An investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study.
J Biomol Struct Dyn 2020;
39:3347-3357. [PMID:
32362245 PMCID:
PMC7232884 DOI:
10.1080/07391102.2020.1763201]
[Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A new strain of a novel infectious disease affecting millions of people, caused by severe
acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has recently been declared as a
pandemic by the World Health Organization (WHO). Currently, several clinical trials are
underway to identify specific drugs for the treatment of this novel virus. The inhibition
of the SARS-CoV-2 main protease is necessary for the blockage of the viral replication.
Here, in this study, we have utilized a blind molecular docking approach to identify the
possible inhibitors of the SARS-CoV-2 main protease, by screening a total of 33 molecules
which includes natural products, anti-virals, anti-fungals, anti-nematodes and
anti-protozoals. All the studied molecules could bind to the active site of the SARS-CoV-2
protease (PDB: 6Y84), out of which rutin (a natural compound) has the highest inhibitor
efficiency among the 33 molecules studied, followed by ritonavir (control drug), emetine
(anti-protozoal), hesperidin (a natural compound), lopinavir (control drug) and indinavir
(anti-viral drug). All the molecules, studied out here could bind near the crucial
catalytic residues, HIS41 and CYS145 of the main protease, and the molecules were
surrounded by other active site residues like MET49, GLY143, HIS163, HIS164, GLU166,
PRO168, and GLN189. As this study is based on molecular docking, hence being particular
about the results obtained, requires extensive wet-lab experimentation and clinical trials
under in vitro as well as in vivo conditions.
Communicated by Ramaswamy H. Sarma
Collapse