Z-FA-FMK is commonly used as an irreversible inhibitor of cysteine proteases, particularly cathepsins and caspases. It is widely applied in biochemical and cellular research to study apoptosis and lysosomal function. By covalently binding to the active site of these enzymes, it effectively blocks their activity, allowing researchers to investigate the role of specific proteases in signaling pathways. It is also used in control experiments to confirm the specificity of other protease inhibitors. Due to its cell permeability, Z-FA-FMK is suitable for both in vitro and cell-based assays.