Cysteine proteases peptide synthesis

M Baca, TW Muir, M Schnolzer, SBH Kent. Chemical ligation of cysteine-containing peptides synthesis of a 22 kDa tethered dimer of HIV-1 protease. J Am Chem Soc 117, 1881, 1995. 

Baca M, Muir TW, Schnolzer M, Kent SBH. Chemical hgation of cysteine-containing peptides synthesis of a 22kDa tethered dimer of HlV-1 protease. J. Am. Chem. Soc. 1995 117 1881-1887. 

As discussed above, proteases are peptide bond hydrolases and act as catalysts in this reaction. Consequently, as catalysts they also have the potential to catalyze the reverse reaction, the formation of a peptide bond. Peptide synthesis with proteases can occur via one of two routes either in an equilibrium controlled or a kinetically controlled manner 60). In the kinetically controlled process, the enzyme acts as a transferase. The protease catalyzes the transfer of an acyl group to a nucleophile. This requires an activated substrate preferably in the form of an ester and a protected P carboxyl group. This process occurs through an acyl covalent intermediate. Hence, for kineticmly controlled reactions the eii me must go through an acyl intermediate in its mechanism and thus only serine and cysteine proteases are of use. In equilibrium controlled synthesis, the enzyme serves omy to expedite the rate at which the equilibrium is reached, however, the position of the equilibrium is unaffected by the protease. 

Extensive studies of enzyme-substrate complexes by resonance Raman spectroscopy (RR) have prompted the synthesis of new peptide bond modifications such as thionoesters and dithioesters (Scheme l7)t82-83l within simple model substrates. The resulting acyl-enzyme complexes are especially amenable to RR analysis with cysteine proteases such as papain due to formation of the transient dithioester intermediates. 

Fluoromethyl ketones are one of the most widely used classes of peptidyl a-fluoroalkyl ketones, second only to trifluoromethyl ketones. Peptidyl fluoromethyl ketones are very effective as irreversible inhibitors of cysteine proteases the first reported use of a fluoromethyl ketone compound was the use of Z-Phe-Ala-CH2F as an irreversible inhibitor of cathepsin BJ2,31 Today, many lysine and arginine derivatives have been synthesized as potential inhibitors for trypsin and trypsin-like enzymesJ3 There are four basic methods for the synthesis of peptide fluoromethyl ketones (1) the reaction of HF with peptide diazomethyl ketones (Section 15.1.4.1.1), (2) a halogen-exchange reaction with a chloro-, bromo-, or iodomethyl ketone (Section 15.1.4.1.2), (3) a Henry nitro-aldol condensation reaction (Section 15.1.4.1.3), and (4) a modified Dakin-West acylation reaction (Section 15.1.4.1.4). 

Peptide mimetics containing the a-ketoamide moiety are very important because they act as cysteine protease inhibitors. In fact, the a-ketoamide residue forms hemithioacetals with the -SH group of the cysteine residue of the enzyme [32], Nakamura et al. [26b] reported the preparation of a 100-member combinatorial library of a-ketoamides by means of a two-step one-pot synthesis. The first step consisted of the Ugi-4CR between (+/— )lactic acid, amines, isocyanides, and aldehydes leading to the formation of the lactamides 40 which were oxidized to the corresponding pyruvamides 41. This one-pot procedure was performed in THF since the PDC oxidation was incompatible with the presence of methanol. Five a-ketoamides showed an 80% average purity (Scheme 2.17). 

With regard to the use of protease in the synthetic mode, the reaction can be carried out using a kinetic or thermodynamic approach. The kinetic approach requires a serine or cysteine protease that forms an acyl-enzyme intermediate, such as trypsin (E.C. 3.4.21.4), a-chymotrypsin (E.C. 3.4.21.1), subtilisin (E.C. 3.4.21.62), or papain (E.C. 3.4.22.2), and the amino donor substrate must be activated as the ester (Scheme 19.27) or amide (not shown). Here the nucleophile R3-NH2 competes with water to form the peptide bond. Besides amines, other nucleophiles such as alcohols or thiols can be used to compete with water to form new esters or thioesters. Reaction conditions such as pH, temperature, and organic solvent modifiers are manipulated to maximize synthesis. Examples of this approach using carboxypeptidase Y (E.C. 3.4.16.5) from baker s yeast have been described.219... 

The constmction of synthetic selenocysteine-containing proteins or selenium-containing proteins attracts considerable interest at present, mainly for the reason that it can be used to solve the phase problem in X-ray crystallography. Selenomethionine incorporation has been used mostly uutil now for this purpose. There are also two reports ou uew synthetic selenocysteine-containing proteins. In one case, the active site serine of subtUisin has been converted into a selenocysteine residue by chemical means, with the result that the enzyme gains a predominant esterase instead of protease activity. In the second case, automated peptide synthesis was carried out to produce a peptide in which all seven-cysteine residues of the Neurospora crassa metallothioueiu (Cu) were replaced by selenocysteine. The replacement resulted iu au alteration of both the stoichiometry and the affinity of copper binding. ... 

A step-by-step peptide synthesis from the N- to the C-terminus is not possible with chemical methods as it risks partial epimerization due to the repeated carboxy activation procedures, In constrast, the stereo- and regiospecificity of serine and cysteine proteases ensures integrity of the stereogenic center and allows ecological reaction conditions without side-chain protection. Scheme 4 shows the synthesis scheme using clostripain and chymo-trypsin as catalysts.The second coupling reaction was carried out by enzyme catalysis in a frozen aqueous system (see Section 4.2.3.1). 

Azapeptides, -NH-CHRi-CO-NH-NR -CO-NH-CHR -CO-, a dass of backbone-modified peptides in which the a-CH of one or more amino add residues in the peptide chain is isoelectronicaUy replaced by a trivalent nitrogen atom. This alteration results in a loss of asymmetry associated with the a-CH, and yields a structure that can be considered intermediate in configuration between d- and t-amino acids. This a-carbon replacement is connected with the capability to provide resistance to enzymatic deavage, and the capacity to act as selective inhibitor of serine and cysteine proteases [J. Gante, Synthesis 1989, 405 J. Magrathetal.,J. Med. Chem. 1992,35,4279 R. Xing et al., J. Med. Chem. 1998, 42,1344 E. Wieczerzak et al., J. Med. Chem. 2002, 45, 4202]. 

The serine, cysteine, and aspartic proteases and the metalloproteases have all been applied in peptide synthesis. Nevertheless, shortcomings still exist and at an industrial scale chemoenzymatic peptide synthesis is certainly not always the preferred method. Since the properties of the catalyst to a large extent determine the feasibility of industrial application, the discovery and engineering of better variants are an intensive field of research. 

SERINE AND CYSTEINE PROTEASES FOR PEPTIDE SYNTHESIS 15.3.1 Chymotrypsin, Trypsin, and Related Enzymes... 

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