Molecular docking and dynamics study to explore phytochemical ligand molecules against the main protease of SARS-CoV-2 from extensive phytochemical datasets
Shafi Mahmud, Mohasana Akter Mita, Suvro Biswas, Gobindo Kumar Paul, Maria Meha Promi, Shamima Afrose, Robiul Hasan, Sharmin Sultana Shimu, Shahriar Zaman, Salah Uddin, Trina Ekawati Tallei, Talha Bin Emran, Abu Saleh
Abstract
BACKGROUND: ) of SARS-CoV-2 can act as a potential target due to its role in viral replication and conservation level. METHODS: of SARS-CoV-2. RESULTS: The selected three ligands, Flemichin, Delta-Oleanolic acid, and Emodin 1-O-beta-D-glucoside had a binding energy of -8.9, -8.9, -8.7 KJ/mol respectively. The compounds bind to the active groove of the main protease at; Cys145, Glu166, His41, Met49, Pro168, Met165, Gln189. The multiple descriptors from the simulation study; root mean square deviation, root mean square fluctuation, radius of gyration, hydrogen bond, solvent accessible surface area confirms the stable nature of the protein-ligand complexes. Furthermore, post-md analysis confirms the rigidness in the docked poses over the simulation trajectories. CONCLUSIONS: Our combinatorial drug design approaches may help researchers to identify suitable drug candidates against SARS-CoV-2.