E-64d is widely used in biological research as a cell-permeable inhibitor of cysteine proteases, particularly calpains and cathepsins. It is commonly applied in studies involving apoptosis, necrosis, and other cellular processes where protease activity plays a key role. Due to its ability to cross cell membranes, E-64d is effective in live-cell assays, helping to prevent unwanted protein degradation during experiments. It is also used in neuroscience research to protect neurons from ischemic damage by inhibiting proteolytic enzymes activated during injury. Additionally, E-64d serves as a tool in parasitology, especially in studies of protozoan parasites like Plasmodium and Trypanosoma, where it helps block cysteine protease-dependent pathways essential for parasite survival.