Target Protein Identification Using Pharmacophore Screening and Molecular Docking

To discover potential target proteins for a target molecule, we screened the target compounds against a pharmacophore library. Short peptide molecules were constructed using the Maestro module of the Schrodinger2021-1 software package. The pharmacophore library used in this study was based on the latest PDB co-crystal structures and contained 16,646 pharmacophore models, as reported by Aurélien et al. This allowed for a comprehensive exploration of the potential target proteins of the target compounds. Target screening was performed using the Phase module of the Schrodinger2021-1 software package. Considering the large number of rotatable bonds, we generated 200 conformations of the target molecule during the screening process to explore the conformational space as much as possible. All pharmacophores of the protein were considered as hits. After screening, target proteins were further filtered based on the screening score (Fitness) and manual selection.