Study of Antiviral Activity of Some Pyrimidine Ring Containing Compounds against COVID-19 Based on Molecular Docking and Quantum Chemical Calculations by DFT Method

Abstract

The novel coronavirus, COVID-19, caused by SARS-CoV-2, is a global health pandemic and currently no specific drug is available to prevent or cure this novel coronavirus (SARS-CoV-2) disease. We have been put forth five pyrimidine ring containing compounds as potential antiviral candidatures for the treatment of COVID-19 diseases based on quantum chemical properties predicted by molecular docking study and DFT calculations at the level of B3LYP method with 6-311++G (d,p) basis set. Our findings were also compared to remdesivir, a control ligand. Blind docking with the main protease revealed that the ligands preferentially bind to the active site. Interestingly, all of the ligands exhibited low binding free energies i.e., strong inhibitory interactions with the active sites of the main protease. Ligand L1 was one of them, which revealed significantly low binding energies (-8.8 kcal/mol) with SARS-CoV-2 Mpro. These binding energies are even lower than those of remdesivir’s potent active metabolite. All of the drugs interact with the key active site residues, including His41 and Cys145. These findings are also strongly supported by quantum chemical investigations.