COVID-19 in Indonesia is considered to be entering the endemic phase, and the population is expected to live side by side with the SARS-CoV 2 viruses and their variants. In this study, procyanidin, oleic acid, methyl linoleic acid, and vitexin, four compounds from binahong leaves-tropical/subtropical plant, were examined for their interactions with the major protease (Mpro) of the SARS-CoV 2 virus. Molecular dynamics simulation shows that procyanidin and vitexin have the best docking scores of −9.132 and −8.433, respectively. Molecular dynamics simulation also shows that procyanidin and vitexin have the best Root Mean Square Displacement (RMSD) and Root Mean Square Fluctuation (RMSF) performance due to dominant hydrogen, hydrophobic, and water bridge interactions. However, further strain energy calculation obtained from ligand torsion analyses, procyanidin and vitexin do not conform as much as quercetin as ligand control even though these two ligands have good performance in terms of interaction with the target protein.
COVID-19 is an infectious disease caused by SARS-CoV-2, which attacks the respiratory tract as the primary target. Until now, no cure for COVID-19 has been found and the efforts made are vaccine distribution, so it is necessary to increase daily human immunity. M pro SARS-CoV-2 is an enzyme for viral replication in host cells so that it can be a target of inhibition. In this study, an in-silico simulation of flavonoid compounds in green meniran plants was carried out: Astragalin, Isoquercitrin, Quercitrin, and Rutin with Quercetin as a control ligand. Predictive analysis of ADMET properties showed that all ligands showed good safety for drug use in humans, except Rutin. The four ligands showed good scores on molecular docking results, which had lower binding scores and MM-GBSA than Quercetin. Molecular dynamics simulation for 20 ns showed that all ligands had good interaction stability, and Quercetin and Isoquercitrin tended to have the most stable interaction. Overall, it was found that Isoquercitrin showed better potential as a M pro SARS-CoV-2 inhibitor with a binding score of -11.973 kcal/mol, an average RMSD of 1.652Å, the highest RMSF value of 2.12Å, interacted with 25 protein residues, and had 12 torsions with strain energy of 0.748 kcal/mol.
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