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Sample records for alkylaminocarbene ligand leads

  1. A Cyclic Alkyl(amino)carbene as Two-Atom π-Chromophore Leading to the First Phosphorescent Linear CuIComplexes.

    Science.gov (United States)

    Gernert, Markus; Müller, Ulrich; Haehnel, Martin; Pflaum, Jens; Steffen, Andreas

    2017-02-10

    The members of a series of linear and trigonal copper(I) complexes bearing a cyclic alkyl(amino)carbene (CAAC) ligand show surprising photophysical properties compared to those of the corresponding N-heterocyclic carbene (NHC) complexes. Whereas the linear NHC complexes [CuX(NHC)] are almost non-emissive, [CuX(CAAC)] (X=Cl, Br, I) and [Cu(CAAC) 2 ]PF 6 show very bright emissions from their triplet excited states in the blue to green region, displaying quantum yields of up to 65 % in the solid state, even though the π-acceptor comprises only the carbene C and N atoms with no other π conjugation. [Cu(CAAC) 2 ]PF 6 is the fastest Cu I -based triplet state emitter characterized to date, not displaying thermally activated delayed fluorescence (TADF), with an intrinsic lifetime of only 10.6 μs, that is, k r =9.4×10 4  s -1 , competitive with many Pt II - and Ir III -based emitters. In order to test the stability of such linear copper CAAC complexes in devices, some of our compounds have been applied in proof-of-principle organic light-emitting diodes (OLEDs). This case study thus demonstrates for the first time the use of CAACs as suitable π-chromophores for Cu I -based phosphorescent emitters, and their implementation in OLEDs underlines the general applicability of this class of ligands in materials science. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Phosphorescent 2-, 3- and 4-coordinate cyclic (alkyl)(amino)carbene (CAAC) Cu(i) complexes.

    Science.gov (United States)

    Hamze, Rasha; Jazzar, Rodolphe; Soleilhavoup, Michele; Djurovich, Peter I; Bertrand, Guy; Thompson, Mark E

    2017-08-08

    The photophysical properties of several Cu(i) complexes coordinated with cyclic (alkyl)(amino)carbene (CAAC) ligands were examined. All the compounds were found to be phosphorescent, regardless of whether they are 2-, 3- or 4-coordinated. Aggregate and excimer emission were observed from 2-coordinate CAAC-CuCl derivatives in methylcyclohexane solution. Emission from the complex 4-coordinated with a trispyrazolylborate ligand is red-shifted with respect to both the chloro-derivative and an analogous complex with an NHC ligand.

  3. Stereochemistry of lead(II) complexes with oxygen donor ligands.

    Energy Technology Data Exchange (ETDEWEB)

    Stavilla, Vitalie; Davidovich, Ruven L.; Whitmire, Kenton Herbert (Rice University); Voit, Elena I.; Marinin, Dmitry V.

    2008-10-01

    This review discusses the coordination number (CN) and the coordination geometry of the first coordination sphere of Pb(II) atoms in crystal structures of 98 lead(II) complexes with O-donor ligands and the stereochemically active lone pair of electrons (LP, E) in the terms of the valence shell electron-pair repulsion (VSEPR) model. The CN of Pb(II) atoms of the first coordination sphere has values falling into the range (3 + E) to (6 + E). The following coordination polyhedra-{psi}-tetrahedron (I), {psi}-trigonal bipyramid (II), {psi}-octahedron (III), {psi}-pentagonal bipyramid with an axial (IV) or equatorial (V) vacant position are formed. For the investigated structures of the Pb(II) complexes, the formula of each compound, the overall CN of the Pb(II) atom considered as the sum of the CN in the first coordination sphere and the number of secondary bonds, the polyhedron shape, the Pb-O bond lengths, and O-Pb-O bond angles in the first coordination sphere, secondary bond lengths, references and REFCODEs are presented in the comprehensive Tables. The quantum chemical investigations performed using density functional theory (DFT) method have confirmed the stereochemical activity of the LP of Pb(II) atoms in the studied structures of lead(II) complexes with O-donor ligands.

  4. Kinetic Selectivity of Olefin Metathesis Catalysts Bearing Cyclic (Alkyl)(Amino)Carbenes

    Science.gov (United States)

    Anderson, Donde R.; Ung, Thay; Mkrtumyan, Garik; Bertrand, Guy; Grubbs, Robert H.; Schrodi, Yann

    2008-01-01

    The evaluation of ruthenium olefin metathesis catalysts 4–6 bearing cyclic (alkyl)(amino)carbenes (CAACs) in the cross-metathesis of cis-1,4-diacetoxy-2-butene (7) with allylbenzene (8) and the ethenolysis of methyl oleate (11) is reported. Relative to most NHC-substituted complexes, CAAC-substituted catalysts exhibit lower E/Z ratios (3:1 at 70% conversion) in the cross-metathesis of 7 and 8. Additionally, complexes 4–6 demonstrate good selectivity for the formation of terminal olefins versus internal olefins in the ethenolysis of 11. Indeed, complex 6 achieved 35 000 TONs, the highest recorded to date. CAAC-substituted complexes exhibit markedly different kinetic selectivity than most NHC-substituted complexes. PMID:18584055

  5. When Ligand Exchange Leads to Ion Exchange: Nanocrystal Facets Dictate the Outcome.

    Science.gov (United States)

    Hewavitharana, Indika K; Brock, Stephanie L

    2017-11-28

    This study demonstrates that ligand exchange of nanocrystals (NCs) is not always an innocuous process, but can lead to facile (room temperature) ion exchange, depending on the surface crystal faceting. Rock salt PbTe NCs prepared as cubes with neutral facets undergo room-temperature ligand exchange with sulfide ions, whereas cuboctahedron-shaped particles with neutral {100} and polar {111} facets are transformed to PbS, driven by ion exchange along the ⟨111⟩ direction. Likewise, cation exchange (with Ag + ) occurs rapidly for cuboctahedra, whereas cubes remain inert. This dramatic difference is attributed to the relative surface area of {111} facets that promote rapid ion exchange and shows how facet engineering is a powerful knob for the control of reaction pathways in nanoparticles.

  6. Novel ligands of Choline Acetyltransferase designed by in silico molecular docking, hologram QSAR and lead optimization

    Science.gov (United States)

    Kumar, Rajnish; Långström, Bengt; Darreh-Shori, Taher

    2016-08-01

    Recent reports have brought back the acetylcholine synthesizing enzyme, choline acetyltransferase in the mainstream research in dementia and the cholinergic anti-inflammatory pathway. Here we report, a specific strategy for the design of novel ChAT ligands based on molecular docking, Hologram Quantitative Structure Activity Relationship (HQSAR) and lead optimization. Molecular docking was performed on a series of ChAT inhibitors to decipher the molecular fingerprint of their interaction with the active site of ChAT. Then robust statistical fragment HQSAR models were developed. A library of novel ligands was generated based on the pharmacophoric and shape similarity scoring function, and evaluated in silico for their molecular interactions with ChAT. Ten of the top scoring invented compounds are reported here. We confirmed the activity of α-NETA, the only commercially available ChAT inhibitor, and one of the seed compounds in our model, using a new simple colorimetric ChAT assay (IC50 ~ 88 nM). In contrast, α-NETA exhibited an IC50 of ~30 μM for the ACh-degrading cholinesterases. In conclusion, the overall results may provide useful insight for discovering novel ChAT ligands and potential positron emission tomography tracers as in vivo functional biomarkers of the health of central cholinergic system in neurodegenerative disorders, such as Alzheimer’s disease.

  7. Integration of ligand and structure-based virtual screening for identification of leading anabolic steroids.

    Science.gov (United States)

    Alvarez-Ginarte, Yoanna María; Montero-Cabrera, Luis Alberto; García-de la Vega, José Manuel; Bencomo-Martínez, Alberto; Pupo, Amaury; Agramonte-Delgado, Alina; Marrero-Ponce, Yovani; Ruiz-García, José Alberto; Mikosch, Hans

    2013-11-01

    Parallel ligand- and structure-based virtual screenings of 269 steroids with anabolic activity evaluated in vivo were performed. The quantitative structure-activity relationship (QSAR) model expressed by selected descriptors as the octanol-water partition coefficient, the molar volume and the quantum mechanical calculated charge values on atoms C1, C2, C5, C9, C10, C14 and C17 of the steroid skeleton, expresses structural features of anabolic steroids (AS) contributing to the transport and steroid-receptor interaction. On the other hand, computational simulations of a candidate ligand binding to a receptor study (a "docking" procedure) predict the association of these AS with the human androgen receptor (AR). Fourteen compounds were identified as lead; the most potent was the 7α-methylestr-4-en-3, 17-dione. It was concluded that a good anabolic activity requires hydrogen bonding interactions between both Arg752 and Gln711 residues in the cycles A with O3 atom of the steroid and either Asn705 and Thr877 residues in the cycles D of steroid with O17 atom. Copyright © 2013 Elsevier Ltd. All rights reserved.

  8. Spatio-temporal regulation of Hsp90-ligand complex leads to immune activation.

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    Yasuaki eTamura

    2016-05-01

    Full Text Available Hsp90 is the most abundant cytosolic HSP and is known to act as a molecular chaperone. We found that an Hsp90-cancer antigen peptide complex was efficiently cross-presented by human monocyte-derived dendritic cells and induced peptide-specific cytotoxic T lymphocytes. Furthermore, we observed that the internalized Hsp90-peptide complex was strictly sorted to the Rab5+, EEA1+ static early endosome and the Hsp90-chaperoned peptide was processed and bound to MHC class I molecules through a endosome-recycling pathway. We also found that extracellular Hsp90 complexed with CpG-A or self-DNA stimulates production of a large amount of IFN-α from pDCs via static early endosome targeting. Thus, extracellular Hsp90 can target the antigen or nucleic acid to a static early endosome by spatio-temporal regulation. Moreover, we showed that Hsp90 associates with and delivers TLR7/9 from the ER to early endosomes for ligand recognition. Hsp90 inhibitor, geldanamycin derivative inhibited the Hsp90 association with TLR7/9, resulting in inhibition IFN-α production, leading to improvement of SLE symptoms. Interstingly, we observed that serum Hsp90 is clearly increased in patients with active SLE compared with that in patients with inactive disease. Serum Hsp90 detected in SLE patients binds to self-DNA and/or anti-DNA Ab, thus leading to stimulation of pDCs to produce IFN-α. Thus, Hsp90 plays a crucial role in the pathogenesis of SLE and that an Hsp90 inhibitor will therefore provide a new therapeutic approach to SLE and other nucleic acid-related autoimmune diseases. We will discuss how spatio-temporal regulation of Hsp90-ligand complexes within antigen-presenting cells affects the innate immunity and adaptive immunity.

  9. Polar self-assembly: steric effects leading to polar mixed-ligand coordination cages.

    Science.gov (United States)

    Zhang, Jianyong; Miller, Philip W; Nieuwenhuyzen, Mark; James, Stuart L

    2006-03-08

    We present a highly unusual example of self-assembly, specifically a polar, mixed-ligand cage which forms in preference to symmetrical homo-ligand products, and which suggests that steric effects can be exploited to obtain novel non-uniform polyhedral cages. In particular, reaction between the bulky tripodal triphosphine 2,4,6-tris(diphenylphosphino)triazine, L1, the non-bulky tripodal trinitrile 2,4,6-tris(cyanomethyl)trimethylbenzene, L2 and silver hexafluoroantimonate, AgSbF6, in a 3:1:4 ratio gives the mixed-ligand aggregate [Ag4(L1)3(L2)(SbF6)]3+, 1-SbF6, instantly as the only product in quantitative yield. The X-ray crystal structure of complex 1-SbF6 is consistent with the suspected solution-state structure. The cage derives from trigonal-pyramidal geometry, the basal vertices of which are defined by three bulky triphosphines, L1, and the apical vertex by the non-bulky trinitrile, L2. There is apical elongation amounting to 19% in comparison to the ideal uniform tetrahedron. The cage also encapsulates an SbF6 anion. 19F NMR spectra in solution for the analogous PF6 complex [Ag4(L1)3(L2)(PF6)]3+, 1-PF6, confirm that one anion is also encapsulated in solution. The synthesis of the analogous CF3SO3(-) complex, [Ag4(L1)3(L2)(OTf)]3+, 1-OTf, in solution is also described, although 1-PF6 and 1-OTf could not be isolated due to slow decomposition in solution. The selective formation of these mixed-ligand cages is discussed in terms of ligand-ligand and ligand-included anion steric repulsions, which we propose prevent the formation of the competing hypothetical homo-ligand tetrahedral structure [Ag4(L1)4(SbF6)]3+, and thus favour the mixed ligand cage. "Cage cone angles" for L1 and L2 are estimated at 115 degrees and 101 degrees, respectively. Variable-temperature 31P NMR spectroscopy shows that complex 1-SbF6 and the related previously reported partial tetrahedral complex [Ag4(L1)3(anion)]3+ undergo dynamic twisting processes in solution between enantiomeric C3

  10. Extraction of uranium and lead from mixed waste debris using a variety of metal/ligand complexes

    International Nuclear Information System (INIS)

    Needham, D.A.; Duran, B.L.; Ehler, D.S.; Sauer, N.N.

    1997-01-01

    To ensure the safety of our Nation's nuclear stockpile, Los Alamos National Laboratory is in the process of constructing the DARHT (Dual Axis Radiographic Hydrodynamic Test) facility. DARHT will examine the effects of aging and the stability of our stockpile. Contained testing will be phased in to reduce the impact of these tests, which contain depleted uranium, on our environment. The main focus of this research is to develop a treatment scheme for the recovery of depleted uranium and lead from shot debris that will result from these tests. The goals of this research are to optimize the conditions on a bench scale using a commercially available water soluble polymer to bind the lead and a variety of metal/ligand complexes such as 4,5-dihydroxy-1,3-benzene-disulfonic acid, dithionite, sodium carbonate/bicarbonate, and sodium hypochlorite to bind the uranium. Studies were conducted on a mixture of debris, such as wood, cable, paper towels, and tubing that contained both uranium and lead ranging in concentration from 10-1000's of ppm of contaminants. Experiments were done varying combinations and successions of extractant solutions as well as a number of sequential extractions. Studies show that a mixture of sodium hypochlorite and carbonate removed 90+% of both uranium and lead. We then focused on a separation scheme for the lead and uranium

  11. Phase-Transfer Ligand Exchange of Lead Chalcogenide Quantum Dots for Direct Deposition of Thick, Highly Conductive Films.

    Science.gov (United States)

    Lin, Qianglu; Yun, Hyeong Jin; Liu, Wenyong; Song, Hyung-Jun; Makarov, Nikolay S; Isaienko, Oleksandr; Nakotte, Tom; Chen, Gen; Luo, Hongmei; Klimov, Victor I; Pietryga, Jeffrey M

    2017-05-17

    The use of semiconductor nanocrystal quantum dots (QDs) in optoelectronic devices typically requires postsynthetic chemical surface treatments to enhance electronic coupling between QDs and allow for efficient charge transport in QD films. Despite their importance in solar cells and infrared (IR) light-emitting diodes and photodetectors, advances in these chemical treatments for lead chalcogenide (PbE; E = S, Se, Te) QDs have lagged behind those of, for instance, II-VI semiconductor QDs. Here, we introduce a method for fast and effective ligand exchange for PbE QDs in solution, resulting in QDs completely passivated by a wide range of small anionic ligands. Due to electrostatic stabilization, these QDs are readily dispersible in polar solvents, in which they form highly concentrated solutions that remain stable for months. QDs of all three Pb chalcogenides retain their photoluminescence, allowing for a detailed study of the effect of the surface ionic double layer on electronic passivation of QD surfaces, which we find can be explained using the hard/soft acid-base theory. Importantly, we prepare highly conductive films of PbS, PbSe, and PbTe QDs by directly casting from solution without further chemical treatment, as determined by field-effect transistor measurements. This method allows for precise control over the surface chemistry, and therefore the transport properties of deposited films. It also permits single-step deposition of films of unprecedented thickness via continuous processing techniques, as we demonstrate by preparing a dense, smooth, 5.3-μm-thick PbSe QD film via doctor-blading. As such, it offers important advantages over laborious layer-by-layer methods for solar cells and photodetectors, while opening the door to new possibilities in ionizing-radiation detectors.

  12. Coordination chemistry of two heavy metals: I, Ligand preferences in lead(II) complexation, toward the development of therapeutic agents for lead poisoning: II, Plutonium solubility and speciation relevant to the environment

    Energy Technology Data Exchange (ETDEWEB)

    Neu, Mary Patricia [Univ. of California, Berkeley, CA (United States)

    1993-11-01

    The coordination chemistry and solution behavior of the toxic ions lead(II) and plutonium(IV, V, VI) have been investigated. The ligand pKas and ligand-lead(II) stability constants of one hydroxamic acid and four thiohydroaxamic acids were determined. Solution thermodynamic results indicate that thiohydroxamic acids are more acidic and slightly better lead chelators than hydroxamates, e.g., N-methylthioaceto-hydroxamic acid, pKa = 5.94, logβ120 = 10.92; acetohydroxamic acid, pKa = 9.34, logβ120 = 9.52. The syntheses of lead complexes of two bulky hydroxamate ligands are presented. The X-ray crystal structures show the lead hydroxamates are di-bridged dimers with irregular five-coordinate geometry about the metal atom and a stereochemically active lone pair of electrons. Molecular orbital calculations of a lead hydroxamate and a highly symmetric pseudo octahedral lead complex were performed. The thermodynamic stability of plutonium(IV) complexes of the siderophore, desferrioxamine B (DFO), and two octadentate derivatives of DFO were investigated using competition spectrophotometric titrations. The stability constant measured for the plutonium(IV) complex of DFO-methylterephthalamide is logβ120 = 41.7. The solubility limited speciation of 242Pu as a function of time in near neutral carbonate solution was measured. Individual solutions of plutonium in a single oxidation state were added to individual solutions at pH = 6.0, T = 30.0, 1.93 mM dissolved carbonate, and sampled over intervals up to 150 days. Plutonium solubility was measured, and speciation was investigated using laser photoacoustic spectroscopy and chemical methods.

  13. Coordination chemistry of two heavy metals: I, Ligand preferences in lead(II) complexation, toward the development of therapeutic agents for lead poisoning: II, Plutonium solubility and speciation relevant to the environment

    International Nuclear Information System (INIS)

    Neu, M.P.

    1993-11-01

    The coordination chemistry and solution behavior of the toxic ions lead(II) and plutonium(IV, V, VI) have been investigated. The ligand pK a s and ligand-lead(II) stability constants of one hydroxamic acid and four thiohydroaxamic acids were determined. Solution thermodynamic results indicate that thiohydroxamic acids are more acidic and slightly better lead chelators than hydroxamates, e.g., N-methylthioaceto-hydroxamic acid, pK a = 5.94, logβ 120 = 10.92; acetohydroxamic acid, pK a = 9.34, logβ l20 = 9.52. The syntheses of lead complexes of two bulky hydroxamate ligands are presented. The X-ray crystal structures show the lead hydroxamates are di-bridged dimers with irregular five-coordinate geometry about the metal atom and a stereochemically active lone pair of electrons. Molecular orbital calculations of a lead hydroxamate and a highly symmetric pseudo octahedral lead complex were performed. The thermodynamic stability of plutonium(IV) complexes of the siderophore, desferrioxamine B (DFO), and two octadentate derivatives of DFO were investigated using competition spectrophotometric titrations. The stability constant measured for the plutonium(IV) complex of DFO-methylterephthalamide is logβ 110 = 41.7. The solubility limited speciation of 242 Pu as a function of time in near neutral carbonate solution was measured. Individual solutions of plutonium in a single oxidation state were added to individual solutions at pH = 6.0, T = 30.0, 1.93 mM dissolved carbonate, and sampled over intervals up to 150 days. Plutonium solubility was measured, and speciation was investigated using laser photoacoustic spectroscopy and chemical methods

  14. Transient Inhibition of FGFR2b-ligands signaling leads to irreversible loss of cellular β-catenin organization and signaling in AER during mouse limb development.

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    Soula Danopoulos

    Full Text Available The vertebrate limbs develop through coordinated series of inductive, growth and patterning events. Fibroblast Growth Factor receptor 2b (FGFR2b signaling controls the induction of the Apical Ectodermal Ridge (AER but its putative roles in limb outgrowth and patterning, as well as in AER morphology and cell behavior have remained unclear. We have investigated these roles through graded and reversible expression of soluble dominant-negative FGFR2b molecules at various times during mouse limb development, using a doxycycline/transactivator/tet(O-responsive system. Transient attenuation (≤ 24 hours of FGFR2b-ligands signaling at E8.5, prior to limb bud induction, leads mostly to the loss or truncation of proximal skeletal elements with less severe impact on distal elements. Attenuation from E9.5 onwards, however, has an irreversible effect on the stability of the AER, resulting in a progressive loss of distal limb skeletal elements. The primary consequences of FGFR2b-ligands attenuation is a transient loss of cell adhesion and down-regulation of P63, β1-integrin and E-cadherin, and a permanent loss of cellular β-catenin organization and WNT signaling within the AER. Combined, these effects lead to the progressive transformation of the AER cells from pluristratified to squamous epithelial-like cells within 24 hours of doxycycline administration. These findings show that FGFR2b-ligands signaling has critical stage-specific roles in maintaining the AER during limb development.

  15. Lead

    Science.gov (United States)

    ... about the health effects of lead in drinking water The law mandates no-lead products for drinking water after ... Waste, and Cleanup Lead Mold Pesticides Radon Science Water A-Z Index Laws & Regulations By Business Sector By Topic Compliance Enforcement ...

  16. Mechanistic Insight Leads to a Ligand Which Facilitates the Palladium-Catalyzed Formation of 2-(Hetero)Arylaminooxazoles and 4-(Hetero)Arylaminothiazoles.

    Science.gov (United States)

    Olsen, Esben P K; Arrechea, Pedro L; Buchwald, Stephen L

    2017-08-21

    By using mechanistic insight, a new ligand (EPhos) for the palladium-catalyzed C-N cross-coupling between primary amines and aryl halides has been developed. Employing an isopropoxy group at the C3-position favors the C-bound isomer of the ligand-supported palladium(II) complexes and leads to significantly improved reactivity. The use of a catalyst system based on EPhos with NaOPh as a mild homogeneous base proved to be very effective in the formation of 4-arylaminothiazoles and highly functionalized 2-arylaminooxazoles. Previously, these were not readily accessible using palladium catalysis. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Organic-ligand-assisted supercritical hydrothermal synthesis of titanium oxide nanocrystals leading to perfectly dispersed titanium oxide nanoparticle in organic phase

    International Nuclear Information System (INIS)

    Mousavand, Tahereh; Zhang Jing; Ohara, Satoshi; Umetsu, Mitsuo; Naka, Takashi; Adschiri, Tadafumi

    2007-01-01

    Titanium oxide (TiO 2 ) nanocyrstals which are perfectly dispersed in organic solvents are synthesized by organic-ligand-assisted supercritical hydrothermal synthesis. The addition of hexaldehyde to the supercritical hydrothermal synthesis of TiO 2 leads to the in-situ surface modification, which enables the synthsized TiO 2 nanocrystals to be perfectly dispersed in iso-octane because of its hydrophobic nature. Further, the one-pot synthesis of hybrid materials results in the significant reduction of the particles size, probably due to the capping effect of hexaldehyde to suppress the particles growth

  18. A Saccharomyces cerevisiae assay system to investigate ligand/AdipoR1 interactions that lead to cellular signaling.

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    Mustapha Aouida

    Full Text Available Adiponectin is a mammalian hormone that exerts anti-diabetic, anti-cancer and cardioprotective effects through interaction with its major ubiquitously expressed plasma membrane localized receptors, AdipoR1 and AdipoR2. Here, we report a Saccharomyces cerevisiae based method for investigating agonist-AdipoR interactions that is amenable for high-throughput scale-up and can be used to study both AdipoRs separately. Agonist-AdipoR1 interactions are detected using a split firefly luciferase assay based on reconstitution of firefly luciferase (Luc activity due to juxtaposition of its N- and C-terminal fragments, NLuc and CLuc, by ligand induced interaction of the chimeric proteins CLuc-AdipoR1 and APPL1-NLuc (adaptor protein containing pleckstrin homology domain, phosphotyrosine binding domain and leucine zipper motif 1-NLuc in a S. cerevisiae strain lacking the yeast homolog of AdipoRs (Izh2p. The assay monitors the earliest known step in the adiponectin-AdipoR anti-diabetic signaling cascade. We demonstrate that reconstituted Luc activity can be detected in colonies or cells using a CCD camera and quantified in cell suspensions using a microplate reader. AdipoR1-APPL1 interaction occurs in absence of ligand but can be stimulated specifically by agonists such as adiponectin and the tobacco protein osmotin that was shown to have AdipoR-dependent adiponectin-like biological activity in mammalian cells. To further validate this assay, we have modeled the three dimensional structures of receptor-ligand complexes of membrane-embedded AdipoR1 with cyclic peptides derived from osmotin or osmotin-like plant proteins. We demonstrate that the calculated AdipoR1-peptide binding energies correlate with the peptides' ability to behave as AdipoR1 agonists in the split luciferase assay. Further, we demonstrate agonist-AdipoR dependent activation of protein kinase A (PKA signaling and AMP activated protein kinase (AMPK phosphorylation in S. cerevisiae, which are

  19. A Saccharomyces cerevisiae Assay System to Investigate Ligand/AdipoR1 Interactions That Lead to Cellular Signaling

    KAUST Repository

    Aouida, Mustapha

    2013-06-07

    Adiponectin is a mammalian hormone that exerts anti-diabetic, anti-cancer and cardioprotective effects through interaction with its major ubiquitously expressed plasma membrane localized receptors, AdipoR1 and AdipoR2. Here, we report a Saccharomyces cerevisiae based method for investigating agonist-AdipoR interactions that is amenable for high-throughput scale-up and can be used to study both AdipoRs separately. Agonist-AdipoR1 interactions are detected using a split firefly luciferase assay based on reconstitution of firefly luciferase (Luc) activity due to juxtaposition of its N- and C-terminal fragments, NLuc and CLuc, by ligand induced interaction of the chimeric proteins CLuc-AdipoR1 and APPL1-NLuc (adaptor protein containing pleckstrin homology domain, phosphotyrosine binding domain and leucine zipper motif 1-NLuc) in a S. cerevisiae strain lacking the yeast homolog of AdipoRs (Izh2p). The assay monitors the earliest known step in the adiponectin-AdipoR anti-diabetic signaling cascade. We demonstrate that reconstituted Luc activity can be detected in colonies or cells using a CCD camera and quantified in cell suspensions using a microplate reader. AdipoR1-APPL1 interaction occurs in absence of ligand but can be stimulated specifically by agonists such as adiponectin and the tobacco protein osmotin that was shown to have AdipoR-dependent adiponectin-like biological activity in mammalian cells. To further validate this assay, we have modeled the three dimensional structures of receptor-ligand complexes of membrane-embedded AdipoR1 with cyclic peptides derived from osmotin or osmotin-like plant proteins. We demonstrate that the calculated AdipoR1-peptide binding energies correlate with the peptides\\' ability to behave as AdipoR1 agonists in the split luciferase assay. Further, we demonstrate agonist-AdipoR dependent activation of protein kinase A (PKA) signaling and AMP activated protein kinase (AMPK) phosphorylation in S. cerevisiae, which are homologous to

  20. Sonochemical Synthesis of a New Nano Lead(II Coordination Polymer with 2,5-bis(2-pyridyl-3,4-diaza-2,4- hexadiene ligand: A Precursor to Produce Pure Phase Nano- sized Lead(II Oxide

    Directory of Open Access Journals (Sweden)

    A. Morsali

    2011-04-01

    Full Text Available A new nano-sized lead(II coordination polymer, [Pb(2-bpdh(NO32]n (1; (2-bpdh = 2,5-bis(2-pyridyl-3,4-diaza-2,4-hexadiene}, was synthesized by a sonochemical method. The structure of 1 may be considered coordination polymer of lead(II consist of metallocyclicchains formed by bridging NO3- and 2-bpdh ligands. The thermal stability of compound was studied by thermal gravimetric and differential thermal analyses. The new nano-structure coordination polymer was characterized by scanning electron microscopy, powder X-ray diffraction, elemental analyses and IR spectroscopy. The size of the samples was about 50 nm. Nano-particles of PbO were obtained by thermolysis of compound 1in oleic acid as a surfactant at 180 °C under air atmosphere and the size of this PbO particles were about 50 nm.

  1. Synthesis and physicochemical characterization of two lead(II) complexes with O-, N-donor ligands. Lone pair functionality and crystal structure

    Science.gov (United States)

    Masternak, Joanna; Barszcz, Barbara; Hodorowicz, Maciej; Khavryuchenko, Oleksiy V.; Majka, Alina

    2015-02-01

    A dinuclear [Pb2(4-CHO-5-MeIm)6(NO3)2](NO3)2 (1) and a polynuclear [Pb(2-pzc)2(H2O)]n (2) complexes (where 5(4)-carbaldehyde-4(5)-methylimidazole (5(4)-CHO-4(5)-MeIm) and pyrazine-2-carboxylic acid (2-pzcH)) have been synthesized and characterized by elemental analysis, IR spectroscopy and X-ray crystallography. Structural determination for complex 1 reveals a cationic species [Pb(4-CHO-5-MeIm)3]2+ connected through bridging nitrate(V) ions. There are also an uncoordinated nitrate ions as counterions. Complex 2 is a three-dimensional architecture consisting of Pb6O12 building units. The pyrazine-2-carboxylato ligand behaves as a chelating agent and a bi-connective bridge. The coordination polyhedra around lead(II) ion could be described as a distorted docecahedron (1) or monocapped trigonal prism (2). The luminescent properties of 1 and 2 investigated in the solid state at room temperature indicate structure-dependent photoluminescent properties. The DFT calculations and the X-ray structural data point on rather hemidirected type of coordination around Pb(II) ions of 1 and 2.

  2. Delivery of the TLR ligand poly(I:C) to liver cells in vitro and in vivo by calcium phosphate nanoparticles leads to a pronounced immunostimulation.

    Science.gov (United States)

    Sokolova, Viktoriya; Shi, Zou; Huang, Shunmei; Du, Yanqin; Kopp, Mathis; Frede, Annika; Knuschke, Torben; Buer, Jan; Yang, Dongliang; Wu, Jun; Westendorf, Astrid Maria; Epple, Matthias

    2017-12-01

    The selective activation of the immune system is a concurrent problem in the treatment of persistent diseases like viral infections (e.g. hepatitis). For the delivery of the toll-like receptor ligand poly(I:C), an immunostimulatory action was discovered earlier by hydrodynamic injection. However, this technique is not clinically transferable to human patients. A modular system where the immunoactive toll-like-receptor ligand 3 (TLR-3) poly(I:C) was incorporated into calcium phosphate nanoparticles was developed. The nanoparticles had a hydrodynamic diameter of 275nm and a zeta potential of +20mV, measured by dynamic light scattering. The diameter of the solid core was 120nm by scanning electron microscopy. In vitro, the nanoparticle uptake was investigated after 1 and 24h of incubation of THP-1 cells (macrophages) with nanoparticles by fluorescence microscopy. After intravenous injection into BALB/c and C57BL/6J mice, respectively, the in vivo uptake was especially prominent in lung and liver, 1 and 3h after the injection. Pronounced immunostimulatory effects of the nanoparticles were found in vitro with primary liver cells, i.e. Kupffer cells (KC) and liver sinusoidal endothelial cells (LSEC) from wild-type C57BL/6J mice. Thus, they represent a suitable alternative to hydrodynamic injection treatments for future vaccination concepts. The selective activation of the immune system is a concurrent problem in the treatment of persistent diseases like viral infections (e.g. hepatitis). For the delivery of the toll-like receptor ligand poly(I:C), an immunostimulatory action has been discovered earlier by hydrodynamic injection. However, this technique is not clinically transferable to human patients. We have developed a modular system where poly(I:C) was incorporated into calcium phosphate nanoparticles. The uptake into relevant liver cells was studied both in vitro and in vivo. After intravenous injection into mice, the in vivo uptake was especially prominent in lung

  3. Post-translational Modification of the NKG2D Ligand RAET1G Leads to Cell Surface Expression of a Glycosylphosphatidylinositol-linked Isoform*

    Science.gov (United States)

    Ohashi, Maki; Eagle, Robert A.; Trowsdale, John

    2010-01-01

    NKG2D is an important activating receptor on lymphocytes. In human, it interacts with two groups of ligands: the major histocompatibility complex class I chain-related A/B (MICA/B) family and the UL-16 binding protein (ULBP) family, also known as retinoic acid early transcript (RAET1). MIC proteins are membrane-anchored, but all of the ULBP/RAET1 proteins, except for RAET1E and RAET1G, are glycosylphosphatidylinositol (GPI)-anchored. To address the reason for these differences we studied the association of RAET1G with the membrane. Using epitope-tagged RAET1G protein in conjunction with antibodies to different parts of the molecule and in pulse-chase experiments, we showed that the C terminus of the protein was cleaved soon after protein synthesis. Endoglycosidase H and peptide N-glycosidase treatment and cell surface immunoprecipitation indicated that most of the protein stayed in the endoplasmic reticulum, but some of the cleaved form was modified in the Golgi and transported to the cell surface. We examined the possibility of GPI anchoring of the protein in three ways: (i) Phosphatidylinositol (PI)-specific phospholipase C released the PI-linked form of the protein. (ii) The surface expression pattern of RAET1G decreased in cells defective in GPI anchoring through mutant GPI-amidase. (iii) Site-directed mutagenesis, to disrupt residues predicted to facilitate GPI-anchoring, resulted in diminished surface expression of RAET1G. Thus, a form of RAET1G is GPI-anchored, in line with most other ULBP/RAET1 family proteins. The cytoplasmic tail and transmembrane domains appear to result from gene duplication and frameshift mutation. Together with our previous results, our data suggest that RAET1G is regulated post-translationally to produce a GPI-anchored isoform. PMID:20304922

  4. Post-translational modification of the NKG2D ligand RAET1G leads to cell surface expression of a glycosylphosphatidylinositol-linked isoform.

    Science.gov (United States)

    Ohashi, Maki; Eagle, Robert A; Trowsdale, John

    2010-05-28

    NKG2D is an important activating receptor on lymphocytes. In human, it interacts with two groups of ligands: the major histocompatibility complex class I chain-related A/B (MICA/B) family and the UL-16 binding protein (ULBP) family, also known as retinoic acid early transcript (RAET1). MIC proteins are membrane-anchored, but all of the ULBP/RAET1 proteins, except for RAET1E and RAET1G, are glycosylphosphatidylinositol (GPI)-anchored. To address the reason for these differences we studied the association of RAET1G with the membrane. Using epitope-tagged RAET1G protein in conjunction with antibodies to different parts of the molecule and in pulse-chase experiments, we showed that the C terminus of the protein was cleaved soon after protein synthesis. Endoglycosidase H and peptide N-glycosidase treatment and cell surface immunoprecipitation indicated that most of the protein stayed in the endoplasmic reticulum, but some of the cleaved form was modified in the Golgi and transported to the cell surface. We examined the possibility of GPI anchoring of the protein in three ways: (i) Phosphatidylinositol (PI)-specific phospholipase C released the PI-linked form of the protein. (ii) The surface expression pattern of RAET1G decreased in cells defective in GPI anchoring through mutant GPI-amidase. (iii) Site-directed mutagenesis, to disrupt residues predicted to facilitate GPI-anchoring, resulted in diminished surface expression of RAET1G. Thus, a form of RAET1G is GPI-anchored, in line with most other ULBP/RAET1 family proteins. The cytoplasmic tail and transmembrane domains appear to result from gene duplication and frameshift mutation. Together with our previous results, our data suggest that RAET1G is regulated post-translationally to produce a GPI-anchored isoform.

  5. Cloud point extraction for determination of lead in blood samples of children, using different ligands prior to analysis by flame atomic absorption spectrometry: A multivariate study

    Energy Technology Data Exchange (ETDEWEB)

    Shah, Faheem, E-mail: shah_ceac@yahoo.com [National Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan); Kazi, Tasneem Gul, E-mail: tgkazi@yahoo.com [National Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan); Afridi, Hassan Imran, E-mail: hassanimranafridi@yahoo.com [National Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan); Naeemullah, E-mail: khannaeemullah@ymail.com [National Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan); Arain, Muhammad Balal, E-mail: bilal_ku2004@yahoo.com [Department of Chemistry, University of Science and Technology, Bannu, KPK (Pakistan); Baig, Jameel Ahmed, E-mail: jab_mughal@yahoo.com [National Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan)

    2011-09-15

    Highlights: {yields} Trace levels of lead in blood samples of healthy children and with different kidney disorders {yields} Pre-concentration of Pb{sup +2} in acid digested blood samples after chelating with two complexing reagents. {yields} Multivariate technique was used for screening of significant factors that influence the CPE of Pb{sup +2} {yields} The level of Pb{sup +2} in diseased children was significantly higher than referents of same age group. - Abstract: The phase-separation phenomenon of non-ionic surfactants occurring in aqueous solution was used for the extraction of lead (Pb{sup 2+}) from digested blood samples after simultaneous complexation with ammonium pyrrolidinedithiocarbamate (APDC) and diethyldithiocarbamate (DDTC) separately. The complexed analyte was quantitatively extracted with octylphenoxypolyethoxyethanol (Triton X-114). The multivariate strategy was applied to estimate the optimum values of experimental factors. Acidic ethanol was added to the surfactant-rich phase prior to its analysis by flame atomic absorption spectrometer (FAAS). The detection limit value of Pb{sup 2+} for the preconcentration of 10 mL of acid digested blood sample was 1.14 {mu}g L{sup -1}. The accuracy of the proposed methods was assessed by analyzing certified reference material (whole blood). Under the optimized conditions of both CPE methods, 10 mL of Pb{sup 2+} standards (10 {mu}g L{sup -1}) complexed with APDC and DDTC, permitted the enhancement factors of 56 and 42, respectively. The proposed method was used for determination of Pb{sup 2+} in blood samples of children with kidney disorders and healthy controls.

  6. Haploinsufficiency of E-selectin ligand-1 is Associated with Reduced Atherosclerotic Plaque Macrophage Content while Complete Deficiency Leads to Early Embryonic Lethality in Mice

    Science.gov (United States)

    Luo, Wei; Wang, Hui; Guo, Chiao; Wang, Jintao; Kwak, Jeffrey; Bahrou, Kristina L; Eitzman, Daniel T.

    2012-01-01

    E-selectin-1 (ESL-1), also known as golgi complex-localized glycoprotein-1 (GLG1), homocysteine-rich fibroblast growth factor receptor (CGR-1), and latent transforming growth factor-β complex protein 1 (LTCP-1), is a multifunctional protein with widespread tissue distribution. To determine the functional consequences of ESL-1 deficiency, mice were generated carrying an ESL-1 gene trap. After backcrossing to C57BL6/J for 6 generations, mice heterozygous for the gene trap (ESL-1+/-) were intercrossed to produce ESL-1-/- mice, however ESL-1-/- mice were not viable, even at embryonic day E10.5. To determine the effect of heterozygous ESL-1 deficiency on atherosclerosis, apolipoprotein E deficient (ApoE-/-), ESL-1+/- mice were generated and fed western diet. Compared to ApoE-/-, ESL-1++ mice, atherosclerotic lesions from ApoE-/-, ESL-1+/- contained more collagen and fewer macrophages, suggesting increased plaque stability. In conclusion, heterozygous deficiency of ESL-1 is associated with features of increased atherosclerotic plaque stability while complete deficiency of ESL-1 leads to embryonic lethality. PMID:22939356

  7. HIV-mediated phosphatidylinositol 3-kinase/serine-threonine kinase activation in APCs leads to programmed death-1 ligand upregulation and suppression of HIV-specific CD8 T cells.

    Science.gov (United States)

    Muthumani, Karuppiah; Shedlock, Devon J; Choo, Daniel K; Fagone, Paolo; Kawalekar, Omkar U; Goodman, Jonathan; Bian, Chaoran B; Ramanathan, Aarti A; Atman, Parikh; Tebas, Pablo; Chattergoon, Michael A; Choo, Andrew Y; Weiner, David B

    2011-09-15

    Recent evidence demonstrates that HIV-1 infection leads to the attenuation of cellular immune responses, which has been correlated with the increased expression of programmed death (PD)-1 on virus-specific CD8(+) T cells. PD-1 is induced upon T cell activation, and its prolonged expression facilitates CD8(+) T cell inhibitory signals when bound to its B7 family ligands, PD-ligand (L)1/2, which are expressed on APCs. Importantly, early reports demonstrated that blockade of the PD-1/PD-L interaction by Abs may help to counter the development of immune exhaustion driven by HIV viral persistence. To better understand the regulation of the PD-1 pathway during HIV infection, we examined the ability of the virus to induce PD-L expression on macrophages and dendritic cells. We found a direct relationship between the infection of APCs and the expression of PD-L1 in which virus-mediated upregulation induced a state of nonresponsiveness in uninfected HIV-specific T cells. Furthermore, this exhaustion phenotype was revitalized by the blockade of PD-L1, after which T cells regained their capacity for proliferation and the secretion of proinflammatory cytokines IFN-γ, IL-2, and IL-12 upon restimulation. In addition, we identify a critical role for the PI3K/serine-threonine kinase signaling pathway in PD-L1 upregulation of APCs by HIV, because inhibition of these intracellular signal transducer enzymes significantly reduced PD-L1 induction by infection. These data identify a novel mechanism by which HIV exploits the immunosuppressive PD-1 pathway and suggest a new role for virus-infected cells in the local corruption of immune responses required for viral suppression.

  8. Bitopic Ligands and Metastable Binding Sites

    DEFF Research Database (Denmark)

    Fronik, Philipp; Gaiser, Birgit I; Sejer Pedersen, Daniel

    2017-01-01

    of orthosteric binding sites. Bitopic ligands have been employed to address the selectivity problem by combining (linking) an orthosteric ligand with an allosteric modulator, theoretically leading to high-affinity subtype selective ligands. However, it remains a challenge to identify suitable allosteric binding...... that have been reported to date, this type of bitopic ligands would be composed of two identical pharmacophores. Herein, we outline the concept of bitopic ligands, review metastable binding sites, and discuss their potential as a new source of allosteric binding sites....

  9. Ligands in PSI structures

    International Nuclear Information System (INIS)

    Kumar, Abhinav; Chiu, Hsiu-Ju; Axelrod, Herbert L.; Morse, Andrew; Elsliger, Marc-André; Wilson, Ian A.; Deacon, Ashley

    2010-01-01

    A survey of the types and frequency of ligands that are bound to PSI structures is analyzed as well as their utility in functional annotation of previously uncharacterized proteins. Approximately 65% of PSI structures report some type of ligand(s) that is bound in the crystal structure. Here, a description is given of how such ligands are handled and analyzed at the JCSG and a survey of the types, variety and frequency of ligands that are observed in the PSI structures is also compiled and analyzed, including illustrations of how these bound ligands have provided functional clues for annotation of proteins with little or no previous experimental characterization. Furthermore, a web server was developed as a tool to mine and analyze the PSI structures for bound ligands and other identifying features

  10. AutoSite: an automated approach for pseudo-ligands prediction—from ligand-binding sites identification to predicting key ligand atoms

    Science.gov (United States)

    Ravindranath, Pradeep Anand; Sanner, Michel F.

    2016-01-01

    Motivation: The identification of ligand-binding sites from a protein structure facilitates computational drug design and optimization, and protein function assignment. We introduce AutoSite: an efficient software tool for identifying ligand-binding sites and predicting pseudo ligand corresponding to each binding site identified. Binding sites are reported as clusters of 3D points called fills in which every point is labelled as hydrophobic or as hydrogen bond donor or acceptor. From these fills AutoSite derives feature points: a set of putative positions of hydrophobic-, and hydrogen-bond forming ligand atoms. Results: We show that AutoSite identifies ligand-binding sites with higher accuracy than other leading methods, and produces fills that better matches the ligand shape and properties, than the fills obtained with a software program with similar capabilities, AutoLigand. In addition, we demonstrate that for the Astex Diverse Set, the feature points identify 79% of hydrophobic ligand atoms, and 81% and 62% of the hydrogen acceptor and donor hydrogen ligand atoms interacting with the receptor, and predict 81.2% of water molecules mediating interactions between ligand and receptor. Finally, we illustrate potential uses of the predicted feature points in the context of lead optimization in drug discovery projects. Availability and Implementation: http://adfr.scripps.edu/AutoDockFR/autosite.html Contact: sanner@scripps.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27354702

  11. Radiation alters PD-L1/NKG2D ligand levels in lung cancer cells and leads to immune escape from NK cell cytotoxicity via IL-6-MEK/Erk signaling pathway.

    Science.gov (United States)

    Shen, Ming Jing; Xu, Li Jun; Yang, Li; Tsai, Ying; Keng, Peter C; Chen, Yongbing; Lee, Soo Ok; Chen, Yuhchyau

    2017-10-06

    We investigated whether radiation influences the susceptibility of non-small cell lung cancer (NSCLC) cells to NK cell mediated cytotoxicity. We found radiation treatment increased expression of programmed cell death ligand 1 (PD-L1), but decreased NK group 2, member D (NKG2D) ligand expressions in A549 and H157 NSCLC cells. Both types of changes would have protected tumor cells from the cytotoxic action of NK cells. Consistently, we detected similar alteration in these molecules in radioresistant A549R26-1 and H157R24-1 subline cells. Higher PD-L1 level was also observed in tumors of A549R26-1 cell-derived xenografts than tumors of parental A549 (A549P) cell-derived xenografts. Accordingly, we found radioresistant cells were more resistant to the cytotoxic action of NK cells than parental cells, and such resistance was decreased when neutralizing antibody (Ab) of PD-L1 was added to the radioresistant cell/NK cell co-cultures. In mechanism studies, we found that IL-6-MEK/Erk signaling contributed most significantly to the up-regulation of PD-L1/down-regulation of NKG2D ligands in radioresistant cells. The addition of the MEK/Erk inhibitor increased the susceptibility of A549R26-1 and H157R24-1 cells to NK-cell cytotoxicity while no significant effect was observed in parental cells. Moreover, we detected enhanced NK-cell cytotoxicity to radioresistant cells when PD-L1 Ab and MEK/Erk inhibitor were added together to co-cultures of tumor/NK cells compared to when PD-L1 Ab was used alone. We suggest that combined use of PD-L1 Ab and MEK/Erk inhibitor may offer better therapeutic benefits than PD-L1 Ab alone to treat NSCLC patients who are receiving radiotherapy or who are at the radioresistant stage.

  12. Radiation alters PD-L1/NKG2D ligand levels in lung cancer cells and leads to immune escape from NK cell cytotoxicity via IL-6-MEK/Erk signaling pathway

    Science.gov (United States)

    Shen, Ming Jing; Xu, Li Jun; Yang, Li; Tsai, Ying; Keng, Peter C.; Chen, Yongbing; Lee, Soo Ok; Chen, Yuhchyau

    2017-01-01

    We investigated whether radiation influences the susceptibility of non-small cell lung cancer (NSCLC) cells to NK cell mediated cytotoxicity. We found radiation treatment increased expression of programmed cell death ligand 1 (PD-L1), but decreased NK group 2, member D (NKG2D) ligand expressions in A549 and H157 NSCLC cells. Both types of changes would have protected tumor cells from the cytotoxic action of NK cells. Consistently, we detected similar alteration in these molecules in radioresistant A549R26-1 and H157R24-1 subline cells. Higher PD-L1 level was also observed in tumors of A549R26-1 cell-derived xenografts than tumors of parental A549 (A549P) cell-derived xenografts. Accordingly, we found radioresistant cells were more resistant to the cytotoxic action of NK cells than parental cells, and such resistance was decreased when neutralizing antibody (Ab) of PD-L1 was added to the radioresistant cell/NK cell co-cultures. In mechanism studies, we found that IL-6-MEK/Erk signaling contributed most significantly to the up-regulation of PD-L1/down-regulation of NKG2D ligands in radioresistant cells. The addition of the MEK/Erk inhibitor increased the susceptibility of A549R26-1 and H157R24-1 cells to NK-cell cytotoxicity while no significant effect was observed in parental cells. Moreover, we detected enhanced NK-cell cytotoxicity to radioresistant cells when PD-L1 Ab and MEK/Erk inhibitor were added together to co-cultures of tumor/NK cells compared to when PD-L1 Ab was used alone. We suggest that combined use of PD-L1 Ab and MEK/Erk inhibitor may offer better therapeutic benefits than PD-L1 Ab alone to treat NSCLC patients who are receiving radiotherapy or who are at the radioresistant stage. PMID:29113321

  13. Autocrine signal transmission with extracellular ligand degradation

    International Nuclear Information System (INIS)

    Muratov, C B; Posta, F; Shvartsman, S Y

    2009-01-01

    Traveling waves of cell signaling in epithelial layers orchestrate a number of important processes in developing and adult tissues. These waves can be mediated by positive feedback autocrine loops, a mode of cell signaling where binding of a diffusible extracellular ligand to a cell surface receptor can lead to further ligand release. We formulate and analyze a biophysical model that accounts for ligand-induced ligand release, extracellular ligand diffusion and ligand–receptor interaction. We focus on the case when the main mode for ligand degradation is extracellular and analyze the problem with the sharp threshold positive feedback nonlinearity. We derive expressions that link the speed of propagation and other characteristics of traveling waves to the parameters of the biophysical processes, such as diffusion rates, receptor expression level, etc. Analyzing the derived expressions we found that traveling waves in such systems can exhibit a number of unusual properties, e.g. non-monotonic dependence of the speed of propagation on ligand diffusivity. Our results for the fully developed traveling fronts can be used to analyze wave initiation from localized perturbations, a scenario that frequently arises in the in vitro models of epithelial wound healing, and guide future modeling studies of cell communication in epithelial layers

  14. Impact of protein and ligand impurities on ITC-derived protein-ligand thermodynamics.

    Science.gov (United States)

    Grüner, Stefan; Neeb, Manuel; Barandun, Luzi Jakob; Sielaff, Frank; Hohn, Christoph; Kojima, Shun; Steinmetzer, Torsten; Diederich, François; Klebe, Gerhard

    2014-09-01

    The thermodynamic characterization of protein-ligand interactions by isothermal titration calorimetry (ITC) is a powerful tool in drug design, giving valuable insight into the interaction driving forces. ITC is thought to require protein and ligand solutions of high quality, meaning both the absence of contaminants as well as accurately determined concentrations. Ligands synthesized to deviating purity and protein of different pureness were titrated by ITC. Data curation was attempted also considering information from analytical techniques to correct stoichiometry. We used trypsin and tRNA-guanine transglycosylase (TGT), together with high affinity ligands to investigate the effect of errors in protein concentration as well as the impact of ligand impurities on the apparent thermodynamics. We found that errors in protein concentration did not change the thermodynamic properties obtained significantly. However, most ligand impurities led to pronounced changes in binding enthalpy. If protein binding of the respective impurity is not expected, the actual ligand concentration was corrected for and the thus revised data compared to thermodynamic properties obtained with the respective pure ligand. Even in these cases, we observed differences in binding enthalpy of about 4kJ⋅mol(-1), which is considered significant. Our results indicate that ligand purity is the critical parameter to monitor if accurate thermodynamic data of a protein-ligand complex are to be recorded. Furthermore, artificially changing fitting parameters to obtain a sound interaction stoichiometry in the presence of uncharacterized ligand impurities may lead to thermodynamic parameters significantly deviating from the accurate thermodynamic signature. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. Cyclopalladated complexes containing 2-C6R4PPh2 ligands (R = H, F): one-electron electrochemical reduction leading to metal-carbon σ-bond cleavage via palladium(I).

    Science.gov (United States)

    Kar, Gopa; Privér, Steven H; Jones, Lathe A; Guo, Si-Xuan; Torriero, Angel A J; Bond, Alan M; Bennett, Martin A; Bhargava, Suresh K

    2015-02-21

    Three new ortho-metallated palladium complexes, [Pd(O,O'-hfacac)(κ(2)-2-C6F4PPh2)] (), [Pd2(O,O'-hfacac)2(μ-2-C6F4PPh2)2] () and [Pd(O,O'-hfacac)(κC-2-C6F4PPh2)(PPh3)] () (hfacac = hexafluoroacetylacetonate), have been prepared and fully characterised. The electrochemical reductions of complexes , together with those of other cyclopalladated complexes containing 2-C6R4PPh2 ligands (R = H, F) were studied by cyclic, rotating disk and microelectrode voltammetry. Evidence for the one-electron reduction of [PdI(κ(2)-2-C6F4PPh2)(PPh2Fc)] () was obtained from coulometric analysis, although the product is unstable and undergoes further chemical processes. Preparative electro-reduction of [Pd2(μ-Br)2(κ(2)-2-C6F4PPh2)2] () in CH2Cl2 causes reductive cleavage of its Pd-C σ-bonds and formation of the complex [PdBr2{PPh2(2-C6F4H)}2] (); possible mechanisms are discussed.

  16. Ligand based pharmacophore modelling of anticancer histone ...

    African Journals Online (AJOL)

    like myocardium damage and bone marrow depression even leading to cell death have been observed in the treatment of caner cells using HDAC inhibitors. The discovery and development of type-specific HDAC inhibitors is of both research and clinical interests. Ligand based pharmacophore modelling is playing a key ...

  17. Synthesis and characterization of new coordination polymer with l-proline amino acid ligand, new precursor for preparation of pure phase lead(II) oxide nanoparticles via thermal decomposition

    Czech Academy of Sciences Publication Activity Database

    Varzdar, S.; Hashemi, L.; Morsali, A.; Dušek, Michal

    2017-01-01

    Roč. 14, č. 11 (2017), s. 2255-2261 ISSN 1735-207X Institutional support: RVO:68378271 Keywords : coordination polymer * nanoparticle * lead(II) oxide * proline amino acid Subject RIV: BM - Solid Matter Physics ; Magnetism OBOR OECD: Condensed matter physics (including formerly solid state physics, supercond.) Impact factor: 1.407, year: 2016

  18. LEADING WITH LEADING INDICATORS

    International Nuclear Information System (INIS)

    PREVETTE, S.S.

    2005-01-01

    This paper documents Fluor Hanford's use of Leading Indicators, management leadership, and statistical methodology in order to improve safe performance of work. By applying these methods, Fluor Hanford achieved a significant reduction in injury rates in 2003 and 2004, and the improvement continues today. The integration of data, leadership, and teamwork pays off with improved safety performance and credibility with the customer. The use of Statistical Process Control, Pareto Charts, and Systems Thinking and their effect on management decisions and employee involvement are discussed. Included are practical examples of choosing leading indicators. A statistically based color coded dashboard presentation system methodology is provided. These tools, management theories and methods, coupled with involved leadership and employee efforts, directly led to significant improvements in worker safety and health, and environmental protection and restoration at one of the nation's largest nuclear cleanup sites

  19. Properties of myelin altered peptide ligand cyclo(87-99)(Ala91,Ala96)MBP87-99 render it a promising drug lead for immunotherapy of multiple sclerosis.

    Science.gov (United States)

    Deraos, George; Rodi, Maria; Kalbacher, Hubert; Chatzantoni, Kokona; Karagiannis, Fotios; Synodinos, Loukas; Plotas, Panayiotis; Papalois, Apostolos; Dimisianos, Nikolaos; Papathanasopoulos, Panagiotis; Gatos, Dimitrios; Tselios, Theodore; Apostolopoulos, Vasso; Mouzaki, Athanasia; Matsoukas, John

    2015-08-28

    Multiple sclerosis (MS) is an inflammatory, demyelinating disease of the central nervous system, and it has been established that autoreactive T helper (Th) cells play a crucial role in its pathogenesis. Myelin basic protein (MBP) epitopes are major autoantigens in MS, and the sequence MBP87-99 is an immunodominant epitope. We have previously reported that MBP87-99 peptides with modifications at principal T-cell receptor (TCR) contact sites suppressed the induction of EAE symptoms in rats and SJL/J mice, diverted the immune response from Th1 to Th2 and generated antibodies that did not cross react with the native MBP protein. In this study, the linear and cyclic analogs of the MBP87-99 epitope, namely linear (Ala91,Ala96)MBP87-99 (P2) and cyclo(87-99)(Ala91,Ala96)MBP87-99 (P3), were evaluated for their binding to HLA-DR4, stability to lysosomal enzymes, their effect on cytokine secretion by peripheral blood mononuclear cells (PBMC) derived from MS patients or healthy subjects (controls), and their effect in rat EAE. P1 peptide (wild-type, MBP87-99) was used as control. P2 and P3 did not alter significantly the cytokine secretion by control PBMC, in contrast to P1 that induced moderate IL-10 production. In MS PBMC, P2 and P3 induced the production of IL-2 and IFN-γ, with a simultaneous decrease of IL-10, whereas P1 caused a reduction of IL-10 secretion only. The cellular response to P3 indicated that cyclization did not affect the critical TCR contact sites in MS PBMC. Interestingly, the cyclic P3 analog was found to be a stronger binder to HLA-DR4 compared to linear P2. Moreover, cyclic P3 was more stable to proteolysis compared to linear P2. Finally, both P2 and P3 suppressed EAE induced by an encephalitogenic guinea pig MBP74-85 epitope in Lewis rats whereas P1 failed to do so. In conclusion, cyclization of myelin altered peptide ligand (Ala91,Ala96)MBP87-99 improved binding affinity to HLA-DR4, resistance to proteolysis and antigen-specific immunomodulation

  20. Predicting Nanocrystal Shape through Consideration of Surface-Ligand Interactions

    KAUST Repository

    Bealing, Clive R.

    2012-03-27

    Density functional calculations for the binding energy of oleic acid-based ligands on Pb-rich {100} and {111} facets of PbSe nanocrystals determine the surface energies as a function of ligand coverage. Oleic acid is expected to bind to the nanocrystal surface in the form of lead oleate. The Wulff construction predicts the thermodynamic equilibrium shape of the PbSe nanocrystals. The equilibrium shape is a function of the ligand surface coverage, which can be controlled by changing the concentration of oleic acid during synthesis. The different binding energy of the ligand on the {100} and {111} facets results in different equilibrium ligand coverages on the facets, and a transition in the equilibrium shape from octahedral to cubic is predicted when increasing the ligand concentration during synthesis. © 2012 American Chemical Society.

  1. Sonochemical synthesis of nano-scale mixed-ligands lead(II) coordination polymers as precursors for preparation of PbO and PbBr(OH) nano-structures; thermal, structural and X-ray powder diffraction studies.

    Science.gov (United States)

    Sadeghzadeh, Homa; Morsali, Ali; Yilmaz, Veysel T; Büyükgüngör, Orhan

    2010-03-01

    Nano-structures of two new lead(II) two-dimensional coordination polymers, [Pb(2)(2-pyc)(2)(I)(2)](n) (1) and [Pb(2)(2-pyc)(2)(Br)(2)](n) (2), {2-Hpyc=2-pyridinecarboxilic acid } were synthesized by a sonochemical method that produce the coordination polymers at nano-size. The new nano-structures were characterized by scanning electron microscopy, X-ray powder diffraction, IR spectroscopy and elemental analyses. Compounds 1 and 2 were structurally characterized by single crystal X-ray diffraction and consist of two-dimensional polymeric units. The thermal stability of compounds 1 and 2 were studied by thermal gravimetric and differential thermal analyses. PbO and PbBr(OH) nano-structures were obtained by calcination of the nano-structures of compounds 1 and 2 at 400 degrees C, respectively. Copyright 2009 Elsevier B.V. All rights reserved.

  2. LIBRA: LIgand Binding site Recognition Application.

    Science.gov (United States)

    Hung, Le Viet; Caprari, Silvia; Bizai, Massimiliano; Toti, Daniele; Polticelli, Fabio

    2015-12-15

    In recent years, structural genomics and ab initio molecular modeling activities are leading to the availability of a large number of structural models of proteins whose biochemical function is not known. The aim of this study was the development of a novel software tool that, given a protein's structural model, predicts the presence and identity of active sites and/or ligand binding sites. The algorithm implemented by ligand binding site recognition application (LIBRA) is based on a graph theory approach to find the largest subset of similar residues between an input protein and a collection of known functional sites. The algorithm makes use of two predefined databases for active sites and ligand binding sites, respectively, derived from the Catalytic Site Atlas and the Protein Data Bank. Tests indicate that LIBRA is able to identify the correct binding/active site in 90% of the cases analyzed, 90% of which feature the identified site as ranking first. As far as ligand binding site recognition is concerned, LIBRA outperforms other structure-based ligand binding sites detection tools with which it has been compared. The application, developed in Java SE 7 with a Swing GUI embedding a JMol applet, can be run on any OS equipped with a suitable Java Virtual Machine (JVM), and is available at the following URL: http://www.computationalbiology.it/software/LIBRAv1.zip. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  3. Emergence of a Promising Lead Compound in the Treatment of Triple Negative Breast Cancer: An Insight into Conformational Features and Ligand Binding Landscape of c-Src Protein with UM-164.

    Science.gov (United States)

    Ndagi, Umar; Mhlongo, Ndumiso N; Soliman, Mahmoud E

    2017-12-27

    UM-164, a potent Src/p38 inhibitor, is a promising lead compound for developing the first targeted therapeutic strategy against triple-negative breast cancer (TNBC). However, lack of understanding of conformational features of UM-164 in complex with Src serves a challenge in the rational design of novel Src dual inhibitors. Herein, we provide an in-depth insight into conformational features of Src-UM-164 using different computational approaches. This involved molecular dynamics (MD) simulation, principal component analysis (PCA), thermodynamics calculations, dynamic cross-correlation (DCCM) analysis, and hydrogen bond formation. Findings from this study revealed that (1) the binding of UM-164 to Src induces a more stable and compact conformation; (2) the binding of UM-164 results in increased correlation among the active site residue; (3) the presence of multiple phenyl rings and fluorinated phenyl group in UM-164 contributes to the steric effect; (4) a relatively high-binding free energy estimated for the Src-UM-164 system is affirmative of its experimental potency; (5) hydrophobic packing contributes significantly to the drug binding in Src-UM-164; and (6) observed increase in H-bond distance of interacting residue atoms and Dasatinib compared to UM-164. Findings from this study can serve as a baseline in the design of novel Src inhibitors with dual inhibitory properties.

  4. Sterically demanding iminopyridine ligands

    NARCIS (Netherlands)

    Irrgang, Torsten; Keller, Sandra; Maisel, Heidi; Kretschmer, Winfried; Kempe, Rhett

    Two sterically demanding iminopyridine ligands, (2,6-diisopropylphenyl)[6-(2,4,6-triisopropylphenyl)pyridin-2-ylmeth- ylene]amine and (2,6-diisopropylphenyl)]6-(2,6-dimethylphenyl)pyridin-2-ylmethylene]amine, were prepared by a two-step process: first, condensation of 6-bromopyridine-2-carbaldehyde

  5. Characterization of Ligand Shell for Mixed-Ligand Coated Gold Nanoparticles.

    Science.gov (United States)

    Ong, Quy; Luo, Zhi; Stellacci, Francesco

    2017-08-15

    Gold nanoparticles owe a large number of their properties to their ligand shell. Indeed, many researchers routinely use mixtures of ligand molecules for their nanoparticles to impart complex property sets. It has been shown that the morphology of ligand shells (e.g., Janus, random, stripelike) leads to specific properties. Examples include wettability, solubility, protein nonspecific adsorption, cell penetration, catalysis, and cation-capturing abilities. Yet, it remains a great challenge to evaluate such morphologies in even the most fundamental terms such as dimension and shape. In this Account, we review recent progress in characterization techniques applicable to gold nanoparticles with ligand shells composed of mixed ligands. We divide the characterization into three major categories, namely, microscopy, spectroscopy, and simulation. In microscopy, we review progresses in scanning tunneling microscopy (STM), atomic force microscopy (AFM), and scanning/transmission electron microscopy. In spectroscopy, we mainly highlight recent achievements in nuclear magnetic resonance (NMR), mass spectrometry (MS), small angle neutron scattering (SANS), electron spin resonance (EPR), and adsorption based spectroscopies. In simulation, we point out the latest results in understanding thermodynamic stability of ligand shell morphology and emphasize the role of computer simulation for helping interpretation of experimental data. We conclude with a perspective of future development.

  6. Analysis of macromolecules, ligands and macromolecule-ligand complexes

    Science.gov (United States)

    Von Dreele, Robert B [Los Alamos, NM

    2008-12-23

    A method for determining atomic level structures of macromolecule-ligand complexes through high-resolution powder diffraction analysis and a method for providing suitable microcrystalline powder for diffraction analysis are provided. In one embodiment, powder diffraction data is collected from samples of polycrystalline macromolecule and macromolecule-ligand complex and the refined structure of the macromolecule is used as an approximate model for a combined Rietveld and stereochemical restraint refinement of the macromolecule-ligand complex. A difference Fourier map is calculated and the ligand position and points of interaction between the atoms of the macromolecule and the atoms of the ligand can be deduced and visualized. A suitable polycrystalline sample of macromolecule-ligand complex can be produced by physically agitating a mixture of lyophilized macromolecule, ligand and a solvent.

  7. Radiobiology with DNA ligands

    International Nuclear Information System (INIS)

    Weinreich, R.; Argentini, M.; Guenther, I.; Koziorowski, J.; Larsson, B.; Nievergelt-Egido, M.C.; Salt, C.; Wyer, L.; Dos Santos, D.F.; Hansen, H.J.

    1997-01-01

    The paper deals with the following topics: labelling of DNA ligands and other tumour-affinic compounds with 4.15-d 124 I, radiotoxicity of Hoechst 33258 and 33342 and of iodinated Hoechst 33258 in cell cultures, preparation of 76 Br-, 123 I-, and 221 At-labelled 5-halo-2'-deoxyuridine, chemical syntheses of boron derivatives of Hoechst 33258.III., Gadolinium neutron capture therapy

  8. Therapeutic androgen receptor ligands

    Science.gov (United States)

    Allan, George F.; Sui, Zhihua

    2003-01-01

    In the past several years, the concept of tissue-selective nuclear receptor ligands has emerged. This concept has come to fruition with estrogens, with the successful marketing of drugs such as raloxifene. The discovery of raloxifene and other selective estrogen receptor modulators (SERMs) has raised the possibility of generating selective compounds for other pathways, including androgens (that is, selective androgen receptor modulators, or SARMs). PMID:16604181

  9. Lead Poisoning

    Science.gov (United States)

    Lead is a metal that occurs naturally in the earth's crust. Lead can be found in all parts of our ... from human activities such as mining and manufacturing. Lead used to be in paint; older houses may ...

  10. Lead Toxicity

    Science.gov (United States)

    ... time may lead to reduced IQ, slow learning, Attention Deficit Hyperactivity Disorder (ADHD), or behavioral issues. • Lead also affects other parts ... 800-424-5323) • U.S. Environmental Protection Agency Lead Awareness Program http: / / www. epa. gov/ lead • EPA publication “ ...

  11. Bexarotene ligand pharmaceuticals.

    Science.gov (United States)

    Hurst, R E

    2000-12-01

    Bexarotene (LGD-1069), from Ligand, was the first retinoid X receptor (RXR)-selective, antitumor retinoid to enter clinical trials. The company launched the drug for the treatment of cutaneous T-cell lymphoma (CTCL), as Targretin capsules, in the US in January 2000 [359023]. The company filed an NDA for Targretin capsules in June 1999, and for topical gel in December 1999 [329011], [349982] specifically for once-daily oral administration for the treatment of patients with early-stage CTCL who have not tolerated other therapies, patients with refractory or persistent early stage CTCL and patients with refractory advanced stage CTCL. The FDA approved Targretin capsules at the end of December 1999 for once-daily oral treatment of all stages of CTCL in patients refractory to at least one prior systemic therapy, at an initial dose of 300 mg/m2/day. After an NDA was submitted in December 1999 for Targretin gel, the drug received Priority Review status for use as a treatment of cutaneous lesions in patients with stage IA, IB or IIA CTCL [354836]. The FDA issued an approvable letter in June 2000, and granted marketing clearance for CTCL in the same month [370687], [372768], [372769], [373279]. Ligand had received Orphan Drug designation for this indication [329011]. At the request of the FDA, Ligand agreed to carry out certain post-approval phase IV and pharmacokinetic studies [351604]. The company filed an MAA with the EMEA for Targretin Capsules to treat lymphoma in November 1999 [348944]. The NDA for Targretin gel is based on a multicenter phase III trial that was conducted in the US, Canada, Europe and Australia involving 50 patients and a multicenter phase I/II clinical program involving 67 patients. Targretin gel was evaluated for the treatment of patients with early stage CTCL (IA-IIA) who were refractory to, intolerant to, or reached a response plateau for at least 6 months on at least two prior therapies. Efficacy results exceeded the protocol-defined response

  12. A ligand's view of target similarity

    DEFF Research Database (Denmark)

    Garland, Stephen L; Gloriam, David E

    2011-01-01

    -finding and, potentially, to produce ligands for previously intractable receptors. Sequence motifs correlated with ligands can be applied in the design of target-specific focused libraries that are both efficient and cost-effective and should provide increased hit-rates over diversity screening. Furthermore...... shows with several examples how focusing on the binding site(s) has a clear advantage when it comes to establishing sequence-correlated pharmacological profiles. By organizing and comparing sequence and structural data it is possible to "borrow" SAR from similar targets to increase the speed of lead......, in the optimization phase, the binding motif approach offers the possibility to identify quickly the most likely off-target candidates to be chosen for selectivity screening, as well as potentially characterizing those pockets which may best be exploited for improved selectivity....

  13. Ligand Depot: a data warehouse for ligands bound to macromolecules.

    Science.gov (United States)

    Feng, Zukang; Chen, Li; Maddula, Himabindu; Akcan, Ozgur; Oughtred, Rose; Berman, Helen M; Westbrook, John

    2004-09-01

    Ligand Depot is an integrated data resource for finding information about small molecules bound to proteins and nucleic acids. The initial release (version 1.0, November, 2003) focuses on providing chemical and structural information for small molecules found as part of the structures deposited in the Protein Data Bank. Ligand Depot accepts keyword-based queries and also provides a graphical interface for performing chemical substructure searches. A wide variety of web resources that contain information on small molecules may also be accessed through Ligand Depot. Ligand Depot is available at http://ligand-depot.rutgers.edu/. Version 1.0 supports multiple operating systems including Windows, Unix, Linux and the Macintosh operating system. The current drawing tool works in Internet Explorer, Netscape and Mozilla on Windows, Unix and Linux.

  14. Effects of electrostatic interactions on ligand dissociation kinetics

    Science.gov (United States)

    Erbaş, Aykut; de la Cruz, Monica Olvera; Marko, John F.

    2018-02-01

    We study unbinding of multivalent cationic ligands from oppositely charged polymeric binding sites sparsely grafted on a flat neutral substrate. Our molecular dynamics simulations are suggested by single-molecule studies of protein-DNA interactions. We consider univalent salt concentrations spanning roughly a 1000-fold range, together with various concentrations of excess ligands in solution. To reveal the ionic effects on unbinding kinetics of spontaneous and facilitated dissociation mechanisms, we treat electrostatic interactions both at a Debye-Hückel (DH) (or implicit ions, i.e., use of an electrostatic potential with a prescribed decay length) level and by the more precise approach of considering all ionic species explicitly in the simulations. We find that the DH approach systematically overestimates unbinding rates, relative to the calculations where all ion pairs are present explicitly in solution, although many aspects of the two types of calculation are qualitatively similar. For facilitated dissociation (FD) (acceleration of unbinding by free ligands in solution) explicit-ion simulations lead to unbinding at lower free-ligand concentrations. Our simulations predict a variety of FD regimes as a function of free-ligand and ion concentrations; a particularly interesting regime is at intermediate concentrations of ligands where nonelectrostatic binding strength controls FD. We conclude that explicit-ion electrostatic modeling is an essential component to quantitatively tackle problems in molecular ligand dissociation, including nucleic-acid-binding proteins.

  15. Melatonin: functions and ligands.

    Science.gov (United States)

    Singh, Mahaveer; Jadhav, Hemant R

    2014-09-01

    Melatonin is a chronobiotic substance that acts as synchronizer by stabilizing bodily rhythms. Its synthesis occurs in various locations throughout the body, including the pineal gland, skin, lymphocytes and gastrointestinal tract (GIT). Its synthesis and secretion is controlled by light and dark conditions, whereby light decreases and darkness increases its production. Thus, melatonin is also known as the 'hormone of darkness'. Melatonin and analogs that bind to the melatonin receptors are important because of their role in the management of depression, insomnia, epilepsy, Alzheimer's disease (AD), diabetes, obesity, alopecia, migraine, cancer, and immune and cardiac disorders. In this review, we discuss the mechanism of action of melatonin in these disorders, which could aid in the design of novel melatonin receptor ligands. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Ligand and structure-based methodologies for the prediction of the activity of G protein-coupled receptor ligands

    Science.gov (United States)

    Costanzi, Stefano; Tikhonova, Irina G.; Harden, T. Kendall; Jacobson, Kenneth A.

    2009-11-01

    Accurate in silico models for the quantitative prediction of the activity of G protein-coupled receptor (GPCR) ligands would greatly facilitate the process of drug discovery and development. Several methodologies have been developed based on the properties of the ligands, the direct study of the receptor-ligand interactions, or a combination of both approaches. Ligand-based three-dimensional quantitative structure-activity relationships (3D-QSAR) techniques, not requiring knowledge of the receptor structure, have been historically the first to be applied to the prediction of the activity of GPCR ligands. They are generally endowed with robustness and good ranking ability; however they are highly dependent on training sets. Structure-based techniques generally do not provide the level of accuracy necessary to yield meaningful rankings when applied to GPCR homology models. However, they are essentially independent from training sets and have a sufficient level of accuracy to allow an effective discrimination between binders and nonbinders, thus qualifying as viable lead discovery tools. The combination of ligand and structure-based methodologies in the form of receptor-based 3D-QSAR and ligand and structure-based consensus models results in robust and accurate quantitative predictions. The contribution of the structure-based component to these combined approaches is expected to become more substantial and effective in the future, as more sophisticated scoring functions are developed and more detailed structural information on GPCRs is gathered.

  17. Database of ligand-induced domain movements in enzymes

    Directory of Open Access Journals (Sweden)

    Hayward Steven

    2009-03-01

    Full Text Available Abstract Background Conformational change induced by the binding of a substrate or coenzyme is a poorly understood stage in the process of enzyme catalysed reactions. For enzymes that exhibit a domain movement, the conformational change can be clearly characterized and therefore the opportunity exists to gain an understanding of the mechanisms involved. The development of the non-redundant database of protein domain movements contains examples of ligand-induced domain movements in enzymes, but this valuable data has remained unexploited. Description The domain movements in the non-redundant database of protein domain movements are those found by applying the DynDom program to pairs of crystallographic structures contained in Protein Data Bank files. For each pair of structures cross-checking ligands in their Protein Data Bank files with the KEGG-LIGAND database and using methods that search for ligands that contact the enzyme in one conformation but not the other, the non-redundant database of protein domain movements was refined down to a set of 203 enzymes where a domain movement is apparently triggered by the binding of a functional ligand. For these cases, ligand binding information, including hydrogen bonds and salt-bridges between the ligand and specific residues on the enzyme is presented in the context of dynamical information such as the regions that form the dynamic domains, the hinge bending residues, and the hinge axes. Conclusion The presentation at a single website of data on interactions between a ligand and specific residues on the enzyme alongside data on the movement that these interactions induce, should lead to new insights into the mechanisms of these enzymes in particular, and help in trying to understand the general process of ligand-induced domain closure in enzymes. The website can be found at: http://www.cmp.uea.ac.uk/dyndom/enzymeList.do

  18. Lead poisoning

    Science.gov (United States)

    ... help if this information is not immediately available. Poison Control If someone has severe symptoms from possible ... be caused by lead poisoning, call your local poison control center. Your local poison center can be ...

  19. Targeting Selectins and Their Ligands in Cancer

    Directory of Open Access Journals (Sweden)

    Alessandro eNatoni

    2016-04-01

    Full Text Available Aberrant glycosylation is a hallmark of cancer cells with increased evidence pointing to a role in tumor progression. In particular, aberrant sialylation of glycoproteins and glycolipids have been linked to increased immune cell evasion, drug evasion, drug resistance, tumor invasiveness, and vascular dissemination leading to metastases. Hypersialylation of cancer cells is largely the result of overexpression of sialyltransferases. Humans differentially express twenty different sialyltransferases in a tissue-specific manner, each of which catalyze the attachment of sialic acids via different glycosidic linkages (2-3; 2-6 or 2-8 to the underlying glycan chain. One important mechanism whereby overexpression of sialyltransferases contributes to an enhanced metastatic phenotype is via the generation of selectin ligands. Selectin ligand function requires the expression of sialyl-Lewis X and its structural-isomer sialyl-Lewis A, which are synthesized by the combined action of alpha 1-3-fucosyltransferases, 2-3-sialyltransferases, 1-4-galactosyltranferases, and N-acetyl--glucosaminyltransferases. The α2-3-sialyltransferases ST3Gal4 and ST3Gal6 are critical to the generation of functional E- and P-selectin ligands and overexpression of these sialyltransferases have been linked to increased risk of metastatic disease in solid tumors and poor outcome in multiple myeloma. Thus, targeting selectins and their ligands as well as the enzymes involved in their generation, in particular sialyltransferases, could be beneficial to many cancer patients. Potential strategies include sialyltransferase inhibition and the use of selectin antagonists, such as glycomimetic drugs and antibodies. Here, we review ongoing efforts to optimize the potency and selectivity of sialyltransferase inhibitors, including the potential for targeted delivery approaches, as well as evaluate the potential utility of selectin inhibitors, which are now in early clinical

  20. Glutamate receptor ligands

    DEFF Research Database (Denmark)

    Guldbrandt, Mette; Johansen, Tommy N; Frydenvang, Karla Andrea

    2002-01-01

    Homologation and substitution on the carbon backbone of (S)-glutamic acid [(S)-Glu, 1], as well as absolute stereochemistry, are structural parameters of key importance for the pharmacological profile of (S)-Glu receptor ligands. We describe a series of methyl-substituted 2-aminoadipic acid (AA...... or slightly lower potencies than (S)-AA [e.g., EC(50) = 76 microM for (2S,4S)-4-methyl-AA (5a) as compared to EC(50) = 35 microM for (S)-AA]. The position of the methyl substituent had a profound effect on the observed pharmacology, whereas the absolute stereochemistry at the methylated carbon atom had a very......) analogs, and the synthesis, stereochemistry, and enantiopharmacology of 3-methyl-AA (4a-d), 4-methyl-AA (5a-d), 5-methyl-AA (6a-d), and (E)-Delta(4)-5-methyl-AA (7a and 7b) are reported. The compounds were resolved using chiral HPLC and the configurational assignments of the enantiomers were based on X...

  1. Discovery of GPCR ligands for probing signal transduction pathways.

    Science.gov (United States)

    Brogi, Simone; Tafi, Andrea; Désaubry, Laurent; Nebigil, Canan G

    2014-01-01

    G protein-coupled receptors (GPCRs) are seven integral transmembrane proteins that are the primary targets of almost 30% of approved drugs and continue to represent a major focus of pharmaceutical research. All of GPCR targeted medicines were discovered by classical medicinal chemistry approaches. After the first GPCR crystal structures were determined, the docking screens using these structures lead to discovery of more novel and potent ligands. There are over 360 pharmaceutically relevant GPCRs in the human genome and to date about only 30 of structures have been determined. For these reasons, computational techniques such as homology modeling and molecular dynamics simulations have proven their usefulness to explore the structure and function of GPCRs. Furthermore, structure-based drug design and in silico screening (High Throughput Docking) are still the most common computational procedures in GPCRs drug discovery. Moreover, ligand-based methods such as three-dimensional quantitative structure-selectivity relationships, are the ideal molecular modeling approaches to rationalize the activity of tested GPCR ligands and identify novel GPCR ligands. In this review, we discuss the most recent advances for the computational approaches to effectively guide selectivity and affinity of ligands. We also describe novel approaches in medicinal chemistry, such as the development of biased agonists, allosteric modulators, and bivalent ligands for class A GPCRs. Furthermore, we highlight some knockout mice models in discovering biased signaling selectivity.

  2. Discovery of GPCR ligands for probing signal transduction pathways

    Science.gov (United States)

    Brogi, Simone; Tafi, Andrea; Désaubry, Laurent; Nebigil, Canan G.

    2014-01-01

    G protein-coupled receptors (GPCRs) are seven integral transmembrane proteins that are the primary targets of almost 30% of approved drugs and continue to represent a major focus of pharmaceutical research. All of GPCR targeted medicines were discovered by classical medicinal chemistry approaches. After the first GPCR crystal structures were determined, the docking screens using these structures lead to discovery of more novel and potent ligands. There are over 360 pharmaceutically relevant GPCRs in the human genome and to date about only 30 of structures have been determined. For these reasons, computational techniques such as homology modeling and molecular dynamics simulations have proven their usefulness to explore the structure and function of GPCRs. Furthermore, structure-based drug design and in silico screening (High Throughput Docking) are still the most common computational procedures in GPCRs drug discovery. Moreover, ligand-based methods such as three-dimensional quantitative structure–selectivity relationships, are the ideal molecular modeling approaches to rationalize the activity of tested GPCR ligands and identify novel GPCR ligands. In this review, we discuss the most recent advances for the computational approaches to effectively guide selectivity and affinity of ligands. We also describe novel approaches in medicinal chemistry, such as the development of biased agonists, allosteric modulators, and bivalent ligands for class A GPCRs. Furthermore, we highlight some knockout mice models in discovering biased signaling selectivity. PMID:25506327

  3. Assessment and Challenges of Ligand Docking into Comparative Models of G-Protein Coupled Receptors

    DEFF Research Database (Denmark)

    Nguyen, E.D.; Meiler, J.; Norn, C.

    2013-01-01

    is increased by one order of magnitude for every 10 residues known to contact the ligand. Additionally, in the case of DOR, knowledge of a single specific ligand-protein contact improved sampling efficiency 7 fold. These findings offer specific guidelines which may lead to increased success in determining...

  4. The therapeutic potential of allosteric ligands for free fatty acid sensitive GPCRs

    DEFF Research Database (Denmark)

    Hudson, Brian D; Ulven, Trond; Milligan, Graeme

    2013-01-01

    of identifying allosteric leads and their often flat or confusing SAR. The present review will consider the advantages and challenges associated with allosteric GPCR ligands, and examine how the particular properties of these ligands may be exploited to uncover the therapeutic potential for free fatty acid...

  5. Ecotoxicology: Lead

    Science.gov (United States)

    Scheuhammer, A.M.; Beyer, W.N.; Schmitt, C.J.; Jorgensen, Sven Erik; Fath, Brian D.

    2008-01-01

    Lead (Pb) is a naturally occurring metallic element; trace concentrations are found in all environmental media and in all living things. However, certain human activities, especially base metal mining and smelting; combustion of leaded gasoline; the use of Pb in hunting, target shooting, and recreational angling; the use of Pb-based paints; and the uncontrolled disposal of Pb-containing products such as old vehicle batteries and electronic devices have resulted in increased environmental levels of Pb, and have created risks for Pb exposure and toxicity in invertebrates, fish, and wildlife in some ecosystems.

  6. Ligand-guided receptor optimization.

    Science.gov (United States)

    Katritch, Vsevolod; Rueda, Manuel; Abagyan, Ruben

    2012-01-01

    Receptor models generated by homology or even obtained by crystallography often have their binding pockets suboptimal for ligand docking and virtual screening applications due to insufficient accuracy or induced fit bias. Knowledge of previously discovered receptor ligands provides key information that can be used for improving docking and screening performance of the receptor. Here, we present a comprehensive ligand-guided receptor optimization (LiBERO) algorithm that exploits ligand information for selecting the best performing protein models from an ensemble. The energetically feasible protein conformers are generated through normal mode analysis and Monte Carlo conformational sampling. The algorithm allows iteration of the conformer generation and selection steps until convergence of a specially developed fitness function which quantifies the conformer's ability to select known ligands from decoys in a small-scale virtual screening test. Because of the requirement for a large number of computationally intensive docking calculations, the automated algorithm has been implemented to use Linux clusters allowing easy parallel scaling. Here, we will discuss the setup of LiBERO calculations, selection of parameters, and a range of possible uses of the algorithm which has already proven itself in several practical applications to binding pocket optimization and prospective virtual ligand screening.

  7. Lead grids

    CERN Multimedia

    1974-01-01

    One of the 150 lead grids used in the multiwire proportional chamber g-ray detector. The 0.75 mm diameter holes are spaced 1 mm centre to centre. The grids were made by chemical cutting techniques in the Godet Workshop of the SB Physics.

  8. Leading men

    DEFF Research Database (Denmark)

    Bekker-Nielsen, Tønnes

    2016-01-01

    Through a systematic comparison of c. 50 careers leading to the koinarchate or high priesthood of Asia, Bithynia, Galatia, Lycia, Macedonia and coastal Pontus, as described in funeral or honorary inscriptions of individual koinarchs, it is possible to identify common denominators but also disting...

  9. Novel olfactory ligands via terpene synthases.

    Science.gov (United States)

    Touchet, Sabrina; Chamberlain, Keith; Woodcock, Christine M; Miller, David J; Birkett, Michael A; Pickett, John A; Allemann, Rudolf K

    2015-05-01

    A synthetic biology approach to the rational design of analogues of olfactory ligands by providing unnatural substrates for the enzyme synthesising (S)-germacrene D, an olfactory ligand acting as a plant derived insect repellent, to produce novel ligands is described as a viable alternative to largely unsuccessful ligand docking studies. (S)-14,15-Dimethylgermacrene D shows an unexpected reversal in behavioural activity.

  10. Synthesis and transition metal coordination chemistry of a novel hexadentate bispidine ligand.

    Science.gov (United States)

    Comba, Peter; Rudolf, Henning; Wadepohl, Hubert

    2015-02-14

    Reported is the new bispidine-derived hexadentate ligand (L = 3-(2-methylpyridyl)-7-(bis-2-methylpyridyl)-3,7-diazabicyclo[3.3.1]nonane) with two tertiary amine and four pyridine donor groups. This ligand can form heterodinuclear and mononuclear complexes and, in the mononuclear compounds discussed here, the ligand may coordinate as a pentadentate ligand, with one of the bispyridinemethane-based pyridine groups un- or semi-coordinated, or as a hexadentate ligand, leading to a pentagonal pyramidal coordination geometry or, with an additional monodentate ligand, to a heptacoordinate pentagonal bipyramidal structure. The solution and solid state data presented here indicate that, with the relatively small Cu(II) and high-spin Fe(II) ions the fourth pyridine group is only semi-coordinated for steric reasons and, with the larger high-spin Mn(II) ion genuine heptacoordination is observed but with a relatively large distortion in the pentagonal equatorial plane.

  11. Controlling Nanocrystal Superlattice Symmetry and Shape-Anisotropic Interactions through Variable Ligand Surface Coverage

    KAUST Repository

    Choi, Joshua J.

    2011-03-09

    The assembly of colloidal nanocrystals (NCs) into superstructures with long-range translational and orientational order is sensitive to the molecular interactions between ligands bound to the NC surface. We illustrate how ligand coverage on colloidal PbS NCs can be exploited as a tunable parameter to direct the self-assembly of superlattices with predefined symmetry. We show that PbS NCs with dense ligand coverage assemble into face-centered cubic (fcc) superlattices whereas NCs with sparse ligand coverage assemble into body-centered cubic (bcc) superlattices which also exhibit orientational ordering of NCs in their lattice sites. Surface chemistry characterization combined with density functional theory calculations suggest that the loss of ligands occurs preferentially on {100} than on reconstructed {111} NC facets. The resulting anisotropic ligand distribution amplifies the role of NC shape in the assembly and leads to the formation of superlattices with translational and orientational order. © 2011 American Chemical Society.

  12. Memetic algorithms for ligand expulsion from protein cavities

    Science.gov (United States)

    Rydzewski, J.; Nowak, W.

    2015-09-01

    Ligand diffusion through a protein interior is a fundamental process governing biological signaling and enzymatic catalysis. A complex topology of channels in proteins leads often to difficulties in modeling ligand escape pathways by classical molecular dynamics simulations. In this paper, two novel memetic methods for searching the exit paths and cavity space exploration are proposed: Memory Enhanced Random Acceleration (MERA) Molecular Dynamics (MD) and Immune Algorithm (IA). In MERA, a pheromone concept is introduced to optimize an expulsion force. In IA, hybrid learning protocols are exploited to predict ligand exit paths. They are tested on three protein channels with increasing complexity: M2 muscarinic G-protein-coupled receptor, enzyme nitrile hydratase, and heme-protein cytochrome P450cam. In these cases, the memetic methods outperform simulated annealing and random acceleration molecular dynamics. The proposed algorithms are general and appropriate in all problems where an accelerated transport of an object through a network of channels is studied.

  13. Ligand-based virtual screening under partial shape constraints

    Science.gov (United States)

    von Behren, Mathias M.; Rarey, Matthias

    2017-04-01

    Ligand-based virtual screening has proven to be a viable technology during the search for new lead structures in drug discovery. Despite the rapidly increasing number of published methods, meaningful shape matching as well as ligand and target flexibility still remain open challenges. In this work, we analyze the influence of knowledge-based sterical constraints on the performance of the recently published ligand-based virtual screening method mRAISE. We introduce the concept of partial shape matching enabling a more differentiated view on chemical structure. The new method is integrated into the LBVS tool mRAISE providing multiple options for such constraints. The applied constraints can either be derived automatically from a protein-ligand complex structure or by manual selection of ligand atoms. In this way, the descriptor directly encodes the fit of a ligand into the binding site. Furthermore, the conservation of close contacts between the binding site surface and the query ligand can be enforced. We validated our new method on the DUD and DUD-E datasets. Although the statistical performance remains on the same level, detailed analysis reveal that for certain and especially very flexible targets a significant improvement can be achieved. This is further highlighted looking at the quality of calculated molecular alignments using the recently introduced mRAISE dataset. The new partial shape constraints improved the overall quality of molecular alignments especially for difficult targets with highly flexible or different sized molecules. The software tool mRAISE is freely available on Linux operating systems for evaluation purposes and academic use (see http://www.zbh.uni-hamburg.de/raise).

  14. Rosetta Ligand docking with flexible XML protocols.

    Science.gov (United States)

    Lemmon, Gordon; Meiler, Jens

    2012-01-01

    RosettaLigand is premiere software for predicting how a protein and a small molecule interact. Benchmark studies demonstrate that 70% of the top scoring RosettaLigand predicted interfaces are within 2Å RMSD from the crystal structure [1]. The latest release of Rosetta ligand software includes many new features, such as (1) docking of multiple ligands simultaneously, (2) representing ligands as fragments for greater flexibility, (3) redesign of the interface during docking, and (4) an XML script based interface that gives the user full control of the ligand docking protocol.

  15. THERMODYNAMIC ASSESSMENT OF ANIONIC LIGANDS ...

    African Journals Online (AJOL)

    DJFLEX

    2010-06-30

    Jun 30, 2010 ... The presence of the ligands (ethylenediaminettraacetic acid, EDTA, enthylenediamine, en,and chloride ion, Cl-) generally improved the sorption capacity for the adsorbent, the best being. Cl- at optimum pH of 2.0 (for Co2+) and 5.0 (for Ni2+ and Cd2+). The thermodynamic studies reveal that the adsorption.

  16. Polysulfide ligand exchange on zinc sulfide nanocrystal surfaces for improved film formation

    Science.gov (United States)

    Herron, Steven M.; Lawal, Qudus O.; Bent, Stacey F.

    2015-12-01

    The physical and chemical properties of nanocrystals can be modified by changing the ligands attached at their surfaces. A ligand exchange procedure with ammonium polysulfides has been developed to replace the native ligands on cubic zinc sulfide nanocrystals. Several mixtures of polysulfides in formamide and other solvents were prepared with different average chain lengths and used to achieve high yield ligand exchange, as confirmed by UV-vis spectroscopy, infrared spectroscopy and X-ray photoelectron spectroscopy. The results show that polysulfide content can be increased with longer surface ligands and that the exchange process yields compositionally pure surfaces before and after high temperature anneals. X-ray diffraction and scanning electron microscopy show that, when annealed in nitrogen at 525 °C, polysulfide ligands lead to average crystal sizes 2-3 times larger than in the un-exchanged control sample. The ligand exchange procedure itself does not alter nanocrystal size. Nanocrystal inks prepared from the exchanged samples form thin films that exhibit superior grain growth, morphology, mass retention, and composition compared to the un-exchanged material. Overall, polysulfide species are demonstrated as alternative ligands for the surfaces of metal chalcogenide nanocrystals which, when incorporated in an efficient ligand-exchange procedure, can improve the quality of ZnS nanocrystal inks.

  17. Residue preference mapping of ligand fragments in the Protein Data Bank.

    Science.gov (United States)

    Wang, Lirong; Xie, Zhaojun; Wipf, Peter; Xie, Xiang-Qun

    2011-04-25

    The interaction between small molecules and proteins is one of the major concerns for structure-based drug design because the principles of protein-ligand interactions and molecular recognition are not thoroughly understood. Fortunately, the analysis of protein-ligand complexes in the Protein Data Bank (PDB) enables unprecedented possibilities for new insights. Herein, we applied molecule-fragmentation algorithms to split the ligands extracted from PDB crystal structures into small fragments. Subsequently, we have developed a ligand fragment and residue preference mapping (LigFrag-RPM) algorithm to map the profiles of the interactions between these fragments and the 20 proteinogenic amino acid residues. A total of 4032 fragments were generated from 71 798 PDB ligands by a ring cleavage (RC) algorithm. Among these ligand fragments, 315 unique fragments were characterized with the corresponding fragment-residue interaction profiles by counting residues close to these fragments. The interaction profiles revealed that these fragments have specific preferences for certain types of residues. The applications of these interaction profiles were also explored and evaluated in case studies, showing great potential for the study of protein-ligand interactions and drug design. Our studies demonstrated that the fragment-residue interaction profiles generated from the PDB ligand fragments can be used to detect whether these fragments are in their favorable or unfavorable environments. The algorithm for a ligand fragment and residue preference mapping (LigFrag-RPM) developed here also has the potential to guide lead chemistry modifications as well as binding residues predictions.

  18. NKG2D and Its Ligands: “One for All, All for One”

    Directory of Open Access Journals (Sweden)

    Alessandra Zingoni

    2018-03-01

    Full Text Available The activating receptor NKG2D is peculiar in its capability to bind to numerous and highly diversified MHC class I-like self-molecules. These ligands are poorly expressed on normal cells but can be induced on damaged, transformed or infected cells, with the final NKG2D ligand expression resulting from multiple levels of regulation. Although redundant molecular mechanisms can converge in the regulation of all NKG2D ligands, different stimuli can induce specific cellular responses, leading to the expression of one or few ligands. A large body of evidence demonstrates that NK cell activation can be triggered by different NKG2D ligands, often expressed on the same cell, suggesting a functional redundancy of these molecules. However, since a number of evasion mechanisms can reduce membrane expression of these molecules both on virus-infected and tumor cells, the co-expression of different ligands and/or the presence of allelic forms of the same ligand guarantee NKG2D activation in various stressful conditions and cell contexts. Noteworthy, NKG2D ligands can differ in their ability to down-modulate NKG2D membrane expression in human NK cells supporting the idea that NKG2D transduces different signals upon binding various ligands. Moreover, whether proteolytically shed and exosome-associated soluble NKG2D ligands share with their membrane-bound counterparts the same ability to induce NKG2D-mediated signaling is still a matter of debate. Here, we will review recent studies on the NKG2D/NKG2D ligand biology to summarize and discuss the redundancy and/or diversity in ligand expression, regulation, and receptor specificity.

  19. Crystallization of protein–ligand complexes

    International Nuclear Information System (INIS)

    Hassell, Anne M.; An, Gang; Bledsoe, Randy K.; Bynum, Jane M.; Carter, H. Luke III; Deng, Su-Jun J.; Gampe, Robert T.; Grisard, Tamara E.; Madauss, Kevin P.; Nolte, Robert T.; Rocque, Warren J.; Wang, Liping; Weaver, Kurt L.; Williams, Shawn P.; Wisely, G. Bruce; Xu, Robert; Shewchuk, Lisa M.

    2007-01-01

    Methods presented for growing protein–ligand complexes fall into the categories of co-expression of the protein with the ligands of interest, use of the ligands during protein purification, cocrystallization and soaking the ligands into existing crystals. Obtaining diffraction-quality crystals has long been a bottleneck in solving the three-dimensional structures of proteins. Often proteins may be stabilized when they are complexed with a substrate, nucleic acid, cofactor or small molecule. These ligands, on the other hand, have the potential to induce significant conformational changes to the protein and ab initio screening may be required to find a new crystal form. This paper presents an overview of strategies in the following areas for obtaining crystals of protein–ligand complexes: (i) co-expression of the protein with the ligands of interest, (ii) use of the ligands during protein purification, (iii) cocrystallization and (iv) soaks

  20. Using chemical shift perturbation to characterise ligand binding.

    Science.gov (United States)

    Williamson, Mike P

    2013-08-01

    Chemical shift perturbation (CSP, chemical shift mapping or complexation-induced changes in chemical shift, CIS) follows changes in the chemical shifts of a protein when a ligand is added, and uses these to determine the location of the binding site, the affinity of the ligand, and/or possibly the structure of the complex. A key factor in determining the appearance of spectra during a titration is the exchange rate between free and bound, or more specifically the off-rate koff. When koff is greater than the chemical shift difference between free and bound, which typically equates to an affinity Kd weaker than about 3μM, then exchange is fast on the chemical shift timescale. Under these circumstances, the observed shift is the population-weighted average of free and bound, which allows Kd to be determined from measurement of peak positions, provided the measurements are made appropriately. (1)H shifts are influenced to a large extent by through-space interactions, whereas (13)Cα and (13)Cβ shifts are influenced more by through-bond effects. (15)N and (13)C' shifts are influenced both by through-bond and by through-space (hydrogen bonding) interactions. For determining the location of a bound ligand on the basis of shift change, the most appropriate method is therefore usually to measure (15)N HSQC spectra, calculate the geometrical distance moved by the peak, weighting (15)N shifts by a factor of about 0.14 compared to (1)H shifts, and select those residues for which the weighted shift change is larger than the standard deviation of the shift for all residues. Other methods are discussed, in particular the measurement of (13)CH3 signals. Slow to intermediate exchange rates lead to line broadening, and make Kd values very difficult to obtain. There is no good way to distinguish changes in chemical shift due to direct binding of the ligand from changes in chemical shift due to allosteric change. Ligand binding at multiple sites can often be characterised, by

  1. Force loading explains spatial sensing of ligands by cells

    Science.gov (United States)

    Oria, Roger; Wiegand, Tina; Escribano, Jorge; Elosegui-Artola, Alberto; Uriarte, Juan Jose; Moreno-Pulido, Cristian; Platzman, Ilia; Delcanale, Pietro; Albertazzi, Lorenzo; Navajas, Daniel; Trepat, Xavier; García-Aznar, José Manuel; Cavalcanti-Adam, Elisabetta Ada; Roca-Cusachs, Pere

    2017-12-01

    Cells can sense the density and distribution of extracellular matrix (ECM) molecules by means of individual integrin proteins and larger, integrin-containing adhesion complexes within the cell membrane. This spatial sensing drives cellular activity in a variety of normal and pathological contexts. Previous studies of cells on rigid glass surfaces have shown that spatial sensing of ECM ligands takes place at the nanometre scale, with integrin clustering and subsequent formation of focal adhesions impaired when single integrin-ligand bonds are separated by more than a few tens of nanometres. It has thus been suggested that a crosslinking ‘adaptor’ protein of this size might connect integrins to the actin cytoskeleton, acting as a molecular ruler that senses ligand spacing directly. Here, we develop gels whose rigidity and nanometre-scale distribution of ECM ligands can be controlled and altered. We find that increasing the spacing between ligands promotes the growth of focal adhesions on low-rigidity substrates, but leads to adhesion collapse on more-rigid substrates. Furthermore, disordering the ligand distribution drastically increases adhesion growth, but reduces the rigidity threshold for adhesion collapse. The growth and collapse of focal adhesions are mirrored by, respectively, the nuclear or cytosolic localization of the transcriptional regulator protein YAP. We explain these findings not through direct sensing of ligand spacing, but by using an expanded computational molecular-clutch model, in which individual integrin-ECM bonds—the molecular clutches—respond to force loading by recruiting extra integrins, up to a maximum value. This generates more clutches, redistributing the overall force among them, and reducing the force loading per clutch. At high rigidity and high ligand spacing, maximum recruitment is reached, preventing further force redistribution and leading to adhesion collapse. Measurements of cellular traction forces and actin flow speeds

  2. -Pincer Ligand Family through Ligand Post-Modification

    KAUST Repository

    Huang, Mei-Hui

    2017-10-02

    A series of air-stable nickel complexes containing triazine-based PN3P-pincer ligands were synthesized and fully characterized. Complex 3 contains a de-aromatized central triazine ring from the deprotonation of one of the N–H arms. With a post-modification strategy, the Me-PN3P*NiCl complex (3) could be converted into a new class of diimine–traizine PN3P-pincer nickel complexes.

  3. Chelating ligands for nanocrystals' surface functionalization

    NARCIS (Netherlands)

    Querner, Claudia; Reiss, Peter; Bleuse, Joël; Pron, Adam

    2004-01-01

    A new family of ligands for the surface functionalization of CdSe nanocrystals is proposed, namely alkyl or aryl derivatives of carbodithioic acids (R-C(S)SH). The main advantages of these new ligands are as follows: they nearly quantitatively exchange the initial surface ligands (TOPO) in very mild

  4. The therapeutic potential of allosteric ligands for free fatty acid sensitive GPCRs

    DEFF Research Database (Denmark)

    Hudson, Brian D; Ulven, Trond; Milligan, Graeme

    2013-01-01

    G protein coupled receptors (GPCRs) are the most historically successful therapeutic targets. Despite this success there are many important aspects of GPCR pharmacology and function that have yet to be exploited to their full therapeutic potential. One in particular that has been gaining attention...... in recent times is that of GPCR ligands that bind to allosteric sites on the receptor distinct from the orthosteric site of the endogenous ligand. As therapeutics, allosteric ligands possess many theoretical advantages over their orthosteric counterparts, including more complex modes of action, improved...... of identifying allosteric leads and their often flat or confusing SAR. The present review will consider the advantages and challenges associated with allosteric GPCR ligands, and examine how the particular properties of these ligands may be exploited to uncover the therapeutic potential for free fatty acid...

  5. Structural parameterization of the binding enthalpy of small ligands.

    Science.gov (United States)

    Luque, Irene; Freire, Ernesto

    2002-11-01

    A major goal in ligand and drug design is the optimization of the binding affinity of selected lead molecules. However, the binding affinity is defined by the free energy of binding, which, in turn, is determined by the enthalpy and entropy changes. Because the binding enthalpy is the term that predominantly reflects the strength of the interactions of the ligand with its target relative to those with the solvent, it is desirable to develop ways of predicting enthalpy changes from structural considerations. The application of structure/enthalpy correlations derived from protein stability data has yielded inconsistent results when applied to small ligands of pharmaceutical interest (MW the enthalpy associated with any possible conformational change in the protein or ligand upon binding; and, (3) the enthalpy associated with protonation/deprotonation events, if present. As in the case of protein stability, the intrinsic binding enthalpy scales with changes in solvent accessible surface areas. However, an accurate estimation of the intrinsic binding enthalpy requires explicit consideration of long-lived water molecules at the binding interface. The best statistical structure/enthalpy correlation is obtained when buried water molecules within 5-7 A of the ligand are included in the calculations. For all seven protein systems considered (HIV-1 protease, dihydrodipicolinate reductase, Rnase T1, streptavidin, pp60c-Src SH2 domain, Hsp90 molecular chaperone, and bovine beta-trypsin) the binding enthalpy of 25 small molecular weight peptide and nonpeptide ligands can be accounted for with a standard error of +/-0.3 kcal x mol(-1). Copyright 2002 Wiley-Liss, Inc.

  6. Alternative Affinity Ligands for Immunoglobulins.

    Science.gov (United States)

    Kruljec, Nika; Bratkovič, Tomaž

    2017-08-16

    The demand for recombinant therapeutic antibodies and Fc-fusion proteins is expected to increase in the years to come. Hence, extensive efforts are concentrated on improving the downstream processing. In particular, the development of better-affinity chromatography matrices, supporting robust time- and cost-effective antibody purification, is warranted. With the advances in molecular design and high-throughput screening approaches from chemical and biological combinatorial libraries, novel affinity ligands representing alternatives to bacterial immunoglobulin (Ig)-binding proteins have entered the scene. Here, we review the design, development, and properties of diverse classes of alternative antibody-binding ligands, ranging from engineered versions of Ig-binding proteins, to artificial binding proteins, peptides, aptamers, and synthetic small-molecular-weight compounds. We also provide examples of applications for the novel affinity matrices in chromatography and beyond.

  7. Ligand binding by PDZ domains

    DEFF Research Database (Denmark)

    Chi, Celestine N.; Bach, Anders; Strømgaard, Kristian

    2012-01-01

    The postsynaptic density protein-95/disks large/zonula occludens-1 (PDZ) protein domain family is one of the most common protein-protein interaction modules in mammalian cells, with paralogs present in several hundred human proteins. PDZ domains are found in most cell types, but neuronal proteins...... as pathological conditions have been reviewed recently. In this review, we focus on the molecular details of how PDZ domains bind their protein ligands and their potential as drug targets in this context....

  8. Radioiodinated ligands for dopamine receptors

    International Nuclear Information System (INIS)

    Kung, H.F.

    1994-01-01

    The dopamine receptor system is important for normal brain function; it is also the apparent action site for various neuroleptic drugs for the treatment of schizophrenia and other metal disorders. In the past few years radioiodinated ligands for single photon emission tomography (SPECT) have been successfully developed and tested in humans: [ 123 I]TISCH for D1 dopamine receptors; [ 123 I]IBZM, epidepride, IBF and FIDA2, four iodobenzamide derivatives, for D2/D3 dopamine receptors. In addition, [ 123 I]β-CIT (RTI-55) and IPT, cocaine derivatives, for the dopamine reuptake site are potentially useful for diagnosis of loss of dopamine neurons. The first iodinated ligand, (R)trans-7-OH-PIPAT, for D3 dopamine receptors, was synthesized and characterized with cloned cell lines (Spodoptera frugiperda, Sf9) expressing the D2 and D3 dopamine receptors and with rat basal forebrain membrane preparations. Most of the known iodobenzamides displayed similar potency in binding to both D2 and D3 dopamine receptors expressed in the cell lines. Initial studies appear to suggest that by fine tuning the structures it may be possible to develop agents specific for D2 and D3 dopamine receptors. It is important to investigate D2/D3 selectivity for this series of potent ligands

  9. Tumor targeting via integrin ligands

    Directory of Open Access Journals (Sweden)

    Udaya Kiran eMarelli

    2013-08-01

    Full Text Available Selective and targeted delivery of drugs to tumors is a major challenge for an effective cancer therapy and also to overcome the side effects associated with current treatments. Overexpression of various receptors on tumor cells is a characteristic structural and biochemical aspect of tumors and distinguishes them from physiologically normal cells. This abnormal feature is therefore suitable for selectively directing anticancer molecules to tumors by using ligands that can preferentially recognize such receptors. Several subtypes of integrin receptors that are crucial for cell adhesion, cell signaling, cell viability and motility have been shown to have an upregulated expression on cancer cells. Thus, ligands that recognize specific integrin subtypes represent excellent candidates to be conjugated to drugs or drug carrier systems and be targeted to tumors. In this regard, integrins recognizing the RGD cell adhesive sequence have been extensively targeted for tumor specific drug delivery. Here we review key recent examples on the presentation of RGD-based integrin ligands by means of distinct drug delivery systems, and discuss the prospects of such therapies to specifically target tumor cells.

  10. The Evaluation of Novel Camphor-derived Pyridyl Ligands as ...

    African Journals Online (AJOL)

    NJD

    2009-03-03

    Mar 3, 2009 ... Lewis acids under very mild conditions led to a number of researchers investigating the development of chiral ligands which could complex these Lewis acids, hence leading to asym- metric products from the ..... halides such as NiBr2, CaBr2, MnBr2, FeCl2, CoBr2, CuCl2 and. ZnI2 and complexation time ...

  11. Polysulfide ligand exchange on zinc sulfide nanocrystal surfaces for improved film formation

    Energy Technology Data Exchange (ETDEWEB)

    Herron, Steven M. [Department of Chemistry, Stanford University, Stanford, CA 94305 (United States); Lawal, Qudus O. [Department of Chemical Engineering, Stanford University, Stanford, CA 94305 (United States); Bent, Stacey F., E-mail: sbent@stanford.edu [Department of Chemical Engineering, Stanford University, Stanford, CA 94305 (United States)

    2015-12-30

    Graphical abstract: - Highlights: • Ammonium polysulfides are prepared in aprotic solvents. • Native ligands on surfaces of colloidal ZnS nanocrystals are efficiently exchanged with polysulfides. • Ligand exchange improves crystallinity and composition in annealed ZnS thin films. • Polysulfide nanocrystal inks increase mass retention from 62% to 88%. - Abstract: The physical and chemical properties of nanocrystals can be modified by changing the ligands attached at their surfaces. A ligand exchange procedure with ammonium polysulfides has been developed to replace the native ligands on cubic zinc sulfide nanocrystals. Several mixtures of polysulfides in formamide and other solvents were prepared with different average chain lengths and used to achieve high yield ligand exchange, as confirmed by UV–vis spectroscopy, infrared spectroscopy and X-ray photoelectron spectroscopy. The results show that polysulfide content can be increased with longer surface ligands and that the exchange process yields compositionally pure surfaces before and after high temperature anneals. X-ray diffraction and scanning electron microscopy show that, when annealed in nitrogen at 525 °C, polysulfide ligands lead to average crystal sizes 2–3 times larger than in the un-exchanged control sample. The ligand exchange procedure itself does not alter nanocrystal size. Nanocrystal inks prepared from the exchanged samples form thin films that exhibit superior grain growth, morphology, mass retention, and composition compared to the un-exchanged material. Overall, polysulfide species are demonstrated as alternative ligands for the surfaces of metal chalcogenide nanocrystals which, when incorporated in an efficient ligand-exchange procedure, can improve the quality of ZnS nanocrystal inks.

  12. Contrasting roles for TLR ligands in HIV-1 pathogenesis.

    Directory of Open Access Journals (Sweden)

    Beda Brichacek

    2010-09-01

    Full Text Available The first line of a host's response to various pathogens is triggered by their engagement of cellular pattern recognition receptors (PRRs. Binding of microbial ligands to these receptors leads to the induction of a variety of cellular factors that alter intracellular and extracellular environment and interfere directly or indirectly with the life cycle of the triggering pathogen. Such changes may also affect any coinfecting microbe. Using ligands to Toll-like receptors (TLRs 5 and 9, we examined their effect on human immunodeficiency virus (HIV-1 replication in lymphoid tissue ex vivo. We found marked differences in the outcomes of such treatment. While flagellin (TLR5 agonist treatment enhanced replication of CC chemokine receptor 5 (CCR 5-tropic and CXC chemokine receptor 4 (CXCR4-tropic HIV-1, treatment with oligodeoxynucleotide (ODN M362 (TLR9 agonist suppressed both viral variants. The differential effects of these TLR ligands on HIV-1 replication correlated with changes in production of CC chemokines CCL3, CCL4, CCL5, and of CXC chemokines CXCL10, and CXCL12 in the ligand-treated HIV-1-infected tissues. The nature and/or magnitude of these changes were dependent on the ligand as well as on the HIV-1 viral strain. Moreover, the tested ligands differed in their ability to induce cellular activation as evaluated by the expression of the cluster of differentiation markers (CD 25, CD38, CD39, CD69, CD154, and human leukocyte antigen D related (HLA-DR as well as of a cell proliferation marker, Ki67, and of CCR5. No significant effect of the ligand treatment was observed on apoptosis and cell death/loss in the treated lymphoid tissue ex vivo. Our results suggest that binding of microbial ligands to TLRs is one of the mechanisms that mediate interactions between coinfected microbes and HIV-1 in human tissues. Thus, the engagement of appropriate TLRs by microbial molecules or their mimetic might become a new strategy for HIV therapy or prevention.

  13. Colloidal-quantum-dot photovoltaics using atomic-ligand passivation

    KAUST Repository

    Tang, Jiang

    2011-09-18

    Colloidal-quantum-dot (CQD) optoelectronics offer a compelling combination of solution processing and spectral tunability through quantum size effects. So far, CQD solar cells have relied on the use of organic ligands to passivate the surface of the semiconductor nanoparticles. Although inorganic metal chalcogenide ligands have led to record electronic transport parameters in CQD films, no photovoltaic device has been reported based on such compounds. Here we establish an atomic ligand strategy that makes use of monovalent halide anions to enhance electronic transport and successfully passivate surface defects in PbS CQD films. Both time-resolved infrared spectroscopy and transient device characterization indicate that the scheme leads to a shallower trap state distribution than the best organic ligands. Solar cells fabricated following this strategy show up to 6% solar AM1.5G power-conversion efficiency. The CQD films are deposited at room temperature and under ambient atmosphere, rendering the process amenable to low-cost, roll-by-roll fabrication. © 2011 Macmillan Publishers Limited. All rights reserved.

  14. Ligand-directed trafficking of receptor stimulus.

    Science.gov (United States)

    Chilmonczyk, Zdzisław; Bojarski, Andrzej J; Sylte, Ingebrigt

    2014-12-01

    GPCRs are seven transmembrane-spanning receptors that convey specific extracellular stimuli to intracellular signalling. They represent the largest family of cell surface proteins that are therapeutically targeted. According to the traditional two-state model of receptor theory, GPCRs were considered as operating in equilibrium between two functional conformations, an active (R*) and inactive (R) state. Thus, it was assumed that a GPCR can exist either in an "off" or "on" conformation causing either no activation or equal activation of all its signalling pathways. Over the past several years it has become evident that this model is too simple and that GPCR signalling is far more complex. Different studies have presented a multistate model of receptor activation in which ligand-specific receptor conformations are able to differentiate between distinct signalling partners. Recent data show that beside G proteins numerous other proteins, such as β-arrestins and kinases, may interact with GPCRs and activate intracellular signalling pathways. GPCR activation may therefore involve receptor desensitization, coupling to multiple G proteins, Gα or Gβγ signalling, and pathway activation that is independent of G proteins. This latter effect leads to agonist "functional selectivity" (also called ligand-directed receptor trafficking, stimulus trafficking, biased agonism, biased signalling), and agonist intervention with functional selectivity may improve the therapy. Many commercially available drugs with beneficial efficacy also show various undesirable side effects. Further studies of biased signalling might facilitate our understanding of the side effects of current drugs and take us to new avenues to efficiently design pathway-specific medications. Copyright © 2014 Institute of Pharmacology, Polish Academy of Sciences. Published by Elsevier Urban & Partner Sp. z o.o. All rights reserved.

  15. Natural products as tools for studies of ligand-gated ion channels

    DEFF Research Database (Denmark)

    Strømgaard, Kristian

    2005-01-01

    in the brain. Historically, natural products have been used extensively in biomedical studies and ultimately as drugs or leads for drug design. In studies of ligand-gated ion channels, natural products have been essential for the understanding of their structure and function. In the following a short survey...... of natural products and their use in studies of ligand-gated ion channels is given....

  16. Drop amalgam voltammetric study of lead complexation by natural ...

    African Journals Online (AJOL)

    Drop amalgam voltammetric study of lead complexation by natural inorganic ligands in a salt lake. ... Bulletin of the Chemical Society of Ethiopia ... The results obtained indicate that in Lake Katwe water (25 oC, carbonate alkalinity = 0.11 M, pH 11) approximately 0.00% of total inorganic lead exists as the free ion, and at ...

  17. Drop amalgam voltammetric study of lead complexation by natural ...

    African Journals Online (AJOL)

    A study of inorganic complexation of lead using drop amalgam voltammetry is described. The study has been carried out in simulated salt lake water and at ionic strength of 7.35 M, the predetermined ionic strength of Lake Katwe. The complexation of lead with the simple ligands (Cl-, CO32-) created anodic waves and the ...

  18. Ligand photo-isomerization triggers conformational changes in iGluR2 ligand binding domain.

    Directory of Open Access Journals (Sweden)

    Tino Wolter

    Full Text Available Neurological glutamate receptors bind a variety of artificial ligands, both agonistic and antagonistic, in addition to glutamate. Studying their small molecule binding properties increases our understanding of the central nervous system and a variety of associated pathologies. The large, oligomeric multidomain membrane protein contains a large and flexible ligand binding domains which undergoes large conformational changes upon binding different ligands. A recent application of glutamate receptors is their activation or inhibition via photo-switchable ligands, making them key systems in the emerging field of optochemical genetics. In this work, we present a theoretical study on the binding mode and complex stability of a novel photo-switchable ligand, ATA-3, which reversibly binds to glutamate receptors ligand binding domains (LBDs. We propose two possible binding modes for this ligand based on flexible ligand docking calculations and show one of them to be analogues to the binding mode of a similar ligand, 2-BnTetAMPA. In long MD simulations, it was observed that transitions between both binding poses involve breaking and reforming the T686-E402 protein hydrogen bond. Simulating the ligand photo-isomerization process shows that the two possible configurations of the ligand azo-group have markedly different complex stabilities and equilibrium binding modes. A strong but slow protein response is observed after ligand configuration changes. This provides a microscopic foundation for the observed difference in ligand activity upon light-switching.

  19. Targeting protein-protein interactions with trimeric ligands: high affinity inhibitors of the MAGUK protein family.

    Science.gov (United States)

    Nissen, Klaus B; Haugaard-Kedström, Linda M; Wilbek, Theis S; Nielsen, Line S; Åberg, Emma; Kristensen, Anders S; Bach, Anders; Jemth, Per; Strømgaard, Kristian

    2015-01-01

    PDZ domains in general, and those of PSD-95 in particular, are emerging as promising drug targets for diseases such as ischemic stroke. We have previously shown that dimeric ligands that simultaneously target PDZ1 and PDZ2 of PSD-95 are highly potent inhibitors of PSD-95. However, PSD-95 and the related MAGUK proteins contain three consecutive PDZ domains, hence we envisioned that targeting all three PDZ domains simultaneously would lead to more potent and potentially more specific interactions with the MAGUK proteins. Here we describe the design, synthesis and characterization of a series of trimeric ligands targeting all three PDZ domains of PSD-95 and the related MAGUK proteins, PSD-93, SAP-97 and SAP-102. Using our dimeric ligands targeting the PDZ1-2 tandem as starting point, we designed novel trimeric ligands by introducing a PDZ3-binding peptide moiety via a cysteine-derivatized NPEG linker. The trimeric ligands generally displayed increased affinities compared to the dimeric ligands in fluorescence polarization binding experiments and optimized trimeric ligands showed low nanomolar inhibition towards the four MAGUK proteins, thus being the most potent inhibitors described. Kinetic experiments using stopped-flow spectrometry showed that the increase in affinity is caused by a decrease in the dissociation rate of the trimeric ligand as compared to the dimeric ligands, likely reflecting the lower probability of simultaneous dissociation of all three PDZ ligands. Thus, we have provided novel inhibitors of the MAGUK proteins with exceptionally high affinity, which can be used to further elucidate the therapeutic potential of these proteins.

  20. Ruthenium Cumulenylidene Complexes Bearing Heteroscorpionate Ligands

    OpenAIRE

    Strinitz, Frank

    2014-01-01

    In previous work of the BURZLAFF group, the design of suitable N,N,O ligands for a wide variety of applications ranging from catalysis to bioinorganic model compounds has been extensively investigated. Especially the methyl substituted bis(3,5-dimethylpyrazol-1-yl) acetate (bdmpza) ligand has shown manifold chemistry, comparable to the anionic cyclopentadienyl (Cp) and hydridotris(pyrazol-1-yl)borato (Tp) ligand. In the first part of this thesis the new tricarbonylmanganese(I) complexes be...

  1. From Widely Accepted Concepts in Coordination Chemistry to Inverted Ligand Fields.

    Science.gov (United States)

    Hoffmann, Roald; Alvarez, Santiago; Mealli, Carlo; Falceto, Andrés; Cahill, Thomas J; Zeng, Tao; Manca, Gabriele

    2016-07-27

    We begin with a brief historical review of the development of our understanding of the normal ordering of nd orbitals of a transition metal interacting with ligands, the most common cases being three below two in an octahedral environment, two below three in tetrahedral coordination, and four below one in a square-planar environment. From the molecular orbital construction of these ligand field splittings evolves a strategy for inverting the normal order: the obvious way to achieve this is to raise the ligand levels above the metal d's; that is, make the ligands better Lewis bases. However, things are not so simple, for such metal/ligand level placement may lead to redox processes. For 18-electron octahedral complexes one can create the inverted situation, but it manifests itself in the makeup of valence orbitals (are they mainly on metal or ligands?) rather than energy. One can also see the effect, in small ways, in tetrahedral Zn(II) complexes. We construct several examples of inverted ligand field systems with a hypothetical but not unrealistic AlCH3 ligand and sketch the consequences of inversion on reactivity. Special attention is paid to the square-planar case, exemplified by [Cu(CF3)4](-), in which Snyder had the foresight to see a case of an inverted field, with the empty valence orbital being primarily ligand centered, the dx2-y2 orbital heavily occupied, in what would normally be called a Cu(III) complex. For [Cu(CF3)4](-) we provide theoretical evidence from electron distributions, geometry of the ligands, thermochemistry of molecule formation, and the energetics of abstraction of a CF3 ligand by a base, all consistent with oxidation of the ligands in this molecule. In [Cu(CF3)4](-), and perhaps more complexes on the right side of the transition series than one has imagined, some ligands are σ-noninnocent. Exploration of inverted ligand fields helps us see the continuous, borderless transition from transition metal to main group bonding. We also give

  2. Development of immobilized ligands for actinide separations

    International Nuclear Information System (INIS)

    Paine, R.T.

    1994-01-01

    Primary goals during this grant period were to (1) synthesize new bifunctional chelating ligands, (2) characterize the structural features of the Ln and An coordination complexes formed by these ligands, (3) use structural data to iteratively design new classes of multifunctional ligands, and (4) explore additional routes for attachment of key ligands to solid supports that could be useful for chromatographic separations. Some highlights of recently published work as well as a summary of submitted, unpublished and/or still in progress research are outlined

  3. Macrocyclic ligands for uranium complexation

    Energy Technology Data Exchange (ETDEWEB)

    Potts, K.T.

    1991-04-01

    A highly preorganized 24-macrocycle containing biuret, thiobiuret and pyridine subunits has been prepared by high dilution ring-closure procedures. Intermediate products to this macrocycle have been utilized to extend this synthetic route to include further representatives where solubility and stability will be influenced by substituent variation. A 1:1 complex has been formed from uranyl acetate and a quinquepyridine derivative, this representing a new type of ligand for the uranyl ion. A very convenient synthetic procedure that will allow the incorporation of these macrocycles into polymeric systems has been developed for the introduction of a vinyl substituent into the 4-position of the pyridine ring. Using triflate, vinyltributyltin and Pd{sup 0} chemistry, this procedure should make a variety of substituted 4-vinylpyridines available for the first time. 3 refs.

  4. Macrocyclic ligands for uranium complexation

    International Nuclear Information System (INIS)

    Potts, K.T.

    1991-04-01

    A highly preorganized 24-macrocycle containing biuret, thiobiuret and pyridine subunits has been prepared by high dilution ring-closure procedures. Intermediate products to this macrocycle have been utilized to extend this synthetic route to include further representatives where solubility and stability will be influenced by substituent variation. A 1:1 complex has been formed from uranyl acetate and a quinquepyridine derivative, this representing a new type of ligand for the uranyl ion. A very convenient synthetic procedure that will allow the incorporation of these macrocycles into polymeric systems has been developed for the introduction of a vinyl substituent into the 4-position of the pyridine ring. Using triflate, vinyltributyltin and Pd 0 chemistry, this procedure should make a variety of substituted 4-vinylpyridines available for the first time. 3 refs

  5. Internalization Mechanisms of the Epidermal Growth Factor Receptor after Activation with Different Ligands

    Science.gov (United States)

    Henriksen, Lasse; Grandal, Michael Vibo; Knudsen, Stine Louise Jeppe; van Deurs, Bo; Grøvdal, Lene Melsæther

    2013-01-01

    The epidermal growth factor receptor (EGFR) regulates normal growth and differentiation, but dysregulation of the receptor or one of the EGFR ligands is involved in the pathogenesis of many cancers. There are eight ligands for EGFR, however most of the research into trafficking of the receptor after ligand activation focuses on the effect of epidermal growth factor (EGF) and transforming growth factor-α (TGF-α). For a long time it was believed that clathrin-mediated endocytosis was the major pathway for internalization of the receptor, but recent work suggests that different pathways exist. Here we show that clathrin ablation completely inhibits internalization of EGF- and TGF-α-stimulated receptor, however the inhibition of receptor internalization in cells treated with heparin-binding EGF-like growth factor (HB-EGF) or betacellulin (BTC) was only partial. In contrast, clathrin knockdown fully inhibits EGFR degradation after all ligands tested. Furthermore, inhibition of dynamin function blocked EGFR internalization after stimulation with all ligands. Knocking out a number of clathrin-independent dynamin-dependent pathways of internalization had no effect on the ligand-induced endocytosis of the EGFR. We suggest that EGF and TGF-α lead to EGFR endocytosis mainly via the clathrin-mediated pathway. Furthermore, we suggest that HB-EGF and BTC also lead to EGFR endocytosis via a clathrin-mediated pathway, but can additionally use an unidentified internalization pathway or better recruit the small amount of clathrin remaining after clathrin knockdown. PMID:23472148

  6. Internalization mechanisms of the epidermal growth factor receptor after activation with different ligands.

    Directory of Open Access Journals (Sweden)

    Lasse Henriksen

    Full Text Available The epidermal growth factor receptor (EGFR regulates normal growth and differentiation, but dysregulation of the receptor or one of the EGFR ligands is involved in the pathogenesis of many cancers. There are eight ligands for EGFR, however most of the research into trafficking of the receptor after ligand activation focuses on the effect of epidermal growth factor (EGF and transforming growth factor-α (TGF-α. For a long time it was believed that clathrin-mediated endocytosis was the major pathway for internalization of the receptor, but recent work suggests that different pathways exist. Here we show that clathrin ablation completely inhibits internalization of EGF- and TGF-α-stimulated receptor, however the inhibition of receptor internalization in cells treated with heparin-binding EGF-like growth factor (HB-EGF or betacellulin (BTC was only partial. In contrast, clathrin knockdown fully inhibits EGFR degradation after all ligands tested. Furthermore, inhibition of dynamin function blocked EGFR internalization after stimulation with all ligands. Knocking out a number of clathrin-independent dynamin-dependent pathways of internalization had no effect on the ligand-induced endocytosis of the EGFR. We suggest that EGF and TGF-α lead to EGFR endocytosis mainly via the clathrin-mediated pathway. Furthermore, we suggest that HB-EGF and BTC also lead to EGFR endocytosis via a clathrin-mediated pathway, but can additionally use an unidentified internalization pathway or better recruit the small amount of clathrin remaining after clathrin knockdown.

  7. Ligand based pharmacophore modelling of anticancer histone ...

    African Journals Online (AJOL)

    USER

    2010-06-21

    Jun 21, 2010 ... HDAC ligands (Chen et al., 2008b). The knowledge of common properties of the binding group is essential for the determination of the type of inhibitor binding the target. Major goal of modern drug design is identification and development of new ligands with high affinity of binding toward a given protein.

  8. Organometallic chemistry of chiral diphosphazane ligands ...

    Indian Academy of Sciences (India)

    Unknown

    1. Introduction. Diphosphazanes constitute a class of versatile short-bite bidentate P-donor ligands that have given rise to a varied and extensive transition metal organometallic chemistry. The organometallic chemistry of diphosphazane ligands with almost every transition metal in the periodic table is well documented1–3.

  9. Cofactor-Controlled Chirality of Tropoisomeric Ligand

    NARCIS (Netherlands)

    Théveau, L.; Bellini, R.; Dydio, P.; Szabo, Z.; van der Werf, A.; Sander, R.A.; Reek, J.N.H.; Moberg, C.

    2016-01-01

    A new tropos ligand with an integrated anion receptor receptor site has been prepared. Chiral carboxylate and phosphate anions that bind in the anion receptor unit proved capable of stabilizing chiral conformations of the achiral flexible bidentate biaryl phosphite ligand, as shown by variable

  10. Ligand modification for mono- and biphasic oxosynthesis

    Energy Technology Data Exchange (ETDEWEB)

    Haerter, P.; Herrmann, W.A.; Baskakov, D. [Technische Univ. Muenchen (Germany). Dept. Chemie

    2006-07-01

    The use of aqueous/organic biphasic systems has attracted huge interest in catalytic reactions by transition metal complexes. [1,2,3] The biphasic systems have benefits in catalyst separation and recycling, and the reduction or elimination of organic solvents is also advantageous for the development of economical and environmentally friendly processes. The key for such biphasic catalysis is the use of water soluble phosphines as ligands. Since the launch of the commercial propylene hydroformylation process by Ruhrchemie/Rhone-Poulenc, sulfonated ligands such as TPPTS (1), and BINAS (2) have been widely used as ligands in hydroformylation, hydrogenation and related reactions catalyzed by transition metals. One of the draw backs of ligands 1 and 2 are corrosive production conditions and therefore unfavorable costs. With the synthesis of aminoacid based trishydroxymethylphosphine derivatives (THMP-aminoacid) we introduce to our knowledge a new group of water soluble and cheap to produce ligands [8]. The properties of catalysts based on these compounds in the hydroformylation reaction of propene are discussed in comparison to normally used catalyst systems. In a second part the performance of catalysts containing NHC-ligands in the hydroformylation of 1-octene is discussed [9]. These investigations show, that the activity can be influenced by the electron donating ability of the NHC ligand. Sterical variations on the NHC ligands have no effect on the selectivity performance of the the catalysts. (orig.)

  11. Organometallic chemistry of chiral diphosphazane ligands ...

    Indian Academy of Sciences (India)

    Unknown

    organometallic chemistry of diphosphazane ligands with almost every transition metal in the periodic table is well documented1–3. A very attractive feature of diphosphazane ligands is that 'chirality' can be incorporated at the phosphorus centres as well as at the substituents attached to the nitrogen and the two phosphorus ...

  12. Ligand sphere conversions in terminal carbide complexes

    DEFF Research Database (Denmark)

    Morsing, Thorbjørn Juul; Reinholdt, Anders; Sauer, Stephan P. A.

    2016-01-01

    Metathesis is introduced as a preparative route to terminal carbide complexes. The chloride ligands of the terminal carbide complex [RuC(Cl)2(PCy3)2] (RuC) can be exchanged, paving the way for a systematic variation of the ligand sphere. A series of substituted complexes, including the first exam...

  13. Segregation of receptor-ligand complexes in cell adhesion zones: phase diagrams and the role of thermal membrane roughness

    Science.gov (United States)

    Różycki, B.; Lipowsky, R.; Weikl, T. R.

    2010-09-01

    The adhesion zone of immune cells, the 'immunological synapse', exhibits characteristic domains of receptor-ligand complexes. The domain formation is probably caused by a length difference of the receptor-ligand complexes, and has been investigated in experiments in which T cells adhere to supported membranes with anchored ligands. For supported membranes with two types of anchored ligands, MHCp and ICAM1, which bind to the T-cell receptor (TCR) and the receptor LFA1 in the cell membrane, the coexistence of domains of the TCR-MHCp and LFA1-ICAM1 complexes in the cell adhesion zone has been observed for a wide range of ligand concentrations and affinities. For supported membranes with long and short ligands that bind to the same cell receptor CD2, in contrast, domain coexistence has been observed for a quite narrow ratio of ligand concentrations. In this paper, we determine detailed phase diagrams for cells adhering to supported membranes with a statistical-physical model of cell adhesion. We find a characteristic difference between the adhesion scenarios in which two types of ligands in a supported membrane bind (i) to the same cell receptor or (ii) to two different cell receptors, which helps us to explain the experimental observations. Our phase diagrams fully include thermal shape fluctuations of the cell membranes on nanometer scales, which lead to a critical point for the domain formation and to a cooperative binding of the receptors and ligands.

  14. Biomimetic affinity ligands for protein purification.

    Science.gov (United States)

    Sousa, Isabel T; Taipa, M Angela

    2014-01-01

    The development of sophisticated molecular modeling software and new bioinformatic tools, as well as the emergence of data banks containing detailed information about a huge number of proteins, enabled the de novo intelligent design of synthetic affinity ligands. Such synthetic compounds can be tailored to mimic natural biological recognition motifs or to interact with key surface-exposed residues on target proteins and are designated as "biomimetic ligands." A well-established methodology for generating biomimetic or synthetic affinity ligands integrates rational design with combinatorial solid-phase synthesis and screening, using the triazine scaffold and analogues of amino acids side chains to create molecular diversity.Triazine-based synthetic ligands are nontoxic, low-cost, highly stable compounds that can replace advantageously natural biological ligands in the purification of proteins by affinity-based methodologies.

  15. Passivating ligand and solvent contributions to the electronic properties of semiconductor nanocrystals

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, S.; Crotty, A.; Kilina, S.; Ivanov, I.; Tretiak, S

    2012-01-01

    We examine in detail the impact of passivating ligands (i.e., amines, phosphines, phosphine oxides and pyridines) on the electronic and optical spectra of Cd{sub 33}Se{sub 33} quantum dots (QDs) using density functional theory (DFT) and time-dependent DFT (TDDFT) quantum-chemical methodologies. Most ligand orbitals are found deep inside in the valence and conduction bands of the QD, with pyridine being an exception by introducing new states close to the conduction band edge. Importantly, all ligands contribute states which are highly delocalized over both the QD surface and ligands, forming hybridized orbitals rather than ligand-localized trap states. In contrast, the states close to the band gap are delocalized over the QD atoms only and define the lower energy absorption spectra. The random detachment of one of ligands from the QD surface results in the appearance of a highly localized unoccupied state inside the energy gap of the QD. Such changes in the electronic structure are correlated with the respective QD-ligand binding energy and steric ligand-ligand interactions. Polar solvent significantly reduces both effects leading to delocalization and stabilization of the surface states. Thus, trap and surface states are substantially eliminated by the solvent. Polar solvent also blue-shifts (e.g., 0.3-0.4 eV in acetonitrile) the calculated absorption spectra. This shift increases with an increase of the dielectric constant of the solvent. We also found that the approximate single-particle Kohn-Sham (KS) approach is adequate for calculating the absorption spectra of the ligated QDs. Besides a systematic blue-shift, the KS spectra are in very good agreement with their respective counterparts calculated with the more accurate TDDFT method.

  16. A look at ligand binding thermodynamics in drug discovery.

    Science.gov (United States)

    Claveria-Gimeno, Rafael; Vega, Sonia; Abian, Olga; Velazquez-Campoy, Adrian

    2017-04-01

    Drug discovery is a challenging endeavor requiring the interplay of many different research areas. Gathering information on ligand binding thermodynamics may help considerably in reducing the risk within a high uncertainty scenario, allowing early rejection of flawed compounds and pushing forward optimal candidates. In particular, the free energy, the enthalpy, and the entropy of binding provide fundamental information on the intermolecular forces driving such interaction. Areas covered: The authors review the current status and recent developments in the application of ligand binding thermodynamics in drug discovery. The thermodynamic binding profile (Gibbs energy, enthalpy, and entropy of binding) can be used for lead selection and optimization (binding enthalpy, selectivity, and adaptability). Expert opinion: Binding thermodynamics provides fundamental information on the forces driving the formation of the drug-target complex. It has been widely accepted that binding thermodynamics may be used as a decision criterion along the ligand optimization process in drug discovery and development. In particular, the binding enthalpy may be used as a guide when selecting and optimizing compounds over a set of potential candidates. However, this has been recently called into question by arguing certain difficulties and in the light of certain experimental examples.

  17. A2A receptor ligands: past, present and future trends.

    Science.gov (United States)

    Clementina, Manera; Giuseppe, Saccomanni

    2010-01-01

    The adenosine A(2A) receptor is a member of the G protein-coupled receptor family and mediates multiple physiological effects of adenosine, both at the central nervous system and at peripheral tissues. Increasing evidence relates the A(2A) receptor with several pathological conditions such as neurodegenerative disorders, inflammation, pharmacological stress, and wound healing renewing the interest in A(2A) receptor agonists and antagonists as promising leads for drugs. However some of them initially tested in clinical trials presented several side effects, short half-life, lower solubility, and in some cases a lack of effects, perhaps attributable to receptor desensitization or to low receptor density in the targeted tissue. For these reasons it is evident that additional rational chemical modifications of the existing A(2A) receptor ligands to improve their affinity/selectivity and bioavailability as well as further studies to get new template for A(2A)AR ligands are necessary. The purpose of this review is to analyze and summarize the past and the present aspects related to the medicinal chemistry of A(2A) receptor ligands. Moreover their current and possible therapeutic applications have been also highlighted.

  18. Correcting ligands, metabolites, and pathways

    Directory of Open Access Journals (Sweden)

    Vriend Gert

    2006-11-01

    Full Text Available Abstract Background A wide range of research areas in bioinformatics, molecular biology and medicinal chemistry require precise chemical structure information about molecules and reactions, e.g. drug design, ligand docking, metabolic network reconstruction, and systems biology. Most available databases, however, treat chemical structures more as illustrations than as a datafield in its own right. Lack of chemical accuracy impedes progress in the areas mentioned above. We present a database of metabolites called BioMeta that augments the existing pathway databases by explicitly assessing the validity, correctness, and completeness of chemical structure and reaction information. Description The main bulk of the data in BioMeta were obtained from the KEGG Ligand database. We developed a tool for chemical structure validation which assesses the chemical validity and stereochemical completeness of a molecule description. The validation tool was used to examine the compounds in BioMeta, showing that a relatively small number of compounds had an incorrect constitution (connectivity only, not considering stereochemistry and that a considerable number (about one third had incomplete or even incorrect stereochemistry. We made a large effort to correct the errors and to complete the structural descriptions. A total of 1468 structures were corrected and/or completed. We also established the reaction balance of the reactions in BioMeta and corrected 55% of the unbalanced (stoichiometrically incorrect reactions in an automatic procedure. The BioMeta database was implemented in PostgreSQL and provided with a web-based interface. Conclusion We demonstrate that the validation of metabolite structures and reactions is a feasible and worthwhile undertaking, and that the validation results can be used to trigger corrections and improvements to BioMeta, our metabolite database. BioMeta provides some tools for rational drug design, reaction searches, and

  19. Chemistry of marine ligands and siderophores.

    Science.gov (United States)

    Vraspir, Julia M; Butler, Alison

    2009-01-01

    Marine microorganisms are presented with unique challenges to obtain essential metal ions required to survive and thrive in the ocean. The production of organic ligands to complex transition metal ions is one strategy to both facilitate uptake of specific metals, such as iron, and to mitigate the potential toxic effects of other metal ions, such as copper. A number of important trace metal ions are complexed by organic ligands in seawater, including iron, cobalt, nickel, copper, zinc, and cadmium, thus defining the speciation of these metal ions in the ocean. In the case of iron, siderophores have been identified and structurally characterized. Siderophores are low molecular weight iron-binding ligands produced by marine bacteria. Although progress has been made toward the identity of in situ iron-binding ligands, few compounds have been identified that coordinate the other trace metals. Deciphering the chemical structures and production stimuli of naturally produced organic ligands and the organisms they come from is fundamental to understanding metal speciation and bioavailability. The current evidence for marine ligands, with an emphasis on siderophores, and discussion of the importance and implications of metal-binding ligands in controlling metal speciation and cycling within the world's oceans are presented.

  20. Radiation induced ligand loss from cobalt complexes

    International Nuclear Information System (INIS)

    Funston, A. M.; McFadyen, W.D.; Tregloan, P.A.

    2000-01-01

    Full text: Due to the rapid nature of ligand dissociation from cobalt(II) complexes the study of the rate of ligand dissociation necessitates the use of a technique such as pulse radiolysis. This allows the rapid reduction of the corresponding cobalt(III) complex by a reducing radical, such as the aquated electron, to form the cobalt(II) complex. However, to date, no systematic study of either the mechanism of reduction or the influence of the electronic structure on the rate of ligand dissociation has been carried out. In order to understand these processes more fully the mechanism of reduction of a range of related cobalt(III) complexes by the aquated electron and the subsequent rate of ligand dissociation from the resulting cobalt(II) complexes is being investigated. It has been found that a number of processes are observed following the initial rapid reaction of the cobalt(III) complex with the aquated electron. Ultimately ligand loss is observed. Depending upon the complex, the initial processes observed may include the formation of coordinated radicals and electron transfer within the complex. For complexes containing aromatic ligands such as 2,2'-bipyridine, 1,10-phenanthroline and dipyrido[3,2-a:2',3'-c]phenazine the formation of a coordinated radical is observed as the initial reduction step. The kinetics of ligand dissociation of these complexes has been determined. The loss of monodentate ligands is fast and has been indistinguishable from the reduction processes when aromatic ligands are also present in the complex. However, for diamine chelates and diimine chelates spectra of the transient species can be resolved

  1. Optimizing Ligand Efficiency of Selective Androgen Receptor Modulators (SARMs).

    Science.gov (United States)

    Handlon, Anthony L; Schaller, Lee T; Leesnitzer, Lisa M; Merrihew, Raymond V; Poole, Chuck; Ulrich, John C; Wilson, Joseph W; Cadilla, Rodolfo; Turnbull, Philip

    2016-01-14

    A series of selective androgen receptor modulators (SARMs) containing the 1-(trifluoromethyl)benzyl alcohol core have been optimized for androgen receptor (AR) potency and drug-like properties. We have taken advantage of the lipophilic ligand efficiency (LLE) parameter as a guide to interpret the effect of structural changes on AR activity. Over the course of optimization efforts the LLE increased over 3 log units leading to a SARM 43 with nanomolar potency, good aqueous kinetic solubility (>700 μM), and high oral bioavailability in rats (83%).

  2. Stabilization of enzyme by using hydrophobic ligands

    Energy Technology Data Exchange (ETDEWEB)

    Ota, H.; Yamahara, K.; Kuboi, R. [Osaka University, Osaka (Japan)

    1998-02-01

    The protection (stabilization) effect of various hydrophobic ligands on the denaturation and aggregation of carbonic anhydrase from bovine (CAB) has been quantitatively investigated under various heat stress conditions. In a limited temperature range (40-60degC), where the protein was only partially denatured and the local hydrophobicities (LH) of CAB were positive effective stabilization of the protein is achieved by the addition of various ligands. The importance of balance between hydrophobic head and hydrophilic tail of the ligands is hypothesized. 18 refs., 5 figs.

  3. A versatile dinucleating ligand containing sulfonamide groups

    DEFF Research Database (Denmark)

    Sundberg, Jonas; Witt, Hannes; Cameron, Lisa

    2014-01-01

    ligand can be prepared in aqueous solutions using only divalent metal ions. Two of the copper(II) complexes, [Cu2(psmp)(OH)] and [Cu2(psmp)(OAc)2]-, demonstrate the anticipated 1:2 ligand/metal stoichiometry and show that the dimetallic binding site created for exogenous ligands possesses high inherent...... of antiferromagnetic coupling. This is corroborated computationally by broken-symmetry density functional theory, which for isotropic modeling of the coupling predicts an antiferromagnetic coupling strength of J = 70.5 cm-1....

  4. Ligand-Controlled Synthesis of Azoles via Ir-Catalyzed Reactions of Sulfoxonium Ylides with 2-Amino Heterocycles.

    Science.gov (United States)

    Phelps, Alicia M; Chan, Vincent S; Napolitano, José G; Krabbe, Scott W; Schomaker, Jennifer M; Shekhar, Shashank

    2016-05-20

    An iridium-catalyzed method was developed for the synthesis of imidazo-fused pyrrolopyrazines. The presence or absence of a nitrogenated ligand controlled the outcome of the reaction, leading to simple β-keto amine products in the absence of added ligand and the cyclized 7- and 8-substituted-imidazo[1,2-a]pyrrolo[2,3-e]pyrazine products in the presence of ligand. This catalyst control was conserved across a variety of ylide and amine coupling partners. The substrate was shown to act as a ligand for the iridium catalyst in the absence of other ligands via NMR spectroscopy. Kinetic studies indicated that formation of the Ir-carbene was reversible and the slow step of the reaction. These mechanistic investigations suggest that the β-keto amine products form via an intramolecular carbene N-H insertion, and the imidazopyrrolopyrazines form via an intermolecular carbene N-H insertion.

  5. CADASIL-associated Notch3 mutations have differential effects both on ligand binding and ligand-induced Notch3 receptor signaling through RBP-Jk.

    Science.gov (United States)

    Peters, Nils; Opherk, Christian; Zacherle, Simone; Capell, Anja; Gempel, Petra; Dichgans, Martin

    2004-10-01

    Mutations in the NOTCH3 gene are the cause of cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL), a hereditary angiopathy leading to strokes and dementia. Pathogenic mutations remove or insert cysteine residues within epidermal growth factor (EGF) repeats in the extracellular domain of the Notch3 receptor (N3ECD). Vascular smooth muscle cells (VSMC) are the predominant site of Notch3 expression in adults. In CADASIL patients, VSMC degenerate and N3ECD is deposited within the vasculature. However, the mechanisms underlying VSMC degeneration and N3ECD accumulation are still unknown. In this study, we investigated the consequences of three pathogenic Notch3 mutations on the biological activity of the receptor by analyzing ligand (Delta-/Jagged-)-induced signaling via RBP-Jk. Two mutations (R133C and C183R) that are located outside the putative ligand binding domain (LBD) of the receptor were found to result in normal Jagged1-induced signaling in A7r5 VSMC, whereas the third mutation (C455R located within the putative LBD) showed strongly reduced signaling activity. Ligand binding assays with soluble Delta1 and Jagged1 revealed that C455R interferes with ligand binding through disruption of the LBD which, as we show here, is located in EGF repeats 10/11 of Notch3. All mutant receptors including Notch3C455R were targeted to the cell surface but showed an elevated ratio between the unprocessed full-length 280-kDa receptor and S1-cleaved receptor fragments. Taken together, these data indicate that CADASIL-associated Notch3 mutations differ with respect to their consequences both on ligand binding and ligand-induced signaling through RBP-Jk, whereas they have similar effects on receptor maturation. Moreover, the data suggest that ligand-induced receptor shedding may not be required for N3ECD deposition in CADASIL. Copyright 2004 Elsevier Inc.

  6. Lead poisoning in children.

    Science.gov (United States)

    Dapul, Heda; Laraque, Danielle

    2014-08-01

    There is no safe lead level in children. Primary prevention is the most effective way to bring about the complete removal of lead from the environment and eliminate lead poisoning as a public health concern. The National Lead Information Center can be reached via the Internet at www.epa.gov/lead and www.hud.gov/lead, or via phone at 1-800-424-LEAD (5323).

  7. Protein stabilization with a dipeptide-mimic triazine-scaffolded synthetic affinity ligand.

    Science.gov (United States)

    Sousa, I T; Lourenço, N M T; Afonso, C A M; Taipa, M A

    2013-02-01

    Protein stabilization was achieved by a novel approach based on the adsorption and establishment of affinity-like interactions with a biomimetic triazine-scaffolded ligand. A synthetic lead compound (ligand 3'/11, K(a) ≈ 10(4) M(-1)) was selected from a previously screened solid-phase library of affinity ligands for studies of adsorption and stabilization of cutinase from Fusarium solani pisi used as a model system. This ligand, directly synthesized in agarose by a well-established solid-phase synthesis method, was able to strongly bind cutinase and led to impressive half-lives of more than 8 h at 70 °C, and of approximately 34 h at 60 °C for bound protein (a 25- and 57-fold increase as compared with the free enzyme, respectively). The ligand density in the solid matrix was found to be a determinant parameter for cutinase stabilization. It is conceivable that the highly stabilizing effect observed results from the binding of more than one ligand residue to the enzyme, creating specific macromolecular configurations that lock structural mobility thus improving molecular stability. Copyright © 2013 John Wiley & Sons, Ltd.

  8. New Proton-Ionizable, Calixarene-Based Ligands for Selective Metal Ion Separations

    Energy Technology Data Exchange (ETDEWEB)

    Bartsch, Richard A.

    2012-06-04

    The project objective was the discovery of new ligands for performing metal ion separations. The research effort entailed the preparation of new metal ion complexing agents and polymers and their evaluation in metal ion separation processes of solvent extraction, synthetic liquid membrane transport, and sorption. Structural variations in acyclic, cyclic, and bicyclic organic ligands were used to probe their influence upon the efficiency and selectivity with which metal ion separations can be performed. A unifying feature of the ligand structures is the presence of one (or more) side arm with a pendent acidic function. When a metal ion is complexed within the central cavity of the ligand, ionization of the side arm(s) produces the requisite anion(s) for formation of an overall electroneutral complex. This markedly enhances extraction/transport efficiency for separations in which movement of aqueous phase anions of chloride, nitrate, or sulfate into an organic medium would be required. Through systematic structural variations, new ligands have been developed for efficient and selective separations of monovalent metal ions (e.g., alkali metal, silver, and thallium cations) and of divalent metal ion species (e.g., alkaline earth metal, lead, and mercury cations). Research results obtained in these fundamental investigations provide important insight for the design and development of ligands suitable for practical metal ion separation applications.

  9. Controlling Signal Transduction with Synthetic Ligands

    Science.gov (United States)

    Spencer, David M.; Wandless, Thomas J.; Schreiber, Stuart L.; Crabtree, Gerald R.

    1993-11-01

    Dimerization and oligomerization are general biological control mechanisms contributing to the activation of cell membrane receptors, transcription factors, vesicle fusion proteins, and other classes of intra- and extracellular proteins. Cell permeable, synthetic ligands were devised that can be used to control the intracellular oligomerization of specific proteins. To demonstrate their utility, these ligands were used to reduce intracellular oligomerization of cell surface receptors that lacked their transmembrane and extracellular regions but contained intracellular signaling domains. Addition of these ligands to cells in culture resulted in signal transmission and specific target gene activation. Monomeric forms of the ligands blocked the pathway. This method of ligandregulated activation and termination of signaling pathways has the potential to be applied wherever precise control of a signal transduction pathway is desired.

  10. Allyl functionalized phosphinite and phosphonite ligands: Synthesis ...

    Indian Academy of Sciences (India)

    Allyl functionalized phosphinite and phosphonite ligands: Synthesis, transition metal chemistry and orthopalladation reactions. SINGAPPAGUDEM GOVINDARAJUa, GUDDEKOPPA S ANANTHNAGa, SUSMITA NAIKa,. SHAIKH M MOBINb and MARAVANJI S BALAKRISHNAa,∗. aPhosphorus Laboratory, Department of ...

  11. Organometallic chemistry of chiral diphosphazane ligands ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 114; Issue 4. Organometallic chemistry of chiral diphosphazane ligands: Synthesis and structural characterisation. Kannan Raghuraman Swadhin K Mandal T S Venkatakrishnan Setharampattu S Krishnamurthy Munirathinam Nethaji. Volume 114 Issue 4 August 2002 ...

  12. EGFR Activation by Spatially Restricted Ligands

    National Research Council Canada - National Science Library

    Clouse, Katherine N; Goodrich, Jennifer S

    2006-01-01

    ...) activity has been associated with an increased prognosis of breast cancer. During cogenesis in Drosophila melanogaster local Egfr activation by the spatially-restricted TGFalpha-like ligand Gurken (Grk...

  13. EGFR Activation by Spatially Restricted Ligands

    National Research Council Canada - National Science Library

    Goodrich, Jennifer S

    2005-01-01

    ...) activity has been associated with an increased prognosis of breast cancer. During oogenesis in Drosophila melanogaster, local EGFR activation by the spatially restricted TGF alpha-like ligand, Gurken (Grk...

  14. Ligand and Metal Based Multielectron Redox Chemistry of Cobalt Supported by Tetradentate Schiff Bases.

    Science.gov (United States)

    Andrez, Julie; Guidal, Valentin; Scopelliti, Rosario; Pécaut, Jacques; Gambarelli, Serge; Mazzanti, Marinella

    2017-06-28

    We have investigated the influence of bound cations on the reduction of cobalt complexes of redox active ligands and explored the reactivity of reduced species with CO 2 . The one electron reduction of [Co II ( R salophen)] with alkali metals (M = Li, Na, K) leads to either ligand-centered or metal-centered reduction depending on the alkali ion. It affords either the [Co I ( R salophen)K] complexes or the [Co II 2 (bis-salophen)M 2 ] (M = Li, Na) dimers that are present in solution in equilibrium with the respective [Co I (salophen)M] complexes. The two electron reduction of [Co II ( OMe salophen)] results in both ligand centered and metal centered reduction affording the Co(I)-Co(II)-Co(I) [Co 3 (tris- OMe salophen)Na 6 (THF) 6 ], 6 complex supported by a bridging deca-anionic tris- OMe salophen 10- ligand where three OMe salophen units are connected by two C-C bonds. Removal of the Na ion from 6 leads to a redistribution of the electrons affording the complex [(Co( OMe salophen)) 2 Na][Na(cryptand)] 3 , 7. The EPR spectrum of 7 suggests the presence of a Co(I) bound to a radical anionic ligand. Dissolution of 7 in pyridine leads to the isolation of [Co I 2 (bis- OMe salophen)Na 2 Py 4 ][Na(cryptand)] 2 , 8. Complex 6 reacts with ambient CO 2 leading to multiple CO 2 reduction products. The product of CO 2 addition to the OMe salophen ligand, [Co( OMe salophen-CO 2 )Na] 2 [Na(cryptand)] 2 , 9, was isolated but CO 3 2- formation in 53% yield was also detected. Thus, the electrons stored in the reversible C-C bonds may be used for the transformation of carbon dioxide.

  15. Chemistry of Marine Ligands and Siderophores

    OpenAIRE

    Vraspir, Julia M.; Butler, Alison

    2009-01-01

    Marine microorganisms are presented with unique challenges to obtain essential metal ions required to survive and thrive in the ocean. The production of organic ligands to complex transition metal ions is one strategy to both facilitate uptake of specific metals, such as iron, and to mitigate the potential toxic effects of other metal ions, such as copper. A number of important trace metal ions are complexed by organic ligands in seawater, including iron, cobalt, nickel, copper, zinc, and cad...

  16. N-H bond activation by palladium(ii) and copper(i) complexes featuring a reactive bidentate PN-ligand

    NARCIS (Netherlands)

    de Boer, S.Y.; Gloaguen, Y.; Reek, J.N.H.; Lutz, M.; van der Vlugt, J.I.

    2012-01-01

    The first examples of reactivity at the backbone of a bidentate PN-ligand L1H relevant to N-H activation are described, leading to novel PdII and CuI amido complexes. Activation of the PN-ligand backbone led to selective dearomatization of the pyridyl ring structure. In the case of PdII, the

  17. Application of a supramolecular-ligand library for the automated search for catalysts for the asymmetric hydrogenation of industrially relevant substrates

    NARCIS (Netherlands)

    Meeuwissen, J.; Kuil, M.; van der Burg, A.M.; Sandee, A.J.; Reek, J.N.H.

    2009-01-01

    A procedure is described for the automated screening and lead optimization of a supramolecular-ligand library for the rhodium-catalyzed asymmetric hydrogenation of five challenging substrates relevant to industry. Each catalyst is (self-) assembled from two urea-functionalized ligands and a

  18. Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations.

    Science.gov (United States)

    Moraca, Federica; Amato, Jussara; Ortuso, Francesco; Artese, Anna; Pagano, Bruno; Novellino, Ettore; Alcaro, Stefano; Parrinello, Michele; Limongelli, Vittorio

    2017-03-14

    G-quadruplexes (G4s) are higher-order DNA structures typically present at promoter regions of genes and telomeres. Here, the G4 formation decreases the replicative DNA at each cell cycle, finally leading to apoptosis. The ability to control this mitotic clock, particularly in cancer cells, is fascinating and passes through a rational understanding of the ligand/G4 interaction. We demonstrate that an accurate description of the ligand/G4 binding mechanism is possible using an innovative free-energy method called funnel-metadynamics (FM), which we have recently developed to investigate ligand/protein interaction. Using FM simulations, we have elucidated the binding mechanism of the anticancer alkaloid berberine to the human telomeric G4 ( d [AG 3 (T 2 AG 3 ) 3 ]), computing also the binding free-energy landscape. Two ligand binding modes have been identified as the lowest energy states. Furthermore, we have found prebinding sites, which are preparatory to reach the final binding mode. In our simulations, the ions and the water molecules have been explicitly represented and the energetic contribution of the solvent during ligand binding evaluated. Our theoretical results provide an accurate estimate of the absolute ligand/DNA binding free energy ([Formula: see text] = -10.3 ± 0.5 kcal/mol) that we validated through steady-state fluorescence binding assays. The good agreement between the theoretical and experimental value demonstrates that FM is a most powerful method to investigate ligand/DNA interaction and can be a useful tool for the rational design also of G4 ligands.

  19. Designer TGFβ superfamily ligands with diversified functionality.

    Directory of Open Access Journals (Sweden)

    George P Allendorph

    Full Text Available Transforming Growth Factor--beta (TGFβ superfamily ligands, including Activins, Growth and Differentiation Factors (GDFs, and Bone Morphogenetic Proteins (BMPs, are excellent targets for protein-based therapeutics because of their pervasiveness in numerous developmental and cellular processes. We developed a strategy termed RASCH (Random Assembly of Segmental Chimera and Heteromer, to engineer chemically-refoldable TGFβ superfamily ligands with unique signaling properties. One of these engineered ligands, AB208, created from Activin-βA and BMP-2 sequences, exhibits the refolding characteristics of BMP-2 while possessing Activin-like signaling attributes. Further, we find several additional ligands, AB204, AB211, and AB215, which initiate the intracellular Smad1-mediated signaling pathways more strongly than BMP-2 but show no sensitivity to the natural BMP antagonist Noggin unlike natural BMP-2. In another design, incorporation of a short N-terminal segment from BMP-2 was sufficient to enable chemical refolding of BMP-9, without which was never produced nor refolded. Our studies show that the RASCH strategy enables us to expand the functional repertoire of TGFβ superfamily ligands through development of novel chimeric TGFβ ligands with diverse biological and clinical values.

  20. Exploiting ligand-protein conjugates to monitor ligand-receptor interactions.

    Directory of Open Access Journals (Sweden)

    Hirohito Haruki

    Full Text Available We introduce three assays for analyzing ligand-receptor interactions based on the specific conjugation of ligands to SNAP-tag fusion proteins. Conjugation of ligands to different SNAP-tag fusions permits the validation of suspected interactions in cell extracts and fixed cells as well as the establishment of high-throughput assays. The different assays allow the analysis of strong and weak interactions. Conversion of ligands into SNAP-tag substrates thus provides access to a powerful toolbox for the analysis of their interactions with proteins.

  1. Li+-ligand binding energies and the effect of ligand fluorination on the binding energies

    Science.gov (United States)

    Bauschlicher, Charles W.

    2018-02-01

    The Li+-ligand binding energies are computed for seven ligands and their perfluoro analogs using Density Functional Theory. The bonding is mostly electrostatic in origin. Thus the size of the binding energy tends to correlate with the ligand dipole moment, however, the charge-induced dipole contribution can be sufficiently large to affect the dipole-binding energy correlation. The perfluoro species are significantly less strongly bound than their parents, because the electron withdrawing power of the fluorine reduces the ligand dipole moment.

  2. LigandRFs: random forest ensemble to identify ligand-binding residues from sequence information alone

    KAUST Repository

    Chen, Peng

    2014-12-03

    Background Protein-ligand binding is important for some proteins to perform their functions. Protein-ligand binding sites are the residues of proteins that physically bind to ligands. Despite of the recent advances in computational prediction for protein-ligand binding sites, the state-of-the-art methods search for similar, known structures of the query and predict the binding sites based on the solved structures. However, such structural information is not commonly available. Results In this paper, we propose a sequence-based approach to identify protein-ligand binding residues. We propose a combination technique to reduce the effects of different sliding residue windows in the process of encoding input feature vectors. Moreover, due to the highly imbalanced samples between the ligand-binding sites and non ligand-binding sites, we construct several balanced data sets, for each of which a random forest (RF)-based classifier is trained. The ensemble of these RF classifiers forms a sequence-based protein-ligand binding site predictor. Conclusions Experimental results on CASP9 and CASP8 data sets demonstrate that our method compares favorably with the state-of-the-art protein-ligand binding site prediction methods.

  3. Synthesis and screening of a rationally designed combinatorial library of affinity ligands mimicking protein L from Peptostreptococcus magnus.

    Science.gov (United States)

    Roque, A Cecília A; Taipa, M Angela; Lowe, Christopher R

    2005-01-01

    Rational design and combinatorial chemistry were utilized to search for lead protein L (PpL) mimetics for application as affinity ligands for the purification of antibodies and small fragments, such as Fab and scFv, and as potential diagnostic or therapeutic agents. Inspection of the key structural features of the complex between PpL and human Fab prompted the de novo design and combinatorial synthesis of a 169-membered solid-phase ligand library, which was assessed for binding to human IgG and subsequent selectivity for the Fab fragment. Eight ligands were selected, chemically characterized and compared with a commercial PpL-adsorbent for binding pure immunoglobulin fractions. The most promising lead, ligand 8/7, when immobilized on an agarose support, behaved in a similar fashion to PpL in isolating Fab fragments from papain digests of human IgG to a final purity of 97%. Copyright 2005 John Wiley & Sons, Ltd.

  4. Identification of Histamine H3 Receptor Ligands Using a New Crystal Structure Fragment-based Method

    DEFF Research Database (Denmark)

    Frandsen, Ida Osborn; Boesgaard, Michael W; Fidom, Kimberley

    2017-01-01

    Virtual screening offers an efficient alternative to high-throughput screening in the identification of pharmacological tools and lead compounds. Virtual screening is typically based on the matching of target structures or ligand pharmacophores to commercial or in-house compound catalogues. This ...

  5. Electrochemical Study on Ligand Substitution Reactions in Oxofluoro Boron Containing Melts

    DEFF Research Database (Denmark)

    Polyakova, L.P.; Bukatova, G.A.; Polyakov, E.G.

    1997-01-01

    Linear voltammetry was used for study of the ligand substitution reactions in the process of titration of FLINAK-KBF4, melt with different oxides. At molar ratio O/B=1 complexes BF4- which are characteristic for oxygenless melt transform into BOF2- Further increasing of O/B ratio up to 2 leads to...

  6. Vesicular Stomatitis Virus Infection Promotes Immune Evasion by Preventing NKG2D-Ligand Surface Expression

    DEFF Research Database (Denmark)

    Jensen, Helle; Andresen, Lars; Nielsen, Jens

    2011-01-01

    leads to a robust induction of MICA mRNA expression, however the subsequent surface expression is potently hindered. Thus, VSV lines up with human cytomegalovirus (HCMV) and adenovirus, which actively subvert the immune system by negatively affecting NKG2D-ligand surface expression. VSV infection caused...

  7. Synthesis and characterization of mixed ligand chiral nanoclusters

    KAUST Repository

    Guven, Zekiye P.

    2016-06-22

    Chiral mixed ligand silver nanoclusters were synthesized in the presence of a chiral and an achiral ligand. While the chiral ligand led mostly to the formation of nanoparticles, the presence of the achiral ligand drastically increased the yield of nanoclusters with enhanced chiral properties. © 2016 The Royal Society of Chemistry.

  8. Learn about Lead

    Science.gov (United States)

    ... and dust-free Clean around painted areas where friction can generate dust, such as doors, windows, and ... Us to ask a question, provide feedback, or report a problem. Lead Lead Home Learn About Lead ...

  9. Lead (Pb) Air Pollution

    Science.gov (United States)

    ... Environmental Protection Agency Search Search Lead (Pb) Air Pollution Contact Us Share As a result of EPA's ... protect aquatic and terrestrial ecosystems. Lead (Pb) Air Pollution Basic Information How does lead get in the ...

  10. Immobilisation of ligands by radio-derivatized polymers; Immobilisering av ligander med radioderiverte polymerer

    Energy Technology Data Exchange (ETDEWEB)

    Varga, J.M.; Fritsch, P.

    1995-01-30

    The invention relates to radio-derivatized polymers and a method of producing them by contacting non-polymerizable conjugands with radiolysable polymers in the presence of irradiation. The resulting radio-derivatized polymers can be further linked with ligand of organic or inorganic nature to immobilize such ligands. 2 figs., 5 tabs.

  11. Catalytic ethylene dimerization and oligomerization: recent developments with nickel complexes containing P,N-chelating ligands.

    Science.gov (United States)

    Speiser, Fredy; Braunstein, Pierre; Saussine, Lucien

    2005-10-01

    Catalytic ethylene oligomerization represents a topic of considerable current academic and industrial interest, in particular for the production of linear alpha-olefins in the C4-C10 range, whose demand is growing fast. Identifying and fine-tuning the parameters that influence the activity and selectivity of metal catalysts constitute major challenges at the interface between ligand design, coordination/organometallic chemistry, and homogeneous catalysis. In this Account, we show how comparative studies aiming at modulating the coordinating properties of functional ligands for a metal, such as nickel, which is used in industrial processes, lead to beneficial effects in catalytic ethylene oligomerization.

  12. Toxicokinetics of bone lead.

    OpenAIRE

    Rabinowitz, M B

    1991-01-01

    This article discusses bone as a source of lead to the rest of the body and as a record of past lead exposure. Bone lead levels generally increase with age at rates dependent on the skeletal site and lead exposure. After occupational exposure, the slow decline in blood lead, a 5- to 19-year half-life, reflects the long skeletal half-life. Repeated measurements of bone lead demonstrate the slow elimination of lead from bone. Stable isotope ratios have revealed many details of skeletal uptake a...

  13. A General Ligand Design for Gold Catalysis allowing Ligand-Directed Anti Nucleophilic Attack of Alkynes

    Science.gov (United States)

    Wang, Yanzhao; Wang, Zhixun; Li, Yuxue; Wu, Gongde; Cao, Zheng; Zhang, Liming

    2014-01-01

    Most homogenous gold catalyses demand ≥0.5 mol % catalyst loading. Due to the high cost of gold, these reactions are unlikely to be applicable in medium or large scale applications. Here we disclose a novel ligand design based on the privileged biphenyl-2-phosphine framework that offers a potentially general approach to dramatically lowering catalyst loading. In this design, an amide group at the 3’ position of the ligand framework directs and promotes nucleophilic attack at the ligand gold complex-activated alkyne, which is unprecedented in homogeneous gold catalysis considering the spatial challenge of using ligand to reach antiapproaching nucleophile in a linear P-Au-alkyne centroid structure. With such a ligand, the gold(I) complex becomes highly efficient in catalyzing acid addition to alkynes, with a turnover number up to 99,000. Density functional theory calculations support the role of the amide moiety in directing the attack of carboxylic acid via hydrogen bonding. PMID:24704803

  14. A new class of PN3-pincer ligands for metal–ligand cooperative catalysis

    KAUST Repository

    Li, Huaifeng

    2014-12-01

    Work on a new class of PN3-pincer ligands for metal-ligand cooperative catalysis is reviewed. While the field of the pyridine-based PN3-transition metal pincer complexes is still relatively young, many important applications of these complexes have already emerged. In several cases, the PN3-pincer complexes for metal-ligand cooperative catalysis result in significantly improved or unprecedented activities. The synthesis and coordination chemistry of PN3-pincer ligands are briefly summarized first to cover the synthetic routes for their preparation, followed by a focus review on their applications in catalysis. A specific emphasis is placed on the later section about the role of PN3-pincer ligands\\' dearomatization-rearomatization steps during the catalytic cycles. The mechanistic insights from density functional theory (DFT) calculations are also discussed.

  15. Complexation of lead by organic matter in Luanda Bay, Angola.

    Science.gov (United States)

    Leitão, Anabela; Santos, Ana Maria; Boaventura, Rui A R

    2015-10-01

    Speciation is defined as the distribution of an element among different chemical species. Although the relation between speciation and bioavailability is complex, the metal present as free hydrated ion, or as weak complexes able to dissociate, is usually more bioavailable than the metal incorporated in strong complexes or adsorbed on colloidal or particulate matter. Among the analytical techniques currently available, anodic stripping voltammetry (ASV) has been one of the most used in the identification and quantification of several heavy metal species in aquatic systems. This work concerns the speciation study of lead, in original (natural, non-filtered) and filtered water samples and in suspensions of particulate matter and sediments from Luanda Bay (Angola). Complexes of lead with organics were identified and quantified by differential pulse anodic stripping voltammetry technique. Each sample was progressively titrated with a Pb(II) standard solution until complete saturation of the organic ligands. After each addition of Pb(II), the intensity, potential and peak width of the voltammetric signal were measured. The results obtained in this work show that more than 95 % of the lead in the aquatic environment is bound in inert organic complexes, considering all samples from different sampling sites. In sediment samples, the lead is totally (100 %) complexed with ligands adsorbed on the particles surface. Two kinds of dominant lead complexes, very strong (logK >11) and strong to moderately strong (8< logK <11), were found, revealing the lead affinity for the stronger ligands.

  16. Effects of PPARγ ligands on vascular tone.

    Science.gov (United States)

    Salomone, Salvatore; Drago, Filippo

    2012-06-01

    Peroxisome Proliferator-Activated Receptor γ (PPARγ), originally described as a transcription factor for genes of carbohydrate and lipid metabolism, has been more recently studied in the context of cardiovascular pathophysiology. Here, we review the available data on PPARγ ligands as modulator of vascular tone. PPARγ ligands include: thiazolidinediones (used in the treatment of type 2 diabetes mellitus), glitazars (bind and activate both PPARγ and PPARα), and other experimental drugs (still in development) that exploit the chemistry of thiazolidinediones as a scaffold for PPARγ-independent pharmacological properties. In this review, we examine both short (mostly from in vitro data)- and long (mostly from in vivo data)-term effects of PPARγ ligands that extend from PPARγ-independent vascular effects to PPARγ-dependent gene expression. Because endothelium is a master regulator of vascular tone, we have attempted to differentiate between endothelium-dependent and endothelium-independent effects of PPARγ ligands. Based on available data, we conclude that PPARγ ligands appear to influence vascular tone in different experimental paradigms, most often in terms of vasodilatation (potentially increasing blood flow to some tissues). These effects on vascular tone, although potentially beneficial, must be weighed against specific cardiovascular warnings that may apply to some drugs, such as rosiglitazone.

  17. Dockomatic - automated ligand creation and docking.

    Science.gov (United States)

    Bullock, Casey W; Jacob, Reed B; McDougal, Owen M; Hampikian, Greg; Andersen, Tim

    2010-11-08

    The application of computational modeling to rationally design drugs and characterize macro biomolecular receptors has proven increasingly useful due to the accessibility of computing clusters and clouds. AutoDock is a well-known and powerful software program used to model ligand to receptor binding interactions. In its current version, AutoDock requires significant amounts of user time to setup and run jobs, and collect results. This paper presents DockoMatic, a user friendly Graphical User Interface (GUI) application that eases and automates the creation and management of AutoDock jobs for high throughput screening of ligand to receptor interactions. DockoMatic allows the user to invoke and manage AutoDock jobs on a single computer or cluster, including jobs for evaluating secondary ligand interactions. It also automates the process of collecting, summarizing, and viewing results. In addition, DockoMatic automates creation of peptide ligand .pdb files from strings of single-letter amino acid abbreviations. DockoMatic significantly reduces the complexity of managing multiple AutoDock jobs by facilitating ligand and AutoDock job creation and management.

  18. Dockomatic - automated ligand creation and docking

    Directory of Open Access Journals (Sweden)

    Hampikian Greg

    2010-11-01

    Full Text Available Abstract Background The application of computational modeling to rationally design drugs and characterize macro biomolecular receptors has proven increasingly useful due to the accessibility of computing clusters and clouds. AutoDock is a well-known and powerful software program used to model ligand to receptor binding interactions. In its current version, AutoDock requires significant amounts of user time to setup and run jobs, and collect results. This paper presents DockoMatic, a user friendly Graphical User Interface (GUI application that eases and automates the creation and management of AutoDock jobs for high throughput screening of ligand to receptor interactions. Results DockoMatic allows the user to invoke and manage AutoDock jobs on a single computer or cluster, including jobs for evaluating secondary ligand interactions. It also automates the process of collecting, summarizing, and viewing results. In addition, DockoMatic automates creation of peptide ligand .pdb files from strings of single-letter amino acid abbreviations. Conclusions DockoMatic significantly reduces the complexity of managing multiple AutoDock jobs by facilitating ligand and AutoDock job creation and management.

  19. Chelating ligands for nanocrystals' surface functionalization.

    Science.gov (United States)

    Querner, Claudia; Reiss, Peter; Bleuse, Joël; Pron, Adam

    2004-09-22

    A new family of ligands for the surface functionalization of CdSe nanocrystals is proposed, namely alkyl or aryl derivatives of carbodithioic acids (R-C(S)SH). The main advantages of these new ligands are as follows: they nearly quantitatively exchange the initial surface ligands (TOPO) in very mild conditions; they significantly improve the resistance of nanocrystals against photooxidation because of their ability of strong chelate-type binding to metal atoms; their relatively simple preparation via Grignard intermediates facilitates the development of new bifunctional ligands containing, in addition to the anchoring carbodithioate group, a second function, which enables the grafting of molecules or macromolecules of interest on the nanocrystal surface. To give an example of this approach, we report, for the first time, the grafting of an electroactive oligomer from the polyaniline family-aniline tetramer-on CdSe nanocrystals after their functionalization with 4-formyldithiobenzoic acid. The grafting proceeds via a condensation reaction between the aldehyde group of the ligand and the terminal primary amine group of the tetramer. The resulting organic/inorganic hybrid exhibits complete extinction of the fluorescence of its constituents, indicating efficient charge or energy transfer between the organic and the inorganic semiconductors.

  20. Ligand identification using electron-density map correlations

    International Nuclear Information System (INIS)

    Terwilliger, Thomas C.; Adams, Paul D.; Moriarty, Nigel W.; Cohn, Judith D.

    2007-01-01

    An automated ligand-fitting procedure is applied to (F o − F c )exp(iϕ c ) difference density for 200 commonly found ligands from macromolecular structures in the Protein Data Bank to identify ligands from density maps. A procedure for the identification of ligands bound in crystal structures of macromolecules is described. Two characteristics of the density corresponding to a ligand are used in the identification procedure. One is the correlation of the ligand density with each of a set of test ligands after optimization of the fit of that ligand to the density. The other is the correlation of a fingerprint of the density with the fingerprint of model density for each possible ligand. The fingerprints consist of an ordered list of correlations of each the test ligands with the density. The two characteristics are scored using a Z-score approach in which the correlations are normalized to the mean and standard deviation of correlations found for a variety of mismatched ligand-density pairs, so that the Z scores are related to the probability of observing a particular value of the correlation by chance. The procedure was tested with a set of 200 of the most commonly found ligands in the Protein Data Bank, collectively representing 57% of all ligands in the Protein Data Bank. Using a combination of these two characteristics of ligand density, ranked lists of ligand identifications were made for representative (F o − F c )exp(iϕ c ) difference density from entries in the Protein Data Bank. In 48% of the 200 cases, the correct ligand was at the top of the ranked list of ligands. This approach may be useful in identification of unknown ligands in new macromolecular structures as well as in the identification of which ligands in a mixture have bound to a macromolecule

  1. Characteristic molecular vibrations of adenosine receptor ligands.

    Science.gov (United States)

    Chee, Hyun Keun; Yang, Jin-San; Joung, Je-Gun; Zhang, Byoung-Tak; Oh, S June

    2015-02-13

    Although the regulation of membrane receptor activation is known to be crucial for molecular signal transduction, the molecular mechanism underlying receptor activation is not fully elucidated. Here we study the physicochemical nature of membrane receptor behavior by investigating the characteristic molecular vibrations of receptor ligands using computational chemistry and informatics methods. By using information gain, t-tests, and support vector machines, we have identified highly informative features of adenosine receptor (AdoR) ligand and corresponding functional amino acid residues such as Asn (6.55) of AdoR that has informative significance and is indispensable for ligand recognition of AdoRs. These findings may provide new perspectives and insights into the fundamental mechanism of class A G protein-coupled receptor activation. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  2. Effects of PPARγ Ligands on Leukemia

    Directory of Open Access Journals (Sweden)

    Yoko Tabe

    2012-01-01

    Full Text Available Peroxisome proliferator-activated receptors (PPARs and retinoic acid receptors (RARs, members of the nuclear receptor superfamily, are transcription factors that regulate a variety of important cellular functions. PPARs form heterodimers retinoid X receptor (RXR, an obligate heterodimeric partner for other nuclear receptors. Several novel links between retinoid metabolism and PPAR responses have been identified, and activation of PPAR/RXR expression has been shown to increase response to retinoids. PPARγ has emerged as a key regulator of cell growth and survival, whose activity is modulated by a number of synthetic and natural ligands. While clinical trials in cancer patients with thiazolidinediones (TZD have been disappointing, novel structurally different PPARγ ligands, including triterpenoids, have entered clinical arena as therapeutic agents for epithelial and hematopoietic malignancies. Here we shall review the antitumor advances of PPARγ, alone and in combination with RARα ligands in control of cell proliferation, differentiation, and apoptosis and their potential therapeutic applications in hematological malignancies.

  3. Toxicokinetics of bone lead.

    Science.gov (United States)

    Rabinowitz, M B

    1991-02-01

    This article discusses bone as a source of lead to the rest of the body and as a record of past lead exposure. Bone lead levels generally increase with age at rates dependent on the skeletal site and lead exposure. After occupational exposure, the slow decline in blood lead, a 5- to 19-year half-life, reflects the long skeletal half-life. Repeated measurements of bone lead demonstrate the slow elimination of lead from bone. Stable isotope ratios have revealed many details of skeletal uptake and subsequent release. The bulk turnover rates for compact bone are about 2% per year and 8% for spine. Turnover activity varies with age and health. Even though lead approximates calcium, radium, strontium, barium, fluorine, and other bone seekers, the rates for each are different. A simple, two-pool (bone and blood) kinetic model is presented with proposed numerical values for the changes in blood lead levels that occur with changes in turnover rates. Two approaches are offered to further quantify lead turnover. One involves a study of subjects with known past exposure. Changes in the ratio of blood lead to bone lead with time would reflect the course of bone lead availability. Also, stable isotopes and subjects who move from one geographical area to another offer opportunities. Sequential isotope measurements would indicate how much of the lead in blood is from current exposure or bone stores, distinct from changes in absorption or excretion.

  4. Lead in alcoholic beverages.

    Science.gov (United States)

    Sherlock, J C; Pickford, C J; White, G F

    1986-01-01

    Following the finding that blood lead concentrations in middle-aged men were positively associated with alcohol consumption, the Royal Commission on Environmental Pollution recommended that information on lead in alcoholic beverages be obtained. The results reported here were obtained in response to the Royal Commission's request. About 90% of canned and bottled beers contained less than or equal to 10 micrograms/l of lead, whereas nearly half the draught beers sampled contained greater than 10 micrograms/l and 4% contained greater than 100 micrograms/l. Opening the cans and bottles and pouring the contents into a glass had no significant effect on the lead concentration in the beer. All wines sampled directly from the bottle, that is without pouring, contained less than 250 micrograms/l of lead. However the lead concentration in some wines contained in lead-capped bottles increased significantly when the wine was poured from the bottle, in one instance the increment was 1890 micrograms/l. It is concluded that consumption of beer containing 50 micrograms/l of lead could make a substantial contribution to blood lead concentrations in man. Consumption of 1 l/day of wine containing 150 micrograms/l of lead could also make a major contribution to blood lead concentrations. Lead contamination of wine when it is poured from a bottle, which had been lead-capped, can sometimes greatly increase lead concentrations in the wine.

  5. Metal-ligand cooperation by aromatization-dearomatization as a tool in single bond activation.

    Science.gov (United States)

    Milstein, David

    2015-03-13

    Metal-ligand cooperation (MLC) plays an important role in bond activation processes, enabling many chemical and biological catalytic reactions. A recent new mode of activation of chemical bonds involves ligand aromatization-dearomatization processes in pyridine-based pincer complexes in which chemical bonds are broken reversibly across the metal centre and the pincer-ligand arm, leading to new bond-making and -breaking processes, and new catalysis. In this short review, such processes are briefly exemplified in the activation of C-H, H-H, O-H, N-H and B-H bonds, and mechanistic insight is provided. This new bond activation mode has led to the development of various catalytic reactions, mainly based on alcohols and amines, and to a stepwise approach to thermal H2 and light-induced O2 liberation from water. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  6. Transition Metal Complexes Coordinated by Water Soluble Phosphane Ligands: How Cyclodextrins Can Alter the Coordination Sphere?

    Directory of Open Access Journals (Sweden)

    Michel Ferreira

    2017-01-01

    Full Text Available The behaviour of platinum(II and palladium(0 complexes coordinated by various hydrosoluble monodentate phosphane ligands has been investigated by 31P{1H} NMR spectroscopy in the presence of randomly methylated β-cyclodextrin (RAME-β-CD. This molecular receptor can have no impact on the organometallic complexes, induce the formation of phosphane low-coordinated complexes or form coordination second sphere species. These three behaviours are under thermodynamic control and are governed not only by the affinity of RAME-β-CD for the phosphane but also by the phosphane stereoelectronic properties. When observed, the low-coordinated complexes may be formed either via a preliminary decoordination of the phosphane followed by a complexation of the free ligand by the CD or via the generation of organometallic species complexed by CD which then lead to expulsion of ligands to decrease their internal steric hindrance.

  7. Fabricating Water Dispersible Superparamagnetic Iron Oxide Nanoparticles for Biomedical Applications through Ligand Exchange and Direct Conjugation

    Directory of Open Access Journals (Sweden)

    Tina Lam

    2016-05-01

    Full Text Available Stable superparamagnetic iron oxide nanoparticles (SPIONs, which can be easily dispersed in an aqueous medium and exhibit high magnetic relaxivities, are ideal candidates for biomedical applications including contrast agents for magnetic resonance imaging. We describe a versatile methodology to render water dispersibility to SPIONs using tetraethylene glycol (TEG-based phosphonate ligands, which are easily introduced onto SPIONs by either a ligand exchange process of surface-anchored oleic-acid (OA molecules or via direct conjugation. Both protocols confer good colloidal stability to SPIONs at different NaCl concentrations. A detailed characterization of functionalized SPIONs suggests that the ligand exchange method leads to nanoparticles with better magnetic properties but higher toxicity and cell death, than the direct conjugation methodology.

  8. Lead inclusions in aluminium

    International Nuclear Information System (INIS)

    Johnson, E.; Johansen, A.; Sarholt-Kristensen, L.; Andersen, H.H.; Grabaek, L.; Bohr, J.

    1990-01-01

    Ion implantation at room temperature of lead into aluminum leads to spontaneous phase separation and formation of lead precipitates growing topotactically with the matrix. Unlike the highly pressurized (∼ 1-5 GPa) solid inclusions formed after noble gas implantations, the pressure in the lead precipitates is found to be less than 0.12 GPa. Recently the authors have observed the result that the lead inclusions in aluminum exhibit both superheating and supercooling. In this paper they review and elaborate on these results. Small implantation-induced lead precipitates embedded in an aluminum matrix were studied by x-ray diffraction

  9. Homology model-based virtual screening for GPCR ligands using docking and target-biased scoring.

    Science.gov (United States)

    Radestock, Sebastian; Weil, Tanja; Renner, Steffen

    2008-05-01

    The current study investigates the combination of two recently reported techniques for the improvement of homology model-based virtual screening for G-protein coupled receptor (GPCR) ligands. First, ligand-supported homology modeling was used to generate receptor models that were in agreement with mutagenesis data and structure-activity relationship information of the ligands. Second, interaction patterns from known ligands to the receptor were applied for scoring and rank ordering compounds from a virtual library using ligand-receptor interaction fingerprint-based similarity (IFS). Our approach was evaluated in retrospective virtual screening experiments for antagonists of the metabotropic glutamate receptor (mGluR) subtype 5. The results of our approach were compared to the results obtained by conventional scoring functions (Dock-Score, PMF-Score, Gold-Score, ChemScore, and FlexX-Score). The IFS lead to significantly higher enrichment rates, relative to the competing scoring functions. Though using a target-biased scoring approach, the results were not biased toward the chemical classes of the reference structures. Our results indicate that the presented approach has the potential to serve as a general setup for successful structure-based GPCR virtual screening.

  10. Identification of small molecular ligands as potent inhibitors of fatty acid metabolism in Mycobacterium tuberculosis

    Science.gov (United States)

    Malikanti, Ramesh; Vadija, Rajender; Veeravarapu, Hymavathi; Mustyala, Kiran Kumar; Malkhed, Vasavi; Vuruputuri, Uma

    2017-12-01

    Tuberculosis (Tb) is one of the major health challenges for the global scientific community. The 3-hydroxy butyryl-CoA dehydrogenase (Fad B2) protein belongs to 3-hydroxyl acetyl-CoA dehydrogenase family, which plays a key role in the fatty acid metabolism and β-oxidation in the cell membrane of Mycobacterium tuberculosis (Mtb). In the present study the Fad B2 protein is targeted for the identification of potential drug candidates for tuberculosis. The 3D model of the target protein Fad B2, was generated using homology modeling approach and was validated. The plausible binding site of the Fad B2 protein was identified from computational binding pocket prediction tools, which ranges from ASN120 to VAL150 amino acid residues. Virtual screening was carried out with the databases, Ligand box UOS and hit definder, at the binding site region. 133 docked complex structures were generated as an output. The identified ligands show good glide scores and glide energies. All the ligand molecules contain benzyl amine pharmacophore in common, which show specific and selective binding interactions with the SER122 and ASN146 residues of the Fad B2 protein. The ADME properties of all the ligand molecules were observed to be within the acceptable range. It is suggested from the result of the present study that the docked molecular structures with a benzyl amine pharmacophore act as potential ligands for Fad B2 protein binding and as leads in Tb drug discovery.

  11. Multifunctionality and mechanism of ligand binding in a mosquito antiinflammatory protein

    Energy Technology Data Exchange (ETDEWEB)

    Calvo, Eric; Mans, Ben J.; Ribeiro, José M.C.; Andersen, John F.; (NIH)

    2009-04-07

    The mosquito D7 salivary proteins are encoded by a multigene family related to the arthropod odorant-binding protein (OBP) superfamily. Forms having either one or two OBP domains are found in mosquito saliva. Four single-domain and one two-domain D7 proteins from Anopheles gambiae and Aedes aegypti (AeD7), respectively, were shown to bind biogenic amines with high affinity and with a stoichiometry of one ligand per protein molecule. Sequence comparisons indicated that only the C-terminal domain of AeD7 is homologous to the single-domain proteins from A. gambiae, suggesting that the N-terminal domain may bind a different class of ligands. Here, we describe the 3D structure of AeD7 and examine the ligand-binding characteristics of the N- and C-terminal domains. Isothermal titration calorimetry and ligand complex crystal structures show that the N-terminal domain binds cysteinyl leukotrienes (cysLTs) with high affinities (50-60 nM) whereas the C-terminal domain binds biogenic amines. The lipid chain of the cysLT binds in a hydrophobic pocket of the N-terminal domain, whereas binding of norepinephrine leads to an ordering of the C-terminal portion of the C-terminal domain into an alpha-helix that, along with rotations of Arg-176 and Glu-268 side chains, acts to bury the bound ligand.

  12. Synthesis and spectral characterisation of a new metal complex with a bidentate ligand

    Science.gov (United States)

    Niculescu, Violeta; Tamaian, Radu; Păun, Nadia; Pîrnău, Adrian; Szabo, Laszlo

    2009-08-01

    Literature mentions the important biologic-active, antimalaric, antiviral, antitumoural, tuberculostatic properties of 3-alkyl-and 3-alkenyl-substituted derivatives of 2-hydroxy-1,4-naphthoquinone and arylamino-1,4-naphthoquinones; the same properties are shown by the complexes that these ligands form with metal ions, which act in the biological structures as essential microelement. This paper reports the study of the structure of some new electron-transfer complexes with bidentate ligands of the naphthoquinone series by using IR, visible and UV spectra. A quantum-mechanical interpretation of the electronic transitions for the free and coordinated ligand has been performed in order to get information on the coordination of the heteroatoms to the M(II). The complexes of transitional metals with naphthoquinonic ligand have been prepared by following the procedure described by Jensen and Nielsen. The structural formula of the free and coordinated organic ligand has been modelled on the computer. The electronic spectra of the complexes studied lead to the conclusion that they are square-planar.

  13. Vesicular stomatitis virus infection promotes immune evasion by preventing NKG2D-ligand surface expression.

    Science.gov (United States)

    Jensen, Helle; Andresen, Lars; Nielsen, Jens; Christensen, Jan Pravsgaard; Skov, Søren

    2011-01-01

    Vesicular stomatitis virus (VSV) has recently gained attention for its oncolytic ability in cancer treatment. Initially, we hypothesized that VSV infection could increase immune recognition of cancer cells through induction of the immune stimulatory NKG2D-ligands. Here we show that VSV infection leads to a robust induction of MICA mRNA expression, however the subsequent surface expression is potently hindered. Thus, VSV lines up with human cytomegalovirus (HCMV) and adenovirus, which actively subvert the immune system by negatively affecting NKG2D-ligand surface expression. VSV infection caused an active suppression of NKG2D-ligand surface expression, affecting both endogenous and histone deacetylase (HDAC)-inhibitor induced MICA, MICB and ULBP-2 expression. The classical immune escape mechanism of VSV (i.e., the M protein blockade of nucleocytoplasmic mRNA transport) was not involved, as the VSV mutant strain, VSV(ΔM51), which possess a defective M protein, prevented MICA surface expression similarly to wild-type VSV. The VSV mediated down modulation of NKG2D-ligand expression did not involve apoptosis. Constitutive expression of MICA bypassed the escape mechanism, suggesting that VSV affect NKG2D-ligand expression at an early post-transcriptional level. Our results show that VSV possess an escape mechanism, which could affect the immune recognition of VSV infected cancer cells. This may also have implications for immune recognition of cancer cells after combined treatment with VSV and chemotherapeutic drugs.

  14. Lead and tap water

    Science.gov (United States)

    Water contaminated with lead ... The Environmental Protection Agency (EPA) monitors drinking water in the United States. It requires water suppliers to produce annual water quality reports. These reports include information about lead amounts, and they ...

  15. VOLUMETRIC LEAD ASSAY

    International Nuclear Information System (INIS)

    Ebadian, M.A.; Dua, S.K.; Roelant, David; Kumar, Sachin

    2001-01-01

    This report describes a system for handling and radioassay of lead, consisting of a robot, a conveyor, and a gamma spectrometer. The report also presents a cost-benefit analysis of options: radioassay and recycling lead vs. disposal as waste

  16. Leading Causes of Blindness

    Science.gov (United States)

    ... Home Current Issue Past Issues Feature: Vision Leading Causes of Blindness Past Issues / Summer 2008 Table of ... million Americans have cataracts. They are the leading cause of blindness in the world. By age 80, ...

  17. NA49: lead-lead collision

    CERN Multimedia

    1996-01-01

    This is an image of an actual lead ion collision taken from tracking detectors on the NA49 experiment, part of the heavy ion project at CERN. These collisions produce a very complicated array of hadrons as the heavy ions break up. It is hoped that one of these collisions will eventually create a new state of matter known as quark-gluon plasma.

  18. Ligand Exchange and 1H NMR Quantification of Single- and Mixed-Moiety Thiolated Ligand Shells on Gold Nanoparticles.

    Science.gov (United States)

    Smith, Ashley M; Millstone, Jill E

    2017-01-01

    The use of nanoparticles in biomedicine critically depends on their surface chemistry. For metal nanoparticles, a common way to tune this surface chemistry is through mass action ligand exchange, where ligand exchange can be used to expand the functionality of the resulting nanoparticle conjugates. Specifically, the quantity, identity, and arrangement of the molecules in the resulting ligand shell each can be tuned significantly. Here, we describe methods to exchange and quantify thiolated and non-thiolated ligands on gold nanoparticle surfaces. Importantly, these strategies allow the quantification of multiple ligand types within a single ligand shell, simultaneously providing ligand composition and ligand density information. These results are crucial for both designing and assigning structure-function relationships in bio-functionalized nanoparticles, and these methods can be applied to a broad range of nanoparticle cores and ligand types including peptides, small molecule drugs, and oligonucleotides.

  19. Anatomy of lead poisoning

    African Journals Online (AJOL)

    ABEOLUGBENGAS

    Abstract. Objective: Lead poisoning and lead toxicity is usually often interchangeably used by different Scientists. The Anatomy of lead poisoning encompasses its effects on different organ-systems of different species of organisms. It also includes environmental, functional and biochemical components associated with most.

  20. Synthesis of freestanding water-soluble indium oxide nanocrystals capped by alanine nitric acid via ligand exchange for thin film transistors and effects of ligands on the electrical properties

    International Nuclear Information System (INIS)

    Choi, Jin-Kyu; Koh, Ye-Seul; Jeong, Hyun-Dam

    2015-01-01

    We demonstrate synthesis of freestanding water-soluble indium oxide nanocrystals (In 2 O 3 NCs) by ligand exchange to β-alanine nitric acid (Ala·HNO 3 ) and its application for active channel layer in thin film transistors (TFTs), with investigation of the effect of curing temperatures on the TFT properties in terms of thermal behaviour of the ligand molecules at 150, 300, and 350 °C. After ligand exchange from long alkyl ligand (myristic acid, MA) to short Ala·HNO 3 , the mobility of NC TFTs cured at 150 °C increased by over 1 order of magnitude, from 1.3 × 10 −4 cm 2 V -1 s −1 to 4.5 × 10 −3 cm 2 V -1 s −1 , due to enhanced tunnelling rate (Γ) between adjective NCs. Higher curing temperatures such as 300 and 350 °C, inducing thermal decomposition of the organic ligands, led to further enhancement of the mobility, particularly up to 2.2 cm 2 V -1 s −1 for the In 2 O 3 NC-Ala·HNO 3 TFT cured at 350 °C. It is also found that the ligand exchange of In 2 O 3 NC in acidic condition (e.g. HNO 3 ) would be simple and effective to reduce the surface defects by surface etching, which may lead to better device performances. - Graphical abstract: Display Omitted - Highlights: • Freestanding water-soluble In 2 O 3 nanocrystals (NCs) were synthesized by ligand exchange. • Thin film transistors (TFTs) of colloidal NCs were fabricated by spin-coating method. • Water-soluble In 2 O 3 NC TFTs showed higher mobilities due to shorter ligand length. • Surface defects of NCs were notably reduced by surface etching during ligand exchange

  1. Structural Diversity of Metallosupramolecular Assemblies Based on the Bent Bridging Ligand 4,4′-Dithiodipyridine

    Directory of Open Access Journals (Sweden)

    Rüdiger W. Seidel

    2013-05-01

    Full Text Available 4,4′-Dithiodipyridine (dtdp, also termed 4,4′-dipyridyldisulfide, is a bridging ligand of the 4,4′-bipyridine type. The introduction of the disulfide moiety inevitably leads to a relatively rigid angular structure, which exhibits axial chirality. More than 90 metal complexes containing the dtdp ligand have been crystallographically characterised until now. This review focuses on the preparation and structural diversity of discrete and polymeric metallosupramolecular assemblies constructed from dtdp as bridging ligands. These encompass metallamacrocycles with M2L2 topology and coordination polymers with periodicity in one or two dimensions. One-dimensional coordination polymers represent the vast majority of the metallosupramolecular structures obtained from dtdp. These include repeated rhomboids, zigzag, helical and arched chains among other types. In this contribution, we make an attempt to provide a comprehensive account of the structural data that are currently available for metallosupramolecular assemblies based on the bent bridging ligand dtdp.

  2. Ligand field theory and the origin of life as an emergent feature of the periodic table of elements.

    Science.gov (United States)

    Morowitz, Harold J; Srinivasan, Vijayasarathy; Smith, Eric

    2010-08-01

    The assumption that all biological catalysts are either proteins or ribozymes leads to an outstanding enigma of biogenesis-how to determine the synthetic pathways to the monomers for the efficient formation of catalytic macromolecules in the absence of any such macromolecules. The last 60 years have witnessed chemists developing an understanding of organocatalysis and ligand field theory, both of which give demonstrable low-molecular-weight catalysts. We assume that transition-metal-ligand complexes are likely to have occurred in the deep ocean trenches by the combination of naturally occurring oceanic metals and ligands synthesized from the emergent CO(2), H(2), NH(3), H(2)S, and H(3)PO(4). We are now in a position to investigate experimentally the metal-ligand complexes, their catalytic function, and the reaction networks that could have played a role in the development of metabolism and life itself.

  3. A2AR Binding Kinetics in the Ligand Depletion Regime.

    Science.gov (United States)

    McNeely, Patrick M; Naranjo, Andrea N; Forsten-Williams, Kimberly; Robinson, Anne Skaja

    2017-02-01

    Ligand binding plays a fundamental role in stimulating the downstream signaling of membrane receptors. Here, ligand-binding kinetics of the full-length human adenosine A 2A receptor (A 2A R) reconstituted in detergent micelles were measured using a fluorescently labeled ligand via fluorescence anisotropy. Importantly, to optimize the signal-to-noise ratio, these experiments were conducted in the ligand depletion regime. In the ligand depletion regime, the assumptions used to determine analytical solutions for one-site binding models for either one or two ligands in competition are no longer valid. We therefore implemented a numerical solution approach to analyze kinetic binding data as experimental conditions approach the ligand depletion regime. By comparing the results from the numerical and the analytical solutions, we highlight the ligand-receptor ratios at which the analytical solution begins to lose predictive accuracy. Using the numerical solution approach, we determined the kinetic rate constants of the fluorescent ligand, FITC-APEC, and those for three unlabeled ligands using competitive association experiments. The association and dissociation rate constants of the unlabeled ligands determined from the competitive association experiments were then independently validated using competitive dissociation data. Based on this study, a numerical solution is recommended to determine kinetic ligand-binding parameters for experiments conducted in the ligand-depletion regime.

  4. CHELATING LIGANDS: ENHANCERS OF QUALITY AND PURITY ...

    African Journals Online (AJOL)

    Nwokem et al.

    ABSTRACT. The quality of biogas depends largely on the percentage of methane and hydrogen sulphide gas present. High concentration of hydrogen sulphide results in low quality biogas. This work employed the use of chelating ligands in scrubbing hydrogen sulphide gas while improving the yield of methane gas.

  5. Ligand iron catalysts for selective hydrogenation

    Science.gov (United States)

    Casey, Charles P.; Guan, Hairong

    2010-11-16

    Disclosed are iron ligand catalysts for selective hydrogenation of aldehydes, ketones and imines. A catalyst such as dicarbonyl iron hydride hydroxycyclopentadiene) complex uses the OH on the five member ring and hydrogen linked to the iron to facilitate hydrogenation reactions, particularly in the presence of hydrogen gas.

  6. Versatile phosphite ligands based on silsesquioxane backbones

    NARCIS (Netherlands)

    van der Vlugt, JI; Ackerstaff, J; Dijkstra, TW; Mills, AM; Kooijman, H; Spek, AL; Meetsma, A; Abbenhuis, HCL; Vogt, D

    Silsesquioxanes are employed as ligand backbones for the synthesis of novel phosphite compounds with 3,3'-5,5'-tetrakis(tert-butyl)-2,2'-di-oxa-1,1'-biphenyl substituents. Both mono- and bidentate phosphites are prepared in good yields. Two types of silsesquioxanes are employed as starting

  7. Constitutive and ligand-induced TCR degradation

    DEFF Research Database (Denmark)

    von Essen, Marina; Bonefeld, Charlotte Menné; Siersma, Volkert

    2004-01-01

    divergent models for TCR down-regulation and degradation have been suggested. The aims of this study were to determine the rate constants for constitutive and ligand-induced TCR degradation and to determine whether the TCR subunits segregate or are processed as an intact unit during TCR down...

  8. Ligand Exchange Kinetics of Environmentally Relevant Metals

    Energy Technology Data Exchange (ETDEWEB)

    Panasci, Adele Frances [Univ. of California, Davis, CA (United States)

    2014-07-15

    The interactions of ground water with minerals and contaminants are of broad interest for geochemists but are not well understood. Experiments on the molecular scale can determine reaction parameters (i.e. rates of ligand exchange, activation entropy, activation entropy, and activation volume) that can be used in computations to gain insight into reactions that occur in natural groundwaters. Experiments to determine the rate of isotopic ligand exchange for three environmentally relevant metals, rhodium (Rh), iron (Fe), and neptunium (Np), are described. Many environmental transformations of metals (e.g. reduction) in soil occur at trivalent centers, Fe(III) in particular. Contaminant ions absorb to mineral surfaces via ligand exchange, and the reversal of this reaction can be dangerous, releasing contaminants into the environment. Ferric iron is difficult to study spectroscopically because most of its complexes are paramagnetic and are generally reactive toward ligand exchange; therefore, Rh(III), which is diamagnetic and less reactive, was used to study substitution reactions that are analogous to those that occur on mineral oxide surfaces. Studies on both Np(V) and Np(VI) are important in their own right, as 237Np is a radioactive transuranic element with a half-life of 2 million years.

  9. Dynamic Ligand Based Pharmacophore Modeling and Virtual ...

    Indian Academy of Sciences (India)

    user

    ChEMBL-HIV https://www.ebi.ac.uk/chembl/index.php/assay/results (ChEMBL Bioassay was searched with the key word “Human. Immunodefficiency virus”, display bioactivity option was chosen and then “Download All Bioactivity Data” was ... Ligand based pharmacophore models generated from the crystal structure and.

  10. Mixed-ligand binuclear copper(II)

    Indian Academy of Sciences (India)

    A new mixed-ligand binuclear copper(II) complex [Cu(MS)(bpy)]2.(ClO4)2, built of 5-methylsalicylaldehyde and 2,2'-bipyridyl has been synthesized and characterized by using elemental analysis, IR and UV-Vis spectroscopy. Crystal structure of the complex shows that copper(II) ion lies in a square pyramidal coordination ...

  11. A versatile dinucleating ligand containing sulfonamide groups

    DEFF Research Database (Denmark)

    Sundberg, Jonas; Witt, Hannes; Cameron, Lisa

    2014-01-01

    Copper, iron, and gallium coordination chemistries of the new pentadentate bis-sulfonamide ligand 2,6-bis(N-2-pyridylmethylsulfonamido)-4-methylphenol (psmpH3) were investigated. PsmpH3 is capable of varying degrees of deprotonation, and notably, complexes containing the fully trideprotonated...

  12. Amidinate Ligands in Zinc coordination sphere

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 128; Issue 6. Amidinate Ligands in Zinc coordination sphere: Synthesis and structural diversity. SRINIVAS ANGA INDRANI BANERJEE TARUN K PANDA. Regular Article Volume 128 Issue 6 June 2016 pp ... Keywords. Zinc; carbodiimides; amidinate; alkyl migration.

  13. Simple tertiary phosphines to hexaphosphane ligands: Syntheses ...

    Indian Academy of Sciences (India)

    In this context, we have developed new synthetic methodologies for making unusual inorganic ring systems containing trivalent phosphorus centres, novel phosphorus-based multidentate and hybrid ligands and explored their rich transition metal chemistry and catalytic applications. We have also fine tuned a few existing ...

  14. Lead in the environment

    Science.gov (United States)

    Pattee, Oliver H.; Pain, Deborah J.; Hoffman, David J.; Rattner, Barnett A.; Burton, G. Allen; Cairns, John

    2003-01-01

    Anthropogenic uses of lead have probably altered its availability and environmental distribution more than any other toxic element. Consequently, lead concentrations in many living organisms may be approaching thresholds of toxicity for the adverse effects of lead. Such thresholds are difficult to define, as they vary with the chemical and physical form of lead, exposure regime, other elements present and also vary both within and between species. The technological capability to accurately quantify low lead concentrations has increased over the last decade, and physiological and behavioral effects have been measured in wildlife with tissue lead concentrations below those previously considered safe for humans.s.236 Consequently. lead criteria for the protection of wildlife and human health are frequently under review, and 'thresholds' of lead toxicity are being reconsidered. Proposed lead criteria for the protection of natural resources have been reviewed by Eisler. Uptake of lead by plants is limited by its generally low availability in soils and sediments, and toxicity may be limited by storage mechanisms and its apparently limited translocation within most plants. Lead does not generally accumulate within the foliar parts of plants, which limits its transfer to higher trophic levels. Although lead may concentrate in plant and animal tissues, no evidence of biomagnification exists. Acid deposition onto surface waters and soils with low buffering capacity may influence the availability of lead for uptake by plants and animals, and this may merit investigation at susceptible sites. The biological significance of chronic low-level lead exposure to wildlife is sometimes difficult to quantify. Animals living in urban environments or near point sources of lead emission are inevitably subject to greater exposure to lead and enhanced risk of lead poisoning. Increasingly strict controls on lead emissions in many countries have reduced exposure to lead from some sources

  15. ALICE: Simulated lead-lead collision

    CERN Document Server

    2003-01-01

    This track is an example of simulated data modelled for the ALICE detector on the Large Hadron Collider (LHC) at CERN, which will begin taking data in 2008. ALICE will focus on the study of collisions between nuclei of lead, a heavy element that produces many different particles when collided. It is hoped that these collisions will produce a new state of matter known as the quark-gluon plasma, which existed billionths of a second after the Big Bang.

  16. Ammonia formation by metal-ligand cooperative hydrogenolysis of a nitrido ligand

    Science.gov (United States)

    Askevold, Bjorn; Nieto, Jorge Torres; Tussupbayev, Samat; Diefenbach, Martin; Herdtweck, Eberhardt; Holthausen, Max C.; Schneider, Sven

    2011-07-01

    Bioinspired hydrogenation of N2 to ammonia at ambient conditions by stepwise nitrogen protonation/reduction with metal complexes in solution has experienced remarkable progress. In contrast, the highly desirable direct hydrogenation with H2 remains difficult. In analogy to the heterogeneously catalysed Haber-Bosch process, such a reaction is conceivable via metal-centred N2 splitting and unprecedented hydrogenolysis of the nitrido ligands to ammonia. We report the synthesis of a ruthenium(IV) nitrido complex. The high nucleophilicity of the nitrido ligand is demonstrated by unusual N-C coupling with π-acidic CO. Furthermore, the terminal nitrido ligand undergoes facile hydrogenolysis with H2 at ambient conditions to produce ammonia in high yield. Kinetic and quantum chemical examinations of this reaction suggest cooperative behaviour of a phosphorus-nitrogen-phosphorus pincer ligand in rate-determining heterolytic hydrogen splitting.

  17. Nucleotide-mimetic synthetic ligands for DNA-recognizing enzymes One-step purification of Pfu DNA polymerase.

    Science.gov (United States)

    Melissis, S; Labrou, N E; Clonis, Y D

    2006-07-28

    The commercial availability of DNA polymerases has revolutionized molecular biotechnology and certain sectors of the bio-industry. Therefore, the development of affinity adsorbents for purification of DNA polymerases is of academic interest and practical importance. In the present study we describe the design, synthesis and evaluation of a combinatorial library of novel affinity ligands for the purification of DNA polymerases (Pols). Pyrococcus furiosus DNA polymerase (Pfu Pol) was employed as a proof-of-principle example. Affinity ligand design was based on mimicking the natural interactions between deoxynucleoside-triphosphates (dNTPs) and the B-motif, a conserved structural moiety found in Pol-I and Pol-II family of enzymes. Solid-phase 'structure-guided' combinatorial chemistry was used to construct a library of 26 variants of the B-motif-binding 'lead' ligand X-Trz-Y (X is a purine derivative and Y is an aliphatic/aromatic sulphonate or phosphonate derivative) using 1,3,5-triazine (Trz) as the scaffold for assembly. The 'lead' ligand showed complementarity against a Lys and a Tyr residue of the polymerase B-motif. The ligand library was screened for its ability to bind and purify Pfu Pol from Escherichia coli extract. One immobilized ligand (oABSAd), bearing 9-aminoethyladenine (AEAd) and sulfanilic acid (oABS) linked on the triazine scaffold, displayed the highest purifying ability and binding capacity (0,55 mg Pfu Pol/g wet gel). Adsorption equilibrium studies with this affinity ligand and Pfu Pol determined a dissociation constant (K(D)) of 83 nM for the respective complex. The oABSAd affinity adsorbent was exploited in the development of a facile Pfu Pol purification protocol, affording homogeneous enzyme (>99% purity) in a single chromatography step. Quality control tests showed that Pfu Pol purified on the B-motif-complementing ligand is free of nucleic acids and contaminating nuclease activities, therefore, suitable for experimental use.

  18. Ab initio calculation of transport properties between PbSe quantum dots facets with iodide ligands

    Science.gov (United States)

    Wang, B.; Patterson, R.; Chen, W.; Zhang, Z.; Yang, J.; Huang, S.; Shrestha, S.; Conibeer, G.

    2018-01-01

    The transport properties between Lead Selenide (PbSe) quantum dots decorated with iodide ligands has been studied using density functional theory (DFT). Quantum conductance at each selected energy levels has been calculated along with total density of states and projected density of states. The DFT calculation is carried on using a grid-based planar augmented wave (GPAW) code incorporated with the linear combination of atomic orbital (LCAO) mode and Perdew Burke Ernzerhof (PBE) exchange-correlation functional. Three iodide ligand attached low index facets including (001), (011), (111) are investigated in this work. P-orbital of iodide ligand majorly contributes to density of state (DOS) at near top valence band resulting a significant quantum conductance, whereas DOS of Pb p-orbital shows minor influence. Various values of quantum conductance observed along different planes are possibly reasoned from a combined effect electrical field over topmost surface and total distance between adjacent facets. Ligands attached to (001) and (011) planes possess similar bond length whereas it is significantly shortened in (111) plane, whereas transport between (011) has an overall low value due to newly formed electric field. On the other hand, (111) plane with a net surface dipole perpendicular to surface layers leading to stronger electron coupling suggests an apparent increase of transport probability. Apart from previously mentioned, the maximum transport energy levels located several eVs (1 2 eVs) from the edge of valence band top.

  19. Role of Lanthanide-Ligand bonding in the magnetization relaxation ...

    Indian Academy of Sciences (India)

    Ligand bonding. Our calculations transpire comparatively improved Single-Ion Magnet (SIM) behaviour for carbene analogues due to the more axially compressed trigonal prismatic ligand environment. Furthermore, our detailed Mulliken charge, ...

  20. Substrate coated with receptor and labelled ligand for assays

    International Nuclear Information System (INIS)

    1980-01-01

    Improvements in the procedures for assaying ligands are described. The assay consists of a polystyrene tube on which receptors are present for both the ligand to be assayed and a radioactively labelled form of the ligand. The receptors on the bottom portion of the tube are also coated with labelled ligands, thus eliminating the necessity for separate addition of the labelled ligand and sample during an assay. Examples of ligands to which this method is applicable include polypeptides, nucleotides, nucleosides and proteins. Specific examples are given in which the ligand to be assayed is digoxin, the labelled form of the ligand is 3-0-succinyl digoxyigenin tyrosine ( 125 I) and the receptor is digoxin antibody. (U.K.)

  1. Ligand-Mediated Coating of Liposomes with Human Serum Albumin.

    Science.gov (United States)

    Sato, Hikari; Nakhaei, Elnaz; Kawano, Takahito; Murata, Masaharu; Kishimura, Akihiro; Mori, Takeshi; Katayama, Yoshiki

    2018-02-13

    Coating liposome surfaces with human serum albumin (HSA) can improve the colloidal stability and prevent opsonization. HSA coating via specific binding with alkyl ligands is promising because although the ligand-mediated coating is relatively stable it can spontaneously exchange with fresh HSA. However, to achieve surface coating with HSA, multiple hydrophobic ligands must be exposed to an aqueous medium prior to binding with HSA. This presents a challenge, as hydrophobic ligands tend to be buried in the liposomal membrane. Here we present the first HSA modification of liposome surfaces via alkyl ligands. We found that a relatively short alkyl ligand, or a long alkyl ligand with a terminal carboxylate, could be exposed on the liposome surface without causing aggregation of the liposomes and these ligands could subsequently bind HSA. The resulting HSA-coated liposomes were as inert as conventional PEGylated liposomes in terms of macrophage recognition.

  2. Quantum.Ligand.Dock: protein-ligand docking with quantum entanglement refinement on a GPU system.

    Science.gov (United States)

    Kantardjiev, Alexander A

    2012-07-01

    Quantum.Ligand.Dock (protein-ligand docking with graphic processing unit (GPU) quantum entanglement refinement on a GPU system) is an original modern method for in silico prediction of protein-ligand interactions via high-performance docking code. The main flavour of our approach is a combination of fast search with a special account for overlooked physical interactions. On the one hand, we take care of self-consistency and proton equilibria mutual effects of docking partners. On the other hand, Quantum.Ligand.Dock is the the only docking server offering such a subtle supplement to protein docking algorithms as quantum entanglement contributions. The motivation for development and proposition of the method to the community hinges upon two arguments-the fundamental importance of quantum entanglement contribution in molecular interaction and the realistic possibility to implement it by the availability of supercomputing power. The implementation of sophisticated quantum methods is made possible by parallelization at several bottlenecks on a GPU supercomputer. The high-performance implementation will be of use for large-scale virtual screening projects, structural bioinformatics, systems biology and fundamental research in understanding protein-ligand recognition. The design of the interface is focused on feasibility and ease of use. Protein and ligand molecule structures are supposed to be submitted as atomic coordinate files in PDB format. A customization section is offered for addition of user-specified charges, extra ionogenic groups with intrinsic pK(a) values or fixed ions. Final predicted complexes are ranked according to obtained scores and provided in PDB format as well as interactive visualization in a molecular viewer. Quantum.Ligand.Dock server can be accessed at http://87.116.85.141/LigandDock.html.

  3. Quantum.Ligand.Dock: protein–ligand docking with quantum entanglement refinement on a GPU system

    Science.gov (United States)

    Kantardjiev, Alexander A.

    2012-01-01

    Quantum.Ligand.Dock (protein–ligand docking with graphic processing unit (GPU) quantum entanglement refinement on a GPU system) is an original modern method for in silico prediction of protein–ligand interactions via high-performance docking code. The main flavour of our approach is a combination of fast search with a special account for overlooked physical interactions. On the one hand, we take care of self-consistency and proton equilibria mutual effects of docking partners. On the other hand, Quantum.Ligand.Dock is the the only docking server offering such a subtle supplement to protein docking algorithms as quantum entanglement contributions. The motivation for development and proposition of the method to the community hinges upon two arguments—the fundamental importance of quantum entanglement contribution in molecular interaction and the realistic possibility to implement it by the availability of supercomputing power. The implementation of sophisticated quantum methods is made possible by parallelization at several bottlenecks on a GPU supercomputer. The high-performance implementation will be of use for large-scale virtual screening projects, structural bioinformatics, systems biology and fundamental research in understanding protein–ligand recognition. The design of the interface is focused on feasibility and ease of use. Protein and ligand molecule structures are supposed to be submitted as atomic coordinate files in PDB format. A customization section is offered for addition of user-specified charges, extra ionogenic groups with intrinsic pKa values or fixed ions. Final predicted complexes are ranked according to obtained scores and provided in PDB format as well as interactive visualization in a molecular viewer. Quantum.Ligand.Dock server can be accessed at http://87.116.85.141/LigandDock.html. PMID:22669908

  4. Ligand-based modeling of Akt3 lead to potent dual Akt1/Akt3 inhibitor.

    Science.gov (United States)

    Al-Sha'er, Mahmoud A; Taha, Mutasem O

    2018-02-13

    Akt1 and Akt3 are important serine/threonine-specific protein kinases involved in G2 phase required by cancer cells to maintain cell cycle and to prevent cell death. Accordingly, inhibitors of these kinases should have potent anti-cancer properties. This prompted us to use pharmacophore/QSAR modeling to identify optimal binding models and physicochemical descriptors that explain bioactivity variation within a set of 74 diverse Akt3 inhibitors. Two successful orthogonal pharmacophores were identified and further validated using receiver operating characteristic (ROC) curve analyses. The pharmacophoric models and associated QSAR equation were applied to screen the national cancer institute (NCI) list of compounds for new Akt3 inhibitors. Six hits showed significant experimental anti-Akt3 IC 50 values, out of which one compound exhibited dual low micromolar anti-Akt1 and anti-Akt3 inhibitory profiles. Copyright © 2018 Elsevier Inc. All rights reserved.

  5. The role of halides on a chromium ligand field in lead borate glasses

    Science.gov (United States)

    Sekhar, K. Chandra; Srinivas, B.; Narsimlu, N.; Narasimha Chary, M.; Shareefuddin, Md

    2017-10-01

    Glasses with a composition of PbX–PbO–B2O3 (X  =  F2, Cl2 and Br2) containing Cr3+ ions were prepared by a melt quenching technique and investigated by using x-ray diffraction (XRD), optical absorption and electron paramagnetic resonance (EPR) studies. X-ray diffractograms revealed the amorphous nature of the glasses. The density and molar volume were determined. Density values increased for the PFPBCR glass system and decreased for the PCPBCR and PBPBCR glass systems with the composition. Optical absorption spectra were recorded at room temperature (RT) to evaluate the optical band gap E opt and Urbach energies. All the spectra showed characteristic peaks at around 450 nm, 600 nm and 690 nm, and they are assigned to 4 A 2g  →  4 T 1g, 4 A 2g  →  4 T 2g, 4 A 2g  →  2 E transitions respectively. From the optical absorption spectral data, the crystal field (D q ) and Racah parameters (B and C) have been evaluated. Variations in optical band gaps were explained using the electro negativity of halide ions. Electron paramagnetic resonance (EPR) studies were carried out by introducing Cr3+ as the spin probe. The EPR spectra of all the glass samples were recorded at X-band frequencies. The EPR spectra exhibit two resonance signals with effective g values at g  ≈  4.82 and g  ≈  1.99 and are attributed to isolated Cr3+ ions and exchange coupled Cr3+ pairs respectively. The number of spins along with susceptibility are also calculated from the EPR spectra.

  6. Hydrogenation and dehydrogenation iron pincer catalysts capable of metal-ligand cooperation by aromatization/dearomatization.

    Science.gov (United States)

    Zell, Thomas; Milstein, David

    2015-07-21

    The substitution of expensive and potentially toxic noble-metal catalysts by cheap, abundant, environmentally benign, and less toxic metals is highly desirable and in line with green chemistry guidelines. We have recently discovered a new type of metal-ligand cooperation, which is based on the reversible dearomatization/aromatization of different heteroaromatic ligand cores caused by deprotonation/protonation of the ligand. More specifically, we have studied complexes of various transition metals (Ru, Fe, Co, Rh, Ir, Ni, Pd, Pt, and Re) bearing pyridine- and bipyridine-based PNP and PNN pincer ligands, which have slightly acidic methylene protons. In addition, we have discovered long-range metal-ligand cooperation in acridine-based pincer ligands, where the cooperation takes place at the electrophilic C-9 position of the acridine moiety leading to dearomatization of its middle ring. This type of metal-ligand cooperation was used for the activation of chemical bonds, including H-H, C-H (sp(2) and sp(3)), O-H, N-H, and B-H bonds. This unusual reactivity likely takes place in various catalytic hydrogenation, dehydrogenation, and related reactions. In this Account, we summarize our studies on novel bifunctional iron PNP and PNN pincer complexes, which were designed on the basis of their ruthenium congeners. Iron PNP pincer complexes serve as efficient (pre)catalysts for hydrogenation and dehydrogenation reactions under remarkably mild conditions. Their catalytic applications include atom-efficient and industrially important hydrogenation reactions of ketones, aldehydes, and esters to the corresponding alcohols. Moreover, they catalyze the hydrogenation of carbon dioxide to sodium formate in the presence of sodium hydroxide, the selective decomposition of formic acid to carbon dioxide and hydrogen, and the E-selective semihydrogenation of alkynes to give E-alkenes. These catalysts feature, compared to other iron-based catalysts, very high catalytic activities which in

  7. GLIDA: GPCR-ligand database for chemical genomic drug discovery

    OpenAIRE

    Okuno, Yasushi; Yang, Jiyoon; Taneishi, Kei; Yabuuchi, Hiroaki; Tsujimoto, Gozoh

    2005-01-01

    G-protein coupled receptors (GPCRs) represent one of the most important families of drug targets in pharmaceutical development. GPCR-LIgand DAtabase (GLIDA) is a novel public GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands, as well as access information to the various web databases regarding GPCRs. Thes...

  8. Lead-Free Piezoelectrics

    CERN Document Server

    Nahm, Sahn

    2012-01-01

    Ecological restrictions in many parts of the world are demanding the elimination of Pb from all consumer items. At this moment in the piezoelectric ceramics industry, there is no issue of more importance than the transition to lead-free materials. The goal of Lead-Free Piezoelectrics is to provide a comprehensive overview of the fundamentals and developments in the field of lead-free materials and products to leading researchers in the world. The text presents chapters on demonstrated applications of the lead-free materials, which will allow readers to conceptualize the present possibilities and will be useful for both students and professionals conducting research on ferroelectrics, piezoelectrics, smart materials, lead-free materials, and a variety of applications including sensors, actuators, ultrasonic transducers and energy harvesters.

  9. Lead Poison Detection

    Science.gov (United States)

    1976-01-01

    With NASA contracts, Whittaker Corporations Space Science division has developed an electro-optical instrument to mass screen for lead poisoning. Device is portable and detects protoporphyrin in whole blood. Free corpuscular porphyrins occur as an early effect of lead ingestion. Also detects lead in urine used to confirm blood tests. Test is inexpensive and can be applied by relatively unskilled personnel. Similar Whittaker fluorometry device called "drug screen" can measure morphine and quinine in urine much faster and cheaper than other methods.

  10. REVIEW ARTICLE:Future of Lead Chelation – Distribution and Treatment

    Directory of Open Access Journals (Sweden)

    Venkatesh Thuppil

    2012-01-01

    Full Text Available Lead is the major environmental toxin resulting in the ill health and deleterious effect on almost all organs in the human body in a slow and effective manner. The best treatment for lead poisoning is chelation therapy which is next only to prevention. The authors describe the disruption of homeostasis of the human body by lead in various tissues like blood, bones, liver, kidneys and brain; and the ability of lead to enter the cell using calcium channels and calcium receptors like Ca++ dependant K+ ion channels, transient receptor potential channels, T-tubules, calmodulin receptors, inositol trisphosphate receptors and ryanodine receptors. We report a few novel chelating agents like ionophores, decadentate ligands, picolinate ligands, octadentate ligand, allicin, thiamine, that show good potential for being used in chelation therapy. Future of leadpoisoning is a challenge to all and it needs to be meticulously studies to have an economic and health approach.

  11. Integrating structural and mutagenesis data to elucidate GPCR ligand binding

    DEFF Research Database (Denmark)

    Munk, Christian; Harpsøe, Kasper; Hauser, Alexander S

    2016-01-01

    G protein-coupled receptors (GPCRs) represent the largest family of human membrane proteins, as well as drug targets. A recent boom in GPCR structural biology has provided detailed images of receptor ligand binding sites and interactions on the molecular level. An ever-increasing number of ligands...... elucidate new GPCR ligand binding sites, and ultimately design drugs with tailored pharmacological activity....

  12. New pinene-derived pyridines as bidentate chiral ligands

    Czech Academy of Sciences Publication Activity Database

    Malkov, A. V.; Stewart-Liddon, A.; Teplý, Filip; Kobr, L.; Muir, K. W.; Haigh, D.; Kočovský, P.

    2008-01-01

    Roč. 64, č. 18 (2008), s. 4011-4025 ISSN 0040-4020 Institutional research plan: CEZ:AV0Z40550506 Keywords : chiral ligands * transition metal catalysis * asymmetric catalysis * pyridine ligands * oxazoline ligands Subject RIV: CC - Organic Chemistry Impact factor: 2.897, year: 2008

  13. Study of the spectroscopic characteristics of methyl (ligand ...

    Indian Academy of Sciences (India)

    TECS

    Abstract. Spectroscopic characterization (IR, NMR and electronic spectra) of methyl (ligand) coba- loxime was done, where ligand = pyrazole, dimethyl pyrazole, alanine and alanine methyl ester. The fre- quency changes in the IR spectra and shifts in the NMR were explained on the basis of basicity of the ligand, steric ...

  14. Equilibrium and kinetic studies on ligand substitution reactions of ...

    Indian Academy of Sciences (India)

    Unknown

    The rate constants and equilibrium constants are correlated to the hardness and softness of the ligands and the Co(III) of cobaloxime. Keywords. Alkylcobaloximes; ligand substitution reactions; hard and soft ligands. 1. Introduction. B12-based enzymes are among the few cofactors known till now contain a metal–carbon.

  15. Design and use of conditional MHC class I ligands

    NARCIS (Netherlands)

    Toebes, Mireille; Coccoris, Miriam; Bins, Adriaan; Rodenko, Boris; Gomez, Raquel; Nieuwkoop, Nella J.; van de Kasteele, Willeke; Rimmelzwaan, Guus F.; Haanen, John B. A. G.; Ovaa, Huib; Schumacher, Ton N. M.

    2006-01-01

    Major histocompatibility complex (MHC) class I molecules associate with a variety of peptide ligands during biosynthesis and present these ligands on the cell surface for recognition by cytotoxic T cells. We have designed conditional MHC ligands that form stable complexes with MHC molecules but

  16. Hydrogen exchange and ligand binding: Ligand-dependent and ligand-independent protection in the Src SH3 domain

    OpenAIRE

    Wildes, David; Marqusee, Susan

    2005-01-01

    Amide hydrogen-deuterium exchange has proven to be a powerful tool for detecting and characterizing high-energy conformations in protein ensembles. Since interactions with ligands can modulate these high-energy conformations, hydrogen exchange appears to be an ideal experimental probe of the physical mechanisms underlying processes like allosteric regulation. The chemical mechanism of hydrogen exchange, however, can complicate such studies. Here, we examine hydrogen exchange rates in a simple...

  17. Blood lead concentrations age.

    Science.gov (United States)

    Jusko, Todd A; Henderson, Charles R; Lanphear, Bruce P; Cory-Slechta, Deborah A; Parsons, Patrick J; Canfield, Richard L

    2008-02-01

    Few studies provide data directly relevant to the question of whether blood lead concentrations affect children's cognitive function. We examined the association between blood lead concentrations assessed throughout early childhood and children's IQ at 6 years of age. Children were followed from 6 months to 6 years of age, with determination of blood lead concentrations at 6, 12, 18, and 24 months, and 3, 4, 5, and 6 years of age. At 6 years of age, intelligence was assessed in 194 children using the Wechsler Preschool and Primary Scale of Intelligence-Revised. We used general linear and semiparametic models to estimate and test the association between blood lead concentration and IQ. After adjustment for maternal IQ, HOME scale scores, and other potential confounding factors, lifetime average blood lead concentration (mean = 7.2 microg/dL; median = 6.2 microg/dL) was inversely associated with Full-Scale IQ (p = 0.006) and Performance IQ scores (p = 0.002). Compared with children who had lifetime average blood lead concentrations IQ (91.3 vs. 86.4, p = 0.03). Nonlinear modeling of the peak blood lead concentration revealed an inverse association (p = 0.003) between peak blood lead levels and Full-Scale IQ down to 2.1 microg/dL, the lowest observed peak blood lead concentration in our study. Evidence from this cohort indicates that children's intellectual functioning at 6 years of age is impaired by blood lead concentrations well below 10 microg/dL, the Centers for Disease Control and Prevention definition of an elevated blood lead level.

  18. Solvent-induced synthesis of cobalt(II) coordination polymers based on a rigid ligand and flexible carboxylic acid ligands: syntheses, structures and magnetic properties.

    Science.gov (United States)

    Wang, Ting; Zhang, Chuanlei; Ju, Zemin; Zheng, Hegen

    2015-04-21

    Five new cobalt(ii) coordination architectures, {[Co(L)2(H2O)2]·2H2O·2NO3}n (), {[Co(L)(ppda)]·2H2O}n (), {[Co2(L)(ppda)2]2·H2O}n (), {[Co(L)(nba)]·5H2O}n (), and {[Co(L)(oba)]2·3H2O}n (), have been constructed from the rigid ligand L [L = 2,8-di(1H-imidazol-1-yl)dibenzofuran] and different flexible carboxylic acid ligands [H2ppda = 4,4'-(perfluoropropane-2,2-diyl)dibenzoic acid, H2nba = 4,4'-azanediyldibenzoic acid, and H2oba = 4,4'-oxydibenzoic acid]. Depending on the nature of the solvent systems, these five different coordination polymers were synthesized and characterized by single-crystal X-ray diffraction, IR, PXRD and elemental analysis. Compounds , and were obtained by a one-pot method, and then we utilized the solvent-induced effect to obtain almost pure crystals of , respectively. Compound is an infinite 1D chain which is formed by L ligands and Co atoms. Compound contains a [Co2(CO2)4] secondary building unit (SBU), and can be topologically represented as a 6-connected 2-fold interpenetrating pcu net with the point symbol of {4(12)·6(3)}. Compound can be characterized as a 4-connected sql tetragonal planar network with the point symbol of {4(4)·6(2)}. In compounds and , there is a 1D chain which is formed by flexible carboxylic acid ligands and Co atoms; then the 1D chain is linked by L ligands in the tilting direction, leading to the formation of a 2D layer. Furthermore, UV-vis, TGA and magnetic properties have been investigated in detail.

  19. Crystal structure of di-μ-chlorido-bis[dichloridobis(methanol-κOiridium(III] dihydrate: a surprisingly simple chloridoiridium(III dinuclear complex with methanol ligands

    Directory of Open Access Journals (Sweden)

    Joseph S. Merola

    2015-05-01

    Full Text Available The reaction between IrCl3·xH2O in methanol led to the formation of small amounts of the title compound, [Ir2Cl6(CH3OH4]·2H2O, which consists of two IrCl4O2 octahedra sharing an edge via chloride bridges. The molecule lies across an inversion center. Each octahedron can be envisioned as being comprised of four chloride ligands in the equatorial plane with methanol ligands in the axial positions. A lattice water molecule is strongly hydrogen-bonded to the coordinating methanol ligands and weak interactions with coordinating chloride ligands lead to the formation of a three-dimensional network. This is a surprising structure given that, while many reactions of iridium chloride hydrate are carried out in alcoholic solvents, especially methanol and ethanol, this is the first structure of a chloridoiridium compound with only methanol ligands.

  20. Human PD-1 binds differently to its human ligands: a comprehensive modeling study.

    Science.gov (United States)

    Viricel, Clement; Ahmed, Marawan; Barakat, Khaled

    2015-04-01

    Programmed death-1 (PD-1) is a potent inhibitory receptor of T cells which binds to two different ligands, namely PD-L1 and PD-L2, and upon binding, it inhibits T cell activation, differentiation, and proliferation, leading to a state of immune tolerance. Blocking these interactions recently emerged as a 'game changer' approach in immunotherapy. Despite the significant therapeutic potential of targeting the PD-1 pathway, the interaction between human PD-1 and its two human ligands is not fully understood. Current crystal structures describe the interactions of mouse PD-1 with human PD-L1 or mouse PD-L2. However, recent mutational and nuclear magnetic resonance (NMR) analyses suggest that human PD-1 binds its human ligands differently compared to their mouse counterparts. No detailed model is currently available to consistently fit these data. The lack of these accurate structures constitutes a high barrier against rationally developing more effective and safer agents targeting these interactions. Here we describe for the first time two accurate models for human PD-1 bound to its two human ligands. Our methodology involved combining molecular dynamics (MD) simulations with protein-protein docking and binding energy analysis to predict the most probable binding conformations for PD1 to its ligands. Our results confirm the available experimental NMR and mutational data and reveal the most accurate atomistic details so far of how human PD-1 binds to human PD-Ls and why the two ligands bind with different affinities to the same receptor. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. EFFECT OF LEAD ACETATE

    African Journals Online (AJOL)

    MICROSOFT

    A significant (P<0.05) increase was recorded in GPT, creatinine and uric acid levels ... chemical composition of the compound containing lead, ... their body weight. Each group comprised five chicks. Treatment. Groups A, B, C, D, E and F were treated once a day with lead acetate at a dose rate of 80, 120, 160, 200, 240 and ...

  2. Leadership, Leaders, and Leading

    Science.gov (United States)

    Dean, Peter J.

    2004-01-01

    Arguably, the most important need in society today is to create individuals who will take action positively and progressively to lead in the private organization, in the the public institution, or in the governmental agency. Leadership action should not be held hostage by the notion that only those in formal positions of leadership can lead.…

  3. Developmental immunotoxicology of lead

    International Nuclear Information System (INIS)

    Dietert, Rodney R.; Lee, Ji-Eun; Hussain, Irshad; Piepenbrink, Michael

    2004-01-01

    The heavy metal, lead, is a known developmental immunotoxicant that has been shown to produce immune alterations in humans as well as other species. Unlike many compounds that exert adverse immune effects, lead exposure at low to moderate levels does not produce widespread loss of immune cells. In contrast, changes resulting from lead exposure are subtle at the immune cell population level but, nevertheless, can be functionally dramatic. A hallmark of lead-induced immunotoxicity is a pronounced shift in the balance in T helper cell function toward T helper 2 responses at the expense of T helper 1 functions. This bias alters the nature and range of immune responses that can be produced thereby influencing host susceptibility to various diseases. Immunotoxic responses to lead appear to differ across life stages not only quantitatively with regard to dose response, but also qualitatively in terms of the spectrum of immune alterations. Experimental studies in several lab animal species suggest the latter stages of gestation are a period of considerable sensitivity for lead-induced immunotoxicity. This review describes the basic characteristics of lead-induced immunotoxicity emphasizing experimental animal results. It also provides a framework for the consideration of toxicant exposure effects across life stages. The existence of and probable basis for developmental windows of immune hyper-susceptibility are presented. Finally, the potential for lead to serve as a perinatal risk factor for childhood asthma as well as other diseases is considered

  4. Up-regulation of osteopontin expression by aryl hydrocarbon receptor via both ligand-dependent and ligand-independent pathways in lung cancer.

    Science.gov (United States)

    Chuang, Cheng-Yen; Chang, Han; Lin, Pinpin; Sun, Shih-Jung; Chen, Po-Hung; Lin, Yu-Ying; Sheu, Gwo-Tarng; Ko, Jiunn-Liang; Hsu, Shih-Lan; Chang, Jinghua Tsai

    2012-01-15

    The secreted glycol-phosphoprotein OPN not only plays important roles in immune responses and tissue remodeling but is also intimately involved in tumorigenesis. It is up-regulated in various cancers and correlated with poor prognosis. It is evident by enhancing growth and migration of cancer cells. However, the mechanisms that participate in up-regulation of OPN in lung cancer are largely unknown. Up-regulation of aryl hydrocarbon receptor (AhR), a transcription factor activated by xenobiotics, has been observed in lung cancer as well as premalignant lesions. In this study we demonstrated that AhR positively regulates OPN expression in lung cancer. We observed positive correlation of OPN and AhR expression in lung cancer specimen. Knockdown or overexpression of AhR exhibited down- or up-regulation of OPN expression in lung cancer cells. We identified an OPN promoter region between positions -268 and +435 that was activated by both ligand-independent and ligand-activated AhR. However, this region does not contain AhR response element/dioxin response element (DRE/XRE). Further truncations and internal deletions of the promoter revealed that the ligand-independent and ligand-activated AhR function through different regions of OPN promoter. The region between -268 and -100 was required for ligand-independent AhR activity. This region contains several cis-elements including AP2, C/EBP, SP1 and AP1 sites. On the other hand, the ligand-activated AhR up-regulates OPN activity through two regions of OPN promoter; one contains NFκB site at +137 and the other is between positions -100 and +126. This study suggested that both overexpression of un-induced AhR (in cases of non-smokers with high level of AhR) and ligand-activated AhR (such as smokers) contribute to up-regulation of OPN that in turn leads to lung tumorigenesis. Copyright © 2011 Elsevier B.V. All rights reserved.

  5. Complexes of .beta.-galactosidase with ligands

    Czech Academy of Sciences Publication Activity Database

    Štěpánková, Andrea; Skálová, Tereza; Dohnálek, Jan; Dušková, Jarmila; Koval, Tomáš; Hašek, Jindřich; Lipovová, P.

    2010-01-01

    Roč. 17, 1a (2010), b54 ISSN 1211-5894. [Discussions in Structural Molecular Biology /8./. 18.03.2010-20.03.2010, Nové Hrady] R&D Projects: GA ČR GA305/07/1073 Institutional research plan: CEZ:AV0Z40500505; CEZ:AV0Z10100521 Keywords : ligands * enzyme * galactosidase Subject RIV: CD - Macromolecular Chemistry

  6. Polyfluoroalkylated tripyrazolylmethane ligands: Synthesis and complexes

    Czech Academy of Sciences Publication Activity Database

    Skalická, V.; Rybáčková, M.; Skalický, M.; Kvíčalová, Magdalena; Cvačka, Josef; Březinová, Anna; Čejka, J.; Kvíčala, J.

    2011-01-01

    Roč. 132, č. 7 (2011), s. 434-440 ISSN 0022-1139 R&D Projects: GA MŠk ME 857; GA MŠk ME09114 Institutional research plan: CEZ:AV0Z40320502; CEZ:AV0Z40550506 Keywords : tripyrazolylmethane * Tpm * tripyrazolylethanol * fluorinated * perfluoroalkylation * ligand Subject RIV: CC - Organic Chemistry Impact factor: 2.033, year: 2011

  7. Organotellurium ligands – designing and complexation reactions

    Indian Academy of Sciences (India)

    Unknown

    which can be compared to the values of 82⋅0(3) and 79⋅6(3)° for Te–Pd–Te angles in the complexes 9 and 10. However in the complex 11 the ditelluroether ligand is not in meso form. The distortions from all 90° angles in the octahedron about ruthenium are apparently not equally shared between the two tellurium atoms.

  8. Displacement of aqua ligands from the hydroxopentaaquarhodium ...

    Indian Academy of Sciences (India)

    cis-Pt(NH3)2Cl2 (cisplatin) is well-known as an anti- tumour drug.1,2 However, there are still difficulties related to its use, ... Cisplatin is not very soluble in water and tends to hydrolyse at neutral pH. Replacement ... cancer agents, but some of them exhibited marked toxic effects.17,18 For certain ligands, the anation reaction.

  9. Effects of ligands on unfolding of the amyloid β-peptide central helix: mechanistic insights from molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Mika Ito

    Full Text Available Polymerization of the amyloid β-peptide (Aβ, a process which requires that the helical structure of Aβ unfolds beforehand, is suspected to cause neurodegeneration in Alzheimer's disease. According to recent experimental studies, stabilization of the Aβ central helix counteracts Aβ polymerization into toxic assemblies. The effects of two ligands (Dec-DETA and Pep1b, which were designed to bind to and stabilize the Aβ central helix, on unfolding of the Aβ central helix were investigated by molecular dynamics simulations. It was quantitatively demonstrated that the stability of the Aβ central helix is increased by both ligands, and more effectively by Pep1b than by Dec-DETA. In addition, it was shown that Dec-DETA forms parallel conformations with β-strand-like Aβ, whereas Pep1b does not and instead tends to bend unwound Aβ. The molecular dynamics results correlate well with previous experiments for these ligands, which suggest that the simulation method should be useful in predicting the effectiveness of novel ligands in stabilizing the Aβ central helix. Detailed Aβ structural changes upon loss of helicity in the presence of the ligands are also revealed, which gives further insight into which ligand may lead to which path subsequent to unwinding of the Aβ central helix.

  10. Access Path to the Ligand Binding Pocket May Play a Role in Xenobiotics Selection by AhR

    Science.gov (United States)

    Szöllősi, Dániel; Erdei, Áron; Gyimesi, Gergely; Magyar, Csaba; Hegedűs, Tamás

    2016-01-01

    Understanding of multidrug binding at the atomic level would facilitate drug design and strategies to modulate drug metabolism, including drug transport, oxidation, and conjugation. Therefore we explored the mechanism of promiscuous binding of small molecules by studying the ligand binding domain, the PAS-B domain of the aryl hydrocarbon receptor (AhR). Because of the low sequence identities of PAS domains to be used for homology modeling, structural features of the widely employed HIF-2α and a more recent suitable template, CLOCK were compared. These structures were used to build AhR PAS-B homology models. We performed molecular dynamics simulations to characterize dynamic properties of the PAS-B domain and the generated conformational ensembles were employed in in silico docking. In order to understand structural and ligand binding features we compared the stability and dynamics of the promiscuous AhR PAS-B to other PAS domains exhibiting specific interactions or no ligand binding function. Our exhaustive in silico binding studies, in which we dock a wide spectrum of ligand molecules to the conformational ensembles, suggest that ligand specificity and selection may be determined not only by the PAS-B domain itself, but also by other parts of AhR and its protein interacting partners. We propose that ligand binding pocket and access channels leading to the pocket play equally important roles in discrimination of endogenous molecules and xenobiotics. PMID:26727491

  11. Access Path to the Ligand Binding Pocket May Play a Role in Xenobiotics Selection by AhR.

    Directory of Open Access Journals (Sweden)

    Dániel Szöllősi

    Full Text Available Understanding of multidrug binding at the atomic level would facilitate drug design and strategies to modulate drug metabolism, including drug transport, oxidation, and conjugation. Therefore we explored the mechanism of promiscuous binding of small molecules by studying the ligand binding domain, the PAS-B domain of the aryl hydrocarbon receptor (AhR. Because of the low sequence identities of PAS domains to be used for homology modeling, structural features of the widely employed HIF-2α and a more recent suitable template, CLOCK were compared. These structures were used to build AhR PAS-B homology models. We performed molecular dynamics simulations to characterize dynamic properties of the PAS-B domain and the generated conformational ensembles were employed in in silico docking. In order to understand structural and ligand binding features we compared the stability and dynamics of the promiscuous AhR PAS-B to other PAS domains exhibiting specific interactions or no ligand binding function. Our exhaustive in silico binding studies, in which we dock a wide spectrum of ligand molecules to the conformational ensembles, suggest that ligand specificity and selection may be determined not only by the PAS-B domain itself, but also by other parts of AhR and its protein interacting partners. We propose that ligand binding pocket and access channels leading to the pocket play equally important roles in discrimination of endogenous molecules and xenobiotics.

  12. Access Path to the Ligand Binding Pocket May Play a Role in Xenobiotics Selection by AhR.

    Science.gov (United States)

    Szöllősi, Dániel; Erdei, Áron; Gyimesi, Gergely; Magyar, Csaba; Hegedűs, Tamás

    2016-01-01

    Understanding of multidrug binding at the atomic level would facilitate drug design and strategies to modulate drug metabolism, including drug transport, oxidation, and conjugation. Therefore we explored the mechanism of promiscuous binding of small molecules by studying the ligand binding domain, the PAS-B domain of the aryl hydrocarbon receptor (AhR). Because of the low sequence identities of PAS domains to be used for homology modeling, structural features of the widely employed HIF-2α and a more recent suitable template, CLOCK were compared. These structures were used to build AhR PAS-B homology models. We performed molecular dynamics simulations to characterize dynamic properties of the PAS-B domain and the generated conformational ensembles were employed in in silico docking. In order to understand structural and ligand binding features we compared the stability and dynamics of the promiscuous AhR PAS-B to other PAS domains exhibiting specific interactions or no ligand binding function. Our exhaustive in silico binding studies, in which we dock a wide spectrum of ligand molecules to the conformational ensembles, suggest that ligand specificity and selection may be determined not only by the PAS-B domain itself, but also by other parts of AhR and its protein interacting partners. We propose that ligand binding pocket and access channels leading to the pocket play equally important roles in discrimination of endogenous molecules and xenobiotics.

  13. Lifetime, Mobility, and Diffusion of Photoexcited Carriers in Ligand-Exchanged PbSe Nanocrystal Films Measured by Time-Resolved Terahertz Spectroscopy

    Science.gov (United States)

    Li, Siming; Guglietta, Glenn; Wu, Yaoting; Gogotsi, Natalie; Murray, Christopher; Baxter, Jason

    Colloidal semiconductor nanocrystals have been used as building blocks for electronic and optoelectronic devices ranging from field effect transistors to solar cells. Properties of the nanocrystal films depend sensitively on the choice of capping ligand to replace the insulating synthesis ligands. Thus far, ligands leading to the best performance in transistors result in poor solar cell performance, and vice versa. To understand this dichotomy, we used time-resolved terahertz spectroscopy to study the mobility and lifetime of PbSe nanocrystal films with five common ligand-exchange reagents. The films treated with different displacing ligands show more than an order of magnitude difference in the peak conductivities and a bifurcation of time-dynamics. Inorganic chalcogenide ligand-exchanges with Na2S or NH4SCN show high mobilities but nearly complete decay of transient photocurrent in 1.4 ns. In contrast, ligand exchanges with EDA, EDT, and TBAI show lower mobilities but longer lifetimes, resulting in longer diffusion lengths. This bifurcated behavior may explain the divergent performance of field-effect transistors and photovoltaics constructed from nanocrystal building blocks with different ligand exchanges. Ref: Guglietta et al., ACS Nano, 2015. NSF

  14. Lead levels - blood

    Science.gov (United States)

    Blood lead levels ... A blood sample is needed. Most of the time blood is drawn from a vein located on the inside ... may be used to puncture the skin. The blood collects in a small glass tube called a ...

  15. Lead User Innovation

    DEFF Research Database (Denmark)

    Brem, Alexander; Larsen, Henry

    2015-01-01

    User innovation and especially the integration of lead users is a key topic in the innovation management literature of recent years. This paper contributes by providing a rare perspective into what easily could be seen as innovation failure, shown from two perspectives. We show how a lack of shared...... imagination hampers participation and kills innovation between interdependent stakeholders at the threshold between invention and innovation in practice. We present a first case in the fun-sport industry where an external lead user and diverse firm representatives in different functions fail to create......, deliver and capture the value of an innovatively new device together. From the perspective of the lead user, we show antecedents and effects of social interaction between organizational actors and the lead user on the development of social capital, especially trust and shared imagination. The second case...

  16. Lead in Construction

    National Research Council Canada - National Science Library

    1993-01-01

    Although Occupational Safety and Health Administration (OSHA) regulations for occupational lead exposure have been in effect since 1971 for the construction and general industries, the agency regulations for general industry in 1978...

  17. Assessment and challenges of ligand docking into comparative models of G-protein coupled receptors.

    Directory of Open Access Journals (Sweden)

    Elizabeth Dong Nguyen

    ligand-protein contact improved sampling efficiency 7 fold. These findings offer specific guidelines which may lead to increased success in determining receptor-ligand complexes.

  18. Lead poisoning in dogs

    International Nuclear Information System (INIS)

    Zook, B.C.; Carpenter, J.L.; Leeds, E.B.

    1969-01-01

    Lead poisoning was diagnosed and studied in 60 dogs. It was found that lead poisoning is a common disease of young dogs, especially in the summer and fall, and is related to their chewing and eating habits resulting in the ingestion of paint, linoleum, or other lead-containing materials. The signs were characterized by gastrointestinal dysfunction (colic, vomiting, and diarrhea) and nervous disorders (convulsions, hysteria, nervousness, behavioral changes). The blood findings, which the authors consider nearly pathognomonic, consisted of numerous stippled and immature (especially nucleated) erythrocytes in the absence of severe anemia. Protein and casts were frequently found in the urine. Radiography sometimes revealed lead-containing particles in the gastro-intestinal tract, and lead lines were occasionally detected in the metaphysis of long bones in immature dogs. Treatment with calcium ethylenediamine-tetraacetic acid resulted in rapid and often dramatic recoveries in nearly all instances. Removal of lead from the gastrointestinal tract and treatment to relieve pronounced central nervous disorders was sometimes necessary. 40 references, 6 figures, 7 tables

  19. ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites.

    Science.gov (United States)

    Konc, Janez; Janežič, Dušanka

    2014-07-01

    The ProBiS-ligands web server predicts binding of ligands to a protein structure. Starting with a protein structure or binding site, ProBiS-ligands first identifies template proteins in the Protein Data Bank that share similar binding sites. Based on the superimpositions of the query protein and the similar binding sites found, the server then transposes the ligand structures from those sites to the query protein. Such ligand prediction supports many activities, e.g. drug repurposing. The ProBiS-ligands web server, an extension of the ProBiS web server, is open and free to all users at http://probis.cmm.ki.si/ligands. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Ligand activation of the prokaryotic pentameric ligand-gated ion channel ELIC.

    Directory of Open Access Journals (Sweden)

    Iwan Zimmermann

    2011-06-01

    Full Text Available While the pentameric ligand-gated ion channel ELIC has recently provided first insight into the architecture of the family at high resolution, its detailed investigation was so far prevented by the fact that activating ligands were unknown. Here we describe a study on the functional characterization of ELIC by electrophysiology and X-ray crystallography. ELIC is activated by a class of primary amines that include the neurotransmitter GABA at high micro- to millimolar concentrations. The ligands bind to a conserved site and evoke currents that slowly desensitize over time. The protein forms cation selective channels with properties that resemble the nicotinic acetylcholine receptor. The high single channel conductance and the comparably simple functional behavior make ELIC an attractive model system to study general mechanisms of ion conduction and gating in this important family of neurotransmitter receptors.

  1. Hydrogenation of imines catalysed by ruthenium(II) complexes based on lutidine-derived CNC pincer ligands.

    Science.gov (United States)

    Hernández-Juárez, Martín; Vaquero, Mónica; Álvarez, Eleuterio; Salazar, Verónica; Suárez, Andrés

    2013-01-14

    The preparation of new Ru(II) complexes incorporating fac-coordinated lutidine-derived CNC ligands is reported. These derivatives are selectively deprotonated by (t)BuOK at one of the methylene arms of the pincer, leading to catalytically active species in the hydrogenation of imines.

  2. The impact of Metal-Ligand Cooperation in Hydrogenation of Carbon Dioxide Catalyzed by Ruthenium PNP Pincer

    NARCIS (Netherlands)

    Filonenko, G.A.; Conley, M.P.; Copéret, C.; Lutz, M.; Hensen, E.J.M.; Pidko, E.A.

    2013-01-01

    The metal–ligand cooperative activation of CO2 with pyridine-based ruthenium PNP pincer catalysts leads to pronounced inhibition of the activity in the catalytic CO2 hydrogenation to formic acid. The addition of water restores catalytic performance by activating alternative reaction pathways and

  3. Cobalt and Nickel Complexes Bearing 2,6-Bis(imino)phenoxy Ligands:Synthesis and Ethylene Oligomerization Study

    OpenAIRE

    Du, Jian-Long; Li, Li-Jun

    2006-01-01

    A series of new cobalt and nickel complexes MLX2 (M = Co or Ni, X = Cl) bearing 2,6-bis(imino)phenoxy ligands have been synthesized. Treatment of the complexes with methylaluminoxane (MAO) leads to active catalysts for ethylene oligomerization. The oligomers are olefins from C4 to C6.

  4. Cobalt and Nickel Complexes Bearing 2,6-Bis(iminophenoxy Ligands:Synthesis and Ethylene Oligomerization Study

    Directory of Open Access Journals (Sweden)

    Jian-Long Du

    2006-01-01

    Full Text Available A series of new cobalt and nickel complexes MLX2 (M = Co or Ni, X = Cl bearing 2,6-bis(iminophenoxy ligands have been synthesized. Treatment of the complexes with methylaluminoxane (MAO leads to active catalysts for ethylene oligomerization. The oligomers are olefins from C4 to C6.

  5. Determinants of Ligand Subtype-Selectivity at α1A-Adrenoceptor Revealed Using Saturation Transfer Difference (STD) NMR.

    Science.gov (United States)

    Yong, Kelvin J; Vaid, Tasneem M; Shilling, Patrick J; Wu, Feng-Jie; Williams, Lisa M; Deluigi, Mattia; Plückthun, Andreas; Bathgate, Ross A D; Gooley, Paul R; Scott, Daniel J

    2018-03-22

    α 1A - and α 1B -adrenoceptors (α 1A -AR and α 1B -AR) are closely related G protein-coupled receptors (GPCRs) that modulate the cardiovascular and nervous systems in response to binding epinephrine and norepinephrine. The GPCR gene superfamily is made up of numerous subfamilies that, like α 1A -AR and α 1B -AR, are activated by the same endogenous agonists but may modulate different physiological processes. A major challenge in GPCR research and drug discovery is determining how compounds interact with receptors at the molecular level, especially to assist in the optimization of drug leads. Nuclear magnetic resonance spectroscopy (NMR) can provide great insight into ligand-binding epitopes, modes, and kinetics. Ideally, ligand-based NMR methods require purified, well-behaved protein samples. The instability of GPCRs upon purification in detergents, however, makes the application of NMR to study ligand binding challenging. Here, stabilized α 1A -AR and α 1B -AR variants were engineered using Cellular High-throughput Encapsulation, Solubilization, and Screening (CHESS), allowing the analysis of ligand binding with Saturation Transfer Difference NMR (STD NMR). STD NMR was used to map the binding epitopes of epinephrine and A-61603 to both receptors, revealing the molecular determinants for the selectivity of A-61603 for α 1A -AR over α 1B -AR. The use of stabilized GPCRs for ligand-observed NMR experiments will lead to a deeper understanding of binding processes and assist structure-based drug design.

  6. Direct synthesis of aqueous quantum dots through 4,4'-bipyridine-based twin ligand strategy.

    Science.gov (United States)

    Kalita, Mausam; Cingarapu, Sreeram; Roy, Santanu; Park, Seok Chan; Higgins, Daniel; Jankowiak, Ryszard; Chikan, Viktor; Klabunde, Kenneth J; Bossmann, Stefan H

    2012-04-16

    We report a new class of derivatized 4,4'-bipyridinium ligands for use in synthesizing highly fluorescent, extremely stable, water-soluble CdSe and CdTe quantum dots (QDs) for bioconjugation. We employed an evaporation-condensation technique, also known as solvated metal atom dispersion (SMAD), followed by a digestive ripening procedure. This method has been used to synthesize both metal nanoparticles and semiconductors in the gram scale with several stabilizing ligands in various solvents. The SMAD technique comprised evaporation condensation and stabilization of CdSe or CdTe in tetrahydrofuran. The as-prepared product was then digestively ripened in both water and dimethyl formamide, leading to narrowing of the particle size distributions. The ligands were synthesized by nucleophilic substitution (S(N)2) reactions using 4,4'-bipyridine as a nucleophile. Confocal microscopy images revealed the orange color of the nanocrystalline QDs with diameters of ~5 nm. The size has been confirmed by using transmission electron microscopy. As a part of our strategy, 85% of the 4,4'-bipyridinium salt was synthesized as propionic acid derivative and used to both stabilize the QDs in water and label basic amino acids and different biomarkers utilizing the carboxylic acid functional group. Fifteen percent of the 4,4'-bipyridinium salt was synthesized as N-propyl maleimide and used as a second ligand to label any protein containing the amino acid cysteine by means of a 1,4-Michael addition. © 2012 American Chemical Society

  7. Synthesis, Structures and Properties of Cobalt Thiocyanate Coordination Compounds with 4-(hydroxymethylpyridine as Co-ligand

    Directory of Open Access Journals (Sweden)

    Stefan Suckert

    2016-04-01

    Full Text Available Reaction of Co(NCS2 with 4-(hydroxymethylpyridine (hmpy leads to the formation of six new coordination compounds with the composition [Co(NCS2(hmpy4] (1, [Co(NCS2(hmpy4] × H2O (1-H2O, [Co(NCS2(hmpy2(EtOH2] (2, [Co(NCS2(hmpy2(H2O2] (3, [Co(NCS2(hmpy2]n∙4 H2O (4 and [Co(NCS2(hmpy2]n (5. They were characterized by single crystal and powder X-ray diffraction experiments, thermal and elemental analysis, IR and magnetic measurements. Compound 1 and 1-H2O form discrete complexes, in which the Co(II cations are octahedrally coordinated by two terminal thiocyanato anions and four 4-(hydroxymethylpyridine ligands. Discrete complexes were also observed for compounds 2 and 3 where two of the hmpy ligands were substituted by solvent, either water (3 or ethanol (2. In contrast, in compounds 4 and 5, the Co(II cations are linked into chains by bridging 4-(hydroxymethylpyridine ligands. The phase purity was checked with X-ray powder diffraction. Thermogravimetric measurements showed that compound 3 transforms into 5 upon heating, whereas the back transformation occurs upon resolvation. Magnetic measurements did not show any magnetic exchange via the hmpy ligand for compound 5.

  8. Differential Epitope Mapping by STD NMR Spectroscopy To Reveal the Nature of Protein-Ligand Contacts.

    Science.gov (United States)

    Monaco, Serena; Tailford, Louise E; Juge, Nathalie; Angulo, Jesus

    2017-11-27

    Saturation transfer difference (STD) NMR spectroscopy is extensively used to obtain epitope maps of ligands binding to protein receptors, thereby revealing structural details of the interaction, which is key to direct lead optimization efforts in drug discovery. However, it does not give information about the nature of the amino acids surrounding the ligand in the binding pocket. Herein, we report the development of the novel method differential epitope mapping by STD NMR (DEEP-STD NMR) for identifying the type of protein residues contacting the ligand. The method produces differential epitope maps through 1) differential frequency STD NMR and/or 2) differential solvent (D 2 O/H 2 O) STD NMR experiments. The two approaches provide different complementary information on the binding pocket. We demonstrate that DEEP-STD NMR can be used to readily obtain pharmacophore information on the protein. Furthermore, if the 3D structure of the protein is known, this information also helps in orienting the ligand in the binding pocket. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  9. Entropy-enthalpy compensation: Role and ramifications in biomolecular ligand recognition and design

    Science.gov (United States)

    Chodera, John D.; Mobley, David L.

    2014-01-01

    Recent calorimetric studies of small molecule interactions with biomolecular targets have generated renewed interest in the phenomenon of entropy-enthalpy compensation. In these studies, entropic and enthalpic contributions to binding are observed to vary substantially and in an opposing manner as the ligand or protein is modified while the binding free energy varies little. In severe examples, engineered enthalpic gains can lead to completely compensating entropic penalties, frustrating ligand design. Here, we examine the evidence for compensation, as well as its potential origins, prevalence, severity, and ramifications for ligand engineering. We find the evidence for severe compensation to be weak in light of the large magnitude of and correlation between errors in experimental measurements of entropic and enthalpic contributions to binding, though a limited form of compensation may be common. Given the difficulty of predicting or measuring entropic and enthalpic changes to useful precision, or using this information in design, we recommend ligand engineering efforts instead focus on computational and experimental methodologies to directly assess changes in binding free energy. PMID:23654303

  10. Ligand-modulated conformational switching in a fully synthetic membrane-bound receptor

    Science.gov (United States)

    Lister, Francis G. A.; Le Bailly, Bryden A. F.; Webb, Simon J.; Clayden, Jonathan

    2017-05-01

    Signal transduction through G-protein-coupled receptors (GPCRs) involves binding to signalling molecules at the cell surface, which leads to global changes in molecular conformation that are communicated through the membrane. Artificial mechanisms for communication involving ligand binding and global conformational switching have been demonstrated so far only in the solution phase. Here, we report a membrane-bound synthetic receptor that responds to binding of a ligand by undergoing a conformational change that is propagated over several nanometres, deep into the phospholipid bilayer. Our design uses a helical foldamer core, with structural features borrowed from a class of membrane-active fungal antibiotics, ligated to a water-compatible, metal-centred binding site and a conformationally responsive fluorophore. Using the fluorophore as a remote reporter of conformational change, we find that binding of specific carboxylate ligands to a Cu(II) cofactor at the binding site perturbs the foldamer's global conformation, mimicking the conformational response of a GPCR to ligand binding.

  11. Magnesium Diboride Current Leads

    Science.gov (United States)

    Panek, John

    2010-01-01

    A recently discovered superconductor, magnesium diboride (MgB2), can be used to fabricate conducting leads used in cryogenic applications. Dis covered to be superconducting in 2001, MgB2 has the advantage of remaining superconducting at higher temperatures than the previously used material, NbTi. The purpose of these leads is to provide 2 A of electricity to motors located in a 1.3 K environment. The providing environment is a relatively warm 17 K. Requirements for these leads are to survive temperature fluctuations in the 5 K and 11 K heat sinks, and not conduct excessive heat into the 1.3 K environment. Test data showed that each lead in the assembly could conduct 5 A at 4 K, which, when scaled to 17 K, still provided more than the required 2 A. The lead assembly consists of 12 steelclad MgB2 wires, a tensioned Kevlar support, a thermal heat sink interface at 4 K, and base plates. The wires are soldered to heavy copper leads at the 17 K end, and to thin copper-clad NbTi leads at the 1.3 K end. The leads were designed, fabricated, and tested at the Forschungszentrum Karlsruhe - Institut foer Technische Physik before inclusion in Goddard's XRS (X-Ray Spectrometer) instrument onboard the Astro-E2 spacecraft. A key factor is that MgB2 remains superconducting up to 30 K, which means that it does not introduce joule heating as a resistive wire would. Because the required temperature ranges are 1.3-17 K, this provides a large margin of safety. Previous designs lost superconductivity at around 8 K. The disadvantage to MgB2 is that it is a brittle ceramic, and making thin wires from it is challenging. The solution was to encase the leads in thin steel tubes for strength. Previous designs were so brittle as to risk instrument survival. MgB2 leads can be used in any cryogenic application where small currents need to be conducted at below 30 K. Because previous designs would superconduct only at up to 8 K, this new design would be ideal for the 8-30 K range.

  12. Spectrophotometric method for determination of bifunctional macrocyclic ligands in macrocyclic ligand-protein conjugates

    International Nuclear Information System (INIS)

    Dadachova, E.; Chappell, L.L.; Brechbiel, M.W.

    1999-01-01

    A simple spectrophotometric assay for determination of bifunctional polyazacarboxylate-macrocyclic ligands of different sizes that are conjugated to proteins has been developed for: 12-membered macrocycle DOTA (2-[4-nitrobenzyl]-1, 4, 7, 10-tetraazacyclododecane-N,N',N'',N'''-tetraacetic acid) and analogs, the 15-membered PEPA macrocycle (2-[4-nitrobenzyl]-1,4,7,10,13-pentaazacyclopentadecane-N,N',N'',N''',N'''' -pentaacetic acid), and the large 18-membered macrocycle HEHA (1,4,7,10,13,16-hexaazacyclooctadecane-N,N',N'',N''',N''''-hexaacetic acid). The method is based on titration of the blue-colored 1:1 Pb(II)-Arsenazo III (AAIII) complex with the polyazacarboxylate macrocyclic ligand in the concentration range of 0-2.5 μM, wherein color change occurring upon transchelation of the Pb(II) from the AAIII to the polyazamacrocyclic ligand is monitored at 656 nm. The assay is performed at ambient temperature within 20 min without any interfering interaction between the protein and Pb(II)-AA(III) complex. Thus, this method also provides a ligand-to-protein ratio (L/P ratio) that reflects the effective number of ligands per protein molecule available to radiolabeling. The method is not suitable for 14-membered TETA macrocycle (2-[4-nitrobenzyl]-1, 4, 8, 11-tetraazacyclotetradecane N,N',N'',N'''-tetraacetic acid) because of low stability constant of Pb(II)-TETA complex. The method is rapid, simple and may be customized for other polyazacarboxylate macrocyclic ligands

  13. Characterizing common substructures of ligands for GPCR protein subfamilies.

    Science.gov (United States)

    Erguner, Bekir; Hattori, Masahiro; Goto, Susumu; Kanehisa, Minoru

    2010-01-01

    The G-protein coupled receptor (GPCR) superfamily is the largest class of proteins with therapeutic value. More than 40% of present prescription drugs are GPCR ligands. The high therapeutic value of GPCR proteins and recent advancements in virtual screening methods gave rise to many virtual screening studies for GPCR ligands. However, in spite of vast amounts of research studying their functions and characteristics, 3D structures of most GPCRs are still unknown. This makes target-based virtual screenings of GPCR ligands extremely difficult, and successful virtual screening techniques rely heavily on ligand information. These virtual screening methods focus on specific features of ligands on GPCR protein level, and common features of ligands on higher levels of GPCR classification are yet to be studied. Here we extracted common substructures of GPCR ligands of GPCR protein subfamilies. We used the SIMCOMP, a graph-based chemical structure comparison program, and hierarchical clustering to reveal common substructures. We applied our method to 850 GPCR ligands and we found 53 common substructures covering 439 ligands. These substructures contribute to deeper understanding of structural features of GPCR ligands which can be used in new drug discovery methods.

  14. Mutations in G-protein coupled receptors and their ligands as the molecular cause of endocrine diseases: from mutation detection to structure-function relation-ships

    OpenAIRE

    Biebermann, Heike

    2010-01-01

    G protein coupled receptors (GPCR) are the largest family of integral membrane proteins. GPCR transmit the information of extracellular signal into the cell where they influence the activity of effector systems that in turn modulated the concentration of second messengers. Genetic variations in GPCR are the molecular cause of a variety of human diseases. Mutations could lead to inactivation of the receptors or to ligand-independent constitutive activation. Moreover mutations in ligands fo...

  15. Identification of Novel Smoothened Ligands Using Structure-Based Docking

    Science.gov (United States)

    Torosyan, Hayarpi; Parathaman, Pranavan; Irwin, John J.; Shoichet, Brian K.

    2016-01-01

    The seven transmembrane protein Smoothened is required for Hedgehog signaling during embryonic development and adult tissue homeostasis. Inappropriate activation of the Hedgehog signalling pathway leads to cancers such as basal cell carcinoma and medulloblastoma, and Smoothened inhibitors are now available clinically to treat these diseases. However, resistance to these inhibitors rapidly develops thereby limiting their efficacy. The determination of Smoothened crystal structures enables structure-based discovery of new ligands with new chemotypes that will be critical to combat resistance. In this study, we docked 3.2 million available, lead-like molecules against Smoothened, looking for those with high physical complementarity to its structure; this represents the first such campaign against the class Frizzled G-protein coupled receptor family. Twenty-one high-ranking compounds were selected for experimental testing, and four, representing three different chemotypes, were identified to antagonize Smoothened with IC50 values better than 50 μM. A screen for analogs revealed another six molecules, with IC50 values in the low micromolar range. Importantly, one of the most active of the new antagonists continued to be efficacious at the D473H mutant of Smoothened, which confers clinical resistance to the antagonist vismodegib in cancer treatment. PMID:27490099

  16. Gas cooled leads

    International Nuclear Information System (INIS)

    Shutt, R.P.; Rehak, M.L.; Hornik, K.E.

    1993-01-01

    The intent of this paper is to cover as completely as possible and in sufficient detail the topics relevant to lead design. The first part identifies the problems associated with lead design, states the mathematical formulation, and shows the results of numerical and analytical solutions. The second part presents the results of a parametric study whose object is to determine the best choice for cooling method, material, and geometry. These findings axe applied in a third part to the design of high-current leads whose end temperatures are determined from the surrounding equipment. It is found that cooling method or improved heat transfer are not critical once good heat exchange is established. The range 5 5 but extends over a large of values. Mass flow needed to prevent thermal runaway varies linearly with current above a given threshold. Below that value, the mass flow is constant with current. Transient analysis shows no evidence of hysteresis. If cooling is interrupted, the mass flow needed to restore the lead to its initially cooled state grows exponentially with the time that the lead was left without cooling

  17. Leading healthcare in complexity.

    Science.gov (United States)

    Cohn, Jeffrey

    2014-12-01

    Healthcare institutions and providers are in complexity. Networks of interconnections from relationships and technology create conditions in which interdependencies and non-linear dynamics lead to surprising, unpredictable outcomes. Previous effective approaches to leadership, focusing on top-down bureaucratic methods, are no longer effective. Leading in complexity requires leaders to accept the complexity, create an adaptive space in which innovation and creativity can flourish and then integrate the successful practices that emerge into the formal organizational structure. Several methods for doing adaptive space work will be discussed. Readers will be able to contrast traditional leadership approaches with leading in complexity. They will learn new behaviours that are required of complexity leaders, along with challenges they will face, often from other leaders within the organization.

  18. Lead toxicity in plants

    OpenAIRE

    Sharma, Pallavi; Dubey, Rama Shanker

    2005-01-01

    Contamination of soils by heavy metals is of widespread occurrence as a result of human, agricultural and industrial activities. Among heavy metals, lead is a potential pollutant that readily accumulates in soils and sediments. Although lead is not an essential element for plants, it gets easily absorbed and accumulated in different plant parts. Uptake of Pb in plants is regulated by pH, particle size and cation exchange capacity of the soils as well as by root exudation and other physico-che...

  19. Role of Acid–Base Equilibria in the Size, Shape, and Phase Control of Cesium Lead Bromide Nanocrystals

    Science.gov (United States)

    2018-01-01

    A binary ligand system composed of aliphatic carboxylic acids and primary amines of various chain lengths is commonly employed in diverse synthesis methods for CsPbBr3 nanocrystals (NCs). In this work, we have carried out a systematic study examining how the concentration of ligands (oleylamine and oleic acid) and the resulting acidity (or basicity) affects the hot-injection synthesis of CsPbBr3 NCs. We devise a general synthesis scheme for cesium lead bromide NCs which allows control over size, size distribution, shape, and phase (CsPbBr3 or Cs4PbBr6) by combining key insights on the acid–base interactions that rule this ligand system. Furthermore, our findings shed light upon the solubility of PbBr2 in this binary ligand system, and plausible mechanisms are suggested in order to understand the ligand-mediated phase control and structural stability of CsPbBr3 NCs. PMID:29381326

  20. Prediction of GPCR-Ligand Binding Using Machine Learning Algorithms

    Directory of Open Access Journals (Sweden)

    Sangmin Seo

    2018-01-01

    Full Text Available We propose a novel method that predicts binding of G-protein coupled receptors (GPCRs and ligands. The proposed method uses hub and cycle structures of ligands and amino acid motif sequences of GPCRs, rather than the 3D structure of a receptor or similarity of receptors or ligands. The experimental results show that these new features can be effective in predicting GPCR-ligand binding (average area under the curve [AUC] of 0.944, because they are thought to include hidden properties of good ligand-receptor binding. Using the proposed method, we were able to identify novel ligand-GPCR bindings, some of which are supported by several studies.

  1. The autoxidation activity of new mixed-ligand manganese and iron complexes with tripodal ligands

    NARCIS (Netherlands)

    van Gorkum, R.; Berding, J.; Tooke, D.M.; Spek, A.L.|info:eu-repo/dai/nl/156517566; Reedijk, J.; Bouwman, E.

    2007-01-01

    The activity of new manganese and iron complexes of dianionic tripodal ligands in the autoxidation of ethyl linoleate (EL) is reported. EL consumption rates were monitored using time-resolved FTIR and the degree of oligomerisation was determined by SEC. Almost all complexes showed the same trend in

  2. LASSO-ligand activity by surface similarity order: a new tool for ligand based virtual screening.

    Science.gov (United States)

    Reid, Darryl; Sadjad, Bashir S; Zsoldos, Zsolt; Simon, Aniko

    2008-01-01

    Virtual Ligand Screening (VLS) has become an integral part of the drug discovery process for many pharmaceutical companies. Ligand similarity searches provide a very powerful method of screening large databases of ligands to identify possible hits. If these hits belong to new chemotypes the method is deemed even more successful. eHiTS LASSO uses a new interacting surface point types (ISPT) molecular descriptor that is generated from the 3D structure of the ligand, but unlike most 3D descriptors it is conformation independent. Combined with a neural network machine learning technique, LASSO screens molecular databases at an ultra fast speed of 1 million structures in under 1 min on a standard PC. The results obtained from eHiTS LASSO trained on relatively small training sets of just 2, 4 or 8 actives are presented using the diverse directory of useful decoys (DUD) dataset. It is shown that over a wide range of receptor families, eHiTS LASSO is consistently able to enrich screened databases and provides scaffold hopping ability.

  3. LASSO—ligand activity by surface similarity order: a new tool for ligand based virtual screening

    Science.gov (United States)

    Reid, Darryl; Sadjad, Bashir S.; Zsoldos, Zsolt; Simon, Aniko

    2008-06-01

    Virtual Ligand Screening (VLS) has become an integral part of the drug discovery process for many pharmaceutical companies. Ligand similarity searches provide a very powerful method of screening large databases of ligands to identify possible hits. If these hits belong to new chemotypes the method is deemed even more successful. eHiTS LASSO uses a new interacting surface point types (ISPT) molecular descriptor that is generated from the 3D structure of the ligand, but unlike most 3D descriptors it is conformation independent. Combined with a neural network machine learning technique, LASSO screens molecular databases at an ultra fast speed of 1 million structures in under 1 min on a standard PC. The results obtained from eHiTS LASSO trained on relatively small training sets of just 2, 4 or 8 actives are presented using the diverse directory of useful decoys (DUD) dataset. It is shown that over a wide range of receptor families, eHiTS LASSO is consistently able to enrich screened databases and provides scaffold hopping ability.

  4. New Quinoxaline Derivatives as Potential MT1 and MT2 Receptor Ligands

    Directory of Open Access Journals (Sweden)

    Saioa Ancizu

    2012-06-01

    Full Text Available Ever since the idea arose that melatonin might promote sleep and resynchronize circadian rhythms, many research groups have centered their efforts on obtaining new melatonin receptor ligands whose pharmacophores include an aliphatic chain of variable length united to an N-alkylamide and a methoxy group (or a bioisostere, linked to a central ring. Substitution of the indole ring found in melatonin with a naphthalene or quinoline ring leads to compounds of similar affinity. The next step in this structural approximation is to introduce a quinoxaline ring (a bioisostere of the quinoline and naphthalene rings as the central nucleus of future melatoninergic ligands.

  5. Girls Leading Outward

    Science.gov (United States)

    Hamed, Heather; Reyes, Jazmin; Moceri, Dominic C.; Morana, Laura; Elias, Maurice J.

    2011-01-01

    The authors describe a program implemented in Red Bank Middle School in New Jersey to help at-risk, minority middle school girls realize their leadership potential. The GLO (Girls Leading Outward) program was developed by the Developing Safe and Civil Schools Project at Rutgers University and is facilitated by university students. Selected middle…

  6. Turning lead into gold

    DEFF Research Database (Denmark)

    Jensen, Steffen Moltrup Ernø

    For years the field of entrepreneurship has been blinded by the alchemical promise of turning lead into gold, of finding the ones most likely to become the next Branson, Zuckerberg or Gates. The promise has been created in the midst of political and scientific agendas where certain individuals...

  7. Relational Perspectives on Leading

    DEFF Research Database (Denmark)

    Relational Perspectives on Leading discusses leadership from a relational and social constructionism perspective as practiced on an everyday basis between people. The book pursues a fast growing, practice-based approach - particularly within the Anglo-Saxon parts of the world - to organization...

  8. Scientometry Leading us Astray

    Czech Academy of Sciences Publication Activity Database

    Haindl, Michal

    2010-01-01

    Roč. 2010, č. 82 (2010), s. 8-8 ISSN 0926-4981 Institutional research plan: CEZ:AV0Z10750506 Keywords : scientometry Subject RIV: BD - Theory of Information http://ercim-news.ercim.eu/en82/european-scene/ scientometry -leading-us-astray

  9. Selective engagement of G protein coupled receptor kinases (GRKs) encodes distinct functions of biased ligands

    Science.gov (United States)

    Zidar, David A.; Violin, Jonathan D.; Whalen, Erin J.; Lefkowitz, Robert J.

    2009-01-01

    CCL19 and CCL21 are endogenous agonists for the seven-transmembrane receptor CCR7. They are equally active in promoting G protein stimulation and chemotaxis. Yet, we find that they result in striking differences in activation of the G protein-coupled receptor kinase (GRK)/ß-arrestin system. CCL19 leads to robust CCR7 phosphorylation and β-arrestin2 recruitment catalyzed by both GRK3 and GRK6 whereas CCL21 activates GRK6 alone. This differential GRK activation leads to distinct functional consequences. Although each ligand leads to β-arrestin2 recruitment, only CCL19 leads to redistribution of β-arrestin2-GFP into endocytic vesicles and classical receptor desensitization. In contrast, these agonists are both capable of signaling through GRK6 and β-arrestin2 to ERK kinases. Thus, this mechanism for “ligand bias” whereby endogenous agonists activate different GRK isoforms leads to functionally distinct pools of β-arrestin. PMID:19497875

  10. Ligands hybrides : synthèse et chimie de coordination

    OpenAIRE

    Massard, Alexandre

    2011-01-01

    This manuscript deals with the synthesis of hybrids ligands and their coordination ability. The first part is dedicated to Cp-imidazole, Cp-imidazolium and Cp-phosphine ligands. Several synthetic routes have been developed to reach these mixed ligands and their coordination chemistry has been studied with titanium. In a second part, a method developed in our laboratory to synthesize phosphine-olefines was applied to obtain a phosphino-diene bearing three potential coordination sites. We have ...

  11. Functionalization of new PN ligands with steroids

    International Nuclear Information System (INIS)

    Jimenez, H.; Volkert, W.A.; Singh, P.R.; Ketring, A.R.; Katti, K.V.

    1993-01-01

    Efforts are currently underway to radiolabel steroids for possible imaging and treatment of breast cancer. The authors are exploring the ligating properties of phosphorus hydrazides to anchor radionuclides of diagnostic and therapeutic use (e.g. 99m Tc or 186 Re/ 188 Re) to estrogen and progesterone steroids which abound around breast tumor cells. The phenolic ring of estrone undergoes nucleophilic reaction with the pentavalent trichloro phosphorus sulfide (or oxide) in the presence of a weak base such as Et 3 N or pyridine. The chlorines were then substituted with hydrazine to produce the phosphorus attached steroid ligands in excellent yields. These ligands formed stable complexes with the metals at the open-quotes non-tracerclose quotes (Pd(II) and Re) and open-quotes tracerclose quotes ( 99m Tc and 109 Pd) levels. The alcohol functionalities as in 11-hydroxy progesterone and protected estradiol were also utilized with the use of a strong base LiN(SiMe 3 ) 2 and KH. Carbonyl containing steroid such as pregnenolone was directly added to a bishydrazido phosphine chelate by Schiff base coupling in a dean stark set-up. For estrone, which contains a hindered ketone, one hydrazone unit was first formed before the phosphorus chloride was introduced. C-O-P bond formation was also achieved from enolates of these ketones. By applying 2 eq of LDA or BuLi, α C-P bonding was accomplished. Structures and reactivities of these phosphorus hydrazide bound steroids are discussed

  12. Novel Somatostatin Receptor Ligands Therapies for Acromegaly

    Directory of Open Access Journals (Sweden)

    Rosa Maria Paragliola

    2018-03-01

    Full Text Available Surgery is considered the treatment of choice in acromegaly, but patients with persistent disease after surgery or in whom surgery cannot be considered require medical therapy. Somatostatin receptor ligands (SRLs octreotide (OCT, lanreotide, and the more recently approved pasireotide, characterized by a broader receptor ligand binding profile, are considered the mainstay in the medical management of acromegaly. However, in the attempt to offer a more efficacious and better tolerated medical approach, recent research has been aimed to override some limitations related to the use of currently approved drugs and novel SRLs therapies, with potential attractive features, have been proposed. These include both new formulation of older molecules and new molecules. Novel OCT formulations are aimed in particular to improve patients’ compliance and to reduce injection discomfort. They include an investigational ready-to-use subcutaneous depot OCT formulation (CAM2029, delivered via prefilled syringes and oral OCT that uses a “transient permeability enhancer” technology, which allows for OCT oral absorption. Another new delivery system is a long-lasting OCT implant (VP-003, which provide stable doses of OCT throughout a period of several months. Finally, a new SRL DG3173 (somatoprim seems to be more selective for GH secretion, suggesting possible advantages in the presence of hyperglycemia or diabetes. How much these innovations will actually be beneficial to acromegaly patients in real clinical practice remains to be seen.

  13. Crystallographic study of novel transthyretin ligands exhibiting negative-cooperativity between two thyroxine binding sites.

    Directory of Open Access Journals (Sweden)

    Divya Tomar

    Full Text Available BACKGROUND: Transthyretin (TTR is a homotetrameric serum and cerebrospinal fluid protein that transports thyroxine (T4 and retinol by binding to retinol binding protein. Rate-limiting tetramer dissociation and rapid monomer misfolding and disassembly of TTR lead to amyloid fibril formation in different tissues causing various amyloid diseases. Based on the current understanding of the pathogenesis of TTR amyloidosis, it is considered that the inhibition of amyloid fibril formation by stabilization of TTR in native tetrameric form is a viable approach for the treatment of TTR amyloidosis. METHODOLOGY AND PRINCIPAL FINDINGS: We have examined interactions of the wtTTR with a series of compounds containing various substitutions at biphenyl ether skeleton and a novel compound, previously evaluated for binding and inhibiting tetramer dissociation, by x-ray crystallographic approach. High resolution crystal structures of five ligands in complex with wtTTR provided snapshots of negatively cooperative binding of ligands in two T4 binding sites besides characterizing their binding orientations, conformations, and interactions with binding site residues. In all complexes, the ligand has better fit and more potent interactions in first T4 site i.e. (AC site than the second T4 site (BD site. Together, these results suggest that AC site is a preferred ligand binding site and retention of ordered water molecules between the dimer interfaces further stabilizes the tetramer by bridging a hydrogen bond interaction between Ser117 and its symmetric copy. CONCLUSION: Novel biphenyl ether based compounds exhibit negative-cooperativity while binding to two T4 sites which suggests that binding of only single ligand molecule is sufficient to inhibit the TTR tetramer dissociation.

  14. Discovery of Peptidomimetic Ligands of EED as Allosteric Inhibitors of PRC2

    Energy Technology Data Exchange (ETDEWEB)

    Barnash, Kimberly D.; The, Juliana; Norris-Drouin, Jacqueline L.; Cholensky, Stephanie H.; Worley, Beau M.; Li, Fengling; Stuckey, Jacob I.; Brown, Peter J.; Vedadi, Masoud; Arrowsmith, Cheryl H.; Frye, Stephen V.; James, Lindsey I. (UNC); (Toronto)

    2017-02-06

    The function of EED within polycomb repressive complex 2 (PRC2) is mediated by a complex network of protein–protein interactions. Allosteric activation of PRC2 by binding of methylated proteins to the embryonic ectoderm development (EED) aromatic cage is essential for full catalytic activity, but details of this regulation are not fully understood. EED’s recognition of the product of PRC2 activity, histone H3 lysine 27 trimethylation (H3K27me3), stimulates PRC2 methyltransferase activity at adjacent nucleosomes leading to H3K27me3 propagation and, ultimately, gene repression. By coupling combinatorial chemistry and structure-based design, we optimized a low-affinity methylated jumonji, AT-rich interactive domain 2 (Jarid2) peptide to a smaller, more potent peptidomimetic ligand (Kd = 1.14 ± 0.14 μM) of the aromatic cage of EED. Our strategy illustrates the effectiveness of applying combinatorial chemistry to achieve both ligand potency and property optimization. Furthermore, the resulting ligands, UNC5114 and UNC5115, demonstrate that targeted disruption of EED’s reader function can lead to allosteric inhibition of PRC2 catalytic activity.

  15. Nanomolar anti-sickling compounds identified by ligand-based pharmacophore approach.

    Science.gov (United States)

    Paz, Odailson Santos; de Jesus Pinheiro, Milena; do Espirito Santo, Renan Fernandes; Villarreal, Cristiane Flora; Castilho, Marcelo Santos

    2017-08-18

    Adenosine receptors are considered as potential targets for drug development against several diseases. The discovery of subtype 2B adenosine receptors role in erythrocyte sickling process proved its importance to neglected diseases such as sickle cell anemia, which affects approximately 29.000 people around the world, but whose treatment is restricted to just one FDA approved drug (hydroxyurea). In order to widen the therapeutic arsenal available to treat sickle cell anemia patients, it is imperative to identify new lead compounds that modify the sickling course and not just its symptoms. In order to accomplish this goal, ligand-based pharmacophore models that differentiate true ligands from decoys and enlighten the structure-activity relationship of known RA2B antagonists were employed screen the lead-like subset of the ZINC database. Following a chemical diversity analysis, 18 compounds were selected for biological evaluation. Among them, one molecule Z1139491704 (pEC50 = 7.77 ± 0.17) has shown better anti-sickling activity than MRS1754 (pEC50 = 7.63 ± 0.12), a commercial RA2B antagonist. Moreover, these compounds exhibited no cytotoxic effect at low micromolar range on mammalian cells. In conclusion, the sound development of validated ligand-based pharmacophore models proved essential to identify novel chemical scaffolds that might be useful to develop anti-sickling drugs. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  16. Treatment of autoimmune inflammation by a TLR7 ligand regulating the innate immune system.

    Directory of Open Access Journals (Sweden)

    Tomoko Hayashi

    Full Text Available The Toll-like receptors (TLR have been advocated as attractive therapeutic targets because TLR signaling plays dual roles in initiating adaptive immune responses and perpetuating inflammation. Paradoxically, repeated stimulation of bone marrow mononuclear cells with a synthetic TLR7 ligand 9-benzyl-8-hydroxy-2-(2-methoxyethoxy adenine (called 1V136 leads to subsequent TLR hyporesponsiveness. Further studies on the mechanism of action of this pharmacologic agent demonstrated that the TLR7 ligand treatment depressed dendritic cell activation, but did not directly affect T cell function. To verify this mechanism, we utilized experimental allergic encephalitis (EAE as an in vivo T cell dependent autoimmune model. Drug treated SJL/J mice immunized with proteolipid protein (PLP(139-151 peptide had attenuated disease severity, reduced accumulation of mononuclear cells in the central nervous system (CNS, and limited demyelination, without any apparent systemic toxicity. Splenic T cells from treated mice produced less cytokines upon antigenic rechallenge. In the spinal cords of 1V136-treated EAE mice, the expression of chemoattractants was also reduced, suggesting innate immune cell hyposensitization in the CNS. Indeed, systemic 1V136 did penetrate the CNS. These experiments indicated that repeated doses of a TLR7 ligand may desensitize dendritic cells in lymphoid organs, leading to diminished T cell responses. This treatment strategy might be a new modality to treat T cell mediated autoimmune diseases.

  17. Design of targeting ligands in medicinal inorganic chemistry.

    Science.gov (United States)

    Storr, Tim; Thompson, Katherine H; Orvig, Chris

    2006-06-01

    This tutorial review will highlight recent advances in medicinal inorganic chemistry pertaining to the use of multifunctional ligands for enhanced effect. Ligands that adequately bind metal ions and also include specific targeting features are gaining in popularity due to their ability to enhance the efficacy of less complicated metal-based agents. Moving beyond the traditional view of ligands modifying reactivity, stabilizing specific oxidation states, and contributing to substitution inertness, we will discuss recent work involving metal complexes with multifunctional ligands that target specific tissues, membrane receptors, or endogenous molecules, including enzymes.

  18. Competitive antagonism of AMPA receptors by ligands of different classes

    DEFF Research Database (Denmark)

    Hogner, Anders; Greenwood, Jeremy R; Liljefors, Tommy

    2003-01-01

    that ATPO and DNQX stabilize an open form of the ligand-binding core by different sets of interactions. Computational techniques are used to quantify the differences between these two ligands and to map the binding site. The isoxazole moiety of ATPO acts primarily as a spacer, and other scaffolds could......-(phosphonomethoxy)-4-isoxazolyl]propionic acid (ATPO) in complex with the ligand-binding core of the receptor. Comparison with the only previous structure of the ligand-binding core in complex with an antagonist, 6,7-dinitro-2,3-quinoxalinedione (DNQX) (Armstrong, N.; Gouaux, E. Neuron 2000, 28, 165-181), reveals...

  19. Biased ligands: pathway validation for novel GPCR therapeutics.

    Science.gov (United States)

    Rominger, David H; Cowan, Conrad L; Gowen-MacDonald, William; Violin, Jonathan D

    2014-06-01

    G protein-coupled receptors (GPCRs), in recent years, have been shown to signal via multiple distinct pathways. Furthermore, biased ligands for some receptors can differentially stimulate or inhibit these pathways versus unbiased endogenous ligands or drugs. Biased ligands can be used to gain a deeper understanding of the molecular targets and cellular responses associated with a GPCR, and may be developed into therapeutics with improved efficacy, safety and/or tolerability. Here we review examples and approaches to pathway validation that establish the relevance and therapeutic potential of distinct pathways that can be selectively activated or blocked by biased ligands. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. Ligand-controlled Fe mobilization catalyzed by adsorbed Fe(II) on Fe(hydr)oxides

    Science.gov (United States)

    Kang, Kyounglim; Biswakarma, Jagannath; Borowski, Susan C.; Hug, Stephan J.; Hering, Janet G.; Schenkeveld, Walter D. C.; Kraemer, Stephan M.

    2017-04-01

    Dissolution of Fe(hydr)oxides is a key process in biological iron acquisition. Due to the low solubility of iron oxides in environments with a circumneutral pH, organisms may exude organic compounds catalyzing iron mobilization by reductive and ligand controlled dissolution mechanisms. Recently, we have shown synergistic effects between reductive dissolution and ligand-controlled dissolution that may operate in biological iron acquisition. The synergistic effects were observed in Fe mobilization from single goethite suspensions as well as in suspensions containing calcareous soil[1],[2]. However, how the redox reaction accelerates Fe(hydr)oxide dissolution by ligands is not studied intensively. In our study, we hypothesized that electron transfer to structural Fe(III) labilizes the Fe(hydr)oxide structure, and that this can accelerate ligand controlled dissolution. Systematical batch dissolution experiments were carried out under anoxic conditions at environmentally relevant pH values in which various Fe(hydr)oxides (goethite, hematite, lepidocrocite) interacted with two different types of ligand (desferrioxamine B (DFOB) and N,N'-Di(2-hydroxybenzyl)ethylenediamine-N,N'-diacetic acid monohydrochloride (HBED)). Electron transfer to the structure was induced by adsorbing Fe(II) to the mineral surface at various Fe(II) concentrations. Our results show a distinct catalytic effect of adsorbed Fe(II) on ligand controlled dissolution, even at submicromolar Fe(II) concentrations. We observed the effect for a range of iron oxides, but it was strongest in lepidocrocite, most likely due to anisotropy in conductivity leading to higher near-surface concentration of reduced iron. Our results demonstrate that the catalytic effect of reductive processes on ligand controlled dissolution require a very low degree of reduction making this an efficient process for biological iron acquisition and a potentially important effect in natural iron cycling. References 1. Wang, Z. M

  1. LEAD SEVERING CONTRIVANCE

    Science.gov (United States)

    Widmaier, W.

    1958-04-01

    A means for breaking an electrical circuit within an electronic tube during the process of manufacture is described. Frequently such circuits must be employed for gettering or vapor coating purposes, however, since an external pair of corector pins having no use after manufacture, is undesirable, this invention permits the use of existing leads to form a temporary circuit during manufacture, and severing it thereafter. One portion of the temporary circuit, made from a springy material such as tungsten, is spot welded to a fusable member. To cut the circuit an external radiant heat source melts the fusable member, allowing the tensed tungsten spring to contract and break the circuit. This inexpensive arrangement is particularly useful when the tube has a great many external leads crowded into the tube base.

  2. CMS lead tungstate crystals

    CERN Multimedia

    Laurent Guiraud

    2000-01-01

    These crystals are made from lead tungstate, a crystal that is as clear as glass yet with nearly four times the density. They have been produced in Russia to be used as scintillators in the electromagnetic calorimeter on the CMS experiment, part of the LHC project at CERN. When an electron, positron or photon passes through the calorimeter it will cause a cascade of particles that will then be absorbed by these scintillating crystals, allowing the particle's energy to be measured.

  3. Design, synthesis, and cocrystal structure of a nonpeptide Src SH2 domain ligand.

    Science.gov (United States)

    Plummer, M S; Holland, D R; Shahripour, A; Lunney, E A; Fergus, J H; Marks, J S; McConnell, P; Mueller, W T; Sawyer, T K

    1997-11-07

    The specific association of an SH2 domain with a phosphotyrosine (pTyr)-containing sequence of another protein precipitates a cascade of intracellular molecular interactions (signals) which effect a wide range of intracellular processes. The nonreceptor tyrosine kinase Src, which has been associated with breast cancer and osteoporosis, contains an SH2 domain. Inhibition of Src SH2-phosphoprotein interactions by small molecules will aid biological proof-of-concept studies which may lead to the development of novel therapeutic agents. Structure-based design efforts have focused on reducing the size and charge of Src SH2 ligands while increasing their ability to penetrate cells and reach the intracellular Src SH2 domain target. In this report we describe the synthesis, binding affinity, and Src SH2 cocrystal structure of a small, novel, nonpeptide, urea-containing SH2 domain ligand.

  4. Synthesis and Doping of Ligand-Protected Atomically-Precise Metal Nanoclusters

    KAUST Repository

    Aljuhani, Maha A.

    2016-05-01

    Rapidly expanding research in nanotechnology has led to exciting progress in a versatile array of applications from medical diagnostics to catalysis. This success resulted from the manipulation of the desired properties of nanomaterials by controlling their size, shape, and composition. Among the most thriving areas of research about nanoparticle is the synthesis and doping of the ligand-protected atomically-precise metal nanoclusters. In this thesis, we developed three different novel metal nanoclusters, such as doped Ag29 with five gold (Au) atoms leading to enhance its quantum yield with remarkable stability. We also developed half-doped (alloyed) cluster of Ni6 nanocluster with molybdenum (Mo). This enabled enhanced stability and better catalytic activity. The third metal nanocluster that we synthesized was Au28 nanocluster by using di-thiolate as the ligand stabilizer instead of mono-thiolate. The new metal clusters obtained have been characterized by spectroscopic, electrochemical and crystallographic methods.

  5. Comparative analysis of machine learning methods in ligand-based virtual screening of large compound libraries.

    Science.gov (United States)

    Ma, Xiao H; Jia, Jia; Zhu, Feng; Xue, Ying; Li, Ze R; Chen, Yu Z

    2009-05-01

    Machine learning methods have been explored as ligand-based virtual screening tools for facilitating drug lead discovery. These methods predict compounds of specific pharmacodynamic, pharmacokinetic or toxicological properties based on their structure-derived structural and physicochemical properties. Increasing attention has been directed at these methods because of their capability in predicting compounds of diverse structures and complex structure-activity relationships without requiring the knowledge of target 3D structure. This article reviews current progresses in using machine learning methods for virtual screening of pharmacodynamically active compounds from large compound libraries, and analyzes and compares the reported performances of machine learning tools with those of structure-based and other ligand-based (such as pharmacophore and clustering) virtual screening methods. The feasibility to improve the performance of machine learning methods in screening large libraries is discussed.

  6. Protozoacidal Trojan-Horse: use of a ligand-lytic peptide for selective destruction of symbiotic protozoa within termite guts.

    Science.gov (United States)

    Sethi, Amit; Delatte, Jennifer; Foil, Lane; Husseneder, Claudia

    2014-01-01

    For novel biotechnology-based termite control, we developed a cellulose bait containing freeze-dried genetically engineered yeast which expresses a protozoacidal lytic peptide attached to a protozoa-recognizing ligand. The yeast acts as a 'Trojan-Horse' that kills the cellulose-digesting protozoa in the termite gut, which leads to the death of termites, presumably due to inefficient cellulose digestion. The ligand targets the lytic peptide specifically to protozoa, thereby increasing its protozoacidal efficiency while protecting non-target organisms. After ingestion of the bait, the yeast propagates in the termite's gut and is spread throughout the termite colony via social interactions. This novel paratransgenesis-based strategy could be a good supplement for current termite control using fortified biological control agents in addition to chemical insecticides. Moreover, this ligand-lytic peptide system could be used for drug development to selectively target disease-causing protozoa in humans or other vertebrates.

  7. Unique contributions of an arginine side chain to ligand recognition in a glutamate-gated chloride channel

    DEFF Research Database (Denmark)

    Lynagh, Timothy; Komnatnyy, Vitaly V; Pless, Stephan A

    2017-01-01

    Glutamate recognition by neurotransmitter receptors often relies on arginine (Arg) residues in the binding site, leading to the assumption that charge-charge interactions underlie ligand recognition. However, assessing the precise chemical contribution of Arg side chains to protein function...... and pharmacology has proven to be exceedingly difficult in such large and complex proteins. Using the in vivo nonsense suppression approach, we report the first successful incorporation of the isosteric, titratable Arg analog, canavanine, into a neurotransmitter receptor in a living cell, utilizing a glutamate......-gated chloride channel from the nematode Haemonchus contortus. Our data unveil a surprisingly small contribution of charge at a conserved arginine side chain previously suggested to form a salt bridge with the ligand, glutamate. Instead, our data show that Arg contributes crucially to ligand sensitivity via...

  8. Comparing and combining implicit ligand sampling with multiple steered molecular dynamics to study ligand migration processes in heme proteins.

    Science.gov (United States)

    Forti, Flavio; Boechi, Leonardo; Estrin, Dario A; Marti, Marcelo A

    2011-07-30

    The ubiquitous heme proteins perform a wide variety of tasks that rely on the subtle regulation of their affinity for small ligands like O2, CO, and NO. Ligand affinity is characterized by kinetic association and dissociation rate constants, that partially depend on ligand migration between the solvent and active site, mediated by the presence of internal cavities or tunnels. Different computational methods have been developed to study these processes which can be roughly divided in two strategies: those costly methods in which the ligand is treated explicitly during the simulations, and the free energy landscape of the process is computed; and those faster methods that use prior computed Molecular Dynamics simulation without the ligand, and incorporate it afterwards, called implicit ligand sampling (ILS) methods. To compare both approaches performance and to provide a combined protocol to study ligand migration in heme proteins, we performed ILS and multiple steered molecular dynamics (MSMD) free energy calculations of the ligand migration process in three representative and well theoretically and experimentally studied cases that cover a wide range of complex situations presenting a challenging benchmark for the aim of the present work. Our results show that ILS provides a good description of the tunnel topology and a reasonable approximation to the free energy landscape, while MSMD provides more accurate and detailed free energy profile description of each tunnel. Based on these results, a combined strategy is presented for the study of internal ligand migration in heme proteins. Copyright © 2011 Wiley Periodicals, Inc.

  9. Calculating the mean time to capture for tethered ligands and its effect on the chemical equilibrium of bound ligand pairs.

    Science.gov (United States)

    Shen, Lu; Decker, Caitlin G; Maynard, Heather D; Levine, Alex J

    2016-09-01

    We present here the calculation of the mean time to capture of a tethered ligand to the receptor. This calculation is then used to determine the shift in the partitioning between (1) free, (2) singly bound, and (3) doubly bound ligands in chemical equilibrium as a function of the length of the tether. These calculations are used in the research article Fibroblast Growth Factor 2 Dimer with Superagonist in vitro Activity Improves Granulation Tissue Formation During Wound Healing (Decker et al., in press [1]) to explain quantitatively how changes in polymeric linker length in the ligand dimers modifies the efficacy of these molecules relative to that of free ligands.

  10. Process of Fragment-Based Lead Discovery—A Perspective from NMR

    Directory of Open Access Journals (Sweden)

    Rongsheng Ma

    2016-07-01

    Full Text Available Fragment-based lead discovery (FBLD has proven fruitful during the past two decades for a variety of targets, even challenging protein–protein interaction (PPI systems. Nuclear magnetic resonance (NMR spectroscopy plays a vital role, from initial fragment-based screening to lead generation, because of its power to probe the intrinsically weak interactions between targets and low-molecular-weight fragments. Here, we review the NMR FBLD process from initial library construction to lead generation. We describe technical aspects regarding fragment library design, ligand- and protein-observed screening, and protein–ligand structure model generation. For weak binders, the initial hit-to-lead evolution can be guided by structural information retrieved from NMR spectroscopy, including chemical shift perturbation, transferred pseudocontact shifts, and paramagnetic relaxation enhancement. This perspective examines structure-guided optimization from weak fragment screening hits to potent leads for challenging PPI targets.

  11. Synthesis, spectroscopic studies and inhibitory activity against bactria and fungi of acyclic and macrocyclic transition metal complexes containing a triamine coumarine Schiff base ligand

    Science.gov (United States)

    Abou-Hussein, A. A.; Linert, Wolfgang

    2015-04-01

    Two series of new mono and binuclear complexes with a Schiff base ligand derived from the condensation of 3-acetylcoumarine and diethylenetriamine, in the molar ratio 2:1 have been prepared. The ligand was characterized by elemental analysis, IR, UV-visible, 1H-NMR and mass spectra. The reaction of the Schiff base ligand with cobalt(II), nickel(II), copper(II), zinc(II) and oxovanadium(IV) lead to mono or binuclear species of cyclic or macrocyclic complexes, depending on the mole ratio of metal to ligand and as well as on the method of preparation. The Schiff base ligand behaves as a cyclic bidentate, tetradendate or pentaentadentae ligand. The formation of macrocyclic complexes depends significantly on the dimension of the internal cavity, the rigidity of the macrocycles, the nature of its donor atoms and on the complexing properties of the anion involved in the coordination. Electronic spectra and magnetic moments of the complexes indicate that the geometries of the metal centers are either square pyramidal or octahedral for acyclic or macro-cyclic complexes. The structures are consistent with the IR, UV-visible, ESR, 1H-NMR, mass spectra as well as conductivity and magnetic moment measurements. The Schiff base ligand and its metal complexes were tested against two pathogenic bacteria as Gram-positive and Gram-negative bacteria as well as one kind of fungi. Most of the complexes exhibit mild antibacterial and antifungal activities against these organisms.

  12. Identification of cinnabarinic acid as a novel endogenous aryl hydrocarbon receptor ligand that drives IL-22 production.

    Directory of Open Access Journals (Sweden)

    Margaret M Lowe

    Full Text Available The aryl hydrocarbon receptor (AHR binds to environmental toxicants including synthetic halogenated aromatic hydrocarbons and is involved in a diverse array of biological processes. Recently, the AHR was shown to control host immunity by affecting the balance between inflammatory T cells that produce IL-17 (Th17 and IL-22 versus regulatory T cells (Treg involved in tolerance. While environmental AHR ligands can mediate this effect, endogenous ligands are likely to be more relevant in host immune responses. We investigated downstream metabolites of tryptophan as potential AHR ligands because (1 tryptophan metabolites have been implicated in regulating the balance between Th17 and Treg cells and (2 many of the AHR ligands identified thus far are derivatives of tryptophan. We characterized the ability of tryptophan metabolites to bind and activate the AHR and to increase IL-22 production in human T cells. We report that the tryptophan metabolite, cinnabarinic acid (CA, is an AHR ligand that stimulates the differentiation of human and mouse T cells producing IL-22. We compare the IL-22-stimulating activity of CA to that of other tryptophan metabolites and define stimulation conditions that lead to CA production from immune cells. Our findings link tryptophan metabolism to AHR activation and define a novel endogenous AHR agonist with potentially broad biological functions.

  13. Identification of cinnabarinic acid as a novel endogenous aryl hydrocarbon receptor ligand that drives IL-22 production.

    Science.gov (United States)

    Lowe, Margaret M; Mold, Jeff E; Kanwar, Bittoo; Huang, Yong; Louie, Alexander; Pollastri, Michael P; Wang, Cuihua; Patel, Gautam; Franks, Diana G; Schlezinger, Jennifer; Sherr, David H; Silverstone, Allen E; Hahn, Mark E; McCune, Joseph M

    2014-01-01

    The aryl hydrocarbon receptor (AHR) binds to environmental toxicants including synthetic halogenated aromatic hydrocarbons and is involved in a diverse array of biological processes. Recently, the AHR was shown to control host immunity by affecting the balance between inflammatory T cells that produce IL-17 (Th17) and IL-22 versus regulatory T cells (Treg) involved in tolerance. While environmental AHR ligands can mediate this effect, endogenous ligands are likely to be more relevant in host immune responses. We investigated downstream metabolites of tryptophan as potential AHR ligands because (1) tryptophan metabolites have been implicated in regulating the balance between Th17 and Treg cells and (2) many of the AHR ligands identified thus far are derivatives of tryptophan. We characterized the ability of tryptophan metabolites to bind and activate the AHR and to increase IL-22 production in human T cells. We report that the tryptophan metabolite, cinnabarinic acid (CA), is an AHR ligand that stimulates the differentiation of human and mouse T cells producing IL-22. We compare the IL-22-stimulating activity of CA to that of other tryptophan metabolites and define stimulation conditions that lead to CA production from immune cells. Our findings link tryptophan metabolism to AHR activation and define a novel endogenous AHR agonist with potentially broad biological functions.

  14. Programmed Death-Ligand 1 Immunohistochemistry Testing

    DEFF Research Database (Denmark)

    Büttner, Reinhard; Gosney, John R; Skov, Birgit Guldhammer

    2017-01-01

    Purpose Three programmed death-1/programmed death-ligand 1 (PD-L1) inhibitors are currently approved for treatment of non-small-cell lung cancer (NSCLC). Treatment with pembrolizumab in NSCLC requires PD-L1 immunohistochemistry (IHC) testing. Nivolumab and atezolizumab are approved without PD-L1...... testing, though US Food and Drug Administration-cleared complementary PD-L1 tests are available for both. PD-L1 IHC assays used to assess PD-L1 expression in patients treated with programmed death-1/PD-L1 inhibitors in clinical trials include PD-L1 IHC 28-8 pharmDx (28-8), PD-L1 IHC 22C3 pharmDx (22C3...

  15. Lead diffusion in monazite

    International Nuclear Information System (INIS)

    Gardes, E.

    2006-06-01

    Proper knowledge of the diffusion rates of lead in monazite is necessary to understand the U-Th-Pb age anomalies of this mineral, which is one of the most used in geochronology after zircon. Diffusion experiments were performed in NdPO 4 monocrystals and in Nd 0.66 Ca 0.17 Th 0.17 PO 4 polycrystals from Nd 0.66 Pb 0.17 Th 0.17 PO 4 thin films to investigate Pb 2+ + Th 4+ ↔ 2 Nd 3+ and Pb 2+ ↔ Ca 2+ exchanges. Diffusion annealings were run between 1200 and 1500 Celsius degrees, at room pressure, for durations ranging from one hour to one month. The diffusion profiles were analysed using TEM (transmission electronic microscopy) and RBS (Rutherford backscattering spectroscopy). The diffusivities extracted for Pb 2+ + Th 4+ ↔ 2 Nd 3+ exchange follow an Arrhenius law with parameters E equals 509 ± 24 kJ mol -1 and log(D 0 (m 2 s -1 )) equals -3.41 ± 0.77. Preliminary data for Pb 2+ ↔ Ca 2+ exchange are in agreement with this result. The extrapolation of our data to crustal temperatures yields very slow diffusivities. For instance, the time necessary for a 50 μm grain to lose all of its lead at 800 Celsius degrees is greater than the age of the Earth. From these results and other evidence from the literature, we conclude that most of the perturbations in U-Th-Pb ages of monazite cannot be attributed to lead diffusion, but rather to interactions with fluids. (author)

  16. Leading change: 2--planning.

    Science.gov (United States)

    Kerridge, Joanna

    National initiatives have outlined the importance of involving frontline staff in service improvement, and the ability to influence and manage change has been identified as an essential skill for delivering new models of care. Nurses often have to take the lead in managing change in clinical practice. The second in a three-part series is designed to help nurses at all levels develop the knowledge and skills to function as change agents within their organisations. This article focuses on planning the change and dealing with resistance.

  17. lead glass brick

    CERN Multimedia

    When you look through the glass at a picture behind, the picture appears raised up because light is slowed down in the dense glass. It is this density (4.06 gcm-3) that makes lead glass attractive to physicists. The refractive index of the glass is 1.708 at 400nm (violet light), meaning that light travels in the glass at about 58% its normal speed. At CERN, the OPAL detector uses some 12000 blocks of glass like this to measure particle energies.

  18. From three-dimensional GPCR structure to rational ligand discovery

    NARCIS (Netherlands)

    Kooistra, A.J.; Leurs, R.; de Esch, I.J.P.; de Graaf, C.

    2014-01-01

    This chapter will focus on G protein-coupled receptor structure-based virtual screening and ligand design. A generic virtual screening workflow and its individual elements will be introduced, covering amongst others the use of experimental data to steer the virtual screening process, ligand binding

  19. GLIDA: GPCR-ligand database for chemical genomic drug discovery.

    Science.gov (United States)

    Okuno, Yasushi; Yang, Jiyoon; Taneishi, Kei; Yabuuchi, Hiroaki; Tsujimoto, Gozoh

    2006-01-01

    G-protein coupled receptors (GPCRs) represent one of the most important families of drug targets in pharmaceutical development. GPCR-LIgand DAtabase (GLIDA) is a novel public GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands, as well as access information to the various web databases regarding GPCRs. These data are connected with each other in a relational database, allowing users in the field of GPCR-related drug discovery to easily retrieve such information from either biological or chemical starting points. GLIDA includes structure similarity search functions for the GPCRs and for their ligands. Thus, GLIDA can provide correlation maps linking the searched homologous GPCRs (or ligands) with their ligands (or GPCRs). By analyzing the correlation patterns between GPCRs and ligands, we can gain more detailed knowledge about their interactions and improve drug design efforts by focusing on inferred candidates for GPCR-specific drugs. GLIDA is publicly available at http://gdds.pharm.kyoto-u.ac.jp:8081/glida. We hope that it will prove very useful for chemical genomic research and GPCR-related drug discovery.

  20. Immobilisation of ligands by radio-derivatized polymers

    International Nuclear Information System (INIS)

    Varga, J.M.; Fritsch, P.

    1995-01-01

    The invention relates to radio-derivatized polymers and a method of producing them by contacting non-polymerizable conjugands with radiolysable polymers in the presence of irradiation. The resulting radio-derivatized polymers can be further linked with ligand of organic or inorganic nature to immobilize such ligands. 2 figs., 5 tabs

  1. The Evaluation of Novel Camphor-derived Pyridyl Ligands as ...

    African Journals Online (AJOL)

    NJD

    2009-03-03

    Mar 3, 2009 ... group in the field of chiral synthesis and catalytic applications. The first paper involved the synthesis of pentacycloundecane oxazolines and the application of the ligands in an asymmetric. Diels-Alder reaction.1 The second paper made use of camphor- derived ligands in the chiral alkylation of aldehydes ...

  2. Synthesis of meta-substituted monodentate phosphinite ligands and ...

    Indian Academy of Sciences (India)

    SATEJ S DESHMUKH

    and a variety of ligands have been employed to tame the metal.1 Among the wide array of ligands, applica- ... cations in a variety of metal catalyzed transformations as depicted in Figure 1. Notable among these are .... was quenched with water, and organic layer was extracted with ethyl acetate (three times). The combined ...

  3. Mixed-Ligand Complexes Of Nickel (II) With 2-Acetylpyridine ...

    African Journals Online (AJOL)

    The preparation and spectral properties of five nickel (II) mixed-ligands complexes (Ni [2-Actsc.Y]CI2), derived from 2-acetylpyridinethiosermicarbazones and some nitrogen/sulphur monodentate ligands such as thiophene, ammonia, picoline, pyridine and aniline are described. The complexes have been characterized on ...

  4. Kinetics and mechanism of interaction of some bioactive ligands ...

    Indian Academy of Sciences (India)

    The rate constants increase with increasing ligand concentration and the evaluated activation parameters for all reactions suggest an associative substitution mechanism for both the aqua ligand substitution processes. The product of the reaction has been characterized by IR, NMR and ESI-MS spectral analysis; which ...

  5. a review of cyclopentadienyl type ligands in group 4 metallocene

    African Journals Online (AJOL)

    Neil Grimmer

    4. TiCl. Cl. 3. M. M=Ti 1. =Zr 2. Cl. Cl. 2. The Nature of Metallocene Catalysts. Before we commence the discussion of how metallocene ligand design has evolved, .... The use of kinetic isotope effects to probe the polymerisation mechanism, first ...... Here the size of a ligand is measured as a function of distance from the point.

  6. Partial association of restriction polymorphism of the ligand binding ...

    African Journals Online (AJOL)

    Partial association of restriction polymorphism of the ligand binding domain of human androgen receptor in prostate cancer. ... Background: Human androgen receptor (AR) functions as a steroid-hormone activated transcription factor. The receptor binds to its ligand (testosterone or dihydrotestosterone) and is translocated to ...

  7. Lanthanide(III) complexes with tridentate Schiff base ligand ...

    African Journals Online (AJOL)

    The X-ray study reveals isotopic Nd/Sm binuclear structures were each metal ion is nine-coordinated in the same fashion. Both metal centers have distorted tricapped trigonal prism geometry, with the Schiff base acting as tridentate ligand. The DPPH· radical scavenging effects of the Schiff base ligand and its Ln(III) ...

  8. Kinetics and Mechanism of the Ligand Exchange Reaction Between ...

    African Journals Online (AJOL)

    NICO

    Visible spectrophotometry is used to study the kinetics of ligand exchange in the system Ni(salpn)/H2salen with or without triethylamine ... rate of the ligand exchange reaction was accelerated by adding NEt3 to the reaction mixture. However, the ..... 0.05 M. The increase of the reaction rate at low [H2O] could be due to the ...

  9. Synthesis of meta-substituted monodentate phosphinite ligands and ...

    Indian Academy of Sciences (India)

    To demonstrate the synthetic usefulness of 4a and 4b, these ligands were tested in the rhodium catalyzed hydroformylation of 1-octene. The diethylamine substituted ligand 4a was found to be highly active, whereas4bwas less reactive but revealed slightly better regioselectivity of 62% under optimized conditions.

  10. The Evaluation of Novel Camphor-derived Pyridyl Ligands as ...

    African Journals Online (AJOL)

    A series of camphor-derived pyridyl ligands were evaluated in the Diels-Alder reaction of 3-acryloyl-2-oxazolidinone 1 with cyclopentadiene 2. High yields with good endo:exo selectivity, but only moderate enantioselectivities (43 % ee), were obtained. The structures of the copper (II) complexes of the ligands were ...

  11. THERMODYNAMICS OF PROTEIN-LIGAND INTERACTIONS AND THEIR ANALYSIS

    Directory of Open Access Journals (Sweden)

    Rummi Devi Saini

    2017-11-01

    Full Text Available Physiological processes are controlled mainly by intermolecular recognition mechanisms which involve protein–protein and protein–ligand interactions with a high specificity and affinity to form a specific complex. Proteins being an important class of macromolecules in biological systems, it is important to understand their actions through binding to other molecules of proteins or ligands. In fact, the binding of low molecular weight ligands to proteins plays a significant role in regulating biological processes such as cellular metabolism and signal transmission. Therefore knowledge of the protein–ligand interactions and the knowledge of the mechanisms involved in the protein-ligand recognition and binding are key in understanding biology at molecular level which will facilitate the discovery, design, and development of drugs. In this review, the mechanisms involved in protein–ligand binding, the binding kinetics, thermodynamic concepts and binding driving forces are discussed. Thermodynamic mechanisms involved in a few important protein-ligand binding are described. Various spectroscopic, non-spectroscopic and computational method for analysis of protein–ligand binding are also discussed.

  12. Models of protein-ligand crystal structures: trust, but verify

    Science.gov (United States)

    Deller, Marc C.; Rupp, Bernhard

    2015-09-01

    X-ray crystallography provides the most accurate models of protein-ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein-ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein-ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein-ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein-ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein-ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein-ligand models for their computational and biological studies, and we provide an overview of how this can be achieved.

  13. Ligand Binding Domain Protein in Tetracycline-Inducible Expression

    African Journals Online (AJOL)

    Purpose: To investigate tetracycline-inducible expression system for producing clinically usable, highquality liver X receptor ligand-binding domain recombinant protein. Methods: In this study, we have expressed and purified the recombinant liver X receptor β-ligand binding domain proteins in E. coli using a tetracycline ...

  14. Transient ligand docking sites in Cerebratulus lacteus mini-hemoglobin.

    Science.gov (United States)

    Deng, Pengchi; Nienhaus, Karin; Palladino, Pasquale; Olson, John S; Blouin, George; Moens, Luc; Dewilde, Sylvia; Geuens, Eva; Nienhaus, G Ulrich

    2007-08-15

    The monomeric hemoglobin of the nemertean worm Cerebratulus lacteus functions as an oxygen storage protein to maintain neural activity under hypoxic conditions. It shares a large, apolar matrix tunnel with other small hemoglobins, which has been implicated as a potential ligand migration pathway. Here we explore ligand migration and binding within the distal heme pocket, to which the tunnel provides access to ligands from the outside. FTIR/TDS experiments performed at cryogenic temperatures reveal the presence of three transient ligand docking sites within the distal pocket, the primary docking site B on top of pyrrole C and secondary sites C and D. Site C is assigned to a cavity adjacent to the distal portion of the heme pocket, surrounded by the B and E helices. It has an opening to the apolar tunnel and is expected to be on the pathway for ligand entry and exit, whereas site D, circumscribed by TyrB10, GlnE7, and the CD corner, most likely is located on a side pathway of ligand migration. Flash photolysis experiments at ambient temperatures indicate that the rate-limiting step for ligand binding to CerHb is migration through the apolar channel to site C. Movement from C to B and iron-ligand bond formation involve low energy barriers and thus are very rapid processes in the wt protein.

  15. Quantum probability ranking principle for ligand-based virtual screening.

    Science.gov (United States)

    Al-Dabbagh, Mohammed Mumtaz; Salim, Naomie; Himmat, Mubarak; Ahmed, Ali; Saeed, Faisal

    2017-04-01

    Chemical libraries contain thousands of compounds that need screening, which increases the need for computational methods that can rank or prioritize compounds. The tools of virtual screening are widely exploited to enhance the cost effectiveness of lead drug discovery programs by ranking chemical compounds databases in decreasing probability of biological activity based upon probability ranking principle (PRP). In this paper, we developed a novel ranking approach for molecular compounds inspired by quantum mechanics, called quantum probability ranking principle (QPRP). The QPRP ranking criteria would make an attempt to draw an analogy between the physical experiment and molecular structure ranking process for 2D fingerprints in ligand based virtual screening (LBVS). The development of QPRP criteria in LBVS has employed the concepts of quantum at three different levels, firstly at representation level, this model makes an effort to develop a new framework of molecular representation by connecting the molecular compounds with mathematical quantum space. Secondly, estimate the similarity between chemical libraries and references based on quantum-based similarity searching method. Finally, rank the molecules using QPRP approach. Simulated virtual screening experiments with MDL drug data report (MDDR) data sets showed that QPRP outperformed the classical ranking principle (PRP) for molecular chemical compounds.

  16. Quantum probability ranking principle for ligand-based virtual screening

    Science.gov (United States)

    Al-Dabbagh, Mohammed Mumtaz; Salim, Naomie; Himmat, Mubarak; Ahmed, Ali; Saeed, Faisal

    2017-04-01

    Chemical libraries contain thousands of compounds that need screening, which increases the need for computational methods that can rank or prioritize compounds. The tools of virtual screening are widely exploited to enhance the cost effectiveness of lead drug discovery programs by ranking chemical compounds databases in decreasing probability of biological activity based upon probability ranking principle (PRP). In this paper, we developed a novel ranking approach for molecular compounds inspired by quantum mechanics, called quantum probability ranking principle (QPRP). The QPRP ranking criteria would make an attempt to draw an analogy between the physical experiment and molecular structure ranking process for 2D fingerprints in ligand based virtual screening (LBVS). The development of QPRP criteria in LBVS has employed the concepts of quantum at three different levels, firstly at representation level, this model makes an effort to develop a new framework of molecular representation by connecting the molecular compounds with mathematical quantum space. Secondly, estimate the similarity between chemical libraries and references based on quantum-based similarity searching method. Finally, rank the molecules using QPRP approach. Simulated virtual screening experiments with MDL drug data report (MDDR) data sets showed that QPRP outperformed the classical ranking principle (PRP) for molecular chemical compounds.

  17. Blockade of Death Ligand TRAIL Inhibits Renal Ischemia Reperfusion Injury

    International Nuclear Information System (INIS)

    Adachi, Takaomi; Sugiyama, Noriyuki; Gondai, Tatsuro; Yagita, Hideo; Yokoyama, Takahiko

    2013-01-01

    Renal ischemia-reperfusion injury (IRI) is a leading cause of acute kidney injury (AKI). Many investigators have reported that cell death via apoptosis significantly contributed to the pathophysiology of renal IRI. Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a member of the tumor necrosis factor superfamily, and induces apoptosis and inflammation. However, the role of TRAIL in renal IRI is unclear. Here, we investigated whether TRAIL contributes to renal IRI and whether TRAIL blockade could attenuate renal IRI. AKI was induced by unilateral clamping of the renal pedicle for 60 min in male FVB/N mice. We found that the expression of TRAIL and its receptors were highly upregulated in renal tubular cells in renal IRI. Neutralizing anti-TRAIL antibody or its control IgG was given 24 hr before ischemia and a half-dose booster injection was administered into the peritoneal cavity immediately after reperfusion. We found that TRAIL blockade inhibited tubular apoptosis and reduced the accumulation of neutrophils and macrophages. Furthermore, TRAIL blockade attenuated renal fibrosis and atrophy after IRI. In conclusion, our study suggests that TRAIL is a critical pathogenic factor in renal IRI, and that TRAIL could be a new therapeutic target for the prevention of renal IRI

  18. The autoxidation activity of new mixed-ligand manganese and iron complexes with tripodal ligands

    OpenAIRE

    van Gorkum, R.; Berding, J.; Tooke, D.M.; Spek, A.L.; Reedijk, J.; Bouwman, E.

    2007-01-01

    The activity of new manganese and iron complexes of dianionic tripodal ligands in the autoxidation of ethyl linoleate (EL) is reported. EL consumption rates were monitored using time-resolved FTIR and the degree of oligomerisation was determined by SEC. Almost all complexes showed the same trend in the autoxidation of EL. After a short induction time, the reaction started at a relatively high constant rate; later, this rate changes to a lower rate, which was again constant and on average was ...

  19. Luminescence study of praseodymium complexes with selected phosphonate ligands

    Science.gov (United States)

    Pawlicki, G.; Lis, S.

    2011-08-01

    Spectroscopic properties of Pr(III) complexes with diethyl(phthalimidomethyl)phosphonate (DPIP) and diethyl(2-oxo-2phenylethyl)phosphonate (DEPP) ligands were studied using absorption and luminescence spectroscopy. Absorption spectra of praseodymium nitrate hexahydrate complexes with phosphonate ligands in acetonitrile solutions were measured and used to calculate oscillator strength values. Luminescence (excitation and emission) spectra of the Pr(III) complexes with DPIP and DEPP were measured in CH 3CN, DMSO, methanol and toluene solutions. The sensitized emission of Pr(III), observed from different excited states ( 3P 0 or 1D 2), resulted from the intramolecular energy transfer from the ligands to the emissive levels of Pr(III). The Pr(III) complexes with studied ligands were synthesized and their compositions, as Pr(DEPP) 2(NO 3) 3 and Pr(DPIP) 3(NO 3) 3, were confirmed by elemental analyses. Using IR and 31P NMR spectroscopy coordination mode of the ligands were described.

  20. Ligand specificity of nuclear hormone receptors: sifting through promiscuity.

    Science.gov (United States)

    Noy, Noa

    2007-11-27

    The superfamily of nuclear hormone receptors includes transcription factors that play key roles in regulating multiple biological functions during embryonic development and in adult tissues, as well as in many disease states. The quintessential characteristic of nuclear receptors, and the basis for the name of the family, is that their transcriptional activities can be regulated by small molecules, usually comprised of hydrophobic compounds. However, the endogenous ligands for approximately half of the members of the nuclear receptor family are unknown, and these receptors are thus designated as "orphan receptors". One class of orphan receptors encompasses receptors that display a broad ligand selectivity; i.e., they can promiscuously bind to and may be activated by multiple ligands. This characteristic complicates the identification of physiologically meaningful ligands that activate these receptors in vivo. Here, we discuss a few examples of promiscuous receptors and outline strategies that may be employed in shedding light on the nature of bona fide ligands for such receptors.

  1. Mathematical model for determining the binding constants between immunoglobulins, bivalent ligands, and monovalent ligands.

    Science.gov (United States)

    Mack, Eric T; Cummings, Linda; Perez-Castillejos, Raquel

    2011-02-01

    This paper analyzes the equilibria between immunoglobulins (R(2)), homo-bifunctional ligands (L(2)), monovalent ligands (I), and their complexes. We present a mathematical model that can be used to estimate the concentration of each species present in a mixture of R(2), L(2), and I, given the initial conditions defining the total concentration of R(2), L(2), I, and four dissociation constants (K(d)(inter), K(d)(intra), K(d)(mono), and α). This model is based on fewer assumptions than previous models and can be used to describe exactly a broad range of experimental conditions. A series of curves illustrates the dependence of the equilibria upon the total concentrations of receptors and ligands, and the dissociation constants. We provide a set of guidelines for the design and analysis of experiments with a focus on estimating the binding constants from experimental binding isotherms. Two analytical equations relate the conditions for maximum aggregation in this system to the binding constants. This model is a tool to quantify the binding of immunoglobulins to antigens and a guide to understanding and predicting the experimental data of assays and techniques that employ immunoglobulins.

  2. Regulation mechanisms of the FLT3-ligand after irradiation

    International Nuclear Information System (INIS)

    Prat-Lepesant, M.

    2005-06-01

    The hematopoietic compartment is one of the most severely damaged after chemotherapy, radiotherapy or accidental irradiations. Whatever its origin, the resulting damage to the bone marrow remains difficult to evaluate. Thus, it would be of great interest to get a biological indicator of residual hematopoiesis in order to adapt the treatment to each clinical situation. Recent results indicated that the plasma Flt3 ligand concentration was increased in patients suffering from either acquired or induced aplasia, suggesting that Flt3 ligand might be useful as a biological indicator of bone marrow status. We thus followed in a mouse model as well as in several clinical situations the variations in plasma Flt3 ligand concentration, after either homogeneous or heterogeneous irradiations. These variations were correlated to the number of hematopoietic progenitors and to other parameters such as duration and depth of pancytopenia. The results indicated that the concentration of Flt3 ligand in the blood reflects the bone marrow status, and that the follow-up of plasma Flt3 ligand concentration could give predictive information about the bone marrow function and the duration and severity of pancytopenia and thrombocytopenia. Nevertheless, the clinical use of Flt3 ligand as a biological indicator of bone marrow damage require the knowledge of the mechanisms regulating the variations in plasma Flt3 ligand concentration. We thus developed a study in the mouse model. The results indicated that the variations in plasma Flt3 ligand variations were not solely due to a balance between its production by lymphoid cells and its consumption by hematopoietic cells. Moreover, we showed that T lymphocytes are not the main regulator of plasma Flt3 ligand concentration as previously suggested, and that other cell types, possibly including bone marrow stromal cells, might be strongly implicated. These results also suggest that the Flt3 ligand is a main systemic regulator of hematopoiesis

  3. Synthesis of freestanding water-soluble indium oxide nanocrystals capped by alanine nitric acid via ligand exchange for thin film transistors and effects of ligands on the electrical properties

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Jin-Kyu; Koh, Ye-Seul; Jeong, Hyun-Dam, E-mail: hdjeong@chonnam.ac.kr

    2015-07-15

    We demonstrate synthesis of freestanding water-soluble indium oxide nanocrystals (In{sub 2}O{sub 3} NCs) by ligand exchange to β-alanine nitric acid (Ala·HNO{sub 3}) and its application for active channel layer in thin film transistors (TFTs), with investigation of the effect of curing temperatures on the TFT properties in terms of thermal behaviour of the ligand molecules at 150, 300, and 350 °C. After ligand exchange from long alkyl ligand (myristic acid, MA) to short Ala·HNO{sub 3}, the mobility of NC TFTs cured at 150 °C increased by over 1 order of magnitude, from 1.3 × 10{sup −4} cm{sup 2}V{sup -1}s{sup −1} to 4.5 × 10{sup −3} cm{sup 2}V{sup -1}s{sup −1}, due to enhanced tunnelling rate (Γ) between adjective NCs. Higher curing temperatures such as 300 and 350 °C, inducing thermal decomposition of the organic ligands, led to further enhancement of the mobility, particularly up to 2.2 cm{sup 2}V{sup -1}s{sup −1} for the In{sub 2}O{sub 3} NC-Ala·HNO{sub 3} TFT cured at 350 °C. It is also found that the ligand exchange of In{sub 2}O{sub 3} NC in acidic condition (e.g. HNO{sub 3}) would be simple and effective to reduce the surface defects by surface etching, which may lead to better device performances. - Graphical abstract: Display Omitted - Highlights: • Freestanding water-soluble In{sub 2}O{sub 3} nanocrystals (NCs) were synthesized by ligand exchange. • Thin film transistors (TFTs) of colloidal NCs were fabricated by spin-coating method. • Water-soluble In{sub 2}O{sub 3} NC TFTs showed higher mobilities due to shorter ligand length. • Surface defects of NCs were notably reduced by surface etching during ligand exchange.

  4. Developing Ligands for Palladium(II)-Catalyzed C–H Functionalization: Intimate Dialogue between Ligand and Substrate

    Science.gov (United States)

    Engle, Keary M.; Yu, Jin-Quan

    2013-01-01

    Homogeneous transition metal–catalyzed reactions are indispensable to all facets of modern chemical synthesis. It is thus difficult to imagine that for much of the early 20th century, the reactivity and selectivity of all known homogeneous metal catalysts paled in comparison to their heterogeneous and biological counterparts. In the intervening decades, advances in ligand design bridged this divide, such that today some of the most demanding bond-forming events are mediated by ligand-supported homogeneous metal species. While ligand design has propelled many areas of homogeneous catalysis, in the field of Pd(II)-catalyzed C–H functionalization, suitable ligand scaffolds are lacking, which has hampered the development of broadly practical transformations based on C–H functionalization logic. In this review, we offer an account of our research employing three ligand scaffolds, mono-N-protected amino acids, 2,6-disubstituted pyridines, and 2,2′-bipyridines, to address challenges posed by several synthetically versatile substrate classes. Drawing on this work, we discuss principles of ligand design, such as the need to match a ligand to a particular substrate class, and how ligand traits such as tunability and modularity can be advantageous in reaction discovery. PMID:23565982

  5. MYC leads the way.

    Science.gov (United States)

    Venkateswaran, Niranjan; Conacci-Sorrell, Maralice

    2017-11-25

    Members of the MYC family of proto-oncogenes are the most commonly deregulated genes in all human cancers. MYC proteins drive an increase in cellular proliferation and facilitate multiple aspects of tumor initiation and progression, thereby controlling all hallmarks of cancer. MYC's ability to drive metabolic reprogramming of tumor cells leading to biomass accumulation and cellular proliferation is the most studied function of these oncogenes. MYC also regulates tumor progression and is often implicated in resistance to chemotherapy and in metastasis. While most oncogenic functions of MYC are attributed to its role as a transcription factor, more recently, new roles of MYC as a pro-survival factor in the cytoplasm suggest a previously unappreciated diversity in MYC's roles in cancer progression. This review will focus on the role of MYC in invasion and will discuss the canonical functions of MYC in Epithelial to Mesenchymal Transition and the cytoplasmic functions of MYC-nick in collective migration.

  6. Gas adsorption and gas mixture separations using mixed-ligand MOF material

    Science.gov (United States)

    Hupp, Joseph T [Northfield, IL; Mulfort, Karen L [Chicago, IL; Snurr, Randall Q [Evanston, IL; Bae, Youn-Sang [Evanston, IL

    2011-01-04

    A method of separating a mixture of carbon dioxiode and hydrocarbon gas using a mixed-ligand, metal-organic framework (MOF) material having metal ions coordinated to carboxylate ligands and pyridyl ligands.

  7. Lead (Environmental Health Student Portal)

    Science.gov (United States)

    ... Pesticides Climate Change Climate Change Home What is Climate Change ... Lead The Basics Lead is a soft, bluish-white metal that exists naturally in the environment. When lead combines with other chemical elements, it ...

  8. Characterizing low affinity epibatidine binding to α4β2 nicotinic acetylcholine receptors with ligand depletion and nonspecific binding

    Directory of Open Access Journals (Sweden)

    Person Alexandra M

    2011-11-01

    Full Text Available Abstract Background Along with high affinity binding of epibatidine (Kd1≈10 pM to α4β2 nicotinic acetylcholine receptor (nAChR, low affinity binding of epibatidine (Kd2≈1-10 nM to an independent binding site has been reported. Studying this low affinity binding is important because it might contribute understanding about the structure and synthesis of α4β2 nAChR. The binding behavior of epibatidine and α4β2 AChR raises a question about interpreting binding data from two independent sites with ligand depletion and nonspecific binding, both of which can affect equilibrium binding of [3H]epibatidine and α4β2 nAChR. If modeled incorrectly, ligand depletion and nonspecific binding lead to inaccurate estimates of binding constants. Fitting total equilibrium binding as a function of total ligand accurately characterizes a single site with ligand depletion and nonspecific binding. The goal of this study was to determine whether this approach is sufficient with two independent high and low affinity sites. Results Computer simulations of binding revealed complexities beyond fitting total binding for characterizing the second, low affinity site of α4β2 nAChR. First, distinguishing low-affinity specific binding from nonspecific binding was a potential problem with saturation data. Varying the maximum concentration of [3H]epibatidine, simultaneously fitting independently measured nonspecific binding, and varying α4β2 nAChR concentration were effective remedies. Second, ligand depletion helped identify the low affinity site when nonspecific binding was significant in saturation or competition data, contrary to a common belief that ligand depletion always is detrimental. Third, measuring nonspecific binding without α4β2 nAChR distinguished better between nonspecific binding and low-affinity specific binding under some circumstances of competitive binding than did presuming nonspecific binding to be residual [3H]epibatidine binding after

  9. Substituted biurets as uranophilic ligands: A facile DMSO-induced conversion of a 1:1 into a 2:1 uranyl-ligand complex

    Energy Technology Data Exchange (ETDEWEB)

    Potts, K.T.; O' Brien, J.J.; Tham, F.S. (Rensselaer Polytechnic Inst., Troy, NY (United States))

    1990-01-01

    1,5-Bis(6-(1-ethoxycarbonyl-3-thioureido)-2-pyridindiyl)biuret and uranyl acetate gave a crystalline 1:1 uranyl-ligand complex which, on crystallization from DMSO, underwent rearrangement to a crystalline 2:1 uranyl-ligand complex and a stoichiometric amount of the uncomplexed ligand. Spectral characteristics of these ligands and their uranyl complexes together with single crystal x-ray data for the uranyl-ligand complexes are described.

  10. Regulation mechanisms of the FLT3-ligand after irradiation; Mecanismes de regulation du FLT3-ligand apres irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Prat-Lepesant, M

    2005-06-15

    The hematopoietic compartment is one of the most severely damaged after chemotherapy, radiotherapy or accidental irradiations. Whatever its origin, the resulting damage to the bone marrow remains difficult to evaluate. Thus, it would be of great interest to get a biological indicator of residual hematopoiesis in order to adapt the treatment to each clinical situation. Recent results indicated that the plasma Flt3 ligand concentration was increased in patients suffering from either acquired or induced aplasia, suggesting that Flt3 ligand might be useful as a biological indicator of bone marrow status. We thus followed in a mouse model as well as in several clinical situations the variations in plasma Flt3 ligand concentration, after either homogeneous or heterogeneous irradiations. These variations were correlated to the number of hematopoietic progenitors and to other parameters such as duration and depth of pancytopenia. The results indicated that the concentration of Flt3 ligand in the blood reflects the bone marrow status, and that the follow-up of plasma Flt3 ligand concentration could give predictive information about the bone marrow function and the duration and severity of pancytopenia and thrombocytopenia. Nevertheless, the clinical use of Flt3 ligand as a biological indicator of bone marrow damage require the knowledge of the mechanisms regulating the variations in plasma Flt3 ligand concentration. We thus developed a study in the mouse model. The results indicated that the variations in plasma Flt3 ligand variations were not solely due to a balance between its production by lymphoid cells and its consumption by hematopoietic cells. Moreover, we showed that T lymphocytes are not the main regulator of plasma Flt3 ligand concentration as previously suggested, and that other cell types, possibly including bone marrow stromal cells, might be strongly implicated. These results also suggest that the Flt3 ligand is a main systemic regulator of hematopoiesis

  11. Reversibly Switchable, pH-Dependent Peptide Ligand Binding via 3,5-Diiodotyrosine Substitutions.

    Science.gov (United States)

    Ngambenjawong, Chayanon; Sylvestre, Meilyn; Gustafson, Heather H; Pineda, Julio Marco B; Pun, Suzie H

    2018-03-05

    Cell type-specific targeting ligands utilized in drug delivery applications typically recognize receptors that are overexpressed on the cells of interest. Nonetheless, these receptors may also be expressed, to varying extents, on off-target cells, contributing to unintended side effects. For the selectivity profile of targeting ligands in cancer therapy to be improved, stimuli-responsive masking of these ligands with acid-, redox-, or enzyme-cleavable molecules has been reported, whereby the targeting ligands are exposed in specific environments, e.g., acidic tumor hypoxia. One possible drawback of these systems lies in their one-time, permanent trigger, which enables the "demasked" ligands to bind off-target cells if released back into the systemic circulation. A promising strategy to address the aforementioned problem is to design ligands that show selective binding based on ionization state, which may be microenvironment-dependent. In this study, we report a systematic strategy to engineer low pH-selective targeting peptides using an M2 macrophage-targeting peptide (M2pep) as an example. 3,5-Diiodotyrosine mutagenesis into native tyrosine residues of M2pep confers pH-dependent binding behavior specific to acidic environment (pH 6) when the amino acid is protonated into the native tyrosine-like state. At physiological pH of 7.4, the hydroxyl group of 3,5-diiodotyrosine on the peptide is deprotonated leading to interruption of the peptide native binding property. Our engineered pH-responsive M2pep (Ac-Y-Î-Î) binds target M2 macrophages more selectively at pH 6 than at pH 7.4. In addition, 3,5-diiodotyrosine substitutions also improve serum stability of the peptide. Finally, we demonstrate pH-dependent reversibility in target binding via a postbinding peptide elution study. The strategy presented here should be applicable for engineering pH-dependent functionality of other targeting peptides with potential applications in physiology-dependent in vivo targeting

  12. Ligand-induced dynamical change of G-protein-coupled receptor revealed by neutron scattering

    Science.gov (United States)

    Shrestha, Utsab R.; Bhowmik, Debsindhu; Mamontov, Eugene; Chu, Xiang-Qiang

    Light activation of the visual G-protein-coupled receptor rhodopsin leads to the significant change in protein conformation and structural fluctuations, which further activates the cognate G-protein (transducin) and initiates the biological signaling. In this work, we studied the rhodopsin activation dynamics using state-of-the-art neutron scattering technique. Our quasi-elastic neutron scattering (QENS) results revealed a broadly distributed relaxation rate of the hydrogen atom in rhodopsin on the picosecond to nanosecond timescale (beta-relaxation region), which is crucial for the protein function. Furthermore, the application of mode-coupling theory to the QENS analysis uncovers the subtle changes in rhodopsin dynamics due to the retinal cofactor. Comparing the dynamics of the ligand-free apoprotein, opsin versus the dark-state rhodopsin, removal of the retinal cofactor increases the relaxation time in the beta-relaxation region, which is due to the possible open conformation. Moreover, we utilized the concept of free-energy landscape to explain our results for the dark-state rhodopsin and opsin dynamics, which can be further applied to other GPCR systems to interpret various dynamic behaviors in ligand-bound and ligand-free protein.

  13. Biomolecular ligands screening using radiation damping difference WaterLOGSY spectroscopy

    International Nuclear Information System (INIS)

    Sun Peng; Jiang Xianwang; Jiang Bin; Zhang Xu; Liu Maili

    2013-01-01

    Water-ligand observed via gradient spectroscopy (WaterLOGSY) is a widely used nuclear magnetic resonance method for ligand screening. The crucial procedure for the effectiveness of WaterLOGSY is selective excitation of the water resonance. The selective excitation is conventionally achieved by using long selective pulse, which causes partial saturation of the water magnetization leading to reduction of sensitivity, in addition to time consuming and error prone. Therefore, many improvements have been made to enhance the sensitivity and robustness of the method. Here we propose an alternative selective excitation scheme for WaterLOGSY by utilizing radiation damping effect. The pulse scheme starts simply with a hard inversion pulse, instead of selective pulse or pulse train, followed by a pulse field gradient to control the radiation damping effect. The rest parts of the pulse scheme are similar to conventional WaterLOGSY. When the gradient pulse is applied immediately after the inversion pulse, the radiation damping effect is suppressed, and all of the magnetization is inversed. When the gradient pulse and the inversion pulse are about 10–20 ms apart, the radiation damping effect remains active and drives the water magnetization toward +z-axis, resulting in selective non-inversion of the water magnetization. By taking the differences of the spectra obtained under these two conditions, one should get the result of WaterLOGSY. The method is demonstrated to be simple, robust and sensitive for ligand screening

  14. Plasminogen activator inhibitor-1 polymers, induced by inactivating amphipathic organochemical ligands.

    Science.gov (United States)

    Pedersen, Katrine E; Einholm, Anja P; Christensen, Anni; Schack, Lotte; Wind, Troels; Kenney, John M; Andreasen, Peter A

    2003-06-15

    Negatively charged organochemical inactivators of the anti-proteolytic activity of plasminogen activator inhibitor-1 (PAI-1) convert it to inactive polymers. As investigated by native gel electrophoresis, the size of the PAI-1 polymers ranged from dimers to multimers of more than 20 units. As compared with native PAI-1, the polymers exhibited an increased resistance to temperature-induced unfolding. Polymerization was associated with specific changes in patterns of digestion with non-target proteases. During incubation with urokinase-type plasminogen activator, the polymers were slowly converted to reactive centre-cleaved monomers, indicating substrate behaviour of the terminal PAI-1 molecules in the polymers. A quadruple mutant of PAI-1 with a retarded rate of latency transition also had a retarded rate of polymerization. Studying a number of serpins by native gel electrophoresis, ligand-induced polymerization was observed only with PAI-1 and heparin cofactor II, which were also able to copolymerize. On the basis of these results, we suggest that the binding of ligands in a specific region of PAI-1 leads to so-called loop-sheet polymerization, in which the reactive centre loop of one molecule binds to beta-sheet A in another molecule. Induction of serpin polymerization by small organochemical ligands is a novel finding and is of protein chemical interest in relation to pathological protein polymerization in general.

  15. A ligand-directed divergent catalytic approach to establish structural and functional scaffold diversity

    Science.gov (United States)

    Lee, Yen-Chun; Patil, Sumersing; Golz, Christopher; Strohmann, Carsten; Ziegler, Slava; Kumar, Kamal; Waldmann, Herbert

    2017-02-01

    The selective transformation of different starting materials by different metal catalysts under individually optimized reaction conditions to structurally different intermediates and products is a powerful approach to generate diverse molecular scaffolds. In a more unified albeit synthetically challenging strategy, common starting materials would be exposed to a common metal catalysis, leading to a common intermediate and giving rise to different scaffolds by tuning the reactivity of the metal catalyst through different ligands. Herein we present a ligand-directed synthesis approach for the gold(I)-catalysed cycloisomerization of oxindole-derived 1,6-enynes that affords distinct molecular scaffolds following different catalytic reaction pathways. Varying electronic properties and the steric demand of the gold(I) ligands steers the fate of a common intermediary gold carbene to selectively form spirooxindoles, quinolones or df-oxindoles. Investigation of a synthesized compound collection in cell-based assays delivers structurally novel, selective modulators of the Hedgehog and Wnt signalling pathways, autophagy and of cellular proliferation.

  16. Mechanisms of action of ligands of potential-dependent sodium channels.

    Science.gov (United States)

    Tikhonov, D B

    2008-06-01

    Potential-dependent sodium channels play a leading role in generating action potentials in excitable cells. Sodium channels are the site of action of a variety of modulator ligands. Despite numerous studies, the mechanisms of action of many modulators remain incompletely understood. The main reason that many important questions cannot be resolved is that there is a lack of precise data on the structures of the channels themselves. Structurally, potential-dependent sodium channels are members of the P-loop channel superfamily, which also include potassium and calcium channels and glutamate receptor channels. Crystallization of a series of potassium channels showed that it was possible to analyze the structures of different members of the superfamily using the "homologous modeling" method. The present study addresses model investigations of the actions of ligands of sodium channels, including tetrodotoxin and batrachotoxin, as well as local anesthetics. Comparison of experimental data on sodium channel ligands with x-ray analysis data allowed us to reach a new level of understanding of the mechanisms of channel modulation and to propose a series of experimentally verifiable hypotheses.

  17. Improved Free-Energy Landscape Quantification Illustrated with a Computationally Designed Protein-Ligand Interaction.

    Science.gov (United States)

    Van Patten, William J; Walder, Robert; Adhikari, Ayush; Okoniewski, Stephen R; Ravichandran, Rashmi; Tinberg, Christine E; Baker, David; Perkins, Thomas T

    2018-01-05

    Quantifying the energy landscape underlying protein-ligand interactions leads to an enhanced understanding of molecular recognition. A powerful yet accessible single-molecule technique is atomic force microscopy (AFM)-based force spectroscopy, which generally yields the zero-force dissociation rate constant (k off ) and the distance to the transition state (Δx ≠ ). Here, we introduce an enhanced AFM assay and apply it to probe the computationally designed protein DIG10.3 binding to its target ligand, digoxigenin. Enhanced data quality enabled an analysis that yielded the height of the transition state (ΔG ≠ =6.3±0.2 kcal mol -1 ) and the shape of the energy barrier at the transition state (linear-cubic) in addition to the traditional parameters [k off (=4±0.1×10 -4  s -1 ) and Δx ≠ (=8.3±0.1 Å)]. We expect this automated and relatively rapid assay to provide a more complete energy landscape description of protein-ligand interactions and, more broadly, the diverse systems studied by AFM-based force spectroscopy. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Mild and cost-effective green fluorescent protein purification employing small synthetic ligands.

    Science.gov (United States)

    Pina, Ana Sofia; Dias, Ana Margarida G C; Ustok, Fatma Isik; El Khoury, Graziella; Fernandes, Cláudia S M; Branco, Ricardo J F; Lowe, Christopher R; Roque, A Cecília A

    2015-10-30

    The green fluorescent protein (GFP) is a useful indicator in a broad range of applications including cell biology, gene expression and biosensing. However, its full potential is hampered by the lack of a selective, mild and low-cost purification scheme. In order to address this demand, a novel adsorbent was developed as a generic platform for the purification of GFP or GFP fusion proteins, giving GFP a dual function as reporter and purification tag. After screening a solid-phase combinatorial library of small synthetic ligands based on the Ugi-reaction, the lead ligand (A4C7) selectively recovered GFP with 94% yield and 94% purity under mild conditions and directly from Escherichia coli extracts. Adsorbents containing the ligand A4C7 maintained the selectivity to recover other proteins fused to GFP. The performance of A4C7 adsorbents was compared with two commercially available methods (immunoprecipitation and hydrophobic interaction chromatography), confirming the new adsorbent as a low-cost viable alternative for GFP purification. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. Fringe proteins modulate Notch-ligand cis and trans interactions to specify signaling states.

    Science.gov (United States)

    LeBon, Lauren; Lee, Tom V; Sprinzak, David; Jafar-Nejad, Hamed; Elowitz, Michael B

    2014-09-25

    The Notch signaling pathway consists of multiple types of receptors and ligands, whose interactions can be tuned by Fringe glycosyltransferases. A major challenge is to determine how these components control the specificity and directionality of Notch signaling in developmental contexts. Here, we analyzed same-cell (cis) Notch-ligand interactions for Notch1, Dll1, and Jag1, and their dependence on Fringe protein expression in mammalian cells. We found that Dll1 and Jag1 can cis-inhibit Notch1, and Fringe proteins modulate these interactions in a way that parallels their effects on trans interactions. Fringe similarly modulated Notch-ligand cis interactions during Drosophila development. Based on these and previously identified interactions, we show how the design of the Notch signaling pathway leads to a restricted repertoire of signaling states that promote heterotypic signaling between distinct cell types, providing insight into the design principles of the Notch signaling system, and the specific developmental process of Drosophila dorsal-ventral boundary formation.

  20. Probing protein ligand interactions by automated hydrogen/deuterium exchange mass spectrometry.

    Science.gov (United States)

    Chalmers, Michael J; Busby, Scott A; Pascal, Bruce D; He, Yuanjun; Hendrickson, Christopher L; Marshall, Alan G; Griffin, Patrick R

    2006-02-15

    Amide hydrogen/deuterium exchange is a powerful biophysical technique for probing changes in protein dynamics induced by ligand interaction. The inherent low throughput of the technology has limited its impact on drug screening and lead optimization. Automation increases the throughput of H/D exchange to make it compatible with drug discovery efforts. Here we describe the first fully automated H/D exchange system that provides highly reproducible H/D exchange kinetics from 130 ms to 24 h. Throughput is maximized by parallel sample processing, and the system can run H/D exchange assays in triplicate without user intervention. We demonstrate the utility of this system to differentiate structural perturbations in the ligand-binding domain (LBD) of the nuclear receptor PPARgamma induced upon binding a full agonist and a partial agonist. PPARgamma is the target of glitazones, drugs used for treatment of insulin resistance associated with type II diabetes. Recently it has been shown that partial agonists of PPARgamma have insulin sensitization properties while lacking several adverse effects associated with full agonist drugs. To further examine the mechanism of partial agonist activation of PPARgamma, we extended our studies to the analysis of ligand interactions with the heterodimeric complex of PPARgamma/RXRalpha LBDs. To facilitate analysis of H/D exchange of large protein complexes, we performed the experiment with a 14.5-T Fourier transform ion cyclotron resonance mass spectrometer capable of measuring mass with accuracy in the ppb range.

  1. Molecular evolution of a peptide GPCR ligand driven by artificial neural networks.

    Directory of Open Access Journals (Sweden)

    Sebastian Bandholtz

    Full Text Available Peptide ligands of G protein-coupled receptors constitute valuable natural lead structures for the development of highly selective drugs and high-affinity tools to probe ligand-receptor interaction. Currently, pharmacological and metabolic modification of natural peptides involves either an iterative trial-and-error process based on structure-activity relationships or screening of peptide libraries that contain many structural variants of the native molecule. Here, we present a novel neural network architecture for the improvement of metabolic stability without loss of bioactivity. In this approach the peptide sequence determines the topology of the neural network and each cell corresponds one-to-one to a single amino acid of the peptide chain. Using a training set, the learning algorithm calculated weights for each cell. The resulting network calculated the fitness function in a genetic algorithm to explore the virtual space of all possible peptides. The network training was based on gradient descent techniques which rely on the efficient calculation of the gradient by back-propagation. After three consecutive cycles of sequence design by the neural network, peptide synthesis and bioassay this new approach yielded a ligand with 70fold higher metabolic stability compared to the wild type peptide without loss of the subnanomolar activity in the biological assay. Combining specialized neural networks with an exploration of the combinatorial amino acid sequence space by genetic algorithms represents a novel rational strategy for peptide design and optimization.

  2. Effects of Na/K-ATPase and its ligands on bone marrow stromal cell differentiation

    Directory of Open Access Journals (Sweden)

    Moustafa Sayed

    2014-07-01

    Full Text Available Endogenous ligands of Na/K-ATPase have been demonstrated to increase in kidney dysfunction and heart failure. It is also reported that Na/K-ATPase signaling function effects stem cell differentiation. This study evaluated whether Na/K-ATPase activation through its ligands and associated signaling functions affect bone marrow stromal cells (BMSCs, also known as bone marrow-derived mesenchymal stem cells differentiation capacity. BMSCs were isolated from male Sprague–Dawley rats and cultured in minimal essential medium alpha (MEM-α supplemented with 15% Fetal Bovine serum (FBS. The results showed that marinobufagenin (MBG, a specific Na/K-ATPase ligand, potentiated rosiglitazone-induced adipogenesis in these BMSCs. Meanwhile, it attenuated BMSC osteogenesis. Mechanistically, MBG increased CCAAT/enhancer binding protein alpha (C/EBPα protein expression through activation of an extracellular regulated kinase (ERK signaling pathway, which leads to enhanced rosiglitazone-induced adipogenesis. Inhibition of ERK activation by U0126 blocks the effect of MBG on C/EBPα expression and on rosiglitazone-induced adipogenesis. Reciprocally, MBG reduced runt-related transcription factor 2 (RunX2 expression, which resulted in the inhibition of osteogenesis induced by β-glycerophosphate/ascorbic acid. MBG also potentiated rosiglitazone-induced adipogenesis in 3T3-L1 cells and in mouse BMSCs. These results suggest that Na/K-ATPase and its signaling functions are involved in the regulation of BMSCs differentiation.

  3. Misuse of thermodynamics in the interpretation of isothermal titration calorimetry data for ligand binding to proteins.

    Science.gov (United States)

    Pethica, Brian A

    2015-03-01

    Isothermal titration calorimetry (ITC) has given a mass of data on the binding of small molecules to proteins and other biopolymers, with particular interest in drug binding to proteins chosen as therapeutic indicators. Interpretation of the enthalpy data usually follows an unsound protocol that uses thermodynamic relations in circumstances where they do not apply. Errors of interpretation include incomplete definitions of ligand binding and equilibrium constants and neglect of the non-ideality of the solutions under study, leading to unreliable estimates of standard free energies and entropies of binding. The mass of reported thermodynamic functions for ligand binding to proteins estimated from ITC enthalpies alone is consequently of uncertain thermodynamic significance and utility. ITC and related experiments to test the protocol assumptions are indicated. A thermodynamic procedure avoiding equilibrium constants or other reaction models and not requiring protein activities is given. The discussion draws attention to the fundamental but neglected relation between the thermodynamic activity and bioactivity of drugs and to the generally unknown thermodynamic status of ligand solutions, which for drugs relates directly to effective therapeutic dosimetry. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. Identification of Soft Matter Binding Peptide Ligands Using Phage Display.

    Science.gov (United States)

    Günay, Kemal Arda; Klok, Harm-Anton

    2015-10-21

    Phage display is a powerful tool for the selection of highly affine, short peptide ligands. While originally primarily used for the identification of ligands to proteins, the scope of this technique has significantly expanded over the past two decades. Phage display nowadays is also increasingly applied to identify ligands that selectively bind with high affinity to a broad range of other substrates including natural and biological polymers as well as a variety of low-molecular-weight organic molecules. Such peptides are of interest for various reasons. The ability to selectively and with high affinity bind to the substrate of interest allows the conjugation or immobilization of, e.g., nanoparticles or biomolecules, or generally, facilitates interactions at materials interfaces. On the other hand, presentation of peptide ligands that selectively bind to low-molecular-weight organic materials is of interest for the development of sensor surfaces. The aim of this article is to highlight the opportunities provided by phage display for the identification of peptide ligands that bind to synthetic or natural polymer substrates or to small organic molecules. The article will first provide an overview of the different peptide ligands that have been identified by phage display that bind to these "soft matter" targets. The second part of the article will discuss the different characterization techniques that allow the determination of the affinity of the identified ligands to the respective substrates.

  5. Folding energetics of ligand binding proteins. I. Theoretical model.

    Science.gov (United States)

    Rösgen, J; Hinz, H J

    2001-03-02

    Heat capacity curves as obtained from differential scanning calorimetry are an outstanding source for molecular information on protein folding and ligand-binding energetics. However, deconvolution of C(p) data of proteins in the presence of ligands can be compromised by indeterminacies concerning the correct choice of the statistical thermodynamic ensemble. By convent, the assumption of constant free ligand concentration has been used to derive formulae for the enthalpy. Unless the ligand occurs at large excess, this assumption is incorrect. Still the relevant ensemble is the grand canonical ensemble. We derive formulae for both constraints, constancy of total or free ligand concentration and illustrate the equations by application to the typical equilibrium Nx N + x D + x. It is demonstrated that as long as the thermodynamic properties of the ligand can be completely corrected for by performing a reference measurement, the grand canonical approach provides the proper and mathematically significantly simpler choice. We demonstrate on the two cases of sequential or independent ligand-binding the fact, that similar binding mechanisms result in different and distinguishable heat capacity equations. Finally, we propose adequate strategies for DSC experiments as well as for obtaining first estimates of the characteristic thermodynamic parameters, which can be used as starting values in a global fit of DSC data. Copyright 2001 Academic Press.

  6. Lanthanide mixed ligand chelates for DNA profiling and latent fingerprint detection

    Science.gov (United States)

    Menzel, E. R.; Allred, Clay

    1997-02-01

    It is our aim to develop a universally applicable latent fingerprint detection method using lanthanide (rare-earth) complexes as a source of luminescence. Use of these lanthanide complexes offers advantages on several fronts, including benefits from large Stokes shifts, long luminescence lifetimes, narrow emissions, ability of sequential assembly of complexes, and chemical variability of the ligands. Proper exploitation of these advantages would lead to a latent fingerprint detection method superior to any currently available. These same characteristics also lend themselves to many of the problems associated with DNA processing in the forensic science context.

  7. Synthesis, structures, and dearomatization by deprotonation of iron complexes featuring bipyridine-based PNN pincer ligands.

    Science.gov (United States)

    Zell, Thomas; Langer, Robert; Iron, Mark A; Konstantinovski, Leonid; Shimon, Linda J W; Diskin-Posner, Yael; Leitus, Gregory; Balaraman, Ekambaram; Ben-David, Yehoshoa; Milstein, David

    2013-08-19

    The synthesis and characterization of new iron pincer complexes bearing bipyridine-based PNN ligands is reported. Three phosphine-substituted pincer ligands, namely, the known (t)Bu-PNN (6-((di-tert-butylphosphino)methyl)-2,2'-bipyridine) and the two new (i)Pr-PNN (6-((di-iso-propylphosphino)methyl)-2,2'-bipyridine) and Ph-PNN (6-((diphenylphosphino)methyl)-2,2'-bipyridine) ligands were synthesized and studied in ligation reactions with iron(II) chloride and bromide. These reactions lead to the formation of two types of complexes: mono-chelated neutral complexes of the type [(R-PNN)Fe(X)2] and bis-chelated dicationic complexes of the type [(R-PNN)2Fe](2+). The complexes [(R-PNN)Fe(X)2] (1: R = (t)Bu, X = Cl, 2: R = (t)Bu, X = Br, 3: R = (i)Pr, X = Cl, and 4: R = (i)Pr, X = Br) are readily prepared from reactions of FeX2 with the free R-PNN ligand in a 1:1 ratio. Magnetic susceptibility measurements show that these complexes have a high-spin ground state (S = 2) at room temperature. Employing a 2-fold or higher excess of (i)Pr-PNN, diamagnetic hexacoordinated dicationic complexes of the type [((i)Pr-PNN)2Fe](X)2 (5: X = Cl, and 6: X = Br) are formed. The reactions of Ph-PNN with FeX2 in a 1:1 ratio lead to similar complexes of the type [(Ph-PNN)2Fe](FeX4) (7: X = Cl, and 8: X = Br). Single crystal X-ray studies of 1, 2, 4, 6, and 8 do not indicate electron transfer from the Fe(II) centers to the neutral bipyridine unit based on the determined bond lengths. Density functional theory (DFT) calculations were performed to compare the relative energies of the mono- and bis-chelated complexes. The doubly deprotonated complexes [(R-PNN*)2Fe] (9: R = (i)Pr, and 10: R = Ph) were synthesized by reactions of the dicationic complexes 6 and 8 with KO(t)Bu. The dearomatized nature of the central pyridine of the pincer ligand was established by X-ray diffraction analysis of single crystals of 10. Reactivity studies show that 9 and 10 have a slightly different behavior in

  8. Muscarinic receptors as model targets and antitargets for structure-based ligand discovery.

    Science.gov (United States)

    Kruse, Andrew C; Weiss, Dahlia R; Rossi, Mario; Hu, Jianxin; Hu, Kelly; Eitel, Katrin; Gmeiner, Peter; Wess, Jürgen; Kobilka, Brian K; Shoichet, Brian K

    2013-10-01

    G protein-coupled receptors (GPCRs) regulate virtually all aspects of human physiology and represent an important class of therapeutic drug targets. Many GPCR-targeted drugs resemble endogenous agonists, often resulting in poor selectivity among receptor subtypes and restricted pharmacologic profiles. The muscarinic acetylcholine receptor family exemplifies these problems; thousands of ligands are known, but few are receptor subtype-selective and nearly all are cationic in nature. Using structure-based docking against the M2 and M3 muscarinic receptors, we screened 3.1 million molecules for ligands with new physical properties, chemotypes, and receptor subtype selectivities. Of 19 docking-prioritized molecules tested against the M2 subtype, 11 had substantial activity and 8 represented new chemotypes. Intriguingly, two were uncharged ligands with low micromolar to high nanomolar Ki values, an observation with few precedents among aminergic GPCRs. To exploit a single amino-acid substitution among the binding pockets between the M2 and M3 receptors, we selected molecules predicted by docking to bind to the M3 and but not the M2 receptor. Of 16 molecules tested, 8 bound to the M3 receptor. Whereas selectivity remained modest for most of these, one was a partial agonist at the M3 receptor without measurable M2 agonism. Consistent with this activity, this compound stimulated insulin release from a mouse β-cell line. These results support the ability of structure-based discovery to identify new ligands with unexplored chemotypes and physical properties, leading to new biologic functions, even in an area as heavily explored as muscarinic pharmacology.

  9. Expression of mammalian GPCRs in C. elegans generates novel behavioural responses to human ligands

    Directory of Open Access Journals (Sweden)

    Jansen Gert

    2006-07-01

    Full Text Available Abstract Background G-protein-coupled receptors (GPCRs play a crucial role in many biological processes and represent a major class of drug targets. However, purification of GPCRs for biochemical study is difficult and current methods of studying receptor-ligand interactions involve in vitro systems. Caenorhabditis elegans is a soil-dwelling, bacteria-feeding nematode that uses GPCRs expressed in chemosensory neurons to detect bacteria and environmental compounds, making this an ideal system for studying in vivo GPCR-ligand interactions. We sought to test this by functionally expressing two medically important mammalian GPCRs, somatostatin receptor 2 (Sstr2 and chemokine receptor 5 (CCR5 in the gustatory neurons of C. elegans. Results Expression of Sstr2 and CCR5 in gustatory neurons allow C. elegans to specifically detect and respond to somatostatin and MIP-1α respectively in a robust avoidance assay. We demonstrate that mammalian heterologous GPCRs can signal via different endogenous Gα subunits in C. elegans, depending on which cells it is expressed in. Furthermore, pre-exposure of GPCR transgenic animals to its ligand leads to receptor desensitisation and behavioural adaptation to subsequent ligand exposure, providing further evidence of integration of the mammalian GPCRs into the C. elegans sensory signalling machinery. In structure-function studies using a panel of somatostatin-14 analogues, we identified key residues involved in the interaction of somatostatin-14 with Sstr2. Conclusion Our results illustrate a remarkable evolutionary plasticity in interactions between mammalian GPCRs and C. elegans signalling machinery, spanning 800 million years of evolution. This in vivo system, which imparts novel avoidance behaviour on C. elegans, thus provides a simple means of studying and screening interaction of GPCRs with extracellular agonists, antagonists and intracellular binding partners.

  10. Drowning: a leading killer!

    Directory of Open Access Journals (Sweden)

    Nuno Domingos Garrido

    2016-10-01

    Full Text Available Drowning kills at least 372,000 people worldwide every year and is the 3rd leading cause of unintentional death, accounting for 7% of all deaths stemming from accidents (WHO, 2014. Conceptually, “drowning” is a complex and multi-faceted phenomenon, characterized as a chain of events (Bierens, 2006. Drowning is defined as the process of experiencing respiratory impairment from immersion or submersion in liquid. Research on drowning as a phenomenon presents several difficulties - most of all, that global data concerning the number of occurrences are not accurate. Nevertheless, detailed analysis of the registered incidents allows the identification of risk factors of drowning. An in-depth analysis of the risk factors is the basis for the creation of targeted and effective strategies to prevent drowning. Due to variability of situations which could lead to a drowning episode, experts suggest the adoption of a multi-layer prevention model, rather than opting for isolated measures, since no single measure can prevent all deaths and injuries caused by submersion. Among the preventive measures we would like to emphasize instruction in swimming and water safety. So, what does "knowing how to swim" really mean? Some authors define mastery of this competence as swimming a given distance, while others put the emphasis on how this/any given distance is swum (Stallman, Junge, & Blixt, 2008. It has long been realized that there is no contradiction between learning those competencies which make a person less susceptible to drowning and those competencies which prepare the path towards higher levels of performance and competition. Aquatic movement researchers and practitioners and drowning prevention researchers and practitioners, share in the responsibility for drowning prevention though they are often unaware of it. The question “What should be taught to children?” is too infrequently asked. There remains great variation in what is taught and programs

  11. Leading Your Leaders

    Science.gov (United States)

    Hale, Wayne N.

    2008-01-01

    life is good. More often when an unbelievably difficult test fails, we are left with a very long discussion of why and what was wrong in the design or execution of the test. Make sure that the test is well defined. Even then, it is important to explain to your leaders what inherent accuracy (or error) the test conditions or equipment have and what the assumptions or initial conditions were for the test. Test results without a good understanding of the test's accuracy or the pedigree of the test assumptions are worth very little. Finally, there is flight test data. Always limited, never at the edge of the envelope, it still shows how the real hardware works in a combined environment. Flight experience is dangerous because it typically doesn't show how close to the edge of the cliff the equipment is operating, but it does demonstrate how the hardware really works. A flight test is the ultimate test, again taken with the knowledge that it is probably not the extreme but something more like the middle of the environmental and systems performance. Good understanding of a problem and its solution always relies on a combination of all these methods. Be sure to lead your leaders by using all the tools you have at your disposal. At the end of the day, decisions in space flight always come down to a risk trade. Our business is not remotely safe, not in the sense that the public, the media, or our legislators use the term. Everything we do has a risk, cost, schedule, or performance trade-off. For your leaders to make an appropriate decision, you need to educate them, lead them, talk with them, and engage them in the discussion until full understanding takes place. It's your job. *

  12. Entangled zinc-ditetrazolate frameworks involving in situ ligand synthesis and topological modulation by various secondary N-donor ligands

    International Nuclear Information System (INIS)

    Li Yunwu; Chen Weilin; Wang Yonghui; Li Yangguang; Wang Enbo

    2009-01-01

    The introduction of various secondary N-donor ligands into an in situ ditetrazolate-ligand synthesis system of terephthalonitrile, NaN 3 and ZnCl 2 led to the formation of three new entangled frameworks Zn(pdtz)(4,4'-bipy).3H 2 O (1), [Zn(pdtz)(bpp)] 2 .3H 2 O (2) and Zn(pdtz) 0.5 (N 3 )(2,2'-bipy) (3) (4,4'-bipy=4,4'-bipyridine; bpp=1,3-bis(4-pyridyl)propane; 2,2'-bipy=2,2'-bipyridine; H 2 pdtz=5,5'-1,4-phenylene-ditetrazole). The formation of pdtz 2- ligand involves the Sharpless [2+3] cycloaddition reaction between terephthalonitrile and NaN 3 in the presence of Zn 2+ ion as a Lewis-acid catalyst under hydrothermal conditions. Compound 1 exhibits a fivefold interpenetrating 3D framework based on the diamondoid topology. Compound 2 displays a twofold parallel interpenetrating framework based on the wavelike individual network. Compound 3 possesses a 2D puckered network. These new Zn-ditetrazolate frameworks are highly dependent on the modulation of different secondary N-donor ligands. Their luminescent properties were investigated. - Graphical abstract: Three new entangled frameworks were prepared by an in situ ditetrazolate-ligand synthesis system assisted with various auxiliary N-donor ligands. The entangled structures can be modulated by different secondary ligands.

  13. Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach

    Science.gov (United States)

    Lam, Polo C.-H.; Abagyan, Ruben; Totrov, Maxim

    2018-01-01

    Ligand docking to flexible protein molecules can be efficiently carried out through ensemble docking to multiple protein conformations, either from experimental X-ray structures or from in silico simulations. The success of ensemble docking often requires the careful selection of complementary protein conformations, through docking and scoring of known co-crystallized ligands. False positives, in which a ligand in a wrong pose achieves a better docking score than that of native pose, arise as additional protein conformations are added. In the current study, we developed a new ligand-biased ensemble receptor docking method and composite scoring function which combine the use of ligand-based atomic property field (APF) method with receptor structure-based docking. This method helps us to correctly dock 30 out of 36 ligands presented by the D3R docking challenge. For the six mis-docked ligands, the cognate receptor structures prove to be too different from the 40 available experimental Pocketome conformations used for docking and could be identified only by receptor sampling beyond experimentally explored conformational subspace.

  14. Lead toxicity and nutritional deficiencies

    Energy Technology Data Exchange (ETDEWEB)

    Levander, O.A.

    1979-04-01

    Recent data concerning lead toxicity and nutritional deficiencies are summarized. Lead poisoning can be exacerbated by consumption of either deficient or excessive levels of protein. Mineral deficiencies also exaggerate lead poisoning. Evidence for antagonism between lead and nutritional levels of selenium is inconclusive. Vitamin E deficiency and lead poisoning interact to produce an anemia in rats that is more severe than that caused by either treatment alone. A pro-oxidant stress of lead on red blood cells is hypothesized to cause their accelerated destruction. In addition, disruption of normal membrane structure, leading to peroxidative damage, may occur. Calcium deficiencies in children are negatively correlated with lead concentrations in their blood. Other examples of interactions between minerals and lead poisoning are provided. Nutritional deficiencies have been shown to have an additive effect in potentiating lead toxicity in some cases. (112 references, 4 tables)

  15. Formation of mixed ligand complexes of UO22+ involving some nitrogen and oxygen donor ligands

    International Nuclear Information System (INIS)

    Singh, Mamta; Ram Nayan

    1996-01-01

    The complexation reactions of UO 2 2+ ion with nitrogen and oxygen donor ligands, 1-amino-2-naphthol-4-sulphonic acid, o-aminophenol (ap), 2-hydroxybenzoic acid (sa), 3-carboxy-4-hydroxybenzenesulphonic acid (ss) and 1,2-dihydroxybenzene (ca) have been investigated in aqueous solution employing the pH-titration technique. Analysis of the experimental data recorded at 25 degC and at an ionic strength of 0.10 M KNO 3 indicates formation of binary, hydroxo and ternary complexes of uranium. Formation constant values of the existing species have been evaluated and the results have been discussed. (author). 21 refs., 2 figs., 2 tabs

  16. Inhibition of rat pituitary growth hormone (GH) release by subclinical levels of lead

    International Nuclear Information System (INIS)

    Camoratto, A.M.; White, L.M.; Lau, Y.S.; Moriarty, C.M.

    1990-01-01

    Lead toxicity has been associated with short stature in children. Since growth hormone is a major regulator of growth, the effects of chronic exposure to subclinical lead levels on pituitary function were assessed. Timed pregnant rats were given 125 ppm lead (as lead nitrate) in their drinking water beginning on day 5 of gestation. After weaning, pups were continued on lead until sacrifice at 7 weeks of age. The average blood lead level at this time was 18.9 ug/dl (range 13.7-27.8). On the day of sacrifice the pituitary was removed, hemisected and incubated with vehicle or 40 nM hGRH (human growth hormone releasing hormone). Pituitaries from chronically lead-treated pups were 64% less responsive to GRH than controls. In contrast, no difference in responsiveness was observed in pituitaries from the dams. The specific binding of GRH was also examined. Control animals showed a dose-dependent displacement of 125I-GRH by unlabeled ligand (10-1000 nM). In the pituitaries of lead-treated pups binding of labeled ligand was markedly reduced by unlabeled GRH (less than 100 nM). Chronic exposure to lead had no effect on serum GH or prolactin levels or on pituitary content of GH. These data suggest that one mechanism by which lead can affect growth is by inhibition of GH release

  17. Self-organizing molecular fingerprints: a ligand-based view on drug-like chemical space and off-target prediction.

    Science.gov (United States)

    Schneider, Gisbert; Tanrikulu, Yusuf; Schneider, Petra

    2009-04-01

    Reliable prediction of multiple ligand-receptor interactions for a given bioactive compound helps recognize and understand off-target effects, and enables drug re-purposing and scaffold-hopping in lead discovery. We developed a ligand-based computational method for drug-target prediction that is independent from protein structural analysis. The idea is to infer drug targets from the pharmacophoric feature similarity of known ligands, and define functional target similarity from a ligand perspective, which also provides access to targets with unknown structures. First, known ligands were represented by topological pharmacophoric features. Then, the self-organizing map technique was used to generate fingerprint patterns for similarity analysis, where each resulting fingerprint represents a drug target. Target fingerprints were clustered and analyzed for correlations. Well-structured dendrograms were obtained presenting interpretable and meaningful relationships between drug targets. Self-organization of fingerprints reduces noise from molecular pharmacophore descriptors, captures their essential features, and reveals potential cross-activities of ligand classes and off-target effects of bioactive compounds.

  18. PET and Hormone Receptor Ligands in Breast Cancer

    National Research Council Canada - National Science Library

    Gemignani, Mary

    2006-01-01

    .... To investigate this further, this project's objectives are: To evaluate the use of estrogen-like ligands labeled with positron emitters in preoperatively determining the ER status of breast cancer using PET...

  19. Linkable thiocarbamoylbenzamidines as ligands for bioconjugation of Rhenium and Technetium

    International Nuclear Information System (INIS)

    Castillo Gomez, Juan Daniel

    2015-01-01

    Bioconjugation reactions with Rhenium and Technetium are of high importance for the development of novel radiopharmaceuticals for nuclear medicine. In this thesis the possibilities for bioconjugation using linkable Thiocarmbamoylbenzamidines as ligands for the complexation of Rhenium and Technetium were examined.

  20. Unique advantages of organometallic supporting ligands for uranium complexes

    International Nuclear Information System (INIS)

    Diaconescu, Paula L.; Garcia, Evan

    2014-01-01

    The objective of our research project was to study the reactivity of uranium complexes supported by ferrocene-based ligands. In addition, this research provides training of graduate students as the next generation of actinide scientists.

  1. Synthesis of symmetrical and non-symmetrical bivalent neurotransmitter ligands

    DEFF Research Database (Denmark)

    Stuhr-Hansen, Nicolai; Andersen, Jacob; Thygesen, Mikkel Boas

    2016-01-01

    A novel procedure for synthesis of bivalent neurotransmitter ligands was developed by reacting O-benzyl protected N-nosylated dopamine and serotonin with alkyl- or PEG-linked diols under Fukuyama-Mitsunobu conditions in the presence of DIAD/PPh3 generating three different bivalent neurotransmitter...... ligands in a one-pot reaction. The methodol. establishes a facile route towards bivalent neurotransmitter ligands, and libraries of in total 40 sym. and non-sym. bivalent and monovalent dopamine and serotonin compds. linked through alkyl or PEG spacers of varying length were prepd. Interestingly......, attempted synthesis of an O-tert-Bu analog of the N-nosylated serotonin precursor resulted in unexpected tert-butylations at the 1-, 2- and 6-positions of the indole skeleton. We found that upscaling of selected bivalent serotonin ligands was most efficiently performed via N,O-bis-nosyl-serotonin since...

  2. Mixed-ligand binuclear copper(II) complex of 5 ...

    Indian Academy of Sciences (India)

    ligand binuclear copper(II) complex of 5-methylsalicylaldehyde and 2,2 -bipyridyl: Synthesis, crystal structure, DNA binding and nuclease activity. PERUMAL GURUMOORTHYa, JAYARAM RAVICHANDRANa,b and AZIZ KALILUR RAHIMANa,∗.

  3. Identification of RNA-ligand interactions by affinity electrophoresis.

    Science.gov (United States)

    Boodram, Sherry N; Cho, Chul M; Tavares, Tony J; Johnson, Philip E

    2011-02-01

    We have developed an affinity electrophoresis method to screen for RNA-ligand interactions. Native polyacrylamide gels were polymerized in the absence and presence of different RNA binding molecules. Binding is indicated by a difference in mobility between the gel with ligand present and the gel with no ligand present. The utility of this method was demonstrated using the known interaction between the Escherichia coli ribosomal A-site RNA and different aminoglycoside ligands. The RNA-aminoglycoside interaction observed is dose dependent, and the affinity mirrors what is observed in solution. In addition, we used this method to gauge the affinity to different aminoglycoside molecules of an RNA molecule derived from the thymidylate synthase mRNA construct that contains a CC mismatch. Copyright © 2010 Elsevier Inc. All rights reserved.

  4. Synthesis and Catalytic Activity of Two New Cyclic Tetraaza Ligands

    Directory of Open Access Journals (Sweden)

    Burkhard König

    2003-05-01

    Full Text Available Two new chiral cyclic tetraaza ligands were synthesized and characterized. Their catalytic activity was tested in the asymmetric addition of diethylzinc to benzaldehyde. The expected secondary alcohol was obtained in moderate yields, but with very low enantioselectivity.

  5. Specific activity of radioiodine-labelled human chorionic gonadotropin ligand

    International Nuclear Information System (INIS)

    Crespi, M.; Kay, G.W.; Van der Walt, L.A.

    1983-01-01

    The article deals with the determination of the specific activity of radioiodine-labbelled human chorionic gonadotropin ligand. The iodiation of human chorionic gonadotropin and the counting efficiency of 125 I are discussed

  6. related apoptosis-inducing ligand in transplastomic tobacco

    African Journals Online (AJOL)

    -inducing ligand (sTRAIL) can, as the whole length TRAIL protein, bind with its receptors and specifically induce the apoptosis of cancer cells; therefore, it has been developed as a potential therapeutic agent for various cancer treatments.

  7. Epibatidine-derivatives: ligands for the neuronal nicotinic acetylcholine receptor

    International Nuclear Information System (INIS)

    Westera, G.; Patt, J.T.; Jankowski, K.; Bertrand, D.; Spang, J.; Schubiger, P.A.

    1997-01-01

    Epibatidine, isolated from the Ecuadorian frog Epipedobates tricolar, has been synthesized. 11 C-N-methyl derivate is investigated as useful nicotinergic receptor ligand by electrophysiological methods and in vivo mice experiments. (author) 2 figs., 7 refs

  8. Unique advantages of organometallic supporting ligands for uranium complexes

    Energy Technology Data Exchange (ETDEWEB)

    Diaconescu, Paula L. [Univ. of California, Los Angeles, CA (United States); Garcia, Evan [Univ. of California, Los Angeles, CA (United States)

    2014-05-31

    The objective of our research project was to study the reactivity of uranium complexes supported by ferrocene-based ligands. In addition, this research provides training of graduate students as the next generation of actinide scientists.

  9. Lead in teeth from lead-dosed goats: Microdistribution and relationship to the cumulative lead dose

    International Nuclear Information System (INIS)

    Bellis, David J.; Hetter, Katherine M.; Jones, Joseph; Amarasiriwardena, Dula; Parsons, Patrick J.

    2008-01-01

    Teeth are commonly used as a biomarker of long-term lead exposure. There appear to be few data, however, on the content or distribution of lead in teeth where data on specific lead intake (dose) are also available. This study describes the analysis of a convenience sample of teeth from animals that were dosed with lead for other purposes, i.e., a proficiency testing program for blood lead. Lead concentration of whole teeth obtained from 23 animals, as determined by atomic absorption spectrometry, varied from 0.6 to 80 μg g -1 . Linear regression of whole tooth lead (μg g -1 ) on the cumulative lead dose received by the animal (g) yielded a slope of 1.2, with r 2 =0.647 (p -1 , were found in circumpulpal dentine. Linear regression of circumpulpal lead (μg g -1 ) on cumulative lead dose (g) yielded a slope of 23 with r 2 =0.961 (p=0.0001). The data indicated that whole tooth lead, and especially circumpulpal lead, of dosed goats increased linearly with cumulative lead exposure. These data suggest that circumpulpal dentine is a better biomarker of cumulative lead exposure than is whole tooth lead, at least for lead-dosed goats

  10. The lead industry and lead water pipes "A Modest Campaign".

    Science.gov (United States)

    Rabin, Richard

    2008-09-01

    Lead pipes for carrying drinking water were well recognized as a cause of lead poisoning by the late 1800s in the United States. By the 1920s, many cities and towns were prohibiting or restricting their use. To combat this trend, the lead industry carried out a prolonged and effective campaign to promote the use of lead pipes. Led by the Lead Industries Association (LIA), representatives were sent to speak with plumbers' organizations, local water authorities, architects, and federal officials. The LIA also published numerous articles and books that extolled the advantages of lead over other materials and gave practical advice on the installation and repair of lead pipes. The LIA's activities over several decades therefore contributed to the present-day public health and economic cost of lead water pipes.

  11. The Foundations of Protein-Ligand Interaction

    Science.gov (United States)

    Klebe, Gerhard

    For the specific design of a drug we must first answer the question: How does a drug achieve its activity? An active ingredient must, in order to develop its action, bind to a particular target molecule in the body. Usually this is a protein, but also nucleic acids in the form of RNA and DNA can be target structures for active agents. The most important condition for binding is at first that the active agent exhibits the correct size and shape in order to optimally fit into a cavity exposed to the surface of the protein, the "bindingpocket". It is further necessary for the surface properties of the ligand and protein to be mutually compatible to form specific interactions. In 1894 Emil Fischer compared the exact fit of a substrate for the catalytic centre of an enzyme with the picture of a "lock-and-key". Paul Ehrlich coined in 1913 "Corpora non agunt nisi fixata", literally "bodies do not work when they are not bound". He wanted to imply that active agents that are meant to kill bacteria or parasites must be "fixed" by them, i.e. linked to their structures. Both concepts form the starting point for any rational concept in the development of active pharmaceutical ingredients. In many respects they still apply today. A drug must, after being administered, reach its target and interact with a biological macromolecule. Specific agents have a large affinity and sufficient selectivity to bind to the macromolecule's active site. This is the only way they can develop the desired biological activity without side-effects.

  12. Dysprosium complexes with the tetraphenylporphyrin macrocyclic ligand

    International Nuclear Information System (INIS)

    Martinez M, V.; Padilla, J.; Ramirez, F.M.

    1992-04-01

    In this report, the results obtained on the synthesis, characterization and study of the chemical behavior of dysprosium complex with the acetylacetone chelating agent (Hacac) and the tetraphenylporphyrin macrocyclic ligand (H 2 TFP) are given. Based on the literature but according to our necessities and interest, the appropriate methodology settled down from the synthesis of prime matters until the obtaining and characterization of the products. The acetyl acetonate complex was obtained of mono hydrated dysprosium [Dy(acac) 3 . H 2 0] and trihydrated [Dy(acac) 3 .3 H 2 0], the mono tetra phenyl porphyrinate [Dy(TFP)(acac). 2 ac] the double sandwich of the dysprosium porphyrinate [Dy(TFP) 2 ] and the triple sandwich of the dysprosium porphyrinate [Dy(TFP) 3 . 2 TCB] (TCB = trichlorobenzene). Its were characterized by their melting points, solubility, IR, UV, TGA and DTA both first and besides the techniques already mentioned for NMR'H, RPE and Magnetic susceptibility the three last complexes. From the spectroscopic point of view, IR and RPE its suggested the existence of a complex of inverse mixed valence [Dy(TFP) 2- (TFP) 1- ] for the Dy(TFP) 2 as a result of the existence of the free radical (TFP' 1- and that it was not in none of the other porphyrin compounds. In the NMR'H spectra of the compounds were not observed signals in the region from 0 to 10 ppm that which shows that the dysprosium complexes in special those of the porphyrin type are highly paramagnetic and its could be used as displacement reagents, creators of images and contrast agents of great utility in these days in studies of NMR, technique today by today used in medical diagnoses. (Author)

  13. Lead pollution sources and Impacts

    International Nuclear Information System (INIS)

    El-Haggar, S.M.; Saad, S.G.; Saleh, S.K.; El-Kady, M.A.

    1996-01-01

    Despite the medical awareness of lead toxicity, and despite legislation designed to reduce environmental contamination, lead is one of the most widely used heavy metals. Significant human exposure occurs from automobile exhaust fumes, cigarette smoking, lead-based paints and plumbing systems lead spread in the environment can take place in several ways, the most important of which is through the lead compounds released in automobile exhaust as a direct result of the addition of tetraethyl or tetraethyl lead to gasoline as octane boosting agents. Of special is the effect of lead pollution on children, which affects their behavioral and educational attributes considerably. The major channel through through which lead is absorbed is through inhalation of lead compounds in the atmosphere. Lead is a heavy metal characterized its malleability, ductility and poor conduction of electricity. So, it has a wide range of applications ranging from battery manufacturing to glazing ceramics. It is rarely found free in nature but is present in several minerals and compounds. The aim of this paper is to discuss natural and anthropogenic sources of lead together with its distribution and trends with emphasis on egypt. The effects of lead pollution on human health, vegetation and welfare are also presented. It could be concluded that, the excessive release of lead into the environment, especially through the atmosphere, can produce many detrimental and sometimes fatal effects on human, agriculture and zoological life. Besides, it is very plain that there is a serious problem of pollution lead in egypt and specially in cairo. 7 figs

  14. Metallogel formation in aqueous DMSO by perfluoroalkyl decorated terpyridine ligands.

    Science.gov (United States)

    Tatikonda, Rajendhraprasad; Bhowmik, Sandip; Rissanen, Kari; Haukka, Matti; Cametti, Massimo

    2016-08-09

    Terpyridine based ligands 1 and 2, decorated with a C8F17 perfluorinated tag, are able to form stable thermoreversible gels in the presence of several d-block metal chloride salts. The gel systems obtained have been characterized by NMR, X-ray diffraction, electron microscopies and Tgel experiments in order to gain insights into the observed different behaviour of the two similar ligands, also in terms of the effect of additional common anionic species.

  15. Reversible Size Control of Silver Nanoclusters via Ligand-exchange

    KAUST Repository

    Bootharaju, Megalamane Siddaramappa

    2015-05-21

    The properties of atomically monodisperse noble metal nanoclusters (NCs) are intricately intertwined with their precise molecular formula. The vast majority of size-specific NC syntheses start from the reduction of the metal salt and thiol ligand mixture. Only in gold was it recently shown that ligand-exchange could induce the growth of NCs from one atomically precise species to another; a process of yet unknown reversibility. Here, we present a process for the ligand-exchange-induced growth of atomically precise silver NCs, in a biphasic liquid-liquid system, which is particularly of interest because of its complete reversibility and ability to occur at room temperature. We explore this phenomenon in-depth using Ag35(SG)18 [SG= glutathionate] and Ag44(4-FTP)30 [4-FTP= 4-fluorothiophenol] as model systems. We show that the ligand-exchange conversion of Ag35(SG)18 into Ag44(4-FTP)30 is rapid (< 5 min) and direct, while the reverse process proceeds slowly through intermediate cluster sizes. We adapt a recently developed theory of reverse Ostwald ripening to model the NCs’ interconvertibility. The model’s predictions are in good agreement with the experimental observations, and they highlight the importance of small changes in the ligand-metal binding energy in determining the final equilibrium NC size. Based on the insight provided by this model, we demonstrated experimentally that by varying the choice of ligands, ligand-exchange can be used to obtain different sized NCs. The findings in this work establish ligand-exchange as a versatile tool for tuning cluster sizes.

  16. Reaction chemistry and ligand exchange at cadmium selenide nanocrystal surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Owen, Jonathan; Park, Jungwon; Trudeau, Paul-Emile; Alivisatos, A. Paul

    2008-12-02

    Chemical modification of nanocrystal surfaces is fundamentally important to their assembly, their implementation in biology and medicine, and greatly impacts their electrical and optical properties. However, it remains a major challenge owing to a lack of analytical tools to directly determine nanoparticle surface structure. Early nuclear magnetic resonance (NMR) and X-ray photoelectron spectroscopy (XPS) studies of CdSe nanocrystals prepared in tri-n-octylphosphine oxide (1) and tri-n-octylphosphine (2), suggested these coordinating solvents are datively bound to the particle surface. However, assigning the broad NMR resonances of surface-bound ligands is complicated by significant concentrations of phosphorus-containing impurities in commercial sources of 1, and XPS provides only limited information about the nature of the phosphorus containing molecules in the sample. More recent reports have shown the surface ligands of CdSe nanocrystals prepared in technical grade 1, and in the presence of alkylphosphonic acids, include phosphonic and phosphinic acids. These studies do not, however, distinguish whether these ligands are bound datively, as neutral, L-type ligands, or by X-type interaction of an anionic phosphonate/phosphinate moiety with a surface Cd{sup 2+} ion. Answering this question would help clarify why ligand exchange with such particles does not proceed generally as expected based on a L-type ligand model. By using reagents with reactive silicon-chalcogen and silicon-chlorine bonds to cleave the ligands from the nanocrystal surface, we show that our CdSe and CdSe/ZnS core-shell nanocrystal surfaces are likely terminated by X-type binding of alkylphosphonate ligands to a layer of Cd{sup 2+}/Zn{sup 2+} ions, rather than by dative interactions. Further, we provide spectroscopic evidence that 1 and 2 are not coordinated to our purified nanocrystals.

  17. Tetrapyrroles as Endogenous TSPO Ligands in Eukaryotes and Prokaryotes: Comparisons with Synthetic Ligands

    Directory of Open Access Journals (Sweden)

    Leo Veenman

    2016-06-01

    Full Text Available The 18 kDa translocator protein (TSPO is highly 0conserved in eukaryotes and prokaryotes. Since its discovery in 1977, numerous studies established the TSPO’s importance for life essential functions. For these studies, synthetic TSPO ligands typically are applied. Tetrapyrroles present endogenous ligands for the TSPO. Tetrapyrroles are also evolutionarily conserved and regulate multiple functions. TSPO and tetrapyrroles regulate each other. In animals TSPO-tetrapyrrole interactions range from effects on embryonic development to metabolism, programmed cell death, response to stress, injury and disease, and even to life span extension. In animals TSPOs are primarily located in mitochondria. In plants TSPOs are also present in plastids, the nuclear fraction, the endoplasmic reticulum, and Golgi stacks. This may contribute to translocation of tetrapyrrole intermediates across organelles’ membranes. As in animals, plant TSPO binds heme and protoporphyrin IX. TSPO-tetrapyrrole interactions in plants appear to relate to development as well as stress conditions, including salt tolerance, abscisic acid-induced stress, reactive oxygen species homeostasis, and finally cell death regulation. In bacteria, TSPO is important for switching from aerobic to anaerobic metabolism, including the regulation of photosynthesis. As in mitochondria, in bacteria TSPO is located in the outer membrane. TSPO-tetrapyrrole interactions may be part of the establishment of the bacterial-eukaryote relationships, i.e., mitochondrial-eukaryote and plastid-plant endosymbiotic relationships.

  18. Recent Advances in Ligand and Structure Based Screening of Potent Quorum Sensing Inhibitors Against Antibiotic Resistance Induced Bacterial Virulence.

    Science.gov (United States)

    Nandi, Sisir

    2016-01-01

    Antibiotic resistance is a growing threat in the treatment of bacterial diseases. Bacterial invasion and its virulence can cause damage to the host cells via quorum sensing mechanism which is responsible for the intercellular communication among bacteria that regulates expression of many genes. Quorum sensing (QS) differentially expresses specific sets of genes which may produce resistance. Researchers have been devoted to develop more potent compounds against bacterial resistant quorum sensing inhibitors. A number of anti-quorum sensing approaches have been documented to screen potent inhibitors against quorum sensing induced bacterial virulence. Experimental screening of a large chemical compound library against a quorum sensing biological target is an established technology for lead identification but it is expensive, laborious and time consuming. Therefore, computer-aided high throughput ligand and structure based virtual screening are most effective pharmacoinformatic tools prior to experiment in this context. Ligand based screening includes quantitative structure-activity relationship (QSAR) and pharmacophore generation whereas techniques of structure based virtual screening include molecular docking. The study in this direction can increase the findings of hit rates and decrease cost of drug design and development by producing potent natural as well as synthetic anti-quorum sensing compounds. Most recent patent coverage on ligand and structure based design of novel bioactive quorum sensing inhibitors has been presented here. The paper has also critically reviewed the screening and design of potent quorum sensing inhibitor leads that would help in patenting novel leads active against bacterial virulence and minimizing antibiotic resistance among bacterial pathogens.

  19. Do leading indicators lead peaks more than troughs?

    NARCIS (Netherlands)

    R. Paap (Richard); R. Segers (René); D.J.C. van Dijk (Dick)

    2007-01-01

    textabstractWe develop a formal statistical approach to investigate the possibility that leading indicator variables have different lead times at business cycle peaks and troughs. For this purpose, we propose a novel Markov switching vector autoregressive model, where economic growth and leading

  20. Lead Contamination and Microbial Lead Tolerance in Soils at Major ...

    African Journals Online (AJOL)

    Devika

    ABSTRACT: Lead pollution and lead tolerance levels of microbes in soil at major road junctions in Benin. City were investigated. Results revealed that distance from the road junctions affected the concentrations of lead in soil, as well as the microbial population density and types of microbes present in the soil. The highest ...

  1. Blood lead level as biomarker of environmental lead pollution in ...

    African Journals Online (AJOL)

    The ideal blood lead level is now considered to be zero. Lead pollution of the study area has serious consequences on aquatic fauna and humans who consume such contaminated fish. It is therefore recommended that human and animal health surveillance and environmental monitoring of lead should be initiated.

  2. Lead Contamination and Microbial Lead Tolerance in Soils at Major ...

    African Journals Online (AJOL)

    Lead pollution and lead tolerance levels of microbes in soil at major road junctions in Benin City were investigated. Results revealed that distance from the road junctions affected the concentrations of lead in soil, as well as the microbial population density and types of microbes present in the soil. The highest concentrations ...

  3. Predicting Efficient Antenna Ligands for Tb(III) Emission

    Energy Technology Data Exchange (ETDEWEB)

    Samuel, Amanda P.S.; Xu, Jide; Raymond, Kenneth

    2008-10-06

    A series of highly luminescent Tb(III) complexes of para-substituted 2-hydroxyisophthalamide ligands (5LI-IAM-X) has been prepared (X = H, CH{sub 3}, (C=O)NHCH{sub 3}, SO{sub 3}{sup -}, NO{sub 2}, OCH{sub 3}, F, Cl, Br) to probe the effect of substituting the isophthalamide ring on ligand and Tb(III) emission in order to establish a method for predicting the effects of chromophore modification on Tb(III) luminescence. The energies of the ligand singlet and triplet excited states are found to increase linearly with the {pi}-withdrawing ability of the substituent. The experimental results are supported by time-dependent density functional theory (TD-DFT) calculations performed on model systems, which predict ligand singlet and triplet energies within {approx}5% of the experimental values. The quantum yield ({Phi}) values of the Tb(III) complex increases with the triplet energy of the ligand, which is in part due to the decreased non-radiative deactivation caused by thermal repopulation of the triplet. Together, the experimental and theoretical results serve as a predictive tool that can be used to guide the synthesis of ligands used to sensitize lanthanide luminescence.

  4. Ligand exchange in quaternary alloyed nanocrystals--a spectroscopic study.

    Science.gov (United States)

    Gabka, Grzegorz; Bujak, Piotr; Giedyk, Kamila; Kotwica, Kamil; Ostrowski, Andrzej; Malinowska, Karolina; Lisowski, Wojciech; Sobczak, Janusz W; Pron, Adam

    2014-11-14

    Exchange of initial, predominantly stearate ligands for pyridine in the first step and butylamine (BA) or 11-mercaptoundecanoic acid (MUA) in the second one was studied for alloyed quaternary Cu-In-Zn-S nanocrystals. The NMR results enabled us to demonstrate, for the first time, direct binding of the pyridine labile ligand to the nanocrystal surface as evidenced by paramagnetic shifts of the three signals attributed to its protons to 7.58, 7.95 and 8.75 ppm. XPS investigations indicated, in turn, a significant change in the composition of the nanocrystal surface upon the exchange of initial ligands for pyridine, which being enriched in indium in the 'as prepared' form became enriched in zinc after pyridine binding. This finding indicated that the first step of ligand exchange had to involve the removal of the surface layer enriched in indium with simultaneous exposure of a new, zinc-enriched layer. In the second ligand exchange step (replacement of pyridine with BA or MUA) the changes in the nanocrystal surface compositions were much less significant. The presence of zinc in the nanocrystal surface layer turned out necessary for effective binding of pyridine as shown by a comparative study of ligand exchange in Cu-In-Zn-S, Ag-In-Zn-S and CuInS2, carried out by complementary XPS and NMR investigations.

  5. Leaded gasoline - an environmental problem

    International Nuclear Information System (INIS)

    Petrushevska, Ljubica

    2001-01-01

    In the European countries it is a clear trend towards the increasing consumption of unleaded gasolines. Driving force of this trend is, on the one hand the high toxicity of lead compounds and on the other, the necessity of purification of exhaust gases by catalytic converters, for which the lead represent a catalyst poison. In Macedonia, the limit lead content in the leaded gasolines is relatively high (0,6 g/l), as well as the consumption of the leaded gasolines. Rapid and complete transition to unleaded gasolines can be realized by the concept of step by step reduction of lead in our gasolines. (Original)

  6. Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015.

    Science.gov (United States)

    Deng, Nanjie; Flynn, William F; Xia, Junchao; Vijayan, R S K; Zhang, Baofeng; He, Peng; Mentes, Ahmet; Gallicchio, Emilio; Levy, Ronald M

    2016-09-01

    We describe binding free energy calculations in the D3R Grand Challenge 2015 for blind prediction of the binding affinities of 180 ligands to Hsp90. The present D3R challenge was built around experimental datasets involving Heat shock protein (Hsp) 90, an ATP-dependent molecular chaperone which is an important anticancer drug target. The Hsp90 ATP binding site is known to be a challenging target for accurate calculations of ligand binding affinities because of the ligand-dependent conformational changes in the binding site, the presence of ordered waters and the broad chemical diversity of ligands that can bind at this site. Our primary focus here is to distinguish binders from nonbinders. Large scale absolute binding free energy calculations that cover over 3000 protein-ligand complexes were performed using the BEDAM method starting from docked structures generated by Glide docking. Although the ligand dataset in this study resembles an intermediate to late stage lead optimization project while the BEDAM method is mainly developed for early stage virtual screening of hit molecules, the BEDAM binding free energy scoring has resulted in a moderate enrichment of ligand screening against this challenging drug target. Results show that, using a statistical mechanics based free energy method like BEDAM starting from docked poses offers better enrichment than classical docking scoring functions and rescoring methods like Prime MM-GBSA for the Hsp90 data set in this blind challenge. Importantly, among the three methods tested here, only the mean value of the BEDAM binding free energy scores is able to separate the large group of binders from the small group of nonbinders with a gap of 2.4 kcal/mol. None of the three methods that we have tested provided accurate ranking of the affinities of the 147 active compounds. We discuss the possible sources of errors in the binding free energy calculations. The study suggests that BEDAM can be used strategically to discriminate

  7. A Ferrocene-Based Catecholamide Ligand: the Consequences of Ligand Swivel for Directed Supramolecular Self-Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Mugridge, Jeffrey; Fiedler, Dorothea; Raymond, Kenneth

    2010-02-04

    A ferrocene-based biscatecholamide ligand was prepared and investigated for the formation of metal-ligand supramolecular assemblies with different metals. Reaction with Ge(IV) resulted in the formation of a variety of Ge{sub n}L{sub m} coordination complexes, including [Ge{sub 2}L{sub 3}]{sup 4-} and [Ge{sub 2}L{sub 2}({mu}-OMe){sub 2}]{sup 2-}. The ligand's ability to swivel about the ferrocenyl linker and adopt different conformations accounts for formation of many different Ge{sub n}L{sub m} species. This study demonstrates why conformational ligand rigidity is essential in the rational design and directed self-assembly of supramolecular complexes.

  8. Deprotonation induced ligand-to-metal electron transfer: Synthesis of a mixed-valence Rh(-I,I) dinuclear compound and its reaction with dioxygen

    NARCIS (Netherlands)

    Tejel, C.; Ciriano, M.A.; del Río, M.P.; van den Bruele, F.J.; Hetterscheid, D.G.H.; Tsichlis i Spithas, N.; de Bruin, B.

    2008-01-01

    Treatment of bis(2-picolyl)amine (bpa) with [{Rh(nbd)(mu-OMe))(2)] leads to unexpected and unique redox asymmetric dinuclear Rh-I, Rh+I complex [{Rh(ndb)}(2)(bpa-2H)] (2) with a pi-coordinating imine bound to a tetrahedral low valent rhodate(-I). Mono-oxygenation of the deprotonated bpa ligand in 2

  9. Combining Stochastic Deformation/Relaxation and Intermolecular Contacts Analysis for Extracting Pharmacophores from Ligand-Receptor Complexes.

    Science.gov (United States)

    Hatmal, Ma'mon M; Taha, Mutasem O

    2018-04-23

    We previously combined molecular dynamics (classical or simulated annealing) with ligand-receptor contacts analysis as a means to extract valid pharmacophore model(s) from single ligand-receptor complexes. However, molecular dynamics methods are computationally expensive and time-consuming. Here we describe a novel method for extracting valid pharmacophore model(s) from a single crystallographic structure within a reasonable time scale. The new method is based on ligand-receptor contacts analysis following energy relaxation of a predetermined set of randomly deformed complexes generated from the targeted crystallographic structure. Ligand-receptor contacts maintained across many deformed/relaxed structures are assumed to be critical and used to guide pharmacophore development. This methodology was implemented to develop valid pharmacophore models for PI3K-γ, RENIN, and JAK1. The resulting pharmacophore models were validated by receiver operating characteristic (ROC) analysis against inhibitors extracted from the CHEMBL database. Additionally, we implemented pharmacophores extracted from PI3K-γ to search for new inhibitors from the National Cancer Institute list of compounds. The process culminated in new PI3K-γ/mTOR inhibitory leads of low micromolar IC 50 s.

  10. New organometallic imines of rhenium(i) as potential ligands of GSK-3β: synthesis, characterization and biological studies.

    Science.gov (United States)

    Muñoz-Osses, Michelle; Godoy, Fernando; Fierro, Angélica; Gómez, Alejandra; Metzler-Nolte, Nils

    2018-01-23

    Substituted amino-piperazine derivatives were synthesized and used as precursors for the preparation of a series of new organometallic Re(i) imine complexes with the general formula [(η 5 -C 5 H 4 CH[double bond, length as m-dash]N-(CH 2 ) 5 -Pz-R)Re(CO) 3 ] (Pz-R: -alkyl or aryl piperazine). The piperazine-based ligands were designed to be potential inhibitors of GSK-3β kinase. All the ligands and complexes were fully characterized and evaluated against the HT-29 and PT-45 cancer cell lines, in which GSK-3β plays a crucial role. In this context, we carried out biological evaluation using the MTT colorimetric assay. In terms of structure activity relationship, our findings indicated improved biological activity when aromaticity increased in the organic ligands (3d). In addition, the presence of the rhenium fragment in the imines (5a-d) leads to better activity with IC 50 values in the range of 25-100 μM. In addition, our experimental studies were complemented by computational studies, where the volume and electrostatic surface of the organic ligands and organometallic compounds as well as their binding to the kinase protein are calculated.

  11. Secondary ligand-directed assembly of Co(II) coordination polymers based on a pyridine carboxylate ligand

    International Nuclear Information System (INIS)

    Cao, Ke-Li; Zhang, Yi-Ping; Cai, Yi-Ni; Xu, Xiao-Wei; Feng, Yun-Long

    2014-01-01

    To investigate the influence of hydrogen bonds and secondary ligands on the structures and properties of the resulting frameworks, five new Co(II) compounds have been synthesized by the reactions of Co(II) salts and 3,5-bis(pyridin-4-ylmethoxy)benzoic acid (HL) with four rationally selected dicarboxylic acid ligands. Without secondary ligand, we got one compound [CoL 2 (H 2 O) 2 ] n ·2nH 2 O (1), which possesses a 1D chain structure. In the presence of ancillary ligands, namely, 1,3-adamantanedicarboxylic acid (H 2 adbc), terephthalic acid (H 2 tpa), thiophene-2,5-dicarboxylic acid (H 2 tdc) and 1,4-benzenedithioacetic acid (H 2 bdtc), four 3D structures [Co 2 L 2 (adbc)] n ·nH 2 O (2), [Co 2 L 2 (tpa)] n (3), [Co 2 L 2 (tdc)] n (4), [Co 2 L 2 (bdtc)(H 2 O)] n (5) were obtained, respectively. It can be observed from the architectures of 1–5 that hydrogen bonds and secondary ligands both have great effects on the spatial connective fashions, resulting in the formation of various dimensional compounds. The XRPD, TGA data of title polymers and the magnetic properties for 2 and 5 have also been investigated. - Graphical abstract: The structural differences show that the ancillary ligands have great effects on the spatial connective fashions, resulting in the formation of various dimensional compounds. - Highlights: • Five new Co(II) coordination polymers have been synthesized by solvothermal reactions based on 3,5-bis(pyridin-4-ylmethoxy)benzoic acid (HL). • The long-flexible ligand (HL) is a good candidate to produce interpenetrating architectures. • The secondary dicarboxylic acid ligands play important roles in the spatial connective fashions and the formation of various dimensional compounds. • The magnetism studies show that both 2 and 5 exhibit antiferromagnetic interactions

  12. Integration of screening and identifying ligand(s) from medicinal plant extracts based on target recognition by using NMR spectroscopy

    OpenAIRE

    sprotocols

    2015-01-01

    Authors: Yalin Tang, Qian Shang, Junfeng Xiang, Qianfan Yang, Qiuju Zhou, Lin Li, Hong Zhang, Qian Li, Hongxia Sun, Aijiao Guan, Wei Jiang & Wei Gai ### Abstract This protocol presents the screening of ligand(s) from medicinal plant extracts based on target recognition by using NMR spectroscopy. A detailed description of sample preparation and analysis process is provided. NMR spectroscopies described here are 1H NMR, diffusion-ordered spectroscopy (DOSY), relaxation-edited NMR, 1H–1...

  13. An Analysis of Central Residues Between Ligand-Bound and Ligand-Free Protein Structures Based on Network Approach.

    Science.gov (United States)

    Amala, Arumugam; Emerson, Isacc Arnold

    2017-08-01

    Depiction of protein structures as networks of interacting residues has enabled us to understand the structure and function of the protein. Previous investigations on closeness centrality have identified protein functional sites from three- dimensional structures. It is well recognized that ligand binding to a receptor protein induces a wide range of structural changes. An interesting question is how central residues function during conformational changes triggered during ligand binding? The aim of this study is to comprehend at what extent central residues change during ligand binding to receptor proteins. To determine this, we examined 37 pairs of protein structures consisting of ligand-bound and ligand-free forms. These protein structures were modelled as an undirected network and significant central residues were obtained using residue centrality measures. In addition to these, the basic network parameters were also analysed. On analysing the residue centrality measures, we observed that 60% of central residues were common in both the ligand-bound and ligand-free states. The geometry of the central residues revealed that they were situated closer to the protein center of the mass. Finally, we demonstrated the effectiveness of central residues in amino acids substitutions and in the evolution itself. The closeness centrality was also analyzed among different protein domain sizes and the values gradually declined from single-domains to multi-domain proteins suggesting that the network has potential for hierarchical organization. Betweenness centrality measure was also used to determine the central residues and 31% of these residues were common between the holo/apo states. Findings reveal that central residues play a significant role in determining the functional properties of proteins. These results have implications in predicting binding/active site residues, specifically in the context of drug designing, if additional information concerning ligand binding is

  14. Secondary lead production in Malaysia

    Science.gov (United States)

    Phillips, M. J.; Lim, S. S.

    The increase in the number of vehicles and, subsequently, the volume of batteries made by manufacturers in Malaysia have seen a dramatic rise in lead demand over the last five years. Without any lead mines, the only source of lead in Malaysia has been from the recycling of lead/acid batteries. Metal Reclamation (Industries) has commenced the design of a new and advanced secondary lead plant at West Port, Malaysia to meet the increasing demand for lead and the increasingly stringent environmental regulations. The plant is designed to produce up to 75 000 t of lead and lead alloys per year. The plant will also produce, as by-products: polypropylene chips, wallboard-grade gypsum, non-leachable slag for use in construction. A discussion of the process and the products from the new secondary smelter is outlined.

  15. Safety and Health Topics: Lead

    Science.gov (United States)

    ... enters the body primarily through inhalation and ingestion. Today, adults are mainly exposed to lead by breathing ... can provide a snapshot of industry sectors and business subcategories where lead air concentrations have been found. ...

  16. String method solution of the gating pathways for a pentameric ligand-gated ion channel

    Science.gov (United States)

    Lev, Bogdan; Murail, Samuel; Poitevin, Frédéric; Cromer, Brett A.; Delarue, Marc; Allen, Toby W.

    2017-01-01

    Pentameric ligand-gated ion channels control synaptic neurotransmission by converting chemical signals into electrical signals. Agonist binding leads to rapid signal transduction via an allosteric mechanism, where global protein conformational changes open a pore across the nerve cell membrane. We use all-atom molecular dynamics with a swarm-based string method to solve for the minimum free-energy gating pathways of the proton-activated bacterial GLIC channel. We describe stable wetted/open and dewetted/closed states, and uncover conformational changes in the agonist-binding extracellular domain, ion-conducting transmembrane domain, and gating interface that control communication between these domains. Transition analysis is used to compute free-energy surfaces that suggest allosteric pathways; stabilization with pH; and intermediates, including states that facilitate channel closing in the presence of an agonist. We describe a switching mechanism that senses proton binding by marked reorganization of subunit interface, altering the packing of β-sheets to induce changes that lead to asynchronous pore-lining M2 helix movements. These results provide molecular details of GLIC gating and insight into the allosteric mechanisms for the superfamily of pentameric ligand-gated channels. PMID:28487483

  17. Dual ligand/receptor interactions activate urothelial defenses against uropathogenic E. coli

    Science.gov (United States)

    Liu, Yan; Mémet, Sylvie; Saban, Ricardo; Kong, Xiangpeng; Aprikian, Pavel; Sokurenko, Evgeni; Sun, Tung-Tien; Wu, Xue-Ru

    2015-01-01

    During urinary tract infection (UTI), the second most common bacterial infection, dynamic interactions take place between uropathogenic E. coli (UPEC) and host urothelial cells. While significant strides have been made in the identification of the virulence factors of UPEC, our understanding of how the urothelial cells mobilize innate defenses against the invading UPEC remains rudimentary. Here we show that mouse urothelium responds to the adhesion of type 1-fimbriated UPEC by rapidly activating the canonical NF-κB selectively in terminally differentiated, superficial (umbrella) cells. This activation depends on a dual ligand/receptor system, one between FimH adhesin and uroplakin Ia and another between lipopolysaccharide and Toll-like receptor 4. When activated, all the nuclei (up to 11) of a multinucleated umbrella cell are affected, leading to significant amplification of proinflammatory signals. Intermediate and basal cells of the urothelium undergo NF-κB activation only if the umbrella cells are detached or if the UPEC persistently express type 1-fimbriae. Inhibition of NF-κB prevents the urothelium from clearing the intracellular bacterial communities, leading to prolonged bladder colonization by UPEC. Based on these data, we propose a model of dual ligand/receptor system in innate urothelial defenses against UPEC. PMID:26549759

  18. A thermal responsive affinity ligand for precipitation of sialylated proteins

    Directory of Open Access Journals (Sweden)

    Lindsay Arnold

    2016-01-01

    Full Text Available We report here the development of a thermal responsive affinity ligand specific to sialic acid, sialic acid containing oligosaccharides, glycoproteins, and other sialylated glycoconjugates. The ligand is a fusion protein of 40 repeats of pentapeptide of an elastin like polymer (ELP and the 21 kD sialic acid binding domain of a Vibrio cholera neuraminidase (VCNA. For cost-effective synthesis, the fusion protein was targeted to the periplasmic space of an E. coli lpp deletion mutant, resulting in its secretion to the growth medium. A pre-induction heat-shock step at 42 ˚C for 20 minutes was necessary to achieve high level expression of the ligand. Under optimized induction condition (18 ˚C, 0.1 mM IPTG and 48 hours of post-induction cultivation, the ligand was produced to about 100 mg/L. The ligand exhibited a transition temperature of 52 ˚C, which could be depressed to 37 ˚C with the addition of 0.5 M NaCl. Using fetuin as a model sialylated protein, the ligand was applied in an affinity precipitation process to illustrate its potential application in glycoprotein isolation. The ligand captured 100% fetuin from an aqueous solution when the molar ratio of ligand to fetuin was 10 to 1, which was lower than the expected for full titration of sialic acid on the glycoprotein by the lectin. Elution of fetuin from ligand was achieved with PBS buffer containing 2 mM sialic acid. To evaluate how protein and other contaminants influence the recovery of sialylated proteins, CHO medium was spiked into the fetuin solution. The predominant protein species in CHO medium was found to be albumin. Although its removal of over 94% was evident, purified fetuin contained some albumin due to its over-abundance. Additional experiments with albumin contaminant of varying concentrations showed that below 1 mg/L, albumin had no impact on the affinity precipitation, whereas above 10 mg/L, some albumin was co-purified with fetuin. However, even at 50 mg/ml, fetuin

  19. Environmental Lead and Children's Health.

    Science.gov (United States)

    Lewis, Marie

    This paper discusses the threat to children's health posed by environmental exposure to lead, focusing on public policy issues surrounding lead exposure in New South Wales (NSW), Australia. In Australia, the current blood lead level at which there is a health concern is at or above 25 micrograms per deciliter (ug/dl) of blood for infants and…

  20. Accuracy and precision of protein–ligand interaction kinetics determined from chemical shift titrations

    International Nuclear Information System (INIS)

    Markin, Craig J.; Spyracopoulos, Leo

    2012-01-01

    NMR-monitored chemical shift titrations for the study of weak protein–ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K D ) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K D value of a 1:1 protein–ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125–138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of 1 H– 15 N 2D HSQC NMR spectra acquired using precise protein–ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k off ). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k off ∼ 3,000 s −1 in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k off from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k off values over a wide range, from 100 to 15,000 s −1 . The validity of line shape analysis for k off values approaching intermediate exchange (∼100 s −1 ), may be facilitated by more accurate K D measurements from NMR

  1. Designer ligands. Part 14. Novel Mn(lI), Ni(II) and Zn(II) complexes of benzamide- and biphenyl-derived ligands

    CSIR Research Space (South Africa)

    Wellington, Kevin W

    2009-01-01

    Full Text Available Manganese (II), nickel (II) and zinc (II) complexes have been prepared using various benzamideand biphenyl-derived ligands; their structures have been investigated using infrared spectroscopy and it is apparent that, depending on the ligand...

  2. Presence of lead in opium.

    Science.gov (United States)

    Aghaee-Afshar, Mahmoud; Khazaeli, Payam; Behnam, Behzad; Rezazadehkermani, Mohammad; Ashraf-Ganjooei, Narges

    2008-09-01

    Opium addiction is a common form of addiction in Middle East countries such as Iran. Recently several reports suggested some kinds of pathologic findings such as abdominal pain, nephropathy, and anemia in opium addict patients. Such pathologic findings suggest lead poisoning in the patients. In this study, the concentration of lead in 10 opium samples was evaluated. The mean concentration of lead in the opium samples was 1.88 ppm. This may explain some of the pathologic findings found in addict patients. The authors would suggest further investigations to evaluate the lead concentration in opium addicts' sera and also routine screening for lead poisoning in opium addict patients.

  3. Neurophysiological effects of lead exposure

    Energy Technology Data Exchange (ETDEWEB)

    Rosen, I.; Wildt, K.; Gullberg, B.; Berlin, M.

    1983-10-01

    A series of neurophysiological variables was measured for men occupationally exposed to lead. The results were related to the degree of lead exposure and to the concentrations of lead and zinc protoporphyrin in blood. A small but significant correlation was observed between lead exposure and motor and sensory conduction velocities in the lower limbs, the conduction velocities of slow motor fibers in the upper limbs, and also sensory nerve action potentials. It is suggested that a neurophysiological examination should be considered in the surveillance of the health of lead workers.

  4. 2 : 2 Fe(III): ligand and "adamantane core" 4 : 2 Fe(III): ligand (hydr)oxo complexes of an acyclic ditopic ligand

    DEFF Research Database (Denmark)

    Ghiladi, Morten; Larsen, Frank B.; McKenzie, Christine J.

    2005-01-01

    bond lengths of the two different octahedral iron sites: Fe -mu-OH, 1.953( 5), 2.013( 5) angstrom and Fe-mu-O, 1.803( 5), 1.802( 5) angstrom. The difference in ligand environment is too small for allowing Mossbauer spectroscopy to distinguish between the two crystallographically independent Fe sites...

  5. Microassay for measurement of binding of radiolabelled ligands to cell surface molecules

    International Nuclear Information System (INIS)

    Woof, J.M.; Burton, D.R.

    1988-01-01

    An improved technique for measuring the binding of radiolabelled ligands to cell surface molecules has been developed by modification of a procedure using centrifugation through a water-immiscible oil to separate free and cell-bound ligand. It maximises the percentage of ligand bound since cell-bound and free ligand can be separated easily and reproducibly even when very small reaction volumes are used. This permits low levels of ligand radiolabelling and relatively low numbers of cells to be used

  6. Ligand-specific conformational changes in the alpha1 glycine receptor ligand-binding domain

    DEFF Research Database (Denmark)

    Pless, Stephan Alexander; Lynch, Joseph W

    2009-01-01

    , and by the antagonist, strychnine. Voltage-clamp fluorometry involves labeling introduced cysteines with environmentally sensitive fluorophores and inferring structural rearrangements from ligand-induced fluorescence changes. In the inner beta-sheet, we labeled residues in loop 2 and in binding domain loops D and E....... At each position, strychnine and glycine induced distinct maximal fluorescence responses. The pre-M1 domain responded similarly; at each of four labeled positions glycine produced a strong fluorescence signal, whereas strychnine did not. This suggests that glycine induces conformational changes...... in the inner beta-sheet and pre-M1 domain that may be important for activation, desensitization, or both. In contrast, most labeled residues in loops C and F yielded fluorescence changes identical in magnitude for glycine and strychnine. A notable exception was H201C in loop C. This labeled residue responded...

  7. Blood lead and lead-210 origins in residents of Toulouse

    International Nuclear Information System (INIS)

    Servant, J.; Delapart, M.

    1981-01-01

    Blood lead and lead-210 analyses were performed on blood samples from non-smoking residents of Toulouse (city of 400,000 inhabitants). Simultaneous surface soil lead content determinations were carried out by the same procedure on rural zone samples of southwestern France. The observed isotopic ratios were compared in order to evaluate food chain contamination. For an average of 19.7 +- 5.8 μg 100 cc -1 of lead in blood, atmospheric contamination amounts to 20%, estimated as follows: 6% from direct inhalation and 14% from dry deposits on vegetation absorbed as food. The natural levels carried over by the food chain reach 14.9 μg 100 cc -1 and have a 210 Pb/Pb concentration ratio of 0.055 dpmμg -1 . These results lead to a maximum value of 15 μg 100 cc -1 for natural lead in human blood according to the ICRP model. (author)

  8. Lead content of calcium supplements.

    Science.gov (United States)

    Ross, E A; Szabo, N J; Tebbett, I R

    2000-09-20

    Substantial quantities of lead have been reported in some over-the-counter calcium supplement preparations, including not only bone-meal and dolomite, but also over-the-counter natural and refined calcium carbonate formulations. Examination of this issue is warranted given recent increases in physician recommendations for calcium supplements for prevention and treatment of osteoporosis. To determine the lead content of calcium supplements and to quantify the lead exposure from popular brands of calcium in dosages used for childhood recommended daily allowance, osteoporosis, and phosphate binding in dialysis patients. Analysis of lead content in 21 formulations of nonprescription calcium carbonate (including 7 natural [ie, oyster shell] and 14 refined), 1 brand of prescription-only calcium acetate, and 1 noncalcium synthetic phosphate binder conducted in March 2000. Lead content, assayed using electrothermal atomic absorption, expressed as micrograms of lead per 800 mg/d of elemental calcium, per 1500 mg/d of calcium, and for a range of dosages for patients with renal failure. Six microg/d of lead was considered the absolute dietary limit, with no more than 1 microg/d being the goal for supplements. Four of 7 natural products had measurable lead content, amounting to approximately 1 microg/d for 800 mg/d of calcium, between 1 and 2 microg/d for 1500 mg/d of calcium, and up to 10 microg/d for renal dosages. Four of the 14 refined products had similar lead content, including up to 3 microg/d of lead in osteoporosis calcium dosages and up to 20 microg/d in high renal dosages. No lead was detected in the calcium acetate or polymer products. Lead was present even in some brand name products from major pharmaceutical companies not of natural oyster shell derivation. Despite increasingly stringent limits of lead exposure, many calcium supplement formulations contain lead and thereby may pose an easily avoidable public health concern. JAMA. 2000;284:1425-1429.

  9. Light-Induced Copper(II) Coordination by a Bicyclic Tetraaza Chelator through a Ligand-to-Metal Charge-Transfer Reaction

    DEFF Research Database (Denmark)

    Holm-Jørgensen, Jacob Rørdam; Jensen, Mikael; Bjerrum, Morten J.

    2011-01-01

    To enable utilization of the broad potential of copper isotopes in nuclear medicine, rapid and robust chelation of the copper is required. Bowl adamanzanes (bicyclic tetraaza ligands) can form kinetically stable copper complexes, but they are usually formed at low rates unless high pH values...... coordinated amine groups) at pH above 6. These findings are supported by pH titrations of mixtures of Cu2+ and [24.31]adz in water. Irradiation of this complex in the ligand-to-metal charge-transfer (LMCT) band by a diode-array spectrophotometer leads to photodeprotonation and subsequently to formation...

  10. Aluminum complexes of the redox-active [ONO] pincer ligand.

    Science.gov (United States)

    Szigethy, Géza; Heyduk, Alan F

    2012-07-14

    A series of aluminum complexes containing the tridentate, redox-active ligand bis(3,5-di-tert-butyl-2-phenol)amine ([ONO]H(3)) in three different oxidation states were synthesized. The aluminum halide salts AlCl(3) and AlBr(3) were reacted with the doubly deprotonated form of the ligand to afford five-coordinate [ONHO(cat)]AlX(solv) complexes (1a, X = Cl, solv = OEt(2); 1b, X = Br, solv = THF), each having a trigonal bipyramidal coordination geometry at the aluminum and containing the [ONHO(cat)](2-) ligand with a protonated, sp(3)-hybridized nitrogen donor. The [ONO] ligand platform may also be added to aluminum through the use of the oxidized ligand salt [ONO(q)]K, which was reacted with AlCl(3) in the presence of either diphenylacetylacetonate (acacPh(2)(-)) or 8-oxyquinoline (quinO(-)) to afford [ONO(q)]Al(acacPh(2))Cl (2) or [ONO(q)]Al(quinO)Cl (3), respectively, with well-defined [ONO(q)](-) ligands. Quinonate complexes 2 and 3 were reduced by one electron to afford the corresponding complexes K{[ONO(sq)]Al(acacPh(2))(py)} (4) and K{[ONO(sq)]Al(quinO)(py)} (5), respectively, containing well-defined [ONO(sq)](2-) ligands. The addition of tetrachloro-1,2-quinone to 1a in the presence of pyridine resulted in the expulsion of HCl and the formation of an aluminum complex with two different redox active ligands, [ONO]Al(o-O(2)C(6)Cl(4))(py) (6). Similar results were obtained when 1a was reacted with 9,10-phenanthrenequinone to afford [ONO]Al(o-O(2)C(14)H(8))(py) (7) or with pyrene-4,5-dione to afford [ONO]Al(o-O(2)C(16)H(8))(py) (8). Structural, spectroscopic and preliminary magnetic measurements on 6-8 suggest ligand non-innocent redox behavior in these complexes.

  11. Lead

    Science.gov (United States)

    ... Center for Environmental Health , Division of Emergency and Environmental Health Services Email Recommend Tweet YouTube Instagram Listen Watch RSS ABOUT About CDC Jobs Funding LEGAL Policies Privacy FOIA No Fear Act OIG 1600 Clifton ...

  12. Cloud computing for protein-ligand binding site comparison.

    Science.gov (United States)

    Hung, Che-Lun; Hua, Guan-Jie

    2013-01-01

    The proteome-wide analysis of protein-ligand binding sites and their interactions with ligands is important in structure-based drug design and in understanding ligand cross reactivity and toxicity. The well-known and commonly used software, SMAP, has been designed for 3D ligand binding site comparison and similarity searching of a structural proteome. SMAP can also predict drug side effects and reassign existing drugs to new indications. However, the computing scale of SMAP is limited. We have developed a high availability, high performance system that expands the comparison scale of SMAP. This cloud computing service, called Cloud-PLBS, combines the SMAP and Hadoop frameworks and is deployed on a virtual cloud computing platform. To handle the vast amount of experimental data on protein-ligand binding site pairs, Cloud-PLBS exploits the MapReduce paradigm as a management and parallelizing tool. Cloud-PLBS provides a web portal and scalability through which biologists can address a wide range of computer-intensive questions in biology and drug discovery.

  13. Sensitive and specific detection of ligands using engineered riboswitches.

    Science.gov (United States)

    Morse, Daniel P; Nevins, Colin E; Aggrey-Fynn, Joana; Bravo, Rick J; Pfaeffle, Herman O I; Laney, Jess E

    2018-03-05

    Riboswitches are RNA elements found in non-coding regions of messenger RNAs that regulate gene expression through a ligand-triggered conformational change. Riboswitches typically bind tightly and specifically to their ligands, so they have the potential to serve as highly effective sensors in vitro. In B. subtilis and other gram-positive bacteria, purine nucleotide synthesis is regulated by riboswitches that bind to guanine. We modified the xpt-pbuX guanine riboswitch for use in a fluorescence quenching assay that allowed us to specifically detect and quantify guanine in vitro. Using this assay, we reproducibly detected as little as 5 nM guanine. We then produced sensors for 2'-deoxyguanosine and cyclic diguanylate (c-diGMP) by appending the P1 stem of the guanine riboswitch to the ligand-binding domains of a 2'-deoxyguanosine riboswitch and a c-diGMP riboswitch. These hybrid sensors could detect 15 nM 2'-deoxyguanosine and 3 nM c-diGMP, respectively. Each sensor retained the ligand specificity of its corresponding natural riboswitch. In order to extend the utility of our approach, we developed a strategy for the in vitro selection of sensors with novel ligand specificity. Here we report a proof-of-principle experiment that demonstrated the feasibility of our selection strategy. Published by Elsevier B.V.

  14. Structural basis for EGFR ligand sequestration by Argos.

    Science.gov (United States)

    Klein, Daryl E; Stayrook, Steven E; Shi, Fumin; Narayan, Kartik; Lemmon, Mark A

    2008-06-26

    Members of the epidermal growth factor receptor (EGFR) or ErbB/HER family and their activating ligands are essential regulators of diverse developmental processes. Inappropriate activation of these receptors is a key feature of many human cancers, and its reversal is an important clinical goal. A natural secreted antagonist of EGFR signalling, called Argos, was identified in Drosophila. We showed previously that Argos functions by directly binding (and sequestering) growth factor ligands that activate EGFR. Here we describe the 1.6-A resolution crystal structure of Argos bound to an EGFR ligand. Contrary to expectations, Argos contains no EGF-like domain. Instead, a trio of closely related domains (resembling a three-finger toxin fold) form a clamp-like structure around the bound EGF ligand. Although structurally unrelated to the receptor, Argos mimics EGFR by using a bipartite binding surface to entrap EGF. The individual Argos domains share unexpected structural similarities with the extracellular ligand-binding regions of transforming growth factor-beta family receptors. The three-domain clamp of Argos also resembles the urokinase-type plasminogen activator (uPA) receptor, which uses a similar mechanism to engulf the EGF-like module of uPA. Our results indicate that undiscovered mammalian counterparts of Argos may exist among other poorly characterized structural homologues. In addition, the structures presented here define requirements for the design of artificial EGF-sequestering proteins that would be valuable anti-cancer therapeutics.

  15. Chiral ligand exchange countercurrent chromatography: Enantioseparation of amino acids.

    Science.gov (United States)

    Xiong, Qing; Jin, Jing; Lv, Liqiong; Bu, Zhisi; Tong, Shengqiang

    2018-03-01

    This work deals with the enantioseparation of α-amino acids by chiral ligand exchange high-speed countercurrent chromatography using N-n-dodecyl-l-hydroxyproline as a chiral ligand and copper(II) as a transition metal ion. A biphasic solvent system composed of n-hexane/n-butanol/aqueous phase with different volume ratios was selected for each α-amino acid. The enantioseparation conditions were optimized by enantioselective liquid-liquid extractions, in which the main influence factors, including type of chiral ligand, concentration of chiral ligand and transition metal ion, separation temperature, and pH of the aqueous phase, were investigated for racemic phenylalanine. Altogether, we tried to enantioseparate 15 racemic α-amino acids by the analytical countercurrent chromatography, of which only five of them could be successfully enantioseparated. Different elution sequence for phenylalanine enantiomer was observed compared with traditional liquid chromatography and the proposed interactions between chiral ligand, transition metal ion (Cu 2+ ), and enantiomer are discussed. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. The chemistry of separations ligand degradation by organic radical cations

    International Nuclear Information System (INIS)

    Mezyk, S.P.; Horne, G.P.; Mincher, B.J.; Zalupski, P.R.; Cook, A.R.; Wishart, J.F.

    2016-01-01

    Solvent based extractions of used nuclear fuel use designer ligands in an organic phase extracting ligand complexed metal ions from an acidic aqueous phase. These extractions will be performed in highly radioactive environments, and the radiation chemistry of all these complexing agents and their diluents will play a major role in determining extraction efficiency, separation factors, and solvent-recycle longevity. Although there has been considerable effort in investigating ligand damage occurring in acidic water radiolysis conditions, only minimal fundamental kinetic and mechanistic data has been reported for the degradation of extraction ligands in the organic phase. Extraction solvent phases typically use normal alkanes such as dodecane, TPH, and kerosene as diluents. The radiolysis of such diluents produce a mixture of radical cations (R .+ ), carbon-centered radicals (R . ), solvated electrons, and molecular products such as hydrogen. Typically, the radical species will preferentially react with the dissolved oxygen present to produce relatively inert peroxyl radicals. This isolates the alkane radical cation species, R .+ as the major radiolytically-induced organic species that can react with, and degrade, extraction agents in this phase. Here we report on our recent studies of organic radical cation reactions with 2 ligands: CMPO and TODGA. Elucidating these parameters, and combining them with the known acidic aqueous phase chemistry, will allow a full, fundamental, understanding of the impact of radiation on solvent extraction based separation processes to be achieved. (authors)

  17. High-Temperature Magnetism as a Probe for Structural and Compositional Uniformity in Ligand-Capped Magnetite Nanoparticles.

    Science.gov (United States)

    Kolen'ko, Yury V; Bañobre-López, Manuel; Rodríguez-Abreu, Carlos; Carbó-Argibay, Enrique; Deepak, Francis Leonard; Petrovykh, Dmitri Y; Cerqueira, M Fátima; Kamali, Saeed; Kovnir, Kirill; Shtansky, Dmitry V; Lebedev, Oleg I; Rivas, Jose

    2014-12-04

    To investigate magnetostructural relationships in colloidal magnetite (Fe 3 O 4 ) nanoparticles (NPs) at high temperature (300-900 K), we measured the temperature dependence of magnetization ( M ) of oleate-capped magnetite NPs ca. 20 nm in size. Magnetometry revealed an unusual irreversible high-temperature dependence of M for these NPs, with dip and loop features observed during heating-cooling cycles. Detailed characterizations of as-synthesized and annealed Fe 3 O 4 NPs as well as reference ligand-free Fe 3 O 4 NPs indicate that both types of features in M ( T ) are related to thermal decomposition of the capping ligands. The ligand decomposition upon the initial heating induces a reduction of Fe 3+ to Fe 2+ and the associated dip in M , leading to more structurally and compositionally uniform magnetite NPs. Having lost the protective ligands, the NPs continually sinter during subsequent heating cycles, resulting in divergent M curves featuring loops. The increase in M with sintering proceeds not only through elimination of a magnetically dead layer on the particle surface, as a result of a decrease in specific surface area with increasing size, but also through an uncommonly invoked effect resulting from a significant change in Fe 3+ /Fe 2+ ratio with heat treatment. The interpretation of irreversible features in M ( T ) indicates that reversible M ( T ) behavior, conversely, can be expected only for ligand-free, structurally and compositionally uniform magnetite NPs, suggesting a general applicability of high-temperature M ( T ) measurements as an analytical method for probing the structure and composition of magnetic nanomaterials.

  18. Structural analysis of prolyl oligopeptidases using molecular docking and dynamics: insights into conformational changes and ligand binding.

    Directory of Open Access Journals (Sweden)

    Swati Kaushik

    Full Text Available Prolyl oligopeptidase (POP is considered as an important pharmaceutical target for the treatment of numerous diseases. Despite enormous studies on various aspects of POPs structure and function still some of the questions are intriguing like conformational dynamics of the protein and interplay between ligand entry/egress. Here, we have used molecular modeling and docking based approaches to unravel questions like differences in ligand binding affinities in three POP species (porcine, human and A. thaliana. Despite high sequence and structural similarity, they possess different affinities for the ligands. Interestingly, human POP was found to be more specific, selective and incapable of binding to a few planar ligands which showed extrapolation of porcine POP in human context is more complicated. Possible routes for substrate entry and product egress were also investigated by detailed analyses of molecular dynamics (MD simulations for the three proteins. Trajectory analysis of bound and unbound forms of three species showed differences in conformational dynamics, especially variations in β-propeller pore size, which was found to be hidden by five lysine residues present on blades one and seven. During simulation, β-propeller pore size was increased by ∼2 Å in porcine ligand-bound form which might act as a passage for smaller product movement as free energy barrier was reduced, while there were no significant changes in human and A. thaliana POPs. We also suggest that these differences in pore size could lead to fundamental differences in mode of product egress among three species. This analysis also showed some functionally important residues which can be used further for in vitro mutagenesis and inhibitor design. This study can help us in better understanding of the etiology of POPs in several neurodegenerative diseases.

  19. Combined processing of lead concentrates

    Science.gov (United States)

    Kubasov, V. L.; Paretskii, V. M.; Sidorin, G. N.; Travkin, V. F.

    2013-06-01

    A combined scheme of processing of lead concentrates with the production of pure metallic lead and the important components containing in these concentrates is considered. This scheme includes sulfating roasting of the lead concentrates and two-stage leaching of the formed cinder with the formation of a sulfate solution and lead sulfate. When transformed into a carbonate form, lead sulfate is used for the production of pure metallic lead. Silver, indium, copper, cadmium, nickel, cobalt, and other important components are separately extracted from a solution. At the last stage, zinc is extracted by either extraction followed by electrolytic extraction of a metal or the return of the forming solution of sulfuric acid to cinder leaching.

  20. Taking the Lead : Gender, Social Context and Preference to Lead

    NARCIS (Netherlands)

    Hong, A.P.C.I.; Schaafsma, J.; van der Wijst, P.J.

    2014-01-01

    Previous research has demonstrated that women tend to emerge as leaders less often than men. In the present study, we examined to what extent women's and men's preference to lead is influenced by social context. It was hypothesized that women have a less strong preference to lead than men in a

  1. Genetic susceptibility to lead poisoning.

    OpenAIRE

    Onalaja, A O; Claudio, L

    2000-01-01

    Major strides have been taken in the regulation of lead intoxication in the general population, but studies using genetic markers of susceptibility to environmental toxicants raise the question of whether genes can make certain individuals more vulnerable to environmental toxins such as lead. At least three polymorphic genes have been identified that potentially can influence the bioaccumulation and toxicokinetics of lead in humans. The first gene to be discussed in this review is the gene co...

  2. Archives of Atmospheric Lead Pollution

    Science.gov (United States)

    Weiss, Dominik; Shotyk, William; Kempf, Oliver

    Environmental archives such as peat bogs, sediments, corals, trees, polar ice, plant material from herbarium collections, and human tissue material have greatly helped to assess both ancient and recent atmospheric lead deposition and its sources on a regional and global scale. In Europe detectable atmospheric lead pollution began as early as 6000years ago due to enhanced soil dust and agricultural activities, as studies of peat bogs reveal. Increased lead emissions during ancient Greek and Roman times have been recorded and identified in many long-term archives such as lake sediments in Sweden, ice cores in Greenland, and peat bogs in Spain, Switzerland, the United Kingdom, and the Netherlands. For the period since the Industrial Revolution, other archives such as corals, trees, and herbarium collections provide similar chronologies of atmospheric lead pollution, with periods of enhanced lead deposition occurring at the turn of the century and since 1950. The main sources have been industry, including coal burning, ferrous and nonferrous smelting, and open waste incineration until c.1950 and leaded gasoline use since 1950. The greatest lead emissions to the atmosphere all over Europe occurred between 1950 and 1980 due to traffic exhaust. A marked drop in atmospheric lead fluxes found in most archives since the 1980s has been attributed to the phasing out of leaded gasoline. The isotope ratios of lead in the various archives show qualitatively similar temporal changes, for example, the immediate response to the introduction and phasing out of leaded gasoline. Isotope studies largely confirm source assessments based on lead emission inventories and allow the contributions of various anthropogenic sources to be calculated.

  3. Safe leads and lead changes in competitive team sports

    Science.gov (United States)

    Clauset, A.; Kogan, M.; Redner, S.

    2015-06-01

    We investigate the time evolution of lead changes within individual games of competitive team sports. Exploiting ideas from the theory of random walks, the number of lead changes within a single game follows a Gaussian distribution. We show that the probability that the last lead change and the time of the largest lead size are governed by the same arcsine law, a bimodal distribution that diverges at the start and at the end of the game. We also determine the probability that a given lead is "safe" as a function of its size L and game time t . Our predictions generally agree with comprehensive data on more than 1.25 million scoring events in roughly 40 000 games across four professional or semiprofessional team sports, and are more accurate than popular heuristics currently used in sports analytics.

  4. High temperature superconductor current leads

    Science.gov (United States)

    Hull, John R.; Poeppel, Roger B.

    1995-01-01

    An electrical lead having one end for connection to an apparatus in a cryogenic environment and the other end for connection to an apparatus outside the cryogenic environment. The electrical lead includes a high temperature superconductor wire and an electrically conductive material distributed therein, where the conductive material is present at the one end of the lead at a concentration in the range of from 0 to about 3% by volume, and at the other end of the lead at a concentration of less than about 20% by volume. Various embodiments are shown for groups of high temperature superconductor wires and sheaths.

  5. Lead Poisoning in Wild Birds

    Science.gov (United States)

    Lahner, Lesanna L.; Franson, J. Christian

    2009-01-01

    Lead in its various forms has been used for thousands of years, originally in cooking utensils and glazes and more recently in many industrial and commercial applications. However, lead is a potent, potentially deadly toxin that damages many organs in the body and can affect all animals, including humans. By the mid 1990s, lead had been removed from many products in the United States, such as paint and fuel, but it is still commonly used in ammunition for hunting upland game birds, small mammals, and large game animals, as well as in fishing tackle. Wild birds, such as mourning doves, bald eagles, California condors, and loons, can die from the ingestion of one lead shot, bullet fragment, or sinker. According to a recent study on loon mortality, nearly half of adult loons found sick or dead during the breeding season in New England were diagnosed with confirmed or suspected lead poisoning from ingestion of lead fishing weights. Recent regulations in some states have restricted the use of lead ammunition on certain upland game hunting areas, as well as lead fishing tackle in areas frequented by common loons and trumpeter swans. A variety of alternatives to lead are available for use in hunting, shooting sports, and fishing activities.

  6. Enhanced Leads and Appointment System

    Data.gov (United States)

    Social Security Administration — The data asset contains information on current or upcoming appointments, individuals who will be attending the appointment, potential intent to file a claim (lead),...

  7. Bifunctional cyclam-based ligands with phosphorus acid pendant moieties for radiocopper separation: thermodynamic and kinetic studies.

    Science.gov (United States)

    Paúrová, Monika; Havlíčková, Jana; Pospíšilová, Aneta; Vetrík, Miroslav; Císařová, Ivana; Stephan, Holger; Pietzsch, Hans-Jürgen; Hrubý, Martin; Hermann, Petr; Kotek, Jan

    2015-03-16

    Two macrocyclic ligands based on cyclam with trans-disposed N-methyl and N-(4-aminobenzyl) substituents as well as two methylphosphinic (H2L1) or methylphosphonic (H4L2) acid pendant arms were synthesised and investigated in solution. The ligands form stable complexes with transition metal ions. Both ligands show high thermodynamic selectivity for divalent copper over nickel(II) and zinc(II)-K(CuL) is larger than K(Ni/ZnL) by about seven orders of magnitude. Complexation is significantly faster for the phosphonate ligand H4L2, probably due to the stronger coordination ability of the more basic phosphonate groups, which efficiently bind the metal ion in an "out-of-cage" complex and thus accelerate its "in-cage" binding. The rate of Cu(II) complexation by the phosphinate ligand H2L1 is comparable to that of cyclam itself and its derivatives with non-coordinating substituents. Acid-assisted decomplexation of the copper(II) complexes is relatively fast (τ1/2 = 44 and 42 s in 1 M aq. HClO4 at 25 °C for H2L1 and H4L2, respectively). This combination of properties is convenient for selective copper removal/purification. Thus, the title ligands were employed in the preparation of ion-selective resins for radiocopper(II) separation. Glycidyl methacrylate copolymer beads were modified with the ligands through a diazotisation reaction. The separation ability of the modified polymers was tested with cold copper(II) and non-carrier-added (64)Cu in the presence of a large excess of both nickel(II) and zinc(II). The experiments exhibited high overall separation efficiency leading to 60-70% recovery of radiocopper with high selectivity over the other metal ions, which were originally present in 900-fold molar excess. The results showed that chelating resins with properly tuned selectivity of their complexing moieties can be employed for radiocopper separation. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Structural ordering of disordered ligand-binding loops of biotin protein ligase into active conformations as a consequence of dehydration.

    Directory of Open Access Journals (Sweden)

    Vibha Gupta

    -depth analyses of the sequence and the structure also provide answers to the reported lower affinities of Mtb-BirA toward ATP and biotin substrates. This dehydrated crystal structure not only provides key leads to the understanding of the structure/function relationships in the protein in the absence of any ligand-bound structure, but also demonstrates the merit of dehydration of crystals as an inimitable technique to have a glance at proteins in action.

  9. Hydrogen and copper ion induced molecular reorganizations in two new scorpiand-like ligands appended with pyridine rings.

    Science.gov (United States)

    Blasco, Salvador; Verdejo, Begoña; Clares, M Paz; Castillo, Carmen E; Algarra, Andrés G; Latorre, Julio; Máñez, M Angeles; Basallote, Manuel G; Soriano, Conxa; García-España, Enrique

    2010-08-02

    The synthesis of two new ligands constituted of a tris(2-aminoethyl)amine moiety linked to the 2,6 positions of a pyridine spacer through methylene groups in which the hanging arm is further functionalized with a 2-pycolyl (L1) or 3-pycolyl (L2) group is presented. The protonation of L1 and L2 and formation of Cu(2+) complexes have been studied using potentiometric, NMR, X-ray, and kinetic experiments. The results provide new information about the relevance of molecular movements in the chemistry of this kind of so-called scorpiand ligand. The comparison between these two ligands that only differ in the position of the substituent at the arm reveals important differences in both thermodynamic and kinetic properties. The Cu(2+) complex with L1 is several orders of magnitude more stable than that with L2, surely because in the latter case the pyridine nitrogen at the pendant arm is unable to coordinate to the metal ion with the ligand acting as hexadentate, a possibility that occurs in the case of [CuL1](2+), as demonstrated by its crystal structure. Significant differences are also found between both ligands in the kinetic studies of complex formation and decomposition. For L1, those processes occur in a single kinetic step, whereas for L2 they occur with the formation of a detectable reaction intermediate whose structure corresponds to that resulting from the movement typical of scorpiands. Another interesting conclusion derived from kinetic studies on complex formation is that the reactive form of the ligand is H(3)L(3+) for L1 and H(2)L(2+) for L2. DFT calculations are also reported, and they allow a rationalization of the kinetic results relative to the reactive forms of the ligands in the process of complex formation. In addition, they provide a full picture of the mechanistic pathway leading to the formation of the first Cu-N bond, including outer-sphere complexation, water dissociation, and reorganization of the outer-sphere complex.

  10. Ligands of histamine receptors modulate acid-sensing ion channels.

    Science.gov (United States)

    Shteinikov, V Y; Korosteleva, A S; Tikhonova, T B; Potapieva, N N; Tikhonov, D B

    2017-09-02

    Recently we found that synthetic compounds containing amino group linked to hydrophobic or aromatic moiety are potent modulators of the proton-gated channels (ASICs). These structures have clear similarity with ligands of histamine receptors. We have also demonstrated that histamine potentiates homomeric ASIC1a by shifting its activation dependence to less acidic conditions. In the present work the action of a series of histamine receptors ligands on recombinant ASIC1a and ASIC2a was characterized. Two types of action were found for ASIC1a. 1-methylhistamine, N-alpha-methylhistamine, dimaprit and thioperamide caused significant potentiation, which was pH-dependent and voltage-independent. The H4R antagonist A943931 caused inhibition, which is likely due to voltage-dependent pore block. ASIC2a were virtually insensitive to the drugs tested. We conclude that ligands of histamine receptors should also be considered as ASIC modulators. Copyright © 2017. Published by Elsevier Inc.

  11. Novel peptide ligand with high binding capacity for antibody purification

    DEFF Research Database (Denmark)

    Lund, L. N.; Gustavsson, P. E.; Michael, R.

    2012-01-01

    commonly used capture step in mAb down stream processing; however, the use of Protein A chromatography is less attractive due to toxic ligand leakage as well as high cost. Whether used as an alternative to the Protein A chromatographic media or as a subsequent polishing step, small synthetic peptide...... ligand for purification of human IgG. Immobilized on WorkBeads, an agarose-based base matrix from Bio-Works, the ligand has a dynamic binding capacity of up to 48 mg/mL and purifies IgG from harvest cell culture fluid with purities and recovery of >93%. The binding affinity is similar to 10(5) M-1...

  12. Synthesis and characterization of highly conjugated, chiral bridging ligands.

    Science.gov (United States)

    Sauers, Angela L; Ho, Douglas M; Bernhard, Stefan

    2004-12-10

    This paper describes the synthesis of four chiral derivatives of the electronically highly conjugated tetra-2-pyridylpyrazine (TPPZ) bridging ligand, which are denoted (R)- and (S)-4,5- and 5,6-pineno-tetra-2-pyridylpyrazine (PTPPZ). Preparation of these ligands was undertaken through the use of commercially available, enantiomerically pure (1R)- and (1S)-alpha-pinene, which was functionalized and subsequently employed in a Krohnke pyridine synthesis involving a furan-substituted pyridinium salt to yield a chiral, furan-substituted pyridyl intermediate. Oxidative degradation and subsequent reduction of this furan led to a chiral, substituted 2-pyridylaldehyde, which underwent a pyridoin condensation followed by cyclization to produce the final PTPPZ ligands.

  13. Analytical developments for screening of lanthanides/ligands interactions

    International Nuclear Information System (INIS)

    Varenne, F.

    2012-01-01

    This work investigates the potential of hyphenated capillary electrophoresis and inductively coupled mass spectrometry to classify different ligands according to their europium binding affinity in a hydro-organic medium. On the one hand, this method enables to evaluate the affinity of phosphorus-containing ligands in less than two hours and using less than 15 ng of ligand. On the other hand, complexation constants could be determined. The results are in excellent agreement with the values obtained by spectrophotometric titrations.Moreover, a library of copolymers for solid/liquid extraction of europium is investigated. The extraction protocol enables to classify copolymers according to their europium affinity in a hydro-organic medium. This screening requires 60 mg of copolymers. For the most promising recognition properties and selectivity La 3+ /Eu 3+ /Lu 3+ are evaluated. (author)

  14. Coordination chemistry of N-heterocyclic nitrenium-based ligands.

    Science.gov (United States)

    Tulchinsky, Yuri; Kozuch, Sebastian; Saha, Prasenjit; Mauda, Assaf; Nisnevich, Gennady; Botoshansky, Mark; Shimon, Linda J W; Gandelman, Mark

    2015-05-04

    Comprehensive studies on the coordination properties of tridentate nitrenium-based ligands are presented. N-heterocyclic nitrenium ions demonstrate general and versatile binding abilities to various transition metals, as exemplified by the synthesis and characterization of Rh(I) , Rh(III) , Mo(0) , Ru(0) , Ru(II) , Pd(II) , Pt(II) , Pt(IV) , and Ag(I) complexes based on these unusual ligands. Formation of nitrenium-metal bonds is unambiguously confirmed both in solution by selective (15) N-labeling experiments and in the solid state by X-ray crystallography. The generality of N-heterocyclic nitrenium as a ligand is also validated by a systematic DFT study of its affinity towards all second-row transition and post-transition metals (Y-Cd) in terms of the corresponding bond-dissociation energies. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Ligand screening by saturation-transfer difference (STD) NMR spectroscopy.

    Energy Technology Data Exchange (ETDEWEB)

    Krishnan, V V

    2005-04-26

    NMR based methods to screen for high-affinity ligands have become an indispensable tool for designing rationalized drugs, as these offer a combination of good experimental design of the screening process and data interpretation methods, which together provide unprecedented information on the complex nature of protein-ligand interactions. These methods rely on measuring direct changes in the spectral parameters, that are often simpler than the complex experimental procedures used to study structure and dynamics of proteins. The goal of this review article is to provide the basic details of NMR based ligand-screening methods, with particular focus on the saturation transfer difference (STD) experiment. In addition, we provide an overview of other NMR experimental methods and a practical guide on how to go about designing and implementing them.

  16. Heterobifunctional PEG Ligands for Bioconjugation Reactions on Iron Oxide Nanoparticles

    Science.gov (United States)

    Bloemen, Maarten; Van Stappen, Thomas; Willot, Pieter; Lammertyn, Jeroen; Koeckelberghs, Guy; Geukens, Nick; Gils, Ann; Verbiest, Thierry

    2014-01-01

    Ever since iron oxide nanoparticles have been recognized as promising scaffolds for biomedical applications, their surface functionalization has become even more important. We report the synthesis of a novel polyethylene glycol-based ligand that combines multiple advantageous properties for these applications. The ligand is covalently bound to the surface via a siloxane group, while its polyethylene glycol backbone significantly improves the colloidal stability of the particle in complex environments. End-capping the molecule with a carboxylic acid introduces a variety of coupling chemistry possibilities. In this study an antibody targeting plasminogen activator inhibitor-1 was coupled to the surface and its presence and binding activity was assessed by enzyme-linked immunosorbent assay and surface plasmon resonance experiments. The results indicate that the ligand has high potential towards biomedical applications where colloidal stability and advanced functionality is crucial. PMID:25275378

  17. Xanthene and Xanthone Derivatives as G-Quadruplex Stabilizing Ligands

    Directory of Open Access Journals (Sweden)

    Alessandro Altieri

    2013-10-01

    Full Text Available Following previous studies on anthraquinone and acridine-based G-quadruplex ligands, here we present a study of similar aromatic cores, with the specific aim of increasing G-quadruplex binding and selectivity with respect to duplex DNA. Synthesized compounds include two and three-side chain xanthone and xanthene derivatives, as well as a dimeric “bridged” form. ESI and FRET measurements suggest that all the studied molecules are good G-quadruplex ligands, both at telomeres and on G-quadruplex forming sequences of oncogene promoters. The dimeric compound and the three-side chain xanthone derivative have been shown to represent the best compounds emerging from the different series of ligands presented here, having also high selectivity for G-quadruplex structures with respect to duplex DNA. Molecular modeling simulations are in broad agreement with the experimental data.

  18. The Parathyroid Hormone Family of Ligands and Receptors

    Directory of Open Access Journals (Sweden)

    Damian G. D'Souza

    2015-07-01

    Full Text Available The PTH family of ligands and receptors have a wide range of vital functions from calcium homeostasis to tissue and bone development from the embryo to adult. This family has undergone whole genome duplication events predating vertebrate evolution, indicating more primitive and ancient functions other than skeletal development. The N-terminal region of the ligands, have been widely studied by biophysical and functional analysis, resulting in the discovery of key characteristics essential for ligand-receptor activation being elucidated. Multi-substituted amino acid analogs with differential binding affinities and either antagonistic or agonistic signalling potencies have been created based on these findings allowing for improvement on potential therapies affected by the PTH system in skeletal and embryonic development. The PTH family has diversely evolved to cover a wide range of pivotal pathways crucial to growth and development throughout all animal life.

  19. GPCR biased ligands as novel heart failure therapeutics.

    Science.gov (United States)

    Violin, Jonathan D; Soergel, David G; Boerrigter, Guido; Burnett, John C; Lark, Michael W

    2013-10-01

    G protein-coupled receptors have been successfully targeted by numerous therapeutics including drugs that have transformed the management of cardiovascular disease. However, many GPCRs, when activated or blocked by drugs, elicit both beneficial and adverse pharmacology. Recent work has demonstrated that in some cases, the salutary and deleterious signals linked to a specific GPCR can be selectively targeted by "biased ligands" that entrain subsets of a receptor's normal pharmacology. This review briefly summarizes the advances and current state of the biased ligand field, focusing on an example: biased ligands targeting the angiotensin II type 1 receptor. These compounds exhibit unique pharmacology, distinct from classic agonists or antagonists, and one such molecule is now in clinical development for the treatment of acute heart failure. Copyright © 2013 Elsevier Inc. All rights reserved.

  20. Control of Energy Flow Dynamics between Tetracene Ligands and PbS Quantum Dots by Size Tuning and Ligand Coverage

    Energy Technology Data Exchange (ETDEWEB)

    Kroupa, Daniel M. [National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States; Arias, Dylan H. [National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States; Blackburn, Jeffrey L. [National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States; Carroll, Gerard M. [National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States; Granger, Devin B. [Department; Anthony, John E. [Department; Beard, Matthew C. [National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States; Johnson, Justin C. [National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States

    2018-01-08

    We have prepared a series of samples with the ligand 6,13-bistri(iso-propyl)silylethynyl tetracene 2-carboxylic acid (TIPS-Tc-COOH) attached to PbS quantum dot (QD) samples of three different sizes in order to monitor and control the extent and time scales of energy flow after photoexcitation. Fast energy transfer (~1 ps) to the PbS QD occurs upon direct excitation of the ligand for all samples. The largest size QD maintains the microsecond exciton lifetime characteristic of the as-prepared oleate terminated PbS QDs. However, two smaller QD sizes with lowest exciton energies similar to or larger than the TIPS-Tc-COO- triplet energy undergo energy transfer between QD core and ligand triplet on nanosecond to microsecond timescales. For the intermediate size QDs in particular, energy can be recycled many times between ligand and core, but the triplet remains the dominant excited species at long times, living for ~3 us for fully exchanged QDs and up to 30 us for partial ligand exchange, which is revealed as a method for controlling the triplet lifetime. A unique upconverted luminescence spectrum is observed that results from annihilation of triplets after exclusive excitation of the QD core.

  1. Use of protein-engineered fabrics to identify design rules for integrin ligand clustering in biomaterials.

    Science.gov (United States)

    Benitez, Patrick L; Mascharak, Shamik; Proctor, Amy C; Heilshorn, Sarah C

    2016-01-01

    While ligand clustering is known to enhance integrin activation, this insight has been difficult to apply to the design of implantable biomaterials because the local and global ligand densities that enable clustering-enhanced integrin signaling were unpredictable. Here, two general design principles for biomaterial ligand clustering are elucidated. First, clustering ligands enhances integrin-dependent signals when the global ligand density, i.e., the ligand density across the cellular length scale, is near the ligand's effective dissociation constant (KD,eff). Second, clustering ligands enhances integrin activation when the local ligand density, i.e., the ligand density across the length scale of individual focal adhesions, is less than an overcrowding threshold. To identify these principles, we fabricated a series of elastin-like, electrospun fabrics with independent control over the local (0 to 122 000 ligands μm(-2)) and global (0 to 71 000 ligand μm(-2)) densities of an arginine-glycine-aspartate (RGD) ligand. Antibody blocking studies confirmed that human umbilical vein endothelial cell adhesion to these protein-engineered biomaterials was primarily due to αVβ3 integrin binding. Clustering ligands enhanced cell proliferation, focal adhesion number, and focal adhesion kinase expression near the ligand's KD,eff of 12 000 RGD μm(-2). Near this global ligand density, cells on ligand-clustered fabrics behaved similarly to cells grown on fabrics with significantly larger global ligand densities but without clustering. However, this enhanced ligand-clustering effect was not observed above a threshold cut-off concentration. At a local ligand density of 122 000 RGD μm(-2), cell division, focal adhesion number, and focal adhesion kinase expression were significantly reduced relative to fabrics with identical global ligand density and lesser local ligand densities. Thus, when clustering results in overcrowding of ligands, integrin receptors are no longer

  2. Systematic study of ligand structures of metal oxide EUV nanoparticle photoresists

    KAUST Repository

    Jiang, Jing

    2015-03-19

    Ligand stabilized metal oxide nanoparticle resists are promising candidates for EUV lithography due to their high sensitivity for high-resolution patterning and high etching resistance. As ligand exchange is responsible for the patterning mechanism, we systematically studied the influence of ligand structures of metal oxide EUV nanoparticles on their sensitivity and dissolution behavior. ZrO2 nanoparticles were protected with various aromatic ligands with electron withdrawing and electron donating groups. These nanoparticles have lower sensitivity compared to those with aliphatic ligands suggesting the structures of these ligands is more important than their pka on resist sensitivity. The influence of ligand structure was further studied by comparing the nanoparticles’ solubility for a single type ligand to mixtures of ligands. The mixture of nanoparticles showed improved pattern quality. © (2015) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.

  3. Ruthenium Catalysts Supported by Amino-Substituted N-Heterocyclic Carbene Ligands for Olefin Metathesis of Challenging Substrates.

    Science.gov (United States)

    César, Vincent; Zhang, Yin; Kośnik, Wioletta; Zieliński, Adam; Rajkiewicz, Adam A; Ruamps, Mirko; Bastin, Stéphanie; Lugan, Noël; Lavigne, Guy; Grela, Karol

    2017-02-03

    N-Heterocyclic carbene (NHC) ligands IMesNMe2 and IMes(NMe2)2 derived from the well-known IMes ligand by substituting the carbenic heterocycle with one and two dimethylamino groups, respectively, were employed for the synthesis of second-generation Grubbs- and Grubbs-Hoveyda-type ruthenium metathesis precatalysts. Whereas the stability of the complexes was found to depend on the degree of dimethylamino-substitution and on the type of complex, the backbone-substitution was shown to have a positive impact on their catalytic activity in ring-closing metathesis, with a more pronounced effect in the second-generation Grubbs-type series. The new complexes were successfully implemented in a number of challenging olefin metathesis reactions leading to the formation of tetra-substituted C=C double bonds and/or functionalized compounds. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Selection of ligands for affinity chromatography using quartz crystal biosensor.

    Science.gov (United States)

    Liu, Yang; Tang, Xiaoling; Liu, Feng; Li, Ke'an

    2005-07-01

    This paper described a new strategy for rapid selecting ligands for application in affinity chromatography using a quartz crystal microbalance (QCM) biosensor. An aminoglycoside antibiotic drug, kanamycin (KM), was immobilized on the gold electrodes of the QCM sensor chip. The binding interactions of the immobilized KM with various proteins in solution were monitored as the variations of the resonant frequency of the modified sensor. Such a rapid screen analysis of interactions indicated clearly that KM-immobilized sensor showed strong specific interaction only with lysozyme (LZM). The resultant sensorgrams were rapidly analyzed by using a kinetic analysis software based on a genetic algorithm to derive both the kinetic rate constants (k(ass) and k(diss)) and equilibrium dissociation constants (K(D)) for LZM-KM interactions. The immobilized KM showed higher affinity to LZM with a dissociation constant on the order of 10(-5) M, which is within the range of 10(-4)-10(-8) M and suitable for an affinity ligand. Therefore, KM was demonstrated for the first time as a novel affinity ligand for purification of LZM and immobilized onto the epoxy-activated silica in the presence of a high potassium phosphate concentration. The KM immobilized affinity column has proved useful for a very convenient purification of LZM from chicken egg white. The purity of LZM obtained was higher than 90%, as determined by densitometric scanning of sodium dodecyl sulfate-polyacrylamide gel electrophoresis of purified fraction. These results confirmed that the selected KM ligand is indeed a valuable affinity ligand for purification of LZM. The new screening strategy based on a QCM biosensor is expected to be a promising way for rapid selecting specific ligands for purifying other valuable proteins.

  5. Mapping the Conformational Dynamics of E-selectin upon Interaction with its Ligands

    KAUST Repository

    Aleisa, Fajr A

    2013-05-15

    Selectins are key adhesion molecules responsible for initiating a multistep process that leads a cell out of the blood circulation and into a tissue or organ. The adhesion of cells (expressing ligands) to the endothelium (expressing the selectin i.e.,E-selectin) occurs through spatio-temporally regulated interactions that are mediated by multiple intra- and inter-cellular components. The mechanism of cell adhesion is investigated primarily using ensemble-based experiments, which provides indirect information about how individual molecules work in such a complex system. Recent developments in single-molecule (SM) fluorescence detection allow for the visualization of individual molecules with a good spatio-temporal resolution nanometer spatial resolution and millisecond time resolution). Furthermore, advanced SM fluorescence techniques such as Förster Resonance Energy Transfer (FRET) and super-resolution microscopy provide unique opportunities to obtain information about nanometer-scale conformational dynamics of proteins as well as nano-scale architectures of biological samples. Therefore, the state-of-the-art SM techniques are powerful tools for investigating complex biological system such as the mechanism of cell adhesion. In this project, several constructs of fluorescently labeled E-selectin will be used to study the conformational dynamics of E-selectin binding to its ligand(s) using SM-FRET and combination of SM-FRET and force microscopy. These studies will be beneficial to fully understand the mechanistic details of cell adhesion and migration of cells using the established model system of hematopoietic stem cells (HSCs) adhesion to the selectin expressing endothelial cells (such as the E-selectin expressing endothelial cells in the bone marrow).

  6. Two new coordination polymers with flexible alicyclic carboxylate and bipyridyl co-ligands bearing trinuclear [Ni3(COO)6] SBUs: Synthesis, crystal structures, and magnetic properties

    Science.gov (United States)

    Zhu, Xian-Dong; Li, Yong; Gao, Jian-Gang; Wang, Fen-Hua; Li, Qing-Hai; Yang, Hong-Xun; Chen, Lei

    2017-02-01

    Two new coordination polymers generally formulated as [Ni3(Hchda)2(chda)2(bpy)2(H2O)2]n (1) and [Ni3(Hchda)2(chda)2(bpp)2(H2O)2]n (2) [H2chda = 1,1'-cyclohexanediacetic acid, bpy = 4,4'-bipyridine and bpp = 1,3-bis(4-pyridyl)propane], have been successfully assembled through mixed-ligands synthetic strategy with flexible alicyclic carboxylate and bipyridyl ligands. There structures feature trinuclear nickel secondary building units connected via the bridging bipyridyl spacers to form two-dimensional (4,4) grid layer. The nature of the different N-donor auxiliary ligands leads to the discrepancy in supramolecular structure of the two compounds. Magnetic studies indicate the ferromagnetic intra-complex magnetic interaction in the molecule for 1 and 2.

  7. Molecular dynamics simulations of ligand-induced backbone conformational changes in the binding site of the periplasmic lysine-, arginine-, ornithine-binding protein

    Science.gov (United States)

    Yang, Ami Y.-C.; Mancera, Ricardo L.

    2008-11-01

    The periplasmic lysine-, arginine-, ornithine-binding protein (LAOBP) traps its ligands by a large hinge bending movement between two globular domains. The overall geometry of the binding site remains largely unchanged between the open (unliganded) and closed (liganded) forms, with only a small number of residues exhibiting limited movement of their side chains. However, in the case of the ornithine-bound structure, the backbone peptide bond between Asp11 and Thr12 undergoes a large rotation. Molecular dynamics simulations have been used to investigate the origin and mechanism of this backbone movement. Simulations allowing flexibility of a limited region and of the whole binding site, with and without bound ligands, suggest that this conformational change is induced by the binding of ornithine, leading to the stabilisation of an energetically favourable alternative conformation.

  8. Binding equilibrium and kinetics of membrane-anchored receptors and ligands in cell adhesion: Insights from computational model systems and theory

    Science.gov (United States)

    Weikl, Thomas R.; Hu, Jinglei; Xu, Guang-Kui; Lipowsky, Reinhard

    2016-01-01

    ABSTRACT The adhesion of cell membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. In this article, we review recent results from simulations and theory that lead to novel insights on how the binding equilibrium and kinetics of these proteins is affected by the membranes and by the membrane anchoring and molecular properties of the proteins. Simulations and theory both indicate that the binding equilibrium constant K2D and the on- and off-rate constants of anchored receptors and ligands in their 2-dimensional (2D) membrane environment strongly depend on the membrane roughness from thermally excited shape fluctuations on nanoscales. Recent theory corroborated by simulations provides a general relation between K2D and the binding constant K3D of soluble variants of the receptors and ligands that lack the membrane anchors and are free to diffuse in 3 dimensions (3D). PMID:27294442

  9. Synthesis, spectroscopic studies and inhibitory activity against bacteria and fungi of acyclic and macrocyclic transition metal complexes containing a triamine coumarine Schiff base ligand.

    Science.gov (United States)

    Abou-Hussein, A A; Linert, Wolfgang

    2015-04-15

    Two series of new mono and binuclear complexes with a Schiff base ligand derived from the condensation of 3-acetylcoumarine and diethylenetriamine, in the molar ratio 2:1 have been prepared. The ligand was characterized by elemental analysis, IR, UV-visible, (1)H-NMR and mass spectra. The reaction of the Schiff base ligand with cobalt(II), nickel(II), copper(II), zinc(II) and oxovanadium(IV) lead to mono or binuclear species of cyclic or macrocyclic complexes, depending on the mole ratio of metal to ligand and as well as on the method of preparation. The Schiff base ligand behaves as a cyclic bidentate, tetradendate or pentaentadentae ligand. The formation of macrocyclic complexes depends significantly on the dimension of the internal cavity, the rigidity of the macrocycles, the nature of its donor atoms and on the complexing properties of the anion involved in the coordination. Electronic spectra and magnetic moments of the complexes indicate that the geometries of the metal centers are either square pyramidal or octahedral for acyclic or macro-cyclic complexes. The structures are consistent with the IR, UV-visible, ESR, (1)H-NMR, mass spectra as well as conductivity and magnetic moment measurements. The Schiff base ligand and its metal complexes were tested against two pathogenic bacteria as Gram-positive and Gram-negative bacteria as well as one kind of fungi. Most of the complexes exhibit mild antibacterial and antifungal activities against these organisms. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. Structural studies of Ca2+-ATPase ligand and regulatory complexes

    DEFF Research Database (Denmark)

    Drachmann, Nikolaj Düring

    2015-01-01

    to explore the possibilities for an efficient screening of ligand-bound SERCA structures, serial femtosecond crystallography experiments of microcrystals of SERCA1a in the Ca2+ bound state and in a vanadate stabilised E2 state was conducted. A structure obtained at 2.8 Å maximum resolution of the proof......-of-concept Ca2+ bound crystal form, indicated that the information content of SFX data is higher than synchrotron data, and ligands and ions can be detected with low redundant data. The data of the E2 stabilised form was processed to 5 Å resolution, and it was possible to extract useful anomalous data showing...

  11. Development of catalysts and ligands for enantioselective gold catalysis.

    Science.gov (United States)

    Wang, Yi-Ming; Lackner, Aaron D; Toste, F Dean

    2014-03-18

    During the past decade, the use of Au(I) complexes for the catalytic activation of C-C π-bonds has been investigated intensely. Over this time period, the development of homogeneous gold catalysis has been extraordinarily rapid and has yielded a host of mild and selective methods for the formation of carbon-carbon and carbon-heteroatom bonds. The facile formation of new bonds facilitated by gold naturally led to efforts toward rendering these transformations enantioselective. In this Account, we survey the development of catalysts and ligands for enantioselective gold catalysis by our research group as well as related work by others. We also discuss some of our strategies to address the challenges of enantioselective gold(I) catalysis. Early on, our work with enantioselective gold-catalyzed transformations focused on bis(phosphinegold) complexes derived from axially chiral scaffolds. Although these complexes were highly successful in some reactions like cyclopropanation, the careful choice of the weakly coordinating ligand (or counterion) was necessary to obtain high levels of enantioselectivity for the case of allene hydroamination. These counterion effects led us to use the anion itself as a source of chirality, which was successful in the case of allene hydroalkoxylation. In general, these tactics enhance the steric influence around the reactive gold center beyond the two-coordinate ligand environment. The use of binuclear complexes allowed us to use the second gold center and its associated ligand (or counterion) to exert a further steric influence. In a similar vein, we employed a chiral anion (in place of or in addition to a chiral ligand) to move the chiral information closer to the reactive center. In order to expand the scope of reactions amenable to enantioselective gold catalysis to cycloadditions and other carbocyclization processes, we also developed a new class of mononuclear phosphite and phosphoramidite ligands to supplement the previously widely

  12. Coordination chemistry of poly(thioether)borate ligands

    Science.gov (United States)

    Riordan, Charles G.

    2010-01-01

    This review traces the development and application of the tris(thioether)borate ligands, tripodal ligands with highly polarizable thioether donors. Areas of emphasis include the basic coordination chemistry of the mid-to-late first row transition metals (Fe, Ni, Co, Cu), and the role of the thioether substituent in directing complex formation, the modeling of zinc thiolate protein active sites, high-spin organo-iron and organo-cobalt chemistry, the preparation of monovalent complexes of Fe, Co and Ni, and dioxygen and sulfur activation by monovalent nickel complexes. PMID:20607091

  13. Luminescent cyclometallated iridium(III) complexes having acetylide ligands

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, Mark E.; Bossi, Alberto; Djurovich, Peter Ivan

    2014-09-02

    The present invention relates to phosphorescent (triplet-emitting) organometallic materials. The phosphorescent materials of the present invention comprise Ir(III)cyclometallated alkynyl complexes for use as triplet light-emitting materials. The Ir(III)cyclometallated alkynyl complexes comprise at least one cyclometallating ligand and at least one alkynyl ligand bonded to the iridium. Also provided is an organic light emitting device comprising an anode, a cathode and an emissive layer between the anode and the cathode, wherein the emissive layer comprises a Ir(III)cyclometallated alkynyl complex as a triplet emitting material.

  14. Aluminum Dimer Containing Bulky 1,2,3-Triazolate Ligand

    Directory of Open Access Journals (Sweden)

    Issam Kobrsi

    2014-01-01

    Full Text Available The first molecular aluminum 1,2,3-triazolato complex was synthesized bearing a bulky 1,2,3-triazolate ligand. Oligomers and polymers were avoided due to the bulkiness and noncoordinating nature of the substituents. The novel Al2N4 ring formed contains symmetrical Al-N bond distances unexpectedly having asymmetric Al-N-N angles of 144.55(15° and 115.83(14°. This asymmetry demonstrates the effect of the steric hindrance of the ligand.

  15. Designer ligands: The search for metal ion selectivity

    Directory of Open Access Journals (Sweden)

    Perry T. Kaye

    2011-03-01

    Full Text Available The paper reviews research conducted at Rhodes University towards the development of metal-selective ligands. The research has focused on the rational design, synthesis and evaluation of novel ligands for use in the formation of copper complexes as biomimetic models of the metalloenzyme, tyrosinase, and for the selective extraction of silver, nickel and platinum group metal ions in the presence of contaminating metal ions. Attention has also been given to the development of efficient, metal-selective molecular imprinted polymers.

  16. Structural Basis of Cooperative Ligand Binding by the Glycine Riboswitch

    Energy Technology Data Exchange (ETDEWEB)

    E Butler; J Wang; Y Xiong; S Strobel

    2011-12-31

    The glycine riboswitch regulates gene expression through the cooperative recognition of its amino acid ligand by a tandem pair of aptamers. A 3.6 {angstrom} crystal structure of the tandem riboswitch from the glycine permease operon of Fusobacterium nucleatum reveals the glycine binding sites and an extensive network of interactions, largely mediated by asymmetric A-minor contacts, that serve to communicate ligand binding status between the aptamers. These interactions provide a structural basis for how the glycine riboswitch cooperatively regulates gene expression.

  17. Ligand Receptor-Mediated Regulation of Growth in Plants.

    Science.gov (United States)

    Haruta, Miyoshi; Sussman, Michael R

    2017-01-01

    Growth and development of multicellular organisms are coordinately regulated by various signaling pathways involving the communication of inter- and intracellular components. To form the appropriate body patterns, cellular growth and development are modulated by either stimulating or inhibiting these pathways. Hormones and second messengers help to mediate the initiation and/or interaction of the various signaling pathways in all complex multicellular eukaryotes. In plants, hormones include small organic molecules, as well as larger peptides and small proteins, which, as in animals, act as ligands and interact with receptor proteins to trigger rapid biochemical changes and induce the intracellular transcriptional and long-term physiological responses. During the past two decades, the availability of genetic and genomic resources in the model plant species, Arabidopsis thaliana, has greatly helped in the discovery of plant hormone receptors and the components of signal transduction pathways and mechanisms used by these immobile but highly complex organisms. Recently, it has been shown that two of the most important plant hormones, auxin and abscisic acid (ABA), act through signaling pathways that have not yet been recognized in animals. For example, auxins stimulate cell elongation by bringing negatively acting transcriptional repressor proteins to the proteasome to be degraded, thus unleashing the gene expression program required for increasing cell size. The "dormancy" inducing hormone, ABA, binds to soluble receptor proteins and inhibits a specific class of protein phosphatases (PP2C), which activates phosphorylation signaling leading to transcriptional changes needed for the desiccation of the seeds prior to entering dormancy. While these two hormone receptors have no known animal counterparts, there are also many similarities between animal and plant signaling pathways. For example, in plants, the largest single gene family in the genome is the protein kinase

  18. A ligand channel through the G protein coupled receptor opsin.

    Directory of Open Access Journals (Sweden)

    Peter W Hildebrand

    Full Text Available The G protein coupled receptor rhodopsin contains a pocket within its seven-transmembrane helix (TM structure, which bears the inactivating 11-cis-retinal bound by a protonated Schiff-base to Lys296 in TM7. Light-induced 11-cis-/all-trans-isomerization leads to the Schiff-base deprotonated active Meta II intermediate. With Meta II decay, the Schiff-base bond is hydrolyzed, all-trans-retinal is released from the pocket, and the apoprotein opsin reloaded with new 11-cis-retinal. The crystal structure of opsin in its active Ops* conformation provides the basis for computational modeling of retinal release and uptake. The ligand-free 7TM bundle of opsin opens into the hydrophobic membrane layer through openings A (between TM1 and 7, and B (between TM5 and 6, respectively. Using skeleton search and molecular docking, we find a continuous channel through the protein that connects these two openings and comprises in its central part the retinal binding pocket. The channel traverses the receptor over a distance of ca. 70 A and is between 11.6 and 3.2 A wide. Both openings are lined with aromatic residues, while the central part is highly polar. Four constrictions within the channel are so narrow that they must stretch to allow passage of the retinal beta-ionone-ring. Constrictions are at openings A and B, respectively, and at Trp265 and Lys296 within the retinal pocket. The lysine enforces a 90 degrees elbow-like kink in the channel which limits retinal passage. With a favorable Lys side chain conformation, 11-cis-retinal can take the turn, whereas passage of the all-trans isomer would require more global conformational changes. We discuss possible scenarios for the uptake of 11-cis- and release of all-trans-retinal. If the uptake gate of 11-cis-retinal is assigned to opening B, all-trans is likely to leave through the same gate. The unidirectional passage proposed previously requires uptake of 11-cis-retinal through A and release of photolyzed all

  19. Lead behavior in abalone shell

    Science.gov (United States)

    Hirao, Yoshimitsu; Matsumoto, Akikazu; Yamakawa, Hiroshi; Maeda, Masaru; Kimura, Kan

    1994-08-01

    In order to gain information about the behavior of heavy metals in biological assimilation processes in a marine food chain and to investigate the possibility that lead pollution in a marine environment can be estimated by measurement of a small number of key materials from such a food chain, muscle and shell were analyzed from abalone ( Haliotis) from a shallow water locality in a Japanese coastal region. Lead concentrations in muscle were about 26 ppb for abalone of approximately 3 years old and decreased systematically with increasing age of animals sampled, to about 3.3 ppb for a specimen approximately 8 years old. Lead concentrations in shell material gradually decreased also, from 150 ppb to 82 ppb in the oldest specimen. The decrease of concentration in tissues with increasing age indicates that a mechanism for exclusion of lead during tissue growth becomes more efficient with age. Along the food chain in which abalone is the final stage, lead was enriched at the first stage, from seawater to algae, by a factor of 100. Lead was diminished at all subsequent stages of the chain. Tissue of artificially cultured abalone had four times higher lead values compared to abalone grown in natural conditions, and this appears to reflect the fact that lead concentration was three times higher in seawater in the cultured environment.

  20. Lead-free primary explosives

    Science.gov (United States)

    Huynh, My Hang V.

    2010-06-22

    Lead-free primary explosives of the formula (cat).sub.Y[M.sup.II(T).sub.X(H.sub.2O).sub.6-X].sub.Z, where T is 5-nitrotetrazolate, and syntheses thereof are described. Substantially stoichiometric equivalents of the reactants lead to high yields of pure compositions thereby avoiding dangerous purification steps.

  1. Leading change: a concept analysis.

    Science.gov (United States)

    Nelson-Brantley, Heather V; Ford, Debra J

    2017-04-01

    To report an analysis of the concept of leading change. Nurses have been called to lead change to advance the health of individuals, populations, and systems. Conceptual clarity about leading change in the context of nursing and healthcare systems provides an empirical direction for future research and theory development that can advance the science of leadership studies in nursing. Concept analysis. CINAHL, PubMed, PsycINFO, Psychology and Behavioral Sciences Collection, Health Business Elite and Business Source Premier databases were searched using the terms: leading change, transformation, reform, leadership and change. Literature published in English from 2001 - 2015 in the fields of nursing, medicine, organizational studies, business, education, psychology or sociology were included. Walker and Avant's method was used to identify descriptions, antecedents, consequences and empirical referents of the concept. Model, related and contrary cases were developed. Five defining attributes of leading change were identified: (a) individual and collective leadership; (b) operational support; (c) fostering relationships; (d) organizational learning; and (e) balance. Antecedents were external or internal driving forces and organizational readiness. The consequences of leading change included improved organizational performance and outcomes and new organizational culture and values. A theoretical definition and conceptual model of leading change were developed. Future studies that use and test the model may contribute to the refinement of a middle-range theory to advance nursing leadership research and education. From this, empirically derived interventions that prepare and enable nurses to lead change to advance health may be realized. © 2016 John Wiley & Sons Ltd.

  2. Blood Test: Lead (For Parents)

    Science.gov (United States)

    ... Staying Safe Videos for Educators Search English Español Blood Test: Lead KidsHealth / For Parents / Blood Test: Lead What's ... español Análisis de sangre: plomo What Is a Blood Test? A blood test is when a sample of ...

  3. Selective Liquid-Liquid Extraction of Lead Ions Using Newly Synthesized Extractant 2-(Dibutylcarbamoylbenzoic Acid

    Directory of Open Access Journals (Sweden)

    Hossein Soltani

    2015-12-01

    Full Text Available A new carboxylic acid extractant, named 2-(dibutylcarbamoylbenzoic acid, is prepared and its potential for selective solvent extraction and recovery of lead ions from industrial samples was investigated. The slope analysis indicated that the lead ions are extracted by formation of 1:2 metal to ligand complexes. The effect of the parameters influencing the extraction efficiency including kind of the organic diluent, extractant concentration, type of the salt used for ionic strength adjustment, contact time and temperature was evaluated and discussed. Under optimized conditions (aqueous phase: 5 ml, initial lead concentration 1 × 10-4 M, pH 4, sodium chloride 0.1 M; organic phase: 5 ml dichloromethane, ligand concentration 0.05 M, a quantitative (75.2 ± 0.8% and highly selective extraction of lead ions in the presence of zinc, nickel, cobalt and cadmium ions (each 1 × 10-4 M was achieved, after 20 min. magnetically stirring of the phases, at      25 °C. The extracted lead ions were stripped from the organic phase by diluted nitric acid (0.1 M solution. The proposed method was successfully applied for separation of lead from industrial samples. The study of the effect of temperature allowed evaluating the thermodynamic parameters of the extraction process of lead ions by the studied extractant into dichloromethane.

  4. Biosorption of lead phosphates by lead-tolerant bacteria as a mechanism for lead immobilization.

    Science.gov (United States)

    Rodríguez-Sánchez, Viridiana; Guzmán-Moreno, Jesús; Rodríguez-González, Vicente; Flores-de la Torre, Juan Armando; Ramírez-Santoyo, Rosa María; Vidales-Rodríguez, Luz Elena

    2017-08-01

    The study of metal-tolerant bacteria is important for bioremediation of contaminated environments and development of green technologies for material synthesis due to their potential to transform toxic metal ions into less toxic compounds by mechanisms such as reduction, oxidation and/or sequestration. In this study, we report the isolation of seven lead-tolerant bacteria from a metal-contaminated site at Zacatecas, México. The bacteria were identified as members of the Staphylococcus and Bacillus genera by microscopic, biochemical and 16S rDNA analyses. Minimal inhibitory concentration of these isolates was established between 4.5 and 7.0 mM of Pb(NO 3 ) 2 in solid and 1.0-4.0 mM of Pb(NO 3 ) 2 in liquid media. A quantitative analysis of the lead associated to bacterial biomass in growing cultures, revealed that the percentage of lead associated to biomass was between 1 and 37% in the PbT isolates. A mechanism of complexation/biosorption of lead ions as inorganic phosphates (lead hydroxyapatite and pyromorphite) in bacterial biomass, was determined by Fourier transform infrared spectroscopy and X-ray diffraction analyses. Thus, the ability of the lead-tolerant isolates to transform lead ions into stable and highly insoluble lead minerals make them potentially useful for immobilization of lead in mining waste.

  5. Experimental model of lead nephropathy

    Energy Technology Data Exchange (ETDEWEB)

    Khalil-Manesh, F.; Gonick, H.C. (Cedars-Sinai Medical Center, Los Angeles, CA (United States)); Cohen, A. (UCLA-Harbor General Hospital, Torrance, CA (United States)); Bergamaschi, E.; Mutti, A. (Univ. of Parma (Italy))

    1992-06-01

    Male Sprague-Dawley rats were exposed to high-dose (0.5%) lead acetate for periods ranging from 1 to 9 months; then lead exposure was discontinued, and animals were sacrificed after 12 months. Two additional groups of low-dose (0.01%) and high-dose (0.5%) rats were exposed to lead for 6 months, then lead was discontinued and the rats were treated with three 5-day courses of 0.5% DMSA (dimercaptosuccinic acid) over the next 6 months. Low-dose lead-treated rats showed no significant pathological changes with or without DMSA treatment, but exhibited a significant increase in GFR after DMSA. High-dose lead-treated animals showed no functional or pathological changes when lead exposure was discontinued after 1 month. However, when duration of exposure was 6 or 9 months, GFR was decreased and serum creatinine and urea nitrogen were increased as compared to controls. Tubulointerstitial disease was severe. Administration of DMSA resulted in an improvement in GFR and a decrease in albuminuria, together with a reduction in size and number of nuclear inclusion bodies in proximal tubules. However, tubulointerstitial scarring was only minimally reduced. It may be concluded that, except for brief initial exposure, discontinuation of high-dose lead exposure fails to reverse lead-induced renal damage. Treatment with the chelator, DMSA, improves renal function but has less effect on pathological alterations. As GFR improved after DMSA treatment in both low-dose and high-dose lead-treated rats, irrespective of the degree of pathological alterations, it may be concluded that the DMSA effect is most likely mediated by hemodynamic changes.

  6. Gamma radiolysis of the highly selective ligands CyMe{sub 4}BTBP and CyMe{sub 4}BTPhen: Qualitative and quantitative investigation of radiolysis product

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt, H.; Wilden, A.; Modolo, G.; Bosbach, D. [Forschungszentrum Juelich GmbH, Institute of Energy and Climate Research IEK-6: Nuclear Waste Management, 52425 Juelich (Germany); Santiago-Schuebel, B.; Hupert, M. [Forschungszentrum Juelich GmbH, Central Institute for Engineering, Analytics - ZEA-3, 52425 Juelich (Germany); Svehla, J.; Gruner, B. [Institute of Inorganic Chemistry, Academy of Sciences, Hlavni 1001, 25068 Husinec-Rez (Czech Republic); Ekberg, C. [Department of Chemical and Biochemical Engineering, Chalmers University of Technology, 41296 Gothenburg (Sweden)

    2016-07-01

    The highly selective nitrogen donor ligands CyMe{sub 4}BTBP and CyMe4{sub B}TPhen where γ-irradiated under identical experimental conditions in 1-octanol with and without contact to nitric acid solution. Subsequently, solvent extraction experiments were carried out to evaluate the stability of the extractants against γ-radiation monitoring Am(III) and Eu(III) distribution ratios. Generally, decreasing distribution ratios with increasing absorbed dose were detected for both molecules. Furthermore, qualitative mass spectrometric analyses were performed and ligand concentrations were determined by HPLC-DAD after irradiation to investigate the radiolysis mechanism. An exponential decrease with increasing absorbed dose was observed for both ligands with a faster rate for CyMe{sub 4}BTPhen. Main radiolysis products indicated the addition of one or more diluent molecules (1-octanol) to the ligand via prior production of α-hydroxy-octyl radicals from diluent radiolysis. The addition of nitric acid during the irradiation lead to a remarkable stabilization of the system, as the extraction of Am(III) and Eu(III) did not change significantly over the whole examined dose range. Quantification of the remaining ligand concentration on the other hand showed decreasing concentrations with increasing absorbed dose. The stabilization of D values is therefore explained by the formation of 1-octanol addition products which are also able to extract the studied metal ions. (authors)

  7. Gamma radiolysis of the highly selective ligands CyMe4BTBP and CyMe4BTPhen: Qualitative and quantitative investigation of radiolysis product

    International Nuclear Information System (INIS)

    Schmidt, H.; Wilden, A.; Modolo, G.; Bosbach, D.; Santiago-Schuebel, B.; Hupert, M.; Svehla, J.; Gruner, B.; Ekberg, C.

    2016-01-01

    The highly selective nitrogen donor ligands CyMe 4 BTBP and CyMe4 B TPhen where γ-irradiated under identical experimental conditions in 1-octanol with and without contact to nitric acid solution. Subsequently, solvent extraction experiments were carried out to evaluate the stability of the extractants against γ-radiation monitoring Am(III) and Eu(III) distribution ratios. Generally, decreasing distribution ratios with increasing absorbed dose were detected for both molecules. Furthermore, qualitative mass spectrometric analyses were performed and ligand concentrations were determined by HPLC-DAD after irradiation to investigate the radiolysis mechanism. An exponential decrease with increasing absorbed dose was observed for both ligands with a faster rate for CyMe 4 BTPhen. Main radiolysis products indicated the addition of one or more diluent molecules (1-octanol) to the ligand via prior production of α-hydroxy-octyl radicals from diluent radiolysis. The addition of nitric acid during the irradiation lead to a remarkable stabilization of the system, as the extraction of Am(III) and Eu(III) did not change significantly over the whole examined dose range. Quantification of the remaining ligand concentration on the other hand showed decreasing concentrations with increasing absorbed dose. The stabilization of D values is therefore explained by the formation of 1-octanol addition products which are also able to extract the studied metal ions. (authors)

  8. Molecular Docking Explains Atomic Interaction between Plant-originated Ligands and Oncogenic E7 Protein of High Risk Human Papillomavirus Type 16

    Directory of Open Access Journals (Sweden)

    Satish Kumar

    2014-12-01

    Full Text Available Cervical cancer caused by Human papillomavirus (HPV is one of the leading causes of cancer mortality in women worldwide, particularly in the developing countries. In the last few decades, various compounds from plant origin such as Curcumin, Epigallocatechin gallate (EGCG, Jaceosidin, Resveratrol etc. have been used as anti cancer therapeutic agents. Different studies have shown these plant-originated compounds are able to suppress HPV infection. The E6 and E7 oncoproteins of high-risk HPV play a key role in HPV related cancers. In this study, we explored these ligands from plants origin against E7 oncoprotein of high risk HPV 16, which is known to inactivate tumor suppressor pRb protein. A robust homology model of HPV 16 E7 was built to foresee the interaction mechanism of E7 oncoprotein with these ligands using structure-based drug designing approach. Docking studies demonstrate the interaction of these ligands with pRb binding site of E7 protein by residues Tyr52, Asn53, Val55, Phe57, Cys59, Ser63, Thr64, Thr72, Arg77, Glu80 and Asp81 and help restoration of pRb functioning. This in silico based atomic interaction between these ligands and E7 protein may assist in validating the plant-originated ligands as effective drugs against HPV.

  9. Further Insight into the Lability of MeCN Ligands of Cytotoxic Cycloruthenated Compounds: Evidence for the Antisymbiotic Effect Trans to the Carbon Atom at the Ru Center.

    Science.gov (United States)

    Barbosa, Ana Soraya Lima; Werlé, Christophe; Colunga, Claudia Olivia Oliva; Rodríguez, Cecilia Franco; Toscano, Ruben Alfredo; Le Lagadec, Ronan; Pfeffer, Michel

    2015-08-03

    The two MeCN ligands in [Ru(2-C6H4-2'-Py-κC,N)(Phen, trans-C)(MeCN)2]PF6 (1), both trans to a sp(2) hybridized N atom, cannot be substituted by any other ligand. In contrast, the isomerized derivative [Ru(2-C6H4-2'-Py-κC,N)(Phen, cis-C)(MeCN)2]PF6 (2), in which one MeCN ligand is now trans to the C atom of the phenyl ring orthometalated to Ru, leads to fast and quantitative substitution reactions with several monodentate ligands. With PPh3, 2 affords [Ru(2-C6H4-2'-Py-κC,N)(Phen, cis-C)(PPh3)(MeCN)]PF6 (3), in which PPh3 is trans to the C σ bound to Ru. Compound 3 is not kinetically stable, because, under thermodynamic control, it leads to 4, in which the PPh3 is trans to a N atom of the Phen ligand. Dimethylsulfoxide (DMSO) can also substitute a MeCN ligand in 2, leading to 5, in which DMSO is coordinated to Ru via its S atom trans to the N atom of the Phen ligand, the isomer under thermodynamic control being the only compound observed. We also found evidence for the fast to very fast substitution of MeCN in 2 by water or a chloride anion by studying the electronic spectra of 2 in the presence of water or NBu4Cl, respectively. An isomerization related to that observed between 3 and 4 is also found for the known monophosphine derivative [Ru(2-C6H4-2'-Py-κC,N)(PPh3, trans-C)(MeCN)3]PF6 (10), in which the PPh3 is located trans to the C of the cyclometalated 2-phenylpyridine, since, upon treatment by refluxing MeCN, it leads to its isomer 11, [Ru(2-C6H4-2'-Py-κC,N)(PPh3, cis-C)(MeCN)3]PF6. Further substitutions are also observed on 11, whereby N^N chelates (N^N = 2,2'-bipyridine and phenanthroline) substitute two MeCN ligands, affording [Ru(2-C6H4-2'-Py-κC,N)(PPh3, cis-C)(N^N)(MeCN)]PF6 (12a and 12b). Altogether, the behavior of the obtained complexes by ligand substitution reactions can be rationalized by an antisymbiotic effect on the Ru center, trans to the C atom of the cyclometalated unit, leading to compounds having the least nucleophilic ligand trans to C

  10. Synthesis, structure and reactivity of rare-earth metal complexes containing anionic phosphorus ligands.

    Science.gov (United States)

    Li, Tianshu; Kaercher, Sabrina; Roesky, Peter W

    2014-01-07

    A comprehensive review of structurally characterized rare-earth metal complexes containing anionic phosphorus ligands is presented. Since rare-earth elements form hard ions and phosphorus is considered as a soft ligand, the rare-earth metal phosphorus coordination is regarded as a less favorite combination. Three classes of phosphorus ligands, (1) the monoanionic organophosphide ligands (PR2(-)) bearing one negative charge on the phosphorus atom; (2) the dianionic phosphinidene (PR(2-)) and P(3-) ligands; and (3) the pure inorganic polyphosphide ligands (Pn(x-)), are included here. Particular attention has been paid to the synthesis, structure, and reactivity of the rare-earth metal phosphides.

  11. A liposomal drug platform overrides peptide ligand targeting to a cancer biomarker, irrespective of ligand affinity or density.

    Directory of Open Access Journals (Sweden)

    Bethany Powell Gray

    Full Text Available One method for improving cancer treatment is the use of nanoparticle drugs functionalized with targeting ligands that recognize receptors expressed selectively by tumor cells. In theory such targeting ligands should specifically deliver the nanoparticle drug to the tumor, increasing drug concentration in the tumor and delivering the drug to its site of action within the tumor tissue. However, the leaky vasculature of tumors combined with a poor lymphatic system allows the passive accumulation, and subsequent retention, of nanosized materials in tumors. Furthermore, a large nanoparticle size may impede tumor penetration. As such, the role of active targeting in nanoparticle delivery is controversial, and it is difficult to predict how a targeted nanoparticle drug will behave in vivo. Here we report in vivo studies for αvβ6-specific H2009.1 peptide targeted liposomal doxorubicin, which increased liposomal delivery and toxicity to lung cancer cells in vitro. We systematically varied ligand affinity, ligand density, ligand stability, liposome dosage, and tumor models to assess the role of active targeting of liposomes to αvβ6. In direct contrast to the in vitro results, we demonstrate no difference in in vivo targeting or efficacy for H2009.1 tetrameric peptide liposomal doxorubicin, compared to control peptide and no peptide liposomes. Examining liposome accumulation and distribution within the tumor demonstrates that the liposome, and not the H2009.1 peptide, drives tumor accumulation, and that both targeted H2009.1 and untargeted liposomes remain in perivascular regions, with little tumor penetration. Thus H2009.1 targeted liposomes fail to improve drug efficacy because the liposome drug platform prevents the H2009.1 peptide from both actively targeting the tumor and binding to tumor cells throughout the tumor tissue. Therefore, using a high affinity and high specificity ligand targeting an over-expressed tumor biomarker does not guarantee

  12. Glucagon-like peptide-1 receptor ligand interactions: structural cross talk between ligands and the extracellular domain.

    Directory of Open Access Journals (Sweden)

    Graham M West

    Full Text Available Activation of the glucagon-like peptide-1 receptor (GLP-1R in pancreatic β-cells potentiates insulin production and is a current therapeutic target for the treatment of type 2 diabetes mellitus (T2DM. Like other class B G protein-coupled receptors (GPCRs, the GLP-1R contains an N-terminal extracellular ligand binding domain. N-terminal truncations on the peptide agonist generate antagonists capable of binding to the extracellular domain, but not capable of activating full length receptor. The main objective of this study was to use Hydrogen/deuterium exchange (HDX to identify how the amide hydrogen bonding network of peptide ligands and the extracellular domain of GLP-1R (nGLP-1R were altered by binding interactions and to then use this platform to validate direct binding events for putative GLP-1R small molecule ligands. The HDX studies presented here for two glucagon-like peptide-1 receptor (GLP-1R peptide ligands indicates that the antagonist exendin-4[9-39] is significantly destabilized in the presence of nonionic detergents as compared to the agonist exendin-4. Furthermore, HDX can detect stabilization of exendin-4 and exendin-4[9-39] hydrogen bonding networks at the N-terminal helix [Val19 to Lys27] upon binding to the N-terminal extracellular domain of GLP-1R (nGLP-1R. In addition we show hydrogen bonding network stabilization on nGLP-1R in response to ligand binding, and validate direct binding events with the extracellular domain of the receptor for putative GLP-1R small molecule ligands.

  13. Leading Millennials Motivating And Leading Millennial Service Members

    Science.gov (United States)

    2016-02-20

    mentioned, compared to Baby Boomers and many in Generation X, Millennials have grown up with instantaneous access to limitless information from...www.eremedia.com/ere/helicopter-parents/ Internet ; accessed 12December 2015. 14 Cheryl R. Sturko Grossman, “Gen Y,” Youthwork Information Brief, No...AIR WAR COLLEGE AIR UNIVERSITY LEADING MILLENNIALS MOTIVATING AND LEADING MILLENNIAL SERVICE MEMBERS by Joanne MacGregor, LTC

  14. PATTERN BASED DETECTION OF POTENTIALLY DRUGGABLE BINDING SITES BY LIGAND SCREENING

    Directory of Open Access Journals (Sweden)

    Uttam Pal

    2018-03-01

    Full Text Available This article describes an innovative way of finding the potentially druggable sites on a target protein, which can be used for orthosteric and allosteric lead detection in a single virtual screening setup. Druggability estimation for an alternate binding site other than the canonical ligand-binding pocket of an enzyme is rewarding for several inherent benefits. Allostery is a direct and efficient way of regulating biomacromolecule function. The allosteric modulators can fine-tune protein mechanics. Besides, allosteric sites are evolutionarily less conserved/more diverse even in very similarly related proteins, thus, provides high degree of specificity in targeting a particular protein. Therefore, targeting of allosteric sites is gaining attention as an emerging strategy in rational drug design. However, the experimental approaches provide a limited degree of characterization of new allosteric sites. Computational approaches are useful to analyze and select potential allosteric sites for drug discovery. Here, the use of molecular docking, which has become an integral part of the drug discovery process, has been discussed to predict the druggability of novel allosteric sites as well as the active site on target proteins by ligand screening. Genetic algorithm was used for docking and the whole protein was placed in the search space. For each ligand in the library of small molecules, the genetic algorithm was run for multiple times to populate all the druggable sites in the target protein, which was then translated into two dimensional density maps or “patterns”. High density clusters were observed for lead like molecules in these pattern diagrams. Each cluster in such a pattern diagram indicated a plausible binding site and the density gave its druggability score in terms of weighted probabilities. The patterns were filtered to find the leads for each of the druggable sites on the target protein. Such a novel pattern based analysis of the

  15. 2 : 2 Fe(III): ligand and "adamantane core" 4 : 2 Fe(III): ligand (hydr)oxo complexes of an acyclic ditopic ligand

    DEFF Research Database (Denmark)

    Ghiladi, Morten; Larsen, Frank B.; McKenzie, Christine J.

    2005-01-01

    crystalline platelets. The Fe4O6 core of 2 shows an adamantane-like structure: The six bridging oxygen atoms are provided by the two phenolato groups of the two bpbp(-) ligands, two bridging oxo groups and two bridging hydroxo groups. The hydroxo and oxo ligands could be distinguished on the basis of Fe - O......-ray structure of the dinuclear complex [{( Hbpbp) Fe(mu-OH)}(2)](ClO4)(4) center dot 2C(3)H(6)O ( 1 center dot 2C(3)H(6)O) shows that only one of the metal-binding cavities of each ligand is occupied by an iron( III) atom and two [Fe(Hbpbp)](3+) units are linked together by two hydroxo bridging groups to form...... a [ Fe(III) -(mu-OH)](2) rhomb structure with Fe center dot center dot center dot Fe = 3.109(1) angstrom. The non-coordinated tertiary amine of Hbpbp is protonated. Magnetic susceptibility measurements show a well-behaved weak antiferromagnetic coupling between the two Fe( III) atoms, J =- 8 cm(-1...

  16. Investigation of actinides speciation within the presence of ligands of interest for decorporation

    International Nuclear Information System (INIS)

    Bonin, L.

    2008-01-01

    Data about the behaviour of actinides in biological media are required in order to investigate their decorporation. Those data are obtained through in vivo experiments and the study of chemical speciation of actinides within the presence of biological constituents. A part of this work consists in the development of a method leading to the determination of the speciation of actinides at the oxidation state +IV within the presence of a complexing species, as well as its structure. The method was applied to two types of ligands: 1) a constituent of blood plasma: the citrate anion. The various complexes formed were investigated and their formation constants were quantified. The coordination mode of the ligand was then clarified through a structural study of the complexes, underlining the role of only one carboxylic site and of the alcohol function. 2) chelating agents used for decorporation. The formation constants of complexes of An(IV) with NTA and DTPA were determined. The coordination number of the metallic cation in those complexes as well as the role of the nitrogen atom were proved. Lastly, the behaviour of Pu(IV) within the presence of LIHOPO was investigated. This chelating agent, more efficient than DTPA in the case of in vivo decorporation of Np, forms very stable complexes with the metallic cation. One of those complexes can be assumed to present a stoichiometry 2:3. (author)

  17. In silico identification of new ligands for GPR17: a promising therapeutic target for neurodegenerative diseases

    Science.gov (United States)

    Eberini, Ivano; Daniele, Simona; Parravicini, Chiara; Sensi, Cristina; Trincavelli, Maria L.; Martini, Claudia; Abbracchio, Maria P.

    2011-08-01

    GPR17, a previously orphan receptor responding to both uracil nucleotides and cysteinyl-leukotrienes, has been proposed as a novel promising target for human neurodegenerative diseases. Here, in order to specifically identify novel potent ligands of GPR17, we first modeled in silico the receptor by using a multiple template approach, in which extracellular loops of the receptor, quite complex to treat, were modeled making reference to the most similar parts of all the class-A GPCRs crystallized so far. A high-throughput virtual screening exploration of GPR17 binding site with more than 130,000 lead-like compounds was then applied, followed by the wet functional and pharmacological validation of the top-scoring chemical structures. This approach revealed successful for the proposed aim, and allowed us to identify five agonists or partial agonists with very diverse chemical structure. None of these compounds could have been expected `a priori' to act on a GPCR, and all of them behaved as much more potent ligands than GPR17 endogenous activators.

  18. Synthesis and Characterization of a New Bivalent Ligand Combining Caffeine and Docosahexaenoic Acid

    Directory of Open Access Journals (Sweden)

    Víctor Fernández-Dueñas

    2017-02-01

    Full Text Available Caffeine is a promising drug for the management of neurodegenerative diseases such as Parkinson’s disease (PD, demonstrating neuroprotective properties that have been attributed to its interaction with the basal ganglia adenosine A2A receptor (A2AR. However, the doses needed to exert these neuroprotective effects may be too high. Thus, it is important to design novel approaches that selectively deliver this natural compound to the desired target. Docosahexaenoic acid (DHA is the major omega-3 fatty acid in the brain and can act as a specific carrier of caffeine. Furthermore, DHA displays properties that may lead to its use as a neuroprotective agent. In the present study, we constructed a novel bivalent ligand covalently linking caffeine and DHA and assessed its pharmacological activity and safety profile in a simple cellular model. Interestingly, the new bivalent ligand presented higher potency as an A2AR inverse agonist than caffeine alone. We also determined the range of concentrations inducing toxicity both in a heterologous system and in primary striatal cultures. The novel strategy presented here of attaching DHA to caffeine may enable increased effects of the drug at desired sites, which could be of interest for the treatment of PD.

  19. Surface ligand dependent toxicity of zinc oxide nanoparticles in HepG2 cell model

    International Nuclear Information System (INIS)

    Bartczak, D; Baradez, M-O; Merson, S; Goenaga-Infante, H; Marshall, D

    2013-01-01

    Physicochemical properties of nanoparticles (NP) strongly affect their influence on cell behaviour, but can be significantly distorted by interactions with the proteins present in biological solutions. In this study we show how different surface functionalities of zinc oxide (ZnO) NP lead to changes in the size distribution and dissolution of the NP in serum containing cell culture media and how this impacts on NP toxicity. NPs capped with weakly bound large proteins undergo substantial transformations due to the exchange of the original surface ligands to the components of the cell culture media. Conversely, NP capped with a tight monolayer of small organic molecules or with covalently conjugated proteins show significantly higher stability. These differences in ligand exchange also affect the toxicity of the NP to the HepG2 liver cell model, with the NP capped with small organic molecules being more toxic than those capped with large proteins. This study highlights the importance of characterising NPs in biological media and the effect the media has during in-vitro analysis.

  20. Designing a New Class of Bases for Nucleic Acid Quadruplexes and Quadruplex-Active Ligands.

    Science.gov (United States)

    Bazzi, Sophia; Novotný, Jan; Yurenko, Yevgen P; Marek, Radek

    2015-06-22

    A new class of quadruplex nucleobases, derived from 3-deazaguanine, has been designed for various applications as smart quadruplex ligands as well as quadruplex-based aptamers, receptors, and sensors. An efficient strategy for modifying the guanine quadruplex core has been developed and tested by using quantum chemistry methods. Several potential guanine derivatives modified at the 3- or 8-position or both are analyzed, and the results compared to reference systems containing natural guanine. Analysis of the formation energies (BLYP-D3(BJ)/def2-TZVPP level of theory, in combination with the COSMO model for water) in model systems consisting of two and three stacked tetrads with Na(+) /K(+) ion(s) inside the internal channel indicates that the formation of structures with 3-halo-3-deazaguanine bases leads to a substantial gain in energy, as compared to the corresponding reference guanine complexes. The results cast light on changes in the noncovalent interactions (hydrogen bonding, stacking, and ion coordination) in a quadruplex stem upon modification of the guanine core. In particular, the enhanced stability of the modified quadruplexes was shown to originate mainly from increased π-π stacking. Our study suggests the 3-halo-3-deazaguanine skeleton as a potential building unit for quadruplex systems and smart G-quadruplex ligands. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation

    Directory of Open Access Journals (Sweden)

    Schroeder Michael

    2006-09-01

    Full Text Available Abstract Background Identifying pockets on protein surfaces is of great importance for many structure-based drug design applications and protein-ligand docking algorithms. Over the last ten years, many geometric methods for the prediction of ligand-binding sites have been developed. Results We present LIGSITEcsc, an extension and implementation of the LIGSITE algorithm. LIGSITEcsc is based on the notion of surface-solvent-surface events and the degree of conservation of the involved surface residues. We compare our algorithm to four other approaches, LIGSITE, CAST, PASS, and SURFNET, and evaluate all on a dataset of 48 unbound/bound structures and 210 bound-structures. LIGSITEcsc performs slightly better than the other tools and achieves a success rate of 71% and 75%, respectively. Conclusion The use of the Connolly surface leads to slight improvements, the prediction re-ranking by conservation to significant improvements of the binding site predictions. A web server for LIGSITEcsc and its source code is available at scoppi.biotec.tu-dresden.de/pocket.

  2. Endogenously generated arachidonate-derived ligands for TRPV1 induce cardiac protection in sepsis.

    Science.gov (United States)

    Chen, Jianmin; Hamers, Alexander J P; Finsterbusch, Michaela; Massimo, Gianmichele; Zafar, Maleeha; Corder, Roger; Colas, Romain A; Dalli, Jesmond; Thiemermann, Christoph; Ahluwalia, Amrita

    2018-02-20

    The severity of cardiac dysfunction predicts mortality in sepsis. Activation of transient receptor potential vanilloid receptor type (TRPV)-1, a predominantly neuronal nonselective cation channel, has been shown to improve outcome in sepsis and endotoxemia. However, the role of TRPV1 and the identity of its endogenous ligands in the cardiac dysfunction caused by sepsis and endotoxemia are unknown. Using TRPV1 -/- and TRPV1 +/+ mice, we showed that endogenous activation of cardiac TRPV1 during sepsis is key to limiting the ensuing cardiac dysfunction. Use of liquid chromatography-tandem mass spectrometry lipid analysis and selective inhibitors of arachidonic metabolism suggest that the arachidonate-derived TRPV1 activator, 20-hydroxyeicosateraenoic acid (20-HETE), underlies a substantial component of TRPV1-mediated cardioprotection in sepsis. Moreover, using selective antagonists for neuropeptide receptors, we show that this effect of TRPV1 relates to the activity of neuronally released cardiac calcitonin gene-related peptide (CGRP) and that, accordingly, administration of CGRP can rescue cardiac dysfunction in severe endotoxemia. In sum activation of TRPV1 by 20-HETE leads to the release of CGRP, which protects the heart against the cardiac dysfunction in endotoxemia and identifies both TRPV1 and CGRP receptors as potential therapeutic targets in endotoxemia.-Chen, J., Hamers, A. J. P., Finsterbusch, M., Massimo, G., Zafar, M., Corder, R., Colas, R. A., Dalli, J., Thiemermann, C., Ahluwalia, A. Endogenously generated arachidonate-derived ligands for TRPV1 induce cardiac protection in sepsis.

  3. Bridging-ligand-substitution strategy for the preparation of metal-organic polyhedra

    Science.gov (United States)

    Li, Jian-Rong; Zhou, Hong-Cai

    2010-10-01

    Metal-organic polyhedra-discrete molecular architectures constructed through the coordination of metal ions and organic linkers-have recently attracted considerable attention due to their intriguing structures, their potential for a variety of applications and their relevance to biological self-assembly. Several synthetic routes have been investigated to prepare these complexes. However, to date, these preparative methods have typically been based on the direct assembly of metal ions and organic linkers. Although these routes are convenient, it remains difficult to find suitable reaction conditions or to control the outcome of the assembly process. Here, we demonstrate a synthetic strategy based on the substitution of bridging ligands in soluble metal-organic polyhedra. The introduction of linkers with different properties from those of the initial metal-organic polyhedra can thus lead to new metal-organic polyhedra with distinct properties (including size and shape). Furthermore, partial substitution can also occur and form mixed-ligand species that may be difficult to access by means of other approaches.

  4. Is There an Opportunity for Current Chemotherapeutics to Up-regulate MIC-A/B Ligands?

    Directory of Open Access Journals (Sweden)

    Kendel Quirk

    2017-10-01

    Full Text Available Natural killer (NK cells are critical effectors of the immune system. NK cells recognize unhealthy cells by specific ligands [e.g., MHC- class I chain related protein A or B (MIC-A/B] for further elimination by cytotoxicity. Paradoxically, cancer cells down-regulate MIC-A/B and evade NK cell’s anticancer activity. Recent data indicate that cellular-stress induces MIC-A/B, leading to enhanced sensitivity of cancer cells to NK cell-mediated cytotoxicity. In this Perspective article, we hypothesize that current chemotherapeutics at sub-lethal, non-toxic dose may promote cellular-stress and up-regulate the expression of MIC-A/B ligands to augment cancer’s sensitivity to NK cell-mediated cytotoxicity. Preliminary data from two human breast cancer cell lines, MDA-MB-231 and T47D treated with clinically relevant therapeutics such as doxorubicin, paclitaxel and methotrexate support the hypothesis. The goal of this Perspective is to underscore the prospects of current chemotherapeutics in NK cell immunotherapy, and discuss potential challenges and opportunities to improve cancer therapy.

  5. Surface ligand dependent toxicity of zinc oxide nanoparticles in HepG2 cell model

    Science.gov (United States)

    Bartczak, D.; Baradez, M.-O.; Merson, S.; Goenaga-Infante, H.; Marshall, D.

    2013-04-01

    Physicochemical properties of nanoparticles (NP) strongly affect their influence on cell behaviour, but can be significantly distorted by interactions with the proteins present in biological solutions. In this study we show how different surface functionalities of zinc oxide (ZnO) NP lead to changes in the size distribution and dissolution of the NP in serum containing cell culture media and how this impacts on NP toxicity. NPs capped with weakly bound large proteins undergo substantial transformations due to the exchange of the original surface ligands to the components of the cell culture media. Conversely, NP capped with a tight monolayer of small organic molecules or with covalently conjugated proteins show significantly higher stability. These differences in ligand exchange also affect the toxicity of the NP to the HepG2 liver cell model, with the NP capped with small organic molecules being more toxic than those capped with large proteins. This study highlights the importance of characterising NPs in biological media and the effect the media has during in-vitro analysis.

  6. The Prelude on Novel Receptor and Ligand Targets Involved in the Treatment of Diabetes Mellitus

    Directory of Open Access Journals (Sweden)

    Venu Gopal Jonnalagadda

    2014-05-01

    Full Text Available Metabolic disorders are a group of disorders, due to the disruption of the normal metabolic process at a cellular level. Diabetes Mellitus and Tyrosinaemia are the majorly reported metabolic disorders. Among them, Diabetes Mellitus is a one of the leading metabolic syndrome, affecting 5 to 7 % of the population worldwide and mainly characterised by elevated levels of glucose and is associated with two types of physiological event disturbances such as impaired insulin secretion and insulin resistance. Up to now, various treatment strategies are like insulin, alphaglucosidase inhibitors, biguanides, incretins were being followed. Concurrently, various novel therapeutic strategies are required to advance the therapy of Diabetes mellitus. For the last few decades, there has been an extensive research in understanding the metabolic pathways involved in Diabetes Mellitus at the cellular level and having the profound knowledge on cell-growth, cell-cycle, and apoptosis at a molecular level provides new targets for the treatment of Diabetes Mellitus. Receptor signalling has been involved in these mechanisms, to translate the information coming from outside. To understand the various receptors involved in these pathways, we must have a sound knowledge on receptors and ligands involved in it. This review mainly summarises the receptors and ligands which are involved the Diabetes Mellitus. Finally, researchers have to develop the alternative chemical moieties that retain their affinity to receptors and efficacy. Diabetes Mellitus being a metabolic disorder due to the glucose surfeit, demands the need for regular exercise along with dietary changes.

  7. 1D helical cadmium coordination polymers containing hydrazide ligand: The role of solvent and molar ratio

    Science.gov (United States)

    Notash, Behrouz

    2018-03-01

    Three new cadmium coordination polymers, [Cd(L)(NO3)2CH3OH]n, 1, {[Cd(L)2(NO3)]NO3}n, 2 and {[Cd(L)2(NO3)]NO3.H2O}n3, which L is nicotinohydrazide have been synthesized and characterized by spectroscopic methods as well as single crystal X-ray diffraction. Compounds 1-3 have been synthesized by changing solvent and metal-to-ligand ratio. X-ray crystallography showed that compounds 1-3 have different 1D helical structural motif. Semi-flexible nature of L ligand causes to syn-syn conformation which leading to form 1D helical chains coordination polymers. Compounds 2 and 3 were synthesized under the same reaction conditions with similar molar ratio, but using different solvent system. These compounds are pseudopolymorph which differs in the presence or absence of water molecule in their crystal packing. Hirshfeld surface analysis of the structures 1-3 have been performed and find the percent of participation of intermolecular interactions in the crystal packing of compounds.

  8. Functionalization of Krebs-type polyoxometalates with N,O-chelating ligands: a systematic study.

    Science.gov (United States)

    Artetxe, Beñat; Reinoso, Santiago; San Felices, Leire; Vitoria, Pablo; Pache, Aroa; Martín-Caballero, Jagoba; Gutiérrez-Zorrilla, Juan M

    2015-01-05

    The first organic derivatives of 3d-metal-disubstituted Krebs-type polyoxometalates have been synthesized under mild bench conditions via straightforward replacement of labile aqua ligands with N,O-chelating planar anions on either preformed or in situ-generated precursors. Nine hybrid clusters containing carboxylate derivatives of five- or six-membered aromatic N-heterocycles as antenna ligands have been obtained as pure crystalline phases and characterized by elemental and thermal analyses, infrared spectroscopy, and single-crystal X-ray diffraction. They all show the general formula [{M(II)L(H2O)}2(WO2)2(B-β-XW9O33)2](n-) and can be classified as follows: 1-SbM, where L = 1H-imidazole-4-carboxylate (imc), X = Sb(III), n = 12, and M(II) = Mn, Co, Ni, Zn; 1-TeM, where L = imc, X = Te(IV), n = 10, and M(II) = Mn, Co; 2-SbNi, where L = 1H-pyrazole-3-carboxylate (pzc), X = Sb(III), n = 12, and M(II) = Ni; and 3-SbM, where L = pyrazine-2-carboxylate (pyzc), X =Sb(III), n = 12, and M(II) = Co, Zn. The 3d-metal-disubstituted tungstotellurate(IV) skeleton of compounds 1-TeM is unprecedented in polyoxometalate chemistry. The stability of these hybrid Krebs-type species in aqueous solution has been confirmed by (1)H NMR spectroscopy performed on the diamagnetic 1-SbZn and 3-SbZn derivatives. Our systematic study of the reactivity of disubtituted Krebs-type polyoxotungstates toward diazole-, pyridine-, and diazinecarboxylates demonstrates that organic derivatization is strongly dependent on the nature of the ligand, as follows: imc displays a "universal ligand" character, as functionalization takes place regardless of the external 3d metal and heteroatom; pzc and pyzc show selectivity toward specific 3d metals; pyridazine-3-carboxylate and pyrimidine-4-carboxylate promote partial decomposition of specific precursors, leading to [M(II)L2(H2O)2] complexes; and picolinate is inert under all conditions tested.

  9. Digallane with redox-active diimine ligand: dualism of electron-transfer reactions.

    Science.gov (United States)

    Fedushkin, Igor L; Skatova, Alexandra A; Dodonov, Vladimir A; Chudakova, Valentina A; Bazyakina, Natalia L; Piskunov, Alexander V; Demeshko, Serhiy V; Fukin, Georgy K

    2014-05-19

    The reactivity of digallane (dpp-Bian)Ga-Ga(dpp-Bian) (1), which consists of redox-active ligand 1,2-bis[(2,6-diisopropylphenyl)imino]acenaphthene (dpp-Bian), has been studied. The reaction of 1 with I2 proceeds via one-electron oxidation of each of two dpp-Bian ligands to a radical-anionic state and affords complex (dpp-Bian)IGa-GaI(dpp-Bian) (2). Dissolution of complex 2 in pyridine (Py) gives monomeric compound (dpp-Bian)GaI(Py) (3) as a result of a solvent-induced intramolecular electron transfer from the metal-metal bond to the dpp-Bian ligands. Treatment of compound 3 with B(C6F5)3 leads to removal of pyridine and restores compound 2. The reaction of compound 1 with 3,6-di-tert-butyl-ortho-benzoquinone (3,6-Q) proceeds with oxidation of all the redox-active centers in 1 (the Ga-Ga bond and two dpp-Bian dianions) and results in mononuclear catecholate (dpp-Bian)Ga(Cat) (4) (Cat = [3,6-Q](2-)). Treatment of 4 with AgBF4 gives a mixture of [(dpp-Bian)2Ag][BF4] (5) and (dpp-Bian)GaF(Cat) (6), which both consist of neutral dpp-Bian ligands. The reduction of benzylideneacetone (BA) with 1 generates the BA radical-anions, which dimerize, affording (dpp-Bian)Ga-(BA-BA)-Ga(dpp-Bian) (7). In this case the Ga-Ga bond remains unchanged. Within 10 min at 95 °C in solution compound 7 undergoes transformation to paramagnetic complex (dpp-Bian)Ga(BA-BA) (8) and metal-free compound C36H40N2 (9). The latter is a product of intramolecular addition of the C-H bond of one of the iPr groups to the C═N bond in dpp-Bian. Diamagnetic compounds 3, 5, 6, and 9 have been characterized by NMR spectroscopy, and paramagnetic complexes 2, 4, 7, and 8 by ESR spectroscopy. Molecular structures of 2-7 and 9 have been established by single-crystal X-ray analysis.

  10. The oceanography of winter leads

    Science.gov (United States)

    Morison, J. H.; McPhee, M. G.; Curtin, T. B.; Paulson, C. A.

    1992-07-01

    Leads in pack ice have long been considered important to the thermodynamics of the polar regions. A winter lead affects the ocean around it because it is a density source. As the surface freezes, salt is rejected and forms more dense water which sinks under the lead. This sets up a circulation with freshwater flowing in from the sides near the surface and dense water flowing away from the lead at the base of the mixed layer. If the mixed layer is fully turbulent, this pattern may not occur; rather, the salt rejected at the surface may simply mix into the surface boundary layer. In either event the instability produced at the surface of leads is the primary source of unstable buoyancy flux and, as such, exerts a strong influence on the mixed layer. Here as many as possible of the disparate and almost anecdotal observations of lead oceanography are assembled and combined with theoretical arguments to predict the form and scale of oceanographic disturbances caused by winter leads. The experimental data suggest the velocity disturbances associated with lead convection are about 1-5 cm s-1. These appear as jets near the surface and the base of the mixed layer when ice velocities across the lead are less than about 5 cm s-1. The salinity disturbances are about 0.01 to 0.05 psu. Scaling arguments suggest that the geostrophic currents set up by the lead density disturbances are also of the order of 1-5 cm s-1. The disturbances are most obvious when freezing is rapid and ice velocity is low because the salinity and velocity disturbances in the upper ocean are not smeared out by turbulence. In this vein, lead convection may be characterized at one extreme as free convection in which the density disturbance forces the circulation. At the other extreme, lead convection may be characterized as forced convection in which the density disturbance is mixed rapidly by boundary layer turbulence. The lead number Lo, which is the ratio of the pressure term to the turbulence term in the

  11. Identification of VDR Antagonists among Nuclear Receptor Ligands Using Virtual Screening

    Directory of Open Access Journals (Sweden)

    Kelly Teske

    2014-04-01

    Full Text Available Herein, we described the development of two virtual screens to identify new vitamin D receptor (VDR antagonists among nuclear receptor (NR ligands. Therefore, a database of 14330 nuclear receptor ligands and their NR affinities was assembled using the online available “Binding Database.” Two different virtual screens were carried out in conjunction with a reported VDR crystal structure applying a stringent and less stringent pharmacophore model to filter docked NR ligand conformations. The pharmacophore models were based on the spatial orientation of the hydroxyl functionalities of VDR's natural ligands 1,25(OH2D3 and 25(OH2D3. The first virtual screen identified 32 NR ligands with a calculated free energy of VDR binding of more than -6.0 kJ/mol. All but nordihydroguaiaretic acid (NDGA are VDR ligands, which inhibited the interaction between VDR and coactivator peptide SRC2-3 with an IC50 value of 15.8 μM. The second screen identified 162 NR ligands with a calculated free energy of VDR binding of more than -6.0 kJ/mol. More than half of these ligands were developed to bind VDR followed by ERα/β ligands (26%, TRα/β ligands (7%, and LxRα/β ligands (7%. The binding between VDR and ERα ligand H6036 as well as TRα/β ligand triiodothyronine and a homoserine analog thereof was confirmed by fluorescence polarization.

  12. Molecular dynamics simulations suggest ligand's binding to nicotinamidase/pyrazinamidase.

    Science.gov (United States)

    Zhang, Ji-Long; Zheng, Qing-Chuan; Li, Zheng-Qiang; Zhang, Hong-Xing

    2012-01-01

    The research on the binding process of ligand to pyrazinamidase (PncA) is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA's activity. In the present study, molecular dynamics (MD) simulation methods were performed to investigate the unbinding process of nicotinamide (NAM) from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF) based on the steered molecular dynamics (SMD) simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM's unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand's binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs.

  13. Molecular dynamics simulations suggest ligand's binding to nicotinamidase/pyrazinamidase.

    Directory of Open Access Journals (Sweden)

    Ji-Long Zhang

    Full Text Available The research on the binding process of ligand to pyrazinamidase (PncA is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA's activity. In the present study, molecular dynamics (MD simulation methods were performed to investigate the unbinding process of nicotinamide (NAM from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF based on the steered molecular dynamics (SMD simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM's unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand's binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs.

  14. Synthesis and evaluation of potential ligands for nuclear waste processing

    NARCIS (Netherlands)

    Iqbal, M.

    2012-01-01

    The research presented in this thesis deals with the synthesis and evaluation of new potential ligands for the complexation of actinide and lanthanide ions either for their extraction from bulk radioactive waste or their stripping from an extracted organic phase for final processing of the waste. In

  15. NMR-based screening of membrane protein ligands

    NARCIS (Netherlands)

    Yanamala, Naveena; Dutta, Arpana; Beck, Barbara; Van Fleet, Bart; Hay, Kelly; Yazbak, Ahmad; Ishima, Rieko; Doemling, Alexander; Klein-Seetharaman, Judith

    2010-01-01

    Membrane proteins pose problems for the application of NMR-based ligand-screening methods because of the need to maintain the proteins in a membrane mimetic environment such as detergent micelles: they add to the molecular weight of the protein, increase the viscosity of the solution, interact with

  16. Synthesis and Characterization of Metal Complexes with Schiff Base Ligands

    Science.gov (United States)

    Wilkinson, Shane M.; Sheedy, Timothy M.; New, Elizabeth J.

    2016-01-01

    In order for undergraduate laboratory experiments to reflect modern research practice, it is essential that they include a range of elements, and that synthetic tasks are accompanied by characterization and analysis. This intermediate general chemistry laboratory exercise runs over 2 weeks, and involves the preparation of a Schiff base ligand and…

  17. synthesis and spectra characterization of mixed- ligand complexes

    African Journals Online (AJOL)

    BARTH EKWUEME

    bipyridine(bpy) has been announced to be “the most used ligand in coordination chemistry” (Humphries, et al., 2005), 2,2':6',2''-terpyridine (tpy) also has a rich chemistry. Almost 70 years ago, Burstall and Morgan reported the first synthesis of 2, 2':6', 2''-terpyridine. (Bermejo, et al., 1999). The kinetics and mechanism of ...

  18. Development and Application of Ligand-Exchange Reaction Method ...

    African Journals Online (AJOL)

    Purpose: This paper presents an improved kinetic-spectrophotometric procedure for determining clonazepam (CZP) in pharmaceutical formulations and human serum. Methods: The method is based on ligand-exchange reaction. The reaction was followed spectrophotometrically by measuring the rate of change of ...

  19. Mixed-ligand binuclear copper(II) complex of 5 ...

    Indian Academy of Sciences (India)

    carbon, saturated Ag/AgCl and platinum wire are used as the working, reference and auxiliary electrodes, ... was mounted on a glass fibre for diffraction experiment. X-ray single crystal data were collected on a Kappa ..... with the covalent nature of the metal–ligand bond. 3.4 DNA binding studies. 3.4a Absorption spectral ...

  20. A Simple Ligand for Lanthanide Energy Transfer Luminescence in ...

    African Journals Online (AJOL)

    NJD

    induced electron transfer (P.E.T.) fluorescent-based sensor that responds to the presence of Mg2+ ions by ... phenol tetraacetic acid (bapta).12,13 Owing to the similarity of the structures of bapta and apta, we decided to .... The protonation state can have a profound effect on the ability of the ligand to facilitate the formation of ...