Cl-amidine hydrochloride is primarily used in biochemical research as a potent and selective inhibitor of protein arginine deiminases (PADs). These enzymes play a significant role in post-translational modifications of proteins, particularly in the conversion of arginine residues to citrulline. This process is implicated in various physiological and pathological conditions, including autoimmune diseases like rheumatoid arthritis and multiple sclerosis. By inhibiting PAD activity, Cl-amidine hydrochloride helps researchers study the role of citrullination in disease mechanisms and explore potential therapeutic strategies. Additionally, it is utilized in studies related to epigenetics, as PADs are involved in regulating gene expression through histone modification. Its application extends to cancer research, where abnormal PAD activity is linked to tumor progression and metastasis.