Abstract: Compounds having quinone and quinone analogs useful for pharmaceutical preparations have now been found which inhibit cysteine proteases, in particular, caspases and 3C-cysteine proteases. The cysteine protease inhibitors of the present invention can be identified by their mode of action in disrupting the ability of cysteine proteases and, in particular, caspases to cleave a peptide chain. These compounds are useful in inhibiting cysteine protease or cysteine protease-like proteins and for treating infections diseases or physiopathological diseases or disorders attributed to the presence of excessive or insufficient levels of cysteine proteases.