School of Engineering, RMIT University, Melbourne, Victoria 3001, Australia.
Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.
J Phys Chem B. 2021 Mar 18;125(10):2533-2550. doi: 10.1021/acs.jpcb.0c11321. Epub 2021 Mar 3.
The novel RNA virus, severe acute respiratory syndrome coronavirus II (SARS-CoV-2), is currently the leading cause of mortality in 2020, having led to over 1.6 million deaths and infecting over 75 million people worldwide by December 2020. While vaccination has started and several clinical trials for a number of vaccines are currently underway, there is a pressing need for a cure for those already infected with the virus. Of particular interest in the design of anti-SARS-CoV-2 therapeutics is the human protein angiotensin converting enzyme II (ACE2) to which this virus adheres before entry into the host cell. The SARS-CoV-2 virion binds to cell-surface bound ACE2 via interactions of the spike protein (s-protein) on the viral surface with ACE2. In this paper, we use all-atom molecular dynamics simulations and binding enthalpy calculations to determine the effect that a bound ACE2 active site inhibitor (MLN-4760) would have on the binding affinity of SARS-CoV-2 s-protein with ACE2. Our analysis indicates that the binding enthalpy could be reduced for s-protein adherence to the active site inhibitor-bound ACE2 protein by as much as 1.48-fold as an upper limit. This weakening of binding strength was observed to be due to the destabilization of the interactions between ACE2 residues Glu-35, Glu-37, Tyr-83, Lys-353, and Arg-393 and the SARS-CoV-2 s-protein receptor binding domain (RBD). The conformational changes were shown to lead to weakening of ACE2 interactions with SARS-CoV-2 s-protein, therefore reducing s-protein binding strength. Further, we observed increased conformational lability of the N-terminal helix and a conformational shift of a significant portion of the ACE2 motifs involved in s-protein binding, which may affect the kinetics of the s-protein binding when the small molecule inhibitor is bound to the ACE2 active site. These observations suggest potential new ways for interfering with the SARS-CoV-2 adhesion by modulating ACE2 conformation through distal active site inhibitor binding.
新型 RNA 病毒，严重急性呼吸综合征冠状病毒 2 型（SARS-CoV-2），是目前 2020 年导致死亡率的主要原因，导致全球超过 160 万人死亡，超过 7500 万人感染。虽然疫苗接种已经开始，并且有多项针对多种疫苗的临床试验正在进行，但对于已经感染该病毒的人来说，迫切需要一种治疗方法。在设计抗 SARS-CoV-2 疗法时，特别感兴趣的是人类蛋白血管紧张素转换酶 II（ACE2），该病毒在进入宿主细胞之前与之结合。SARS-CoV-2 病毒粒子通过病毒表面的刺突蛋白（s 蛋白）与 ACE2 之间的相互作用与细胞表面结合的 ACE2 结合。在本文中，我们使用全原子分子动力学模拟和结合焓计算来确定结合 ACE2 活性位点抑制剂（MLN-4760）对 SARS-CoV-2 s 蛋白与 ACE2 结合亲和力的影响。我们的分析表明，s 蛋白与结合 ACE2 活性位点抑制剂的 ACE2 蛋白的结合焓可以降低多达 1.48 倍作为上限。观察到这种结合强度的减弱是由于 ACE2 残基 Glu-35、Glu-37、Tyr-83、Lys-353 和 Arg-393 与 SARS-CoV-2 s 蛋白受体结合域（RBD）之间的相互作用的不稳定。构象变化导致 ACE2 与 SARS-CoV-2 s 蛋白的相互作用减弱，因此降低了 s 蛋白的结合强度。此外，我们观察到 N 端螺旋的构象不稳定性增加，并且参与 s 蛋白结合的 ACE2 基序的大部分发生构象位移，这可能会影响小分子抑制剂与 ACE2 活性位点结合时 s 蛋白结合的动力学。这些观察结果表明，通过调节 ACE2 构象，通过远端活性位点抑制剂结合来干扰 SARS-CoV-2 粘附的潜在新方法。
