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Journal of Molecular Modeling

Journal of Molecular Modeling

IF: 2.5
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Exploring potential SARS-CoV-2 Mpro non-covalent inhibitors through docking, pharmacophore profile matching, molecular dynamic simulation, and MM-GBSA

Published:13 April 2023 DOI: 10.1007/s00894-023-05534-3 PMID: 37055578
Yunfan Shi, Liting Dong, Zhuang Ju, Qiufu Li, Yanru Cui, Yiran Liu, Jiaoyu He, Xianping Ding

Abstract

Context

In the replication of SARS-CoV-2, the main protease (Mpro/3CLpro) is significant. It is conserved in a number of novel coronavirus variations, and no known human proteases share its cleavage sites. Therefore, 3CLpro is an ideal target. In the report, we screened five potential inhibitors (1543, 2308, 3717, 5606, and 9000) of SARS-CoV-2 Mpro through a workflow. The calculation of MM-GBSA binding free energy showed that three of the five potential inhibitors (1543, 2308, 5606) had similar inhibitor effects to X77 against Mpro of SARS-CoV-2. In conclusion, the manuscript lays the groundwork for the design of Mpro inhibitors.

Methods

In the virtual screening phase, we used structure-based virtual screening (Qvina2.1) and ligand-based virtual screening (AncPhore). In the molecular dynamic simulation part, we used the Amber14SB?+?GAFF force field to perform molecular dynamic simulation of the complex for 100?ns (Gromacs2021.5) and performed MM-GBSA binding free energy calculation according to the simulation trajectory.

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