 TCTGCACAGC AGCATGAATT TGCAGGAAGG ACCTCTGGTG

30 81 AAGGTTGCCT TATTTCAGAC GTTACATGGC GATCATTTCT

31 21 TTCTCGCAAT TCATCATTTG GTCGTGGATG GCATTTCCTG

31 61 GCGCATTTTG TTTAAGATTT GGCAACCGGA TACGCGCAGG

33 21 CACTTGCAGG GCAAGCGATC AGTCTGCCCG AAAAAACGGA

32 41 TTCTTTTCAA AGCTGGTCAC AATGGTTGCA AGAATAATGC

32 81 GAACGAGGCG GATTTGCTGA GCGAGATTCC GTACTGGGAG

33 21 AGTCTCGAAT CGCAAGCAAA AAATGTGTCC CTGCCGAAAG

33 61 ACTATGAAGT GACCGACTGC AAACAAAAGA GCGTGCGAAA

34 01 CATGCGGATA CGGCTGCACC CGGAAGAGAC CGAGCAGTTG

34 41 TTGAAGCACG CCAATCAGGC CTATCAAACG GAAATCAACG

34 81 ATCTGTTGTT GGCGGCGCTC GGCTTGGCTT TTGCGGAGTG

35 21 GAGCAAGCTT GCGAAATCGT CATTCATTTG GAGGGGCACG 3561 GGCGCGAGGA CATCATCGAA CAGGCAAACG GTGGCCAGAA

36 01 CGGTCGGATG GTTTACGTCG CAATATCCGG TATTGCTCGA

36 41 CTTGAAGCAA ACCGCTCCCT TGTCCGACTA TATCAAGCTC

36 81 ACCAAAGAGA ATATGCGGAA GATTCCTCGT AAAGGGATCG

37 21 GTTACGACAT CTTGAAGCAT GTGACACTTC CAGAAAATCG

37 61 CGGTTCCTTA TCCTTCCGCG TGCAGCCGGA AGTGACGTTC

38 01 AACTACTTGG GACAGTTTGA TGCGGACATG AGAACGGAAC

38 41 TGTTTACCCG CTCACCCTAC AGCGGCGGCA ACACGTTAGG

38 81 CGCAGATGGC AAAAACAATC TGAGTCCTGA GTCAGAGGTG

39 21 TACACCGCTT TGAATATAAC CGGATTGATT GAAGGCGGAG

39 61 AGCTCGTCCT CACATTCTCT TACAGCTCGG AGCAGTATCG

40 01 GGAAGAGTCC ATCCAGCAAT TGAGCCAAAG TTATCAAAAG

40 41 CATCTGCTTG CCATCATCGC GCATTGCACC GAGAAAAAAG

40 81 AAGTAGAGCG AACGCCCAGC GATTTCAGCG TCAAAGGTCT

41 21 CCAAATGGAA GAAATGGACG ATATCTTCGA ATTGCTTGCA

41 61 AATACACTGC GCTAAACAGA TGTTGGCCAC CATTTTCAGG

42 01 GGCAACTGCG TGCTTTCATT CCCATTTTTA TACATTTATA

42 41 ACAAATAAAG ATATATCCGA GGTGCCGTAA TGAGTGTATT

42 81 TAGCAAAGAA CAAGTTCAGG ATATGTATGC GTTGAC

The coding region of the TycA related protein is at nucleotide positions from about 912 to about 4175 within the SEQ ID NO: 7 sequence.

Related Sequences

As described herein, TycA can catalyze the formation of

aminophenylpropanoyl-CoA in a reaction that proceeds as follows.

Aminophenylpropanoate Aminophenylpropanoyl-CoA

In some embodiments, proteins related to TycA can also catalyze formation of aminophenylpropanoyl-CoA. Such related TycA protein can have sequences that share at least about 85% sequence identity with any of the TycA sequences described herein.

Proteins that share at least about 85% sequence identity with any of the TycA sequences described herein can be obtained by identifying nucleic acids with at least 85% sequence identity to the TycA nucleic acids described herein. Such nucleic acids can readily be identified, isolated and used to facilitate production of aminopropanyl-CoA. Such nucleic acids can encode or hybridize to TycA nucleic acids, or fragments thereof.

For example, related nucleic acids can be isolated and identified by mutation of the SEQ ID NO: 1, SEQ ID NO:3, SEQ ID NO:5, and/or SEQ ID NO: 6 amino acid sequences and/or by hybridization to DNA and/or RNA isolated from other species using the SEQ ID NO:2, SEQ ID NO:4, and/or SEQ ID NO:7 nucleic acids (or fragments thereof) as probes. Sequences of the TycA proteins (e.g., SEQ ID NO: l, 3, and/or 6) or nucleic acids (e.g., SEQ ID NO:2, SEQ ID NO:4, and/or SEQ ID NO:7) can also be examined and used a basis for designing alternative TycA proteins and nucleic acids.

In some embodiments, the TycA nucleic acids that encode useful TycA activities include any nucleic acid that can selectively hybridize to a nucleic acid with any of the SEQ ID NO:2, 4 and 7 sequences.

The term "selectively hybridize" includes hybridization, under stringent hybridization conditions, of a nucleic acid sequence to a specified nucleic acid target sequence (e.g., SEQ ID NO:2, SEQ ID NO:4, and/or SEQ ID NO:7) to a detectably greater degree (e.g., at least 2-fold over background) than its hybridization to non-target nucleic acid sequences. Such selective hybridization substantially excludes non-target nucleic acids.

Related TycA nucleic acids sequences typically have about at least 40% sequence identity, or at least 50% sequence identity, or at least 60% sequence identity, or at least 70% sequence identity, or 60-99% sequence identity, or 70- 99% sequence identity, or 80-99% sequence identity, or 90-95% sequence identity, or 90-99% sequence identity, or 95-97% sequence identity, or 97-99% sequence identity, or 100% sequence identity (or complementarity) with any of SEQ ID NO:2, SEQ ID NO:4, and/or SEQ ID NO:7. In some embodiments, a selectively hybridizing sequence has about at least about 80% or at least about 85% sequence identity or complementarity with any of SEQ ID NO:2, SEQ ID NO:4, and/or SEQ ID NO:7.

Note that if a value of a variable that is necessarily an integer (e.g., the number of nucleotides or amino acids in a nucleic acid or protein), is described as a range, e.g., 80-99% sequence identity what is meant is that the value can be any integer between 80 and 99 inclusive, i.e., 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99, or any range between 80 and 99 inclusive, e.g., 81-99%, 81-98%, 82-99%, etc.

In some embodiments, the nucleic acids used in the methods provided herein can include fragments of TycA nucleic acids. For example, the nucleic acids of the invention include those with about 300 of the same nucleotides as any of the SEQ ID NO:2, 4, 6, 8, 10, 12, 14 and 18 sequences, or about 400 of the same nucleotides as any of the SEQ ID NO: 2, 4, and 7 sequences, or about 500 of the same nucleotides as any of the SEQ ID NO: 2, 4, and 7 sequences, or about 600 of the same nucleotides as any of the SEQ ID NO: 2, 4, and 7 sequences, or about 700 of the same nucleotides as any of the SEQ ID NO: 2, 4, and 7 sequences, or about 800 of the same nucleotides as any of the SEQ ID NO: 2, 4, and 7 sequences, or about 900 of the same nucleotides as any of the SEQ ID NO: 2, 4, and 7 sequences, or about 1000 of the same nucleotides as any of the SEQ ID NO:2, 4, and 7 sequences, or about 1100 of the same nucleotides as any of the SEQ ID NO: 2, 4, and 7 sequences, or about 500-1 100 of the same nucleotides as any of the SEQ ID NO: 2, 4, and 7 sequences. The identical nucleotides can be distributed throughout the nucleic acid, and need not be contiguous. For example, the nucleic acid sequence of a TycA nucleic acid can be optimized for expression in a particular plant species by altering selected codons to encode the same amino acid but use nucleotide codons that are more easily 'read' by the transcription/translation machinery of a selected plant species.

In some embodiments, related nucleic acid hybridize to the nucleic acids described herein under "stringent conditions" or "stringent hybridization conditions."

The terms "stringent conditions" or "stringent hybridization conditions" include conditions under which a probe will hybridize to its target sequence to a detectably greater degree than other sequences (e.g., at least 2-fold over background). Stringent conditions are somewhat sequence-dependent and can vary in different circumstances. By controlling the stringency of the

hybridization and/or washing conditions, target sequences can be hybridized that have up to 100% complementarity to the probe or inhibitory nucleic acid (homologous probing). Alternatively, stringency conditions can be adjusted to allow some mismatching in sequences so that lower degrees of sequence similarity are detected (heterologous probing).

A probe for identifying and/or isolating a related nucleic acid can be approximately 15-500 nucleotides in length, but can vary greatly in length from about 17 nucleotides to equal to the entire length of the target sequence. In some embodiments, the probe is about 10-50 nucleotides in length, or about 15-50 nucleotides in length, or about 16-45 nucleotides in length, or about 18-25 nucleotides in length.

Typically, stringent conditions will be those where the salt concentration is less than about 1.5 M Na ion (or other salts), typically about 0.01 to 1.0 M Na ion concentration (or other salts), at pH 7.0 to 8.3 and the temperature is at least about 30 °C. for shorter probes (e.g., 10 to 50 nucleotides) and at least about 60 °C. for longer probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide or Denhardt's solution. Exemplary low stringency conditions include hybridization with a buffer solution of 30 to 35% formamide, 1M NaCl, 1% SDS (sodium dodecyl sulfate) at 37 °C, and a wash in 1 x SSC to 2 x SSC (where 20 x SSC is 3.0 M NaCl, 0.3 M trisodium citrate) at 50 to 55 °C. Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1M NaCl, 1% SDS at 37 °C, and a wash in 0.5 x SSC to 1 x SSC at 55 to 60 °C. Exemplary high stringency conditions include hybridization in 50% formamide, 1M NaCl, 1% SDS at 37° C, and a wash in 0.1 x SSC at 60 to 65 °C. Specificity is typically a function of post-hybridization washes, where the factors controlling hybridization include the ionic strength and temperature of the final wash solution.

For DNA-DNA hybrids, the T _m can be approximated from the equation of Meinkoth and Wahl (Anal. Biochem. 138:267-84 (1984)): T _m = 81.5 °C + 16.6 (log M) + 0.41 (% GC) - 0.61 (% formamide) -

500/L

where M is the molarity of monovalent cations; % GC is the percentage of guanosine and cytosine nucleotides in the DNA, % formamide is the percentage of formamide in the hybridization solution, and L is the length of the hybrid in base pairs. The T _m is the temperature (under defined ionic strength and pH) at which 50% of a complementary target sequence hybridizes to a perfectly matched probe. The T _m is reduced by about 1 °C. for each 1% of mismatching. Thus, the T _m , hybridization and/or wash conditions can be adjusted to hybridize to sequences of the desired sequence identity. For example, if sequences with greater than or equal to 90% sequence identity are sought, the T _m can be decreased 10 °C. Generally, stringent conditions are selected to be about 5 °C lower than the thermal melting point (T _m ) for the specific sequence and its complement at a defined ionic strength and pH. However, severely stringent conditions can include hybridization and/or a wash at 1, 2, 3 or 4° C lower than the thermal melting point (T _m ). Moderately stringent conditions can include hybridization and/or a wash at 6, 7, 8, 9 or 10 °C lower than the thermal melting point (T _m ). Low stringency conditions can include hybridization and/or a wash at 11, 12, 13, 14, 15 or 20 °C lower than the thermal melting point (T _m ). Using the equation, hybridization and wash compositions, and a desired T _m , those of ordinary skill can identify and isolate nucleic acids with sequences related to any of the SEQ ID NO:2, 4 and 6 sequences. Similarly, those of ordinary skill can identify and isolate inhibitory nucleic acids with sequences that effectively inhibit the expression of a nucleic acid that includes any of the SEQ ID NO:2, 4 and 6 sequences.

Those of skill in the art also understand how to vary the hybridization and/or wash solutions to isolate desirable nucleic acids. For example, if the desired degree of mismatching results in a T _m of less than 45 °C (aqueous solution) or 32 °C (formamide solution) it is preferred to increase the SSC concentration so that a higher temperature can be used.

An extensive guide to the hybridization of nucleic acids is found in Tijssen, LABORATORY TECHNIQUES IN BIOCHEMISTRY AND MOLECULAR

BIOLOGY - HYBRIDIZATION WITH NUCLEIC ACID PROBES, part 1, chapter 2, "Overview of principles of hybridization and the strategy of nucleic acid probe assays," Elsevier, N.Y. (1993); and in CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, chapter 2, Ausubel, et al, eds, Greene Publishing and Wiley- Interscience, New York (1995).

Unless otherwise stated, in the present application, high stringency is defined as a wash in 0.1 x SSC, 0.1% SDS at 65 °C. High stringency hybridization can include hybridization in 4 x SSC, 5 x Denhardt's (5 g Ficoll, 5 g polyvinylpyrrolidone, 5 g bovine serum albumin in 500 ml of water), 0.1 mg/ml boiled salmon sperm DNA, and 25 mM Na phosphate at 65 °C, followed by a wash in 0.1 x SSC, 0.1% SDS at 65 °C.

The following terms are used to describe the sequence relationships between two or more nucleic acids or nucleic acids or polypeptides: (a)

"reference sequence," (b) "comparison window," (c) "sequence identity," (d) "percentage of sequence identity" and (e) "substantial identity."

As used herein, "reference sequence" is a defined sequence used as a basis for sequence comparison. The reference sequence can be a nucleic acid sequence (e.g., any of the SEQ ID NO:2, 4, and 7 nucleic acid sequences) or an amino acid sequence (e.g., any of the SEQ ID NO: l, 3, 5, and 6 amino acid sequences). A reference sequence may be a subset or the entirety of a specified sequence. For example, a reference sequence may be a segment of a full-length cDNA or of a genomic DNA sequence, or the complete cDNA or complete genomic DNA sequence, or a domain of a polypeptide sequence.

As used herein, "comparison window" refers to a contiguous and specified segment of a nucleic acid or an amino acid sequence, wherein the nucleic acid/amino acid sequence can be compared to a reference sequence and wherein the portion of the nucleic acid/amino acid sequence in the comparison window may comprise additions or deletions (i.e., gaps) compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The comparison window can vary for nucleic acid and polypeptide sequences. Generally, for nucleic acids, the comparison window is at least 16 contiguous nucleotides in length, and optionally can be 18, 20, 30, 40, 50, 100 or more nucleotides. For amino acid sequences, the comparison window is at least about 15 amino acids, and can optionally be 20, 30, 40, 50, 100 or more amino acids. Those of skill in the art understand that to avoid a high similarity to a reference sequence due to inclusion of gaps in the nucleic acid or amino acid sequence, a gap penalty is typically introduced and is subtracted from the number of matches.

Methods of alignment of nucleotide and amino acid sequences for comparison are well known in the art. The local homology algorithm (BESTFIT) of Smith and Waterman, (1981) Adv. Appl. Math 2:482, may permit optimal alignment of compared sequences; by the homology alignment algorithm (GAP) of Needleman and Wunsch, (1970) J. Mol. Biol. 48:443-53; by the search for similarity method (Tfasta and Fasta) of Pearson and Lipman, (1988) Proc. Natl. Acad. Sci. USA 85:2444; by computerized implementations of these algorithms, including, but not limited to: CLUSTAL in the PC/Gene program by

Intelligenetics, Mountain View, Calif, GAP, BESTFIT, BLAST, FASTA and TFASTA in the Wisconsin Genetics Software Package, Version 8 (available from Genetics Computer Group (GCG™ programs (Accelrys, Inc., San Diego, Calif.)). The CLUSTAL program is well described by Higgins and Sharp (1988) Gene 73:237-44; Higgins and Sharp, (1989) CABIOS 5: 151-3; Corpet, et al, (1988) Nucleic Acids Res. 16: 10881-90; Huang, et al, (1992) Computer Applications in the Biosciences 8: 155-65 and Pearson, et al, (1994) Meth. Mol. Biol. 24:307-31. An example of a good program to use for optimal global alignment of multiple sequences is PileUp (Feng and Doolittle, (1987) J. Mol. Evol, 25:351-60, which is similar to the method described by Higgins and Sharp, (1989) CABIOS 5: 151-53 (and is hereby incorporated by reference). The BLAST family of programs that can be used for database similarity searches includes: BLASTN for nucleotide query sequences against nucleotide database sequences; BLASTX for nucleotide query sequences against protein database sequences; BLASTP for protein query sequences against protein database sequences; TBLASTN for protein query sequences against nucleotide database sequences; and TBLASTX for nucleotide query sequences against nucleotide database sequences. See, Current Protocols in Molecular Biology, Chapter 19, Ausubel, et al, eds., Greene Publishing and Wiley -Interscience, New York (1995). GAP uses the algorithm of Needleman and Wunsch, (1970) J. Mol. Biol. 48:443-53, to find the alignment of two complete sequences that maximizes the number of matches and minimizes the number of gaps. GAP considers all possible alignments and gap positions and creates the alignment with the largest number of matched bases and the fewest gaps. It allows for the provision of a gap creation penalty and a gap extension penalty in units of matched bases. GAP makes a profit of gap creation penalty number of matches for each gap it inserts. If a gap extension penalty greater than zero is chosen, GAP must, in addition, make a profit for each gap inserted of the length of the gap times the gap extension penalty. Default gap creation penalty values and gap extension penalty values in Version 10 of the Wisconsin Genetics Software Package are 8 and 2, respectively. The gap creation and gap extension penalties can be expressed as an integer selected from the group of integers consisting of from 0 to 100. Thus, for example, the gap creation and gap extension penalties can be 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50 or more.

GAP presents one member of the family of best alignments. There may be many members of this family. GAP displays four figures of merit for alignments: Quality, Ratio, Identity and Similarity. The Quality is the metric maximized in order to align the sequences. Ratio is the quality divided by the number of bases in the shorter segment. Percent Identity is the percent of the symbols that actually match. Percent Similarity is the percent of the symbols that are similar. Symbols that are across from gaps are ignored. A similarity is scored when the scoring matrix value for a pair of symbols is greater than or equal to 0.50, the similarity threshold. The scoring matrix used in Version 10 of the Wisconsin Genetics Software Package is BLOSUM62 (see, Henikoff and Henikoff, (1989) Proc. Natl. Acad. Sci. USA 89: 10915).

Unless otherwise stated, sequence identity/similarity values provided herein refer to the value obtained using the BLAST 2.0 suite of programs using default parameters (Altschul, et al, (1997) Nucleic Acids Res. 25:3389-402).

As those of ordinary skill in the art will understand, BLAST searches assume that proteins can be modeled as random sequences. However, many real proteins comprise regions of nonrandom sequences, which may be

homopolymeric tracts, short-period repeats, or regions enriched in one or more amino acids. Such low-complexity regions may be aligned between unrelated proteins even though other regions of the protein are entirely dissimilar. A number of low-complexity filter programs can be employed to reduce such low- complexity alignments. For example, the SEG (Wooten and Federhen, (1993) Comput. Chem. 17: 149-63) and XNU (C.sub. l-ayerie and States, (1993) Comput. Chem. 17: 191-201) low-complexity filters can be employed alone or in combination.

The terms "substantial identity" indicates that an inhibitory nucleic acid, polypeptide or related nucleic acid comprises a sequence with between 55-100% sequence identity to a reference sequence, with at least 55% sequence identity, or at least 60%, or at least 70%, or at least 80%, or at least 90% or at least 95% sequence identity or any percentage of range between 55-100% sequence identity relative to the reference sequence over a specified comparison window. Optimal alignment may be ascertained or conducted using the homology alignment algorithm of Needleman and Wunsch, supra.

An indication that two polypeptide sequences are substantially identical is that both polypeptides have similar activities. For example, when a polypeptide is related to TycA can catalyze the formation of

aminophenylpropanoyl-CoA in a reaction that proceeds as follows.

Aminophenylpropanoate Aminophenylpropanoyl-CoA

In some embodiments, the polypeptide that is substantially identical to a TycA polypeptide with a SEQ ID NO: 1, 3, 5 or 6 sequence may not have exactly the same level of activity as the TycA with a SEQ ID NO: l, 3, 5 or 6. Instead, the substantially identical polypeptide may exhibit greater or lesser levels of activity than the TycA with SEQ ID NO: 1, 3, 5 or 6, as measured by assays described herein or available in the art. For example, the substantially identical polypeptide may have at least about 40%, or at least about 50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about 90%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 100%, or at least about 105%, or at least about 110%, or at least about 120%, or at least about 130%, or at least about 140%, or at least about 150%, or at least about 200% of the activity of the TycA with the SEQ ID NO: 1, 3, 5 or 6 sequence, when measured by similar assay procedures.

Alternatively, substantial identity is present when a related polypeptide is immunologically reactive with antibodies raised against the TycA polypeptide (e.g., a polypeptide with SEQ ID NO: 1, 3, 5, or 6 sequence). Thus, a polypeptide is substantially identical to a TycA polypeptide, for example, where the two polypeptides differ only by a conservative substitution. In addition, a polypeptide can be substantially identical to a TycA polypeptide when they differ by a non-conservative change if the epitope that the antibody recognizes is substantially identical. In some embodiments, polypeptides that are

"substantially similar" share sequences as noted above except that some residue positions, which are not identical, may differ by conservative amino acid changes.

The TycA polypeptides employed in the methods of the present invention may include the first 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, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98 and 99 N-terminal amino acid residues of a the SEQ ID NO: l, 3, 5 or 7 sequence, or of a sequence related to any of the SEQ ID NO: 1, 3, 5, or 7 sequences. In some embodiments, the related TycA polypeptides may include the first 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, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98 and 99 C- terminal amino acid residues of a the SEQ ID NO: 1, 3, 5, or 7 sequence, or of a sequence related to any of the SEQ ID NO: l, 3, 5, or 7 sequences.

Synthesis of Paclitaxel and Analogs and Derivatives thereof

The enzymes, methods and compounds generated herein can be used to make paclitaxel and it analogs and derivatives.

Taxoid compounds like paclitaxel are synthesized in certain Taxus plants through the 2-C-methyl-D-erythritol phosphate (MEP) pathway that generates of the isoprenes. This pathway provides an isoprenoid precursors isopentenyl

diphosphate (IPP or IDP) and dimethylallyl diphosphate (DMAPP or DMADP), which can be interconverted by the enzyme isopentenyl diphosphate isomerase

(IPPI) in reaction I, shown below.

Isopentenyl diphosphate (IPP) Dimethylallyl diphosphate

(DMAPP)

Isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) are

combined to make geranylgeranyl diphosphate (GGPP or GGDP) in reaction H by the enzyme geranylgeranyl diphosphate synthetase (GGPPS or GGDPS), as shown below.

Dimethylallyl diphosphate (DMAPP) Geranylgeranyl diphosphate (GGPP) The geranylgeranyl diphosphate can then be cyclized to generate taxa- 4(5),l l(12)-diene ("taxadiene") by the enzyme taxadiene synthase (TS) in reaction G, shown below.

Geranylgeranyl diphosphate (GGPP)

The next step in the biosynthesis of paclitaxel and analogs or derivatives thereof involves placement of a hydroxy group at the 5 position of the taxadiene structure, with a tautomeric shift of the double bond at positions 4-5. This hydroxylation reaction (F) can be catalyzed by taxadiene 5-a-hydroxylase (T5H). Reaction F is shown below.

Through additional hydroxylation, acylation and cyclization reactions (E) the taxa-4(5),l l(12)-diene-5a-ol is generally converted to a 2-debenzoyltaxane. These reactions (E) can be catalyzed by enzymes such as taxadiene 13- hydroxylase (T13H), taxadienol 5a-0-acetyl-transferase (TAT), taxadiene 10- hydroxylase (T10H).

A benzoyl group is then linked to the 2-debenzoyltaxane molecule at position 2 to generate 10-deacetyl baccatin III, in reaction D, as illustrated below. An enzyme such as taxane 2a-0-benzoyltransferase (TBT) can catalyze the reaction.

2-Debenzoyltaxane

10-Deacetyl Baccatin 111

An acetyl group is then added to the molecule at position 10 to generate Baccatin III in reaction C, illustrated below. The enzyme 10-deacetylbaccatin III-10-O- acetyltransferase (DBAT) can catalyze the reaction.

10-Deacetyl Baccatin III Baccatin III

It is at this point that the aminopropanoyl-CoA generated

following TycA reaction is employed.

I II

wherein:

X is hydrogen;

Y is hydrogen or OH; and

Ring is a unsubstituted or substituted (C4-C10) aryl, (C4- C9)heteroaryl, (C4-C10)cycloalkyl, or (C4-C9)heterocycloalkyl. The aminopropanoyl-CoA (II) is reacted with Baccatin III in reaction B to thereby make 3'-N-debenzoyltaxol or an analog thereof. The enzyme can be an acyltransferase, for example, a Taxus acyltransferase such as baccatin III O- phenylpropanoyltransferase (BAPT). Reaction B is illustrated below.

3'-N-Debenzoyltaxol or an analog

or derivative thereof

Paclitaxel or an analog or derivative thereof can then be generated from 3'-N-debenzoyltaxol (or an analog or derivative) thereof via reaction A, which adds a benzoyl moiety to the amino group of the aminopropanoyl moiety. The enzyme N -debenzoyl-2'-deoxypaclitaxel: N-benzoyltransferase ( DTBT) can catalyze reaction A, shown below.

3'-N-Debenzoyltaxol or an analog

or derivative thereof

NDTBT

Thus, paclitaxel and its analogs and derivatives can be made by a substantially enzymatic process. The various reactions and steps in a method of making paclitaxel or an analog or derivative thereof can be performed in a cell- free reaction mixture (e.g., in vitro), or in living cells.

For example, any of the enzymes, substrates, intermediates, products, analogs or derivatives thereof described herein can be immobilized or attached to a solid surface (e.g., a bead, a column matrix, a reaction wall and the like). Such immobilization or attachment can facilitate in vitro reaction to generate paclitaxel (or an analog or derivative thereof), as well as purification of the paclitaxel (or analog or derivative thereof) product. For example, substrates and/or intermediates can be attached or immobilized on a solid surface, so that reactants, side products and enzymes can be removed after each step in the synthetic process. Similarly, when the paclitaxel or an analog or derivative thereof is attached or immobilized to a solid surface, the solid surface can be washed to remove reactants, enzymes, side products and the like to facilitate purification of the desired product. Upon cleavage from the solid surface, a purified paclitaxel or an analog or derivative thereof can be obtained.

When any of the reactions or steps of the process is performed in living cells, such living cells can be cultured cells. Such cultured cells can be grown in a cell fermentation apparatus, for example, to facilitate plant cell fermentation production of paclitaxel or an analog or derivative thereof. Alternatively, such living cells can also be plant cells that are present in a plant, for example, in a plant of a Taxus (Yew) species. The living cells can also be transgenic cells, for example, cells recombinantly engineered to express any of the enzymes described herein.

The following non-limiting Examples illustrate aspects of the invention. Some experimental detail relating to the development of the invention is also published as Muchiri & Walker, Taxol Biosynthesis: Tyrocidine Synthetase A Catalyzes the Production of Phenylisoserinyl Co A and Other Amino

Phenylpropanoyl Thioesters, CHEMISTRY & BIOLOGY (June 22, 2012; published online June 21, 2012), the contents of which are specifically incorporated herein in their entirety.

EXAMPLE 1: Materials and Methods

This Example illustrates some of the materials and methods that have been used in the development of the invention.

Chemicals. Bovine serum albumin was obtained from Thermo Scientific (Rockford, IL), (5)-a-phenylalanine, N-Boc-(5)-a-phenylalanine, and N- acetylcysteamine were purchased from Sigma Aldrich, N-Boc-(R/5)- - phenylalanine was obtained from Alfa Aesar, (Ward Hill, MA), (R)- - phenylalanine and N-Boc-(2R,35)-phenylisoserine were obtained from PepTech Corp. (Burlington, MA), (2R,35)-phenylisoserine was purchased from Bachem (Torrance, CA) and CoA was purchased from American Radiolabeled Chemicals Inc. (St. Louis, MO). All other reagents were obtained from Sigma-Aldrich and were used without further purification, unless noted otherwise.

Synthesis of [N-Boc-(S-((S)-a-Phenylalanyl)-N-acetyl) Jcysteamine (referred to as (N-Boc)-(S)-a-Phenylalanyl-SNAC) and [N-Boc-(S-(R/S)-fi- Phenylalanyl)-N-acetyl)]cysteamine (referred to as (N-Boc)-(R/S)-fi- Phenylalanyl-SNA C)

(jV-Boc)-(5 -a-Phenylalanyl-SNAC (jV-Boc)-(ii/5 - -Phenylalanyl-SNAC

[S (S)-a-Phenylalanyl)-N-acetyl]cysteamine and 5"-((R/S)- Phenylalanyl)-N-(acetyl)]cysteamine (i.e., (S)- - and (R/5)- -phenylalanyl- SNAC) were synthesized using a modification of the procedure reported by (Ehmann, et al. (Chem. Biol. 7, 765-772 (2000)). Generally, to N-Boc-(5)-a- or -(R/5)- -phenylalanine (530 mg, 2 mmol) dissolved in tetrahydrofuran (15 - 18 mL) was added N,N'-dicyclohexylcarbodiimide (372 mg, 2 mmol), 1- hydroxybenzotriazole monohydrate (255 mg, 2 mmol), and N,N- diisopropylethylamine (258, 8 mmol) at 24 °C, and the solution was stirred. After 45 min, N-acetylcysteamine (NAC) (238 mg, 2 mmol) was added to the reaction, and the solution was stirred for ~ 12 h. The contents of the reaction mixture were gravity filtered (42.5 mm filter paper, Whatman, Stockton, NJ), and the filtrate was concentrated under vacuum. The resultant residue was then dissolved in ethyl acetate (8 mL), and extracted with an equal volume of 10% aqueous aHC0 ₃ . The aqueous layer was separated, and the organic layer was extracted twice more with 10% aqueous NaHC(¾. The organic fraction was dried (Na ₂ S0 ₄ ), filtered, and the solvent was removed under vacuum. The resultant crude product was purified by silica gel flash chromatography (3 - 5% gradient of methanol in chloroform). The fractions containing the product, as judged by the thin layer chromatography (R _f = 0.15 and 0.12 for N-Boc-a- phenylalanyl-SNAC and N-Boc-(R/5)- -phenylalanyl-SNAC, respectively) were combined separately and concentrated to afford the following products:

N-Boc-a-phenylalanyl-SNAC (552 mg, 75% isolated yield). *H NMR (500 MHz, DMSO- e) δ: 1.32 (s, 9H, methyl-H of Boc), 1.80 (s, 3H, H-2'"), 2.79 (dd, J = 13.7, 10.0 Hz, 1H, H _b -3), 2.87 (t, J = 6.0 Hz, 2H, H _a -1", H _b -1"), 3.05 (dd, J = 13.9, 5.0 Hz, 1H, H _a -3), 3.15 (q, J = 6.0, 2H, H _a -2", H _b -2"), 4.23 (dd, J = 7.2, 5.0 Hz, 1H, H-2), 7.20-7.27 (m, 5H, H-2', H-3', H-4'), 7.67 (d, J = 8.30 Hz, 1H, OC(O)NH); 8.04 (t, J = 5.0 Hz, 1H, C(O)NH). ¹³ C NMR (125 MHz, DMSC δ: 202.33 (C-1), 169.91 (C-1'"), 155.97 (C=0 of Boc), 138.20 (C-1'), 129.78-127.10 (C-2', C-3', C^l'), 79.34 (tert-C of Boc), 62.97 (C-2), 42.85 (C-3), 38.79 (C-2"), 28.83 (methyl-C of Boc), 24.20 (C-1"), 23.22 (C- 2"').

N-Boc-(R/5)- -phenylalanyl-SNAC (487 mg, 66% isolated yield). H NMR (500 MHz, DMSC s) δ: 1.74 (s, 9H, methyl-H of Boc), 2.07 (s, 3H, H _a - 2"'), 2.84 (ddd, J = 12.0, 6.0, 6.0 Hz, 2H, H _a -1", H _b -1"), 3.08 (q, J = 6.0 Hz, 2H, H _a -2", H _b -2"), 3.29 (dd, J = 15.0, 9.0 Hz, 1H, H _a -2), 3.40 (dd, J = 15.0, 5.5 Hz, 2H, H _b -2), 4.64 (m, 1H, H-3), 7.37-7.51 (m, 5H, H-2'a, H-3'a, H-4'a), 8.02 (t, J = 5.5 Hz, 1H, C(O)NH); 8.63 (bs, 1H, OC(O)NH). ¹³ C NMR (125 MHz, DMSC δ: 196.49 (C-1) 169.89 (C-1'"), 155.35 (C=0 of Boc), 141.0 (C-1'), 128.99-127.04 (C-2', C-3', C-4'), 78.67 (tert-C of Boc), 51.93 (C-3), 50.72 (C- 2), 38.86 (C-2"), 28.89 (methyl-C of Boc), 28.68 (C-1"), 23.22 (C-2'").

Synthesis of [(S-((S)-a-Phenylalanyl)-N-acetyl)] cysteamine and f(S- ((S)-(R/S)-fi-Phenylalanyl)-N-acetyl) ] cysteamine.

(S)-a-Phenylalanyl-SNAC (ii/S)- -Phenylalanyl-SNAC ^» HCl salt

To remove the Boc groups, N-Boc-(5)-a-phenylalanyl-SNAC and N-Boc- (R/5)- -phenylalanyl-SNAC were separately dissolved in dichloromethane (4 mL), and trifluoroacetic acid was added dropwise over 4 h at 0 °C. The reaction progress was monitored by normal-phase thin layer chromatography (5% methanol in chloroform). Excess trifluoroacetic acid was removed prior to isolating the (5)-a-phenylalanyl-SNAC by concentrating the reaction volume to 2 mL under vacuum, diluting 2-fold in dichloromethane, and then concentrating to 1 - 2 mL. This dilution/concentration cycle was repeated three times, after which, the solvent was removed completely. To the residue containing (S)-a- phenylalanyl-SNAC was added ethyl acetate and dilute aqueous NaOH at 0 °C to partition the (5)-a-phenylalanyl-SNAC and aqueous soluble contaminants, respectively. The organic layer was decanted and then removed under vacuum. Water (2 mL) was added to the remaining residue to which 1 M HC1 (2 mL) was added at 0 °C. Ethyl acetate was added (2 x 2 mL) to extract any remaining t- butanol and SNAC, and the organic layer was decanted. The water fraction was lyophilized to yield (5)-a-phenylalanyl-SNAC as the hydrochloride salt isolated at ~31 % yield (90 mg,) based on the N-Boc-protected starting material. 1H NMR (500 MHz, DMSC s) δ: 1.78 (s, 3H, H-2"'), 2.69 (dd, J= 13.6, 10.0 Hz, 1H, H _b -3), 2.80 (t, J = 6.0 Hz, 2H, H _a -1", H _b -1"), 2.96 (dd, J = 13.6, 5.0 Hz, 1H, H _a -3), 3.12 (q, J = 6.0 Hz, 2H, H _a -2", H _b -2"), 3.62 (dd, J = 8.7, 5.00 Hz, 1H, H- 2), 7.17-7.29 (m, 5H, H-2', H-3', H^l'), 8.02 (t, J = 5.0 Hz, 1H, C(O)NH). ¹³ C NMR (125 MHz, DMSO- ₆ ) δ: 204.1 (C-1), 168.2 (C-l ^m ), 136.8 (C-1'), 128.3- 125.30 (C-2', C-3', C-4'), 61.74 (C-2), 39.51 (C-3), 37.22 (C-2"), 26.64 (C- 1"), 21.53 (C-2'"). The exact mass was determined in the positive ion mode on a Quadrupole Time-of-Flight Tandem Mass Spectrometer: observed mlz =

267.1164; calculated mlz = 267.1167 for C1 ₃ H19N2O2S.

After deprotection of (N-Boc)-(R/5)- -phenylalanyl-SNAC, excess trifluoroacetic acid was removed prior to isolating the product, as described above, except the residue was dissolved in 1 M HCl (2 mL, at 0 °C) to exchange the trifluoroacetate salt for the hydrochloride salt of the product. The sample was lyophilized to dryness, resulting in the hydrochloride salt of (R/S)-fi- phenylalanyl-SNAC (48 mg, -88.1% yield). ^ MR (500 MHz, DMSC s) δ: 1.74 (s, 3H, H-2'"), 2.84 (ddd, J= 12.0, 6.0, 6.0 Hz, 2H, H _a -1", H _b -1"), 3.08 (q, J= 6.0 Hz, 2H, H _a -2", H _b -2"), 3.31 (dd, J= 15.0, 9.0 Hz, 1H, H _a -2), 3.45 (dd, J = 15.0, 5.5 Hz, 1H, H _b -2), 4.63 (m, 1H, H-3), 7.35-7.60 (m, 5H, 3H, H-2', H- 3', H^l'), 8.06 (t, J= 5.5 Hz, 1H, H-C(O)NH), 8.73 (bs, 1H, H ₃ N ⁺ ). ¹³ C NMR (125 MHz, DMSC δ: 204.1 (C-1), 168.2 (C-1'"), 136.8 (C-1'), 128.3- 125.30 (C-2', C-3', C-4'), 51.64 (C-3), 48.07 (C-2), 38.57 (C-2"), 28.92 (C-1"), 23.18 (C-2'"). The exact mass was determined in the positive ion mode on a Quadrupole Time-of-Flight Tandem Mass Spectrometer: observed mlz = 267.1173; calculated w/z = 267.1167 for C1 ₃ H19 2O2S. Synthesis of [ (S-((2R,3S)-Phenylisoserinyl-N-acetyl)cysteamine.

(2R,3S)-Phenylisoserinyl-SNAC

N-Boc-(25',3R)-Phenylisoserinyl SNAC was synthesized according to the procedure described for the a- and β-phenylalanyl SNAC thioesters, with slight modifications. Briefly, to N-Boc-(25', 3R)-phenylisoserine (100 mg, 0.36 mmol) dissolved in tetrahydrofuran (~6 mL) were added Ν,Ν'- dicyclohexylcarbodiimide (74.3 mg, 0.36 mmol), 1-hydroxybenzotriazole monohydrate (48.6 mg, 0.36 mmol), and N,N-diisopropylethylamine (23.3 mg, 0.72 mmol), and the solution was stirred at 24 °C. After 45 min, NAC (85.6 mg, 0.72 mmol) was added to the reaction, and the solution was stirred for ~ 12 h. The reaction work up and purification were done as described above for the a- and β-amino acid analogs, resulting in residue (~40 mg) containing crude N- Boc-(25',3R)-phenylisoserinyl, which was deprotected without further purification. To the crude mixture containing N-Boc-(25',3R)-phenylisoserinyl dissolved in dichloromethane (4 mL) was added (dropwise) trifluoroacetic acid over 3 h at 0 °C. The reaction progress was monitored by normal-phase thin layer chromatography (5% methanol in chloroform). The work up was similar to the procedure described for (R/5)- -phenylalanyl-SNAC resulting in the hydrochloride salt of (2S, 3R)-phenylisoserinyl SNAC (20 mg, -24% isolated yield based on N-Boc-^S^RHAenylisoserine). H NMR (500 MHz, DMSO- ck) δ: 1.79 (s, 3H, H-2"'), 2.81 (m, 2H, H _a -1", H _b -1"), 3.15 (m, 2H, H _a -2", H _b - 2"), 4.39 (d, J= 5.0 Hz, 1H, H-2), 4.45 (m, 1H, H-3), 7.40-7.47 (m, 5H, H-2', H-3', H-4'), 8.09 (t, J= 5.6 Hz, 1H, C(O)NH), 8.52 (brd, J= 5.0 Hz 1H, H ₃ N ⁺ ). ¹³ C MR (125 MHz, DMSO- ₆ ) δ: 202.06 (C-l), 170.14 (C-l'"), 135.25 (C- 1'), 129.51-128.77 (C-2', C-3', C^l'), 78.24 (C-3), 57.09 (C-2), 38.38 (C-2"), 28.33 (C-l"), 23.24 (C-2'"). The exact mass was determined in the positive ion mode on a Quadrupole Time-of-Flight Tandem Mass Spectrometer: observed mlz = 283.1108; calculated mlz = 283.1116 for C1 ₃ H19 2O ₃ S.

Expression of Wild-type TycA cDNA. A cDNA clone of wild-type tyrocidine synthetase A (iycA) from Brevibacillus brevis was obtained as a gift from Florian Hollfelder (University of Cambridge, UK). Cloned tycA cDNA was inserted into a pSUl 8 vector, and the plasmid was designated pSUl 8-PheATE- His, encoding expression for a C-terminal His6-epitope. The plasmid was used to transform Escherichia coli BL21 (DE3) grown in 2xYT medium (100 mL), containing Bacto Tryptone (1.6 g), Bacto Yeast Extract (1.0 g), NaCl (0.5 g), and chloramphenicol (20 mg'mL ¹ ) at 37 °C for 12 h. A 10-mL aliquot of the seed culture was used to inoculate 2xYT medium (5x 1 L). The bacteria were grown at 37 °C to OD ₆ oo -0.6, at which time isopropyl-D-thiogalactopyranoside was added to a final concentration of 0.5 mM, and the culture was grown for 4 h at 30 °C. The cells were pelleted by centrifugation (30 min, 4000g) at 4 °C, resuspended in Binding Buffer (20 mM Tris-HCl buffer containing 0.5 M NaCl and 5 mM imidazole at pH 7.8), lysed by sonication (Misonix XL 2020 sonicator, Misonix, Inc. Farmingdale, NY), and then centrifuged at 15,000g for 0.5 h. The supernatant was decanted and centrifuged at 149,000g for 2 h to remove cell wall debris and light membranes. Construction and Expression of the S563A TycA mutant. A S563A amino acid mutation was incorporated into the wild-type TycA clone by site-directed mutagenesis. The oligonucleotide primer pair used to incorporate the point mutation (underlined) were as follows: Forward primer S563A-For: 5 -TTA CTC GCT CGG CGG AGA TGC GAT CCA AGC GAT CCA GGT CG-3' (SEQ ID NO:8); Reverse primer S563A-Rev: 5'-CGA CCT GGA TCG CTT GGA TCG CAT CTC CGC CGA GCG AGT AA-3' (SEQ ID NO: 9). The correct synthesis of the mutant cDNA was verified by DNA sequencing. The resultant plasmid encoding a C-terminal His-tag (designated pSU18-S563A- PheATE-His) was used to transform E. coli BL21(DE3) cells. A 10-mL culture οΐΕ. coli transformed with the PSU18 vector was grown in 2xYT medium at 37 °C with chloramphenicol (20 mg'mL ^-1 ) selection for 12 h. The 10-mL inoculum was transferred to a new batch of 2xYT medium (1 L), as described previously for the expression of the wild-type TycA clone. The bacteria were grown at large-scale at 37 °C to OD ₆ oo -0.6, and the cDNA expression was induced by isopropyl-D-thiogalactopyranoside, and the culture was grown for 4 h at 30 °C. The cells were pelleted by centrifugation (30 min, 4000g) at 4 °C, resuspended in Binding Buffer, lysed by sonication, and the corresponding soluble protein fraction was clarified by centrifugation as described earlier to remove cell-wall debris and light membranes.

Purification and characterization of TycA and the TycA-S563A Mutant. Crude soluble enzyme was separately isolated from bacteria expressing the wild-type tycA or tycA-S563A. Each fraction contained ~15 mg total protein as estimated by the Bradford protein assay (Bradford, M. M. Anal. Biochem. 1976, 72, 248-254). These fractions were independently loaded onto a nickel- nitrilotriacetic acid affinity column (Qiagen,

Valencia, CA) and eluted according to the protocol described by the

manufacturer. The column was washed with increasing concentration of imidazole (20 - 250 mM) in Binding Buffer. SDS-PAGE slabs were loaded with aliquots from each fraction that eluted off the nickel-affinity column and stained with Coomassie Blue. Fractions that contained >95% pure protein corresponding to a molecular weight consistent with that of TycA and TycA-S563A at 123 kDa were combined. The enzymes were eluted in ~50 mM imidazole (100 mL) and were separately loaded into a Centriprep size-selective (100,000 MWCO) centrifugal filtration unit (Millipore, Billerica, MA). The protein solutions were concentrated to 1 mL, and the buffer was exchanged with the Assay Buffer (50 mM HEPES containing 100 mM NaCl and 1 mM EDTA at pH 8.0) over several dilution/concentration cycles. The final purity of the enzyme was estimated by SDS-PAGE with Coomassie Blue staining. The final protein concentration was determined by Beer's Law and measuring the absorbance of the protein solution at ^280 on a NanoDrop ND 1000 Spectrophotometer (Thermo Scientific,

Wilmington, DE). The extinction coefficient, D ₂₈₀ , employed was 142685 Μ ¹ cm (Villiers & Hollfelder, Chembiochem, 10: 671-682 (2009)) and the molecular weight of TycA and TycA-S563A were 122675.9 g · moL ¹ and 122,675.9 g · moL ¹ , respectively, consistent with the theoretical value of 123 kDa. The purified protein was stored at 5 mg/mL at -80 °C. The protein sequence of the isolated TycA and TycA-S563A recombinant proteins was confirmed by electrospray ionization tandem mass spectrometry analysis.

Assessing TycA and TycA-S563A as Ligases for Catalysis of a- and β- Amino Phenylpropanoyl-Coenzyme A Thioesters. Substrates (S -a- phenylalanine, (R)- -phenylalanine, and (2R,35)-phenylisoserine (each at 1 mM) were separately incubated at 31 °C in single stopped-time (1 h) reactions containing 100 mM HEPES (pH 8.0), ATP (1 mM), MgCl ₂ (3 mM), CoA (1 mM), and TycA or TycA-S563A (100 μg). Various control reactions were carried out in parallel under the same conditions used for assays containing enzyme, where TycA, TycA-S563A, ATP, or CoA was omitted from the assay. The reactions were quenched by acidification to a pH of about 2 (using 10% formic acid in distilled water) and lyophilized to dryness. The resultant samples were separately dissolved in aqueous 0.01 M HCl (100 μί) and analyzed using a Quattro-Premier Electrospray Tandem Mass Spectrometer coupled with Acquity® UPLC system (LC-QP/ESI-MS/MS) fitted with a CI 8 Ascentis Express column (2.5 x 50 mm, 2.7 μιη) at 30 °C. An aliquot (10 μί) of each sample was loaded onto the column and the analytes were eluted with a solvent gradient of 0 - 15% of acetonitrile (Solvent A) in 0.1% formic acid in distilled water (Solvent B) at a flow rate of 0.2 niL/min. The effluent from the column was directed to the mass spectrometer set to negative ion mode with a scan range oim/z 200 - 1000 atomic mass units. Authentic phenylalanyl CoA was used as a model to identify the diagnostic ion transition ([M - H] → mlz 408) of the three acyl CoA products.

Kinetic Analysis of the CoA Ligase Reaction Catalyzed by TycA and TycA-S563A. After identifying productive substrates for TycA and TycA-S563A in the screen for CoA ligase function, substrates (5)-a-phenylalanine, (^)-β- phenylalanine, and (2R,35)-phenylisoserine (each at 1 mM) were separately incubated (at 31 °C) in 100 μΐ. reactions containing 100 mM HEPES (pH 8.0), ATP (1 mM), MgCl ₂ (3 mM), CoA (1 mM), and TycA or TycA-S563A (50 μg) to establish steady-state conditions with respect to protein concentration and time. Under steady-state conditions, (5)-a-phenylalanine, (R)- -phenylalanine, and (2R,35)-phenylisoserine at 5, 10, 20, 40, 80, 160, 250, 500, 1000 and 2000 μΜ were separately incubated with TycA or TycA-S563A (20 μg) for 30 min. At the end of each reaction, and prior to mass spectrometry analysis, acetyl CoA (1 μΜ) was added as the internal standard to each sample to correct for variations of the analyte. The products of the enzyme-catalyzed reaction were quantified by a liquid chromatography multiple reaction monitoring (LC-ESI-MRM) mass spectrometry technique (Anderson & Hunter, Mol. Cell. Proteomics 5: 573-588 (2006)) on the Quattro-Premier Electro-Spray Mass Spectrometer coupled with Acquity® UPLC system fitted with a CI 8 Ascentis Express column (2.5 x 50 mm, 2.7 μιη) at 30 °C. An aliquot (5 of each sample was loaded onto the column and the analytes were eluted with a solvent gradient of acetonitrile (Solvent A) in 0.05 % triethylamine in distilled water (Solvent B). Elution was held at 2.5 % Solvent A for 3.17 min, increased to 100 % Solvent A over 5 sec with a 2-min hold, and then returned to 2.5 % Solvent A over 5 sec with a 50- sec hold. The flow rate employed was 0.4 mL/min. The effluent from the chromatography column was directed to the mass spectrometer where the first quadrupole mass analyzer (in negative ion mode) was set to select for the molecular ion of a biosynthesized acyl CoA product. The selected ion was then directed to a collision gas chamber where the collision energy was optimized to maximize the abundance of a single signature fragment ion (m/z 408, characteristic of acyl CoA thioesters) resolved in the second quadrupole mass analyzer by the MRM method. The peak area under the curve of fragment ion m/z 408 for each biosynthetic phenylpropionyl CoA thioester was converted to concentration by comparing the peak area of the same ion produced by authentic CoA (at 0.05, 0.1, 0.2, 0.4, 0.8, 1.6, 3.2, 6.4, 12.5, 25, 50, 100 μΜ) using linear regression analysis. The initial velocity (v ₀ ) of (5)-a-phenylalanyl-CoA, (R)- - phenylalanyl-CoA and (2R,35)-phenylisoserinyl-CoA made in separate assays was plotted against substrate concentration and fit by non-linear regression to the Michaelis-Menten equation (R ² was typically between 0.90 and 0.99) to calculate the Michaelis parameters (KM and k _cat ).

The K _M values of TycA and TycA-S563A for CoA were assessed by incubating each enzyme separately with (5)-a-phenylalanine (1 mM), MgC^ (3 mM), ATP (1 mM), and CoA at 0.05, 0.1, 0.2, 0.4, 0.8, 1.6, 3.2, 6.4, 12.8 and 25.6 mM at 31 °C for 20 min. At the end of each reaction and prior to mass spectrometry analysis, acetyl CoA (1 μΜ) was added as the internal standard to each sample to correct for variations of the analyte. The products of the enzyme- catalyzed reaction were quantified by LC-ESI-MRM, and the monitored fragment ion (m/z 408) derived from the CoA moiety of the thioester analytes in the effluent was quantified identically to the procedure described earlier herein. The initial velocity (v ₀ ) production of (5)-a-phenylalanyl CoA made in separate assays was plotted against substrate concentration and fit by non-linear regression to the Michaelis-Menten equation (R ² was typically between 0.92 and 0.98) to calculate the Michaelis constant (KM).

N-Acetylcysteamine, Phenylalanines, and Phenylisoserine Substrates used to Screen TycA and TycA-S563A for Activity. Similar experiments were performed using methods described above for the CoA ligase screen, except N- acetylcysteamine (5 mM, 'NAC') was used in place of CoA with the substrates (5)-a-phenylalanine, (R)- -phenylalanine and (2R,35)-phenylisoserine in different 0.1 mL assays. In general, the enzyme assays for this study contained 100 mM HEPES (pH 8.0), phenylpropanoate (1 mM), ATP (1 mM), MgCl ₂ (3 niM), N-acetylcysteamine (5 niM), and TycA or TycA-S563A (100 μg), and were incubated at 31 °C for 1 h. Various control reactions were carried out in parallel under the same conditions used for the enzyme assay, where either TycA, TycA-S563A, ATP, or N-acetylcysteamine was omitted from the assays. The reactions were quenched by acidification to a pH of about 2 (with 6 M HCl) and lyophilized to dryness. The resultant residues were separately dissolved in aqueous 0.01 M HCl (100 μΐ,) and analyzed using a Quadrupole Time-of-Flight Tandem Mass Spectrometer coupled with 2795 HPLC system fitted with a reverse-phase Halo CI 8 column (5 cm x 2.1 mm) (reverse-phase LC-QToF- MS/MS). The mass analyzer was set to positive ion mode, with a scan range of mlz 0 - 500 atomic mass units. An aliquot (10 μί) of each sample was loaded onto the column (at 30 °C) and the analytes were eluted with a solvent gradient of 0 - 15% of acetonitrile (Solvent A) in 0.1% formic acid in distilled water (Solvent B) at a flow rate of 0.2 mL/min.

Kinetic Analysis of the N-acetylcysteamine Ligase Reaction Catalyzed by TycA or TycA-S563A. Substrates (5)-a-phenylalanine, (R)- -phenylalanine, and (2R,35)-phenylisoserine (each at 1 mM) were separately incubated with TycA or TycA-S563A (20 μg) in the presence of N-acetylcysteamine (NAC; 1 mM), ATP (1 mM), and Mg ²⁺ (3 mM) to establish steady-state conditions with respect to protein concentration and time at 31 °C. Under steady-state conditions, either (5)-phenylalanine, (R)- -phenylalanine, or (2R,35)- phenylisoserine at 5, 10, 20, 40, 80, 160, 250, 500, 1000 and 2000 μΜ was separately incubated with TycA or TycA-S563A (20 μg), ATP (1 mM), Mg ²⁺ (3 mM), and N-acetylcysteamine (1 mM, 'NAC') in duplicate, single stopped-time (20 min) 100 μL· assays. The reactions were quenched by acidification to a pH of about 2 (10% formic acid in distilled water). (N-Boc)-a-phenylalanyl-SNAC (1 μΜ) was added as an internal standard when (5)-a-phenylalanine or (2,3)- phenylisoserine was used as the substrate; alternatively, (N-Boc)-P- phenylalanyl-SNAC (1 μΜ) was added as an internal standard when (Κ)-β- phenylalanine was used as the substrate (the synthesis is described below). The samples were analyzed on a Quattro-Premier Electro-Spray Mass Spectrometer coupled with Acquity® UPLC system fitted with a CI 8 Ascentis Express column (2.5 x 50 mm, 2.7 μιη) at 30 °C. An aliquot (5 μί) of each sample was loaded onto the column and the analytes were eluted with a solvent gradient of (Solvent A) in 0.05% triethylamine in distilled water (Solvent B) (held at 2.5 % Solvent A for 3.17 min, increased to 100 % A over 5 sec with a 2-min hold, and then returned to 2.5 % Solvent A over 5 sec with a 50-sec hold) at a flow rate of 0.4 mL/min. In brief, the effluent from the chromatography column was directed to the Quattro Premier ESI mass spectrometer, in MRM scan mode, to quantify the biosynthetic acyl SNAC products. The transition ions derived from the corresponding molecular ions were mlz 120.06, 131.10 and 105.95 for (<S)-a- phenylalanyl-SNAC, (R)- -phenylalanyl-SNAC and (2R, 35)- phenylisoserinyl-SNAC, respectively. A standard curve was used to convert the peak area under the curve of the monitored fragment ion to concentration for each biosynthetic phenylpropionyl SNAC.

Authentic (S)- - phenylalanyl, (R/S^-phenylalanyl- and (2R,3S)- phenylisoserinyl-SNAC were used to construct the standard curves by correlating the peak area under the curve of the monitored ion to concentration of the standard (at 0.16, 0.32, 0.64, 1.3, 2.5, 5, 10, 20, 40, 80, 160 and 320 μΜ) using linear regression analysis. The initial velocity (v ₀ ) production of (S)-a- phenylalanyl, (R/5)- -phenylalanyl- and (2R,35)-phenylisoserinyl-SNAC was plotted against substrate concentration and fit by non-linear regression to the Michaelis-Menten equation (R ² was typically 0.99) to calculate the Michaelis parameters (KM and k _cat ).

The KM values of TycA and TycA-S563A for N-acetylcysteamine (NAC) was assessed by incubating each enzyme separately with (5)-a-phenylalanine (1 mM), MgCl ₂ (3 mM), ATP (1 mM), and N-acetylcysteamine at 5, 10, 20, 40, 80, 160, 250, 500, 1000 and 2000 μΜ at 31 °C for 20 min. The reactions were quenched by acidification to a pH of about 2 (10% formic acid in distilled water), and an internal standard, (N-Boc)-a-phenylalanyl-SNAC (1 μΜ), was added to each sample to correct for variations of the analyte. The [S-(acy\)-N- (acetyl)] cysteamine (SNAC) thioester products of the enzyme-catalyzed reaction were quantified by a liquid chromatography multiple reaction monitoring (MRM) mass spectrometry technique, and the monitored fragment ion (mlz 120) derived from the SNAC moiety of thioester analyte in the effluent was quantified identically to the procedure described earlier. The initial velocity (v ₀ ) production of (R)-a-phenylalanyl-SNAC made in separate assays was plotted against substrate concentration and fit by non-linear regression to the Michaelis-Menten equation (R ² was typically between 0.97 and 0.99) to calculate the Michaelis constant (KM) and k _cat .

Kinetics of the AMP Ligase Reaction. Each (5)-a-phenylalanine, (Κ)-β- phenylalanine, and (2R,35)-phenylisoserine substrate (at 1 niM) was separately incubated (31 °C) in ΙΟΟ-μί reactions containing 100 niM HEPES (pH 8.0), ATP (1 niM), MgCl ₂ (3 niM) and TycA or TycA-S563A (20 μg in 0.1 -mL assays) to establish steady-state conditions relative to protein concentration and time. Under steady-state conditions, each (5)-a-phenylalanine, (Κ)-β- phenylalanine, and (2R,35)-phenylisoserine substrate, at ten concentration intervals from 5 to 1000 μΜ (in duplicate), was separately incubated with TycA or TycA-S563A for 1 min at 31 °C. The reactions were acid-quenched (pH 3 with 10% formic acid), and the biosynthetic products were quantified by LC- ESI-MRM mass spectrometry (Anderson and Hunter, 2006) on the LC-QP/ESI- MS/MS fitted with a CI 8 Ascentis Express column (2.5 x 50 mm, 2.7 μιη) at 30 °C. An aliquot (5 of each sample was loaded onto the column and the analytes were eluted with the CoA-Elution Gradient (see procedures described above). The effluent from the chromatography column was directed to the mass spectrometer where the first quadrupole mass analyzer (in negative ion mode) was set to select for the molecular ion of a biosynthesized (5)-a-phenylalanine- AMP, (R)- -phenylalanine-AMP, and (2R,35)-phenylisoserine-AMP. The selected ion was directed to the next quadrupole where the collision energy was optimized to maximize the abundance of a single signature fragment ion (m/z 134, the adenine fragment of the adenosine moiety) in negative ion mode. This ion was resolved in the second quadrupole mass analyzer by MRM of the adenine transition ion fragment (m/z 134). The peak area of ion m/z 134 for each biosynthetic (5)-a-phenylalanine-AMP, (R)- -phenylalanine-AMP, and

(2R,35)-phenylisoserine-AMP was converted to concentration units using linear regression of a dilution series of authentic adenosine (at six intervals from 0.01 to 20 μΜ) plotted against the corresponding ion abundance (m/z 134, in negative ion mode). The initial velocity (v ₀ ) of (5)-a-phenylalanine-AMP, (Κ)-β- phenylalanine-AMP, and (2R,35)-phenylisoserine-AMP production was used to calculate KM and k _cat according to the Michaelis-Menten equation (R ² was typically between 0.95 and 0.99).

EXAMPLE 2: Enzymatic Synthesis of Paclitaxel Intermediate

This Example illustrates that tyrocidine synthetase A (TycA) is an adenylating domain of a nonribosomal peptide synthetase (NRPS) tyrocidine synthetase that can produce amino phenylalanyl CoA and amino

phenylisoserinyl CoA thioesters useful for making the antineoplastic drug paclitaxel and its analogs.

Expression and Purification of the ATE Tridomain of Wild-type and Mutant tycA. To test whether the TycA tridomain module is a potential CoA ligase, the wild-type tycA cDNA encoding the A-, T-, and E-domains was subcloned into a pSU18 vector and heterologously expressed as a His6-fusion in Escherichia coli BL21(DE3). E. coli BL21 encodes the 4'-Phosphopantetheine transferase enzyme within its genome that can post-translationally couple 4'- phosphopantetheine (Ppant) to certain serine residues of various polypeptides (Jeong, et al, J. Mol. Biol. 394, 644-652 (2009)). Therefore, Ser563 of TycA was changed to Ala563 (TycA-S563A) to prevent Ppant coupling at Ser563 of the T-domain and thus stall the reaction progress of TycA-S563A at the acyl- adenylate intermediate. The T-domain mutant TycA-S563A was also subcloned into a pSU18 vector and heterologously expressed as a His6-fusion in

Escherichia coli BL21(DE3). The isolated soluble enzymes were Ni-affinity purified to about 95% purity based upon SDS-PAGE analysis with Coomassie Blue staining, and the apparent molecular mass (123 kDa) was consistent with the theoretical value. Wild-type TycA and the S563A mutant (TycAS563A) polypeptides were separately expressed, isolated, and purified from a 5 liter bacterial culture, resulting in about 15 mg of each protein. These wild- type TycA and S563A mutant (TycAS563A) polypeptides were used for activity assays. Assessment ofTycA and TycA-S563A Thiol Ligase Activities. (S)- - Phenylalanine, (R)-P-phenylalanine, and (2R,35)-phenylisoserine were separately added to reaction mixtures containing overexpressed TycA or TycA- S563A along with ATP, MgC^, and CoA or NAC. The product mixtures were screened directly by LC-ESI-mass spectrometry in scan mode. The ion profiles in ESI-MS in negative ion mode (without collision induced ionization) contained a diagnostic, negative molecular ion [M - H] consistent with the value calculated for each putative a-phenylalanyl-CoA (m/z 913, eluting at 2.67 min), β-phenylalanyl-CoA (m/z 913, eluting at 2.47 min), as well as (2R,3S)- phenylisoserinyl-CoA (m/z 929, eluting at 2.26 min) (see FIGs. 1-3).

To confirm the structures of the phenylpropanoid CoA thioesters, the molecular ions were further evaluated by MS/MS analysis (collision-induced dissociation of the [M - H] ion) in negative ion mode. Collision-induced dissociation of the molecular ions confirmed the identity of each CoA thioester. Control assays lacking (5)-a-Phenylalanine, (R)- -phenylalanine, (2R,35)- phenylisoserine, ATP, or CoA from the appropriate enzyme assay mixture did not yield a detectable [M - H] ion that matched any of the corresponding (S)-a- Phenylalanine, (R)- -phenylalanine, and (2R,35)-phenylisoserine CoAs (FIGs. 4-5). The sample incubated with (5)-a-phenylalanine had an m/z 913 ([M - H] ) ion that was consistent with (5)-a-phenylalanyl CoA and fragment ions at 895 (m/z 913 ion - H ₂ 0), 833 (m/z 913 ion - HP0 ₃ ), 566 (m/z 833 ion - adenosine), 426 (adenosine (monohydrogen 3',5'-diphosphate)), 408 (m/z 426 ion - H ₂ 0), and 327 (m/z 426 ion - H ₂ O - HPO ₃ ) that were consistent with TycA-mediated production of a-phenylalanyl CoA. The sample incubated with (^)-β- phenylalanine contained an m/z 913 ([M - H] ) ion was consistent with β- phenylalanyl-CoA and that fragmented ions at m/z 426 (adenosine

(monohydrogen 3',5'-diphosphate)), and 408 (m/z 426 ion -H ₂ 0). After (2R,3S phenylisoserine was incubated with the enzymes, the resultant sample contained an m/z 929 ([M - H] ) ion was consistent with (2R,35)-phenylisoserine-CoA and fragmentation ions m/z 582 (m/z 929 ion - adenosine), 426 (adenosine

(monohydrogen 3',5'-diphosphate)), and 408 (m/z 426 ion -H ₂ 0). Minor fragments ions m/z 842 and 824 were probably derived from the phenylisoserinyl side chain (bearing a hydroxyl group at C2) attached to an intact CoA, all consistent with phenylisoserinyl CoA. Control assays lacking TycA or TycA- S563A, ATP, or CoA from the appropriate enzyme assay mixture did not yield a detectable [M - H] ion consistent with the mass of a-phenylalanyl-CoA, β- phenylalanyl-CoA, nor phenylisoserinyl CoA, as expected for a ATP/Mg ²⁺ - dependent CoA ligase.

The stereochemistry of the amino phenylpropanoyl side chain was not evaluated and so it is unknown whether the products of the CoA reaction interacted with the

E-domain of TycA and its cognate mutant TycA-S563A that could potentially epimerize the stereocenters of the CoA thioester products.

LC-ESI-MS/MS analysis of the products made in assays incubated with N-acetylcysteamine instead of CoA revealed fragment ions of the [M + H] ⁺ ion that were consistent with 5'-(a-phenylalanyl)-N-(acetyl)cysteamine or 5"-(β- phenylalanyl)-N-(acetyl)cysteamine (m/z 267, eluting at 4.49 and 3.01 min, respectively) and 5'-(phenylisoserinyl)-N-(acetyl)cysteamine (m/z 283, eluting at 2.32 min). The MS data for each biosynthetic 5'-(acyl)-N-(acetyl)cysteamine matched those of authentic standards (FIG. 6). Control assays that lacked enzyme from the assay mixture, but included the necessary cofactors and substrate did not yield a detectable molecular ion consistent with the identity of a 5'-(acyl)-N-(acetyl)cysteamine thioester (data not shown).

The data indicate that the following reactions are involved, and that these reactions generate the indicated structures.

The X, Y and Z variables depend upon the aminophenylpropanoate substrate employed. For (5)-a-phenylalanine X is NH ₂ , while Y and Z are both hydrogen. For (R)- -phenylalanine X and Y are both hydrogen while Z is H2. For (2R,35)-phenylisoserine X is hydrogen, Y is OH and Z is H2. The R substituent on the thiol can be a T-domain from the TycA enzyme (e.g., R can be serine 563 of the TycA T-domain); R can also be adenosyl diphosphate; or R can be a methyl group if the thiol is N-acetylcysteamine.

Kinetic Analyses of TycA and TycA-S563A as Thiol Ligases. The kinetic parameters of TycA and TycA-S563A were calculated by separately incubating each catalyst with various dilutions of aminophenylpropanoate substrate along with CoA or NAC and cofactors at apparent saturation. The resulting acyl-CoA and acyl-SNAC thioester products were quantified by LC-ESI-MRM (multiple reaction monitoring).

Kinetics with CoA. The catalytic preference of TycA for (R)- -Phe was 5- and 10-fold higher than for (5)-a-Phe and (2R,35)-Phenylisoserine, respectively. The K _M values of TycA (Error! Reference source not found.) suggested a preference for a-Phe and β-Phe with a C _a - NH or Cp-NH group, but not for phenylisoserine with a C _a -OH and Cp-NH ₂ group. The

stereochemistry of the Cp-NH ₂ of (2R,3S)- phenylisoserine is oriented identically to the amino group of (R)- -Phe; thus, the C _a -OH was considered responsible for affecting the catalysis either by sterics, electronic effects, or H- bonding interactions. Table 1. Stead -state kinetic analysis of the TycA and TycA-S563A

standard deviations of triplicates. ^c PheIso-yl AMP was below the limits of detection. & _cat ^oA , & _cat ^NA and & _cat ^ATP are turnover in the presence of CoA, NAC, and ATP at apparent saturation, respectively.

The catalytic efficiency of TycA-S563A for (R)-P-Phe was highest and followed a similar trend to that of TycA (Table 1). In general, the catalytic efficiency of TycA did not vary more than 3-fold over that of TycA-S563A, suggesting that the concentration of CoA at 1 mM offset the pantetheinylation reaction with the likely small fraction of TycA holoenzyme, containing the 4'-phosphopantetheine at the T-domain. Thus, CoA likely attacked the aminophenylpropanoyl-AMP anhydride while it remained docked in the A- domain of TycA. At this point, the fraction of AMP anhydride that reacted with CoA, after it was released into the medium, could not be determined. TycA was therefore deemed operationally similar to TycA-S563A at high concentrations of CoA.

The kinetic parameters of the enzymes were also calculated using a dilution series of CoA with 1 mM (5)-a-Phe. The resulting thioester product was quantified by LC-ESI- MRM, as before, and the k _c K _M of the TycA congeners for CoA were of a similar order of magnitude (Error! Reference source not found.). However, the difference in catalytic preference between each enzyme was largely influenced by the ~2.5-fold higher KM of TycA, yet similar _ca t, compared to that of TycA-S563A (Error! Reference source not found.). The lower K _M of TycA-S563A may suggest competitive inhibition between CoA, at low concentration, and a small amount of covalent 4'-phosphopantetheine at the T- domain.

Kinetics of the AMP Ligase Reaction. The syntheses of authentic aminophenyl- propanoyl-AMPs using a method described by Owczarek, et al. (Biochemistry 47: 301 - 307 (2008)) for use as quantification standards was low yielding. Therefore, the biosynthetic acyl-AMPs were quantified by LC-ESI-MRM for kinetic analyses. The k^T I KM value of TycA for the conversion of a-phenylalanine and β-phenylalanine (using ATP at apparent saturation (cf. FIG. 2)) to a-Phe-AMP and β-Phe-AMP were about 2- fold and 15-fold, respectively, which is lower than the values for the conversion of a-Phe and β-Phe to their corresponding authentic aminophenylpropanoyl-CoA thioesters

(Error! Reference source not found.). The k^ ^p I KM value of TycA-S563A for similar conversion of a-phenylalanine and β-phenylalanine to the AMP adducts was about 7-fold and about 46-fold lower, respectively. Phenylisoserinyl-AMP was below the limits of detection in a similar assay. The slower steady-state production rate of the

aminophenylpropanoyl-AMP in solution (FIG. 3) did not account for the production rate of the corresponding aminophenylpropanoyl-CoAs. The greater catalytic efficiency for CoA thioester production over aminopropanoyl AMP biosynthesis confirmed that CoA displaced AMP from the aminophenylpropanoyl-AMP in complex with TycA, at steady state, and not from the acyl AMP intermediate in solution to form the thioesters.

Kinetics with NAC. The _ca t and KM values of TycA or TycA-S563A for N- acetylcysteamine (NAC) were obtained by incubating the thiol separately with each aminophenylpropanoate under standard ligase conditions. The reaction products were identified and quantified by LC-ESI-MRM by comparison to the retention time and fragment transition ions of authentic standards. The efficiency of TycA (with NAC) was highest for (R)-P-Phe, followed by (5)-a-Phe, and then by (2R,35)-phenylisoserine, similar (but at lower values) to when CoA was used in place of NAC (Error! Reference source not found.). The K _M values of TycA for each aminophenylpropanoate substrate with NAC at apparent saturation was different, but approximately the same order of magnitude as when CoA was used. These data suggest that the smaller NAC thiol did not affect binding of the aminophenylpropanoate to the PheA domain (Error! Reference source not found.). The kceJKu of TycA for each aminophenylpropanoate and NAC ranged between 1.5- and 3-fold lower than when CoA was used, suggesting that CoA is more catalytically competent than NAC, as anticipated.

The catalytic efficiency of TycA-S563A (compared with TycA) was lower for (R)- β-Phe and (2R,35)-Phenylisoserine and NAC cosubstrate, but increased for the natural substrate (5)-a-Phe. These results somewhat contradicted other findings that the catalytic efficiency of TycA-S563A was highest for β-Phe (Error! Reference source not found.). A 15-fold decrease in turnover and an approximate 2-fold increase in KM caused a -30- fold lower catalytic efficiency of TycA-S563A compared to that of TycA for (R)-P-Phe (Error! Reference source not found.). This disparity was not seen between the catalytic efficiency of each catalyst for CoA and (R)-P-Phe. Apparently, an as yet unknown interaction between NAC, β-Phe, and/or the catalyst affected the turnover. Interestingly, the K _M of both TycA and TycA-S563A for NAC were lower than for CoA (Error! Reference source not found.), despite CoA being a better mimic of the natural Ppant used in the normal TycA reaction (FIG. 2Error! Reference source not found.A). It is unclear whether the smaller NAC has greater reach to the TycA active site than CoA and thus affects the rate of the ligase reaction chemistry.

Comparing the Kinetic Parameters of TycA/TycA-S563A to Other CoA Ligases. Compared to the KM values of bacterial CoA Ligases for CoA (100 - 940 μΜ) and acyl substrates (10 - 6000 μΜ), those of TycA and TycA-S563A for CoA (1976 and 804 μΜ, respectively) are about the same order of magnitude, while the acyl substrates (34 - 132 μΜ) are more variable (Tables Error! Reference source not found, and Error! Reference source not found.).

Table 2

"NL: no listing

CoA ligases active during catabolic pathways in various bacteria convert, for example, propionate (Horswill & Escalante-Semerena, Biochemistry 41 : 2379-2387 (2002)), benzoate (Altenschmidt, et al., J. Bacteriol. 173: 5494-5501 (1991)), and 4- chlorobenzoate (Wu, et al., Biochemistry 48: 41 15-4125 (2009)) to their corresponding CoA thioesters with superior catalytic efficiency (1.65 x 10 ⁶ , 3.94 x 10 ⁷ , and 1.02 x 10 ⁷ s^ 'MT ¹ , respectively) compared to those on secondary metabolic pathways (< 2500 s ^~ '•Mr ¹ ), such as for TycA, (used in tyrocidines A-D biosynthesis, described here as a CoA Ligase), phenylacetate CoA Ligase from Penicillium chrysogenum (Koetsier, et al., Biochem. J. 417: 467-476 (2009)), penicillin G biosynthesis, and cinnamate CoA Ligase from Streptomyces coelicolor (Kaneko, et al., J. Bacteriol. 185, 20-27 (2003)). The role of cinnamoyl CoA is as yet undefined; however, it may play a role in biosynthesis, since Streptomyces sp. are known to produce a variety of secondary products (Ohnishi, et al., J. Bacteriol. 190: 4050-4060 (2008)). Notably, a recent report described a mutation of phenylacetate CoA Ligase from P. chrysogenum that reduced the KM for β-Phe from low mM amount to 68 μΜ in the reaction to make β-Phenylpropanyl CoA (Koetsier, et al., 2009). Likewise, the 1I _C JKM of TycA, which already uses aminophenylpropanoate substrates, may potentially be enhanced through mutagenesis by removing the T- and E- domains to resolve the CoA Ligase activity of the A-domain.

Summary. Under CoA ligation assay conditions, TycA (and TycA-S563A) converted three aryl a- and β-amino acids to their CoA and S-N-acetylcysteamine thioesters via adenylate intermediates kinetically similar to CoA ligases involved in secondary metabolism. The S-N-acetylcysteamine thioesters of each amino acid were biosynthesized when N-acetylcysteamine was used as the thiol donor.

Notably, the β-Phenylpropanyl-CoA and phenylisoserinyl-CoA thioesters made as described herein are useful intermediates on the biosynthetic pathway of paclitaxel, and thus, can be used to make paclitaxel and related antineoplastic drugs.

References

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mechanism of domain alternation in the acyl-adenylate forming ligase superfamily member 4-chlorobenzoate: coenzyme A ligase. Biochemistry 48, 41 15-4125. All patents and publications referenced or mentioned herein are indicative of the levels of skill of those skilled in the art to which the invention pertains, and each such referenced patent or publication is hereby specifically incorporated by reference to the same extent as if it had been incorporated by reference in its entirety individually or set forth herein in its entirety. Applicants reserve the right to physically incorporate into this specification any and all materials and information from any such cited patents or publications.

The specific compositions and methods described herein are representative, exemplary and not intended as limitations on the scope of the invention. Other objects, aspects, and embodiments will occur to those skilled in the art upon consideration of this specification, and are encompassed within the spirit of the invention as defined by the scope of the claims. It will be readily apparent to one skilled in the art that varying substitutions and modifications may be made to the invention disclosed herein without departing from the scope and spirit of the invention. The terms and expressions that have been employed are used as terms of description and not of limitation, and there is no intent in the use of such terms and expressions to exclude any equivalent of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention as claimed. Thus, it will be understood that although the present invention has been specifically disclosed by embodiments and optional features, modification and variation of the concepts herein disclosed may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention as defined by the appended claims and statements of the invention.

The invention illustratively described herein may be practiced in the absence of any element or elements, or limitation or limitations, which is not specifically disclosed herein as essential. The methods and processes illustratively described herein may be practiced in differing orders of steps, and the methods and processes are not necessarily restricted to the orders of steps indicated herein or in the claims.

As used herein and in the appended claims, the singular forms "a," "an," and "the" include plural reference unless the context clearly dictates otherwise. Thus, for example, a reference to "a compound" or "a catalyst" or "a ligand" includes a plurality of such compounds, catalysts or ligands, and so forth. In this document, the term "or" is used to refer to a nonexclusive or, such that "A or B" includes "A but not B," "B but not A," and "A and B," unless otherwise indicated.

Under no circumstances may the patent be interpreted to be limited to the specific examples or embodiments or methods specifically disclosed herein. Under no circumstances may the patent be interpreted to be limited by any statement made by any Examiner or any other official or employee of the Patent and Trademark Office unless such statement is specifically and without qualification or reservation expressly adopted in a responsive writing by Applicants.

The invention has been described broadly and generically herein. Each of the narrower species and subgeneric groupings falling within the generic disclosure also form part of the invention. This includes the generic description of the invention with a proviso or negative limitation removing any subject matter from the genus, regardless of whether or not the excised material is specifically recited herein. In addition, where features or aspects of the invention are described in terms of Markush groups, those skilled in the art will recognize that the invention is also thereby described in terms of any individual member or subgroup of members of the Markush group.

The Abstract is provided to comply with 37 C.F.R. § 1.72(b) to allow the reader to quickly ascertain the nature and gist of the technical disclosure. The Abstract is submitted with the understanding that it will not be used to interpret or limit the scope or meaning of the claims.

The following statements describe aspects of the invention.

Statements describing aspects of the invention:

1. A method of making paclitaxel or an analog thereof, comprising preparing an aminopropanoyl-CoA in a reaction catalyzed by a Tyrocidine synthetase A (TycA) to thereby make paclitaxel or an analog or derivative thereof.

2. The method of statement 1, wherein the aminopropanoyl-CoA is prepared from a substrate of the following formula I:

I

wherein:

X is hydrogen;

Y is hydrogen or OH; and

Ring is a unsubstituted or substituted (C4-C 10) aryl, (C4-C9)heteroaryl,

(C4-C 10)cycloalkyl, or (C4-C9)heterocycloalkyl.

3. The method of statement 1 or 2, wherein the aminopropanoyl-CoA is a compound of formula II:

II

wherein:

X is hydrogen;

Y is hydrogen or OH; and

Ring is a unsubstituted or substituted (C4-C 10) aryl, (C4-C9)heteroaryl, (C4-C 10)cycloalkyl, or (C4-C9)heterocycloalkyl.

The method of any of statements 1-3, wherein the paclitaxel or paclitaxel analog has the follo

Ring is a unsubstituted or substituted (C4-C 10) aryl, (C4-C9)heteroaryl, (C4-C 10)cycloalkyl, or (C4-C9)heterocycloalkyl.

The method of any of statements 1 -4, wherein Ring is a single aryl or heteroaryl ring of about 4-8 carbon atoms, and where the heteroatom is oxygen or nitrogen. The method of any of statements 1-5, wherein the Ring is substituted with 1 or 2 alkyl, amino, hydroxy, cyano, carboxy, nitro, thio, alkoxy, and halogen groups. The method of any of statements 1-6, wherein the aminopropanoyl-CoA prepared from a substrate of the following formula III or IV:

III IV

wherein:

X is hydrogen;

Y is hydrogen or OH;

Z is CH, CH ₂ , oxygen (O) or nitrogen (NH or NH ₂ ); and

Ri is selected from the group consisting of hydrogen, alkyl, amino, hydroxy, cyano, carboxy, nitro, thio, alkoxy, and halogen.

The method of any of statements 1-7, wherein the aminopropanoyl-CoA is

V VI

wherein:

X is hydrogen;

Y is hydrogen or OH;

Z is CH, C¾, oxygen (O), or nitrogen (NH or N¾); and

Ri is selected from the group consisting of hydrogen, alkyl, amino, hydroxy, cyano, carboxy, nitro, thio, alkoxy, and halogen. The method of any of statements 1-8, wherein the Tyrocidine synthetase A has a bacterial amino acid sequence.

The method of any of statements 1-9, wherein the Tyrocidine synthetase A is a Bacillus brevis or Brevibacillus parabrevis Tyrocidine synthetase A.

The method of any of statements 1-10, wherein the Tyrocidine synthetase A has an amino acid sequence of a Tyrocidine synthetase A from bacteria deposited with the American Type Culture Collection under deposit number ATCC 8185.

The method of any of statements 1-1 1, wherein a serine in the Tyrocidine synthetase A is replaced with a substitute amino acid that does not have a hydroxy in its side chain.

The method of any of statements 1- 12, wherein a serine at about position 563 in the Tyrocidine synthetase A is replaced with a substitute amino acid that does not have a hydroxy in its side chain.

The method of statements 12 or 13, wherein the substitute amino acid in the Tyrocidine synthetase A is an alanine, valine, isovaline, leucine, isoleucine, proline, glycine, arginine, lysine, histidine, tryptophan, phenylalanine, methionine or cysteine.

The method of any of statements 1-14, wherein the Tyrocidine synthetase A has an amino acid sequence comprising a sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:6, and an amino acid sequence with 85% sequence identity to any of SEQ ID NO: l, SEQ ID NO:3, SEQ ID NO:5, or SEQ ID NO:6.

The method of any of statements 1-15, wherein the Tyrocidine synthetase A is encoded by a nucleic acid sequence comprising a sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:7, and an nucleic acid sequence with 85% sequence identity to any of SEQ ID NO:2, SEQ ID NO:4 or SEQ ID NO:7.

The method of any of statements 1-16, wherein the reaction comprises a mixture of the Tyrocidine synthetase A, the substrate, ATP and a divalent cation. The method of any of statements 1 - 17, which is performed in vitro.

The method of any of statements 1 - 18, which is performed in a cell- free reaction. The method of any of statements 1 - 17, which occurs in a cultured cell.

The method of any of statements 1 - 17, which occurs in a cultured cell during a plant cell fermentation process.

The method of any of statements 1 -21 , wherein the method further comprises reaction B comprising combining the aminopropanoyl-CoA with Baccatin III:

Baccatin III

to form N-debenzoyl-2'-deoxypaclitaxel or an analog or derivative thereof.

The method of statement 22, wherein the reaction B is catalyzed by an acyltransferase.

The method of statement 22 or 23, wherein the reaction B is catalyzed by a Taxus acyltransferase.

The method of any of statements 22-43, wherein the reaction B is catalyzed by baccatin III O-phenylpropanoyltransferase (BAPT).

The method of any of statements 22-25, wherein the reaction B comprises a mixture of aminopropanyl-CoA, baccatin III O-phenylpropanoyltransferase (BAPT), and Baccatin III. The method of any of statements 22-26, wherein the N-debenzoyl-2'- deoxypaclitaxel or an analog or derivative thereof has the following structure:

3'-N-Debenzoyltaxol or an analog

or derivative thereof

wherein:

X is hydrogen;

Y is hydrogen or OH; and

Ring is a unsubstituted or substituted (C4-C10) aryl, (C4-C9)heteroaryl, (C4-C 10)cycloalkyl, or (C4-C9)heterocycloalkyl.

The method of any of statements 22-27, which is performed in vitro.

The method of any of statements 22-28, which is performed in a cell- free reaction. The method of any of statements 22-27, which is performed in a cultured cell. The method of any of statements 22-27, which is performed in a cultured cell during a plant cell fermentation process.

The method of any of statements 1-31, wherein the method further comprises a reaction A comprising transfer of benzoyl group to a free amine of a propanoid side chain of 3'-N-debenzoyl-paclitaxel or an analog or derivative thereof to form paclitaxel or an analog or derivative thereof.

The method of statement 32, wherein the paclitaxel or an analog or derivative thereof has the following structure:

wherein:

Ring is a unsubstituted or substituted (C4-C 10) aryl, (C4-C9)heteroaryl, (C4-C 10)cycloalkyl, or (C4-C9)heterocycloalkyl.

The method of statement 33, wherein Ring is a single aryl or heteroaryl ring of about 4-8 carbon atoms, and where the heteroatom is oxygen or nitrogen.

The method of statement 33 or 34, wherein the Ring is substituted with 1 or 2 alkyl, amino, hydroxy, cyano, carboxy, nitro, thio, alkoxy, and halogen groups. The method of any of statements 32-35, wherein the reaction A is catalyzed by an acyltransferase.

The method of any of statements 32-36, wherein the reaction A is catalyzed by a Taxus acyltransferase.

The method of any of statements 32-37, wherein the reaction A is catalyzed by N - debenzoyl-2'-deoxypaclitaxel: N-benzoyltransferase (NDTBT).

The method of any of statements 32-38, wherein the reaction A comprises a mixture of 3'-N-debenzoyl-paclitaxel, a benzoyl-contributing agent and N - debenzoyl-2'-deoxypaclitaxel: N-benzoyltransferase (NDTBT).

The method of any of statements 32-39, which is performed in vitro.

The method of any of statements 32-40, which is performed in a cell- free reaction. The method of any of statements 31-39, which is performed in a cultured cell. The method of any of statements 31-39, which is performed in a cultured cell during a plant cell fermentation process.

The method of any of any of statements 1 -43, wherein the method further comprises a reaction C comprising acyl transfer of an acetyl group to 10-deacetyl Baccatin III to generate Baccatin III:

The method of statement 44, wherein reaction C is catalyzed by an acetyl transferase.

The method of statement 44 or 45, wherein reaction C is catalyzed by 10- deacetylbacctin III acetyltransferase.

The method of any of statements 44-46, which is performed in vitro.

The method of any of statements 44-47, which is performed in a cell-free reaction. The method of any of statements 44-46, which is performed in a cultured cell. The method of any of statements 44-46, which is performed in a cultured cell during a plant cell fermentation process.

The method of any of statements 1 -50, wherein the method further comprises a reaction D comprising transfer of a benzoyl group to 2-debenzoyltaxane to generate 10-deacetyl Baccatin III.

The method of statement 51 , wherein reaction D proceeds as follows:

2-Debenzoyltaxane

10-Deacetyl Baccatin III

The method of statement 51 or 52, wherein reaction D is catalyzed by taxane 2a-0- benzoyltransferase.

The method of any of statements 51-53, which is performed in vitro.

The method of any of statements 51-54, which is performed in a cell-free reaction. The method of any of statements 51-53, which is performed in a cultured cell. The method of any of statements 51-53, which is performed in a cultured cell during a plant cell fermentation process.

The method of any of statements 1-57, wherein the method further comprises a reaction E comprising acylation and hydroxylation of taxa-4(5), l l(12)-diene-5a-ol to generate 2-debenzoyltaxane.

The method of statement 58, wherein reaction E proceeds as follows:

axa-4(5),1 l(12)-diene-5a-ol

2-Debenzoyltaxane The method of statement 58 or 59, wherein reaction E is catalyzed by an enzyme selected from the group consisting of taxadiene 13 -hydroxylase (T13H), taxadienol 5a-0-acetyl transferase (TAT), taxadiene 10-hydroxylase (T10H), or a combination thereof. 61. The method of any of statements 58-60, which is performed in vitro.

62. The method of any of statements 58-61, which is performed in a cell- free reaction.

63. The method of any of statements 58-60, which is performed in a cultured cell.

64. The method of any of statements 58-60, which is performed in a cultured cell during a plant cell fermentation process.

65. The method of any of statements 1-64, wherein the method further comprises a reaction F comprising hydroxylation of taxa-4(5), l l(12)-diene to generate taxa- 4(5),l l(12)-diene-5a-ol.

66. wherein reaction F proceeds as follows:

Taxa-4(5),1 l(12)-diene Taxa-4(5),1 l(12)-diene-5a-ol

67. The method of statement 65 or 66, wherein reaction F is catalyzed by taxadiene 5a-hydroxylase.

68. The method of any of statements 65-67, which is performed in vitro.

69. The method of any of statements 65-68, which is performed in a cell-free reaction.

70. The method of any of statements 65-67, which is performed in a cultured cell.

71. The method of any of statements 65-67, which is performed in a cultured cell during a plant cell fermentation process.

72. The method of any of statements 1-71, wherein the method further comprises a reaction G comprising ring closure of geranylgeranyl diphosphate.

73. The method of statement 72, wherein reaction G generates taxa-4(5),l l(12)-diene.

74. The method of statement 72 or 73, wherein reaction G proceeds as follows:

Geranylgeranyl diphosphate (GGPP)

75. The method of any of statements 72-73, wherein reaction G is catalyzed by

taxadiene synthase.

76. The method of any of statements 72-75, which is performed in vitro.

77. The method of any of statements 72-76, which is performed in a cell- free reaction.

78. The method of any of statements 72-75, which is performed in a cultured cell.

79. The method of any of statements 71-75, which is performed in a cultured cell during a plant cell fermentation process.

80. The method of any of statements 1-79, wherein the method further comprises a reaction H comprising condensation of geranylgeranyl diphosphate and dimethylallyl diphosphate.

81. The method of statement 80, wherein the condensation generates taxa-4(5),l 1(12)- diene.

82. The method of statement 80 or 81, wherein reaction H proceeds as follows:

Dimethylallyl diphosphate (DMAPP) Geranylgeranyl diphosphate (GGPP)

83. The method of any of statements 80-82, wherein reaction H is catalyzed by

geranylgeranyl diphosphate synthetase.

84. The method of any of statements 80-83, which is performed in vitro.

85. The method of any of statements 80-84, which is performed in a cell- free reaction.

86. The method of any of statements 80-83, which is performed in a cultured cell.

87. The method of any of statements 80-83, which is performed in a cultured cell during a plant cell fermentation process.

The following claims describe aspects of the invention.