Molecular Docking and Molecular Dynamics of Herbal Plants Phylantus Niruri Linn (Green Meniran) towards of SARS-CoV-2 Main Protease

Abstract

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.