Discovery of highly potent naphthalene/quinoline-based PAD inhibitors: Structure-activity relationship, selectivity,...

This study focuses on developing highly potent inhibitors targeting peptidyl arginine deiminases (PADs), particularly PAD4 and PAD1, which play critical roles in citrullination-linked diseases such as cancer and autoimmune disorders. A series of benzylamine- and benzimidazole-substituted compounds were synthesized and evaluated for their inhibitory activity. Key findings include the identification of naphthalene and quinoline-based scaffolds with hydroxyl substitutions, which exhibited superior inhibition of PAD1 and PAD4 (IC₅₀ values as low as 0.273 μM and 0.204 μM, respectively), compared with their precursor, Cl-amidine. While the most potent compounds 13 and 16 showed very low cytotoxicity (CC₅₀ > 80 μM), thus providing a wide therapeutic window. Structural modifications provided valuable insights into structure-activity relationships and strategies for activity optimization. The hydroxy-naphthalene scaffold of 13 and 16 revealed a previously unrecognized binding site (Glu575) on the PAD4 enzyme, which was visualized through docking simulations. These inhibitors serve as valuable tools for investigating PAD functions and exploring potential therapeutic applications.