Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19). As of October 21, 2020, more than 41.4 million confirmed cases and 1.1 million deaths have been reported. Thus, it is immensely important to develop drugs and vaccines to combat COVID-19. The spike protein present on the outer surface of the virion plays a major role in viral infection by binding to receptor proteins present on the outer membrane of host cells, triggering membrane fusion and internalization, which enables release of viral ssRNA into the host cell. Understanding the interactions between the SARS-CoV-2 trimeric spike protein and its host cell receptor protein, angiotensin converting enzyme 2 (ACE2), is important for developing drugs and vaccines to prevent and treat COVID-19. Several crystal structures of partial and mutant SARS-CoV-2 spike proteins have been reported; however, an atomistic structure of the wild-type SARS-CoV-2 trimeric spike protein complexed with ACE2 is not yet available. Therefore, in our study, homology modeling was used to build the trimeric form of the spike protein complexed with human ACE2, followed by all-atom molecular dynamics simulations to elucidate interactions at the interface between the spike protein and ACE2. Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) and in silico alanine scanning were employed to characterize the interacting residues at the interface. Twenty interacting residues in the spike protein were identified that are likely to be responsible for tightly binding to ACE2, of which five residues (Val445, Thr478, Gly485, Phe490, and Ser494) were not reported in the crystal structure of the truncated spike protein receptor binding domain (RBD) complexed with ACE2. These data indicate that the interactions between ACE2 and the tertiary structure of the full-length spike protein trimer are different from those between ACE2 and the truncated monomer of the spike protein RBD. These findings could facilitate the development of drugs and vaccines to prevent SARS-CoV-2 infection and combat COVID-19.

严重急性呼吸系统综合症冠状病毒-2 (SARS-CoV-2) 会导致 2019 年冠状病毒病 (COVID-19)。截至2020年10月21日，已报告确诊病例超过4140万例，死亡病例110万例。因此，开发抗击 COVID-19 的药物和疫苗非常重要。病毒颗粒外表面的刺突蛋白通过与宿主细胞外膜上的受体蛋白结合，触发膜融合和内化，从而将病毒 ssRNA 释放到宿主细胞中，从而在病毒感染中发挥重要作用。了解 SARS-CoV-2 三聚体刺突蛋白与其宿主细胞受体蛋白血管紧张素转换酶 2 (ACE2) 之间的相互作用对于开发预防和治疗 COVID-19 的药物和疫苗非常重要。已报道部分和突变 SARS-CoV-2 刺突蛋白的几种晶体结构；然而，与 ACE2 复合的野生型 SARS-CoV-2 三聚刺突蛋白的原子结构尚不清楚。因此，在我们的研究中，使用同源模型构建了与人 ACE2 复合的刺突蛋白的三聚体形式，然后进行全原子分子动力学模拟以阐明刺突蛋白和 ACE2 之间界面的相互作用。分子力学泊松-玻尔兹曼表面积 (MMPBSA) 和计算机模拟采用丙氨酸扫描来表征界面处相互作用的残基。鉴定出刺突蛋白中的 20 个相互作用残基可能与 ACE2 紧密结合有关，其中 5 个残基（Val445、Thr478、Gly485、Phe490 和 Ser494）在截短的刺突蛋白受体的晶体结构中未报告与 ACE2 复合的结合域 (RBD)。 这些数据表明ACE2和全长刺突蛋白三聚体的三级结构之间的相互作用不同于ACE2和刺突蛋白RBD的截短单体之间的相互作用。这些发现可以促进药物和疫苗的开发，以预防 SARS-CoV-2 感染和对抗 COVID-19。