Peripheral but crucial: a hydrophobic pocket (Tyr(706), Leu(337), and Met(336)) for potent and selective inhibition of neuronal nitric oxide synthase.

Abstract Selective inhibition of the neuronal isoform of nitric oxide synthase (nNOS) over endothelial nitric oxide synthase (eNOS) and inducible nitric oxide synthase (iNOS) has become a promising strategy for the discovery of new therapeutic agents for neurodegenerative diseases. However, because of the high sequence homology of different isozymes in the substrate binding pocket, developing inhibitors with both potency and excellent isoform selectivity remains a challenging problem. Herein, we report the evaluation of a recently discovered peripheral hydrophobic pocket (Tyr 706 , Leu 337 , and Met 336 ) that opens up upon inhibitor binding and its potential in designing potent and selective nNOS inhibitors using three compounds, 2a , 2b , and 3 . Crystal structure results show that inhibitors 2a and 3 adopted the same binding mode as lead compound 1 . We also found that hydrophobic interactions between the 4-methyl group of the aminopyridine ring of these compounds with the side chain of Met 336 , as well as the π–π stacking interaction between the pyridinyl motif and the side chain of Tyr 706 are important for the high potency and selectivity of these nNOS inhibitors.