Docking and Molecular Dynamic Simulations of Cholecalciferol (Vitamin D3) as a Promising Inhibitor of Main Protease of Coronavirus to Prevent COVID-19 Infection

Abstract

Coronavirus infectious disease - 2019 (COVID-19) is a pandemic that has no potential drug as of today to cure it. Some recent studies showed both supportive and contradictory results of using some chemicals such as hydroxychloroquine in fighting against the cure or spread of this infective disease. This article focuses on the investigation of binding of Cholecalciferol (Vitamin D3) ligand to the main protease of COVID-19. In addition to the Vitamin D3 (VD3), the prospects of using Resveratrol and Curcumin as potential drugs are also studied by conducting molecular docking studies. The docking score for VD3 is observed to be on par with that of hydroxychloroquine. With VD3 obtained naturally from sunlight, it is a cheaper, essential and more promising candidate for the inhibition or spread of COVID-19. Molecular dynamic (MD) simulations of the binding of VD3 to the main protease are conducted using LAMMPS software with CHARMM force field. Several performances such as the root mean square deviation, root mean square fluctuation and number of hydrogen bonds are obtained and compared between protease and docked protease at different time steps. The MD simulations show that VD3 plays very vital role in inhibiting the main protease of coronavirus. © 2021 ACM.

Keywords Cholecalciferol, Coronavirus, COVID-19, Molecular docking, Molecular dynamics