HIV-1 Integrase Structural Biology

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DESCRIPTION (provided by applicant): Like all retroviruses, HIV-1 must integrate the cDNA copy made by reverse transcription into a cell chromosome in order to replicate. HIV-1 integration is catalyzed by the essential viral enzyme integrase. This makes the integrase an attractive drug target, and anti-integrase compounds are in US clinical trials. Rational drug design benefits from visualizing three-dimensional enzyme structures, and numerous structures of the HIV-1 integrase catalytic core domain have been solved. Although two domain N-terminal/core and core/C-terminal structures are also solved, there is no structure for the intact integrase protein, which in large part can be attributed to poor protein solubility. In cells, integrase is likely to interact with normal human proteins, and the interaction between integrase and the transcriptional co-activator lens epithelium-derived growth factor (LEDGF) forms the basis for this application. We recently solved the three-dimensional structure of the integrase-binding domain (IBD) in LEDGF using NMR spectroscopy and herein present the crystal structure of the IBD bound to the dimeric core domain of HIV-1 integrase. Building from these results, we propose to utilize the LEDGF IBD to form novel LEDGF-IN complexes and to solve the three-dimensional structure of the full-length integrase protein. Our novel structure revealed a pocket at the core domain dimer interface that is occupied by LEDGF hot spot residues upon complex formation. Because integrase mutations that ablate the interaction with LEDGF kill HIV-1, we hypothesize that compounds that bind to this region of the core and preclude LEDGF binding might similarly cripple HIV-1. Previous results revealed that certain integrase inhibitors bind at or near this pocket, but those compounds did not inhibit the LEDGF-integrase interaction. A novel assay system will be designed to select for inhibitors of the LEDGF-integrase interaction. The results of these experiments will significantly aid the design of inhibitors of HIV-1 integrase function, as the three-dimensional structure of the intact enzyme will be elucidated and an assay that could select for novel inhibitors of HIV-1 replication will be developed.