Isoform-Selective PAD2/PAD4 Substrates with Unnatural Amino Acids Enable Cellular Peptidylarginine Deiminase Activity Profiling and Reveal Vimentin Citrullination Effects in Macrophages

Peptidylarginine deiminases (PADs) catalyze the calcium-dependent conversion of arginine to citrulline, which affects diverse cellular processes. Among the human PAD isoforms, PAD2 and PAD4 are particularly relevant because of their distinct tissue distributions and substrate preferences. However, the lack of isoform-selective substrates has limited our ability to discriminate between their activities in biological systems. In this study, we developed PAD2- and PAD4-selective fluorogenic peptide substrates using the Hybrid Combinatorial Substrate Library (HyCoSuL) strategy, which incorporates both natural and over 100 unnatural amino acids. Substrate specificity profiling at P4-P2 positions revealed that PAD2 tolerates a broader range of residues, particularly at the P2 position, whereas PAD4 displays more selective preferences, favoring aspartic acid at this site. Based on these insights, we designed and validated peptide substrates with high selectivity for PAD2 or PAD4, enabling isoform-specific kinetic analysis <i>in vitro</i>. We demonstrated the utility of these substrates in profiling PAD activity in THP-1 macrophages, revealing dominant PAD2 activity in PMA (phorbol 12-myristate 13-acetate)/LPS (lipopolysaccharide)-stimulated monocytes. Furthermore, PAD4-mediated citrullination of vimentin modulates its susceptibility to caspase and calpain cleavage, potentially altering its function as a damage-associated molecular pattern (DAMP). Our findings provide a framework for the development of PAD-selective inhibitors and chemical probes, enabling the precise dissection of isozyme-specific PAD functions in health and disease.