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.     

<Superscript>1</Superscript>H NMR signal at 2.10 ppm in the spectrum of KMnO<Subscript>4</Subscript>-bleached heparin sodium: identification of the chemical origin using an NMR-only approach

The recently revised European Pharmacopeia and US Pharmacopeia heparin sodium monographs include nuclear magnetic resonance (NMR) tests on both identity and purity. In KMnO₄-bleached heparin, an unidentified NMR signal is present at 2.10 ppm at a level of 15–20% of the mean of signal height of the major glucosamine (GlcNAc/GlcNS,6S) anomeric proton signal at 5.42 ppm and of the major iduronic acid (IdoA2S) anomeric proton signal at 5.21 ppm. According to the new monographs, no unidentified signals greater than 4% should be detected at that position. Thus, the material did not meet the acceptance criterion. The signal at 2.10 ppm has been present at the same level in all released MSD KMnO₄-bleached heparin sodium batches analyzed over the past 10 years. The signal is a result of the KMnO₄ bleaching. No (oversulfated) chondroitin sulfate or dermatan sulfate was detected in this material. A comprehensive NMR study using long-range heteronuclear 2D techniques identifies this signal at 2.10 ppm as originating from the acetyl methyl group of (6-sulfated) 2-N-acetyl-2-deoxy-glucono-1,5-lactone. This modified monosaccharide is formed by the KMnO₄ oxidation of the reducing end of a terminal N-acetylglucosamine.     

Solution NMR approaches for establishing specificity of weak heterodimerization of membrane proteins

Solution NMR provides a powerful approach for detecting complex formation involving weak to moderate intermolecular affinity. However, solution NMR has only rarely been used to detect complex formation between two membrane proteins in model membranes. The impact of specific binding on the NMR spectrum of a membrane protein can be difficult to distinguish from spectral changes that are induced by nonspecific binding and/or by changes that arise from forced cohabitation of the two proteins in a single model membrane assembly. This is particularly the case when solubility limits make it impossible to complete a titration to the point of near saturation of complex formation. In this work experiments are presented that provide the basis for establishing whether specific complex formation occurs between two membrane proteins under conditions where binding is not of high avidity. Application of these methods led to the conclusion that the membrane protein CD147 (also known as EMMPRIN or basigin) forms a specific heterodimeric complex in the membrane with the 99-residue transmembrane C-terminal fragment of the amyloid precursor protein (C99 or APP-βCTF), the latter being the immediate precursor of the amyloid-β polypeptides that are closely linked to the etiology of Alzheimer's disease.     

Application of thermal analysis in preservation and restoration of historic masonry materials

Thermal analysis techniques have been used in characterizing building materials from significant historic properties in the Charleston, South Carolina area. Determining the chemical and physical effects of deterioration resulting from long periods of exposure is a first step in formulating preservation strategies. In this regard, simultaneous thermal analysis coupled with evolved gas analysis has been used to study reactions between air, seawater, and masonry materials. Further, the traditional petrographic identification of mortar composition is greatly facilitated through use of thermal analysis. Simultaneous thermal analysis allows for an exact determination of the calcium carbonate content in mortars as an alternative to the use of an inferred value based on chemical analysis data. The partial dissolution of calcium carbonate in the presence of sea salt is a major deterioration process. Further, natural cements manufactured in the United States are identified, in part, based on their thermogravimetric (TG) traces and their evolved gases. The data indicates that natural cements form some carbonate phases in addition to the major hydrate phases. Clay bricks are found to exhibit interaction with sea water, with uptake of bicarbonate suggested. Additionally, there is evidence of re-hydroxylation in the 160 year old bricks. The bricks made in coastal zones contain a considerable free silica fraction that is composed of a small percentage of cristobalite. The silica content of the clay bricks is seen to result in very high thermal expansion coefficients in the area of 10 × 10⁻⁶ to 12 × 10⁻⁶ K⁻¹. These studies provide guidance in restoration efforts where authenticity of cements is important. In the event that replacement bricks are required, matching the thermal expansion coefficient of the original bricks is a requirement for preservation of the masonry structure.     

Puroindoline-a, a lipid binding protein from common wheat, spontaneously forms prolate protein micelles in solution

The self-assembly in solution of puroindoline-a (Pin-a), an amphiphilic lipid binding protein from common wheat, was investigated by small angle neutron scattering, dynamic light scattering and size exclusion chromatography. Pin-a was found to form monodisperse prolate ellipsoidal micelles with a major axial radius of 112 ± 4.5 ? and minor axial radius of 40.4 ± 0.18 ?. These protein micelles were formed by the spontaneous self-assembly of 38 Pin-a molecules in solution and were stable over a wide pH range (3.5-11) and at elevated temperatures (20-65 °C). Pin-a micelles could be disrupted upon addition of the non-ionic surfactant dodecyl-β-maltoside, suggesting that the protein self-assembly is driven by hydrophobic forces, consisting of intermolecular interactions between Trp residues located within a well-defined Trp-rich domain of Pin-a.     

Fluorescence lifetime imaging of oxygen in living cells

The usefulness of the fluorescent probe ruthenium tris(2,2′-dipyridyl) dichloride hydrate (RTDP) for the quantitative imaging of oxygen in single cells was investigated utilizing fluorescence lifetime imaging. The results indicate that the fluorescence behavior of RTDP in the presence of oxygen can be described by the Stem-Volmer equation. This shows that fluorescence quenching by oxygen is a dynamic quenching process. In addition, it was demonstrated that the fluorescence lifetime of RTDP is insensitive to pH, ion concentration, and cellular contents. This implies that a simple calibration procedure in buffers can be used to quantify oxygen concentrations within cells. First fluorescence imaging experiments on J774 macrophages show a nonuniform fluorescence intensity and a uniform fluorescence lifetime image. This indicates that the RTDP is heterogeneously partitioned throughout the cells, while the oxygen concentration is constant.     

Generation of ultraviolet broadband light in a single-mode fiber

Ultraviolet broadband light spanning 337–405 nm was produced in a single-mode optical fiber primarily by stimulated Raman scattering. Pulses of 4 ns duration at 337 nm were coupled into a 50 m long ultraviolet-grade fiber featuring single-mode operation in the 320–450 nm range. Significant spectral broadening was achieved with pulses of only ∼10 W peak power. Our experiments demonstrate the potential for a source with ∼10⁴ times the spectral radiance of a quartz tungsten halogen lamp, which is currently used for many applications in this wavelength range. PACS 42.65.Ky; 42.81.Wg     

Circuit preserving edge maps

It is proved that any one-to-one edge map f from a 3-connected graph G onto a graph G′, G and G′ possibly infinite, satisfying f(C) is a circuit in G′ whenever C is a circuit in G is induced by a vertex isomorphism. This generalizes a result of Whitney which hypothesizes f(C) is a circuit in G′ if and only if C is a circuit in G.