The high level of amino acid conservation and structural similarity of the substrate-binding sites of the oxygenase domains of the nitric oxide synthase (NOS) isoforms (eNOSoxy, iNOSoxy, nNOSoxy) make the interpretation of the structural basis of inhibitor isoform specificity a challenge, and provide few clues for the design of new selective compounds. Crystal structures of iNOSoxy and nNOSoxy complexed with the neuronal NOS-specific inhibitor AR-R17447 suggest that specificity is provided by the interaction of the chlorophenyl group with an isoform-unique substrate access channel residue (L337 in rat neuronal NOS, N115 in mouse inducible NOS). This is confirmed by biochemical analysis of site-directed mutants. Inhibitors combining guanidinium-like structural motifs with long chains specifically targeting this residue are good candidates for rational isoform-specific drug design. Based on this finding, modifications of AR-R17447 to improve the specificity for the human isoforms are suggested. N itric oxide (NO), a ubiquitous signaling molecule, is currently one of the most intensely studied small molecules in biology because of its involvement in numerous biological events such as vasodilation, neurotransmission, and the immune response. The isozymes of NO synthase (NOS) that produce NO are dimeric multidomain polypeptides consisting of three main components: a heme-containing catalytic oxygenase domain (NOSoxy), a calmodulin binding linker, and a NADPH reductase domain. NOS transforms L-arginine to citrulline and NO in two sequential steps consuming oxygen and electrons (1). The cofactor tetrahydrobiopterin bound at the interface of the two oxygenase domains in the NOS dimer is required for NO synthesis (2, 3). In mammals, three NOS isoforms have been identified sharing 50-60% sequence identity, which differ in cellular distribution, regulation, and activity (1). Endothelial NOS (eNOS) regulates vascular tone and smooth muscle tension (4). Neuronal NOS (nNOS) produced NO functions as a diffusible neurotransmitter (5), whereas NO generated by inducible NOS (iNOS) generates cytotoxins with both protective and pathologic effects (1, 6). In line with NO's central biological role, there are a number of pathological processes associated with its over-or underproduction. For example, nNOS is implicated in stroke and migraine, and iNOS is implicated in septic shock, arthritis, and multiple sclerosis. The possibility of treating these and other conditions by inhibiting NOS has elicited intense efforts to identify or design NOS inhibitors. Because the three isoforms of NOS have unique roles in separate tissues, selective inhibition of one isozyme over the others is essential. In particular, it is important not to inhibit eNOS because of its critical role in maintaining vascular tone. Numerous inhibitors of NOS have been developed (7). The majority of the inhibitors contain amidino or ureido functional groups that mimic the guanidino group of the substrate L-arginine. The high level of amino acid conservation and striking...