In-silico Study to Identify Dietary Molecules as Potential SARS-CoV-2 Agents

Abstract

Background: Recently, Coronavirus Disease-2019 (COVID-19), caused by a fatal strain of coronavirus named Severe Acute Respiratory Syndrome-2 (SARS-CoV-2), has been declared as a pandemic by the World Health Organisation (WHO) on 11 March 2020. Globally, no therapy such as vaccines and specific therapeutic agents is available so far despite some protease inhibitors and antiviral agents. Introduction: Due to no therapeutic drug or vaccine against SARS-CoV-2 so far, phytomedicine may be developed as therapeutic agents in the prevention and treatment of current COVID-19 disease. Thus, the aim of this study was to find out a suitable therapeutic agent from selected 17 dietary molecules, which could target SARS-CoV-2 encoded proteins. Materials and Methods: In this study, 3D structures of selected dietary molecules were obtained from the PubChem database, which have previously been reported for their antiviral and anti-inflammatory effects. Then, molecular docking analysis by using AutoDoc4 and AutoDockVina software was conducted to evaluate their anti-SARS-CoV-2 activity. Lipinski’s rule of five and drug-likeness properties were also discussed with the help of Molinspiration and the OSIRIS property explorer methods. Results: Our results revealed that, among all, epigallocatechin gallate (EGCG) (7) is a lead compound that could fit well into the binding sites of docked proteins of SARS-CoV-2. EGCG showed very strong molecular interactions with the free enzyme of main protease (6y2e), chimeric receptorbinding domain complexed with human ACE2 (6vw1), and NSP15 endoribonuclease (6vww) encoded proteins of SARS-CoV-2, by showing binding energies -9.30, -8.66, and -8.38, kcal/mole, respectively. Conclusion: In the present study, EGCG (7) is more active than two standard drugs that are currently being used in COVID 19, namely remdesivir and nafamostat. Therefore, EGCG (7), as per our results, might be explored as a therapeutic agent for the treatment of COVID-19.