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 (3CL^pro) 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 3CL^pro-substrate complexes hinders the screening of potential inhibitors. In this study, we aimed to identify antiviral agents that target PRRSV 3CL^pro 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 3CL^pro 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 3CL^pro inhibitors.