Cysteine proteases are widespread in nature. Their implication in numerous vital processes and pathologies make them highly attractive targets for drug design. The proper functioning and regulation of activity of cysteine proteases is a delicate balance of many factors, one of the most crucial being the protease inhibitors. In this review the basic principles of physiological protease inhibition by protein inhibitors are discussed with the focus on papain-like cathepsins and the caspases, and their inhibitors.
INTRODUCING THE TARGETS: CYSTEINE PRO-TEASESCysteine proteases represent one of the five mechanistic classes of proteases. Their common feature is their catalytic mechanism: all cysteine proteases utilize a Cys residue as the nucleophile and a His residue as the general base for proton shuttling. Cysteine proteases are widespread in nature and can be found in organisms from viruses and eubacteria to humans. Based on sequence homology and implied structural organization, they are divided into clans, each consisting of one or more families. The most abundant among all cysteine proteases is clan CA, which includes the papain family and the calpain family. The second abundant clan is CD, containing the caspase family. Whereas in the first two families the catalytic Cys and His residues are in the Cys-His order in the sequence, this order is reversed in caspases (His-Cys) and other members of clan CD, including gingipains, legumains, clostripains and separases [reviewed in 1, 2].
Papain-Like CathepsinsThe family comprises papain and related plant proteases, such as chymopapain, caricain, bromelain and actinidin, cysteine proteases from Trypanosomatids, Leishmania, Schistosoma, Giardia, Fasciola and other parasites, bleomycin hydrolase and the lysosomal cathepsins B, C, H, L, S, K, O, F, X, V and W (human members). Lysosomal cathepsins are monomeric proteins with M r ~30 kDa with the exception of tetrameric cathepsin C with M r ~200 kDa [reviewed in 1, 3].The enzymes are synthesized as preproenzymes and share similar sequences and tertiary structures. Their structures consist of two domains, referred to as the R-and Ldomains, with a 'V' shaped active site cleft situated between them. The most dominant feature of the L-domain is about30 residue central α-helix, whereas the R-domain is folded into a β-barrel. Propeptides are mainly alpha helical and sterically block access to the active site, thereby inhibiting activity and endowing latency on the pro-enzymes [reviewed in 3-5]. The enzymes are optimally active in slightly acidic, reducing environments (pH 4.5-6.5). In the active form the two catalytic residues Cys 25 and His 159 (papain numbering) form a thiolate-imidazolium ion pair, which is essential for the enzyme activity [6]. Most of the enzymes' specificity is governed by the substrate binding sites S2 and S1' [7].The enzymes are mostly endopeptidases with cathepsins B and H being also a carboxydipeptidase and an aminopeptidase, respectively. The only true exopeptidases are carboxymono/carboxydipeptidase cat...