Marked difference in saxitoxin and tetrodotoxin affinity for the human nociceptive voltage-gated sodium channel (Nav1.7) [corrected].

Human nociceptive voltage-gated sodium channel (Na(v)1.7), a target of significant interest for the development of antinociceptive agents, is blocked by low nanomolar concentrations of (-)-tetrodotoxin(TTX) but not (+)-saxitoxin (STX) and (+)-gonyautoxin-III (GTX-III). These findings question the long-accepted view that the 1.7 isoform is both tetrodotoxin- and saxitoxin-sensitive and identify the outer pore region of the channel as a possible target for the design of Na(v)1.7-selective inhibitors. Single- and double-point amino acid mutagenesis studies along with whole-cell electrophysiology recordings establish two domain III residues (T1398 and I1399), which occur as methionine and aspartate in other Na(v) isoforms, as critical determinants of STX and gonyautoxin-III binding affinity. An advanced homology model of the Na(v) pore region is used to provide a structural rationalization for these surprising results.

Potent, orally bioavailable, liver-selective stearoyl-CoA desaturase (SCD) inhibitors.

Two structurally distinct series of SCD (Delta9 desaturase) inhibitors (1 and 2) have been previously reported by our group. In the present work, we merged the structural features of the two series. This led to the discovery of compound 5b (CVT-12,012) which is highly potent in a human cell-based (HEPG2) SCD assay (IC(50)=6nM). This compound has 78% oral bioavailability in rats and is preferentially distributed into liver (76 times vs plasma) with relatively low brain penetration. In a five-day study (sucrose fed rats) compound 5b significantly reduced SCD activity in a dose-dependent manner as determined by GC analysis of fatty acid composition in plasma and liver, and significantly reduced liver triglycerides versus the control group ( approximately 50%).

A pharmacophore map of small molecule protein kinase inhibitors.

Protein kinases have emerged as one of the major drug target classes that are amenable to the development of small molecule inhibitors. They share a conserved structural similarity in the region of the ATP binding site, where most inhibitors interact. Using a pharmacophore approach, we have explored the features of protein-ligand interactions for a set of 220 kinase crystal structures from the Protein Data Bank (PDB). The resulting "pharmacophore map" shows the interactions made by all ligands with their receptors simultaneously. This gives insight that has been applied in the design of kinase screening sets and combinatorial libraries. An algorithm is described that scores small molecule structures for goodness of fit to the resulting binding site description obtained from the analysis. The algorithm identifies a pose that is close to the crystal structure pose for the majority of ligands, with only the 2D chemical structure as input and no knowledge of the crystal structure from which it was derived. Application of the algorithm to a test screening set gave a useful enrichment of active compounds.

Diverse biochemical properties of Shp2 mutants. Implications for disease phenotypes.

Mutations in the Src homology 2 (SH2)-containing protein-tyrosine phosphatase Shp2 (PTPN11) underlie half of the cases of the autosomal dominant genetic disorder Noonan syndrome, and somatic Shp2 mutations are found in several hematologic and solid malignancies. Earlier studies of small numbers of mutants suggested that disease-associated mutations cause constitutive (SH2 binding-independent) activation and that cancer-associated mutants are more active than those associated with Noonan syndrome. We have characterized a larger panel of Shp2 mutants and find that this "activity-centric" model cannot explain the behaviors of all pathogenic Shp2 mutations. Instead, enzymatic, structural, and mathematical modeling analyses show that these mutants can affect basal activation, SH2 domain-phosphopeptide affinity, and/or substrate specificity to varying degrees. Furthermore, there is no absolute correlation between the mutants' extents of basal activation and the diseases they induce. We propose that activated mutants of Shp2 modulate signaling from specific stimuli to a subset of effectors and provide a theoretical framework for understanding the complex relationship between Shp2 activation, intracellular signaling, and pathology.

Prediction of ultraviolet spectral absorbance using quantitative structure-property relationships.

High performance liquid chromatography (HPLC) with ultraviolet (UV) spectrophotometric detection is a common method for analyzing reaction products in organic chemistry. This procedure would benefit from a computational model for predicting the relative response of organic molecules. Models are now reported for the prediction of the integrated UV absorbance for a diverse set of organic compounds using a quantitative structure-property relationship (QSPR) approach. A seven-descriptor linear correlation with a squared correlation coefficient (R2) of 0.815 is reported for a data set of 521 compounds. Using the sum of ZINDO oscillator strengths in the integration range as an additional descriptor allowed reduction in the number of descriptors producing a robust model for 460 compounds with five descriptors and a squared correlation coefficient 0.857. The descriptors used in the models are discussed with respect to the physical nature of the UV absorption process.