Reconstruction of the unbinding pathways of new inhibitors of the SARS-CoV-2 papain-like protease using molecular dynamics simulation

Developing novel antiviral drugs against the SARS-CoV-2 virus and COVID-19 disease is imperative as the vaccines may not offer absolute protection. PLpro plays a crucial role in the viral life cycle, making it an attractive target for drug development. Several PLpro inhibitors have been developed, and their 3D structures in complex with PLpro are available. In this work, we employed Supervised Molecular Dynamics (SuMD), a specific Unbiased Molecular Dynamics (UMD) method, to investigate unbinding pathways of the novel inhibitors of PLpro (PDB IDs: 7LBR, 7RZC, 7SDR and 7E35) and GRL0617 (PDB ID: 7JRN) as a reference. We conducted three simulations for each ligand and achieved unbinding events in the nanosecond timescale in all simulations. We found that unbinding events are commonly affected by altering the conformation of the BL2 loop, which is caused by the natural fluctuations of the loop that are required to trap the substrate and throw out the product. BL2 loop is crucial for keeping the ligand and unbinding and acts as a double-edged sword. Any inhibitor designed to be effective must prevent the loop’s natural fluctuations. We perceived that increasing ligands interactions with the binding pocket interior and the BL2 loop will help prevent natural fluctuation of the BL2 loop, Although the interactions with the binding pocket’s inner side are more critical than the BL2 loop. These findings may be helpful in developing more potent inhibitors against SARS-CoV-2.
Communicated by Ramaswamy H. Sarma

鉴于疫苗无法提供绝对防护，开发针对新型冠状病毒（SARS-CoV-2）及新型冠状病毒肺炎（COVID-19）的新型抗病毒药物实属当务之急。木瓜样蛋白酶（PLpro）在病毒生命周期中发挥关键调控作用，因此成为药物开发的极具吸引力的靶点。目前已有多款PLpro抑制剂被开发出来，且其与PLpro形成复合物的三维结构已公开可用。
本研究采用监督分子动力学（SuMD）——一种特定的非偏分子动力学（UMD）方法——探究了新型PLpro抑制剂（蛋白质数据库编号（PDB IDs）：7LBR、7RZC、7SDR及7E35）以及参比化合物GRL0617（蛋白质数据库编号（PDB IDs）：7JRN）的配体解离通路。我们针对每个配体开展了三次模拟实验，所有模拟均在纳秒级时间尺度内成功观测到解离事件。
研究发现，配体解离事件通常受BL2环（BL2 loop）构象改变的影响，而该构象改变源于捕获底物并释放产物所需的环自然波动。BL2环对于维持配体结合与解离过程至关重要，堪称一把双刃剑。任何旨在实现高效活性的抑制剂，均需抑制该环的自然波动。我们进一步发现，增强配体与结合口袋内部以及BL2环之间的相互作用，将有助于抑制BL2环的自然波动，尽管与结合口袋内侧的相互作用相较BL2环更为关键。上述研究结果可为开发更高效的抗SARS-CoV-2抑制剂提供有益参考。
本文由Ramaswamy H. Sarma转交