Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Simrol, Indore, 453552, India.
Institute of Microbial Chemistry (BIKAKEN), Microbial Chemistry Research Foundation, Numazu-shi, Shizuoka, Japan.
Drugs R D. 2021 Sep;21(3):273-283. doi: 10.1007/s40268-021-00357-0. Epub 2021 Jul 29.
BACKGROUND AND OBJECTIVE: Coronavirus disease 2019 is a novel disease caused by the severe acute respiratory syndrome coronavirus (SARS-CoV)-2 virus. It was first detected in December 2019 and has since been declared a pandemic causing millions of deaths worldwide. Therefore, there is an urgent need to develop effective therapeutics against coronavirus disease 2019. A critical step in the crosstalk between the virus and the host cell is the binding of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein to the peptidase domain of the angiotensin-converting enzyme 2 (ACE2) receptor present on the surface of host cells. METHODS: An in silico approach was employed to design a 13-amino acid peptide inhibitor (13AApi) against the RBD of the SARS-CoV-2 spike protein. Its binding specificity for RBD was confirmed by molecular docking using pyDockWEB, ClusPro 2.0, and HDOCK web servers. The stability of 13AApi and the SARS-CoV-2 spike protein complex was determined by molecular dynamics simulation using the GROMACS program while the physicochemical and ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties of 13AApi were determined using the ExPASy tool and pkCSM server. Finally, in vitro validation of the inhibitory activity of 13AApi against the spike protein was performed by an enzyme-linked immunosorbent assay. RESULTS: In silico analyses indicated that the 13AApi could bind to the RBD of the SARS-CoV-2 spike protein at the ACE2 binding site with high affinity. In vitro experiments validated the in silico findings, showing that 13AApi could significantly block the RBD of the SARS-CoV-2 spike protein. CONCLUSIONS: Blockage of binding of the SARS-CoV-2 spike protein with ACE2 in the presence of the 13AApi may prevent virus entry into host cells. Therefore, the 13AApi can be utilized as a promising therapeutic agent to combat coronavirus disease 2019.
背景与目的:2019 年冠状病毒病是一种由严重急性呼吸系统综合征冠状病毒(SARS-CoV-2 病毒)引起的新型疾病。该病毒于 2019 年 12 月首次被发现,此后已被宣布为大流行,在全球范围内造成数百万人死亡。因此,迫切需要开发针对 2019 年冠状病毒病的有效治疗方法。病毒与宿主细胞相互作用的关键步骤是 SARS-CoV-2 刺突蛋白的受体结合结构域(RBD)与宿主细胞表面存在的血管紧张素转换酶 2(ACE2)受体的肽酶结构域结合。
方法:采用计算机模拟方法设计针对 SARS-CoV-2 刺突蛋白 RBD 的 13 个氨基酸肽抑制剂(13AApi)。使用 pyDockWEB、ClusPro 2.0 和 HDOCK web 服务器进行分子对接,证实了其与 RBD 的结合特异性。使用 GROMACS 程序进行分子动力学模拟,确定 13AApi 和 SARS-CoV-2 刺突蛋白复合物的稳定性,使用 ExPASy 工具和 pkCSM 服务器确定 13AApi 的物理化学和 ADMET(吸收、分布、代谢、排泄和毒性)特性。最后,通过酶联免疫吸附试验进行体外验证 13AApi 对刺突蛋白的抑制活性。
结果:计算机分析表明,13AApi 可以与 SARS-CoV-2 刺突蛋白的 RBD 在 ACE2 结合位点以高亲和力结合。体外实验验证了计算机模拟的结果,表明 13AApi 可以显著阻断 SARS-CoV-2 刺突蛋白的 RBD。
结论:在存在 13AApi 的情况下,阻止 SARS-CoV-2 刺突蛋白与 ACE2 的结合可能会阻止病毒进入宿主细胞。因此,13AApi 可作为治疗 2019 年冠状病毒病的有前途的治疗剂。
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