Structure and Function of Integrase

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DESCRIPTION (provided by applicant): Integrase (IN) is one of three virus-encoded enzymes that are essential for retroviral replication and a validated target for the development of drugs t treat HIV/AIDS. Although there has been success in developing clinically useful drugs that block the final step in the integration reaction, the so-called strand transfer inhibitors, there is a continuing need to augment or replace existing IN therapeutics as viral resistance is encountered. A detailed knowledge of all aspects of the structure, assembly, and catalysis by HIV-1 IN, will reveal unexploited vulnerabilities and novel strategies for inhibiting this critical enzyme. In the current funding period, we applied small angle X-ray scattering (SAXS) and protein-protein cross-linking methods to obtain the first experimentally-derived models of full-length unliganded apo-IN monomers and dimers in solution, using avian sarcoma virus (ASV) IN. The results revealed a dimer architecture (called a reaching dimer) that was previously unsuspected. The configuration of the reaching dimer resembles that of the viral DNA-binding, "inner" dimer in the crystal structure of the prototype foamy virus (PFV) IN. From these and other data, we have constructed a structural model for an HIV IN reaching dimer, which we hypothesize is pre-positioned to interact with viral DNA ends. In Aim 1 of this competitive renewal we propose to test this model by determining the solution structures of monomers, dimers, and tetramers of HIV IN, using methods successfully employed with ASV IN. We will identify the interactions that stabilize HIV dimers and determine the effects of substrate binding on their conformation. In Aim 2 we will identify compounds that alter the stability of HIV apo-IN dimers and inhibit the conformational changes that are required for IN function. The results of our studies will provide critical new information concerning HIV IN structure and function, and contribute to the design of new, allosterically-acting drugs that can complement the active site inhibitors now in clinical use.