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化合物的结构和结构方面发挥着越来越大的作用 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 艾滋病毒生命周期中关键结构和组件的功能分析和荧光标记，以及 在耐药靶点设计新的抑制模式。该项目将采取多管齐下的方法，建立 围绕高度创新的硫(VI)氟交换(SuFEx)化学进行发现和设计 反应性但生物正交的特定分子，选择性地靶向病毒生命中涉及的大分子 周而复始。SuFEx化学在发现各种新的结合模式方面取得了巨大成功 目标。计算方法将补充这一化学：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，中尺度模拟将整合不同的数据 从艾滋病毒结构社区到病毒和宿主蛋白组装的模型。该项目涉及Close 与其他蜂巢调查人员合作，他们将提供实验分析和验证 已开发的方法、假设和试剂。化学和计算的结合将会 补充和扩展由其他项目中提出的实验收集的结构和功能数据， 服务于以下具体目标： 1)设计和创建面向多样性的Rational SuFEx部分不可逆结合探针文库 用于艾滋病毒目标的活动/功能调节； 2)蛋白质调控的虚拟筛选、反应对接和自由能微扰计算 病毒和宿主大分子的蛋白质和蛋白质-核酸相互作用； 3)基于建模、结构和进化序列的新型变构HIV整合酶的合理设计 抑制剂； 4)针对抑制剂和药物靶点发现的中尺度HIV综合模型的发展。 该项目将设计新的计算协议来生成和测试新的假设，通过整合 在其他蜂巢项目中产生的大量结构和生化数据。这些型号将提供 理性支持推动新分子探针的设计，并导致新的药物设计方法学和 治疗对标准疗法产生抗药性的艾滋病毒感染者的治疗进展。 SuFEx的化学工作将由夏普莱斯领导，计算工作将涉及Olson，Goodsell 利维，与外部合作者维奥拉和韦德。实验分析和假设验证将 涉及蜂巢调查人员Torbett，Kvaratskhelia，Sarafianos，Arnold，Musier-Forsyth， Lyumkis，Millar，Williamson，Marcotrigiano和Griffin。

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.