HIV-1 Protease crystallography at BARC

Abstract

Human Immunodeficiency Virus (HIV) is a complex retrovirus, and is the causative agent of Aquired Immuno Deficiency Syndrome (AIDS), a disease condition that is proving fatal to millions of Indians. Since a HIV/AIDS pandemic can destroy the very fabric of nations, devastate the most productive members of the societies, and orphan children, there is an urgent need to rein-in this disease. Crystallography can play a major role in this endeavour by providing accurate structural data on the chemical interactions between a chosen target and the designed inhibitor. Because of its essential role in the maturation process of HIV, the viral protease (HIV-1 PR) is an important target for inhibitor design. Many of the effective anti-HIV drugs in the market are inhibitors of HIV-1 PR, optimized for active-site binding through high-resolution crystal structures. However, occurence of drug resistant mutations in the protease necessitates continuous development of newer inhibitors through novel strategies. Inhibitors based on the mechanism of the enzyme are less likely to be overcome by point mutations, and thus may represent a novel class of inhibitors. Although hundreds of structures of active HIV-1 protease inhibitor complexes are reported, there are no reports of active enzyme substrate complexes. We have produced, for the first time, atomic-level snap-shots of enzyme-substrate complexes trapped at different stages of the cleavage reaction. These crystal structures may provide insight into the molecular mechanism of HIV-1 PR. For example, the formation of a low barrier hydrogen bond between catalytic aspartates had not been envisaged in earlier mechanistic proposals. Similarly, the hydrogen bond between cleavage products suggests protonation of scissile nitrogen atom by the hydroxyl group of the tetrahedral intermediate, in the reaction mechanism. The structures also open up the possibility that the enzyme uses different mechanisms to cleave substrates containing either a proline residue or a non-proline residue at the cleavage site. Finally, the structures provide a template for the design of mechanism-based inhibitors.