Virtual flavonoids screening identifies potent compounds against enterovirus A71 and coxsackievirus A16

Worldwide outbreaks of hand, foot, and mouth disease (HFMD) are caused by enterovirus A71 (EV-A71) and coxsackievirus A16 (CV-A16). Since no anti-HFMD drugs are currently available, it is interesting to study potential viral inhibitors. Rupintrivir is a rhinovirus 3C protease (3Cpro) inhibitor with apparent inhibitory activity against HFMD. This study constructs pharmacophore models of the EV-A71 and CV-A16 3Cpro complexed with rupintrivir using molecular dynamics (MD) simulations. Both models had similar pharmacophore features, including hydrogen bond donors and acceptors and hydrophobic interactions. These pharmacophore models were then used as a template to screen 39 flavonoid compounds as potential novel inhibitors. Diosmin, epigallocatechin gallate (EGCG), and RTH-011 showed high binding affinities for EV-A71 and CV-A16 3Cpro. They formed hydrogen bonds with important surrounding residues in both proteins, including H40, L127, T142, A144, T145, H161, I162, G163, and G164. In addition, their effective concentrations against rhabdomyosarcoma (RD) cell infection by EV-A71 and CV-A16 were determined. EGCG had the highest half maximal effective concentration (EC 50 ) of 12.86 ± 1.30 µM for EV-A71 and 15.54 ± 1.50 µM for CV-A16, while diosmin had EC 50 of 21.01 ± 1.57 µM for EV-A71 and 30.68 ± 3.25 µM for CV-A16. Both compounds were non-toxic in RD cells, with 50% cytotoxic concentrations of > 100 µM for EGCG and > 500 µM for diosmin. In addition, MD simulation analysis showed that EGCG had a higher binding affinity than diosmin, supported by its significantly lower solvated binding free energies and greater numbers of contact atoms and key binding residues. Moreover, previous studies reported EGCG’s inhibitory effect on other viruses, such as severe acute respiratory syndrome coronavirus 2. Therefore, our findings suggest that EGCG can effectively inhibit the EV-A71 and CV-A16 3Cpro.