Discovery and use of chemical probes through SuFEx chemistry, computational design and predictive modeling

摘要 化学生物学在帮助发现和阐明生物体的结构和功能方面起着越来越重要的作用。 复杂生物分子系统的机械方面。项目6将开发化学探针，用于 HIV生命周期中关键结构和组装的功能分析和荧光标记，以及 设计新的耐药靶点抑制模式。该项目将采取多管齐下的方法， 围绕高度创新的硫（VI）氟交换（SuFEx）化学， 反应性但生物正交的特异性分子，以选择性靶向参与病毒生命的大分子 周期SuFEx化学在发现与各种各样的蛋白质的新结合模式方面取得了巨大成功。 目标的计算方法将补充这种化学：超高通量虚拟筛选， 反应式对接将为该方法增加合理的设计，而中尺度模拟将整合各种数据 从HIV结构社区到病毒和宿主蛋白质组装的模型。该项目涉及近 与其他HIVE研究人员合作，他们将提供实验分析和验证 方法，假设，和开发的试剂。化学和计算的结合 补充和扩展其他项目中提出的实验收集的结构和功能数据， 具体目标如下： 1)设计和创建面向多样性的合理的含SuFEx部分的不可逆结合探针库 用于HIV靶标的活性/功能调节; 2)虚拟筛选、反应对接和自由能微扰计算用于蛋白质- 病毒和宿主大分子的蛋白质和蛋白质-核酸相互作用; 3)基于模型、结构和进化序列的新型变构HIV整合酶合理设计 抑制剂; 4)发展中尺度综合艾滋病毒模型的抑制剂和药物靶点发现。 该项目将设计新的计算协议，通过整合 在其他HIVE项目中产生的大量结构和生物化学数据。这些模型将提供 合理的支持驱动新的分子探针的设计，并导致新的药物设计方法， 治疗进展，以治疗对标准疗法产生耐药性的HIV感染患者。 SuFEx化学工作将由Sharpless领导，计算工作将涉及Olson，Goodsell 和利维，以及外部合作者维奥拉和韦德。实验分析和假设验证将 涉及HIVE研究人员Torbett，Kvaratskhelia，Sarafianos，Arnold，Musier-Forsyth的实验室， 莱姆基斯，米勒，威廉姆森，马可特里贾诺和格里芬。

ABSTRACT Chemical biology is playing an increasing role in helping to discover and elucidate the structural and mechanistic aspects of complex biomolecular systems. Project 6 will develop chemical probes for use in functional analysis and fluorescent labeling of critical structures and assemblies in the HIV life cycle, as well as design new modes of inhibition in drug resistant targets. The project will take a multipronged approach, built around the highly innovative Sulfur (VI) Fluorine Exchange (SuFEx) chemistry for discovering and designing reactive yet bioorthogonal specific molecules to selectively target macromolecules involved in the viral life cycle. SuFEx chemistry has shown great success in discovery of new binding modes to a wide variety of targets. Computational methods will complement this chemistry: ultrahigh-throughput virtual screening with reactive docking will add rational design to the method, and mesoscale modeling will integrate diverse data from the HIV structural community into models of viral and host protein assemblies. The project involves close collaborations with other HIVE investigators who will provide experimental assays and verification of the methods, hypotheses, and reagents that are developed. The combination of chemistry and computation will complement and extend the structural and functional data gathered by experiments proposed in other projects, serving the following specific aims: 1) Design and create diversity oriented rational SuFEx moiety-containing library of irreversible binding probes for activity/function modulation of HIV targets; 2) Virtual screening, reactive docking and free energy perturbation calculations for modulation of protein- protein and protein-nucleic acid interactions of viral and host macromolecules; 3) Modeling, structure- and evolutionary sequence-based rational design of new allosteric HIV Integrase inhibitors; 4) Development of mesoscale integrative HIV modeling for inhibitor and drug target discovery. The project will design novel computational protocols to generate and test new hypotheses by integrating the large amount of structural and biochemical data generated in other HIVE Projects. These models will provide rational support driving the design of new molecular probes, and lead to new drug design methodologies and therapeutic advances to treat HIV infected patients who have developed drug resistance to standard therapies. The SuFEx chemistry effort will be led by Sharpless, and the computational work will involve Olson, Goodsell and Levy, with outside collaborators Viola, and Wade. Experimental assays and hypothesis validation will involve the laboratories of HIVE investigators Torbett, Kvaratskhelia, Sarafianos, Arnold, Musier-Forsyth, Lyumkis, Millar, Williamson, Marcotrigiano and Griffin.