Leishmania major:Molecular Modeling of Cysteine Proteases and Prediction of New Nonpeptide Inhibitors

Abstract

The crystal structures of papain, cruzain, and human liver cathepsin B were used to build homology-based enzyme models of a cathepsin L-like cysteine protease (cpL) and a cathepsin B-like cysteine protease (cpB) from the protozoan parasiteLeishmania major.Although structurally a member of the cathepsin B subfamily, theL. majorcpB is not able to cleave synthetic substrates having an arginine in position P2. This biochemical property correlates with the prediction of a glycine instead of a glutamic acid at position 205 (papain numbering). The modeled active sites of theL. majorcpB and cpL were used to screen the Available Chemicals Directory (a database of about 150,000 commercially available compounds) for potential cysteine protease inhibitors, using DOCK3.5. Based on both steric and force field considerations, 69 compounds were selected. Of these, 18 showed IC50's between 50 and 100 μM and 3 had IC50's below 50 μM. A secondary library of compounds, originally derived from a structural screen against the homologous protease ofPlasmodium falciparum(falcipain), and subsequently expanded by combinatorial chemistry, was also screened. Three inhibitors were identified which were not only effective against theL. majorprotease but also inhibited parasite growth at 5–50 μM.