Molecular modelling on SARS-CoV-2 papain-like protease: an integrated study with homology modelling, molecular docking, and molecular dynamics simulations

SARS-CoV-2 PLpro was investigated as a therapeutic target for potent antiviral drugs due to its essential role in not only viral replication but also regulating the inborn immune response. Several computational approaches, including homology modelling, molecular docking, and dynamics (MD) studies, were employed search promising treating SARS-CoV-2. Eighty-one compounds, sub-structurally similar drug, used potential inhibitors of PLpro. From our results, three complexes containing ligands with Pubchem IDs: 153012995, 12149203, 123608715 showed lower binding energies than control (Ritonavir), indicating that they may become MD performed water solvent validate stability complexes. All achieved stable structure during simulation no significant fluctuations observed validation parameters. Moreover, energy each complex estimated using MM-GBSA method. Complex 1 most based on lowest score remained cavity docket snapshot. Based assumed be inhibitors. The ligand drug against targeting