Integrating Chemo- and Bioinformatics with In Vitro Biological Assays to Discover Potential ACE2 and Mpro Inhibitors against SARS-CoV‑2

Abstract

The study aims to identify potential SARS-CoV-2 inhibitors and investigate the mechanism of action on the viral ACE2 receptor and main protease (Mpro), using chemo- and bioinformatics approaches. Ligand-based virtual screening was performed in the Molport database (∼4.79 million compounds), and after applying physicochemical filters, 313 molecules with characteristics such as hydroxychloroquine were obtained. After obtaining bioactive conformations, the molecular structures were subjected to the study of pharmacokinetic predictions, in which 106 molecules presented properties for oral bioavailability, penetration of the BBB, PPB, and solubility (average). The toxicological property predictions proved plausible for the molecules, as they did not present warnings of hepatotoxicity, mutagenicity, potential risk of carcinogenicity, and LC50 and LD50 values higher than the controls. Subsequently, 81 structures were subjected to a molecular docking study of ACE2 receptor/Spike and Mpro. In the ACE2 receptor, four (4) ligands showed high binding affinity value, in which the molecule MolPort-010-778-422 had the best ΔG value of −9.414 kcal/mol, followed by MolPort-009-093-282 with ΔG = −8.978 kcal/mol. In the Mpro receptor, four (4) ligands showed high binding affinity values compared to control 11b, with emphasis on molecule MolPort-005-766-143 with ΔG = −8.829 kcal/mol, followed by molecule MolPort-046-186-743. To study the antiviral effects of the molecules in vitro, TopHits8 molecules were tested against the SARS-CoV-2 virus. MolPort-010-778-422 had the best result on the screening and presented an IC50 of 8.9 nM.