Computational investigations of three main drugs and its comparison with synthesized compounds as potent inhibitors of SARS-CoV-2 main protease (M(pro)): DFT, QSAR, Molecular docking, and in silico toxicity analysis

Mohapatra, Ranjan K.; Perekhoda, Lina; Azam, Mohammad; Suleiman, Marharyta; Sarangi, Ashish K.; Semenets, Anton; Pintilie, Lucia; Al-Resayes, Saud I.

In this study, we examined five previously synthesized compounds and checked their binding affinity towards the SARS-CoV-2 main protease (M(pro)) by molecular docking study, and compared the data with three FDA approved drugs, i.e., Remdesivir, Ivermectine and Hydroxychlorochine. In addition, we have investigated the docking study against the main protease of SARS-CoV-2 (M(pro)) by using Autodock 4.2 software package. The results suggested that the investigated compounds have property to bind the active position of the protein as reported in approved drugs. Hence, further experimental studies are required. The formation of intermolecular interactions, negative values of scoring functions, free binding energy and the calculated binding constants confirmed that the studied compounds have significant affinity for the specified biotarget. These studied compounds were passed the drug-likeness criteria as suggested by calculating ADME data by SwissADME server. Moreover, the ADMET properties suggested that the investigated compounds to be orally active compounds in human. Furthermore, density functional computations (DFT) were executed by applying GAUSSIAN 09 suit program. In addition, Quantitative Structure-Activity Relationship (QSAR) was studied by applying HyperChem Professional 8.0.3 program.