Identification of natural compounds as potent inhibitors of SARS-CoV-2 main protease using combined docking and molecular dynamics simulations

Coronavirus disease 2019 (COVID-19) has emerged from China and globally affected the entire population through the human-to-human transmission of a newly emerged virus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The genome of SARS-CoV-2 encodes several proteins that are essential for multiplication and pathogenesis. The main protease (M-pro or 3CL(pro)) of SARS-CoV-2 plays a central role in its pathogenesis and thus is considered as an attractive drug target for the drug design and development of small-molecule inhibitors. We have employed an extensive structure-based high-throughput virtual screening to discover potential natural compounds from the ZINC database which could inhibit the M-pro of SARS-CoV-2. Initially, the hits were selected on the basis of their physicochemical and drug-like properties. Subsequently, the PAINS filter, estimation of binding affinities using molecular docking, and interaction analyses were performed to find safe and potential inhibitors of SARS-CoV-2 M-pro. We have identified ZINC02123811 (1-(3-(2,5,9-trimethyl-7-oxo-3-phenyl-7H-furo[3,2-g]chromen-6-yl)propanoyl)piperidine-4-carboxamide), a natural compound bearing appreciable affinity, efficiency, and specificity towards the binding pocket of SARS-CoV-2 M-pro. The identified compound showed a set of drug-like properties and preferentially binds to the active site of SARS-CoV-2 M-pro. All-atom molecular dynamics (MD) simulations were per- formed to evaluate the conformational dynamics, stability and interaction mechanism of M-pro with ZINC02123811. MD simulation results indicated that M-pro with ZINCO2123811 forms a stable complex throughout the trajectory of 100 ns. These findings suggest that ZINC02123811 may be further exploited as a promising scaffold for the development of potential inhibitors of SARS-CoV-2 M-pro to address COVID-19. (C) 2021 The Author(s). Published by Elsevier B.V. on behalf of King Saud University.

Automated summary

COVID-19 originated in China and spread globally through human-to-human transmission, caused by a newly emerged virus called SARS-CoV-2. The main protease of SARS-CoV-2, M-pro, is a key target for drug design. A high-throughput virtual screening process identified potential natural compounds to inhibit the M-pro of SARS-CoV-2.