In Silico Discovery of a Novel Antiviral Scaffold for SARS-CoV‑2 Targeting the Spike Glycoprotein through the Fatty Acid Binding Pocket.

The key viral protein for infection by SARS-CoV-2 is the spike glycoprotein (S protein), mediating entry into host cells, which therefore represents a strong focus for the development of targeted therapeutics. In this work, we explored the fatty acid binding pocket within the S protein, which stabilizes an inactive conformation and disrupts cell recognition and infection. To explore the potential of this site as a drug target, molecular dynamics simulations were performed, followed by a docking-based virtual screening of commercial druglike compounds. This in silico procedure enabled the identification of potential inhibitors of SARS-CoV-2 cell infection, likely by stabilizing an inactive spike conformation, detected in binding assays, although further experiments are required to directly confirm this action. The antiviral effect of the virtual hits was analyzed in cell-based assays, and one molecule displayed a low micromolar activity. Starting from the best antiviral compound found, structural analogues were purchased and evaluated in antiviral assays. An increase in activity was observed for multiple analogues, with the strongest antiviral compound showing submicromolar activity and low cytotoxicity. The successful identification of a new antiviral scaffold through in silico studies might pave the way for the further development of antivirals against SARS-CoV-2 and shows the reliability of the methodologies applied.