Virtual Screening of Phytochemicals in Search of a Potential Drug Candidate for COVID-19: DFT Study and Molecular Docking

Abstract

The global health pandemic due to COVID-19 caused by SARS-CoV-2, affected and changed the world’s condition drastically. Herein, we evaluated the bioactivity of some phytochemicals as inhibitors against SARS-CoV-2 M provirus (6LU7) using computational models. We reported the optimization of phytochemicals employing density functional theory (DFT) with B3LYP/6-311G+(d,p) level theory. DFT calculations were employed to determine the free energy, dipole moment as well as chemical reactivity descriptors. Molecular docking has been performed against the SARS-CoV-2 M provirus to search the binding affinity and interactions of all compounds with the respective protein. The known drug, Chloroquine of SARS-CoV-2 main protease, was also docked to evaluate its binding affinity. Besides, the data from DFT, the docking studies predicted that flavonoids (Quercetin, Myricetin, Apigenin and Daidzein) have the least binding affinity and might serve as a potent inhibitor against SARS-CoV-2 comparable with the approved medicine, Chloroquine. The high binding affinity of flavonoids was attributed to the presence of hydrogen bonds along with different hydrophobic interactions between the flavonoid and the critical amino acid residues of the receptor. The DFT calculations showed that flavonoids have high lying HOMO, electrophilicity index and dipole moment. All these parameters could share a different extent to significantly affect the binding affinity of these phytochemicals with active protein sites.<br>