Molecular docking studies on synthetic therapeutic agents for COVID-19

Coronavirus disease (COVID-19) is an infectious disease caused by coronavirus 2 (SARS CoV-2) who have been detected for the first time in Wuhan China in December 2019. The rapid spread of this highly contagious and pathogenic virus led to the declaration of the pandemic by the World Health Organization (WHO) on March 11, 2020. In these conditions, the discovery of new antiviral agents is extremely important. For the development of the anti-SARS-CoV-2 drugs, the fastest way is to find potential molecules from the marketed drugs by molecular docking studies. Molecular docking studies have been performed to identify and visualize the most likely interaction of the ligand with the protein/enzyme receptor. The docking score and hydrogen bonds formed with the amino acids from of the group interaction atoms are used to predict the binding modes, the binding affinity, and the orientation of the docked ligands in the active site of the protein/enzyme receptor. The docking study have been carried out with synthetic anti-viral agents (13) and anti-inflammatory agents (2) as ligands against the SARS-CoV-2 main protease (PD ID: 6W63, PD ID: 6WNP), SARS-CoV-2 spike glycoprotein (closed state) (PD ID: 6VXX), SARS-CoV-2 chimeric receptor-binding domain complexed with its receptor human ACE2 (PD ID: 6VW1), SARS-CoV-2 RNA-dependent RNA polymerase (PD ID: 6M71), SARS-CoV-2 3CL protease (3CL pro) (PD ID: 6M2N).