Snooker: a structure-based pharmacophore generation tool applied to class A GPCRs

G-protein coupled receptors (GPCRs) are important drug targets for various diseases and of major interest to pharmaceutical companies. The function of individual members of this protein family can be modulated by the binding of small molecules at the extracellular side of the structurally conserved transmembrane (TM) domain. Here, we present Snooker, a structure-based approach to generate pharmacophore hypotheses for compounds binding to this extracellular side of the TM domain. Snooker does not require knowledge of ligands, is therefore suitable for apo-proteins, and can be applied to all receptors of the GPCR protein family. The method comprises the construction of a homology model of the TM domains and prioritization of residues on the probability of being ligand binding. Subsequently, protein properties are converted to ligand space, and pharmacophore features are generated at positions where protein ligand interactions are likely. Using this semiautomated knowledge-driven bioinformatics approach we have created pharmacophore hypotheses for 15 different GPCRs from several different subfamilies. For the beta-2-adrenergic receptor we show that ligand poses predicted by Snooker pharmacophore hypotheses reproduce literature supported binding modes for ～75% of compounds fulfilling pharmacophore constraints. All 15 pharmacophore hypotheses represent interactions with essential residues for ligand binding as observed in mutagenesis experiments and compound selections based on these hypotheses are shown to be target specific. For 8 out of 15 targets enrichment factors above 10-fold are observed in the top 0.5% ranked compounds in a virtual screen. Additionally, prospectively predicted ligand binding poses in the human dopamine D3 receptor based on Snooker pharmacophores were ranked among the best models in the community wide GPCR dock 2010.     

The effect of bias-temperature stress on Na<Superscript>+</Superscript> incorporation into thin insulating films

The action of Na⁺ incorporation into thin insulating films and transport therein under influence of a bias voltage and temperature (BT stress) is the subject of this work. Deposited onto highly n-doped Si wafers, the insulators get BT stressed and subsequently investigated by means of time-of-flight–secondary ion mass spectrometry (ToF-SIMS). A thin PMMA film, spin-coated onto the insulator, serves as host matrix for a defined amount of Na⁺, provided via sodium triflate. Combining BT stress and ToF-SIMS depth profiling enables the unambiguous detection of Na⁺, incorporated into the insulating material. The insulators of interest vary in their nitride content: SiO₂, SiO_xN_y, and Si₃N₄. For SiO₂, it is shown that once a threshold BT stress is exceeded, Na⁺ gets quantitatively incorporated from PMMA into the underlying insulator, finally accumulating at the SiO₂/Si interface. A quantitative assessment by combination of Butler–Volmer kinetics with hopping dynamics reveals activation energies of E _a = 1.55 − 2.04 eV for Na⁺ transport in SiO₂ with varying thickness. On the other hand, SiO_xN_y and Si₃N₄ films show a different Na⁺ incorporation characteristic in this type of experiment, which can be explained by the higher coordination of nitrogen and hence the reduced Na⁺ permeability within these insulators.     

Determination of the binding sites for oxaliplatin on insulin using mass spectrometry-based approaches

Using insulin as a model protein for binding of oxaliplatin to proteins, various mass spectrometric approaches and techniques were compared. Several different platinum adducts were observed, e.g. addition of one or two diaminocyclohexane platinum(II) (Pt(dach)) molecules. By top-down analysis and fragmentation of the intact insulin–oxaliplatin adduct using nano-electrospray ionisation quadrupole time-of-flight mass spectrometry (nESI-Q-ToF-MS), the major binding site was assigned to histidine5 on the insulin B chain. In order to simplify the interpretation of the mass spectrum, the disulphide bridges were reduced. This led to the additional identification of cysteine6 on the A chain as a binding site along with histidine5 on the B chain. Digestion of insulin–oxaliplatin with endoproteinase Glu-C (GluC) followed by reduction led to the formation of five peptides with Pt(dach) attached. Identification of several of the binding sites was obtained using matrix-assisted laser desorption/ionization (MALDI)-ToF-ToF-MS and liquid chromatography-nESI-Q-ToF-MS. Upon comparing the top-down and bottom-up approaches, the suitability of the bottom-up approach for determining binding sites was questioned, as the release and possible re-association of Pt(dach) were demonstrated upon enzymatic digestion. The associated advantages and disadvantages of ESI and MALDI were also pointed out.     

Cellulose nanofibrils as filler for adhesives: effect on specific fracture energy of solid wood-adhesive bonds

Cellulose nanofibrils were prepared by mechanical fibrillation of never-dried beech pulp and bacterial cellulose. To facilitate the separation of individual fibrils, one part of the wood pulp was surface-carboxylated by a catalytic oxidation using (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO) as a catalyst. After fibrillation by a high pressure homogenizer, the obtained aqueous fibril dispersions were directly mixed with different urea–formaldehyde-(UF)-adhesives. To investigate the effect of added cellulose filler on the fracture mechanical properties of wood adhesive bonds, double cantilever beam specimens were prepared from spruce wood. While the highest fracture energy values were observed for UF-bonds filled with untreated nanofibrils prepared from wood pulp, bonds filled with TEMPO-oxidized fibrils showed less satisfying performance. It is proposed that UF-adhesive bonds can be significantly toughened by the addition of only small amounts of cellulose nanofibrils. Thereby, the optimum filler content is largely depending on the adhesive and type of cellulose filler used.     

Fluorescence detected circular dichroism of a red-shifted exciton-coupling chromophore <Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>′-carbonyl-bridged dipyrrinone derivative using an ellipsoidal device

A fluorescent red-shifted exciton-coupling chromophore, N,N′-carbonyl-bridged dipyrrinone, was subjected to fluorescence-detected CD (FDCD) measurements as a primitive structure-elucidating probe with trans-1,2-cyclohexanediol template in several solvents under various instrumental conditions. With the help of a JASCO ellipsoidal mirror device FDCD465, a chloroform solution achieved the sensitivity enhancement by 50 times of the transmission CD and 5 times of the conventional FDCD. All FDCD spectra were completely free from the polarization artifacts. Correspondence: Tatsuo Nehira and David A. Lightner, Graduate School of Integrated Arts and Sciences, Hiroshima University, Higashi-hiroshima 739-8521, Japan; Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA.