In silico discovery of small-molecule inhibitors targeting PRRSV 3C-like proteases.

Porcine reproductive and respiratory syndrome virus (PRRSV) poses a substantial threat to the swine industry. Current commercial vaccines lack sufficient safety and efficacy, highlighting the necessity for effective anti-PRRSV therapeutics. The 3C-like protease (3CLpro) of PRRSV is a promising target for antiviral drug development because of its essential role in viral protein processing. However, the absence of resolved crystal structures for PRRSV 3CLpro-substrate complexes hinders the screening of potential inhibitors. In this study, we aimed to identify antiviral agents that target PRRSV 3CLpro from a compound library comprising 1049,397 small molecules. Through virtual screening, we selected the top 14 candidates on the basis of docking scores and protein-ligand interactions. Subsequent molecular dynamics simulations and binding free energy calculations via the Molecular Mechanics-Poisson Boltzmann Surface Area method identified five putative lead compounds. Among these compounds, CL01790761 exhibited the most significant inhibition of PRRSV 3CLpro enzymatic activity and viral proliferation, as evidenced by enzyme inhibition and antiviral assays. Our study presents a novel antiviral candidate for PRRSV and provides valuable insights into the in silico discovery of 3CLpro inhibitors.