In Silico Structural-based Virtual Screening and Molecular Docking Analysis of Plant-derived Small Molecules for Treatment of COVID-19

Abstract

Background and Objectives Despite many studies on the new Coronavirus disease 2019 (COVID-19), there is still a rate of disease mortality, which has made researchers to focus more on finding successful antiviral drugs. In this regard, small molecule inhibitors have been suggested for their higher safety, lower toxicity, and cost-effectiveness. In this study, we applied virtual screening and docking analysis to identify the prospective inhibitors of 3CL protease and ACE-2 receptors Subjects and Methods In this study, 1,600 natural compounds were assessed by virtual screening. The ligands with a high affinity to bind to active site residues of target proteins were identified using the glide docking method and then were included in the induced-fit docking analysis in Schrödinger-Maestro software. Results The found compounds such as Theaflavin and Delphinidin had a high affinity to bind to the receptors. They had higher binding energy and a potent inhibitory effect compared to common drugs such as chloroquine. Conclusion The introduced natural compounds can be used to suppress COVID-19. The results may help develop new drugs or formulations to combat COVID-19; however, clinical trials are needed to examine the potential of these small molecules alone or in combination with other medical procedures.