The Identification of Natural Products that are Predicted to Bind to the SARS‐CoV‐2 3CL Protease

Abstract

Considerable attention has been paid to immunological approaches to dealing with the Covid‐19 pandemic. In addition, existing pharmaceuticals, such as the modified mononucleotide Remdesvir, have been studied in the context of the viral infection.This study looks at different classes of compounds, natural products, some already ingested by millions of people every day, and asks if there is evidence that they might bind to Covid‐19 viral proteins and possibly interfere with viral replication.In this study, the Universal Natural Products Database was used to search for compounds that bind to the SARS‐CoV‐2 3CL Protease. The database was interrogated using the Smina docking program, a branch of Autodock Vina. Those compounds that were predicted by Smina to bind better than ‐9 kcal/mole were then successively interrogated with LeDock, a program that gives results that are considerably different from Smina.The compounds with predicted binding values of ‐11 kcal/mole or lower by both programs were then studied by observing their predicted binding using several programs that enable the examination of ligand‐protein interactions.While this study identified many compounds of potential interest, this report concentrates on compounds that are commonly found in foodstuffs. Some but not all of these compounds are structurally close to those compounds that have been classified by others as Pan‐Assay Interference Compounds, PAINS.