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

The main protease (M^pro) 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 M^pro 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 M^pro 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 M^pro. Molecular dynamics simulations and binding free energy calculations were employed to reveal the atomic details of the binding of these compounds with M^pro. 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 M^pro inhibitors with high potency.