Virtual Screening with a Structure-Based Pharmacophore Model to Identify Small-Molecule Inhibitors of CARM1

CARM1 (coactivator-associated arginine methyltransferase 1), also known as PRMT4 (protein arginine N-methyltransferase 4), belongs to the protein arginine methyltransferase (PRMT) family, which has emerged as a potential anticancer drug target. To discover new CARM1 inhibitors, we performed virtual screening against the substrate-binding site in CARM1. Structure-based pharmacophore models, which were generated according to three druggable subpockets embedding critical residues for ligand binding, were applied for virtual screening. The importance of the solvent-exposed substrate-binding cavity was highlighted due to significant hydrophobicity. Aided by molecular docking, 15 compounds structurally distinct from known CARM1 inhibitors were selected to evaluate their inhibitory effects on CARM1 methyltransferase activity, which resulted in seven compounds exhibiting micromolar inhibition, with selectivity over other members in the PRMT protein family. Moreover, three of them exhibited potent antiproliferation activities in breast cancer cells. Particularly, compound NO.2 exhibited potent activity both in vitro and in cultured cells, which will serve as a leading hit for developing CARM1 inhibitors with improved efficacy. The virtual screening strategy in this study will be applicable for the discovery of substrate-competitive inhibitors targeting other members in the PRMT protein family.