E-64 is widely used in biochemical research as a potent and irreversible inhibitor of cysteine proteases. It is particularly valuable in studies involving enzymes like cathepsins, calpains, and papain, where it helps to block their activity, allowing researchers to investigate their roles in biological processes. In cell biology, E-64 is employed to study protein degradation pathways, including autophagy and lysosomal function, by preventing the breakdown of proteins by cysteine proteases. Additionally, it is used in the development of therapeutic strategies for diseases where cysteine proteases are implicated, such as cancer, neurodegenerative disorders, and parasitic infections. Its ability to selectively inhibit these enzymes makes it a crucial tool in both basic research and drug discovery.