Pharmacophore Model for SARS-CoV-2 3CLpro Small-Molecule Inhibitors and in Vitro Experimental Validation of Computationally Screened Inhibitors

= 31 μM). In combination with the developed pharmacophore model, these and other confirmed 3CLpro inhibitors may provide a basis for further similarity-based screening in independent compound databases and structural design optimization efforts to identify 3CLpro ligands with improved potency and selectivity. Overall, this study suggests that the integration of virtual screening, MD simulations, and machine learning can facilitate 3CLpro-targeted small-molecule screening investigations. Different receptor-, ligand-, and machine learning-based screening strategies provided complementary information, helping to increase the number and diversity of the identified active compounds. Finally, the resulting pharmacophore model and experimentally validated small-molecule inhibitors for 3CLpro provide resources to support follow-up computational screening efforts for this drug target.