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

• Published in: Journal of molecular modeling Vol. 29; no. 5; p. 138
• Main Authors: Shi, Yunfan, Dong, Liting, Ju, Zhuang, Li, Qiufu, Cui, Yanru, Liu, Yiran, He, Jiaoyu, Ding, Xianping
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.05.2023; Springer Nature B.V
• Subjects: Binding; Binding energy; Characterization and Evaluation of Materials; Chemistry; Chemistry and Materials Science; Computer Appl. in Life Sciences; Computer Applications in Chemistry; COVID-19; Endopeptidases; Free energy; Gibbs free energy; Humans; Inhibitors; Mathematical analysis; Molecular docking; Molecular Docking Simulation; Molecular dynamics; Molecular Dynamics Simulation; Molecular Medicine; Original Paper; pharmacology; Pharmacophore; Protease Inhibitors - pharmacology; proteinases; SARS-CoV-2; Screening; Severe acute respiratory syndrome coronavirus 2; Simulation; Theoretical and Computational Chemistry; Workflow; Virtual screening; 3CLpro; MM-GBSA; MD

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 (15...