BB-Cl-Amidine is primarily utilized in biochemical research as a potent and selective inhibitor of protein arginine deiminases (PADs). These enzymes play a crucial role in post-translational modifications of proteins, particularly in the conversion of arginine residues to citrulline. By inhibiting PAD activity, BB-Cl-Amidine helps researchers study the biological functions of these enzymes in various physiological and pathological processes, such as inflammation, autoimmune diseases, and cancer. Its application extends to understanding the role of citrullination in diseases like rheumatoid arthritis and multiple sclerosis, providing insights into potential therapeutic targets. Additionally, BB-Cl-Amidine is used in drug discovery efforts to develop treatments for conditions linked to dysregulated PAD activity.