Chapter 29. Macromolecular X-Ray Crystallography and NMR as Tools for Structure-based Drug Design

Structure-based design of symmetric inhibitors of HIV-1 protease

HIV-1, the causative agent of AIDS, encodes a protease that processes the viral polyproteins into the structural proteins and replicative enzymes found in mature virions. Protease activity has been shown to be essential for the proper assembly and maturation of fully infectious HIV-1. Thus, the HIV-1 protease (HIV PR) has become an important target for the design of antiviral agents for AIDS. Analysis of the three-dimensional structures of related aspartic proteinases, and later of Rous sarcoma virus protease, indicated that the active site and extended substrate binding cleft exhibits two-fold (C2) symmetry at the atomic level. We therefore set out to test whether compounds that contained a C2 axis of symmetry, and that were structurally complementary to the active site region, could be potent and selective inhibitors of HIV PR. Two novel classes of C2 or pseudo-C2 symmetric inhibitors were designed, synthesized and shown to display potent inhibitory activity towards HIV PR, and one of these, A-77003, recently entered clinical trials. The structure of the complex with A-74704 was solved using X-ray crystallographic methods and revealed a highly symmetric mode of binding, confirming our initial design principles. These studies demonstrate that relatively simple symmetry considerations can give rise to novel compound designs, allowing access to imaginative new templates for synthesis that can be translated into experimental therapeutic agents.

Empirical and rational approaches for development of inhibitors of the human immunodeficiency virus--HIV-1

The human immunodeficiency virus, HIV-1, is generally accepted to be responsible for AIDS. It is imperative that all approaches, empirical and rational, be taken for development of a drug for therapy of this disease. These approaches are discussed, with emphasis on the direction being pursued in our laboratory. Empirically, we found 3'-deoxy-2',3'-didehydrothymidine, a compound first synthesized for potential anticancer activity by J. Horwitz in the 1960s, to be a potent inhibitor of HIV-1. It is now in Phase II/III clinical trials. We have also synthesized several 2,5'-anhydro pyrimidine nucleoside analogs, which have interesting chemical and biological properties. We have evaluated a natural product, gossypol and synthesized various derivatives for anti-HIV-1 activity, but none were appreciably more inhibitory than the parent compound. More recently, we have taken the rational approach and synthesized a boron-modified tetrapeptide, Ac-Thr-Leu-Asn-boro-Phe, which corresponds to the COOH-terminal of the Phe-Pro scissle bond of the gag/pol gene polyprotein product. Potent inhibition of the HIV-1 encoded protease was observed. These approaches and findings will be discussed.