Identification of PEDV inhibitors targeting 3CL protease

Porcine epidemic diarrhea (PED), caused by porcine epidemic diarrhea virus (PEDV), is a highly contagious gastrointestinal disease characterized by vomiting, diarrhea, and dehydration, with mortality rates approaching 100% among suckling piglets. The PEDV 3C-like protease (3CLpro) is essential for viral replication and regarded as a critical target for antiviral inhibitor development. In this study, we aimed to identify small-molecule inhibitors of PEDV by targeting 3CLpro. Virtual screening of 1.6 million compounds from the ChemDiv library identified four potential candidates. Molecular dynamics simulations, specifically analyzing RMSD, RMSF, and Rg, demonstrated increased structural stability of the compound-protease complexes compared to the monomeric enzyme. All compounds had low cytotoxicity in Vero cells (CC₅₀ ​> ​200 ​μM). Fluorescence resonance energy transfer-based assays demonstrated dose-dependent inhibitory activity of the compounds against 3CLpro. Among the candidates, compound F366-0161 exhibited the weakest inhibition, with an IC₅₀ value of 151.5 ​μM. Two analogues, 3238-0395 (IC₅₀ of 121.4 ​μM) and L878-0493 (IC₅₀ of 123.6 ​μM), exhibited moderately enhanced activity. Y041-1672 was identified as the most effective inhibitor, with an IC₅₀ of 86.48 ​μM. In viral replication inhibition assays, Y041-1672 reduced PEDV replication, with an EC₅₀ of 17.97 ​μM and a selectivity index (SI) of 15.5 (CC₅₀/EC₅₀). These results were validated by RT-qPCR, plaque assays, immunofluorescence, and Western blot analyses. In vitro validation confirmed Y041-1672 as the optimal antiviral candidate, and time-of-addition experiments indicated that inhibition primarily occurred during viral replication. This study identifies scaffold molecules for PEDV antiviral drug development, providing strategic insights for PED treatment.