Molecular dynamics simulation perception study of the binding affinity performance for main protease of SARS-CoV-2

Abstract

Like common cold and flu, SARC-CoV-2 virus spreads by droplets of sneezes or coughs which virus affects people of various age groups. Today, this virus is almost distributed all over the world. Since binding process plays a crucial role between host and receptor, therefore, we studied the molecules intended toward inhibition process through molecular docking and molecular dynamics simulation process. From the molecular docking study, it is noteworthy that remdesivir shows better binding affinity toward the main protease of SARS-CoV2 compared to other studied drugs. Within studied phytochemicals, carnosic acid shows better binding poses toward main protease of SARS-CoV2 among studied phytochemicals. The amino acid residues GLN110 and PHE294 were almost found in all the studied interactions of drugs and phytochemicals with main protease of SARS-CoV-2. Furthermore, the results show a larger contribution of the Van der Waals energies as compared to others like electrostatic energies suggesting that ligands at the binding pocket are predominantly stabilized by hydrophobic interactions. The conformational change during ligand binding was predicted from Gibbs free energy landscape analysis through molecular dynamics simulation. We observed that, there were two main free energy basins for both docked carnosic acid complex and for docked remdesivir complex, only one main free energy basin was found in the global free energy minimum region.

Communicated by Ramaswamy H. Sarma

Keywords:

• SARC-CoV-2 virus
• binding affinity
• drug likeness properties
• molecular dynamics simulations
• Gibbs free energy landscape

Acknowledgments

S.N. Sahu, B. Mishra, R. Sahu acknowledge Kalinga Institute of Industrial Technology (KIIT), Deemed to be Bhubaneswar University. S.K. Pattanayak is grateful to National Institute of Technology, Raipur.

Disclosure statement

No potential conflict of interest was reported by the authors.