Current Pharmaceutical Design - Volume 8, Issue 18, 2002

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 lysosomal cysteine proteases and the caspases, and their inhibitors.

Thirteen papain-like cysteine proteases (cathepsins) are coded in the human genome from which two represent pseudogenes. Initially it was believed that lysosomal cysteine proteases primarily fulfill house-keeping functions which would exclude them as potential drug targets. Within the last decade, this view has dramatically changed and highly specific and therapeutically relevant functions have been assigned to individual cathepsins. Cathepsins are critical for osteoclast-mediated bone resorption and cartilage erosion in arthritis. They are involved in various aspects of immune responses, in the development and proliferation of various cell types, as well as in tumor invasion and metastasis. Cathepsins qualify as pharmaceutical targets for the treatment of osteoporosis, arthritis, asthma, autoimmune diseases, and potentially for certain forms of cancer. The major challenge in using cysteine protease inhibitors will be the design of highly selective, potent, and bioavailable compounds. Emerging novel functions of long-known and recently discovered cathepsins will require more emphasis on the selectivity of drug candidates to avoid adverse side effects. This review will focus on the discussion of presently known functions of papain-like cathepsins and on recent advances in the design of cysteine protease inhibitors.

New drugs to treat malaria are urgently needed. Cysteine proteases of malaria parasites offer potential new chemotherapeutic targets. Cysteine protease inhibitors block parasite hemoglobin hydrolysis and development, indicating that cysteine proteases play a key role in hemoglobin degradation, a necessary function of erythrocytic trophozoites. These inhibitors also block the rupture of erythrocytes by mature parasites, suggesting an additional role for cysteine proteases in the hydrolysis of erythrocyte cytoskeletal proteins. Recent studies have shown that the repertoire of cysteine proteases of malaria parasites is larger than was previously realized. Plasmodium falciparum, the most virulent human malaria parasite, expresses three papain-family cysteine proteases, known as falcipains. All three proteases are expressed by trophozoites and hydrolyze hemoglobin at acidic pH, suggesting roles in this process. Falcipain-2 also hydrolyzes ankyrin at neutral pH, suggesting additional activity against erythrocyte cytoskeletal targets. Multiple orthologs of the falcipains have been identified in other plasmodial species. Analysis of orthologs from animal model rodent parasites identified similar features, but some noteworthy biochemical differences between the cysteine proteases. These differences must be taken into account in interpreting in vivo experiments. A number of small molecule cysteine protease inhibitors blocked parasite hemoglobin hydrolysis and development, and inhibitory effects against parasites generally correlated with inhibition of falcipain-2. Some compounds also cured mice infected with otherwise lethal malaria infections. Current research priorities are to better characterize the biological roles and biochemical features of the falcipains. In addition, efforts to identify optimal falcipain inhibitors as antimalarials are underway.

The application of various molecular modeling techniques has been recently reported in the design of several new cysteine protease inhibitors. Computational chemistry techniques have been used to understand and predict enzyme-inhibitor interactions and also to study enzyme mechanism and inhibitor reactivity. This review focuses on examples that use structure-based design or reflect cysteine proteases as a target class. In several cases X-ray crystallography and molecular modeling have significantly facilitated the inhibitor design process. Cysteine proteases can present extra challenges in molecular modeling, due to the covalent binding modes and the reactive nature of many of the inhibitors. We also discuss some of the key challenges in developing new tools to evaluate these properties and help in making informed decisions about new templates and leads.