Identification of Potential Inhibitors of SARS-CoV-2 Main Protease from Allium roseum L. Molecular Docking Study

Abstract

The recent outbreak of the respiratory pandemic known as novel coronavirus SARS-CoV-2 disease “COVID-19” was first identified in Wuhan, China and quickly spread to other countries. The 3CL protease (3CLpro) enzyme is the main protease of the SARS-CoV-2, which is responsible for coronavirus replication and therefore, the 3CLpro is considered a drug discovery target. The study reports that the molecular docking approach of 30 compounds had been identified from Allium roseum against two 3CL proteases (3CLpro) targets (PDB: 6LU7) (PDB: 6M2N) of SARS-CoV-2 using Autodock Vina. The docking results revealed that the top three compounds, Kaempferol-7-O-rutinoside, Kaempferol-3-O-glucuronoside and Apigenin-7-O-glucoside, displayed high affinity against the two 3CLproteas binding pockets. The free energy of binding (FEB) were − 12.10, − 11.80 and − 11.52 against 6LU7 and − 11.83, − 11.34 and − 11.01 kcal/mol against 6M2N for Autodock, while AutoDock Vina scores were − 11.6, − 11.2 and − 10.3 kcal/mol against 6LU7 and − 11.1, − 10.8 and − 10.5 kcal/mol against 6M2N. The results reveal that the three compounds fully interact with the essential amino acids in the binding pocket catalytic dyad Cys145 and His41 of the two 3CLpro. Consequently, they are expected to hinder SARS-CoV-2 3CLpro activity. In conclusion, our In-silico results suggest that the three identified compounds could serve as a potential lead that could inhibit the function of 3CLprotease (3CL pro) of Coronavirus. However, in-vitro and in-vivo experiments are necessary to certify and confirm the docking results reported here.