Binding modes of a new epoxysuccinyl-peptide inhibitor of cysteine proteases. Where and how do cysteine proteases express their selectivity?

Papain from Carica papaya, an easily available cysteine protease, is the be st-studied representative of this family of enzymes. The three dimensional structure of papain is very similar to that of other cysteine proteases of either plant (actinidin, caricain, papaya protease IV) or animal (cathepsin s B, K, L, H) origin. As abnormalities in the activities of mammalian cyste ine proteases accompany a variety of diseases, there has been a long-lastin g interest in the development of potent and selective inhibitors for these enzymes. A covalent inhibitor of cysteine proteases, designed as a combinat ion of epoxysuccinyl and peptide moieties, has been modeled in the catalyti c pocket of papain. A number of its configurations have been generated and relaxed by constrained simulated annealing-molecular dynamics in water. A c lear conformational variability of this inhibitor is discussed in the conte xt of a conspicuous conformational diversity observed earlier in several so lid-state structures of other complexes between cysteine proteases and cova lent inhibitors. The catalytic pockets S2 and even more so S3, as defined b y the pioneering studies on the papain-ZPACK, papain-E64c and papain-leupep tin complexes, appear elusive in view of the evident flexibility of the pre sent inhibitor and in confrontation with the obvious conformational scatter seen in other examples. This predicts limited chances for the development of selective structure-based inhibitors of thiol proteases, designed to exp loit the minute differences in the catalytic pockets of various members of this family. A simultaneous comparison of the three published proenzyme str uctures suggests the enzyme's prosegment binding loop-prosegment interface as a new potential target for selective inhibitors of papain-related thiol proteases, (C) 1999 Elsevier Science B.V. All rights reserved.