Identifying Natural Products as Feline Coronavirus Mpro Inhibitors by Structural-Based Virtual Screening and Enzyme-Based Assays

The main protease (Mpro) is a pivotal target in the life cycle of feline coronavirus (FCoV), which causes a high mortality feline disease, feline infectious peritonitis (FIP). Virtual screening was performed against the feline coronavirus Mpro to find active compounds with low toxicity from a library of natural products. Eighty-six compounds were selected by using the rank of docking score and binding pose analysis. In the enzyme-based assay, 12 compounds showed a more than 40% inhibitory effect on Mpro at a concentration of 200 μmol/L. The IC50 values of theaflavin 3,3′-digallate (25.0 μmol/L), sennoside C (25.2 μmol/L), pinocembrin-galloyl-HHDP-G (33.3 μmol/L), and thonningianin A (50.6 μmol/L) were determined. In addition, curcuminoids (51.7–64.3% under 200 μmol/L) and flavonoids (41.3–60.3% under 200 μmol/L) also exhibited certain inhibitory effects on Mpro. Molecular dynamics simulations and binding free energy calculations were employed to reveal the atomic details of the binding of these compounds with Mpro. The results showed that most of the compounds formed significant interactions with key residues on the catalytic site, such as His-41, Cys-144, and Glu-165. These compounds could serve as a starting point to develop FCoV Mpro inhibitors with high potency.