In Silico Approach to Identify Substrates and Inhibitors of Malaria Proteases

Abstract

Malaria affects over 500 million people and causes 1.3 million deaths annually. The parasite, Plasmodium falciparum, is responsible for the most deadly variant of malaria in humans. Due to evolving resistance to current treatments, it is necessary to develop new drugs targeting the parasite. Potential drug targets are the malaria proteases; several proteases are critical in both the liver and blood stages of the parasite's life cycle, essential for both invasion and egress of cells. Proteases have been effective drug targets for the treatment of several diseases evidenced by the development of HIV protease inhibitors, ACE inhibitors treating hypertension, and anticoagulants treating thrombosis. In developing new therapies, we are taking a structure-based drug design approach to design inhibitors of proteases key to parasite survival. While several vital proteases have been identified, relatively little else is known and substrates for many proteases have yet to be identified. To identify these substrates, we are using an in silico approach to screen for peptides that bind to the protease active site, identify sequence preference, and possibly identify proteins cleaved by the protease. To achieve protease substrate identification, we have created peptide conformer libraries and docked peptides into crystal structures and homology models of several proteases. Understanding the substrate spectrum of these proteases can facilitate the design of peptide mimics that can be developed into inhibitors. In addition to identification of substrates, we are taking a fragment-based approach to design new inhibitors. Drug-like fragments from multiple compound libraries are docked into the protease active site and top hits are later screened in crystal soaking experiments and in parasites. An in silico approach followed with in vitro confirmation and in vivo evaluation is a starting point for developing new anti-malarial therapies.