Resistance Driven Structural Design for HIV Therapies

描述（由申请人提供）：我们拟在HIV蛋白酶抑制的背景下研究耐药的发展，以开发和测试针对这一机制的结构和合成策略。该项目的总体目标是了解病毒耐药性的机制，使建模和设计更可持续的抗病毒治疗策略成为可能。该计划包括四个高度集成的项目和三个支持核心设施：项目1将通过开发和应用药物/靶点相互作用的详细原子模型，模拟病毒种群动态和药物选择压力下的患者反应，利用自动学习和隐马尔可夫建模方法来提供和完善这些模型，从而增强和扩展计算协同进化方法来研究耐药性；项目2将利用高通量晶体学的能力，利用片段文库寻找和表征蛋白质靶点上的新结合位点，以帮助构建新的抑制剂先导物，保持对多位点PR突变体的有效性，分别与项目1和项目3的优化和合成工作相联系；项目3将利用他们的“Click Chemistry”合成方法，与项目1和项目2一起快速开发和进化新型基于片段的抑制剂，并与项目4一起开发抗性探针；项目4将通过实验表征PR和Gag-Pol其余部分的蛋白酶抑制对HIV耐药性的演变，方法是利用组织培养时间过程评估在已确定的抑制剂存在下传代病毒，以及对选定患者样本进行深度遗传分析；Core A将为该项目提供突变型和野生型蛋白酶、功能分析和化学探针以及抑制剂分析；Core B将提供必要的x射线结构数据和计算分析，以整合有关蛋白酶突变体和蛋白酶抑制剂相互作用的新信息；C核心将收集并向项目1和项目4提供艾滋病毒感染者抗逆转录病毒治疗的时间过程数据以及来自高度耐药个体的血液样本，用于深入的生物信息学和病毒基因组分析。艾滋病仍然是我们时代的主要流行病。虽然感染艾滋病毒的患者现在可以用药物治疗，使他们能够过上富有成效的生活，但这种病毒可以通过对这些药物产生耐药性来破坏这种治疗。本研究旨在详细了解HIV耐药性，目的是开发新的治疗策略，以更可持续的治疗方法来预防艾滋病。

DESCRIPTION (provided by applicant): 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.