Used as an irreversible inhibitor of cysteine proteases, particularly cathepsins, Z-FA-FMK is widely applied in biochemical and cellular research to study protease function and regulation. It helps in blocking proteolytic activity in lysosomal pathways, enabling researchers to investigate the role of specific proteases in apoptosis, antigen presentation, and disease progression such as cancer and neurodegenerative disorders. Due to its cell permeability, it is effective in live cell assays for monitoring intracellular protease inhibition. It also serves as a control agent in enzyme activity studies and supports the development of targeted protease inhibitors for therapeutic use.