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.