We propose to study the development of drug resistance in the context of HIV protease inhibition to develop and test structural and synthetic strategies in response to this mechanism. The overall goal of this Program Project is to understand the mechanisms of viral resistance, enabling modeling and design of more sustainable anti-viral therapeutic strategies. The Program consist of four highly integrated Projects and three supporting Core facilities: Project 1, will enhance and extend a computational co-evolution approach to drug resistance by developing and applying detailed atomic models of drug/target interactions, modeling viral population dynamics and patient response under drug selection pressure, exploiting automated learning and hidden Markov modeling approaches to inform and refine these models;Project 2 will exploit the capabilities of high throughput crystallography to find and characterize novel binding sites on the protein target using fragment libraries to help construct new inhibitor leads to maintain efficacy against multi-site PR mutants, linking with optimization and synthetic efforts in Projects 1 and 3 respectively;Project 3 will utilize their "Click Chemistry" synthetic approaches for rapid development and evolution of novel fragment-based inhibitors in conjunction with Projects 1 and 2, and develop resistance probes with Project 4;Project 4 will experimentally characterize the evolution of HIV resistance in response to protease inhibition both within PR and in the rest of Gag-Pol, by exploiting tissue-culture time-course evaluation passaged virus in the presence of identified inhibitors, as well as from deep genetic analysis of selected patient samples;Core A will provide mutant and wildtype proteases, functional assays and chemical probes, and inhibitor analyses for the Program;Core B will provide the necessary x-ray structural data and computational analysis to integrate new information on protease mutants, and protease-inhibitor interactions;and Core C will assemble and make available to projects 1 and 4 time-course anti-retroviral treatment data on HIV infected patients as well as blood samples from highly resistant individuals for in-depth bioinformatic and viral genomic analyses. AIDS remains the major pandemic of our time. While patients infected with HIV can now be treated with drugs that enable them to live productive lives, the virus can subvert this treatment by developing resistance to these drugs. This study is aimed at a detailed understanding of HIV drug resistance, with the goal of developing new therapeutic strategies for more sustainable treatments to prevent AIDS.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Program Projects (P01)
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Special Emphasis Panel (ZRG1-AARR-A (40))
Program Officer
Sakalian, Michael
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Scripps Research Institute
La Jolla
United States
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Tiefenbrunn, Theresa; Forli, Stefano; Happer, Meaghan et al. (2014) Crystallographic fragment-based drug discovery: use of a brominated fragment library targeting HIV protease. Chem Biol Drug Des 83:141-8
Tsai, Yingssu; McPhillips, Scott E; Gonzalez, Ana et al. (2013) AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery. Acta Crystallogr D Biol Crystallogr 69:796-803
Chang, Max W; Oliveira, Glenn; Yuan, Jinyun et al. (2013) Rapid deep sequencing of patient-derived HIV with ion semiconductor technology. J Virol Methods 189:232-4
Joshi, Pheroze; Sloan, Barbara; Torbett, Bruce E et al. (2013) Heat shock protein 90AB1 and hyperthermia rescue infectivity of HIV with defective cores. Virology 436:162-72
Lin, Ying-Chuan; Happer, Meaghan; Elder, John H (2013) Selection of drug-resistant feline immunodeficiency virus (FIV) encoding FIV/HIV chimeric protease in the presence of HIV-specific protease inhibitors. J Virol 87:8524-34
Tiefenbrunn, Theresa; Forli, Stefano; Baksh, Michael M et al. (2013) Small molecule regulation of protein conformation by binding in the Flap of HIV protease. ACS Chem Biol 8:1223-31
Kislukhin, Alexander A; Higginson, Cody J; Hong, Vu P et al. (2012) Degradable conjugates from oxanorbornadiene reagents. J Am Chem Soc 134:6491-7
Breuer, Sebastian; Sepulveda, Homero; Chen, Yu et al. (2011) A cleavage enzyme-cytometric bead array provides biochemical profiling of resistance mutations in HIV-1 Gag and protease. Biochemistry 50:4371-81
Chang, Max W; Torbett, Bruce E (2011) Accessory mutations maintain stability in drug-resistant HIV-1 protease. J Mol Biol 410:756-60
Lin, Ying Chuan; Perryman, Alexander L; Olson, Arthur J et al. (2011) Structural basis for drug and substrate specificity exhibited by FIV encoding a chimeric FIV/HIV protease. Acta Crystallogr D Biol Crystallogr 67:540-8

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