We report the structure-based design and synthesis of a unique NOS inhibitor, called nanoshutter NS1, with two-photon absorption properties. NS1 targets the NADPH site of NOS by a nucleotide moiety mimicking NADPH linked to a conjugated push-pull chromophore with nonlinear absorption properties. Because NS1 could not provide reducing equivalents to the protein and competed with NADPH binding, it efficiently inhibited NOS catalysis. NS1 became fluorescent once bound to NOS with an excellent signalto-noise ratio because of two-photon excitation avoiding interference from the flavin-autofluorescence and because free NS1 was not fluorescent in aqueous solutions. NS1 fluorescence enhancement was selective for constitutive NOS in vitro, in particular for endothelial NOS (eNOS). Molecular dynamics simulations suggested that two variable residues among NOS isoforms induced differences in binding of NS1 and in local solvation around NS1 nitro group, consistent with changes of NS1 fluorescence yield. NS1 colocalized with eNOS in living human umbilical vein endothelial cells. Thus, NS1 constitutes a unique class of eNOS probe with two-photon excitation in the 800-950-nm range, with great perspectives for eNOS imaging in living tissues.chemical biology | inhibition of enzymatic catalysis | structure-based design and molecular modeling | two-photon fluorescence imaging | fluorescence spectroscopy I n mammals, NO is a gaseous signaling mediator that exerts a wide range of key physiological functions, including blood pressure regulation, neurotransmission, and immune responses (1). NO is formed by nitric-oxide synthases, a family of hemoproteins that catalyzes the oxidation of L-arginine leading to L-citrulline and NO (2, 3). NOS catalysis is driven by reducing equivalents supplied by NADPH. NOS enzymes are constituted by oxygenase and reductase domains linked by a calmodulin (CaM)-binding domain. The oxygenase domain binds the heme, L-arginine, and the cofactor (6R)-5,6,7,8-tetrahydro-L-biopterin (H 4 B). The reductase domain binds two flavins, FMN and FAD, and NADPH (4). CaM binding allows the electron transfer from FMN to the heme (2, 3). The biological activities of NO are closely linked to the specific NOS isoform involved in its synthesis and deregulation of its biosynthesis leads to various pathologies (5). Data support the notion that inhibition of the inducible and neuronal isoforms iNOS and nNOS have therapeutic utility in the treatment of a variety of diseases, including septic shock, neurodegeneration, inflammation, and cancer (5, 6). It was shown that the endothelial isoform eNOS participates in tumor initiation and maintenance, thus its inhibition could be beneficial in this context (7,8). Based on crystallographic studies (9, 10), much effort was dedicated to the development of specific NOS inhibitors by targeting the heme site. However, most of these inhibitors are not specific and cannot avoid NOS uncoupling and formation of deleterious radical oxygen species (ROS) at the reductase domain. Although the struct...