Xu David, Si Yubing, Meroueh Samy O
Department of BioHealth Informatics, Indiana University School of Informatics and Computing , Indianapolis, Indiana 46202, United States.
J Chem Inf Model. 2017 Sep 25;57(9):2250-2272. doi: 10.1021/acs.jcim.7b00181. Epub 2017 Aug 29.
The binding affinity of a protein-protein interaction is concentrated at amino acids known as hot spots. It has been suggested that small molecules disrupt protein-protein interactions by either (i) engaging receptor protein hot spots or (ii) mimicking hot spots of the protein ligand. Yet, no systematic studies have been done to explore how effectively existing small-molecule protein-protein interaction inhibitors mimic or engage hot spots at protein interfaces. Here, we employ explicit-solvent molecular dynamics simulations and end-point MM-GBSA free energy calculations to explore this question. We select 36 compounds for which high-quality binding affinity and cocrystal structures are available. Five complexes that belong to three classes of protein-protein interactions (primary, secondary, and tertiary) were considered, namely, BRD4•H4, XIAP•Smac, MDM2•p53, Bcl-xL•Bak, and IL-2•IL-2Rα. Computational alanine scanning using MM-GBSA identified hot-spot residues at the interface of these protein interactions. Decomposition energies compared the interaction of small molecules with individual receptor hot spots to those of the native protein ligand. Pharmacophore analysis was used to investigate how effectively small molecules mimic the position of hot spots of the protein ligand. Finally, we study whether small molecules mimic the effects of the native protein ligand on the receptor dynamics. Our results show that, in general, existing small-molecule inhibitors of protein-protein interactions do not optimally mimic protein-ligand hot spots, nor do they effectively engage protein receptor hot spots. The more effective use of hot spots in future drug design efforts may result in smaller compounds with higher ligand efficiencies that may lead to greater success in clinical trials.
蛋白质 - 蛋白质相互作用的结合亲和力集中在被称为热点的氨基酸上。有人提出,小分子通过以下两种方式破坏蛋白质 - 蛋白质相互作用:(i)结合受体蛋白热点;(ii)模拟蛋白质配体的热点。然而,尚未进行系统研究来探索现有小分子蛋白质 - 蛋白质相互作用抑制剂在蛋白质界面模拟或结合热点的有效程度。在此,我们采用显式溶剂分子动力学模拟和终点MM - GBSA自由能计算来探讨这个问题。我们选择了36种具有高质量结合亲和力和共晶体结构的化合物。考虑了属于三类蛋白质 - 蛋白质相互作用(一级、二级和三级)的五个复合物,即BRD4•H4、XIAP•Smac、MDM2•p53、Bcl - xL•Bak和IL - 2•IL - 2Rα。使用MM - GBSA进行的计算丙氨酸扫描确定了这些蛋白质相互作用界面处的热点残基。分解能量比较了小分子与单个受体热点的相互作用以及与天然蛋白质配体的相互作用。药效团分析用于研究小分子模拟蛋白质配体热点位置的有效程度。最后,我们研究小分子是否模拟天然蛋白质配体对受体动力学的影响。我们的结果表明,一般来说,现有的蛋白质 - 蛋白质相互作用小分子抑制剂不能最佳地模拟蛋白质 - 配体热点,也不能有效地结合蛋白质受体热点。在未来的药物设计中更有效地利用热点可能会产生具有更高配体效率的更小化合物,这可能会在临床试验中取得更大成功。