MODULATING STRUCTURE AND DYNAMICS AT ALLOSTERIC SITES USING SMALL MOLECULES

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 变构位点已经显示出选择性抑制特定蛋白质靶点的巨大潜力，但探索有限。这些位点很难用小分子靶向，因为它们是高度灵活的;然而，基于片段的方法，特别是系链，在这些位点的小分子发现中显示出希望。在系链中，在还原条件下针对内源性或工程化的表面半胱氨酸筛选一组含二硫化物的双链体，以使用LC/MS鉴定即使在低亲和力下的良好结合剂。预测双链体文库的相对亲和力的计算方法将可用于指导命中-先导SAR化学和预测特定位点的可药性。我正在开发一种分子动力学分析方法来寻找相关的运动，以确定耦合残基的变构位点和变构网络。我还开发了一个全原子，基于物理学的扭转角采样分子力学方法来预测半胱氨酸共轭化合物的相对结合亲和力，并正在研究这些共价化合物或可溶性化合物的变构效应，结合到同一网站使用分子动力学，自由能扰动，和多尺度蒙特卡罗方法。我计划验证这些预测使用的热力学循环的变性结合和弛豫分散NMR动力学。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Allosteric sites have shown great potential for selective inhibition of particular protein targets but limited exploration. Such sites are difficult to target with small molecules because they are highly flexible; yet, fragment-based apporaches, and Tethering in particular, have shown promise in small molecule discovery at these sites. In Tethering, one screens a set of disulfide-containing monophores against an endogenous or engineered surface cysteine under reducing conditions to identify good binders even at low affinity using LC/MS. A computational approach to predict relative affinities of a library of monophores would be useful in guiding hit-to-lead SAR chemistry and in predicting the druggability of particular sites. I am developing a molecular dynamics analysis method to search for correlated motions to identify allosteric sites and allosteric networks of coupled residues. I am also developing an all-atoms, physics-based torsion-angle sampling molecular mechanics approach to predict relative binding affinities of cysteine-conjugating compounds and am studying the allosteric effects of these covalent compounds or soluble compounds that bind to the same site using molecular dynamics, free energy pertubation, and multiscale Monte Carlo methods. I plan to validate these predictions using a thermodynamic cycle of denaturation for binding and relaxation-dispersion NMR for dynamics.