<i>In silico</i> analysis of marine natural product from sponge (<i>Clathria</i> Sp.) for their activity as inhibitor of SARS-CoV-2 Main Protease
Dwi Syah Fitra Ramadhan, Fatmasari Siharis, Syawal Abdurrahman, Muhammad Isrul, Taufik Muhammad Fakih
Abstract
method. The ligand structures were obtained from the Knapsack database and the protein structure obtained from the RCSB site with the PDB code: 6LU7. The molecular docking method was validated by re-docked the native ligand and calculated the RMSD value. The compounds contained in Sponge were docked into the active site of the protein based on the validated methods. Afterward, the molecular dynamics were performed for 100 ns simulation, then analyzed its system complex stability. The RMSD 1.329 Å was obtained by re-docked of native ligand which indicates that the docking method was valid. Molecular docking of the ligands showed mirabilin_G has binding energy -7.38 kcal/mol, compared to the native ligand N3 inhibitor that is -7.30 kcal/mol, and the ligand showed good stability from molecular dynamics simulation indicated by RMSD, RMSF and MM-PBSA binding free energy similar to the inhibitor during 100 ns simulation. Its indicated the potential of the compounds contained in the sponge as inhibitor of SARS-CoV-2 main protease.Communicated by Ramaswamy H. Sarma.