Peptide inhibitors, specificity

Hoppe-Seyler, F., Crnkovic-Mertens, I., Tomai, E., and Butz, K. 2004. Peptide aptamers specific inhibitors of protein function. Current Molecular Medicine 4(5), 529-583. 

Protein Kinase Inhibitors Pseudosubstrate-based peptide inhibitors, 201, 287 utilization of the inhibitor protein of adenosine cyclic monophosphate-dependent protein kinase, and peptides derived from it, as tools to study adenosine cyclic monophosphate-mediated cellular processes, 201, 304 use of sphingosine as inhibitor of protein kinase C, 201, 316 properties and use of H-series compounds as protein kinase inhibitors, 201, 328 use and specificity of staurosporine, UCN-01, and calphostin C as protein kinase inhibitors, 201, 340 inhibition of protein-tyrosine kinases by tyrphostins, 201, 347 use and specificity of genistein as inhibitor of protein-tyrosine kinases, 201, 362 use and selectivity of herbimycin a as inhibitor of protein-tyrosine kinases,... 

Schematic representation of the specificity subsites of the PR active site with bound peptidic inhibitor JG-365. Amino acids forming the boundaries of the particular...

Stereo view of the peptidic inhibitor AG1002 bound to the active site of PR. The distribution of the specificity subsites S and S is similar to that shown in Figure 2. The boundaries of the HIV PR active site are indicated by the dotted... 

In the analysis of the structural data of other protein kinases, it is noted that only cAPK has been crystallized with its specific peptide inhibitor. Nevertheless, three other structures of protein kinases compared with the structure of the cAPK-PKI complex provide substantial evidence for the conservation of the substrate binding cleft. The substrate binding cleft of the phosphorylase kinase structure has been analyzed in detail and it is clear that all amino acids of the known specific substrate can be built into the PKI model and all required corresponding charges can be found in the cleft of the phosphorylase kinase structure. In the CK-1 structure determined without a peptide, the requirement of the peptide specificity resides on the P-3 site, which has to be phosphorylated. An analysis of the surface charges of the cleft of the CK-1 structure reveals the exact correspondence of the residues required to interact with a phosphorylated substrate at this site. 

A straightforward approach is to hunt for short polypeptides that meet the specificity requirement of an enzyme but which, because of peculiarities of the sequence, are acted upon very slowly. Such a peptide may contain unusual or chemically modified amino acids. For example, the peptide Thr-Pro-nVal-NMeLeu-Tyr-Thr (nVal=norvaline NMeLeu = N-methylleucine) is a very slow elastase substrate whose binding can be studied by X-ray diffraction and NMR spectroscopy.6 Thiol proteases are inhibited by succinyl-Gln-Val-Val-Ala-Ala-p-nitroanilide, which includes a sequence common to a number of naturally occurring peptide inhibitors called cystatins.f They are found in various animal tissues where they inhibit cysteine proteases. 

I. SCHECHTEE, A. Bergee On the active site of proteases. 3. Mapping the active site of papain specific peptide inhibitors... 

Dhanraj, V., Dealwis, C.G., Frazo, C, Badasso, M., Sibanda, B.L., Tickle, I.J., and Cooper, J.B. et al. (1992). X-ray analysis of peptide-inhibitor complexes define the structural basis of specificity for human and mouse renins. Nature 357,466 472. 

Hara H, et al. Inhibition of interleukin Ibeta converting enzyme family proteases reduces ischemic and excitotoxic neuronal damage. Proc. Natl. Acad. Sci. U. S. A., 1997 94 2007-2012. Schotte P, et al. Non-specific effects of methyl ketone peptide inhibitors of caspases. FEBS Lett. 1999 442 117-121. 

Figure 7 Structure of ATP-peptide substrate linked "bifunctional" kinase inhibitors are a general strategy to generate specific inhibitors of any protein kinase whose peptide substrate specificity is known.

Phosphonates (Fig. 8) and sulfonates represent a third class of covalent irreversible inhibitors. These inhibitors adopt a stable tetrahedral geometry and are covalently bound transition-state analogs. They often have a peptide-like specificity element, and the electrophilicity of the leaving groups can be modified to mne the reactivity of the inhibitor. These inhibitors are specific for serine proteases, because the serine protease active site has a well-defined oxyanion hole, which stabilizes the transition-state mimic. 

Sanschagrin, F., Levesque, R. C. (2005). A specific peptide inhibitor of the class B metallo-beta-lactamase L-1 from Stenotrophomonas maltophilia identified using phage display. J. Antimicrob. Chemother., 55, 252-255. 

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