Inhibition of SARS-CoV-2 main protease: a repurposing study that targets the dimer interface of the protein

Coronavirus disease-2019 (COVID-19) was firstly reported in Wuhan, China, towards the end of 2019, and emerged as a pandemic. The spread and lethality rates of the COVID-19 have ignited studies that focus on the development of therapeutics for either treatment or prophylaxis purposes. In parallel, drug repurposing studies have also come into prominence. Herein, we aimed at having a holistic understanding of conformational and dynamical changes induced by an experimentally characterized inhibitor on main protease (M^pro) which would enable the discovery of novel inhibitors. To this end, we performed molecular dynamics simulations using crystal structures of <i>apo</i> and <i>α</i>-ketoamide 13b-bound M^pro homodimer. Analysis of trajectories pertaining to <i>apo</i> M^pro revealed a new target site, which is located at the homodimer interface, next to the catalytic dyad. Thereafter, we performed ensemble-based virtual screening by exploiting the ZINC and DrugBank databases and identified three candidate molecules, namely eluxadoline, diosmin, and ZINC02948810 that could invoke local and global conformational rearrangements which were also elicited by <i>α</i>-ketoamide 13b on the catalytic dyad of M^pro. Furthermore, ZINC23881687 stably interacted with catalytically important residues Glu166 and Ser1 and the target site throughout the simulation. However, it gave positive binding energy, presumably, due to displaying higher flexibility that might dominate the entropic term, which is not included in the MM-PBSA method. Finally, ZINC20425029, whose mode of action was different, modulated dynamical properties of catalytically important residue, Ala285. As such, this study presents valuable findings that might be used in the development of novel therapeutics against M^pro. Communicated by Ramaswamy H. Sarma

2019新型冠状病毒病（Coronavirus disease 2019, COVID-19）于2019年末首次在中国武汉被报道，并迅速演变为全球大流行疫情。新冠疫情的传播性与致死率，催生了大量针对治疗或预防性治疗药物开发的研究。与此同时，药物重定位研究也逐渐成为研究热点。本研究旨在全面解析经实验验证的抑制剂对新冠病毒主蛋白酶（main protease, M^pro）所诱导的构象与动态变化，以期为新型抑制剂的发现提供支撑。为此，我们分别以空载型（apo）与α-酮酰胺13b结合型新冠病毒主蛋白酶同源二聚体的晶体结构为对象，开展分子动力学模拟。对空载型主蛋白酶的模拟轨迹进行分析后，我们发现了一个全新的靶点位点：该位点位于主蛋白酶同源二聚体的界面处，紧邻催化二联体。随后，我们依托ZINC与DrugBank数据库开展基于集合的虚拟筛选，最终筛选出3种候选分子：依来多林（eluxadoline）、地奥司明（diosmin）以及ZINC02948810。这三种分子可诱导主蛋白酶催化二联体发生局部与全局构象重排，该效应与α-酮酰胺13b所引发的效应一致。此外，ZINC23881687在整个模拟过程中，可与催化关键残基Glu166、Ser1以及上述靶点位点保持稳定相互作用。但该分子的结合能为正值，推测是由于其具有较高的柔性，该柔性主导了未被分子力学-泊松玻尔兹曼表面积（MM-PBSA）方法纳入考量的熵项。最后，ZINC20425029的作用模式有所不同，它可调控催化关键残基Ala285的动态特性。综上，本研究获得了具有重要价值的研究成果，可为靶向主蛋白酶的新型治疗药物开发提供参考。本文由Ramaswamy H. Sarma供稿。