AND PROTEIN SEQUENCING

This application is a continuation-in-part of Serial No. 271,328 filed November 15, 1988 and Serial No. 311,966 filed February 17, 1989, both pending.

FIELD OF THE INVENTION

This invention relates to the carboxyl-terminal (C-terminal) amino acid sequence analysis of peptides and proteins. More particularly, the invention relates to novel C-terminal coupling reagents, to the methodology for using these reagents, and to the novel coupling reaction products produced. BACKGROUND OF THE INVENTION

Known C-terminal sequencing methodologies are enzymatic physical or chemical. The enzymatic approach is basically a time-course carboxypeptidase procedure. It is limited by differential hydrolysis rates of the involved peptide bonds and by potential unaccessibility of the COOH carboxyl terminus in proteins. The approach may yield the correct amino acids but in the wrong order and may not extend to more than three to five amino acids.

Physical approaches include mass spectrometry and nuclear magnetic resonance (NMR) and are most suitable for small peptides. Fast atom bombardment—Mass Spectrometry (FAB/MS) sensitivity for determining an entire peptide sequence is in the range of 1-10 nmol and is limited to expensive multisector instruments. Micro olar samples are required for NMR analysis.

Four chemical methods of some interest are known. In 1978 Parkam and Loudon reported a method in which the carboxya ido peptide derivative is treated with bis(1,1 trifluoroacetoxy)- iodobenzene to yield a derivative of the amino acid. Free COOH groups were treated with bis-p-nitrophenylphosphoryl

azide to generate the carboxyamido derivative through a Curtius rearrangement. Parham, M.E. and Loudon G.M. Biochem. Biophys. Res. Commun. 80;1;7 (1978).

Loudon and coworkers presented another version of the method which entailed reaction of the COOH terminus with pivaloylhydroxyl amine in the presence of carbodimide to effect a Lossen rearrangement. This method failed to degrade aspartic and glutamine residues. Miller, M.J. and Loudon, G.M. , J. Am. Chem. Soc. 97:5296 (1975); Miller, M.J. , et al. , J. Orcf. Chem. 42:1750 (1977).

The method reported by Stark releases the COOH-terminal amino acid as a thiohydantoin. Stark, G.R. Biochemistry Σ5:4735 (1968) ; Stark, G.R. in "Methods in Enzymology", Vol. 25, p. 369, Academic Press, New York, New York (1972) . It entails activation of the COOH group with acetic anhydride, followed by reaction with ammonium thiocyanate and cleavage by acid or base hydrolysis to release the thiohydantoin from the peptide chain.

Hawke reported a modification of the Stark chemistry in which trimethylsilylisothiocyanate is utilized as the coupling reagent. Hawke, et al. Analytical Biochemistry 166:298-307 (1987) .

Notwithstanding these procedures, there is a continuing substantial need for a generally- applicable chemical method for C-terminal sequencing. Such a method would have particular value with respect to, among other things, sequencing N-terminal blocked polypeptides and proteins, verifying the primary protein structures predicted from DNA sequences, providing practical detection of post translational processing of gene products from known codon sequences, and as an aid in the design of oligonucleotide cDNA or gene bank probes.

SUMMARY OF THE INVENTION This invention provides practical C-terminal peptide sequencing methodology utilizing novel phosphoryl amide preferably phosphoryl thioa ide coupling reagents which yield arylhydantoin, arylthiohydantoin or aryliminohydantoin cleavage products. The peptide may be preactivated with acetic anhydride and acetic acid. As compared with the prior art chemical procedures yielding thiohydantoin, aldehyde or iminohydantoin cleavage products, elaboration of the aryl ring imparts enhanced molar absorptivity to the cleavage product molecule and hence greater sensitivity to detection either in the UV or fluorescent spectra. Practical C-terminal sequencing of nanomole and sub-nanomole peptide and protein samples with positive identification, for example, by capillary electrophoresis, of released amino acids is facilitated.

DESCRIPTION OF THE PREFERRED EMBODIMENTS The Coupling Reagents The novel phosphoryl amide coupling reagents of this invention are of the schematic Formula I:

Xc Xd

II II

I. (Rι ⁾ n ^{Xa fcp N} — ^c — ^{Xe (} ₂ ⁾ _n Xb R3 in which Xa and Xb are 0 (oxygen) , S (sulfur) or N

(nitrogen)

R _l and R ₂ are H, or any alkyl or aryl radical having not more than about 10 carbon atoms, n is 1 when Xa and Xb are O or S; n is 2 when Xa or Xb is N when Xa and Xb are both N (Ri _n Xa and

( ^R 2)n ^{xb ma} Y ^be included in an acylic amine or a nitrogen heterocycle;

R ₄ is an alkyl or aryl radical having not more than about 10 carbon atoms;

Xc is O or S

Xd is O, S or NR4 wherein R4 is H or any alkyl or aryl radical having not more than about 10 carbon atoms

Xe is OR ₅ , SR ₅ or N(Rs) ₂ wherein R5 is an alkyl or aryl radical having not more than about 12 carbon atoms, and in which

Xd

II N C Xe may be included in a ring system.

The alkyl or aryl groups which may constitute R^, ^R ₂ r ^R ₃ r ^{or R} 4 preferably have from 3 to about 6 carbon atoms. The alkyl groups may be straight or branch chain. The aryl groups may be substituted or unsubstituted phenyl or napthyl groups.

Representative phosphoryl amide coupling reagents of this invention are represented by the compounds of formulas A, B, C, and D in which "PhO" is 0 _/ —°— and Z is O or S:

A.

B.

(PhO) ₂ — —N/ ^N 0

Additional phosphoryl amide coupling agents of the invention include the compounds of formulas E, F, and G:

E .

N-H

0 S

II II

(PhO) 2 P — — C — SR

G .

Any of the coupling reagents can be utilized as the free amides preferably after preactivation of the C-terminal acid of the peptide samples with acetic acid and acetic anhydride.

SYNTHESIS OF THE COUPLING AGENTS

The coupling agents of the invention apparently are not reported in the literature. They may be synthesized by chemistry related to that used to produce certain known phosphoryl(thio)amide compounds. See, e.g., Kirsanov, A.V. , and Levchenko, E.S. Zhur. Obsschcheu Khim, 2ϊ:2285-2289 (1956) ; ibid 22 _^ :673-676 (1956); ibid. 3_1:210-216 (1961); Kulka, M. , Can. J. Chem. 37:525-528 (1959); Ballester-Rodes, M. and Palomo-Coll, A.L. , Synthetic Communications, 14:515-520 (1984) and Kuneida, T. , Abe, Y. , Higuchi, T. , and Hirobe, M. Tetrahedron Letters, 22:1257-1258 (1981) . For example a phosphorylating agent such as

. O

II (PhO)2—P—Cl may be reacted with a mercaptobenzo- thiazole, aminobenzothiazole, mercaptobenzoxazole or

N, N' trisubstituted thiourea such as pyridyl, methyl, N'-m-nitrophenyl thiourea, to produce the compounds of formulas A through H. The reaction proceeds in the manner illustrated by Equation 1:

The synthesis is appropriately accomplished at a temperature from about 20°C to about 100°C in an inert solvent in the presence of an amine.

Appropriate solvents include dimethyl formamide, dichloromethane, acetonitrile, saturated aliphatic hydrocarbons having from about 5 to about 10 carbon atoms, aromatic hydrocarbons including benzene, toluene, xylene and mesitylene. Tertiary amines which do not react with the phosphorylating agent under the reaction conditions may be utilized. Trialkyl amines having from 1 to about 5 carbon atom alkyl groups are appropriate. Triethylamine is preferred. The reaction time may range from about 15 min. to .about 60 min. The reaction is normally complete in about 30 min.

EXAMPLE I—SYNTHESIS OF COMPOUND OF FORMULA A

1 millimole of 2-mercaptobenzothiazole was dissolved in 0.5 ml of toluene followed by the addition of 1 millimole of triethylamine. This solution was added to a solution of l millimole of diphenylchlorophosphate in 1 ml of toluene heated at 70°C. The mixture was reacted for two hours at 70°C, allowed to cool, filtered, and the filtrate evaporated to yield a yellow solid analyzed for the compound of Formula A. Calculated exact mass of the Formula A compound is 400.0231 atomic mass units (amu) . The average of several exact mass determinations of the compound produced in Example I as determined by FAB-MS was 400.0256 amu. A yield of 40% to 50% of theoretical was obtained.

EXAMPLE II—SYNTHESIS OF COMPOUND OF FORMULA B

This example illustrates the synthesis of the compound of Formula B. 1 millimole of 2-mercaptobenzoxazol'e was dissolved in 0.5 ml toluene followed by the addition of 1 millimole of triethylamine. This solution was added to a solution of 1 millimole of diphenyldichlorophosphate in 1 ml of toluene heated to 70°C and the mixture was reacted for 30 minutes. The reaction mixture was filtered and the filtrate evaporated leaving a white solid.

The yield of Formula B compound from a plurality of such reactions of ranged from 20% to 50% of theoretical. The calculated exact mass for the compound of Formula B is 384.0460 amu. The average of several exact mass determinations of the product of Example II as determined by FAB-MS is 384.0415 amu.

Formula C and D compounds are produced in like manner by reacting 2-mercaptobenzothiazole or

2-mercaptobenzoxazole with

O II

The Coupling Reaction

The reaction of dansylnorvaline with the compound of Formula A provides a model for carboxylic acid activation as the first coupling step requires in the C-terminal sequencing methodology of this invention.

As illustrated by Equation 2, in a model reaction the piperidine salt of dansylnorvaline is utilized to permit direct reaction of an amino acid carboxylate with the compound of Formula A.

CH

418 amu 503 amu

Under the conditions shown by Equation 2, the reaction proceeds at 25°C in an acetonitrile solvent. Molecular ions of 418 and 503 amu are detected by FAB-MS after 2 minutes reaction time and persist after three hours.

Figure 1 is a FAB mass spectrum evidencing a molecular ion of 503 amu after the Equation 2 reaction had proceeded for three hours.

Figure 2 is a FAB mass spectrum evidencing a molecular ion of 418 amu after the Equation 2 reaction had proceeded for two minutes.

These two products are consistent with the carboxyl activation of the amino acid by the compound of Formula A to provide the intermediate activated carboxylate:

which decomposes or reacts with the initially present nucleophilic amine piperidine.

Generalized coupling reactions involving the Formula A compound and the subsequent cyclization reaction are illustrated by Equations 3a and 3b. A peptide is depicted from the amino-terminal residue (R ¹ through R ³ ) up to the carboxy terminal residue which is labelled as R ³ , although peptides or proteins of any length may be considered.

3a:

EXAMPLE III

This example illustrates a peptide coupling reaction with the use of the amino-terminally blocked tripeptide N-dansyltriglycine (DG3) .

About 20 nanomoles of N-dansyltriglycine, dissolved in 20 μl (microliters) of acetonitrile, was reacted with about 10-20 μmoles of compound A in 15 μmoles of triethylamine. The reaction was performed several times at about 25"C over time courses of from one to 24 hours. FAB-MS data show a molecular ion of 673 amu (see Fig. 3) which is consistent with the triethylamine (TEA)' salt of the coupled peptide molecular ion formed pursuant to Equation 4:

(DG3-coupled product)

This structure indicates the cyclization of the intermediate coupled peptide, i.e.,

The cyclized product exists as its triethylamine salt and gives rise to the 673 amu molecular ion.

A molecular ion of 348 amu (see Fig. 4) is consistent with a fragmentation

of the cyclized product.

A FAB mass spectral ion detected at 571 amu, consistent with the parent molecular ion calculated for the coupled peptide (not as its triethylamine salt) , was found when N-dansyltriglycine was reacted with a 5,000-fold molar excess of compound A and triethylamine for 30 minutes at 50°C and subsequent brief (1 to 2 minute) exposure to a dilute aqueous sodium hydroxide solution (0.1N).

Coupling utilizing the novel reagents of this invention, is facilitated by immobilization, preferably covalent, of the protein in known manner to a solid support. Preferred solid supports include derivatized polyvinyldifluoride membranes (Millipore Immobilon) and inert carriers such as polystyrene beads and controlled pore glass (CPG) . Immobilization through nucleophilic groups, e.g., protein lysine residues is preferred. In this way the requirement for pretreatment of the protein with an amino-blocking reagent such as acetic anhydride may be avoided.

The coupling reaction may be accomplished in the presence of various bases. Triethyl amine is preferred. Other amines which may be utilized include trialkyl amines in which the alkyl groups have from one to about 5 carbon atoms, aryl amines such as pyridine or the Aldrich proton sponge.

The coupling reaction rate is a function of reaction temperature. A preferred temperature range is from about 25°C to about 60°C. Any appropriate solvent may be utilized. Acetonitrile is preferred. N,N-dimethylformamide and dimethylsulfoxide are useful solvents.

EXAMPLE IV

This example illustrates, by comparative experiments, the acetic anhydride-acetic acid preactivation of a peptide to be sequenced.

(i) About 20 nmoles of the hexapeptide, Arg-Gly-Tyr-Ala- Leu-Gly, were treated with about 5 μmoles of triethylamine and 5 moles of diphenylphosphorylmercaptobenzothiazole in 10 μl of N,N-dimethylformamide for 30 minutes at 50"C. The product mixture was fractionated by reversed phase HPLC. The coupled peptide was recovered as an individual peak and gave a FAB-MS molecular ion consistent with the calculated value of 786 amu depicted by Figu-e 5.

The coupling reaction is illustrated by Equation 5:

Arg-Gly-Tyr-Ala-Leu-Gly +

s

Arg-Gly-Tyr-Ala-Leu-Glycyl N S

As Figure 6 shows, a molecular ion of 1018 amu was found after product mixture fractionation when acetonitrile replaced N,N-dimethylformamide as the solvent. The ion is consistent with the diphenylphosphorylpeptidyl mercaptobenzothiazole produced by Equation 6:

Arg-Gly-Tyr-Ala-Leu-Gly + (PhO)

(ii) When 20 nmoles of the above hexapeptide were treated with acetic acid and acetic anhydride for 30 minutes at 50°C, a product mixture composed of various acetylated peptides was found by FAB-MS analysis. Subsequent exposure of the mixture to triethylamine in N,N-dimethylformamide yielded a series of azlactone peptides resulting from the elimination of acetic acid at the Glycyl terminus and five-membered ring closure. Subsequent addition of 2-mercaptobenzothiazole (about 5 μmoles) and triethylamine (5 μmoles) in N,N-dimethylformamide for 30 minutes at 50°C resulted in a product mixture containing acetylated peptidyl mercaptobenzothiazole. As Figure 7 shows, a molecular ion of 869 amu was found which corresponds to the diacetylated peptidylmercaptobenzothiazole.

This result is consistent with the following reactions collectively identified as Equation 7:

7.

Arg-Gly-Tyr-Ala-Leu-Gly Acetic Acid

Acetic Anhydride

30 min.

50°C

O 0

(CH ₃ C) ₂ c Acid/TE

ide) 30 m

(CH ₃ C II) ₂

The product peptidyl mercaptobenzothiazole may actually exist as the rearranged peptidyl arylthiothydantoins which are not differentiated by mass value.

coupling condition

O CH ₂

Arg-Gly-Tyr-Ala- eu-C II-N /

The rearrangement (or cyclization) illustrated by Equation 8 is expected to occur under the basic conditions, e.g., the C-terminal azlactone of the peptide Arg-ly-Tyr-Ala-Leu, of the coupling reaction. Additionally observed FAB-MS ion consistent with cleavage products under the coupling conditions are consistent with the cyclized thiohydantoin peptides. A coupling reaction with compound E would yield the corresponding peptidylaryliminohydantoin.

The Cleavage Reaction

Cleavage may be accomplished in known manner, for example, utilizing acetohydroxamic acid, a cation exchange resin or concentrated HCL or dilute NaOH as a cleavage reagent. See, e.g., Stark, G.R. (1968) Biochemistry l i lSG .

Acetohydroxamic acid in a basic medium, preferably triethylamine is preferred. The conditions for acetohydroxamate-assisted cleavage of the protein arylthiohydantoin may be varied to include other organic bases, e.g., pyridine, alkyl-, or arylamines, alternate temperatures, solvent systems, and reaction times. The cleavage reagent is utilized in a mixed organic-aqueous solvent system. Other cleavage reagents and solvent systems which may be utilized include thiolates (mercaptide or

thiophenoxide) such as thiophenol, 2-mercaptopyridine, N-acylcysteine, or 0-acylmercaptoethanol in basic media such as water-acetonitrile with pH greater than 7 adjusted with pyridine, a triakylamine (TEA) , or dilute hydroxide. Dilute triethyl a ine in either an organic solvent such as DMF or in aqueous solution may also serve to cleave the peptidyl hydantoin.

The released arylthiohydantoins (or specifically, thiophenoxy- or phenoxy-thiohydantoins) are identified by separation and detection with reversed-phase HPLC techniques.

Equation 9 illustrates a generalized cleavage reaction applied to the protein-thiophenoxythiohydantoin product generated by Equation 3b:

e NH ₃

Equation 9

The hydrolytic lability of the coupled peptide to release the arylthiohydantoin was evidenced by the FAB-MS molecular ions at 366 and 325 amu which are consistent with the dipeptide, N-dansylglycylglycine, and the thiophenylthiohydantoin of the C-terminal glycyl residue. The generation of these products is attributed to the presence of water, not rigorously excluded, from the basic coupling reaction mixture.

The ion detected at 366 amu (see Fig. 4) is consistent with the dansyldiglycme peptide which is, in effect, the cleavage product that would result from a small amount of water present in the reaction mixture, i.e..

NH-CH ₂ -C It—NH-CH ₂ -COH

366 amu

The ion detected at 325 amu (see Fig. 4) (control reactions also show background at 325 amu) may be contributed in part by the cleaved thiophenyl- thiohydantoin, i.e.,

CH ₃ CH ₃

\ /

-? ^■

325 amu

The molecular ions tend to exhibit low signal intensity due to the anionic charge borne by triethylamine salt moiety of the products.

The C-terminal sequencing methodology of this invention is applicable to protein and peptide samples of all free carboxylic acids and without preclusive restraint consequent from the chain length of amino acid residue. Sequencing pursuant to the

methodology of the invention provides improved sensitivity, speed and yield on sequential degradation cycles. A single cycle of degradation can be accomplished in from about 1 to about 2 hours.

An additional compound H, useful as a carboxyl terminal coupling agent in the sequencing of peptides may be produced pursuant to the following equation:

H.

Compound H, albeit not within the scope of Formula I, implicates a free amide moiety

in the coupling reaction as illustrated by the following equation: