Identification of novel PAD4 inhibitors using pharmacophore-based virtual screening, molecular docking, and molecular dynamics simulations

Protein arginine deiminase 4 (PAD4) is a member of the PAD family of enzymes which catalyze citrullination, or the conversion of the amino acid arginine to citrulline. Overexpression and dysregulation of PAD4 is implicated in the onset and progression of a variety of autoimmune and inflammatory diseases, including rheumatoid arthritis (RA). Thus, PAD4 inhibition via small molecules is an attractive therapeutic avenue. We utilized pharmacophore-based virtual screening of databases including over 120 million commercially available compounds to identify novel small molecule reversible inhibitors of PAD4. Molecular docking and ADME filtering identified our top three compounds that showed high binding affinity and promising ADME/Tox properties. Molecular dynamics (MD) simulations and post-MD analysis metrics such as RMSD, RMSF and Rg were carried out on the final hits to determine the stability of the complexes. All final hits outperform previously discovered reversible PAD4 inhibitors by docking score and ADME properties. Ultimately, MolPort 010-719-973 showed the most promising docking scores, residue interactions, stability, and binding energy as compared to the reference compound. Thus, we identify a novel reversible PAD4 inhibitor that may prove useful for the treatment of RA and can be used as a scaffold to design more potent PAD4 inhibitors.