Abstract
Among a group of 310 natural antiviral natural metabolites, our team identified three compounds as the most potent natural inhibitors against the SARS-CoV-2 main protease (PDB ID: 5R84), M pro . The identified compounds are sattazolin and caprolactin A and B. A validated multistage in silico study was conducted using several techniques. First, the molecular structures of the selected metabolites were compared with that of GWS , the co-crystallized ligand of M pro , in a structural similarity study. The aim of this study was to determine the thirty most similar metabolites (10%) that may bind to the M pro similar to GWS . Then, molecular docking against M pro and pharmacophore studies led to the choice of five metabolites that exhibited good binding modes against the M pro and good fit values against the generated pharmacophore model. Among them, three metabolites were chosen according to ADMET studies. The most promising M pro inhibitor was determined by toxicity and DFT studies to be caprolactin A ( 292 ). Finally, molecular dynamics (MD) simulation studies were performed for caprolactin A to confirm the obtained results and understand the thermodynamic characteristics of the binding. It is hoped that the accomplished results could represent a positive step in the battle against COVID-19 through further in vitro and in vivo studies on the selected compounds.
Keywords: ADMET; DFT; MD simulations; SARS-CoV-2; docking; main protease; pharmacophoric; structural similarity.
【저자키워드】 SARS-CoV-2, main protease, docking, MD simulations, DFT, ADMET, structural similarity., pharmacophoric, 【초록키워드】 COVID-19, Structure, molecular docking, Toxicity, docking, molecular dynamics, protease, in vitro, in silico, SARS-CoV-2 main protease, MD simulations, Characteristics, metabolites, molecular, in vivo, inhibitor, metabolite, binding, compounds, Ligand, similarity, determined by, Compound, PDB ID, M pro, choice, simulation studies, positive, battle, natural antiviral, Simulation study, PDB, FIVE, selected, performed, conducted, exhibited, was determined, determine, thermodynamic, binding mode, co-crystallized, the SARS-CoV-2, 【제목키워드】 natural, targeting, Potential,