Sample records for hexadentate polypyridyl ligands

  1. Synthesis and transition metal coordination chemistry of a novel hexadentate bispidine ligand. (United States)

    Comba, Peter; Rudolf, Henning; Wadepohl, Hubert


    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.

  2. Synthesis, physicochemical studies and biological evaluation of unimetallic and heterobimetallic complexes of hexadentate dihydrazone ligands

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    Fathy A. El Saied


    Full Text Available A new coordination unimetallic and heterobimetallic complexes of hexadentate N2O4 donor dihydrazone ligands were prepared by the condensation of 4-formyl antipyrine with adipic dihydrazide and succinic dihydrazide. The ligands (1 and (11 and their complexes thoroughly characterized using various analytical, physical and spectroscopic techniques, which indicate a distorted octahedral geometry around the metal ions. The ESR spectra of solid copper(II complexes (2–4 and (12–14 showed axial symmetry with g||>g⊥ > ge, indicating distorted octahedral structure and the presence of the unpaired electron in a d(x2−y2 orbital with significant covalent bond character. The antimicrobial activity results of the metal compounds (2–5, (7, (10, (12–15 and (17 show that, all these complexes exhibit inhibitory moderate to mild effects towards Bacillus subtilis, Escherichia coli and Aspergillus niger.

  3. The thermodynamic effects of ligand structure on the molecular recognition of mononuclear ruthenium polypyridyl complexes with B-DNA (United States)

    The ruthenium(II) polypyridyl complexes (RPCs), [(phen)2Ru(tatpp)]Cl2 (3Cl2) and [(phen)2Ru (tatpp)Ru(phen)2]Cl4 (4Cl4), containing the large planar and redox-active tetraazatetrapyrido- pentacene (tatpp) ligand, cleave DNA in the presence of reducing agents in cell-free assays and show significant...

  4. Copper (II) complexes possessing alkyl-substituted polypyridyl ligands: Structural characterization and in vitro antitumor activity. (United States)

    Angel, Noah R; Khatib, Raneen M; Jenkins, Julia; Smith, Michelle; Rubalcava, Justin M; Le, Brian Khoa; Lussier, Daniel; Chen, Zhuo Georgia; Tham, Fook S; Wilson, Emma H; Eichler, Jack F


    In an effort to find alternatives to the antitumor drug cisplatin, a series of copper (II) complexes possessing alkyl-substituted polypyridyl ligands have been synthesized. Eight new complexes are reported herein: μ-dichloro-bis{2,9-di-sec-butyl-1,10-phenanthrolinechlorocopper(II)} {[((di-sec-butyl)phen)ClCu(μ-Cl)2CuCl((di-sec-butyl)phen)]}(1), 2-sec-butyl-1,10-phenanthrolinedichlorocopper(II) {([mono-sec-butyl)phen) CuCl2} (2), 2,9-di-n-butyl-1,10-phenanthrolinedichlorocopper(II) {[(di-n-butyl)phen) CuCl2}(3), 2-n-butyl-1,10-phenanthrolinedichlorocopper(II) {[(mono-n-butyl)phen) CuCl2} (4), 2,9-di-methyl-1,10-phenanthrolineaquadichlorocopper(II) {[(di-methyl)phen) Cu(H2O)Cl2}(5), μ-dichloro-bis{6-sec-butyl-2,2'-bipyridinedichlorocopper(II)} {((mono-sec-butyl)bipy) ClCu(μ-Cl)2CuCl((mono-sec-butyl)bipy)} (6), 6,6'-di-methyl-2,2'-bipyridinedichlorocopper(II) {(6,6'-di-methyl)bipy) CuCl2} (7), and 4,4'-dimethyl-2,2'-bipyridinedichlorocopper(II) {(4,4'-di-methyl)bipy) CuCl2} (8). These complexes have been characterized via elemental analysis, UV-vis spectroscopy, and mass spectrometry. Single crystal X-ray diffraction experiments revealed the complexes synthesized with the (di-sec-butyl)phen ligand (1) and (mono-sec-butyl)bipy ligand (6) crystallized as dimers in which two copper(II) centers are bridged by two chloride ligands. Conversely, complexes 2, 7, and 8 were isolated as monomeric species possessing distorted tetrahedral geometries, and the [((di-methyl)phen)Cu(H2O)Cl2] (5) complex was isolated as a distorted square pyramidal monomer possessing a coordinating aqua ligand. Compounds 1-8 were evaluated for their in vitro antitumor efficacy. Compounds 1, 5, and 7 in particular were found to exhibit remarkable activity against human derived lung cancer cells, yet this class of copper(II) compounds had minimal cytotoxic effect on non-cancerous cells. In vitro control experiments indicate the activity of the copper(II) complexes most likely does not arise from the

  5. Substituent effects on spin state in a series of mononuclear manganese(III) complexes with hexadentate Schiff-Base ligands. (United States)

    Gildea, Brendan; Harris, Michelle M; Gavin, Laurence C; Murray, Caroline A; Ortin, Yannick; Müller-Bunz, Helge; Harding, Charles J; Lan, Yanhua; Powell, Annie K; Morgan, Grace G


    Eleven new mononuclear manganese(III) complexes prepared from two hexadentate ligands, L1 and L2, with different degrees of steric bulk in the substituents are reported. L1 and L2 are Schiff bases resulting from condensation of N,N'-bis(3-aminopropyl)ethylenediamine with 3-methoxy-2-hydroxybenzaldehyde and 3-ethoxy-2-hydroxybenzaldehyde respectively, and are members of a ligand series we have abbreviated as R-Sal2323 to indicate the 323 alkyl connectivity in the starting tetraamine and the substitution (R) on the phenolate ring. L1 hosts a methoxy substituent on both phenolate rings, while L2 bears a larger ethoxy group in the same position. Structural and magnetic properties are reported in comparison with those of a previously reported analogue with L1, namely, [MnL1]NO3, (1e). The BPh4(-) and PF6(-) complexes [MnL1]BPh4, (1a), [MnL2]BPh4, (2a), [MnL1]PF6, (1b'), and [MnL2]PF6, (2b), with both ligands L1 and L2, remain high-spin (HS) over the measured temperature range. However, the monohydrate of (1b') [MnL1]PF6·H2O, (1b), shows gradual spin-crossover (SCO), as do the ClO4(-), BF4(-), and NO3(-) complexes [MnL1]ClO4·H2O, (1c), [MnL2]ClO4, (2c), [MnL1]BF4·H2O, (1d), [MnL2]BF4·0.4H2O, (2d), [MnL1]NO3, (1e), and [MnL2]NO3·EtOH, (2e). The three complexes formed with ethoxy-substituted ligand L2 all show a higher T1/2 than the analogous complexes with methoxy-substituted ligand L1. Analysis of distortion parameters shows that complexes formed with the bulkier ligand L2 exhibit more deformation from perfect octahedral geometry, leading to a higher T1/2 in the SCO examples, where T1/2 is the temperature where the spin state is 50% high spin and 50% low spin. Spin state assignment in the solid state is shown to be solvate-dependent for complexes (1b) and (2e), and room temperature UV-visible and NMR spectra indicate a solution-state spin assignment intermediate between fully HS and fully low spin in 10 complexes, (1a)-(1e) and (2a)-(2e).

  6. Theoretical Insight into the Spectral Characteristics of Fe(II-Based Complexes for Dye-Sensitized Solar Cells—Part I: Polypyridyl Ancillary Ligands

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    Xiaoqing Lu


    Full Text Available The design of light-absorbent dyes with cheaper, safer, and more sustainable materials is one of the key issues for the future development of dye-sensitized solar cells (DSSCs. We report herein a theoretical investigation on a series of polypyridyl Fe(II-based complexes of FeL2(SCN2, [FeL3]2+, [FeL′(SCN3]-, [FeL′2]2+, and FeL′′(SCN2 (L = 2,2′-bipyridyl-4,4′-dicarboxylic acid, L′ = 2,2′,2″-terpyridyl-4,4′,4″-tricarboxylic acid, L″ = 4,4‴-dimethyl-2,2′ : 6′,2″ :6″,2‴-quaterpyridyl-4′,4″-biscarboxylic acid by density functional theory (DFT and time-dependent DFT (TD-DFT. Molecular geometries, electronic structures, and optical absorption spectra are predicted in both the gas phase and methyl cyanide (MeCN solution. Our results show that polypyridyl Fe(II-based complexes display multitransition characters of Fe → polypyridine metal-to-ligand charge transfer and ligand-to-ligand charge transfer in the range of 350–800 nm. Structural optimizations by choosing different polypyridyl ancillary ligands lead to alterations of the molecular orbital energies, oscillator strength, and spectral response range. Compared with Ru(II sensitizers, Fe(II-based complexes show similar characteristics and improving trend of optical absorption spectra along with the introduction of different polypyridyl ancillary ligands.

  7. Selective Photodissociation of Acetonitrile Ligands in Ruthenium Polypyridyl Complexes Studied by Density Functional Theory. (United States)

    Tu, Yi-Jung; Mazumder, Shivnath; Endicott, John F; Turro, Claudia; Kodanko, Jeremy J; Schlegel, H Bernhard


    Metal complexes that release ligands upon photoexcitation are important tools for biological research and show great potential as highly specific therapeutics. Upon excitation with visible light, [Ru(TQA)(MeCN)2](2+) [TQA = tris(2-quinolinylmethyl)amine] exchanges one of the two acetonitriles (MeCNs), whereas [Ru(DPAbpy)MeCN](2+) [DPAbpy = N-(2,2'-bipyridin-6-yl)-N,N-bis(pyridin-2-ylmethyl)amine] does not release MeCN. Furthermore, [Ru(TQA)(MeCN)2](2+) is highly selective for release of the MeCN that is perpendicular to the plane of the two axial quinolines. Density functional theory calculations provide a clear explanation for the photodissociation behavior of these two complexes. Excitation by visible light and intersystem crossing leads to a six-coordinate (3)MLCT state. Dissociation of acetonitrile can occur after internal conversion to a dissociative (3)MC state, which has an occupied dσ* orbital that interacts in an antibonding fashion with acetonitrile. For [Ru(TQA)(MeCN)2](2+), the dissociative (3)MC state is lower than the (3)MLCT state. In contrast, the (3)MC state of [Ru(DPAbpy)MeCN](2+) that releases acetonitrile has an energy higher than that of the (3)MLCT state, indicating dissociation is unfavorable. These results are consistent with the experimental observations that efficient photodissociation of acetonitrile occurs for [Ru(TQA)(MeCN)2](2+) but not for [Ru(DPAbpy)MeCN](2+). For the release of the MeCN ligand in [Ru(TQA)(MeCN)2](2+) that is perpendicular to the axial quinoline rings, the (3)MLCT state has an occupied quinoline π* orbital that can interact with a dσ* Ru-NCCH3 antibonding orbital as the Ru-NCCH3 bond is stretched and the quinolines bend toward the departing acetonitrile. This reduces the barrier for the formation of the dissociative (3)MC state, leading to the selective photodissociation of this acetonitrile. By contrast, when the acetonitrile is in the plane of the quinolines or bpy, no interaction occurs between the ligand

  8. Spectroscopic studies on chromium(III), manganese(II), cobalt(II), nickel(II) and copper(II) complexes with hexadentate nitrogen-sulfur donor [N(2)S(4)] macrocyclic ligand. (United States)

    Shukla, Deepak; Gupta, Lokesh Kumar; Chandra, Sulekh


    Complexes of transition metals have been synthesized with hexadentate ligand (2,6-bis(((2-mercaptophenyl)thio)methyl)pyridinato)metal(II). These complexes have been synthesized via the two step template reaction by using the benzene dithiol, 2,6-bis(chloro)methyl pyridine and corresponding metal salt as key raw materials. The structures of the complexes have been elucidated on the basis of elemental analysis, molar conductance measurements, magnetic susceptibility measurements, IR, electronic and EPR spectral studies. All of the complexes were found to possess six-coordinated geometry and are of high spin type.

  9. Spectroscopic studies on chromium(III), manganese(II), cobalt(II), nickel(II) and copper(II) complexes with hexadentate nitrogen-sulfur donor [N 2S 4] macrocyclic ligand (United States)

    Shukla, Deepak; Gupta, Lokesh Kumar; Chandra, Sulekh


    Complexes of transition metals have been synthesized with hexadentate ligand (2,6-bis(((2-mercaptophenyl)thio)methyl)pyridinato)metal(II). These complexes have been synthesized via the two step template reaction by using the benzene dithiol, 2,6-bis(chloro)methyl pyridine and corresponding metal salt as key raw materials. The structures of the complexes have been elucidated on the basis of elemental analysis, molar conductance measurements, magnetic susceptibility measurements, IR, electronic and EPR spectral studies. All of the complexes were found to possess six-coordinated geometry and are of high spin type.

  10. Cobalt(II), nickel(II) and copper(II) complexes of a hexadentate pyridine amide ligand. Effect of donor atom (ether vs. thioether) on coordination geometry, spin-state of cobalt and M(III)-M(II) redox potential. (United States)

    Pandey, Sharmila; Das, Partha Pratim; Singh, Akhilesh Kumar; Mukherjee, Rabindranath


    Using an acyclic hexadentate pyridine amide ligand, containing a -OCH(2)CH(2)O- spacer between two pyridine-2-carboxamide units (1,4-bis[o-(pyrydine-2-carboxamidophenyl)]-1,4-dioxabutane (H(2)L(9)), in its deprotonated form), four new complexes, [Co(II)(L(9))] (1) and its one-electron oxidized counterpart [Co(III)(L(9))][NO(3)]·2H(2)O (2), [Ni(II)(L(9))] (3) and [Cu(II)(L(9))] (4), have been synthesized. Structural analyses revealed that the Co(II) centre in 1 and the Ni(II) centre in 3 are six-coordinate, utilizing all the available donor sites and the Cu(II) centre in 4 is effectively five-coordinated (one of the ether O atoms does not participate in coordination). The structural parameters associated with the change in the metal coordination environment have been compared with corresponding complexes of thioether-containing hexadentate ligands. The μ(eff) values at 298 K of 1-4 correspond to S = 3/2, S = 0, S = 1 and S = 1/2, respectively. Absorption spectra for all the complexes have been investigated. EPR spectral properties of the copper(II) complex 4 have been investigated, simulated and analyzed. Cyclic voltammetric experiments in CH(2)Cl(2) reveal quasireversible Co(III)-Co(II), Ni(III)-Ni(II) and Cu(II)-Cu(I) redox processes. In going from ether O to thioether S coordination, the effect of the metal coordination environment on the redox potential values of Co(III)-Co(II) (here the effect of spin-state as well), Ni(III)-Ni(II) and Cu(II)-Cu(I) processes have been systematically analyzed.

  11. Electrochemical Polymerization of Iron(III) Polypyridyl Complexes through C-C Coupling of Redox Non-innocent Phenolato Ligands

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    Unjaroen, Duenpen; Swart, Marcel; Browne, Wesley R


    Phenolato moieties impart redox flexibility to metal complexes due their accessible (oxidative) redox chemistry and have been proposed as functional ligand moieties in redox non-innocent ligand based transition metal catalysis. Here, the electro-and spectroelectrochemistry of phenolato based

  12. Rates of nickel(II) capture from complexes with NTA, EDDA, and related tetradentate chelating agents by the hexadentate chelating agents EDTA and CDTA: Evidence of a "semijunctive" ligand exchange pathway (United States)

    Boland, Nathan E.; Stone, Alan T.


    Many siderophores and metallophores produced by soil organisms, as well as anthropogenic chelating agent soil amendments, rely upon amine and carboxylate Lewis base groups for metal ion binding. UV-visible spectra of metal ion-chelating agent complexes are often similar and, as a consequence, whole-sample absorbance measurements are an unreliable means of monitoring the progress of exchange reactions. In the present work, we employ capillary electrophoresis to physically separate Ni(II)-tetradentate chelating agent complexes (NiL) from Ni(II)-hexadentate chelating agent complexes (NiY) prior to UV detection, such that progress of the reaction NiL + Y → NiY + L can be conveniently monitored. Rates of ligand exchange for Ni(II) are lower than for other +II transition metal ions. Ni(II) speciation in environmental media is often under kinetic rather than equilibrium control. Nitrilotriacetic acid (NTA), with three carboxylate groups all tethered to a central amine Lewis base group, ethylenediamine-N,N‧-diacetic acid (EDDA), with carboxylate-amine-amine-carboxylate groups arranged linearly, plus four structurally related compounds, are used as tetradentate chelating agents. Ethylenediaminetetraacetic acid (EDTA) and the structurally more rigid analog trans-cyclohexaneethylenediaminetetraacetic acid (CDTA) are used as hexadentate chelating agents. Effects of pH and reactant concentration are explored. Ni(II) capture by EDTA was consistently more than an order of magnitude faster than capture by CDTA, and too fast to quantify using our capillary electrophoresis-based technique. Using NiNTA as a reactant, Ni(II) capture by CDTA is independent of CDTA concentration and greatly enhanced by a proton-catalyzed pathway at low pH. Using NiEDDA as reactant, Ni(II) capture by CDTA is first order with respect to CDTA concentration, and the contribution from the proton-catalyzed pathway diminished by CDTA protonation. While the convention is to assign either a disjunctive

  13. Electrochemical Polymerization of Iron(III) Polypyridyl Complexes through C-C Coupling of Redox Non-innocent Phenolato Ligands. (United States)

    Unjaroen, Duenpen; Swart, Marcel; Browne, Wesley R


    Phenolato moieties impart redox flexibility to metal complexes due their accessible (oxidative) redox chemistry and have been proposed as functional ligand moieties in redox non-innocent ligand based transition metal catalysis. Here, the electro- and spectroelectrochemistry of phenolato based μ-oxo-diiron(III) complexes [(L 1 )Fe(μ-O)Fe(L 1 )] 2+ (1) and [(L 2 )Fe(μ-O)Fe(L 2 )] 2+ (2), where L 1 = 2-(((di(pyridin-2-yl)methyl)(pyridin-2-ylmethyl)amino)methyl)phenol and L 2 = 3,5-di-tert-butyl-2-(((di(pyridin-2-yl)methyl)(pyridin-2-ylmethyl)amino)methyl)phenol, is described. The electrochemical oxidation of 1 in dichloromethane results in aryl C-C coupling of phenoxyl radical ligand moieties to form tetra nuclear complexes, which undergo subsequent oxidation to form iron(III) phenolato based polymers (poly-1). The coupling is blocked by placing tert-butyl groups at para and ortho positions of phenol units (i.e., 2). Poly-1 shows two fully reversible redox processes in monomer free solution. Assignment of species observed during the electrochemical and chemical {(NH 4 ) 2 [Ce IV (NO 3 ) 6 ]} oxidation of 1 in acetonitrile is made by comparison with the UV-vis-NIR absorption and resonance micro-Raman spectroelectrochemistry of poly-1, and by DFT calculations, which confirms that oxidative coupling occurs in acetonitrile also. However, in contrast to that observed in dichloromethane, in acetonitrile, the oligomers formed are degraded in terms of a loss of the Fe(III)-O-Fe(III) bridge by protonation. The oxidative redox behavior of 1 and 2 is, therefore, dominated by the formation and reactivity of Fe(III) bound phenoxyl radicals, which considerably holds implications in regard to the design of phenolato based complexes for oxidation catalysis.

  14. Mono- and Dinuclear Transition Metal Complexes of the Hexadentate Ligand Tris(4-tert-butyl-2-mercaptobenzyl)-1,4,7-triazacyclononane (L). (United States)

    Beissel, Thomas; Glaser, Thorsten; Kesting, Frank; Wieghardt, Karl; Nuber, Bernhard


    The hexadentate, pendant arm macrocycle 1,4,7-tris(4-tert-butyl-2-mercaptobenzyl)-1,4,7-triazacyclononane (H(3)L) has been synthesized and isolated as its trihydrochloride, H(3)L.3HCl, or sodium salt, Na(3)L, and its coordination chemistry with first-row transition metals has been studied. Mononuclear complexes of the type [LM(III)] (M = Ga (1), In (2), V (3), Cr (4), Mn (5), Fe,Co (6)) have been isolated as have the one-electron-oxidized forms [LM]PF(6) (M = V(IV) (3a), Mn(IV) (5a)). The crystal structure of 6 has been determined by single-crystal X-ray crystallography. Complex 6 crystallizes in the orthorhombic space group Iba2, with cell constants a = 14.206(8) Å, b = 22.53(1) Å, c = 26.07(1) Å, V = 8344.0(3) Å(3), and Z = 8. The cobalt(III) ion is in a distorted octahedral fac-N(3)S(3) donor set. The reaction of L with divalent metal chlorides in a 1:2 ratio in methanol affords the homodinuclear complexes [LM(II)(2)Cl] (M = Mn (7), Co (8), Ni (9), Zn (10), Cd (11)) where one metal is six- (N(3)MS(3)) and the other is four-coordinate (S(3)MCl); the two polyhedra are linked by three &mgr;(2)-thiolato bridges. Heterodinuclear complexes of the type [LM(1)M(2)Cl] have been obtained from [LM(2)Cl] species by abstraction of the four-coordinate metal ion and replacement by a different metal ion. The complexes [LZn(II)M(II)Cl] (M = Fe (12), Co (13), Ni (14)), [LNi(II)M(II)Cl] (M = Co (15), Zn (16)), and [LMn(II)M(II)Cl] (M = Fe (17), Co (18), Ni (19), Zn (20), Cd (21), Hg (22)) have been isolated as solid materials. The crystal structure of 14 has been determined by X-ray crystallography. Complex 14 crystallizes in the orthorhombic space group P2(1)2(1)2(1), with cell constants a = 15.45(1) Å, b = 17.77(1) Å, c = 17.58(1) Å, V = 4826.5(4) Å(3), and Z = 4. The linkage isomers 14 and 16 show characteristic electronic spectra for octahedrally and tetrahedrally coordinated Ni(II), respectively. The electronic structures of new complexes have been investigated by UV

  15. Synthesis and characterization of monomeric manganese(II and cobalt(III complexes of the hexadentate amine ligand N,N,N',N'-tetrakis(2-pyridylmethylethane-1,2-diamine, C26H28N6(tpen

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    Kirsten Michelsen


    Full Text Available The syntheses and characterization of complexes of manganese(II and cobalt(III with the potentially hexadentate ligand N,N,N',N'-tetrakis(2-pyridylmethylethane-1,2-diamine, C26H28N6 (tpen, are described. The monomeric manganese(II complex [Mn(C26H28N6(H2O](ClO42 (1 crystallizes in the monoclinic space group C2/c with 4 formula units in a cell of dimensions a = 15.080(1 Å, b = 10.101(1 Å, c = 19.426(2 Å and β = 94.6l(l°. The structure has been refined to a final value of the conventional R-factor of 0.0401 based on 2586 observed independent reflections. The geometry at the manganese center is seven-coordinate, and is best described as a capped trigonal pyramid with the water molecule forming the cap and the six nitrogen atoms of the tpen ligand occupying the pyramidal sites. The manganese atom and the water molecule lie on a crystallographic twofold axis. The related cobalt(III complex, [Co(C26H28N6] (C1O43 (4 crystallizes in the monoclinic space group P21/n with 4 formula units in a cell of dimensions a = 9.829(2 Å, b = 18.364(4 Å, c = 18.128(4 Å and β = 93.64(3°. The structure has been refined to a final value of the conventional R-factor of 0.0526 based on 3574 observed independent reflections. The complex is approximately octahedral, the coordination being provided by the six nitrogen atoms of the tpen ligand. The EPR spectrum of 1 diluted into the corresponding Cd(II host has been simulated with the parameters g = 2.00, A = 0.0080 cm-1, D = 0.116 cm-1, and E = 0.0013 cm-1. The small value of E/D is consistent with the observed symmetry of the complex.

  16. Synthesis, structural and biochemical activity studies of a new hexadentate Schiff base ligand and its Cu(II), Ni(II), and Co(II) complexes (United States)

    Ekmekcioglu, Pinar; Karabocek, Nevin; Karabocek, Serdar; Emirik, Mustafa


    A new Schiff base ligand (H2L) and its metal complexes have been prepared and characterized by elemental analysis, magnetic moment and spectral studies. The comparative in-vitro antimicrobial activities against various pathogens with reference to known antibiotics activity under the standard control of different concentrations revealed that the metal complexes (6-8) showed enhanced antimicrobial activities in general as compared to free ligand. As an exception, the free ligand showed better activity against Trichoderma. The antifungal activity experiments were performed in triplicate. The order of biochemical activity for metal complexes were observed as in the following. CuL > CoL > NiL, which is exactly same as the order of stability constants of these complexes. Additionally, we performed DFT and TD-DFT calculation for free ligand and Cu(II) complex to support the experimental data. The geometries of the Cu(II) complex have been optimized using the B3LYP level of theory. The theoretical calculations confirm that the copper (II) center exhibits a distorted square pyramidal geometry which is favored by experimental results.

  17. Design and study of Bi[1,8]naphthyridine ligands as potential photooxidation mediators in Ru(II) polypyridyl aquo complexes. (United States)

    Zong, Ruifa; Naud, Frederic; Segal, Carrie; Burke, John; Wu, Feiyue; Thummel, Randolph


    A series of 3,3'-polymethylene-bridged bi[1,8]naphthyridine (binap) ligands, 3a-c, are complexed with Ru(II) to afford [Ru(tpy)(3a-c)(H(2)O)](2+) where an uncomplexed nitrogen on 3a-c is situated so it can form a H-bond with the coordinated water. An additional complex involving [Ru(4'-NMe(2)tpy)(3b)(H(2)O)](2+) is also prepared. X-ray analyses of the [Ru(tpy)(3a,c)(H(2)O)](2+) complexes indicate well-organized H-bonds even when the binap is nonplanar. In an attempt to realize photooxidation, the effects of light, varying potential, and pH were examined. A Pourbaix diagram indicated that the oxidation potential decreased by approximately 0.5 V in the pH range of 1.9-11.6. The lowest-energy electronic absorption for the binap complexes involves the metal-to-ligand charge transfer to the binap ligand and is sensitive to ligand planarity. The absorbance shifted to a lower energy as the auxiliary ligand became a better donor (4'-NMe(2)tpy) or as the water was deprotonated. Acetonitrile was found to displace water most easily for the complex of 3c, where the ligand is the least planar. Despite promising features, photooxidation of the bound water was not observed.

  18. Synthesis, spectral characterization, structural investigation and antimicrobial studies of mononuclear Cu(II), Ni(II), Co(II), Zn(II) and Cd(II) complexes of a new potentially hexadentate N2O4 Schiff base ligand derived from salicylaldehyde (United States)

    Keypour, Hassan; Shayesteh, Maryam; Rezaeivala, Majid; Chalabian, Firoozeh; Elerman, Yalcin; Buyukgungor, Orhan


    A new potentially hexadentate N2O4 Schiff base ligand, H2L derived from condensation reaction of an aromatic diamine and salicylaldehyde, and its metal complexes were characterized by elemental analyses, IR, UV-Vis, EI-MS, 1H and 13C NMR spectra, as well as conductance measurements. It has been originated that the Schiff base ligand with Cu(II), Ni(II), Co(II), Cd(II) and Zn(II) ions form mononuclear complexes on 1:1 (metal:ligand) stoichiometry. The conductivity data confirm the non-electrolytic nature of the complexes. Also the crystal structures of the complexes [ZnL] and [CoL] have also been determined by using X-ray crystallographic technique. The Zn(II) and Co(II) complexes show a tetrahedral configuration. Electronic absorption spectra of the Cu(II) and Ni(II) complexes suggest a square-planar geometry around the central metal ion. The synthesized compounds have antibacterial activity against the three Gram-positive bacteria: Bacillus cereus, Enterococcus faecalis and Listeria monocytogenes and also against the three Gram-negative bacteria: Salmonella paraB, Citrobacter freundii and Enterobacter aerogenes. The results showed that in some cases the antibacterial activity of complexes were more than nalidixic acid and amoxicillin as standards.

  19. Synthesis, characterization, DNA interaction and antimicrobial screening of isatin-based polypyridyl mixed-ligand Cu(II and Zn(II complexes

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    Full Text Available Several mixed ligand Cu(II/Zn(II complexes using 3-(phenyl-imino-1,3-dihydro-2H-indol-2-one (obtained by the condensation of isatin and aniline as the primary ligand and 1,10-phenanthroline (phen/2,2’-bipyridine (bpy as an additional ligand were synthesized and characterized analytically and spectroscopically by elemental analyses, magnetic susceptibility and molar conductance measurements, as well as by UV–Vis, IR, NMR and FAB mass spectroscopy. The interaction of the complexes with calf thymus (CT DNA was studied using absorption spectra, cyclic voltammetric and viscosity measurements. They exhibit absorption hypochromicity, and the specific viscosity increased during the binding of the complexes to calf thymus DNA. The shifts in the oxidation–reduction potential and changes in peak current on addition of DNA were shown by CV measurements. The Cu(II/Zn(II complexes were found to promote cleavage of pUC19 DNA from the supercoiled form I to the open circular form II and linear form III. The complexes show enhanced antifungal and antibacterial activities compared with the free ligand.

  20. Expanding the family of heteroleptic oxidovanadium(IV) compounds with salicylaldehyde semicarbazones and polypyridyl ligands showing anti-Trypanosoma cruzi activity. (United States)

    Scalese, Gonzalo; Benítez, Julio; Rostán, Santiago; Correia, Isabel; Bradford, Lara; Vieites, Marisol; Minini, Lucía; Merlino, Alicia; Coitiño, E Laura; Birriel, Estefania; Varela, Javier; Cerecetto, Hugo; González, Mercedes; Pessoa, João Costa; Gambino, Dinorah


    Searching for prospective vanadium-based drugs for the treatment of Chagas disease, a new series of heteroleptic [V(IV)O(L-2H)(NN)] compounds was developed by including the lipophilic 3,4,7,8-tetramethyl-1,10-phenanthroline (tmp) NN ligand and seven tridentate salicylaldehyde semicarbazone derivatives (L1-L7). The compounds were characterized in the solid state and in solution. EPR spectroscopy suggests that the NN ligand is bidentate bound through both nitrogen donor atoms in an axial-equatorial mode. The EPR and (51)V-NMR spectra of aerated solutions at room temperature indicate that the compounds are stable to hydrolysis and that no significant oxidation of V(IV) to V(V) takes place at least in 24h. The complexes are more active in vitro against Trypanosoma cruzi, the parasite responsible for Chagas disease, than the reference drug Nifurtimox and most of them are more active than previously reported [V(IV)O(L-2H)(NN)] complexes of other NN co-ligands. Selectivity towards the parasite was analyzed using J-774 murine macrophages as mammalian cell model. Due to both, high activity and high selectivity, L2, L4, L5 and L7 complexes could be considered new hits for further drug development. Lipophilicity probably plays a relevant role in the bioactivity of the new compounds. The [V(IV)O(L-2H)(NN)] compounds were designed aiming DNA as potential molecular target. Therefore, the novel L1-L7 tmp complexes were screened by computational modeling, comparing their DNA-binding features with those of previously reported [V(IV)O(L-2H)(NN)] compounds with different NN co-ligands. Whereas all the complexes interact well with DNA, with binding modes and strength tuned in different extents by the NN and semicarbazone co-ligands, molecular docking suggests that the observed anti-T. cruzi activity cannot be explained upon DNA intercalation as the sole mechanism of action. Copyright © 2015 Elsevier Inc. All rights reserved.


    Directory of Open Access Journals (Sweden)

    Mihaela Cazacu


    Full Text Available Ethylenediaminetetraacetic acid (EDTA (E-385 as such and/or derivatized (salified occupies a separate chapter, of wide interest in food sciences, because of its coordinating (sequestering competences towards various organic and/or inorganic structures (especially metal cations with small geometric dimensions. This paper aims to diversify the structural range of these hexadentate ligands, by accessing a synthetic protocol different from the classic one, the cyanoethylation of primary amine functional groups of ethylenediamine (ED. In this paper are considered the main dependences of the yields of nucleophilic addition of the amino groups to the activated double bond in acrylonitrile (AN monomer, on the operating parameters (temperature, processing time, molar ratio of reactants, and finally the preliminary data on the coordinating (sequestering competence of ethylenediaminetetrapropionic acid (EDTP. The conclusions drawn support further research to extend the area of hexadentate sequestering structures.

  2. Non-bridging ligand effects on the kinetics of reduction of chloro- and azido-pentaamminecobalt(III by some polypyridyl complexes of ruthenium(II

    Directory of Open Access Journals (Sweden)

    Olayinka A. Oyetunji


    Full Text Available Pentaamminecobalt(III complexes, [Co(NH35X]2+ (X = Cl-, N3-, are reduced by [Ru(bipy3]2+ and [Ru(terpy(bipyCl] + in aqueous media at a constant ionic strength of 0.5 M (HCl/LiCl. At 308 K, the second order rate constants (M-1 s-1 are as follows: 17.9 for the reduction of the azidocobalt(III complex by [Ru(bipy3]2+, and 1.41 and 2.63 for the [Ru(terpy(bipyCl]+ reduction of the azido- and chlorocobalt(III complexes, respectively. Activation enthalpies (ΔH‡ and entropies (ΔS‡ were determined from temperature dependence measurements with the following results: ΔH‡= 72.1 kJ mol-1 and ΔS‡ = 13.3 J mol-1 K-1 for the [Ru(bipy3]2+ reduction of the azidocobalt(III complex, while for the reduction of the cobalt(III complexes by [Ru(terpy(bipyCl] +, ΔH‡ (N3- = 20.3 kJ mol-1, ΔH‡ (Cl- = 40.6 kJ mol-1, ΔS‡(N3- = -177 J mol-1 K-1, and ΔS‡ (Cl- = -106 J mol-1 K-1. The relative rates of electron transfer in the different reactions and the influence of π-acceptor ligands on the ruthenium(II reduction of the cobalt(III complexes are discussed.

  3. Palladium polypyridyl complexes: synthesis, characterization, DNA interaction and biological activity on Leishmania (L.) mexicana

    Energy Technology Data Exchange (ETDEWEB)

    Navarro, Maribel [Instituto Venezolano de Investigaciones Cientificas, Caracas (Venezuela). Centro de Quimica; Betancourt, Adelmo [Universidad de Carabobo, Valencia (Venezuela). Facultad Experimental de Ciencia y Tecnologia. Dept. de Quimica; Hernandez, Clara [Universidad de Carabobo Sede Aragua, Maracay (Venezuela). Facultad de Ciencias de la Salud. Dept. de Ciencias Basicas; Marchan, Edgar [Universidad de Oriente, Cumana (Venezuela). Inst. de Investigaciones en Biomedicina y Ciencias Aplicadas. Nucleo de Sucre


    This paper describes the search for new potential chemotherapeutic agents based on transition metal complexes with planar ligands. In this study, palladium polypyridyl complexes were synthesized and characterized by elemental analysis, NMR, UV-VIS and IR spectroscopies. The interaction of the complexes with DNA was also investigated by spectroscopic methods. All metal-to-ligand charge transfer (MLCT) bands of the palladium polypyridyl complexes exhibited hypochromism and red shift in the presence of DNA. The binding constant and viscosity data suggested that the complexes [PdCl{sub 2}(phen)] and [PdCl{sub 2}(phendiamine)] interact with DNA by electrostatic forces. Additionally, these complexes induced an important leishmanistatic effect on L. (L.) mexicana promastigotes at the final concentration of 10 {mu}mol L{sup -1} in 48 h. (author)

  4. Nitroimidazole derivatives of polypyridyl ruthenium complexes: Towards understanding their anticancer activity and mode of action. (United States)

    Mazuryk, Olga; Krysiak-Foria, Oksana; Żak, Agnieszka; Suzenet, Franck; Ptak-Belowska, Agata; Brzozowski, Tomasz; Stochel, Grażyna; Brindell, Małgorzata


    The mechanism of cell death induced by the ruthenium polypyridyl complexes comprising two 4,7-diphenyl-1,10-phenanthroline ligands as well as one unmodified 2,2'-bipyridyl or modified with 2-nitroimidazole moiety attached by shorter (C3H6) or longer (C6H12) linker was investigated. Cytotoxicity and proliferation assays revealed that the studied Ru polypyridyl complexes are more toxic against human pancreas carcinoma PANC-1 cell line than normal human keratinocytes HaCaT with IC50 of 3-5μM. The Ru complexes despite accumulation in mitochondria do not lead to mitochondrial disfunction, though decreasing of mitochondrial Ca(2+) causes mitochondria membrane hyperpolarization. The Ru polypyridyl conjugates induce some phenotypical characteristic of apoptosis, such as condensation of chromatin or phosphatidylserine translocation, however no caspase or calpain activation in the studied cell lines was observed, indicating that detected cell death does not occur via mitochondria- or ER-activated pathways. Caspase-independent cell death is caused by enormous ROS formation, mainly hydrogen peroxide and peroxyl radicals as well as by intracellular Ca(2+) homeostasis disruption. Accumulation of the Ru compounds inhibits the completion of DNA synthesis, arresting cells in S-phase of cell cycle. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Energy transfer pathways in dinuclear heteroleptic polypyridyl complexes : Through-space vs through-bond interaction mechanisms

    NARCIS (Netherlands)

    Weldon, Frances; Hammarström, Leif; Mukhtar, Emad; Hage, Ronald; Gunneweg, Eric; Haasnoot, Jaap G.; Reedijk, Jan; Browne, Wesley R.; Guckian, Adrian L.; Vos, Johannes G.


    A series of homo- and heteronuclear ruthenium and osmium polypyridyl complexes with the bridging ligands 1,3-bis(5-(2-pyridyl)-1H-1,2,4-triazol-3-yl)benzene (H(2)mL) and 1,4-bis(5-(2-pyridyl)-1H-1,2,4-triazol-3-yl)benzene (H(2)pL) are reported. The photophysical properties of these compounds are

  6. Ruthenium(II) and osmium(II) polypyridyl complexes of an asymmetric pyrazinyl- and pyridinyl-containing 1,2,4-triazole based ligand. Connectivity and physical properties of mononuclear complexes

    NARCIS (Netherlands)

    Browne, Wesley R.; O’Connor, Christine M.; Hughes, Helen P.; Hage, Ronald; Walter, Olaf; Doering, Manfred; Gallagher, John F.; Vos, Johannes G.


    The synthesis, purification and characterisation of two coordination isomers of ruthenium(II) and osmium (II) complexes containing the ligand 3-(pyrazin-2'-yl)-5-(pyridin-2"-yl)-1,2,4-triazole (Hppt) are described. The X-ray and molecular structure of the complex [Ru(bipy)(2) (ppt)] PF6.CH3OH (1a)

  7. Copper(II) complexes of a hexadentate mixed-donor N3S3 macrobicyclic cage: facile rearrangements and interconversions. (United States)

    Bell, Craig A; Bernhardt, Paul V; Gahan, Lawrence R; Martínez, Manuel; Monteiro, Michael J; Rodríguez, Carlos; Sharrad, Clint A


    The potentially hexadentate mixed-donor cage ligand 1-methyl-8-amino-3,13,16-trithia-6,10,19-triazabicyclo[6.6.6]eicosane (AMME-N(3)S(3)sar; sar=sarcophagine) displays variable coordination modes in a complex with copper(II). In the absence of coordinating anions, the ligand adopts a conventional hexadentate N(3)S(3) binding mode in the complex [Cu(AMME-N(3)S(3)sar)](ClO(4))(2) that is typical of cage ligands. This structure was determined by X-ray crystallography and solution spectroscopy (EPR and NIR UV/Vis). However, in the presence of bromide ions in DMSO, clean conversion to a five-coordinate bromido complex [Cu(AMME-N(3)S(3)sar)Br](+) is observed that features a novel tetradentate (N(2)S(2))-coordinated form of the cage ligand. This copper(II) complex has also been characterized by X-ray crystallography and solution spectroscopy. The mechanism of the reversible interconversion between the six- and five-coordinated copper(II) complexes has been studied and the reaction has been resolved into two steps; the rate of the first is linearly dependent on bromide ion concentration and the second is bromide independent. Electrochemistry of both [Cu(AMME-N(3)S(3)sar)](2+) and [Cu(AMME-N(3)S(3)sar)Br](+) in DMSO shows that upon reduction to the monovalent state, they share a common five-coordinated form in which the ligand is bound to copper in a tetradentate form exclusively, regardless of whether a six- or five-coordinated copper(II) complex is the precursor.

  8. Ruthenium, osmium and rhodium complexes of polypyridyl ligands ...

    Indian Academy of Sciences (India)


    complexes have been investigated, Rh(III) complexes are excellent catalysts for electrocatalytic reduction ... hydrolysed when it was treated with [Rh(tpy)Cl3] in ethanol–water and resulted in the formation of Rh(III) and .... between the metal centres and the extent of splitting reflects the degree of metal–metal interaction. The.

  9. Polypyridyl iron(II) complexes showing remarkable photocytotoxicity ...

    Indian Academy of Sciences (India)


    Polypyridyl iron(II) complexes showing remarkable photocytotoxicity in visible light. ADITYA GARAI a. , UTTARA BASU a. , ILA PANT b. , PATURU KONDAIAH*. ,b. AND. AKHIL R. CHAKRAVARTY*. ,a a. Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore. 560012, India. E-mail: ...

  10. A study of some transition metal complexes with hexadentate ...

    African Journals Online (AJOL)

    chromophoric type ligands. Mohamed A. Khalifa. Abstract. Bull. Chem. Soc. Ethiop., 3(1) 9-15 (1989). Full Text: EMAIL FREE FULL TEXT EMAIL FREE FULL TEXT · DOWNLOAD FULL TEXT DOWNLOAD FULL TEXT · AJOL African Journals Online.

  11. Synthetic, Crystallographic, and Computational Study of Copper(II) Complexes of Ethylenediaminetetracarboxylate Ligands

    NARCIS (Netherlands)

    Matovic, Zoran D.; Miletic, Vesna D.; Cendic, Marina; Meetsma, Auke; van Koningsbruggen, Petra J.; Deeth, Robert J.; Matović, Zoran D.; Miletić, Vesna D.; Ćendić, Marina


    Copper(II) complexes of hexadentate ethylenediaminetetracarboxylic acid type ligands H(4)eda3p and Rieddadp (H(4)eda3p = ethylenediamine-N-acetic-N,N',N'-tri-3-propionic acid; ateddadp = ethylenediamine-N,N'-diaceticN,N'-di-3-propionic acid) have been prepared. An octahedral trans(O-6) geometry (two

  12. Metal-polypyridyl catalysts for electro- and photochemical reduction of water to hydrogen. (United States)

    Zee, David Z; Chantarojsiri, Teera; Long, Jeffrey R; Chang, Christopher J


    Climate change, rising global energy demand, and energy security concerns motivate research into alternative, sustainable energy sources. In principle, solar energy can meet the world's energy needs, but the intermittent nature of solar illumination means that it is temporally and spatially separated from its consumption. Developing systems that promote solar-to-fuel conversion, such as via reduction of protons to hydrogen, could bridge this production-consumption gap, but this effort requires invention of catalysts that are cheap, robust, and efficient and that use earth-abundant elements. In this context, catalysts that utilize water as both an earth-abundant, environmentally benign substrate and a solvent for proton reduction are highly desirable. This Account summarizes our studies of molecular metal-polypyridyl catalysts for electrochemical and photochemical reduction of protons to hydrogen. Inspired by concept transfer from biological and materials catalysts, these scaffolds are remarkably resistant to decomposition in water, with fast and selective electrocatalytic and photocatalytic conversions that are sustainable for several days. Their modular nature offers a broad range of opportunities for tuning reactivity by molecular design, including altering ancillary ligand electronics, denticity, and/or incorporating redox-active elements. Our first-generation complex, [(PY4)Co(CH3CN)2](2+), catalyzes the reduction of protons from a strong organic acid to hydrogen in 50% water. Subsequent investigations with the pentapyridyl ligand PY5Me2 furnished molybdenum and cobalt complexes capable of catalyzing the reduction of water in fully aqueous electrolyte with 100% Faradaic efficiency. Of particular note, the complex [(PY5Me2)MoO](2+) possesses extremely high activity and durability in neutral water, with turnover frequencies at least 8500 mol of H2 per mole of catalyst per hour and turnover numbers over 600 000 mol of H2 per mole of catalyst over 3 days at an

  13. Photophysics of ruthenium polypyridyl complexes formed with lacunary polyoxotungstates with iron addenda. (United States)

    Seery, Michael K; Fay, Nigel; McCormac, Timothy; Dempsey, Eithne; Forster, Robert J; Keyes, Tia E


    The interactions between luminophore [Ru(bpy)3]2+, and the lacunary Dawson heteropolyanions, [P2W17O61(FeOH2)]7-, [P2W17O61(FeBr)]6- and [P2W17O61]10- were investigated using a combination of photophysics, optical and Raman spectroscopy. Extensive quenching of the excited state of [Ru(bpy)3]2+ was observed in each case. Quenching is attributed to the formation of association complexes between [Ru(bpy)(3)]2+ and the heteropolyanions in which the charge on the heteropolyanions is fully compensated for by the ruthenium polypyridyl species. The interaction appears to be principally electrostatic in nature producing [Ru(bpy)3]3.5[P2W17O61(FeOH2)], [Ru(bpy)3]3[P2W17O61(FeBr)] and [Ru(bpy)3]5[P2W17O61]10-. The association constants for formation of the clusters were obtained from photophysical studies and surprisingly, despite the electrostatic nature of the interaction, there was no correlation between the charge on the polyoxometallate and the association constant. In particular, the unsubstituted lacunary, [P2W17O61]10-, showed considerably weaker association compared to the transition metal substituted lacunaries, in spite of its 10- charge. Difference absorption spectroscopy revealed a new transition at ca. 480 nm for each of the cluster complexes. From resonance Raman spectroscopy the origin of this transition was found to involve the polyoxometallate. Unlike previously reported adducts, the cluster complexes formed were not luminescent. In all cases the cluster complexes exhibit remarkable photostability, with no photodecomposition or photo-induced ligand exchange reactions evident in acetonitrile, under conditions where [Ru(bpy)3]2+ alone exhibits considerable photolability.

  14. Design and development of polynuclear ruthenium and platinum polypyridyl complexes in search of new anticancer agents

    NARCIS (Netherlands)

    Schilden, Karlijn van der


    The research described in this Ph.D. Thesis has been devoted to the design and development of polynuclear polypyridyl ruthenium and ruthenium-platinum complexes in search of new anticancer agents. A variety of polynuclear ruthenium and ruthenium-platinum complexes has been synthesized with a long

  15. Binding of copper(II) polypyridyl complexes to DNA and consequences for DNA-based asymmetric catalysis. (United States)

    Draksharapu, Apparao; Boersma, Arnold J; Leising, Miriam; Meetsma, Auke; Browne, Wesley R; Roelfes, Gerard


    The interaction between salmon testes DNA (st-DNA) and a series of Cu(II) polypyridyl complexes, i.e. [Cu(dmbpy)(NO3)2] (1) (dmbpy = 4,4'-dimethyl-2,2'-bipyridine), [Cu(bpy)(NO3)2] (2) (bpy = 2,2'-bipyridine), [Cu(phen)(NO3)2] (3) (phen = phenanthroline), [Cu(terpy)(NO3)2]·H2O (4) (terpy = 2,2':6',2″-terpyridine), [Cu(dpq)(NO3)2] (5) (dpq = dipyrido-[3,2-d:2',3'-f]-quinoxaline) and [Cu(dppz)(NO3)2] (6) (dppz = dipyrido[3,2-a:2',3'-c]phenazine) was studied by UV/Vis absorption, Circular Dichroism, Linear Dichroism, EPR, Raman and (UV and vis) resonance Raman spectroscopies and viscometry. These complexes catalyse enantioselective C-C bond forming reactions in water with DNA as the source of chirality. Complex 1 crystallizes as an inorganic polymer with nitrate ligands bridging the copper ions, which adopt essentially a distorted square pyramidal structure with a fifth bridging nitrate ligand at the axial position. Raman spectroscopy indicates that in solution the nitrate ligands in 1, 2, 3 and 4 are displaced by solvent (H2O). For complex 1, multiple supramolecular species are observed in the presence of st-DNA in contrast to the other complexes, which appear to interact relatively uniformly as a single species predominantly, when st-DNA is present. Overall the data suggest that complexes 1 and 2 engage primarily through groove binding with st-DNA while 5 and 6 undergo intercalation. For complexes 3 and 4 the data indicates that both groove binding and intercalation takes place, albeit primarily intercalation. Although it is tempting to conclude that the groove binders give highest ee and rate acceleration, it is proposed that the flexibility and dynamics in binding of Cu(II) complexes to DNA are key parameters that determine the outcome of the reaction. These findings provide insight into the complex supramolecular structure of these DNA-based catalysts.

  16. Dinuclear Silver(I) and Copper(II) Complexes of Hexadentate Macrocyclic Ligands Containing p-Xylyl Spacers

    DEFF Research Database (Denmark)

    McKenzie, Christine J.; Nielsen, Lars Preuss; Søtofte, Inger


    The cyclocondensation of terephthalic aldehyde with N,N-bis(3-aminopropyl)-methylamine in the presence of silver(I) gives the dinuclear tetramine Schiff base macrocyclic complex, [Ag2L1](NO3)2 (L1=7,22-N,N'-dimethyl-3,7,11,18, 22,26-hexaazatricyclo[]-tetratricosa-2,11,13,15,1 7...

  17. Synthetic routes to ruthenium (ii) species containing carboxylate-functionalized 2,2`-bipyridine ligands

    Energy Technology Data Exchange (ETDEWEB)

    Bradley, T.; Patterson, A.; Keene, F.R. [James Cook University, Townsville, QLD (Australia). School of Biomedical and Molecular Sciences


    Two methods are reported for the incorporation of carboxylate substituents on polypyridyl ligands coordinated to ruthenium(ll) centres. In the first, a precursor complex is synthesized with ethoxycarbonyl groups which are subsequently base-hydrolysed to produce the carboxylate in high yield (-CO{sub 2}Et{yields} -CO{sub 2}H). In the second method, ruthenyl species were used to chemically catalyse the electochemical oxidation of methyl substituents on the ligands of a precursor complex to produce the target carboxylate species (-CH{sub 3} {yields} -CO{sub 2}H). Copyright (1998) CSIRO Australia 21 refs., 1 tab., 1 fig.

  18. Binding of copper(II) polypyridyl complexes to DNA and consequences for DNA-based asymmetric catalysis

    NARCIS (Netherlands)

    Draksharapu, Apparao; Boersma, Arnold J; Leising, Miriam; Meetsma, Auke; Browne, Wesley R; Roelfes, Gerard


    The interaction between salmon testes DNA (st-DNA) and a series of Cu-II polypyridyl complexes, i.e. [Cu(dmbpy)(NO3)(2)] (1) (dmbpy = 4,4'-dimethyl-2,2'-bipyridine), [Cu(bpy)(NO3)(2)] (2) (bpy = 2,2'-bipyridine), [Cu(phen)(NO3)(2)] (3) (phen = phenanthroline), [Cu(terpy)(NO3)(2)]center dot H2O (4)


    Energy Technology Data Exchange (ETDEWEB)

    Abergel, Rebecca J.; Raymond, Kenneth N.


    The limitations of current therapies for the treatment of iron overload or radioisotope contamination have stimulated efforts to develop new orally bioavailable iron and actinide chelators. Siderophore-inspired tetradentate, hexadentate and octadentate terephthalamidate and hydroxypyridonate ligands were evaluated in vivo as selective and efficacious iron or actinide chelating agents, with several metal loading and ligand assessment procedures, using {sup 59}Fe, {sup 238}Pu, and {sup 241}Am as radioactive tracers. The compounds presented in this study were compared to commercially available therapeutic sequestering agents [deferoxamine (DFO) for iron and diethylenetriaminepentaacetic acid (DPTA) for actinides] and are unrivaled in terms of affinity, selectivity and decorporation efficacy, which attests to the fact that high metal affinity may overcome the low bioavailability properties commonly associated to multidenticity.

  20. Heteroleptic oxidovanadium(IV) complexes of 2-hydroxynaphtylaldimine and polypyridyl ligands against Trypanosoma cruzi and prostate cancer cells. (United States)

    Scalese, Gonzalo; Mosquillo, M Florencia; Rostán, Santiago; Castiglioni, Jorge; Alho, Irina; Pérez, Leticia; Correia, Isabel; Marques, Fernanda; Costa Pessoa, João; Gambino, Dinorah


    In Latin America Chagas disease is an endemic illness caused by the parasite Trypanosoma cruzi (T. cruzi), killing more people than any other parasitic disease. Current chemotherapies are old and inadequate, thus the development of efficient ones is urgently needed. Vanadium-based complexes have been shown to be a promising approach both against parasitic diseases and cancer and this study aims to achieve significant advances in the pursue of effective compounds. Heteroleptic vanadium complexes of Schiff bases and polypyridine compounds were prepared and their stability in solution evaluated by EPR (Electronic Paramagnetic Resonance) and NMR spectroscopy. Their in vitro activities were evaluated against T. cruzi and a set of cells lines representative of human cancer conditions, namely ovarian, breast and prostate cancer. In T. cruzi, most of the complexes depicted IC 50 values in the low μM range, induced changes of mitochondrial membrane potential and apoptosis. In cancer cells, complexes showed good to moderate activity and in metastatic cells (prostate PC3), some complexes inhibited the migratory ability, this suggesting that they display antimetastatic potential. Interestingly, complex 5 seemed to have a dual effect being the most cytotoxic complex on all cancer cells and also the most active anti-T-cruzi compound of the series. Globally the complexes showed promising anticancer and anti T. cruzi activities and also displayed some characteristics indicating they are worth to be further explored as antimetastatic drugs. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. The btp [2,6-bis(1,2,3-triazol-4-yl)pyridine] binding motif: a new versatile terdentate ligand for supramolecular and coordination chemistry. (United States)

    Byrne, Joseph P; Kitchen, Jonathan A; Gunnlaugsson, Thorfinnur


    Ligands containing the btp [2,6-bis(1,2,3-triazol-4-yl)pyridine] motif have appeared with increasing regularity over the last decade. This class of ligands, formed in a one pot ‘click’ reaction, has been studied for various purposes, such as for generating d and f metal coordination complexes and supramolecular self-assemblies, and in the formation of dendritic and polymeric networks, etc. This review article introduces btp as a novel and highly versatile terdentate building block with huge potential in inorganic supramolecular chemistry. We will focus on the coordination chemistry of btp ligands with a wide range of metals, and how it compares with other classical pyridyl and polypyridyl based ligands, and then present a selection of applications including use in catalysis, enzyme inhibition, photochemistry, molecular logic and materials, e.g. polymers, dendrimers and gels. The photovoltaic potential of triazolium derivatives of btp and its interactions with anions will also be discussed.

  2. Comparison of the octadentate bifunctional chelator DFO*-pPhe-NCS and the clinically used hexadentate bifunctional chelator DFO-pPhe-NCS for {sup 89}Zr-immuno-PET

    Energy Technology Data Exchange (ETDEWEB)

    Vugts, Danielle J.; Klaver, Chris; Sewing, Claudia; Poot, Alex J.; Adamzek, Kevin; Visser, Gerard W.M.; Dongen, Guus A.M.S. van [VU University Medical Center, Department of Radiology and Nuclear Medicine, Amsterdam (Netherlands); Huegli, Seraina; Mari, Cristina; Gasser, Gilles [University of Zurich, Department of Chemistry, Zurich (Switzerland); Valverde, Ibai E. [University of Basel Hospital, Division of Radiopharmaceutical Chemistry, Basel (Switzerland); Mindt, Thomas L. [Institute of Pharmaceutical Sciences, ETH Zurich, Zurich (Switzerland); General Hospital of Vienna, Ludwig Boltzmann Institute for Applied Diagnostics, Vienna (Austria)


    All clinical {sup 89}Zr-immuno-PET studies are currently performed with the chelator desferrioxamine (DFO). This chelator provides hexadentate coordination to zirconium, leaving two coordination sites available for coordination with, e.g., water molecules, which are relatively labile ligands. The unsaturated coordination of DFO to zirconium has been suggested to result in impaired stability of the complex in vivo and consequently in unwanted bone uptake of {sup 89}Zr. Aiming at clinical improvements, we report here on a bifunctional isothiocyanate variant of the octadentate chelator DFO* and the in vitro and in vivo comparison of its {sup 89}Zr-DFO*-mAb complex with {sup 89}Zr-DFO-mAb. The bifunctional chelator DFO*-pPhe-NCS was prepared from previously reported DFO* and p-phenylenediisothiocyanate. Subsequently, trastuzumab was conjugated with either DFO*-pPhe-NCS or commercial DFO-pPhe-NCS and radiolabeled with Zr-89 according to published procedures. In vitro stability experiments were carried out in saline, a histidine/sucrose buffer, and blood serum. The in vivo performance of the chelators was compared in N87 tumor-bearing mice by biodistribution studies and PET imaging. In 0.9 % NaCl {sup 89}Zr-DFO*-trastuzumab was more stable than {sup 89}Zr-DFO-trastuzumab; after 72 h incubation at 2-8 C 95 % and 58 % intact tracer were left, respectively, while in a histidine-sucrose buffer no difference was observed, both products were ≥ 92 % intact. In vivo uptake at 144 h post injection (p.i.) in tumors, blood, and most normal organs was similar for both conjugates, except for skin, liver, spleen, ileum, and bone. Tumor uptake was 32.59 ± 11.95 and 29.06 ± 8.66 % ID/g for {sup 89}Zr-DFO*-trastuzumab and {sup 89}Zr-DFO-trastuzumab, respectively. The bone uptake was significantly lower for {sup 89}Zr-DFO*-trastuzumab compared to {sup 89}Zr-DFO-trastuzumab. At 144 h p.i. for {sup 89}Zr-DFO*-trastuzumab and {sup 89}Zr-DFO-trastuzumab, the uptake in sternum was 0.92

  3. Effect of substituent of terpyridines on the DNA-interaction of polypyridyl ruthenium(II) complexes (United States)

    Patel, Mohan N.; Gandhi, Deepen S.; Parmar, Pradhuman A.


    An octahedral complexes of ruthenium with 2,9-dimethyl-1,10-phenanthroline (dmphen) and substituted terpyridine have been synthesized. The Ru II complexes have been characterized by elemental analyses, thermogravimetric analyses, magnetic moment measurements, FT-IR, electronic, 1H NMR and FAB mass spectra. The binding strength and mode of interaction of the complexes with Herring Sperm DNA has been investigated using absorption titration and viscosity measurement studies. Results suggest that the substituent on terpyridine ligand affects the binding mode and binding ability of the complexes. Effect of time and ionic strength on DNA cleavage ability of complex has also been studied by gel electrophoresis. Results suggest that more than 200 mM concentration of NaCl decreases the cleavage ability of complex.

  4. Synthesis, characterization, DNA-binding and cleavage studies of polypyridyl copper(II) complexes (United States)

    Gubendran, Ammavasi; Rajesh, Jegathalaprathaban; Anitha, Kandasamy; Athappan, Periyakaruppan


    Six new mixed-ligand copper(II) complexes were synthesized namely [Cu(phen)2OAc]ClO4ṡH2O(1), [Cu(bpy)2OAc]ClO4ṡH2O(2), [Cu(o-ampacac)(phen)]ClO4(3), [Cu(o-ampbzac)(phen)]ClO4(4), [Cu(o-ampacac)(bpy)]ClO4(5), and [Cu(o-ampbzac)(bpy)]ClO4(6) (phen = 1,10-phenanthroline, bpy = 2, 2‧-bipyridine, o-ampacac = (Z)-4-(2-hydroxylamino)pent-3-ene-2-one,o-ampbzac = (Z)-4-(2-hydroxylamino)-4-phenylbut-3-ene-2-one)and characterized by UV-Vis, IR, EPR and cyclic voltammetry. Ligands were characterized by NMR spectra. Single crystal X-ray studies of the complex 1 shows Cu(II) ions are located in a highly distorted octahedral environment. Absorption spectral studies reveal that the complexes 1-6 exhibit hypochromicity during the interaction with DNA and binding constant values derived from spectral and electrochemical studies indicate that complexes 1, 2 and 3 bind strongly with DNA possibly by an intercalative mode. Electrochemical studies reveal that the complexes 1-4 prefer to bind with DNA in Cu(I) rather than Cu(II) form. The shift in the formal potentials E1/2 and CD spectral studies suggest groove or electrostatic binding mode for the complexes 4-6. Complex 1 can cleave supercoiled (SC) pUC18 DNA efficiently into nicked form II under photolytic conditions and into an open circular form (form II) and linear form (form III) in the presence of H2O2 at pH 8.0 and 37 °C, while the complex 2 does not cleave DNA under similar conditions.

  5. Rational Ligand Design for U(VI) and Pu(IV)

    Energy Technology Data Exchange (ETDEWEB)

    Szigethy, Geza [Univ. of California, Berkeley, CA (United States)


    Nuclear power is an attractive alternative to hydrocarbon-based energy production at a time when moving away from carbon-producing processes is widely accepted as a significant developmental need. Hence, the radioactive actinide power sources for this industry are necessarily becoming more widespread, which is accompanied by the increased risk of exposure to both biological and environmental systems. This, in turn, requires the development of technology designed to remove such radioactive threats efficiently and selectively from contaminated material, whether that be contained nuclear waste streams or the human body. Raymond and coworkers (University of California, Berkeley) have for decades investigated the interaction of biologically-inspired, hard Lewis-base ligands with high-valent, early-actinide cations. It has been established that such ligands bind strongly to the hard Lewis-acidic early actinides, and many poly-bidentate ligands have been developed and shown to be effective chelators of actinide contaminants in vivo. Work reported herein explores the effect of ligand geometry on the linear U(IV) dioxo dication (uranyl, UO2 2+). The goal is to utilize rational ligand design to develop ligands that exhibit shape selectivity towards linear dioxo cations and provides thermodynamically favorable binding interactions. The uranyl complexes with a series of tetradentate 3-hydroxy-pyridin-2-one (3,2-HOPO) ligands were studied in both the crystalline state as well as in solution. Despite significant geometric differences, the uranyl affinities of these ligands vary only slightly but are better than DTPA, the only FDA-approved chelation therapy for actinide contamination. The terepthalamide (TAM) moiety was combined into tris-beidentate ligands with 1,2- and 3,2-HOPO moieties were combined into hexadentate ligands whose structural preferences and solution thermodynamics were measured with the uranyl cation. In addition to achieving coordinative

  6. Synthesis, characterization, electrochemical studies and X-ray structures of mixed-ligand polypyridyl copper(II complexes with the acetate

    Directory of Open Access Journals (Sweden)

    Adekunle Oluwafunmilayo F.


    Full Text Available [Cu(phen2(CH3COO](ClO4.2H2O (1 and [Cu(bipy2(CH3COO]-(ClO4.H2O (2 {phen = 1,10-phenanthroline, bipy = 2,2’-bipyridine}were synthesized and characterized. The complexes were characterized by employying elemental analyses, infrared and UV-Visible spectroscopy, room temperature magnetic measurements and the crystal structures elucidated using X-ray diffraction experiment. The redox properties of the complexes were also investigated. Both structures have a square pyramidal CuN4O chromophore which exhibit significant distortions due to long Cu-O [2.217(3 Å for (1 and 2.179 (1 for (2] and Cu-N [2.631(2 Å for (1 and 2.714(1 Å for (2] bonds. This distortion if further shown by the O-Cu-N bond angles [147.71(8 o for (1 and 153.40(5 o for (2]. The elemental analyses further support the structural details unveiled by the single crystal X-ray diffraction analysis. The infrared spectra shows the acetate vibrational frequencies at 1587 cm-1,1428 cm-1, 1314 cm-1 for (1 and 1571 cm-1, 1441 cm-1, 1319c m-1 for (2 and the perchlo-rate bands at 1059 cm-1, 720 cm-1 (1 and 1080 cm-1,768 cm-1 (2. The broad d-d bands for the copper ion at 14,514 cm-1(1 and 14,535 cm-1(2 support the adoption of square pyramid geometries. The magnetic moments for the two complexes are 1.83 B.M for (1 and 1.72 B.M for (2. The peak to peak values of the two complexes show that the electrode reactions are quasi-reversibile with ΔEp = 0.023V (1 and 0.025V for (2. In both structures, there are π-π intermolecular interactions in addition to hydrogen bonding between the units.

  7. Synthesis, Photophysical and Electrochemical Properties of a Mixed Bipyridyl-Phenanthrolyl Ligand Ru(II Heteroleptic Complex Having trans-2-Methyl-2-butenoic Acid Functionalities

    Directory of Open Access Journals (Sweden)

    Adewale O. Adeloye


    Full Text Available In this work, two ligands: 4-(trans-2-Methyl-2-butenoic acid-2,2'-bipyridine (L1 and 5-(trans-2-methyl-2-butenoic acid-1,10-phenanthroline (L2, with the corresponding mixed-ligand heteroleptic Ru(II complex were synthesized and characterized by FT-IR, 1H-, 13C-NMR spectroscopy and elemental analysis. The influence of the mixed functionalized polypyridyl ruthenium(II complex on the photophysical and electrochemical properties were investigated and compared to individual single-ligand homoleptic complexes. Interestingly, the mixed-ligand complex formulated as [RuL1L2(NCS2] exhibits broad and intense metal-to-ligand charge transfer (MLCT absorption with a high molar extinction coefficient (λmax = 514 nm, ε = 69,700 M−1 cm−1, better than those of individual single-ligand complexes, [Ru(L12(NCS2] and [Ru(L22(NCS2], and a strong photoluminescence intensity ratio in the red region at λem = 686 nm. The electrochemical properties of the complex indicated that the redox processes are ligand-based.

  8. Synthesis, photophysical and electrochemical properties of a mixed bipyridyl-phenanthrolyl ligand Ru(II) heteroleptic complex having trans-2-methyl-2-butenoic acid functionalities. (United States)

    Adeloye, Adewale O


    In this work, two ligands: 4-(trans-2-Methyl-2-butenoic acid)-2,2'-bipyridine) (L(1)) and 5-(trans-2-methyl-2-butenoic acid)-1,10-phenanthroline (L(2)), with the corresponding mixed-ligand heteroleptic Ru(II) complex were synthesized and characterized by FT-IR, 1H-, 13C-NMR spectroscopy and elemental analysis. The influence of the mixed functionalized polypyridyl ruthenium(II) complex on the photophysical and electrochemical properties were investigated and compared to individual single-ligand homoleptic complexes. Interestingly, the mixed-ligand complex formulated as [RuL(1)L(2)(NCS)(2)] exhibits broad and intense metal-to-ligand charge transfer (MLCT) absorption with a high molar extinction coefficient (λ(max) = 514 nm, ε = 69,700 M(-1) cm(-1)), better than those of individual single-ligand complexes, [Ru(L(1))(2)(NCS)(2)] and [Ru(L(2))(2)(NCS)(2)], and a strong photoluminescence intensity ratio in the red region at λ(em) = 686 nm. The electrochemical properties of the complex indicated that the redox processes are ligand-based.

  9. Computational insights on the geometrical arrangements of Cu(II) with a mixed-donor N3S3 macrobicyclic ligand. (United States)

    Algarra, Andrés G; Aullón, Gabriel; Bernhardt, Paul V; Martínez, Manuel


    The macrobicyclic mixed-donor N3S3 cage ligand AMME-N3S3sar (1-methyl-8-amino-3,13,16-trithia-6,10,19-triazabicyclo[6.6.6]eicosane) can form complexes with Cu(II) in which it acts as hexadentate (N3S3) or tetradentate (N2S2) donor. These two complexes are in equilibrium that is strongly influenced by the presence of halide ions (Br(-) and Cl(-)) and the nature of the solvent (DMSO, MeCN, and H2O). In the absence of halides the hexadentate coordination mode of the ligand is preferred and the encapsulated complex ("Cu-in(2+)") is formed. Addition of halide ions in organic solvents (DMSO or MeCN) leads to the tetradentate complex ("Cu-out(+)") in a polyphasic kinetic process, but no Cu-out(+) complex is formed when the reaction is performed in water. Here we applied density functional theory calculations to study the mechanism of this interconversion as well as to understand the changes in the reactivity associated with the presence of water. Calculations were performed at the B3LYP/(SDD,6-31G**) level, in combination with continuum (MeCN) or discrete-continuum (H2O) solvent models. Our results show that formation of Cu-out(+) in organic media is exergonic and involves sequential halide-catalyzed inversion of the configuration of a N-donor of the macrocycle, rapid halide coordination, and inversion of the configuration of a S-donor. In aqueous solution the solvent is found to have an effect on both the thermodynamics and the kinetics of the reaction. Thermodynamically, the process becomes endergonic mainly due to the preferential solvation of halide ions by water, while the kinetics is influenced by formation of a network of H-bonded water molecules that surrounds the complex.

  10. (II) polypyridyls containing multifunctionalized

    Indian Academy of Sciences (India)


    Department of Chemistry, Faculty of Science, Banaras Hindu University,. Varanasi 221 005, India ... with hydrazine to form its N2 complex which is of great interest in the chemistry of N2 fixation. Triazoles are ..... Cotton F A and Wilkinson G 1988 Advanced inorganic chemistry (New York: John Wiley) p. 887. 8. Douglas B ...

  11. Assessment of intercomponent interaction in phenylene bridged dinuclear ruthenium(II) and osmium(II) polypyridyl complexes

    NARCIS (Netherlands)

    Guckian, Adrian L.; Doering, Manfred; Ciesielski, Michael; Walter, Olaf; Hjelm, Johan; O’Boyle, Noel M.; Henry, William; Browne, Wesley R.; McGarvey, John J.; Vos, Johannes G.


    The synthesis and characterisation of [Ru(bipy)(2)(L1)](2+) and the homodinuclear complexes [M(bipy)(2)(L1)M(bipy)(2)](4+) (where M=Ru or Os), employing the ditopic ligand, 1,4-phenylene-bis(1-pyridin-2-ylimidazo [1,5-a] pyridine) (L1), are reported. The complexes are identified by elemental

  12. H2CHXdedpa and H4CHXoctapa-chiral acyclic chelating ligands for (67/68)Ga and (111)In radiopharmaceuticals. (United States)

    Ramogida, Caterina F; Cawthray, Jacqueline F; Boros, Eszter; Ferreira, Cara L; Patrick, Brian O; Adam, Michael J; Orvig, Chris


    The chiral acyclic ligands H2CHXdedpa (N4O2), H2CHXdedpa-bb (N4O2), and H4CHXoctapa (N4O4) (CHX = cyclohexyl/cyclohexane, H2dedpa = 1,2-[[6-carboxy-pyridin-2-yl]-methylamino]ethane, bb = N,N'-dibenzylated, H4octapa = N,N'-bis(6-carboxy-2-pyridylmethyl)-ethylenediamine-N,N'-diacetic acid) were synthesized, complexed with Ga(III) and/or In(III), and evaluated for their potential as chelating agents in radiopharmaceutical applications. The ligands were compared to the previously studied hexadentate H2dedpa and octadentate H4octapa ligands to determine the effect adding a chiral 1R,2R-trans-cyclohexane to replace the ethylenediamine backbone would have on metal complex stability and radiolabeling kinetics. It was found that [Ga(CHXdedpa)](+) showed very similar properties to those of [Ga(dedpa)](+), with only one isomer in solution observed by NMR spectroscopy, and minimal structural changes in the solid-state X-ray structure. Like [Ga(dedpa)](+), [Ga(CHXdedpa)](+) exhibited exceptionally high thermodynamic stability constants (log KML = 28.11(8)), and the chelate retained the ability to label (67)Ga quantitatively in 10 min at room temperature at ligand concentrations of 1 × 10(-5) M. In vitro kinetic inertness assays demonstrated the [(67)Ga(CHXdedpa)](+) complex to be more stable than [(67)Ga(dedpa)](+) in a human serum competition, with 90.5% and 77.8% of (67)Ga remaining chelate-bound after 2 h, respectively. Preliminary coordination studies of H4CHXoctapa with In(III) demonstrated [In(CHXoctapa)](-) to have an equivalently high thermodynamically stable constant as [In(octapa)](-), with log KML values of 27.16(9) and 26.76(14), respectively. The [(111)In(CHXoctapa)](-) complex showed exceptionally high in vitro kinetic inertness over 120 h in human serum, comparing well with previously reported [(111)In(octapa)](-) values, and an improved stability compared to the current industry "gold standards" 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA

  13. Ruthenium Polypyridyl Complex Inhibits Growth and Metastasis of Breast Cancer Cells by Suppressing FAK signaling with Enhancement of TRAIL-induced Apoptosis (United States)

    Cao, Wenqiang; Zheng, Wenjie; Chen, Tianfeng


    Ruthenium-based complexes have emerged as promising antitumor and antimetastatic agents during the past decades. However, the limited understanding of the antimetastatic mechanisms of these agents is a roadblock to their clinical application. Herein, we reported that, RuPOP, a ruthenium polypyridyl complex with potent antitumor activity, was able to effectively inhibit growth and metastasis of MDA-MB-231 cells and synergistically enhance TRAIL-induced apoptosis. The selective intracellular uptake and cytotoxic effect of RuPOP was found associated with transferring receptor (TfR)-mediated endocytosis. Further investigation on intracellular mechanisms reveled that RuPOP notably suppressed FAK-mediated ERK and Akt activation. Pretreatment of cells with ERK inhibitor (U0126) and PI3K inhibitor (LY294002) significantly potentiated the inhibitory effect of RuPOP on cell growth, migration and invasion. Moreover, the alternation in the expression levels of metastatic regulatory proteins, including uPA, MMP-2/-9, and inhibition of VEGF secretion were also observed after RuPOP treatment. These results demonstrate the inhibitory effect of RuPOP on the growth and metastasis of cancer cells and the enhancement of TRAIL-induced apoptosis though suppression of FAK-mediated signaling. Furthermore, RuPOP exhibits the potential to be developed as a metal-based antimetastatic agent and chemosensitizer of TRAIL for the treatment of human metastatic cancers.

  14. Cytotoxic activity, DNA damage, cellular uptake, apoptosis and western blot analysis of ruthenium(II) polypyridyl complex against human lung decarcinoma A549 cell. (United States)

    Lai, Shang-Hai; Jiang, Guang-Bin; Yao, Jun-Hua; Li, Wei; Han, Bing-Jie; Zhang, Cheng; Zeng, Chuan-Chuan; Liu, Yun-Jun


    A new ruthenium(II) polypyridyl complex [Ru(dmp)2(pddppn)](ClO4)2Ru1 was synthesized and characterized. The cytotoxic activity in vitro of the complex was evaluated by MTT method. Ru1 shows high effect on the inhibition of the cell growth against BEL-7402, HeLa, MG-63 and A549 cells with low IC50 values of 1.6±0.4, 9.0±0.8, 1.5±0.2 and 1.5±0.3 μM, respectively. The cellular uptake indicates that Ru1 can enter into the cytoplasm and accumulate in the cell nuclei. Ru1 can induce apoptosis in A549 cells and enhance the levels of reactive oxygen species (ROS) and induce the decrease of mitochondrial membrane potential. In addition, Ru1 can down-regulate the levels of Bcl-2, Bcl-x, Bak, and Bim expression and up-regulate the expression of Bag-1 and Bad. The complex induces apoptosis of A549 cells through an intrinsic ROS-mediated mitochondrial dysfunction pathway, which was accompanied by regulating the expression of caspases and Bcl-2 family proteins. Copyright © 2015 Elsevier Inc. All rights reserved.

  15. The influence of ligand conformation on the thermal spin transitions in iron(III) saltrien complexes. (United States)

    Pritchard, Ruth; Barrett, Simon A; Kilner, Colin A; Halcrow, Malcolm A


    We report the syntheses of six new salts of the iron(III) complexes of four hexadentate Schiff bases of the saltrien-type derived from 1,8-diamino-3,6-diazaoctane and 2 equiv. of the appropriate salicylaldehyde derivative. Three of these new compounds undergo gradual spin-transitions centred between 155-204 K in the solid state, that proceed to 35-50% completeness. One of the other compounds remains high-spin on cooling, another is low-spin, while the last undergoes spin-crossover centred above room temperature. This spin-state variability is typical of solid compounds of this type. As an aid to understanding this behaviour, the crystal structures and magnetochemistry of the known spin-crossover salts [Fe(saltrien)]PF6, [Fe(saltrien)]ClO4 and [Fe(saltrien)]BPh4 have also been reexamined. The structural chemistry of all three salts was found to differ significantly from what has been previously reported. Correlation of the crystal structures and magnetic behaviour of the compounds in this and previous work suggests that the disposition of the two ligand phenoxy groups plays an important role in determining whether high-spin [Fe(saltrien)]+ complexes can undergo thermal spin-transitions.

  16. Structural, luminescent, and magnetic properties of three novel three-dimensional metal-organic frameworks based on hexadentate N,N'-bis(4-picolinoyl)hydrazine. (United States)

    Fang, Zhen-Lan; Yu, Rong-Min; He, Jian-Gang; Zhang, Qi-Sheng; Zhao, Zhen-Guo; Lu, Can-Zhong


    Three novel microporous three-dimensional (3-D) metal-organic framework materials [ML](n) [M = Ni, Co, Cd; L = N,N'-bis(4-picolinoyl)hydrazine] were obtained from hydrothermal reactions. The organic ligand L was formed through the in situ ring-opening hydrolysis reaction of 2,5-bis(4-pyridyl)-1,3,4-oxadiazole with the assistance of metal ions. Single-crystal X-ray diffraction studies reveal that complexes 1-3 adopt 6-connected 3-D networks of distorted alpha-Po topology, which are built from non-interpenetrated (4,4) grids cross-linked by zigzag chains. These isomorphic complexes are all of high thermal stability, but some other physical properties are quite different because of their different metal centers. Antiferromagnetic exchange was observed between Ni(II) centers of complex 1, while ferromagnetic for Co(II) centers of complex 2. Complex 3 exhibits strong fluorescence emission.

  17. Solid state molecular device based on a rhenium(I) polypyridyl complex immobilized on TiO2 films. (United States)

    Patrocinio, Antonio Otavio T; Frin, Karina P M; Murakami Iha, Neyde Y


    The photochemical and photophysical behaviors of fac-[Re(CO)3(phen)(trans-stpyCOOH)](+) (phen = 1,10-phenanthroline, trans-stpyCOOH = 4-[trans-(pyridin-4-yl-vinyl)]benzoic acid) in acetonitrile solution and adsorbed on a TiO2 film have been investigated. The trans-to-cis photoisomerization at 404 nm irradiation of coordinated stpyCOOH occurs efficiently in fluid solution as shown by quantum yield determined spectrophotometrically (Φ(UV-vis) = 0.37 ± 0.04) and, more accurately, by (1)H NMR (Φ(NMR) = 0.48 ± 0.04), following the photoproduct signals in the distinct region of the reactant. For the first time, the trans-to-cis isomerization is also reported for the complex adsorbed on the TiO2 surface (Φ(UV-vis) = 0.23 ± 0.03). The photoproduct, fac-[Re(CO)3(phen)(cis-stpyCOOH)](+), is emissive in acetonitrile (ϕ = 0.032), but its radiative decay is highly quenched on the oxide surface by electron photoinjection into the semiconductor, leading to an increasing photocurrent as the trans-to-cis isomerization takes place. Therefore, the photoinduced trans-to-cis isomerization of coordinated ligand immobilized on TiO2 films acts as a trigger for the electron injection process. This system exemplifies the use of photoinduced molecular motion to yield electrical current, which can be used as a "proof of concept" for molecular machines/devices.

  18. Electrochemical, linear optical, and nonlinear optical properties and interpretation by density functional theory calculations of (4-N,N-dimethylaminostyryl)-pyridinium pendant group associated with polypyridinic ligands and respective multifunctional metal complexes (Ru(II) or Zn(II)). (United States)

    Dumur, Frédéric; Mayer, Cédric R; Hoang-Thi, Khuyen; Ledoux-Rak, Isabelle; Miomandre, Fabien; Clavier, Gilles; Dumas, Eddy; Méallet-Renault, Rachel; Frigoli, Michel; Zyss, Joseph; Sécheresse, Francis


    The synthesis, linear optical and nonlinear optical properties, as well as the electrochemical behavior of a series of pro-ligands containing the 4-(4-N,N-dimethylaminostyryl)-1-methyl pyridinium (DASP(+)) group as a push-pull moiety covalently linked to terpyridine or bipyridine as chelating ligands are reported in this full paper. The corresponding multifunctional Ru(II) and Zn(II) complexes were prepared and investigated. The structural, electronic, and optical properties of the pro-ligands and the ruthenium complexes were investigated using density functional theory (DFT) and time-dependent (TD) DFT calculations. A fairly good agreement was observed between the experimental and the calculated electronic spectra of the pro-ligands and their corresponding ruthenium complexes. A quenching of luminescence was evidenced in all ruthenium complexes compared with the free pro-ligands but even the terpyridine-functionalized metal complexes exhibited detectable luminescence at room temperature. Second order nonlinear optical (NLO) measurements were performed by Harmonic Light Scattering and the contribution of the DASP(+) moieties (and their relative ordering) and the metal-polypyridyl core need to be considered to explain the nonlinear optical properties of the metal complexes.

  19. Hydrogen and copper ion induced molecular reorganizations in two new scorpiand-like ligands appended with pyridine rings. (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


    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.

  20. Ligand modeling and design

    Energy Technology Data Exchange (ETDEWEB)

    Hay, B.P. [Pacific Northwest National Lab., Richland, WA (United States)


    The purpose of this work is to develop and implement a molecular design basis for selecting organic ligands that would be used in the cost-effective removal of specific radionuclides from nuclear waste streams. Organic ligands with metal ion specificity are critical components in the development of solvent extraction and ion exchange processes that are highly selective for targeted radionuclides. The traditional approach to the development of such ligands involves lengthy programs of organic synthesis and testing, which in the absence of reliable methods for screening compounds before synthesis, results in wasted research effort. The author`s approach breaks down and simplifies this costly process with the aid of computer-based molecular modeling techniques. Commercial software for organic molecular modeling is being configured to examine the interactions between organic ligands and metal ions, yielding an inexpensive, commercially or readily available computational tool that can be used to predict the structures and energies of ligand-metal complexes. Users will be able to correlate the large body of existing experimental data on structure, solution binding affinity, and metal ion selectivity to develop structural design criteria. These criteria will provide a basis for selecting ligands that can be implemented in separations technologies through collaboration with other DOE national laboratories and private industry. The initial focus will be to select ether-based ligands that can be applied to the recovery and concentration of the alkali and alkaline earth metal ions including cesium, strontium, and radium.

  1. Structure and Heme-Independent Peroxidase Activity of a Fully-Coordinated Mononuclear Mn(II) Complex with a Schiff-Base Tripodal Ligand Containing Three Imidazole Groups

    Energy Technology Data Exchange (ETDEWEB)

    Sarkar, Shuranjan; Lee, Hong In [Kyungpook National University, Daegu (Korea, Republic of); Moon, Do Hyun [Pohang Accelerator Laboratory, Pohang (Korea, Republic of); Lah, Myoung Soo [Ulsan National Institute of Science and Technology, Ulsan (Korea, Republic of)


    New complex [Mn(II)H{sub 1.5}L]{sub 2}[Mn(II)H{sub 3}L]{sub 2}(ClO{sub 4}){sub 5}·3H{sub 2}O, where H{sub 3}L is tris{2-(4-imidazolyl)methyliminoethyl} amine (imtren), has been prepared by reacting manganese(II) perchlorate hexahydrate with the imtren ligand in methanol. X-ray crystallographic study revealed that the imtren ligand hexadentately binds to Mn(II) ion through the three Schiff-base imine N atoms and three imidazole N atoms with a distorted octahedral geometry, and the apical tertiary amine N atom of the ligand pseudo-coordinates to Mn(II), forming overall a pseudo-seven coordination environment. The hydrogen-bonds between imidazole and imidazolate of [Mn(II)H{sub 1.5}L]{sup 0.5+} complex ions are extended to build a 2D puckered network with trigonal voids. [Mn(II)H{sub 3}L]{sup 2+} complex ions constitutes another extended 2D puckered layer without hydrogen bonds. Two layers are wedged each other to constitute overall stack of the crystal. Peroxidase activity of complex 1 was examined by observing the oxidation of 2,2'-azinobis(3-ethylbenzothiazoline)- 6-sulfonic acid (ABTS) with hydrogen peroxide in the presence of complex 1. Generation of ABTS{sup +·} was observed by UV-vis and EPR spectroscopies, indicating that the complex 1, a fully-coordinated mononuclear Mn(II) complex with nitrogen-only ligand, has a heme-independent peroxidase activity.

  2. Ligand modeling and design

    Energy Technology Data Exchange (ETDEWEB)

    Hay, B. [Pacific Northwest Lab., Richland, WA (United States)


    The purpose of this work is to develop and implement a molecular design basis for selecting organic ligands that would be used tin applications for the cost-effective removal of specific radionuclides from nuclear waste streams.

  3. Iron Pentapyridyl Complexes as Molecular Water Oxidation Catalysts: Strong Influence of a Chloride Ligand and pH in Altering the Mechanism. (United States)

    Das, Biswanath; Orthaber, Andreas; Ott, Sascha; Thapper, Anders


    The development of molecular water oxidation catalysts based on earth-abundant, non-noble metals is essential for artificial photosynthesis research. Iron, which is the most abundant transition metal in the earth's crust, is a prospective candidate for this purpose. Herein, we report two iron complexes based on the polypyridyl ligand Py5OH (Py5OH=pyridine-2,6-diylbis [di(pyridin-2-yl)methanol]) that can catalyse water oxidation to produce O2 in Ru(III) -induced (at pH 8, highest turnover number (TON)=26.5; turnover frequency (TOF)=2.2 s(-1) ), Ce(IV) -induced (at pH≈1.5 highest TON=16; TOF=0.75 s(-1) ) and photo-induced (at pH 8, highest TON=43.5; TOF=0.6 s(-1) ) reactions. A chloride ligand in one of the iron complexes is shown to affect the activity strongly, improve stability and, thereby, the performance at pH 8 but it inhibits oxygen evolution at pH≈1.5. The observations are consistent with a change in mechanism for catalytic water oxidation with the Fe(Py5OH) complexes between acidic (Ce(IV) ) and near-neutral pH (Ru(III) ). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. 3d/4f Metal Complexes of Phenolic Oximes New Binding Sites on Anderson Polyoxometalates Metal Complexes of the New THAME Ligand

    DEFF Research Database (Denmark)

    Sethi, Waqas

    III =DyIII, ErIII, TbIII and YIII). The complexes are synthesised by mixing the appropriate metal salts andligands in basic MeOH or in a mixture of MeOH and MeCN. The metallic skeleton of [LnIII2MnIII4]and [LnIII2MnIII2MnIV2] can be viewed as made of two edge sharing [Ln2Mn2] tetrahedra or...... to be coordinatedto SMMs as well as onto other transition metal complexes, via different synthetic strategies. These synthetic routes did not result in the crystallisation of any new compounds. A new hexadentate ligand tris(((2-hydroxyethyl)-amino)methyl)ethane (THAME) was synthesised and characterised. THAME......Derivatives of phenolic oximes have been used to synthesise two large families of coordinationcomplexes namely [LnIII2MnIII4] and [LnIII2MnIII2MnIV2]. The [LnIII2MnIII4] family can be subdivided into two structural types. Complexes 1 to 9 (Type 1) can be represented by the general formula [LnIII2Mn...

  5. 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

  6. Metal-ligand cooperation at tethered pi-ligands

    NARCIS (Netherlands)

    Verhoeven, Dide G. A.; Moret, Marc-Etienne


    Metal–ligand cooperativity in homogeneous catalysis is emerging as a powerful tool for the design of efficient transition-metal catalysts. This perspective highlights recent advances in the use of neutral π-coordinating ligands, tethered to a transition-metal center by other donor ligands, as

  7. Glutamate receptor ligands

    DEFF Research Database (Denmark)

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


    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.......g., IC(50) = 300 microM for (2R,4S)-4-methyl-AA (5d)]. The two unsaturated analogs (S)- (7a) and (R)-(E)-Delta(4)-5-methyl-AA (7b) turned out to be a weak AMPA receptor agonist and a weak mixed NMDA/AMPA receptor antagonist, respectively....

  8. AMPA receptor ligands

    DEFF Research Database (Denmark)

    Strømgaard, Kristian; Mellor, Ian


    Alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptors (AMPAR), subtype of the ionotropic glutamate receptors (IGRs), mediate fast synaptic transmission in the central nervous system (CNS), and are involved in many neurological disorders, as well as being a key player...... polyamines are known to modulate the function of these receptors in vivo. In this study, recent developments in the medicinal chemistry of polyamine-based ligands are given, particularly focusing on the use of solid-phase synthesis (SPS) as a tool for the facile generation of libraries of polyamine toxin...

  9. Iron coordination chemistry with new ligands containing triazole and pyridine moieties. Comparison of the coordination ability of the N-donors. (United States)

    Ségaud, Nathalie; Rebilly, Jean-Noël; Sénéchal-David, Katell; Guillot, Régis; Billon, Laurianne; Baltaze, Jean-Pierre; Farjon, Jonathan; Reinaud, Olivia; Banse, Frédéric


    We report the synthesis, characterization, and solution chemistry of a series of new Fe(II) complexes based on the tetradentate ligand N-methyl-N,N'-bis(2-pyridyl-methyl)-1,2-diaminoethane or the pentadentate ones N,N',N'-tris(2-pyridyl-methyl)-1,2-diaminoethane and N,N',N'-tris(2-pyridyl-methyl)-1,3-diaminopropane, modified by propynyl or methoxyphenyltriazolyl groups on the amino functions. Six of these complexes are characterized by X-ray crystallography. In particular, two of them exhibit an hexadentate coordination environment around Fe(II) with two amino, three pyridyl, and one triazolyl groups. UV-visible and cyclic voltammetry experiments of acetonitrile solutions of the complexes allow to deduce accurately the structure of all Fe(II) species in equilibrium. The stability of the complexes could be ranked as follows: [L(5)Fe(II)-py](2+) > [L(5)Fe(II)-Cl](+) > [L(5)Fe(II)-triazolyl](2+) > [L(5)Fe(II)-(NCMe)](2+), where L(5) designates a pentadentate coordination sphere composed of the two amines of ethanediamine and three pyridines. For complexes based on propanediamine, the hierarchy determined is [L(5)Fe(II)-Cl](+) > [L(5)Fe(II)(OTf)](+) > [L(5)Fe(II)-(NCMe)](2+), and no ligand exchange could be evidenced for [L(5)Fe(II)-triazolyl](2+). Reactivity of the [L(5)Fe(II)-triazolyl](2+) complexes with hydrogen peroxide and PhIO is similar to the one of the parent complexes that lack this peculiar group, that is, generation of Fe(III)(OOH) and Fe(IV)(O), respectively. Accordingly, the ability of these complexes at catalyzing the oxidation of small organic molecules by these oxidants follows the tendencies of their previously reported counterparts. Noteworthy is the remarkable cyclooctene epoxidation activity by these complexes in the presence of PhIO.

  10. Spectroscopic and electrochemical properties of organic framework of macrocylic OONNOO-donor ligand with its metal organic framework: Host/guest stability measurements (United States)

    Kumar, Rajiv; Singh, R. P.; Singh, R. P.


    In this study, we synthesized 1,2-di( o-aminophenoxy)ethane, as the starting material, used in the preparation of a novel hexadentate OONNOO-donor macrocyclic ligand-1,4,11,14-tetraoxo-7,8-diaza-5,6:9,10;15,16:19,20-terabezocyclododeca-8,17-iene. It has twenty membered organic framework (OF), which has been designed, synthesized and characterized. Our main findings of this paper are related to the organic framework of ligand, its capacity to digest the metal ions and the stability of metal organic framework (MOFs) with cobalt(II), nickel(II) and manganese(II). The authenticity of the used organic framework and its metal complexes have been detected and observed in solid state as well as in aqueous solutions. The main observations were made on the basis of physiochemical measurements viz.: elemental analyses, molar conductance measurements, magnetic susceptibility measurements, IR, 1H NMR, 13C NMR, mass spectroscopy, electronic, ESR spectroscopy. In addition, the magnetic susceptibility and electrochemistry measurements have been made. The 1H NMR spectra suggest stereochemistry and proton movement interaction. Considering the used organic framework there are a lot of carbon atoms in the molecule reflected by the 13C NMR spectrum. All these observations gave a clear view to confirming the encapsulation; arrive at the composition, structure and geometry of encapsulated complexes. In simple words, it confirms the host/guest coordination and its stability. Electrochemical properties of the complexes have been investigated to confirm the various changes in oxidation state of metals with change in potentials with respect to current at different scan rate.

  11. Spectroscopic and electrochemical properties of organic framework of macrocylic OONNOO-donor ligand with its metal organic framework: host/guest stability measurements. (United States)

    Kumar, Rajiv; Singh, R P; Singh, R P


    In this study, we synthesized 1,2-di(o-aminophenoxy)ethane, as the starting material, used in the preparation of a novel hexadentate OONNOO-donor macrocyclic ligand-1,4,11,14-tetraoxo-7,8-diaza-5,6:9,10;15,16:19,20-terabezocyclododeca-8,17-iene. It has twenty membered organic framework (OF), which has been designed, synthesized and characterized. Our main findings of this paper are related to the organic framework of ligand, its capacity to digest the metal ions and the stability of metal organic framework (MOFs) with cobalt(II), nickel(II) and manganese(II). The authenticity of the used organic framework and its metal complexes have been detected and observed in solid state as well as in aqueous solutions. The main observations were made on the basis of physiochemical measurements viz.: elemental analyses, molar conductance measurements, magnetic susceptibility measurements, IR, 1H NMR, 13C NMR, mass spectroscopy, electronic, ESR spectroscopy. In addition, the magnetic susceptibility and electrochemistry measurements have been made. The 1H NMR spectra suggest stereochemistry and proton movement interaction. Considering the used organic framework there are a lot of carbon atoms in the molecule reflected by the 13C NMR spectrum. All these observations gave a clear view to confirming the encapsulation; arrive at the composition, structure and geometry of encapsulated complexes. In simple words, it confirms the host/guest coordination and its stability. Electrochemical properties of the complexes have been investigated to confirm the various changes in oxidation state of metals with change in potentials with respect to current at different scan rate.

  12. Calcium and heterometallic manganese-calcium complexes supported by tripodal pyridine-carboxylate ligands: structural, EPR and theoretical investigations. (United States)

    Gerey, Bertrand; Gennari, Marcello; Gouré, Eric; Pécaut, Jacques; Blackman, Allan; Pantazis, Dimitrios A; Neese, Frank; Molton, Florian; Fortage, Jérôme; Duboc, Carole; Collomb, Marie-Noëlle


    Carboxylate-bridged Mn(II)-Ca(II) complexes are potentially relevant for mimicking the first stages of the Oxygen-Evolving Complex (OEC) assembly process. Here, we report on new homonuclear Ca(II) and heteronuclear Mn(II)–Ca(II) complexes with carboxylate-functionalized tripodal tris(2-pyridylmethyl)amine ligands, the heptadentate H3tpaa, previously reported, and the new hexadentate H2tpada, containing respectively three and two carboxylate units. The mononuclear [Ca(Htpaa)(OH2)] (Ca1) and dinuclear [Ca(tpada)(OH2)2]2 (Ca2) calcium complexes, as well as the tetranuclear [{Mn(tpaa)}2{Ca(OH2)5(μ-OH2)}2][Mn(tpaa)]2 (Mn2Ca2·2Mn) and dinuclear [Mn(tpada)ClCa(OH2)2.67(MeOH)2.33]Cl (MnCa) heterometallic species have been structurally characterized; the syntheses of Ca1 and Mn2Ca2·2Mn being previously reported by us (Inorg. Chem., 2015, 54, 1283). The Mn(II) and Ca(II) are linked by two μ1,1-bridging carboxylates in MnCa, while only one μ1,3-carboxylate bridge connects each Ca2+ ion to each Mn(II) in Mn2Ca2. A variable number of water molecules (n = 1 to 7) are coordinated to Ca in all complexes, most of them being involved in hydrogen-bond networks, in analogy to what occurs in the photosystem II. All donor atoms of the tpaa3- and tpada2- ligands are coordinated to the Mn2+ ions, despite the unusually long distance between the Mn2+ ion and the tertiary amine imposed by the constraining nature of the ligands, as supported by theoretical calculations. Solid state EPR spectroscopy, in combination with DFT calculations, has also shown that the Ca2+ ion has an effect on the electronic parameters (zero field splitting) of the linked Mn(II) in the case of MnCa (μ1,1-carboxylate bridges). In Mn2Ca2 (μ1,3-carboxylate bridge) the Ca2+ ion induces only slight structural changes in the Mn coordination sphere.

  13. Metal-ligand cooperation at tethered π-ligands. (United States)

    Verhoeven, Dide G A; Moret, Marc-Etienne


    Metal-ligand cooperativity in homogeneous catalysis is emerging as a powerful tool for the design of efficient transition-metal catalysts. This perspective highlights recent advances in the use of neutral π-coordinating ligands, tethered to a transition-metal center by other donor ligands, as cooperative reaction centers. The state-of-the-art organometallic complexes, including π-coordinating ligands originating from C[double bond, length as m-dash]C, C[double bond, length as m-dash]E (E = O, N) and boron containing moieties, are described here, with special attention on their specific reactivity. Geometric and electronic aspects of ligand design and their influence on the coordination mode and reactivity of the π-system are discussed.

  14. Macrocyclic G-quadruplex ligands

    DEFF Research Database (Denmark)

    Nielsen, M C; Ulven, Trond


    are macrocyclic structures which have been modeled after the natural product telomestatin or from porphyrin-based ligands discovered in the late 1990s. These two structural classes of G-quadruplex ligands are reviewed here with special attention to selectivity and structure-activity relationships, and with focus...

  15. Two novel mixed-ligand complexes containing organosulfonate ligands. (United States)

    Li, Mingtian; Huang, Jun; Zhou, Xuan; Fang, Hua; Ding, Liyun


    The structures reported herein, viz. bis(4-aminonaphthalene-1-sulfonato-kappaO)bis(4,5-diazafluoren-9-one-kappa(2)N,N')copper(II), [Cu(C(10)H(8)NO(3)S)(2)(C(11)H(6)N(2)O)(2)], (I), and poly[[[diaquacadmium(II)]-bis(mu-4-aminonaphthalene-1-sulfonato)-kappa(2)O:N;kappa(2)N:O] dihydrate], {[Cd(C(10)H(8)NO(3)S)(2)(H(2)O)(2)].2H(2)O}(n), (II), are rare examples of sulfonate-containing complexes where the anion does not fulfill a passive charge-balancing role, but takes an active part in coordination as a monodentate and/or bridging ligand. Monomeric complex (I) possesses a crystallographic inversion center at the Cu(II) atom, and the asymmetric unit contains one-half of a Cu atom, one complete 4-aminonaphthalene-1-sulfonate (ans) ligand and one 4,5-diazafluoren-9-one (DAFO) ligand. The Cu(II) atom has an elongated distorted octahedral coordination geometry formed by two O atoms from two monodentate ans ligands and by four N atoms from two DAFO molecules. Complex (II) is polymeric and its crystal structure is built up by one-dimensional chains and solvent water molecules. Here also the cation (a Cd(II) atom) lies on a crystallographic inversion center and adopts a slightly distorted octahedral geometry. Each ans anion serves as a bridging ligand linking two Cd(II) atoms into one-dimensional infinite chains along the [010] direction, with each Cd(II) center coordinated by four ans ligands via O and N atoms and by two aqua ligands. In both structures, there are significant pi-pi stacking interactions between adjacent ligands and hydrogen bonds contribute to the formation of two- and three-dimensional networks.

  16. Multifaceted interplay between lipophilicity, protein interaction and luminescence parameters of non-intercalative ruthenium(II) polypyridyl complexes controlling cellular imaging and cytotoxic properties. (United States)

    Mazuryk, Olga; Magiera, Katarzyna; Rys, Barbara; Suzenet, Franck; Kieda, Claudine; Brindell, Małgorzata


    Here, we examine the photophysical properties of five ruthenium(II) complexes comprising two 4,7-diphenyl-1,10-phenanthroline (dip) ligands and functionalized bipyridine (R₁bpy-R₂, where R₁= H or CH3, R₂= H, CH₃, COO⁻,4-[3-(2-nitro-1H-imidazol-1-yl)propyl] or 1,3-dicyclohexyl-1-carbonyl-urea) towards development of luminescence probes for cellular imaging. These complexes have been shown to interact with albumin and the formed adducts exhibited up to eightfold increase in the luminescence quantum yield as well as the average lifetime of emission. It was demonstrated that they cannot bind to DNA through the intercalation mode and its luminescence in the presence of DNA is quenching. Cell viability experiments indicated that all complexes possess significant dose-dependent cytotoxicity (with IC₅₀ 5-19 μM) on 4T1 breast cancer cell line and their anti-proliferative activity correlates very well with their lipophilicity. Cellular uptake was studied by measuring the ruthenium content in cells using ICP-MS technique. As expected, the better uptake is directly related to higher lipophilicity of doubly charged ruthenium complexes while uptake of monocationic one is much lower in spite of the highest lipophilicity. Additionally staining properties were assessed using flow cytometry and fluorescence microscopy. These experiments showed that complex with 1,3-dicyclohexyl-1-carbonyl-urea substituent exhibits the best staining properties in spite of the lowest luminescence quantum yield in buffered solution (pH 7.4). Our results point out that both the imaging and cytotoxic properties of the studied ruthenium complexes are strongly influence by the level of internalization and protein interaction.

  17. Correcting ligands, metabolites, and pathways

    NARCIS (Netherlands)

    Ott, M.A.; Vriend, G.


    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,

  18. FAS Ligand Triggers Pulmonary Silicosis (United States)

    Borges, Valéria M.; Falcão, Haroldo; Leite-Júnior, José H.; Alvim, Luciana; Teixeira, Gerlinde P.; Russo, Momtchilo; Nóbrega, Alberto F.; Lopes, Marcela F.; Rocco, Patricia M.; Davidson, Wendy F.; Linden, Rafael; Yagita, Hideo; Zin, Walter A.; DosReis, George A.


    We investigated the role of Fas ligand in murine silicosis. Wild-type mice instilled with silica developed severe pulmonary inflammation, with local production of tumor necrosis factor (TNF)-α, and interstitial neutrophil and macrophage infiltration in the lungs. Strikingly, Fas ligand–deficient generalized lymphoproliferative disease mutant (gld) mice did not develop silicosis. The gld mice had markedly reduced neutrophil extravasation into bronchoalveolar space, and did not show increased TNF-α production, nor pulmonary inflammation. Bone marrow chimeras and local adoptive transfer demonstrated that wild-type, but not Fas ligand–deficient lung macrophages recruit neutrophils and initiate silicosis. Silica induced Fas ligand expression in lung macrophages in vitro and in vivo, and promoted Fas ligand–dependent macrophage apoptosis. Administration of neutralizing anti-Fas ligand antibody in vivo blocked induction of silicosis. Thus, Fas ligand plays a central role in induction of pulmonary silicosis. PMID:11457890

  19. Why mercury prefers soft ligands

    Energy Technology Data Exchange (ETDEWEB)

    Riccardi, Demian M [ORNL; Guo, Hao-Bo [ORNL; Gu, Baohua [ORNL; Parks, Jerry M [ORNL; Summers, Anne [University of Georgia, Athens, GA; Miller, S [University of California, San Francisco; Liang, Liyuan [ORNL; Smith, Jeremy C [ORNL


    Mercury (Hg) is a major global pollutant arising from both natural and anthropogenic sources. Defining the factors that determine the relative affinities of different ligands for the mercuric ion, Hg2+, is critical to understanding its speciation, transformation, and bioaccumulation in the environment. Here, we use quantum chemistry to dissect the relative binding free energies for a series of inorganic anion complexes of Hg2+. Comparison of Hg2+ ligand interactions in the gaseous and aqueous phases shows that differences in interactions with a few, local water molecules led to a clear periodic trend within the chalcogenide and halide groups and resulted in the well-known experimentally observed preference of Hg2+ for soft ligands such as thiols. Our approach establishes a basis for understanding Hg speciation in the biosphere.

  20. Rosetta Ligand docking with flexible XML protocols. (United States)

    Lemmon, Gordon; Meiler, Jens


    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.


    African Journals Online (AJOL)



    Jun 30, 2010 ... ion. This brings about repulsion between the adsorbent and positively charged ion and consequently a reduction in the amount of heavy metal adsorbed at lower pH. (Lee, 1999). The effectiveness of the anionic ligands in the removal of heavy metal ions from aqueous solution seems to be low for the EDTA.

  2. -Pincer Ligand Family through Ligand Post-Modification

    KAUST Repository

    Huang, Mei-Hui


    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. Tumor targeting via integrin ligands

    Directory of Open Access Journals (Sweden)

    Udaya Kiran eMarelli


    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.

  4. 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.

  5. Bitopic Ligands and Metastable Binding Sites

    DEFF Research Database (Denmark)

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


    G protein-coupled receptors (GPCRs) belong to a large superfamily of membrane receptors mediating a variety of physiological functions. As such they are attractive targets for drug therapy. However, it remains a challenge to develop subtype selective GPCR ligands due to the high conservation...... sites. Computational studies on ligand binding to GPCRs have revealed transient, low-affinity binding sites, termed metastable binding sites. Metastable binding sites may provide a new source of allosteric binding sites that could be exploited in the design of bitopic ligands. Unlike the bitopic ligands...

  6. Clinical Use of PPARγ Ligands in Cancer

    Directory of Open Access Journals (Sweden)

    Jennifer L. Hatton


    Full Text Available The role of PPARγ in adipocyte differentiation has fueled intense interest in the function of this steroid nuclear receptor for regulation of malignant cell growth and differentiation. Given the antiproliferative and differentiating effects of PPARγ ligands on liposarcoma cells, investigation of PPARγ expression and ligand activation in other solid tumors such as breast, colon, and prostate cancers ensued. The anticancer effects of PPARγ ligands in cell culture and rodent models of a multitude of tumor types suggest broad applicability of these agents to cancer therapy. This review focuses on the clinical use of PPARγ ligands, specifically the thiazolidinediones, for the treatment and prevention of cancer.

  7. Macrocyclic ligands for uranium complexation

    Energy Technology Data Exchange (ETDEWEB)

    Potts, K.T.


    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.

  8. Ligand-binding kinetics on histamine receptors

    NARCIS (Netherlands)

    Bosma, Reggie; Mocking, T.A.M.; Leurs, R.; Vischer, H.F.


    Equilibrium-binding affinities of ligands for a drug target do not always accurately reflect the success of drug candidates in the clinic. Affinity-based predictions concerning competitive antagonism on the target will only be accurate if equilibrium binding of both ligands is allowed. Unless

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

    African Journals Online (AJOL)



    Jun 21, 2010 ... deacetylases (HDAC) have emerged as an important class of anticancer agents. Various side effects like myocardium damage and ... calculated through the software Jmol. The proposed model has been .... The study was carried out using the software Ligand Scout (version. 2.03[i2_001]). Ligand Scout is a ...

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

    Indian Academy of Sciences (India)

    Abstract. Designing efficient phosphorus-based ligands to make catalysts for homogeneous catalysis has been a great challenge for chemists. Despite a plethora of phosphorus ligands ranging from simple tertiary phosphines to polyphosphines are known, the enthusiasm to generate new ones is mainly due to the demand.

  11. Organotellurium ligands – designing and complexation reactions

    Indian Academy of Sciences (India)


    Abstract. A variety of tellurium ligands has been designed and studied for their complexation reactions in the last decade. Of these hybrid telluroethers, halotellurium ligands and polytellurides are the most notable ones. RTe–and polytelluride ions have also been used to design clusters. Ligation of ditelluroethers and ...

  12. CXCR4 Ligands : The Next Big Hit?

    NARCIS (Netherlands)

    Walenkamp, Annemiek M. E.; Lapa, Constantin; Herrmann, Ken; Wester, Hans-Juergen


    The G protein-coupled protein receptor C-X-C chemokine receptor 4 (CXCR4) is an attractive target for cancer diagnosis and treatment, as it is overexpressed in many solid and hematologic cancers. Binding of its ligand, C-X-C chemokine ligand 12 (CXCL12), results in receptor internalization and

  13. Flexible ligand docking using a genetic algorithm (United States)

    Oshiro, C. M.; Kuntz, I. D.; Dixon, J. Scott


    Two computational techniques have been developed to explore the orientational and conformational space of a flexible ligand within an enzyme. Both methods use the Genetic Algorithm (GA) to generate conformationally flexible ligands in conjunction with algorithms from the DOCK suite of programs to characterize the receptor site. The methods are applied to three enzyme-ligand complexes: dihydrofolate reductase-methotrexate, thymidylate synthase-phenolpthalein and HIV protease-thioketal haloperidol. Conformations and orientations close to the crystallographically determined structures are obtained, as well as alternative structures with low energy. The potential for the GA method to screen a database of compounds is also examined. A collection of ligands is evaluated simultaneously, rather than docking the ligands individually into the enzyme.

  14. Characterizations of chloro and aqua Mn(II) mononuclear complexes with amino-pyridine ligands. Comparison of their electrochemical properties with those of Fe(II) counterparts. (United States)

    Groni, Sihem; Hureau, Christelle; Guillot, Régis; Blondin, Geneviève; Blain, Guillaume; Anxolabéhère-Mallart, Elodie


    The solution behavior of mononuclear Mn(II) complexes, namely, [(L(5)(2))MnCl](+) (1), [(L(5)(3))MnCl](+) (2), [(L(5)(2))Mn(OH(2))](2+) (3), [(L(5)(3))Mn(OH(2))](2+) (4), and [(L(6)(2))Mn(OH(2))](2+) (6), with L(5)(2/3) and L(6)(2) being penta- and hexadentate amino-pyridine ligands, is investigated in MeCN using EPR, UV-vis spectroscopies, and electrochemistry. The addition of one chloride ion onto species 6 leads to the formation of the complex [(L(6)(2))MnCl](+) (5) that is X-ray characterized. EPR and UV-vis spectra indicate that structure and redox states of complexes 1-6 are maintained in MeCN solution. Chloro complexes 1, 2, and 5 show reversible Mn(II)/Mn(III) process at 0.95, 1.02, and 1.05 V vs SCE, respectively, whereas solvated complexes 3, 4, and 6 show an irreversible anodic peak around 1.5 V vs SCE. Electrochemical oxidations of 1 and 5 leading to the Mn(III) complexes [(L(5)(2))MnCl](2+) (7) and [(L(6)(2))MnCl](2+) (8) are successful. The UV-vis signatures of 7 and 8 show features associated with chloro to Mn(III) LMCT and d-d transitions. The X-ray characterization of the heptacoordinated Mn(III) species 8 is also reported. The analogous electrochemical generation of the corresponding Mn(III) complex was not possible when starting from 2. The new mixed-valence di-mu-oxo [(L(5)(2))Mn(muO)(2)Mn(L(5)(2))](3+) species (9) can be obtained from 3, whereas the sister [(L(5)(3))Mn(muO)(2)Mn(L(5)(3))](3+) species can not be generated from 4. Such different responses upon oxidations are commented on with the help of comparison with related Mn/Fe complexes and are discussed in relation with the size of the metallacycle formed between the diamino bridge and the metal center (5- vs 6-membered). Lastly, a comparison between redox potentials of the studied Mn(II) complexes with those of Fe(II) analogues is drawn and completed with previously reported data on Mn/Fe isostructural systems. This gives us the opportunity to get some indirect insights into the metal

  15. Correcting ligands, metabolites, and pathways

    Directory of Open Access Journals (Sweden)

    Vriend Gert


    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

  16. Chemistry of marine ligands and siderophores. (United States)

    Vraspir, Julia M; Butler, Alison


    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.

  17. Coordinate unsaturation with fluorinated ligands

    Energy Technology Data Exchange (ETDEWEB)

    Rack, J.L.; Hurlburt, P.K.; Anderson, O.P.; Strauss, S.H. [Colorado State Univ., Ft. Collins, CO (United States)


    The preparation and characterization of Zn(OTeF{sub 5}){sub 2} has resulted in a model compound with which to explore the concept of coordinative unsaturation. The coordination of solvents of varying donicity and dielectric constant to the Zn(II) ions in Zn(OTeF{sub 5}){sub 2} was studied by vapor phase monometry, NMR and IR spectroscopy, conductimetry, and X-Ray crystallography. The structures of [Zn(C{sub 6}H{sub 5}NO{sub 2}){sub 2}(OTeF{sub 5})2]2 and Zn(C{sub 6}H{sub 5}NO{sub 2}){sub 3}(OTEF{sub 5}){sub 2} demonstrate the electronic flexibility of some weakly coordinating solvents in that nitrobenzene can function as either an {eta}{sup 1}O or {eta}{sup 2}O,O`-ligand. The dependence of the number of bound solvent molecules and the degree of OTeF{sub 5}{minus} dissociation on solvent donor number and dielectric constant will be presented.

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

    African Journals Online (AJOL)



    Jun 21, 2010 ... for designing the pharmacophore onto the set of 70 compounds of three different classes and two subclasses. ... More effective anticancer drug production with novel modes of action .... with Ligand Scout using default settings.

  19. Controlling Signal Transduction with Synthetic Ligands (United States)

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


    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.

  20. Organometallic chemistry of chiral diphosphazane ligands ...

    Indian Academy of Sciences (India)


    Organometallic chemistry of chiral diphosphazane ligands: Synthesis and structural characterisation. KANNAN RAGHURAMAN, SWADHIN K MANDAL,. T S VENKATAKRISHNAN, SETHARAMPATTU S. KRISHNAMURTHY* and MUNIRATHINAM NETHAJI. Department of Inorganic and Physical Chemistry, Indian Institute of ...

  1. EGFR Activation by Spatially Restricted Ligands

    National Research Council Canada - National Science Library

    Goodrich, Jennifer S


    ...) 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...

  2. Asymmetric hydrogenation using monodentate phosphoramidite ligands

    NARCIS (Netherlands)

    Minnaard, Adriaan J.; Feringa, Ben L.; Lefort, Laurent; De Vries, Johannes G.


    Monodentate phosphoramidites are excellent ligands for Rh-catalyzed asymmetric hydrogenations of substituted olefins. Enantioselectivities between 95 and 99% were obtained in the asymmetric hydrogenation of protected alpha- and beta-dehydroamino acids and esters, itaconic acid and esters, aromatic

  3. Ligand Interface Chemistry of Lead Chalcogenide Nanocrystals (United States)

    Liu, Kun; Bealing, Clive; Hennig, Richard; Hennig Group Team


    Lead chalcogenides nanocrystals (NCs) have shown promise in photovoltaic applications. Surface chemistry is one of the most important, yet least understood aspects of NC synthesis and functionalization controlling their properties. For example, an incomplete surface passivation could create trap states that enhance undesired exciton recombination. Clever choices of ligands ensure that neighboring NCs are electronically coupled while maintaining their quantum size effects. These two barriers limiting performance of NC solar cells illustrate the importance of fundamental studies for the interaction between ligands and NC surfaces. We use density functional theory to determine the binding sites and energies of ligands commonly used in NC synthesis and functionalization. Specifically we study amine-, carboxyl-, and thiol-ligands on different PbSe and PbS surfaces. For methylamine ligands we find a similar binding energy on the (100) and (111) facet while carboxylic acid ligands strongly prefer the (111) facet leading to different effective NC shapes. This work was supported in part by Award No. KUS-C1-018-02, made by King Abdullah University of Science and Technology (KAUST) and by the Energy Materials Center at Cornell (EMC2) funded by the U.S. Department of Energy under Award Number DE-SC0001086

  4. 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.

  5. Construction of dinuclear complexes using multidentate ligands

    Energy Technology Data Exchange (ETDEWEB)

    Sampson, C.L


    This work details the synthesis of novel copper(I), copper(II), nickel(II) and zinc(II) dinuclear complexes. Attempts have been made to control the co-ordination architectures of the metal centres by using bis-bidentate and tridentate chelating N,S- and N-donor ligands to generate dinuclear systems. The ligands were both symmetrically and asymmetrically disubstituted pyridazine-based and pyridine-based ligands consisting of a mixture of N-only and mixed N,S-donors. The study using the pyridazine-based ligands continues previous research in our group using 3,6-bis disubstituted pyridazine-based ligands to form complexes with copper(l) and copper(II). The pyridazine-based ligands have been seen to be bis-bidentate upon co-ordination of copper. The pyridazine-based ligands could be envisaged to generate dinuclear complexes by directly bridging between two metal ions. This study involved the formation of copper(l), nickel(II) and zinc(II) complexes with these ligands. The structural properties of two particular complexes have been explored using X-ray crystallography and spectroscopic techniques. Pyridine-based ligands have also been used previously in our group as tridentate chelating ligands. They have been seen to form dinuclear complexes with copper(I) and copper(II) when reacted with an additional bridging ligand e.g. 4,4'-bipyridine. This provides an alternative method for generating dinuclear complexes. Chapter 1 presents an introduction to the area of supramolecular chemistry from which we can learn the principles of polymer formation and them 'in reverse' to generate discrete dinuclear systems. Chapter 2 details the synthesis of the pyridazine and pyridine-based ligands including a detailed nmr study of the ligands. Since the ligands were synthesised using cyclic thioamides as terminal groups it has been found that thiol-thione tautomerisation occurred during synthesis giving rise to two possible ligand conformations. The nmr study has been used

  6. Semiconductor Quantum Dots with Photoresponsive Ligands. (United States)

    Sansalone, Lorenzo; Tang, Sicheng; Zhang, Yang; Thapaliya, Ek Raj; Raymo, Françisco M; Garcia-Amorós, Jaume


    Photochromic or photocaged ligands can be anchored to the outer shell of semiconductor quantum dots in order to control the photophysical properties of these inorganic nanocrystals with optical stimulations. One of the two interconvertible states of the photoresponsive ligands can be designed to accept either an electron or energy from the excited quantum dots and quench their luminescence. Under these conditions, the reversible transformations of photochromic ligands or the irreversible cleavage of photocaged counterparts translates into the possibility to switch luminescence with external control. As an alternative to regulating the photophysics of a quantum dot via the photochemistry of its ligands, the photochemistry of the latter can be controlled by relying on the photophysics of the former. The transfer of excitation energy from a quantum dot to a photocaged ligand populates the excited state of the species adsorbed on the nanocrystal to induce a photochemical reaction. This mechanism, in conjunction with the large two-photon absorption cross section of quantum dots, can be exploited to release nitric oxide or to generate singlet oxygen under near-infrared irradiation. Thus, the combination of semiconductor quantum dots and photoresponsive ligands offers the opportunity to assemble nanostructured constructs with specific functions on the basis of electron or energy transfer processes. The photoswitchable luminescence and ability to photoinduce the release of reactive chemicals, associated with the resulting systems, can be particularly valuable in biomedical research and can, ultimately, lead to the realization of imaging probes for diagnostic applications as well as to therapeutic agents for the treatment of cancer.

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

    KAUST Repository

    Chen, Peng


    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.

  8. Characterization of quinoxolinol salen ligands as selective ligands for chemosensors for uranium

    Energy Technology Data Exchange (ETDEWEB)

    DeVore, Michael A. II; Kerns, Spencer A.; Gorden, Anne E.V. [Department of Chemistry and Biochemistry, Auburn University, Auburn, AL (United States)


    Quinoxalinol salen ligands have been characterized as selective ligands for the rapid identification of uranyl. The absorption maximum of ligand 1 presented a hypsochromic (blue) shift with the addition of UO{sub 2}{sup 2+} (as the acetate salt), and a bathochromic (red) shift in the presence of Cu{sup 2+} or Co{sup 2+} acetate salts, resulting in distinct, visible color changes for all three metal ions. The absorption maximum of ligand 2 was not observed to change with the addition of UO{sub 2}{sup 2+}; however, it does present a bathochromic shift with the addition of Cu{sup 2+}, and a hypsochromic shift with Co{sup 2+} added. Using TDDFT calculations, it was demonstrated that the hypsochromic shift for UO{sub 2}{sup 2+} ion complexation with ligand 1 is caused by a ligand-to-metal charge transfer, while the bathochromic shift observed with Cu{sup 2+} ion addition was caused by a metal-to-ligand charge transfer. Finally, it was found that the addition of Cu{sup 2+} (as metal salts) to either ligand resulted in rapid, complete quenching of the ligand fluorescence. (Copyright copyright 2015 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  9. Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand.

    Directory of Open Access Journals (Sweden)

    Samuel DeLuca

    Full Text Available RosettaLigand has been successfully used to predict binding poses in protein-small molecule complexes. However, the RosettaLigand docking protocol is comparatively slow in identifying an initial starting pose for the small molecule (ligand making it unfeasible for use in virtual High Throughput Screening (vHTS. To overcome this limitation, we developed a new sampling approach for placing the ligand in the protein binding site during the initial 'low-resolution' docking step. It combines the translational and rotational adjustments to the ligand pose in a single transformation step. The new algorithm is both more accurate and more time-efficient. The docking success rate is improved by 10-15% in a benchmark set of 43 protein/ligand complexes, reducing the number of models that typically need to be generated from 1000 to 150. The average time to generate a model is reduced from 50 seconds to 10 seconds. As a result we observe an effective 30-fold speed increase, making RosettaLigand appropriate for docking medium sized ligand libraries. We demonstrate that this improved initial placement of the ligand is critical for successful prediction of an accurate binding position in the 'high-resolution' full atom refinement step.

  10. Copolymerization of Carbon Dioxide with Epoxides Catalyzed by Structurally Well-Characterized Dinickel Bis(benzotriazole iminophenolate) Complexes: Influence of Carboxylate Ligands on the Catalytic Performance. (United States)

    Huang, Li-Shin; Tsai, Chen-Yen; Chuang, Hui-Ju; Ko, Bao-Tsan


    A series of structurally well-defined dinickel carboxylate complexes based on the (R)BiIBTP derivatives [(R)BiIBTP = bis(benzotriazole iminophenolate), where R = 3C for the propyl-bridged backbone and 5C for the 2,2-dimethyl-1,3-propyl-bridged backbone] were synthesized and developed for copolymerization of CO2 and epoxides. The one-pot reactions of nickel perchlorate with the (R)BiIBTP-H2 proligands and an appropriate amount of carboxylic acid derivatives (CF3COOH or 4-X-C6H4CO2H; X = H, CF3, OMe) upon the addition of triethylamine in refluxing methanol (MeOH) afforded dinuclear nickel dicarboxylate complexes, which could be formulated as either [((R)BiIBTP)Ni2(O2CCF3)2] (1 and 2) or [((R)BiIBTP)Ni2(O2CC6H4-4-X)2] (3-7). The dinickel monobenzoate complexes [((R)BiIBTP)Ni2(O2CPh)(ClO4)(H2O)] [R = 3C (8) and 5C (9)] were prepared by using a similar synthetic route in tetrahydrofuran under reflux with a ligand precursor to metal salt to benzoic acid ratio of 1:2:1 in the presence of NEt3. Recrystallization of neutral nickel perchlorate complex 8 in a saturated MeOH or ethanol (EtOH) solution gave ionic and alcohol-solvated monobenzoate bimetallic analogues [((3C)BiIBTP)Ni2(O2CPh)(S)2]ClO4, where S = MeOH (10) and EtOH (11). Single-crystal X-ray crystallography of dinickel analogues 1-11 indicates that the BiIBTP scaffold performs as a N,O,N,N,O,N-hexadentate ligand to chelate two Ni atoms, and the ancillary carboxylate group adopts a bridging bidentate bonding mode. Catalysis for copolymerization of carbon dioxide (CO2) with cyclohexene oxide (CHO) by complexes 1-9 was systematically investigated, and the influence of carboxylate ligands on the catalytic behavior was also studied. Trifluoroacetate-ligated dinickel complex 1 efficiently catalyzed CO2 and CHO with a high turnover frequency (>430 h(-1)) in a controlled fashion, generating perfectly alternating poly(cyclohexenecarbonate) with large molecular weight (Mn > 50000 g/mol). In addition to CO2/CHO

  11. Synthesis and characterization of mixed ligand chiral nanoclusters

    KAUST Repository

    Guven, Zekiye P.


    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Varga, J.M.; Fritsch, P.


    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.

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

    KAUST Repository

    Li, Huaifeng


    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.

  14. PPARα Ligands as Antitumorigenic and Antiangiogenic Agents

    Directory of Open Access Journals (Sweden)

    Ambra Pozzi


    Full Text Available Peroxisome proliferator-activated receptors (PPARs belong to the nuclear receptor family of ligand-activated transcription factors. This subfamily is composed of three members—PPARα, PPARδ, and PPARγ—that differ in their cell and tissue distribution as well as in their target genes. PPARα is abundantly expressed in liver, brown adipose tissue, kidney, intestine, heart, and skeletal muscle; and its ligands have been used to treat diseases such as obesity and diabetes. The recent finding that members of the PPAR family, including the PPARα, are expressed by tumor and endothelial cells together with the observation that PPAR ligands regulate cell growth, survival, migration, and invasion, suggested that PPARs also play a role in cancer. In this review, we focus on the contribution of PPARα to tumor and endothelial cell functions and provide compelling evidence that PPARα can be viewed as a new class of ligand activated tumor “suppressor” gene with antiangiogenic and antitumorigenic activities. Given that PPAR ligands are currently used in medicine as hypolipidemic drugs with excellent tolerance and limited toxicity, PPARα activation might offer a novel and potentially low-toxic approach for the treatment of tumor-associated angiogenesis and cancer.

  15. A screening cascade to identify ERβ ligands. (United States)

    Filgueira, Carly S; Benod, Cindy; Lou, Xiaohua; Gunamalai, Prem S; Villagomez, Rosa A; Strom, Anders; Gustafsson, Jan-Åke; Berkenstam, Anders L; Webb, Paul


    The establishment of effective high throughput screening cascades to identify nuclear receptor (NR) ligands that will trigger defined, therapeutically useful sets of NR activities is of considerable importance. Repositioning of existing approved drugs with known side effect profiles can provide advantages because de novo drug design suffers from high developmental failure rates and undesirable side effects which have dramatically increased costs. Ligands that target estrogen receptor β (ERβ) could be useful in a variety of diseases ranging from cancer to neurological to cardiovascular disorders. In this context, it is important to minimize cross-reactivity with ERα, which has been shown to trigger increased rates of several types of cancer. Because of high sequence similarities between the ligand binding domains of ERα and ERβ, preferentially targeting one subtype can prove challenging. Here, we describe a sequential ligand screening approach comprised of complementary in-house assays to identify small molecules that are selective for ERβ. Methods include differential scanning fluorimetry, fluorescence polarization and a GAL4 transactivation assay. We used this strategy to screen several commercially-available chemical libraries, identifying thirty ERβ binders that were examined for their selectivity for ERβ versus ERα, and tested the effects of selected ligands in a prostate cancer cell proliferation assay. We suggest that this approach could be used to rapidly identify candidates for drug repurposing.

  16. Tris(pyridinealdoximato)metal complexes as ligands for the synthesis of asymmetric heterodinuclear Cr(III)M species [M = Zn(II), Cu(II), Ni(II), Fe(II), Mn(II), Cr(II), Co(III)]: a magneto-structural study. (United States)

    Ross, S; Weyhermüller, T; Bill, E; Wieghardt, K; Chaudhuri, P


    Reactions of the LCr(III) unit with an in situ prepared M(PyA)(3)(n-) ion, where L represents 1,4,7-trimethyl-1,4,7-triazacyclononane and PyA(-) is the monoanion of pyridine-2-aldoxime, yield heterodinuclear complexes of general formula [LCr(III)(PyA)(3)M](2+/3+) as perchlorate salts, where M = Cr(II) (1), Mn(II) (2), low-spin Fe(II) (3), Ni(II) (4), Cu(II) (5), Zn(II) (6), and low-spin Co(III) (7). These compounds contain three oximato anions as bridging ligands. The hexadentate ligand with the identical donor atoms, tris(2-aldoximato-6-pyridyl)phosphine, P(PyA)(3), has been employed to prepare a second Cr(III)Ni(II) species 8, whose magnetic properties differ significantly from those of 4. Complexes 1-8 have been characterized on the basis of elemental analysis, mass spectrometry, IR, UV-vis, Mössbauer, and EPR spectroscopies, and variable-temperature (2-295 K) magnetic susceptibility measurements. They are isostructural in the sense that they all contain a terminal Cr(III) ion in a distorted octahedral environment, CrN(3)O(3), and a second six-coordinated metal ion M in a mostly trigonal prismatic MN(6) geometry. The crystal structures of the perchlorate salts of 2-5, 7, and 8 have been determined by X-ray crystallography at 100 K. The structures consist of mixed-metal Cr(III)M(II) and Cr(III)Co(III) complexes with a geometry in which two pseudooctahedral polyhedra are joined by three oximato (=N-O(-)) groups, with an intramolecular Cr.M(Co) distance in the range of 3.4-3.7 A. The cyclic voltammograms of the complexes reveal ligand oxidation and reduction processes, and in addition, metal-centered oxidation processes have been observed. X-band EPR spectroscopy has been used to establish the electronic ground state of the heterodinuclear complexes. Analysis of the susceptibility data indicates the presence of weak exchange interactions, both ferro- and antiferromagnetic, between the paramagnetic centers. A qualitative rationale on the basis of the Goodenough

  17. Effects of PPARγ Ligands on Leukemia

    Directory of Open Access Journals (Sweden)

    Yoko Tabe


    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.

  18. Flexible Ligand Docking Using Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Thomsen, Rene


    The docking of ligands to proteins can be formulated as a computational problem where the task is to find the most favorable energetic conformation among the large space of possible protein–ligand complexes. Stochastic search methods such as evolutionary algorithms (EAs) can be used to sample large...... search spaces effectively and is one of the commonly used methods for flexible ligand docking. During the last decade, several EAs using different variation operators have been introduced, such as the ones provided with the AutoDock program. In this paper we evaluate the performance of different EA...... settings such as choice of variation operators, population size, and usage of local search. The comparison is performed on a suite of six docking problems previously used to evaluate the performance of search algorithms provided with the AutoDock program package. The results from our investigation confirm...

  19. Isotherm of ligand adsorption on DNA at multiplicative noise. (United States)

    Arakelyan, Valeri; Harutyunyan, Sos; Andriasyan, Vardan; Arakelyan, Hakob


    Fluctuations of the number of ligands adsorbed on macromolecules are considered in the case when the number of ligands in the solution fluctuates under the action of fluctuations of the external medium (external noise). For the case of small filling, the multiplicative type of stochastic differential equation is obtained, describing the time variation of the number of ligands adsorbed on macromolecules. The isotherm of adsorption of ligands on DNA is obtained. It is shown that at small ligand concentrations, for some relations between adsorption parameters and the intensity of the external noise, no macromolecule adsorption of ligands takes place.

  20. Ligand Exchange Kinetics of Environmentally Relevant Metals

    Energy Technology Data Exchange (ETDEWEB)

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


    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.

  1. Supramolecular architectures constructed using angular bipyridyl ligands

    CERN Document Server

    Barnett, S A


    This work details the synthesis and characterization of a series of coordination frameworks that are formed using bidentate angular N-donor ligands. Pyrimidine was reacted with metal(ll) nitrate salts. Reactions using Cd(NO sub 3) sub 2 receive particular focus and the analogous reactions using the linear ligand, pyrazine, were studied for comparison. In all cases, two-dimensional coordination networks were prepared. Structural diversity is observed for the Cd(ll) centres including metal-nitrate bridging. In contrast, first row transition metal nitrates form isostructural one-dimensional chains with only the bridging N-donor ligands generating polymeric propagation. The angular ligand, 2,4-bis(4-pyridyl)-1,3,5-triazine (dpt), was reacted with Cd(NO sub 3) sub 2 and Zn(NO sub 3) sub 2. Whereas Zn(NO sub 3) sub 2 compounds exhibit solvent mediated polymorphism, a range of structures were obtained for the reactions with Cd(NO sub 3) sub 2 , including the first example of a doubly parallel interpenetrated 4.8 sup...

  2. Flexible Ligand Docking Using Differential Evolution

    DEFF Research Database (Denmark)

    Thomsen, René


    Molecular docking of biomolecules is becoming an increasingly important part in the process of developing new drugs, as well as searching compound databases for promising drug candidates. The docking of ligands to proteins can be formulated as an optimization problem where the task is to find...

  3. A versatile dinucleating ligand containing sulfonamide groups

    DEFF Research Database (Denmark)

    Sundberg, Jonas; Witt, Hannes; Cameron, Lisa


    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...

  4. Noncalcemic actions of vitamin D receptor ligands. (United States)

    Nagpal, Sunil; Na, Songqing; Rathnachalam, Radhakrishnan


    1alpha,25-Dihydroxyvitamin D(3) [1,25-(OH)(2)D(3)], the active metabolite of vitamin D(3), is known for the maintenance of mineral homeostasis and normal skeletal architecture. However, apart from these traditional calcium-related actions, 1,25-(OH)(2)D(3) and its synthetic analogs are being increasingly recognized for their potent antiproliferative, prodifferentiative, and immunomodulatory activities. These actions of 1,25-(OH)(2)D(3) are mediated through vitamin D receptor (VDR), which belongs to the superfamily of steroid/thyroid hormone nuclear receptors. Physiological and pharmacological actions of 1,25-(OH)(2)D(3) in various systems, along with the detection of VDR in target cells, have indicated potential therapeutic applications of VDR ligands in inflammation (rheumatoid arthritis, psoriatic arthritis), dermatological indications (psoriasis, actinic keratosis, seborrheic dermatitis, photoaging), osteoporosis (postmenopausal and steroid-induced osteoporosis), cancers (prostate, colon, breast, myelodysplasia, leukemia, head and neck squamous cell carcinoma, and basal cell carcinoma), secondary hyperparathyroidism, and autoimmune diseases (systemic lupus erythematosus, type I diabetes, multiple sclerosis, and organ transplantation). As a result, VDR ligands have been developed for the treatment of psoriasis, osteoporosis, and secondary hyperparathyroidism. Furthermore, encouraging results have been obtained with VDR ligands in clinical trials of prostate cancer and hepatocellular carcinoma. This review deals with the molecular aspects of noncalcemic actions of vitamin D analogs that account for the efficacy of VDR ligands in the above-mentioned indications.


    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.

  6. Ligand sphere conversions in terminal carbide complexes

    DEFF Research Database (Denmark)

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


    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...... demonstrates that details of the coordination geometry affect the carbide chemical shift equally as much as variations in the nature of the auxiliary ligands. Furthermore, the kinetics of formation of the sqaure pyramidal dicyano complex, trans-[RuC(CN)2(PCy3)2], from RuC has been examined and the reaction...... found to be quite sluggish and of first order in both RuC and cyanide with a rate constant of k = 0.0104(6) M–1 s–1. Further reaction with cyanide leads to loss of the carbide ligand and formation of trans-[Ru(CN)4(PCy3)2]2–, which was isolated and structurally characterized as its PPh4+ salt....

  7. 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 ...

  8. Unexpected reversible pyrazine based methylation in a Ru(II) complex bearing a pyrazin-2’-yl-1,2,4-triazolato ligand and its effect on acid/base and photophysical properties

    NARCIS (Netherlands)

    Brennan, Claire; Draksharapu, Apparao; Browne, Wesley R.; McGarvey, John J.; Vos, Johannes G.; Pryce, Mary T.


    The regioselective methylation of a ruthenium polypyridyl complex bearing both a 1,2,4-triazolato and a pyrazine moiety is reported. In contrast to previous studies in which methylation of the 1,2,4-triazolato ring was observed, in the present system methylation takes place exclusively at the

  9. Ammonia formation by metal-ligand cooperative hydrogenolysis of a nitrido ligand (United States)

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


    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.

  10. Quantum.Ligand.Dock: protein-ligand docking with quantum entanglement refinement on a GPU system. (United States)

    Kantardjiev, Alexander A


    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

  11. 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, ...

  12. Fluorescent GPCR ligands as new tools in pharmacology. (United States)

    Kuder, Kamil; Kieć-Kononowicz, Katarzyna


    The expansion of fluorescent techniques for studying the ligand-receptor interaction resulted in a burst of the novel fluorescent ligands development. The discovery of the ligand, that is of high affinity to the receptor and whose localization could be easily visualized, even on the single cell level, gave the researchers a strong impulse to investigate that field of GPCR ligands. Moreover, paying attention to the "non pharmacological" advantages of these ligands, as well as the techniques to be used, fluorescent ligands are becoming treated more seriously, as the ligands themselves, and as novel, useful tools for studying GPCRs. Herein, we review results described in the literature, starting from the year 2000, in the field of the fluorescent GPCR small, non-peptide ligands according to the affinity to the selected receptors (histamine, adenosine, adrenergic, cannabinoid, muscarinie, neuropeptide Y and serotonine) as well as the fluorophores that have been used to tag the molecules.

  13. Ligand-Mediated Coating of Liposomes with Human Serum Albumin. (United States)

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


    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.

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


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


    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...

  15. AutoSite: an automated approach for pseudo-ligands prediction—from ligand-binding sites identification to predicting key ligand atoms (United States)

    Ravindranath, Pradeep Anand; Sanner, Michel F.


    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: Contact: Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27354702

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

    DEFF Research Database (Denmark)

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


    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....

  17. New mixed ligand complexes of ruthenium (II) that incorporate a ...

    Indian Academy of Sciences (India)

    New mixed ligand complexes of ruthenium(II) that incorporate a modified phenanthroline ligand: Synthesis, spectral characterization and DNA binding. S Murali C V ... Fulltext. Click here to view fulltext PDF ... Ruthenium(II) complexes; modified phenanthroline ligand; spectroscopy; DNA binding; fluorescence enhancement.

  18. Novel peptide ligand with high binding capacity for antibody purification

    DEFF Research Database (Denmark)

    Lund, L. N.; Gustavsson, P. E.; Michael, R.


    ligands have an advantage over biological ligands; they are cheaper to produce, ligand leakage by enzymatic degradation is either eliminated or significantly reduced, and they can in general better withstand cleaning in place (CIP) conditions such as 0.1 M NaOH. Here, we present a novel synthetic peptide...


    African Journals Online (AJOL)

    The successive binding energies of up to six water ligands to ferric ion and the reduction in the gross binding energies by ligand-ligand repulsion are determined by electrostatic interaction. The gross binding energy is found to be both geometry and coordination nuitber dependent: whereas it increases with number of ...

  20. Mechanics, thermodynamics, and kinetics of ligand binding to biopolymers. (United States)

    Jarillo, Javier; Morín, José A; Beltrán-Heredia, Elena; Villaluenga, Juan P G; Ibarra, Borja; Cao, Francisco J


    Ligands binding to polymers regulate polymer functions by changing their physical and chemical properties. This ligand regulation plays a key role in many biological processes. We propose here a model to explain the mechanical, thermodynamic, and kinetic properties of the process of binding of small ligands to long biopolymers. These properties can now be measured at the single molecule level using force spectroscopy techniques. Our model performs an effective decomposition of the ligand-polymer system on its covered and uncovered regions, showing that the elastic properties of the ligand-polymer depend explicitly on the ligand coverage of the polymer (i.e., the fraction of the polymer covered by the ligand). The equilibrium coverage that minimizes the free energy of the ligand-polymer system is computed as a function of the applied force. We show how ligands tune the mechanical properties of a polymer, in particular its length and stiffness, in a force dependent manner. In addition, it is shown how ligand binding can be regulated applying mechanical tension on the polymer. Moreover, the binding kinetics study shows that, in the case where the ligand binds and organizes the polymer in different modes, the binding process can present transient shortening or lengthening of the polymer, caused by changes in the relative coverage by the different ligand modes. Our model will be useful to understand ligand-binding regulation of biological processes, such as the metabolism of nucleic acid. In particular, this model allows estimating the coverage fraction and the ligand mode characteristics from the force extension curves of a ligand-polymer system.

  1. Mechanics, thermodynamics, and kinetics of ligand binding to biopolymers.

    Directory of Open Access Journals (Sweden)

    Javier Jarillo

    Full Text Available Ligands binding to polymers regulate polymer functions by changing their physical and chemical properties. This ligand regulation plays a key role in many biological processes. We propose here a model to explain the mechanical, thermodynamic, and kinetic properties of the process of binding of small ligands to long biopolymers. These properties can now be measured at the single molecule level using force spectroscopy techniques. Our model performs an effective decomposition of the ligand-polymer system on its covered and uncovered regions, showing that the elastic properties of the ligand-polymer depend explicitly on the ligand coverage of the polymer (i.e., the fraction of the polymer covered by the ligand. The equilibrium coverage that minimizes the free energy of the ligand-polymer system is computed as a function of the applied force. We show how ligands tune the mechanical properties of a polymer, in particular its length and stiffness, in a force dependent manner. In addition, it is shown how ligand binding can be regulated applying mechanical tension on the polymer. Moreover, the binding kinetics study shows that, in the case where the ligand binds and organizes the polymer in different modes, the binding process can present transient shortening or lengthening of the polymer, caused by changes in the relative coverage by the different ligand modes. Our model will be useful to understand ligand-binding regulation of biological processes, such as the metabolism of nucleic acid. In particular, this model allows estimating the coverage fraction and the ligand mode characteristics from the force extension curves of a ligand-polymer system.

  2. A ligand's view of target similarity

    DEFF Research Database (Denmark)

    Garland, Stephen L; Gloriam, David E


    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......-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......, 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....

  3. Sigma-2 receptor ligands QSAR model dataset

    Directory of Open Access Journals (Sweden)

    Antonio Rescifina


    Full Text Available The data have been obtained from the Sigma-2 Receptor Selective Ligands Database (S2RSLDB and refined according to the QSAR requirements. These data provide information about a set of 548 Sigma-2 (σ2 receptor ligands selective over Sigma-1 (σ1 receptor. The development of the QSAR model has been undertaken with the use of CORAL software using SMILES, molecular graphs and hybrid descriptors (SMILES and graph together. Data here reported include the regression for σ2 receptor pKi QSAR models. The QSAR model was also employed to predict the σ2 receptor pKi values of the FDA approved drugs that are herewith included.

  4. Hydrogen bonding penalty upon ligand binding.

    Directory of Open Access Journals (Sweden)

    Hongtao Zhao

    Full Text Available Ligand binding involves breakage of hydrogen bonds with water molecules and formation of new hydrogen bonds between protein and ligand. In this work, the change of hydrogen bonding energy in the binding process, namely hydrogen bonding penalty, is evaluated with a new method. The hydrogen bonding penalty can not only be used to filter unrealistic poses in docking, but also improve the accuracy of binding energy calculation. A new model integrated with hydrogen bonding penalty for free energy calculation gives a root mean square error of 0.7 kcal/mol on 74 inhibitors in the training set and of 1.1 kcal/mol on 64 inhibitors in the test set. Moreover, an application of hydrogen bonding penalty into a high throughput docking campaign for EphB4 inhibitors is presented, and remarkably, three novel scaffolds are discovered out of seven tested. The binding affinity and ligand efficiency of the most potent compound is about 300 nM and 0.35 kcal/mol per non-hydrogen atom, respectively.

  5. Ligand mediated evolution of size dependent magnetism in cobalt nanoclusters. (United States)

    Hartmann, Michael J; Millstone, Jill E; Häkkinen, Hannu


    We use density functional theory to model the impact of a ligand shell on the magnetic properties of CoN (15 ≤ N ≤ 55) nanoclusters. We study three different ligand shells on each nanocluster core size, each known to have different electronic interactions with the surface: pure Cl ligand shells (X-type), pure PH3 ligand shells (L-type), and two component ligand shells with mixtures of Cl and PH3 ligands. The simulations show that the identity, arrangement, and total coverage of the ligand shell controls the distribution of local magnetic moments across the CoN core. On the surface of an unpassivated CoN nanocluster, the Co-Co coordination number (CN) is known to determine the local magnetic moments. Upon the introduction of a ligand, the Co-Co CN remains important, however the nature of the metal-ligand bond changes the extent to which increasing Co-Co CN quenches magnetism. Further, we identify an additional and significant long-range impact on local magnetic moments (LMM) from the PH3 ligand shells. Thus, we establish important design principles of magnetic nanoclusters, where ligand shell chemistry mediates the distribution of LMMs across a CoNLM nanocluster, allowing a route to rational design of specific magnetic properties.

  6. Separation of tryptophan enantiomers by ligand-exchange chromatography with novel chiral ionic liquids ligand. (United States)

    Qing, Haiqun; Jiang, Xinyu; Yu, Jingang


    Chiral ionic liquids (CILs) with amino acids as cations have been applied as novel chiral ligands coordinated with Cu(2+) to separate tryptophan enantiomers in ligand exchange chromatography. Four kinds of amino acid ionic liquids, including [L-Pro][CF3COO], [L-Pro][NO3], [L-Pro]2[SO4], and [L-Phe][CF3COO] were successfully synthesized and used for separation of tryptophan enantiomers. To optimize the separation conditions, [L-Pro][CF3COO] was selected as the model ligand. Some factors influencing the efficiency of chiral separation, such as copper ion concentration, CILs concentration, methanol ratio (methanol/H2O, v/v), and pH, were investigated. The obtained optimal separation conditions were as follows: 8.0 mmol/L Cu(OAc)2, 4.0 mmol/L [L-Pro][CF3COO], and 20% (v/v) methanol at pH 3.6. Under the optimum conditions, acceptable enantioseparation of tryptophan enantiomers could be observed with a resolution of 1.89. The results demonstrate the good applicability of CILs with amino acids as cations for chiral separation. Furthermore, a comparative study was also conducted for exploring the mechanism of the CILs as new ligands in ligand exchange chromatography. © 2014 Wiley Periodicals, Inc.

  7. Amino acid ionic liquids as chiral ligands in ligand-exchange chiral separations. (United States)

    Liu, Qian; Wu, Kangkang; Tang, Fei; Yao, Lihua; Yang, Fei; Nie, Zhou; Yao, Shouzhuo


    Recently, amino acid ionic liquids (AAILs) have attracted much research interest. In this paper, we present the first application of AAILs in chiral separation based on the chiral ligand exchange principle. By using 1-alkyl-3-methylimidazolium L-proline (L-Pro) as a chiral ligand coordinated with copper(II), four pairs of underivatized amino acid enantiomers-dl-phenylalanine (dl-Phe), dl-histidine (dl-His), dl-tryptophane (dl-Trp), and dl-tyrosine (dl-Tyr)-were successfully separated in two major chiral separation techniques, HPLC and capillary electrophoresis (CE), with higher enantioselectivity than conventionally used amino acid ligands (resolution (R(s))=3.26-10.81 for HPLC; R(s)=1.34-4.27 for CE). Interestingly, increasing the alkyl chain length of the AAIL cation remarkably enhanced the enantioselectivity. It was inferred that the alkylmethylimidazolium cations and L-Pro form ion pairs on the surface of the stationary phase or on the inner surface of the capillary. The ternary copper complexes with L-Pro are consequently attached to the support surface, thus inducing an ion-exchange type of retention for the dl-enantiomers. Therefore, the AAIL cation plays an essential role in the separation. This work demonstrates that AAILs are good alternatives to conventional amino acid ligands for ligand-exchange-based chiral separation. It also reveals the tremendous application potential of this new type of task-specific ILs.

  8. ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites. (United States)

    Konc, Janez; Janežič, Dušanka


    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 © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. Characterizing common substructures of ligands for GPCR protein subfamilies. (United States)

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


    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.

  10. (Ligand intermediates in metal-catalyzed reactions)

    Energy Technology Data Exchange (ETDEWEB)


    This report consists of sections on sigma bond complexes of alkenes, a new carbon-hydrogen bond activation reaction of alkene complexes, carbon-hydrogen bond migrations in alkylidene complexes, carbon- hydrogen bond migrations in alkyne complexes, synthesis, structure and reactivity of C{sub x} complexes, synthesis and reactivity of alcohol and ether complexes, new catalysts for the epimerization of secondary alcohols; carbon-hydrogen bond activation in alkoxide complexes, pi/sigma equilibria in metal/O=CXX' complexes, and other hydrocarbon ligands; miscellaneous.(WET)

  11. Computer-aided design of GPCR ligands. (United States)

    Gutiérrez-de-Terán, Hugo; Keränen, Henrik; Azuaje, Jhonny; Rodríguez, David; Åqvist, Johan; Sotelo, Eddy


    The recent availability of several GPCR crystal structures now contributes decisively to the perspective of structure-based ligand design. In this context, computational approaches are extremely helpful, particularly if properly integrated in drug design projects with cooperation between computational and medicinal chemistry teams. Here, we present the pipelines used in one such project, devoted to the design of novel potent and selective antagonists for the different adenosine receptors. The details of the computational strategies are described, and particular attention is given to explain how these procedures can effectively guide the synthesis of novel chemical entities.

  12. Increased accuracy of ligand sensing by receptor internalization (United States)

    Aquino, Gerardo; Endres, Robert G.


    Many types of cells can sense external ligand concentrations with cell-surface receptors at extremely high accuracy. Interestingly, ligand-bound receptors are often internalized, a process also known as receptor-mediated endocytosis. While internalization is involved in a vast number of important functions for the life of a cell, it was recently also suggested to increase the accuracy of sensing ligand as the overcounting of the same ligand molecules is reduced. Here we show, by extending simple ligand-receptor models to out-of-equilibrium thermodynamics, that internalization increases the accuracy with which cells can measure ligand concentrations in the external environment. Comparison with experimental rates of real receptors demonstrates that our model has indeed biological significance.

  13. Ligands of Therapeutic Utility for the Liver X Receptors

    Directory of Open Access Journals (Sweden)

    Rajesh Komati


    Full Text Available Liver X receptors (LXRs have been increasingly recognized as a potential therapeutic target to treat pathological conditions ranging from vascular and metabolic diseases, neurological degeneration, to cancers that are driven by lipid metabolism. Amidst intensifying efforts to discover ligands that act through LXRs to achieve the sought-after pharmacological outcomes, several lead compounds are already being tested in clinical trials for a variety of disease interventions. While more potent and selective LXR ligands continue to emerge from screening of small molecule libraries, rational design, and empirical medicinal chemistry approaches, challenges remain in minimizing undesirable effects of LXR activation on lipid metabolism. This review provides a summary of known endogenous, naturally occurring, and synthetic ligands. The review also offers considerations from a molecular modeling perspective with which to design more specific LXRβ ligands based on the interaction energies of ligands and the important amino acid residues in the LXRβ ligand binding domain.

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

    Directory of Open Access Journals (Sweden)

    Sangmin Seo


    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.

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

    KAUST Repository

    Bealing, Clive R.


    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.

  16. 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.


    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

  17. Ligand binding by the tandem glycine riboswitch depends on aptamer dimerization but not double ligand occupancy (United States)

    Ruff, Karen M.


    The glycine riboswitch predominantly exists as a tandem structure, with two adjacent, homologous ligand-binding domains (aptamers), followed by a single expression platform. The recent identification of a leader helix, the inclusion of which eliminates cooperativity between the aptamers, has reopened the debate over the purpose of the tandem structure of the glycine riboswitch. An equilibrium dialysis-based assay was combined with binding-site mutations to monitor glycine binding in each ligand-binding site independently to understand the role of each aptamer in glycine binding and riboswitch tertiary interactions. A series of mutations disrupting the dimer interface was used to probe how dimerization impacts ligand binding by the tandem glycine riboswitch. While the wild-type tandem riboswitch binds two glycine equivalents, one for each aptamer, both individual aptamers are capable of binding glycine when the other aptamer is unoccupied. Intriguingly, glycine binding by aptamer-1 is more sensitive to dimerization than glycine binding by aptamer-2 in the context of the tandem riboswitch. However, monomeric aptamer-2 shows dramatically weakened glycine-binding affinity. In addition, dimerization of the two aptamers in trans is dependent on glycine binding in at least one aptamer. We propose a revised model for tandem riboswitch function that is consistent with these results, wherein ligand binding in aptamer-1 is linked to aptamer dimerization and stabilizes the P1 stem of aptamer-2, which controls the expression platform. PMID:25246650

  18. Does the ligand-biopolymer equilibrium binding constant depend on the number of bound ligands? (United States)

    Beshnova, Daria A; Lantushenko, Anastasia O; Evstigneev, Maxim P


    Conventional methods, such as Scatchard or McGhee-von Hippel analyses, used to treat ligand-biopolymer interactions, indirectly make the assumption that the microscopic binding constant is independent of the number of ligands, i, already bound to the biopolymer. Recent results on the aggregation of aromatic molecules (Beshnova et al., J Chem Phys 2009, 130, 165105) indicated that the equilibrium constant of self-association depends intrinsically on the number of molecules in an aggregate due to loss of translational and rotational degrees of freedom on formation of the complex. The influence of these factors on the equilibrium binding constant for ligand-biopolymer complexation was analyzed in this work. It was shown that under the conditions of binding of "small" molecules, these factors can effectively be ignored and, hence, do not provide any hidden systematic error in such widely-used approaches, such as the Scatchard or McGhee-von Hippel methods for analyzing ligand-biopolymer complexation. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 932-935, 2010.

  19. New chiral ligand exchange capillary electrophoresis system with chiral amino amide ionic liquids as ligands. (United States)

    Jiang, Junfang; Mu, Xiaoyu; Qiao, Juan; Su, Yuan; Qi, Li


    Using chiral amino amide ionic liquids as the ligands, a new chiral ligand exchange capillary electrophoresis method with Cu(II) as the central ion was constructed for enantioseparation of labeled D,L-amino acids. The effects of key parameters, including pH value of the running buffer, the ratio of Cu(II) to chiral amino amide ionic liquids, the concentration of complexes based on Cu(II)-chiral amino amide ionic liquids were investigated. It has been observed that eight pairs of labeled D,L-amino acids could be baseline-separated with a running buffer of 15.0mM ammonium acetate, 10.0mM Cu(II) and 20.0mML-phenylalaninamide based ionic liquid at pH 5.0. The quantitation of D,L-amino acids was conducted and good linearity (r2 ≥ 0.964) was obtained. Furthermore, an assay for determining the enantiomeric purity of D,L-amino acids was developed and the possible enantiorecognition mechanism was discussed briefly. The results indicated that the chiral amino amide ionic liquids could play the role of ligands in chiral ligand exchange capillary electrophoresis system and exhibit great potential in chiral analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Quasielastic neutron scattering study of POSS ligand dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Jalarvo, Niina H [ORNL; Tyagi, Madhusudan [NIST Center for Neutron Research (NCRN), Gaithersburg, MD; Crawford, Michael [DuPont Experimental Station


    Polyoligosilsesquioxanes are molecules having cage-like structures composed of silicon and oxygen. These molecules can have a wide variety of functional ligands attached to them. Depending on the nature of the ligand, interesting properties and applications are found. In this work we present results from quasielastic neutron scattering measurements of four different POSS molecules that illustrate the presence of strong coupling between the ligand dynamics and the POSS crystal structures.

  1. Do organic ligands affect calcite dissolution rates? (United States)

    Oelkers, Eric H.; Golubev, Sergey V.; Pokrovsky, Oleg S.; Bénézeth, Pascale


    Steady state Iceland-spar calcite dissolution rates were measured at 25 °C in aqueous solutions containing 0.1 M NaCl and up to 0.05 M dissolved bicarbonate at pH from 7.9 to 9.1 in the presence of 13 distinct dissolved organic ligands in mixed-flow reactors. The organic ligands considered in this study include those most likely to be present in either (1) aquifers at the conditions pertinent to CO 2 sequestration or (2) soil/early diagenetic environments: acetate, phthalate, citrate, EDTA 4-, succinate, D-glucosaminate, L-glutamate, D-gluconate, 2,4-dihydroxybenzoate, 3,4-dihydroxybenzoate, fumarate, malonate, and gallate. Results show that the presence of exopolysaccharides, and analogs of microbial cell envelopes: alginate, lichen extract, humic acid, pectin, and gum xanthan. In no case did the presence of <100 ppm of these organics change calcite dissolution rates by more than a factor of 2.5. Results obtained in this study suggest that the presence of aqueous organic anions negligibly affects calcite forward dissolution rates in most natural environments. Some effect on calcite reactivity may be observed, however, by the presence of organic anions if they change substantially the chemical affinity of the fluid with respect to calcite.

  2. Singular Value Decomposition and Ligand Binding Analysis

    Directory of Open Access Journals (Sweden)

    André Luiz Galo


    Full Text Available Singular values decomposition (SVD is one of the most important computations in linear algebra because of its vast application for data analysis. It is particularly useful for resolving problems involving least-squares minimization, the determination of matrix rank, and the solution of certain problems involving Euclidean norms. Such problems arise in the spectral analysis of ligand binding to macromolecule. Here, we present a spectral data analysis method using SVD (SVD analysis and nonlinear fitting to determine the binding characteristics of intercalating drugs to DNA. This methodology reduces noise and identifies distinct spectral species similar to traditional principal component analysis as well as fitting nonlinear binding parameters. We applied SVD analysis to investigate the interaction of actinomycin D and daunomycin with native DNA. This methodology does not require prior knowledge of ligand molar extinction coefficients (free and bound, which potentially limits binding analysis. Data are acquired simply by reconstructing the experimental data and by adjusting the product of deconvoluted matrices and the matrix of model coefficients determined by the Scatchard and McGee and von Hippel equation.

  3. Superior serum half life of albumin tagged TNF ligands

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, Nicole [Division of Molecular Internal Medicine, Department of Internal Medicine II, University Hospital Wuerzburg, Roentgenring 11, 97070 Wuerzburg (Germany); Schneider, Britta; Pfizenmaier, Klaus [Institute of Cell Biology and Immunology, University of Stuttgart, Allmandring 31, 70569 Stuttgart (Germany); Wajant, Harald, E-mail: [Division of Molecular Internal Medicine, Department of Internal Medicine II, University Hospital Wuerzburg, Roentgenring 11, 97070 Wuerzburg (Germany)


    Due to their immune stimulating and apoptosis inducing properties, ligands of the TNF family attract increasing interest as therapeutic proteins. A general limitation of in vivo applications of recombinant soluble TNF ligands is their notoriously rapid clearance from circulation. To improve the serum half life of the TNF family members TNF, TWEAK and TRAIL, we genetically fused soluble variants of these molecules to human serum albumin (HSA). The serum albumin-TNF ligand fusion proteins were found to be of similar bioactivity as the corresponding HSA-less counterparts. Upon intravenous injection (i.v.), serum half life of HSA-TNF ligand fusion proteins, as determined by ELISA, was around 15 h as compared to approximately 1 h for all of the recombinant control TNF ligands without HSA domain. Moreover, serum samples collected 6 or 24 h after i.v. injection still contained high TNF ligand bioactivity, demonstrating that there is only limited degradation/inactivation of circulating HSA-TNF ligand fusion proteins in vivo. In a xenotransplantation model, significantly less of the HSA-TRAIL fusion protein compared to the respective control TRAIL protein was required to achieve inhibition of tumor growth indicating that the increased half life of HSA-TNF ligand fusion proteins translates into better therapeutic action in vivo. In conclusion, our data suggest that genetic fusion to serum albumin is a powerful and generally applicable mean to improve bioavailability and in vivo activity of TNF ligands.

  4. Design of targeting ligands in medicinal inorganic chemistry. (United States)

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


    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.

  5. A response calculus for immobilized T cell receptor ligands

    DEFF Research Database (Denmark)

    Andersen, P S; Menné, C; Mariuzza, R A


    To address the molecular mechanism of T cell receptor (TCR) signaling, we have formulated a model for T cell activation, termed the 2D-affinity model, in which the density of TCR on the T cell surface, the density of ligand on the presenting surface, and their corresponding two-dimensional affinity...... determine the level of T cell activation. When fitted to T cell responses against purified ligands immobilized on plastic surfaces, the 2D-affinity model adequately simulated changes in cellular activation as a result of varying ligand affinity and ligand density. These observations further demonstrated...

  6. Ligand diffusion in proteins via enhanced sampling in molecular dynamics. (United States)

    Rydzewski, J; Nowak, W


    Computational simulations in biophysics describe the dynamics and functions of biological macromolecules at the atomic level. Among motions particularly important for life are the transport processes in heterogeneous media. The process of ligand diffusion inside proteins is an example of a complex rare event that can be modeled using molecular dynamics simulations. The study of physical interactions between a ligand and its biological target is of paramount importance for the design of novel drugs and enzymes. Unfortunately, the process of ligand diffusion is difficult to study experimentally. The need for identifying the ligand egress pathways and understanding how ligands migrate through protein tunnels has spurred the development of several methodological approaches to this problem. The complex topology of protein channels and the transient nature of the ligand passage pose difficulties in the modeling of the ligand entry/escape pathways by canonical molecular dynamics simulations. In this review, we report a methodology involving a reconstruction of the ligand diffusion reaction coordinates and the free-energy profiles along these reaction coordinates using enhanced sampling of conformational space. We illustrate the above methods on several ligand-protein systems, including cytochromes and G-protein-coupled receptors. The methods are general and may be adopted to other transport processes in living matter. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Ultrafast heme-ligand recombination in truncated hemoglobin HbO from Mycobacterium tuberculosis: A ligand cage (United States)

    Jasaitis, Audrius; Ouellet, Hugues; Lambry, Jean-Christophe; Martin, Jean-Louis; Friedman, Joel M.; Guertin, Michel; Vos, Marten H.


    Truncated hemoglobin HbO from Mycobacterium tuberculosis displays very slow exchange of diatomic ligands with its environment. Using femtosecond spectroscopy, we show that upon photoexcitation, ligands rebind with unusual speed and efficiency. Only ˜1% O2 can escape from the heme pocket and less than 1% NO. Most remarkably, CO rebinding occurs for 95%, predominantly in 1.2 ns. The general CO rebinding properties are unexpectedly robust against changes in the interactions with close by aromatic residues Trp88 (G8) and Tyr36 (CD1). Molecular dynamics simulations of the CO complex suggest that interactions of the ligand with structural water molecules as well as its rotational freedom play a role in the high reactivity of the ligand and the heme. The slow exchange of ligands between heme and environment may result from a combination of hindered ligand access to the heme pocket by the network of distal aromatic residues, and low escape probability from the pocket.

  8. Constitutive and ligand-induced TCR degradation

    DEFF Research Database (Denmark)

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


    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...... to the lysosomes. Similar results were obtained in studies of primary human Vbeta8+ T cells stimulated with superantigen. Based on these results, the simplest model for TCR internalization, sorting, and degradation is proposed.......Modulation of TCR expression levels is a central event during T cell development and activation, and it probably plays an important role in adjusting T cell responsiveness. Conflicting data have been published on down-regulation and degradation rates of the individual TCR subunits, and several...

  9. Ligand interactions with galactose oxidase: mechanistic insights. (United States)

    Whittaker, M M; Whittaker, J W


    Interactions between galactose oxidase and small molecules have been explored using a combination of optical absorption, circular dichroism, and electron paramagnetic resonance (EPR) spectroscopies to detect complex formation and characterize the products. Anions bind directly to the cupric center in both active and inactive galactose oxidase, converting to complexes with optical and EPR spectra that are distinctly different from those of the starting aquo enzyme. Azide binding is coupled to stoichiometric proton uptake by the enzyme, reflecting the generation of a strong base (pKa > 9) in the active site anion adduct. At low temperature, the aquo enzyme converts to a form that exhibits the characteristic optical and EPR spectra of an anion complex, apparently reflecting deprotonation of the coordinated water. Anion binding results in a loss of the optical transition arising from coordinated tyrosine, implying displacement of the axial tyrosine ligand on forming the adduct. Nitric oxide binds to galactose oxidase, forming a specific complex exhibiting an unusual EPR spectrum with all g values below 2. The absence of Cu splitting in this spectrum and the observation that the cupric EPR signal from the active site metal ion is not significantly decreased in the complex suggest a nonmetal interaction site for NO in galactose oxidase. These results have been interpreted in terms of a mechanistic scheme where substrate binding displaces a tyrosinate ligand from the active site cupric ion, generating a base that may serve to deprotonate the coordinated hydroxyl group of the substrate, activating it for oxidation. The protein-NO interactions may probe a nonmetal O2 binding site in this enzyme. PMID:8386015

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

    NARCIS (Netherlands)

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


    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

  11. GLIDA: GPCR-ligand database for chemical genomic drug discovery. (United States)

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


    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 We hope that it will prove very useful for chemical genomic research and GPCR-related drug discovery.

  12. Role of ligands in controlling the regioselectivity in ruthenium ...

    Indian Academy of Sciences (India)

    Keywords. Enol esters; DFT; regio-selectivity; ligands; ruthenium(II) catalyst. Abstract. Density functional studies are performed to understand the role of chelating bi-phosphine ligands [(Ph2P(CH2)mPPh2); m=1–4] in modulating the regio-selectivity of benzoic acid addition to 1-hexyne, in presence of ruthenium(II) catalyst ...

  13. Nickel(II) complexes containing ONS donor ligands: Synthesis ...

    Indian Academy of Sciences (India)

    that the complexes possess a distorted octahedral geometry with the ligand coordinating in a uni-negative tri- dentate ONS fashion. The catalytic activity of complexes towards some C–C ... gen, nitrogen and sulfur was carried out using Vario EL. III Elemental analyzer at SAIF - Cochin India. The IR spectra of the ligand and ...

  14. 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 ...

  15. Iron(III) complexes of certain tetradentate phenolate ligands as ...

    Indian Academy of Sciences (India)

    complexes of tripodal phenolate ligands containing N3O and N2O2 donor sets represent the metal binding re- gion of the iron proteins. ... 1,2-CTD enzymes; functional and structural models; Fe(III) complexes; phenolate ligands; intradiol cleavage. 1. ..... nolates are equatorial in 5, while they are mixed axial–equatorial in the ...

  16. Ligand-modified metal clusters for gas separation and purification (United States)

    Okrut, Alexander; Ouyang, Xiaoying; Runnebaum, Ron; Gates, Bruce C.; Katz, Alexander


    Provided is an organic ligand-bound metal surface that selects one gaseous species over another. The species can be closely sized molecular species having less than 1 Angstrom difference in kinetic diameter. In one embodiment, the species comprise carbon monoxide and ethylene. Such organic ligand-bound metal surfaces can be successfully used in gas phase separations or purifications, sensing, and in catalysis.

  17. Biological Activities of Recombinant Liver X Receptor â- Ligand ...

    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 ...

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

    African Journals Online (AJOL)


    Visible spectrophotometry is used to study the kinetics of ligand exchange in the system Ni(salpn)/H2salen with or without triethylamine (NEt3) and ... coordination chemistry.4,5 However, the kinetics of polydentate ligands exchange ..... chlorides and tetraaza Schiff bases: synthesis and characterization of some novel tin(IV) ...

  19. Proteome-wide covalent ligand discovery in native biological systems. (United States)

    Backus, Keriann M; Correia, Bruno E; Lum, Kenneth M; Forli, Stefano; Horning, Benjamin D; González-Páez, Gonzalo E; Chatterjee, Sandip; Lanning, Bryan R; Teijaro, John R; Olson, Arthur J; Wolan, Dennis W; Cravatt, Benjamin F


    Small molecules are powerful tools for investigating protein function and can serve as leads for new therapeutics. Most human proteins, however, lack small-molecule ligands, and entire protein classes are considered 'undruggable'. Fragment-based ligand discovery can identify small-molecule probes for proteins that have proven difficult to target using high-throughput screening of complex compound libraries. Although reversibly binding ligands are commonly pursued, covalent fragments provide an alternative route to small-molecule probes, including those that can access regions of proteins that are difficult to target through binding affinity alone. Here we report a quantitative analysis of cysteine-reactive small-molecule fragments screened against thousands of proteins in human proteomes and cells. Covalent ligands were identified for >700 cysteines found in both druggable proteins and proteins deficient in chemical probes, including transcription factors, adaptor/scaffolding proteins, and uncharacterized proteins. Among the atypical ligand-protein interactions discovered were compounds that react preferentially with pro- (inactive) caspases. We used these ligands to distinguish extrinsic apoptosis pathways in human cell lines versus primary human T cells, showing that the former is largely mediated by caspase-8 while the latter depends on both caspase-8 and -10. Fragment-based covalent ligand discovery provides a greatly expanded portrait of the ligandable proteome and furnishes compounds that can illuminate protein functions in native biological systems.

  20. Technetium radiodiagnostic fatty acids derived from bisamide bisthiol ligands (United States)

    Jones, Alun G.; Lister-James, John; Davison, Alan


    A bisamide-bisthiol ligand containing fatty acid substituted thiol useful for producing Tc-labelled radiodiagnostic imaging agents is described. The ligand forms a complex with the radionuclide .sup.99m Tc suitable for administration as a radiopharmaceutical to obtain images of the heart for diagnosis of myocardial disfunction.

  1. Biological Activities of Recombinant Liver X Receptor β- Ligand ...

    African Journals Online (AJOL)

    Purpose: To investigate tetracycline-inducible expression system for producing clinically usable, high- quality 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 ...

  2. Improved ligand geometries in crystallographic refinement using AFITT in PHENIX. (United States)

    Janowski, Pawel A; Moriarty, Nigel W; Kelley, Brian P; Case, David A; York, Darrin M; Adams, Paul D; Warren, Gregory L


    Modern crystal structure refinement programs rely on geometry restraints to overcome the challenge of a low data-to-parameter ratio. While the classical Engh and Huber restraints work well for standard amino-acid residues, the chemical complexity of small-molecule ligands presents a particular challenge. Most current approaches either limit ligand restraints to those that can be readily described in the Crystallographic Information File (CIF) format, thus sacrificing chemical flexibility and energetic accuracy, or they employ protocols that substantially lengthen the refinement time, potentially hindering rapid automated refinement workflows. PHENIX-AFITT refinement uses a full molecular-mechanics force field for user-selected small-molecule ligands during refinement, eliminating the potentially difficult problem of finding or generating high-quality geometry restraints. It is fully integrated with a standard refinement protocol and requires practically no additional steps from the user, making it ideal for high-throughput workflows. PHENIX-AFITT refinements also handle multiple ligands in a single model, alternate conformations and covalently bound ligands. Here, the results of combining AFITT and the PHENIX software suite on a data set of 189 protein-ligand PDB structures are presented. Refinements using PHENIX-AFITT significantly reduce ligand conformational energy and lead to improved geometries without detriment to the fit to the experimental data. For the data presented, PHENIX-AFITT refinements result in more chemically accurate models for small-molecule ligands.

  3. Polymerization catalysts containing electron-withdrawing amide ligands (United States)

    Watkin, John G.; Click, Damon R.


    The present invention describes methods of making a series of amine-containing organic compounds which are used as ligands for group 3-10 and lanthanide metal compounds. The ligands have electron-withdrawing groups bonded to them. The metal compounds, when combined with a cocatalyst, are catalysts for the polymerization of olefins.

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

    African Journals Online (AJOL)



    Mar 3, 2009 ... catalysts in the asymmetric Diels-Alder reaction.19–21 These ligands have proven to be reasonably successful in terms of selectivity with enantiomeric excesses in the 80 and low 90 % range. Herein we report the evaluation of a series of recently reported2,3 camphor-derived pyridyl ligands 4-9 (Fig.

  5. Heterogenization of Some PNP Ligands for the Oligomerization of ...

    African Journals Online (AJOL)


    Bis(diphenylphosphino)amine ligands were supported on Merrifield's resin and tested in catalytic ethylene oligomerization reactions with a ... When comparing the homogeneous ligands with their heterogeneous counterparts, the latter showed a four-fold ..... Practice, 3rd edn., Springer-Verlag, Berlin, 2001. 38 J. Emsley and ...

  6. Models of protein-ligand crystal structures: trust, but verify (United States)

    Deller, Marc C.; Rupp, Bernhard


    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.

  7. 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 ...

  8. Receptor-ligand binding assays : Technologies and applications

    NARCIS (Netherlands)

    de Jong, LAA; Uges, DRA; Franke, JP; Bischoff, R; A.A. de Jong, Lutea; Piet Franke, Rainer


    Receptor-ligand interactions play a crucial role in biological systems and their measurement forms an important part of modem pharmaceutical development. Numerous assay formats are available that can be used to screen and quantify receptor ligands. In this review, we give an overview over both

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

    Indian Academy of Sciences (India)

    examples studied. Keywords. Lanthanides; magnetic anisotropy; ligand field environment; QTAIM and wiberg bond index analysis; single ion magnets. 1. Introduction ... their isomeric pyrazole {M(BpMe)3}ligands-based lan- thanide analogues ... from ANO-RCC basis library included in MOLCAS 8.0 suite. The active space ...


    Directory of Open Access Journals (Sweden)

    Rummi Devi Saini


    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.

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


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


    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 ...

  12. Dynamic control of chirality in phosphine ligands for enantioselective catalysis. (United States)

    Zhao, Depeng; Neubauer, Thomas M; Feringa, Ben L


    Chirality plays a fundamental role in biology and chemistry and the precise control of chirality in a catalytic conversion is a key to modern synthesis most prominently seen in the production of pharmaceuticals. In enantioselective metal-based catalysis, access to each product enantiomer is commonly achieved through ligand design with chiral bisphosphines being widely applied as privileged ligands. Switchable phosphine ligands, in which chirality is modulated through an external trigger signal, might offer attractive possibilities to change enantioselectivity in a catalytic process in a non-invasive manner avoiding renewed ligand synthesis. Here we demonstrate that a photoswitchable chiral bisphosphine based on a unidirectional light-driven molecular motor, can be used to invert the stereoselectivity of a palladium-catalysed asymmetric transformation. It is shown that light-induced changes in geometry and helicity of the switchable ligand enable excellent selectivity towards the racemic or individual enantiomers of the product in a Pd-catalysed desymmetrization reaction.

  13. HDX reveals unique fragment ligands for the vitamin D receptor. (United States)

    Carson, Matthew W; Zhang, Jun; Chalmers, Michael J; Bocchinfuso, Wayne P; Holifield, Karol D; Masquelin, Thierry; Stites, Ryan E; Stayrook, Keith R; Griffin, Patrick R; Dodge, Jeffery A


    Modulation of the vitamin D receptor (VDR) with a ligand has the potential to be useful for the oral treatment of osteoporosis. One component of our lead generation strategy to identify synthetic ligands for VDR included a fragment based drug design approach. Screening of ligands in a VDR fluorescence polarization assay and a RXR/VDR conformation sensing assay resulted in the identification of multiple fragment hits (lean >0.30). These fragment scaffolds were subsequently evaluated for interaction with the VDR ligand binding domain using hydrogen-deuterium exchange (HDX) mass spectrometry. Significant protection of H/D exchange was observed for some fragments in helixes 3, 7, and 8 of the ligand binding domain, regions which are similar to those seen for the natural hormone VD3. The fragments appear to mimic the A-ring of VD3 thereby providing viable starting points for synthetic expansion. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. Transporters of ligands for essential metal ions in plants. (United States)

    Haydon, Michael J; Cobbett, Christopher S


    Essential metals are required for healthy plant growth but can be toxic when present in excess. Therefore plants have mechanisms of metal homeostasis which involve coordination of metal ion transporters for uptake, translocation and compartmentalization. However, very little metal in plants is thought to exist as free ions. A number of small, organic molecules have been implicated in metal ion homeostasis as metal ion ligands to facilitate uptake and transport of metal ions with low solubility and also as chelators implicated in sequestration for metal tolerance and storage. Ligands for a number of essential metals have been identified and proteins involved in the transport of these ligands and of metal-ligand complexes have been characterized. Here we review recent advances in understanding the role of mugineic acid, nicotianamine, organic acids (citrate and malate), histidine and phytate as ligands for iron (Fe), zinc (Zn), copper (Cu), manganese (Mn) and nickel (Ni) in plants, and the proteins identified as their transporters.

  15. Automated identification of crystallographic ligands using sparse-density representations

    Energy Technology Data Exchange (ETDEWEB)

    Carolan, C. G.; Lamzin, V. S., E-mail: [European Molecular Biology Laboratory (EMBL), c/o DESY, Notkestrasse 85, 22603 Hamburg (Germany)


    A novel procedure for identifying ligands in macromolecular crystallographic electron-density maps is introduced. Density clusters in such maps can be rapidly attributed to one of 82 different ligands in an automated manner. A novel procedure for the automatic identification of ligands in macromolecular crystallographic electron-density maps is introduced. It is based on the sparse parameterization of density clusters and the matching of the pseudo-atomic grids thus created to conformationally variant ligands using mathematical descriptors of molecular shape, size and topology. In large-scale tests on experimental data derived from the Protein Data Bank, the procedure could quickly identify the deposited ligand within the top-ranked compounds from a database of candidates. This indicates the suitability of the method for the identification of binding entities in fragment-based drug screening and in model completion in macromolecular structure determination.

  16. Polypharmacology: in silico methods of ligand design and development. (United States)

    McKie, Samuel A


    How to design a ligand to bind multiple targets, rather than to a single target, is the focus of this review. Rational polypharmacology draws on knowledge that is both broad ranging and hierarchical. Computer-aided multitarget ligand design methods are described according to their nested knowledge level. Ligand-only and then receptor-ligand strategies are first described; followed by the metabolic network viewpoint. Subsequently strategies that view infectious diseases as multigenomic targets are discussed, and finally the disease level interpretation of medicinal therapy is considered. As yet there is no consensus on how best to proceed in designing a multitarget ligand. The current methodologies are bought together in an attempt to give a practical overview of how polypharmacology design might be best initiated.

  17. Mathematical model for determining the binding constants between immunoglobulins, bivalent ligands, and monovalent ligands. (United States)

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


    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.

  18. Developing ligands for palladium(II)-catalyzed C-H functionalization: intimate dialogue between ligand and substrate. (United States)

    Engle, Keary M; Yu, Jin-Quan


    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 Perspective, 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.

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

    Engle, Keary M.; Yu, Jin-Quan


    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

  20. Polypyridyl iron(II) complexes showing remarkable photocytotoxicity ...

    Indian Academy of Sciences (India)

    immortalized human keratinocyte cells HaCaT and breast cancer cell line MCF-7 giving IC50 values of 0.08 and 13 μM in visible light (400–700 ... [Fe(BHA)(L)Cl] of a dipicolylamine derivative (L) and benzhydroxamic acid (HBHA) which ... μM in various cancer cell lines.31 The iron(II) com- plexes showing the BLM activity ...

  1. Gas adsorption and gas mixture separations using mixed-ligand MOF material (United States)

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


    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.

  2. 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))


    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Prat-Lepesant, M


    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

  4. Structural Analysis of Chemokine Receptor–Ligand Interactions (United States)


    This review focuses on the construction and application of structural chemokine receptor models for the elucidation of molecular determinants of chemokine receptor modulation and the structure-based discovery and design of chemokine receptor ligands. A comparative analysis of ligand binding pockets in chemokine receptors is presented, including a detailed description of the CXCR4, CCR2, CCR5, CCR9, and US28 X-ray structures, and their implication for modeling molecular interactions of chemokine receptors with small-molecule ligands, peptide ligands, and large antibodies and chemokines. These studies demonstrate how the integration of new structural information on chemokine receptors with extensive structure–activity relationship and site-directed mutagenesis data facilitates the prediction of the structure of chemokine receptor–ligand complexes that have not been crystallized. Finally, a review of structure-based ligand discovery and design studies based on chemokine receptor crystal structures and homology models illustrates the possibilities and challenges to find novel ligands for chemokine receptors. PMID:28165741

  5. Ligand-controlled Iron-catalyzed Cross Coupling of Benzylic Chlorides with Aryl Grignard Reagents

    National Research Council Canada - National Science Library

    Kawamura, Shintaro; Nakamura, Masaharu


    .... Although electron-deficient ligands promoted the reductive homocoupling of benzylic halides, electron-rich ligands effectively promoted the desired cross-coupling reaction to afford the corresponding...

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

    DEFF Research Database (Denmark)

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


    Ionotropic glutamate receptors (iGluRs) constitute a family of ligand-gated ion channels that are essential for mediating fast synaptic transmission in the central nervous system. This study presents a high-resolution X-ray structure of the competitive antagonist (S)-2-amino-3-[5-tert-butyl-3......-(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...

  7. Optimal Overlay of Ligands with Flexible Bonds Using Differential Evolution

    DEFF Research Database (Denmark)

    Kristensen, Thomas Greve; Pedersen, Christian Storm


    spatial alignment of a set of active ligands taking the flexibility of chemical bonds into account. We present two implementations of our method. One using Differential Evolution (DE) for numerical optimization, and one using the Nelder-Mead method for numerical optimization. We investigate the quality......When designing novel drugs, the need arise to screen large databases of drug candidates (small synthesizable chemical structures) for structures that resemble active ligands, i.e. small chemical structures that are known to react with the target protein. If several active ligands are known one...

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

    DEFF Research Database (Denmark)

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


    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...

  9. Ligand and structure-based methodologies for the prediction of the activity of G protein-coupled receptor ligands (United States)

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


    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.

  10. Ligand and structure-based methodologies for the prediction of the activity of G protein-coupled receptor ligands. (United States)

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


    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.

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

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


    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.

  12. Residual ligand entropy in the binding of p-substituted benzenesulfonamide ligands to bovine carbonic anhydrase II. (United States)

    Stöckmann, Henning; Bronowska, Agnieszka; Syme, Neil R; Thompson, Gary S; Kalverda, Arnout P; Warriner, Stuart L; Homans, Steve W


    In studies on the thermodynamics of ligand-protein interactions, it is often assumed that the configurational and conformational entropy of the ligand is zero in the bound state (i.e., the ligand is rigidly fixed in the binding pocket). However, there is little direct experimental evidence for this assumption, and in the case of binding of p-substituted benzenesulfonamide inhibitors to bovine carbonic anhydrase II (BCA II), the observed thermodynamic binding signature derived from isothermal titration calorimetry experiments leads indirectly to the conclusion that a considerable degree of residual entropy remains in the bound ligand. Specifically, the entropy of binding increases with glycine chain length n, and strong evidence exists that this thermodynamic signature is not driven by solvent reorganization. By use of heteronuclear (15)N NMR relaxation measurements in a series (n = 1-6) of (15)N-glycine-enriched ligands, we find that the observed thermodynamic binding signature cannot be explained by residual ligand dynamics in the bound state, but rather results from the indirect influence of ligand chain length on protein dynamics.

  13. Investigation of the enantioselectivity of tetramethylammonium L-hydroxyproline ionic liquid as a novel chiral ligand in ligand-exchange CE and ligand-exchange MEKC. (United States)

    Liu, Ruijuan; Du, Yingxiang; Chen, Jiaquan; Zhang, Qi; Du, Shuaijing; Feng, Zijie


    Chiral ionic liquids (ILs) have drawn more and more attention in separation science; however, only a few papers focused on the application of chiral ILs as chiral ligands in LE-CE. In this article, a novel amino acid ionic liquid (AAIL), tetramethylammonium L-hydroxyproline ([TMA][L-OH-Pro]), was first applied as a chiral ligand to evaluate its enantioselectivity towards several aromatic amino acids in ligand-exchange capillary electrophoresis (LE-CE) and ligand-exchange micellar electrokinetic capillary chromatography (LE-MEKC). In the LE-CE system, excellent separations were achieved for tryptophan (Rs = 3.03) and 3, 4-dihydroxyphenylalanine (DOPA) (Rs = 4.35). Several parameters affecting the enantioseparation were systematically investigated, including AAIL concentration, type and concentration of central metal ion, buffer pH, as well as applied voltage. The optimum separation was obtained with 60 mM AAIL containing 30 mM Cu (II) at pH 4.5. Additionally, an LE-MEKC system was established to further study the enantioselectivity of [TMA][L-OH-Pro] towards selected analytes. As observed, the separations of the enantiomers of tryptophan, phenylalanine, and histidine were all improved compared to the LE-CE system. The results indicated that the application of AAILs as chiral ligands is a promising method in chiral separation science. © 2014 Wiley Periodicals, Inc.

  14. Norovirus Binding to Ligands Beyond Histo-Blood Group Antigens (United States)

    Almand, Erin A.; Moore, Matthew D.; Jaykus, Lee-Ann


    Histo-blood group antigens (HBGAs) are commonly accepted as the cellular receptors for human norovirus. However, some human noroviruses have been found not to bind any HBGA ligand, suggesting potential additional co-factors. Some ligands have been found to bind noroviruses and have the potential to be additional cellular receptors/attachment factors for human norovirus or inhibitors of the HBGA interaction. The studies identifying these mostly characterize different chemical, human, food, or bacterial components and their effect on norovirus binding and infection, although the mechanism of interaction is unknown in many cases. This review seeks to supplement the already well-covered HBGA-norovirus literature by covering non-HBGA human norovirus ligands and inhibitors to provide investigators with a more comprehensive view of norovirus ligands. PMID:29312233

  15. Characterization of Ligand-Induced Endocytosis of EGF-Receptors

    National Research Council Canada - National Science Library

    Schmid, Sandra


    Under the auspices of this training Fellowship (May 9, 1994-November 9, 1997) I have undertaken studies on the molecular mechanisms that govern ligand-induced endocytosis of epidermal growth factor receptors (EGFR...

  16. 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)


    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.

  17. (TIQ) Thiazole and Oxazoline Ligands for Asymmetric Henry Reactions

    African Journals Online (AJOL)


    TIQ) backbone were synthesized. Their application in the catalytic asymmetric Henry reaction was investigated with comparison to a corresponding TIQ oxazoline ligand. The Cu(II)-oxazoline complex was more reactive and furnished moderate ...

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

    Directory of Open Access Journals (Sweden)

    Leo Veenman


    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.

  19. A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins. (United States)

    Spyrakis, Francesca; Benedetti, Paolo; Decherchi, Sergio; Rocchia, Walter; Cavalli, Andrea; Alcaro, Stefano; Ortuso, Francesco; Baroni, Massimo; Cruciani, Gabriele


    The importance of taking into account protein flexibility in drug design and virtual ligand screening (VS) has been widely debated in the literature, and molecular dynamics (MD) has been recognized as one of the most powerful tools for investigating intrinsic protein dynamics. Nevertheless, deciphering the amount of information hidden in MD simulations and recognizing a significant minimal set of states to be used in virtual screening experiments can be quite complicated. Here we present an integrated MD-FLAP (molecular dynamics-fingerprints for ligand and proteins) approach, comprising a pipeline of molecular dynamics, clustering and linear discriminant analysis, for enhancing accuracy and efficacy in VS campaigns. We first extracted a limited number of representative structures from tens of nanoseconds of MD trajectories by means of the k-medoids clustering algorithm as implemented in the BiKi Life Science Suite ( [accessed July 21, 2015]). Then, instead of applying arbitrary selection criteria, that is, RMSD, pharmacophore properties, or enrichment performances, we allowed the linear discriminant analysis algorithm implemented in FLAP ( [accessed July 21, 2015]) to automatically choose the best performing conformational states among medoids and X-ray structures. Retrospective virtual screenings confirmed that ensemble receptor protocols outperform single rigid receptor approaches, proved that computationally generated conformations comprise the same quantity/quality of information included in X-ray structures, and pointed to the MD-FLAP approach as a valuable tool for improving VS performances.

  20. Fluorescent and Lanthanide Labeling for Ligand Screens, Assays, and Imaging (United States)

    Josan, Jatinder S.; De Silva, Channa R.; Yoo, Byunghee; Lynch, Ronald M.; Pagel, Mark D.; Vagner, Josef; Hruby, Victor J.


    The use of fluorescent (or luminescent) and metal contrast agents in high-throughput screens, in vitro assays, and molecular imaging procedures has rapidly expanded in recent years. Here we describe the development and utility of high-affinity ligands for cancer theranostics and other in vitro screening studies. In this context, we also illustrate the syntheses and use of heteromultivalent ligands as targeted imaging agents. PMID:21318902

  1. Metal-Ligand Multiple Bonds in High-Spin Complexes


    King, Evan


    The chemistry of late first row transition metals supported by dipyrromethane and dipyrromethene ligands bearing sterically bulky substituents was explored. Transition metal complexes (Mn, Fe, Co, Ni, Zn) of the dipyrromethane ligand 1,9-dimesityl-5,5-dimethyldipyrromethane (dpma) were prepared. Structural and magnetic characterization (SQUID, EPR) of the bis-pyridine adducts \\((dpma)Mn(py)_2\\), \\((dpma)Fe(py)_2\\), and \\((dpma)Co(py)_2\\) showed each tetrahedral divalent ion to be high-spin, w...

  2. Cyclometallated iridium and platinum complexes with noninnocent ligands. (United States)

    Hirani, Bhavna; Li, Jian; Djurovich, Peter I; Yousufuddin, Muhammed; Oxgaard, Jonas; Persson, Petter; Wilson, Scott R; Bau, Robert; Goddard, William A; Thompson, Mark E


    The electronic properties of the cyclometalated (CwedgeN) complexes of iridium and platinum metals with a catechol ligand have been studied experimentally and computationally. The synthesis and characterization of (p-tolylpyridine)Ir(3,5-di-tert-butylcatechol) (abbreviated Ir-sq) and (2,4-diflorophenylpyridine)Pt(3,5-di-tert-butylcatechol) (abbreviated Pt-sq) are reported along with their structural, spectral, and electrochemical properties. Reaction of the 3,5-di-tert-butylcatechol (DTBCat) ligand with the prepared cyclometalated metal complex was carried out in air in the presence of a base. The resulting complexes are air stable and are paramagnetic with the unpaired electron residing mainly on the catechol ligand. The bond lengths obtained from X-ray structure analysis and the theoretical results suggest the semiquinone form of the catechol ligand. Low-energy, intense (approximately 10(3) M-1 cm-1) transitions are observed in the visible to near-infrared region (600-700 nm) of the absorption spectra of the metal complexes. Electrochemically, the complexes exhibit a reversible reduction of the semiquinone form to the catechol form of the ligand and an irreversible oxidation to the unstable quinone form of the ligand. The noninnocent catechol ligand plays a significant role in the electronic properties of the metal complexes. Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations on the two open-shell molecules provide the ground-state and excited-state energies of the molecular orbitals involved in the observed low-energy transitions. The spin density in the two complexes resides mainly on the catechol ligand. The intense transition arises from excitation of the beta electron from a HOMO-n (n = 1 or 2 here) to the LUMO, rather than from the excitation of the unpaired alpha electron.

  3. Increased CD40 ligand in patients with acute anterior uveitis

    DEFF Research Database (Denmark)

    Øgard, Carsten; Sørensen, Torben Lykke; Krogh, Erik


    The inflammatory response in acute anterior uveitis (AU) is believed to be primarily mediated by autoreactive T-cells. We wanted to evaluate whether the T-cell activation marker CD40 ligand is involved in the AU immunopathogenesis.......The inflammatory response in acute anterior uveitis (AU) is believed to be primarily mediated by autoreactive T-cells. We wanted to evaluate whether the T-cell activation marker CD40 ligand is involved in the AU immunopathogenesis....

  4. Synthesis and Characterization of PEGylated Toll Like Receptor 7 Ligands


    Chan, Michael; Hayashi, Tomoko; Mathewson, Richard D.; Yao, Shiyin; Gray, Christine; Tawatao, Rommel; Kalenian, Kevin; Zhang, Yanmei; Hayashi, Yuki; Lao, Fitzgerald S.; Cottam, Howard B.; Carson, Dennis A.


    Toll like receptor 7 (TLR7) is located in the endosomal compartment of immune cells. Signaling through TLR7, mediated by the adaptor protein MyD88, stimulates the innate immune system and shapes adaptive immune responses. Previously, we characterized TLR7 ligands conjugated to protein, lipid or polyethylene glycol (PEG). Among the TLR7 ligand conjugates, the addition of PEG chains reduced the agonistic potency. PEGs are safe in humans and widely used for improvement of pharmacokinetics in exi...

  5. 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


    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.

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

    KAUST Repository

    Bootharaju, Megalamane Siddaramappa


    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.

  7. Synthesis of Copper Nanoparticles Coated with Nitrogen Ligands


    Rubén Sierra-Ávila; Marissa Pérez-Alvarez; Gregorio Cadenas-Pliego; Carlos Alberto Ávila-Orta; Rebeca Betancourt-Galindo; Enrique Jiménez-Regalado; Rosa Martha Jiménez-Barrera; Juan Guillermo Martínez-Colunga


    The synthesis of copper nanoparticles was studied by wet chemical methods using copper sulfate pentahydrate (CuSO4·5H2O) and nitrogen ligands allylamine (AAm) and polyallylamine (PAAm) as stabilizers. The results suggest that the use of these ligands leads to the exclusive formation of metallic copper nanoparticles (Cu-NPs). The use of partially crosslinked polyallylamine (PAAmc) leads to nanoparticles (NPs) with low yields and high coating content, while linear PAAm leads to NPs with high yi...

  8. Discovery of GPCR ligands for probing signal transduction pathways. (United States)

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


    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.

  9. Discovery of GPCR ligands for probing signal transduction pathways (United States)

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


    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

  10. Complexation of cobalt by natural ligands in freshwater

    Energy Technology Data Exchange (ETDEWEB)

    Qian, J.; Xue, H.B. [Swiss Federal Inst. for Environmental Science and Technology, Kastanienbaum (Switzerland); Sigg, L.; Albrecht, A. [Swiss Federal Inst. for Environmental Science and Technology, Duebendorf (Switzerland)


    Ligand exchange with dimethylglyoxime (DMG) and differential pulse cathodic stripping voltammetry (DPCSV) was applied to determine free Co(II) ionic concentrations [Co{sup 2+}] and Co(II) complexation by natural organic ligands in freshwater. [Co{sup 2+}] and the complexing parameters were calculated on the basis of the thermodynamic equilibria between added and natural ligands. The optimal working conditions were carefully evaluated in synthetic solutions and in natural freshwater samples. The results from samples collected at various sites from the Aare and Rhine Rivers and the Biel and Lucerne Lakes, Switzerland, are presented. The total dissolved Co concentrations are in the range of 0.5--6.5 nM, and [Co{sup 2+}] is in the range of 0.05--0.5 nM. Organic complexes of Co are predominant in most samples with 80--96% of total dissolved Co. A one-ligand model could well fit the titrations of freshwater samples with Co(II) (using the FITEQL program). The conditional stability constants of the natural ligands were computed to be log K = 9.5--11.6 (pH 8.0 {+-} 0.1), and the ligand concentrations were [L] = 1.4--7.6 nM. The reliability and applicability of the technique and the implications of the results are discussed.

  11. Ligand binding analysis and screening by chemical denaturation shift. (United States)

    Schön, Arne; Brown, Richard K; Hutchins, Burleigh M; Freire, Ernesto


    The identification of small molecule ligands is an important first step in drug development, especially drugs that target proteins with no intrinsic activity. Toward this goal, it is important to have access to technologies that are able to measure binding affinities for a large number of potential ligands in a fast and accurate way. Because ligand binding stabilizes the protein structure in a manner dependent on concentration and binding affinity, the magnitude of the protein stabilization effect elicited by binding can be used to identify and characterize ligands. For example, the shift in protein denaturation temperature (Tm shift) has become a popular approach to identify potential ligands. However, Tm shifts cannot be readily transformed into binding affinities, and the ligand rank order obtained at denaturation temperatures (≥60°C) does not necessarily coincide with the rank order at physiological temperature. An alternative approach is the use of chemical denaturation, which can be implemented at any temperature. Chemical denaturation shifts allow accurate determination of binding affinities with a surprisingly wide dynamic range (high micromolar to sub nanomolar) and in situations where binding changes the cooperativity of the unfolding transition. In this article, we develop the basic analytical equations and provide several experimental examples. Copyright © 2013 Elsevier Inc. All rights reserved.

  12. Ligand- and receptor-based docking with LiBELa (United States)

    dos Santos Muniz, Heloisa; Nascimento, Alessandro S.


    Methodologies on molecular docking are constantly improving. The problem consists on finding an optimal interplay between the computational cost and a satisfactory physical description of ligand-receptor interaction. In pursuit of an advance in current methods we developed a mixed docking approach combining ligand- and receptor-based strategies in a docking engine, where tridimensional descriptors for shape and charge distribution of a reference ligand guide the initial placement of the docking molecule and an interaction energy-based global minimization follows. This hybrid docking was evaluated with soft-core and force field potentials taking into account ligand pose and scoring. Our approach was found to be competitive to a purely receptor-based dock resulting in improved logAUC values when evaluated with DUD and DUD-E. Furthermore, the smoothed potential as evaluated here, was not advantageous when ligand binding poses were compared to experimentally determined conformations. In conclusion we show that a combination of ligand- and receptor-based strategy docking with a force field energy model results in good reproduction of binding poses and enrichment of active molecules against decoys. This strategy is implemented in our tool, LiBELa, available to the scientific community.

  13. Ligand- and receptor-based docking with LiBELa. (United States)

    dos Santos Muniz, Heloisa; Nascimento, Alessandro S


    Methodologies on molecular docking are constantly improving. The problem consists on finding an optimal interplay between the computational cost and a satisfactory physical description of ligand-receptor interaction. In pursuit of an advance in current methods we developed a mixed docking approach combining ligand- and receptor-based strategies in a docking engine, where tridimensional descriptors for shape and charge distribution of a reference ligand guide the initial placement of the docking molecule and an interaction energy-based global minimization follows. This hybrid docking was evaluated with soft-core and force field potentials taking into account ligand pose and scoring. Our approach was found to be competitive to a purely receptor-based dock resulting in improved logAUC values when evaluated with DUD and DUD-E. Furthermore, the smoothed potential as evaluated here, was not advantageous when ligand binding poses were compared to experimentally determined conformations. In conclusion we show that a combination of ligand- and receptor-based strategy docking with a force field energy model results in good reproduction of binding poses and enrichment of active molecules against decoys. This strategy is implemented in our tool, LiBELa, available to the scientific community.

  14. Ligand-target interactions: what can we learn from NMR? (United States)

    Carlomagno, Teresa


    The conformation of the ligand in complex with a macromolecular target can be studied by nuclear magnetic resonance (NMR) in solution for both tightly and weakly forming complexes. In the weak binding regime (k(off) > 10(4) Hz), the structure of the bound ligand is accessible also for very large complexes (>100 kDa), which are not amenable to NMR studies in the tight binding regime. Here I review the state-of-the-art NMR methodology used for screening ligands and for the structural investigation of bound ligand conformations, in both tight and weak binding regimes. The advantages and disadvantages of each approach are critically described. The NMR methodology used to investigate transiently forming complexes has expanded considerably in the past few years, opening new possibilities for a detailed description of ligand-target interactions. Novel methods for the determination of the bound ligand conformation, in particular transferred cross-correlated relaxation, are thoroughly reviewed, and their advantages with respect to established methodology are discussed, using the epothilone-tubulin complex as a primary example.

  15. A General Strategy for Ligand Exchange on Upconversion Nanoparticles. (United States)

    Kong, Wei; Sun, Tianying; Chen, Bing; Chen, Xian; Ai, Fujin; Zhu, Xiaoyue; Li, Mingyu; Zhang, Wenjun; Zhu, Guangyu; Wang, Feng


    Lanthanide-doped upconversion nanoparticles with a suitable surface coating are appealing for biomedical applications. Because high-quality upconversion nanoparticles are typically prepared in an organic solvent and passivated by hydrophobic oleate ligands, a convenient and reliable method for the surface modification of upconversion nanoparticles is thus highly desired to satisfy downstream biological investigations. In this work, we describe a facile and versatile strategy for displacing native oleate ligands on upconversion nanoparticles with a diversity of hydrophilic molecules. The ligand-exchange procedure involves the removal of original oleate ligands followed by the attachment of new ligands in a separate step. The successful coating of relevant ligands was confirmed by Fourier transform infrared spectroscopy, thermogravimetry analysis, and ζ-potential measurement. The surface-modified nanoparticles display high stability and good biocompatibility, as revealed by electron microscopy, photoluminescence spectroscopy, and cytotoxicity assessment. Our study demonstrates that functional biomolecules such as biotin can be directly immobilized on the nanoparticle surface using this approach for the quick and effective detection of streptavidin.

  16. Predicting Efficient Antenna Ligands for Tb(III) Emission

    Energy Technology Data Exchange (ETDEWEB)

    Samuel, Amanda P.S.; Xu, Jide; Raymond, Kenneth


    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.

  17. Ligands turning around in the midst of protein conformers: the origin of ligand-protein mating. A NMR view. (United States)

    Pertinhez, T A; Spisni, A


    Protein-ligand binding is a puzzling process. Many theories have been devised since the pioneering key-and-lock hypothesis based on the idea that both the protein and the ligand have a rigid single conformation. Indeed, molecular motion is the essence of the universe. Consequently, not only proteins are characterized by an extraordinary conformational freedom, but ligands too can fluctuate in a rather vast conformational space. In this scenario, the quest to understand how do they match is fascinating. Recognizing that the inherent dynamics of molecules is the key factor controlling the success of the binding and, subsequently, their chemical/biological function, here we present a view of this process from the NMR stand point. A description of the most relevant NMR parameters that can provide insights, at atomic level, on the mechanisms of protein-ligand binding is provided in the final section.

  18. The use of fake ligands from computational solvent mapping in ligand and structure-based virtual screening. (United States)

    Hall, David R; Enyedy, Istvan J


    Virtual screening selects compounds that resemble a known modulator or compounds that fit into the binding site of a target protein. Computational solvent mapping defines important chemical features for binding to a target protein. Results/methodology: We have tested the ability to use solvent mapping for generating a 'fake' ligand that is a negative image of the binding site. We used this fake ligand as a query for the program ROCS and to define the search space of the docking programs FRED and HYBRID. The fake ligands perform comparably to or better than the ligands from crystal structures across a set of ten targets. Thus, the approach is suitable for guiding virtual screening and hit-to-lead optimization.

  19. PPARγ ligand production is tightly linked to clonal expansion during initiation of adipocyte differentiation

    DEFF Research Database (Denmark)

    Hallenborg, Philip; Koefoed Petersen, Rasmus; Feddersen, Søren


    Adipocyte differentiation is orchestrated by the ligand-activated nuclear receptor PPAR. Endogenous ligands comprise oxidized derivatives of arachidonic acid and structurally similar PUFAs. Although expression of PPAR peaks in mature adipocytes, ligands are produced primarily at the onset...... expansion for PPAR ligand production at the onset of adipocyte differentiation....

  20. Ligand-based virtual screening under partial shape constraints (United States)

    von Behren, Mathias M.; Rarey, Matthias


    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

  1. Ligand-based virtual screening under partial shape constraints. (United States)

    von Behren, Mathias M; Rarey, Matthias


    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 ).

  2. NALDB: nucleic acid ligand database for small molecules targeting nucleic acid


    Kumar Mishra, Subodh; Kumar, Amit


    Nucleic acid ligand database (NALDB) is a unique database that provides detailed information about the experimental data of small molecules that were reported to target several types of nucleic acid structures. NALDB is the first ligand database that contains ligand information for all type of nucleic acid. NALDB contains more than 3500 ligand entries with detailed pharmacokinetic and pharmacodynamic information such as target name, target sequence, ligand 2D/3D structure, SMILES, molecular f...

  3. Copper(II)-mediated transformation of a tridentate non-innocent ligand into a tetradentate salen-type innocent ligand. (United States)

    Ghorai, Samir; Mukherjee, Chandan


    A non-innocent ligand, H4L(CH2NH2), was synthesized by introducing a -CH2NH2 group at the ortho carbon atom to the aniline moiety of 2-anilino-4,6-di-tert-butylphenol. The new ligand was characterized by IR and NMR spectroscopy and mass spectrometry techniques. Upon treatment with CuCl2⋅2H2O, this non-innocent ligand provided a mononuclear four-coordinate salen-type Cu(II) complex by complete modification of the ligand backbone. The complex was characterized by IR spectroscopy, mass spectrometry, X-ray single-crystal diffraction, electron paramagnetic resonance (EPR) spectroscopy, and UV/Vis/near-IR spectroscopy techniques. X-ray crystallographic analysis showed an asymmetric environment around the Cu(II) center with a small (≈12°) twist between the two biting planes. Analysis of the X-band EPR spectrum also supported the asymmetric environment and also indicated the presence of an unpaired electron on the dx2-y2 orbital. The UV/Vis/near-IR spectrum showed strong absorption bands for metal-to-ligand charge transfer and ligand-to-metal charge transfer along with a Cu(II) -centered d-d transition. Mechanistic investigation of the formation of complex 1 indicated that modification of the ligand backbone proceeded through ligand-centered amine to imine oxidation as well as through C-N bond-breaking processes. During these processes, 3,5-di-tert-butyl-1,2-benzoquinone and 2-aminobenzylidene were produced. Ammonia, generated in situ through hydrolysis of the imine to the aldehyde, reacted with 3,5-di-tert-butyl-1,2-benzoquinone to form the corresponding 3,5-di-tert-butyl-1,2-iminobenzoquinone moiety, which upon two-electron reduction in the reaction medium formed 3,5-di-tert-butyl-1,2-aminophenol. This aminophenol underwent condensation with the H2L5 ligand that was formed by self-condensation of two molecules of 2-aminobenzaldehyde and provided the modified ligand backbone. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Preference for bridging versus terminal ligands in magnesium dimers. (United States)

    Lioe, Hadi; White, Jonathan M; O'Hair, Richard A J


    Magnesium dimers play important roles in inorganic and organometallic chemistry. This study evaluates the inherent bridging ability of a range of different ligands in magnesium dimers. In the first part, the Cambridge Structural Database is interrogated to establish the frequency of different types of ligands found in bridging versus terminal positions in two key structural motifs: one in which there are two bridging ligands (the D(2h) "Mg(2)(μ-X(2))" structure); the other in which there are three bridging ligands (the C(3v) "Mg(2)(μ-X(3))" structure). The most striking finding from the database search is the overwhelming preference for magnesium dimers possessing two bridging ligands. The most common bridging ligands are C-, N-, and O-based. In the second part, DFT calculations (at the B3LYP/6-311+G(d) level of theory) are carried out to examine a wider range of structural types for dimers consisting of the stoichiometries Mg(2)Cl(3)R and Mg(2)Cl(2)R(2), where R = CH(3), SiH(3), NH(2), PH(2), OH, SH, CH(2)CH(3), CH=CH(2), C≡CH, Ph, OAc, F and Br. Consistent with the database search, the most stable magnesium dimers are those that contain two bridging ligands. Furthermore, it was demonstrated that the electronic effect of the bridging ligands is important in influencing the stability of the magnesium dimers. The preference for a bridging ligand, which reflects its ability to stabilize a magnesium dimer, follows the order: OH > NH(2) > C≡CH > SH > Ph > Br > PH(2) = CH=CH(2) > CH(2)CH(3) > CH(3) > SiH(3). Finally, the role that the ether solvent Me(2)O has on the stability of isomeric Mg(2)Cl(2)Me(2) dimers was studied. It was found that the first solvent molecule stabilizes the dimers, while the second solvent molecule can either have a stabilizing or destabilizing effect, depending on the isomer structure.

  5. An efficient computational method for calculating ligand binding affinities.

    Directory of Open Access Journals (Sweden)

    Atsushi Suenaga

    Full Text Available Virtual compound screening using molecular docking is widely used in the discovery of new lead compounds for drug design. However, the docking scores are not sufficiently precise to represent the protein-ligand binding affinity. Here, we developed an efficient computational method for calculating protein-ligand binding affinity, which is based on molecular mechanics generalized Born/surface area (MM-GBSA calculations and Jarzynski identity. Jarzynski identity is an exact relation between free energy differences and the work done through non-equilibrium process, and MM-GBSA is a semimacroscopic approach to calculate the potential energy. To calculate the work distribution when a ligand is pulled out of its binding site, multiple protein-ligand conformations are randomly generated as an alternative to performing an explicit single-molecule pulling simulation. We assessed the new method, multiple random conformation/MM-GBSA (MRC-MMGBSA, by evaluating ligand-binding affinities (scores for four target proteins, and comparing these scores with experimental data. The calculated scores were qualitatively in good agreement with the experimental binding affinities, and the optimal docking structure could be determined by ranking the scores of the multiple docking poses obtained by the molecular docking process. Furthermore, the scores showed a strong linear response to experimental binding free energies, so that the free energy difference of the ligand binding (ΔΔG could be calculated by linear scaling of the scores. The error of calculated ΔΔG was within ≈ ± 1.5 kcal.mol(-1 of the experimental values. Particularly, in the case of flexible target proteins, the MRC-MMGBSA scores were more effective in ranking ligands than those generated by the MM-GBSA method using a single protein-ligand conformation. The results suggest that, owing to its lower computational costs and greater accuracy, the MRC-MMGBSA offers efficient means to rank the ligands, in

  6. Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods (United States)

    Du, Xing; Li, Yi; Xia, Yuan-Ling; Ai, Shi-Meng; Liang, Jing; Sang, Peng; Ji, Xing-Lai; Liu, Shu-Qun


    Molecular recognition, which is the process of biological macromolecules interacting with each other or various small molecules with a high specificity and affinity to form a specific complex, constitutes the basis of all processes in living organisms. Proteins, an important class of biological macromolecules, realize their functions through binding to themselves or other molecules. A detailed understanding of the protein–ligand interactions is therefore central to understanding biology at the molecular level. Moreover, knowledge of the mechanisms responsible for the protein-ligand recognition and binding will also facilitate the discovery, design, and development of drugs. In the present review, first, the physicochemical mechanisms underlying protein–ligand binding, including the binding kinetics, thermodynamic concepts and relationships, and binding driving forces, are introduced and rationalized. Next, three currently existing protein-ligand binding models—the “lock-and-key”, “induced fit”, and “conformational selection”—are described and their underlying thermodynamic mechanisms are discussed. Finally, the methods available for investigating protein–ligand binding affinity, including experimental and theoretical/computational approaches, are introduced, and their advantages, disadvantages, and challenges are discussed. PMID:26821017

  7. Cloud computing for protein-ligand binding site comparison. (United States)

    Hung, Che-Lun; Hua, Guan-Jie


    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.

  8. Cloud Computing for Protein-Ligand Binding Site Comparison

    Directory of Open Access Journals (Sweden)

    Che-Lun Hung


    Full Text Available 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.

  9. Cloud Computing for Protein-Ligand Binding Site Comparison (United States)


    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. PMID:23762824

  10. A motion planning approach to flexible ligand binding. (United States)

    Singh, A P; Latombe, J C; Brutlag, D L


    Most computational models of protein-ligand interactions consider only the energetics of the final bound state of the complex and do not examine the dynamics of the ligand as it enters the binding site. We have developed a novel technique for studying the dynamics of protein-ligand interactions based on motion planning algorithms from the field of robotics. Our algorithm uses electrostatic and van der Waals potentials to compute the most energetically favorable path between any given initial and goal ligand configurations. We use probabilistic motion planning to sample the distribution of possible paths to a given goal configuration and compute an energy-based "difficulty weight" for each path. By statistically averaging this weight over several randomly generated starting configurations, we compute the relative difficulty of entering and leaving a given binding configuration. This approach yields details of the energy contours around the binding site and can be used to characterize and predict good binding sites. Results from tests with three protein-ligand complexes indicate that our algorithm is able to detect energy barriers around the true binding site that distinguish this site from other predicted low-energy binding sites.

  11. Synthesis, structure characterization and biological activity of selected metal complexes of sulfonamide Schiff base as a primary ligand and some mixed ligand complexes with glycine as a secondary ligand (United States)

    Sharaby, Carmen M.; Amine, Mona F.; Hamed, Asmaa A.


    The current work reports synthesis of metal complexes and mixed ligand complexes of a novel sulfonamide Schiff base ligand (HL) resulted from the condensation of sulfametrole [N‧-(4-methoxy-1,2,5-thiadiazol-3-yl]sulfanilamide and acetyl-acetone as a primary ligand and glycine as a secondary ligand. The metal complexes and mixed ligand complexes of HL Schiff base ligand were synthesized and characterized using different physicochemical studies as elemental analyses, mass spectra, conductivity measurement, IR spectra, 1H NMR spectra, UV-vis Spectra, solid reflectance, magnetic susceptibility, thermal analyses (TGA and DTA) and their microbial and anticancer activities. The spectroscopic data of the complexes suggest their 1:2(L1:M) complex structures and 1:2:2(L1:L2:M) mixed ligand complex structures, where L1 = HL and L2 = glycine. Also, the spectroscopic studies suggested the octahedral structure for all complexes. The synthesized Schiff base, its metal and mixed ligand complexes were screened for their bacterial, antifungal and anticancer activity. The activity data show that the metal complexes and mixed ligand complexes exhibited promising microbial and anticancer activities than their parent HL Schiff base ligand, also the data show that the mixed ligand complexes more effective than the metal complexes.

  12. Activation of Neuropeptide FF Receptors by Kisspeptin Receptor Ligands (United States)


    Kisspeptin is a member of the RFamide neuropeptide family that is implicated in gonadotropin secretion. Because kisspeptin-GPR54 signaling is implicated in the neuroendocrine regulation of reproduction, GPR54 ligands represent promising therapeutic agents against endocrine secretion disorders. In the present study, the selectivity profiles of GPR54 agonist peptides were investigated for several GPCRs, including RFamide receptors. Kisspeptin-10 exhibited potent binding and activation of neuropeptide FF receptors (NPFFR1 and NPFFR2). In contrast, short peptide agonists bound with much lower affinity to NPFFRs while showing relatively high selectivity toward GPR54. The possible localization of secondary kisspeptin targets was also demonstrated by variation in the levels of GnRH release from the median eminence and the type of GPR54 agonists used. Negligible affinity of the reported NPFFR ligands to GPR54 was observed and indicates the unidirectional cross-reactivity between both ligands. PMID:24900254

  13. Structure and properties of a new rigid tripodal oxime ligand (United States)

    Premužić, Dejan; Filarowski, Aleksander; Hołyńska, Małgorzata


    Synthesis and properties of a new rigid tripodal oxime ligand are reported. The ligand is a derivative of phloroglucine with three carboxime arms alternate with hydroxyl groups and three intramolecular Osbnd H⋯N hydrogen bonds. Intermolecular Osbnd H⋯O hydrogen bonds result in formation of a characteristic three-dimensional network. The structure of the compound is further analyzed and confirmed by NMR, IR and MS-techniques. DFT calculations were employed to accomplish the analysis of both the hydrogen bonding and the conformational state of the ligand under study. Additionally, the study addresses the way the conformational state and metal-replacement influence the tautomeric equilibrium OH⋯N ⇆ O-⋯+HN in the studied moieties.

  14. Evaluation of macrocyclic hydroxyisophthalamide ligands as chelators for zirconium-89.

    Directory of Open Access Journals (Sweden)

    Nikunj B Bhatt

    Full Text Available The development of bifunctional chelators (BFCs for zirconium-89 immuno-PET applications is an area of active research. Herein we report the synthesis and evaluation of octadentate hydroxyisophthalamide ligands (1 and 2 as zirconium-89 chelators. While both radiometal complexes could be prepared quantitatively and with excellent specific activity, preparation of 89Zr-1 required elevated temperature and an increased reaction time. 89Zr-1 was more stable than 89Zr-2 when challenged in vitro by excess DTPA or serum proteins and in vivo during acute biodistribution studies. Differences in radiometal complex stability arise from structural changes between the two ligand systems, and suggest further ligand optimization is necessary to enhance 89Zr chelation.

  15. Ligand Binding Thermodynamics in Drug Discovery: Still a Hot Tip? (United States)

    Geschwindner, Stefan; Ulander, Johan; Johansson, Patrik


    The use of ligand binding thermodynamics has been proposed as a potential success factor to accelerate drug discovery. However, despite the intuitive appeal of optimizing binding enthalpy, a number of factors complicate routine use of thermodynamic data. On a macroscopic level, a range of experimental parameters including temperature and buffer choice significantly influence the observed thermodynamic signatures. On a microscopic level, solute effects, structural flexibility, and cooperativity lead to nonlinear changes in enthalpy. This multifactorial character hides essential enthalpy contributions of intermolecular contacts, making them experimentally nonobservable. In this perspective, we present three case studies, reflect on some key factors affecting thermodynamic signatures, and investigate their relation to the hydrophobic effect, enthalpy-entropy compensation, lipophilic ligand efficiency, and promiscuity. The studies highlight that enthalpy and entropy cannot be used as direct end points but can together with calculations increase our understanding of ligand binding and identify interesting outliers that do not behave as expected.

  16. Coordination chemistry of N-heterocyclic nitrenium-based ligands. (United States)

    Tulchinsky, Yuri; Kozuch, Sebastian; Saha, Prasenjit; Mauda, Assaf; Nisnevich, Gennady; Botoshansky, Mark; Shimon, Linda J W; Gandelman, Mark


    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.

  17. The Parathyroid Hormone Family of Ligands and Receptors

    Directory of Open Access Journals (Sweden)

    Damian G. D'Souza


    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.

  18. Ligands of histamine receptors modulate acid-sensing ion channels. (United States)

    Shteinikov, V Y; Korosteleva, A S; Tikhonova, T B; Potapieva, N N; Tikhonov, D B


    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.

  19. Thiolate ligands for synthesis of water-soluble gold clusters. (United States)

    Ackerson, Christopher J; Jadzinsky, Pablo D; Kornberg, Roger D


    Water-soluble monolayer-protected gold clusters (MPCs) have been an object of investigation by many research groups since their first syntheses were reported in 1998 and 1999. The basic requirements for a ligand to form a monolayer protecting a gold cluster were established some time ago for alkanethiolate MPCs, but there has been no such information published for water-soluble MPCs. We identify 6 new ligands capable of forming water-soluble MPCs, as well as 22 water-soluble ligands that fail to form MPCs. Our findings contribute not only to the definition of the requirements for MPC formation but also to the variety of MPCs available for applications in chemistry and biology.

  20. Xanthene and Xanthone Derivatives as G-Quadruplex Stabilizing Ligands

    Directory of Open Access Journals (Sweden)

    Alessandro Altieri


    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.

  1. Ligand screening by saturation-transfer difference (STD) NMR spectroscopy.

    Energy Technology Data Exchange (ETDEWEB)

    Krishnan, V V


    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.

  2. The thermodynamic principles of ligand binding in chromatography and biology

    DEFF Research Database (Denmark)

    Mollerup, Jørgen


    In chromatography, macromolecules do not adsorb in the traditional sense of the word but bind to ligands that are covalently bonded to the surface of the porous bead. Therefore, the adsorption must be modelled as a process where protein molecules bind to the immobilised ligands. The paper discusses...... but it is also observed in chromatography due to protein-protein interactions. Retention measurements on P-lactoglobulin A demonstrate this. A discussion of salt effects on hydrophobic interactions in precipitation and chromatography of proteins concludes the paper. (c) 2007 Elsevier B.V. All rights reserved....... the general thermodynamic principles of ligand binding. Models of the multi-component adsorption in ion-exchange and hydrophobic chromatography, HIC and RPLC, are developed. The parameters in the models have a well-defined physical significance. The models are compared to the Langmuir model...

  3. 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


    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.

  4. Complexation of trivalent americium and lanthanides with terdentate 'N' donor ligands: the role of rigidity in the ligand structure. (United States)

    Bhattacharyya, Arunasis; Gadly, Trilochan; Pathak, Priyanath; Ghosh, Sunil K; Mohapatra, Manoj; Ghanty, Tapan K; Mohapatra, Prasanta K


    A systematic study on the Ln(3+) complexation behaviour with two terdentate 'N' donor ligands of varying structural rigidity, viz. 5,6-dimethyl-(1,2,4)-triazinylbipyridine (Me2TBipy) and 5,6-dimethyl-(1,2,4)-triazinylphenanthroline (Me2TPhen), is performed in the present work by UV-Vis spectrophotometry, time resolved fluorescence spectroscopy (TRFS) and electrospray ionization mass spectrometric (ESI-MS) studies. These studies indicate the formation of a 1 : 1 complex of La(3+), 1 : 2 complexes of Eu(3+) and Er(3+) with both the ligands. Density functional theoretical (DFT) study is carried out to determine the solution phase structure of the Eu(3+) complex considering the species (from UV-Vis spectrophotometry) and C2v site symmetry around the Eu(3+) ion (from TRFS study). Me2TPhen is found to be a stronger complexing ligand as compared to Me2TBipy irrespective of the Ln(3+) ions. The solid state crystal structure of the La(3+) complex of Me2TPhen is determined using the single crystal X-ray diffraction (SCXRD) technique. The complexation of the trivalent Am(3+) ion is also studied with both these ligands using UV-Vis spectrophotometric titrations which show the formation of 1 : 2 complexes with higher complexation constant values as compared to all the Ln(3+) ions studied, indicating the selectivity of these ligands for the trivalent actinides over the lanthanides.

  5. Methods for Identifying Ligands that Target Nucleic Acid Molecules and Nucleic Acid Structural Motifs (United States)

    Disney, Matthew D. (Inventor); Childs-Disney, Jessica L. (Inventor)


    Disclosed are methods for identifying a nucleic acid (e.g., RNA, DNA, etc.) motif which interacts with a ligand. The method includes providing a plurality of ligands immobilized on a support, wherein each particular ligand is immobilized at a discrete location on the support; contacting the plurality of immobilized ligands with a nucleic acid motif library under conditions effective for one or more members of the nucleic acid motif library to bind with the immobilized ligands; and identifying members of the nucleic acid motif library that are bound to a particular immobilized ligand. Also disclosed are methods for selecting, from a plurality of candidate ligands, one or more ligands that have increased likelihood of binding to a nucleic acid molecule comprising a particular nucleic acid motif, as well as methods for identifying a nucleic acid which interacts with a ligand.

  6. Systematic study of ligand structures of metal oxide EUV nanoparticle photoresists

    KAUST Repository

    Jiang, Jing


    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.

  7. Use of protein-engineered fabrics to identify design rules for integrin ligand clustering in biomaterials. (United States)

    Benitez, Patrick L; Mascharak, Shamik; Proctor, Amy C; Heilshorn, Sarah C


    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

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

    Directory of Open Access Journals (Sweden)

    Beda Brichacek


    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.

  9. Designer ligands: The search for metal ion selectivity

    Directory of Open Access Journals (Sweden)

    Perry T. Kaye


    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.

  10. Coordination chemistry of poly(thioether)borate ligands. (United States)

    Riordan, Charles G


    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.

  11. Synthesis of Oxovanadium(IV Complexes with Tetraaza Coordinating Ligands

    Directory of Open Access Journals (Sweden)

    Sanjay Singh


    Full Text Available Oxovanadium(IV complexes of the type [VO(mac]SO4 (where mac = tetraaza macrocyclic ligands derived by condensation of thenil with 1,4-diaminobenzene or 3,4-diaminopyridine and their reaction with β-diketones have been prepared using vanadyl ion as kinetic template. The prepared macrocyclic complexes were characterized by elemental analyses, molar conductance, magnetic moments, and infrared, electronic, and electron spin resonance data. From the spectroscopic studies, five-coordinate square-pyramidal geometry for the VO2+ complexes have been proposed wherein derived ligands act as tetradentate chelating agents.

  12. Force loading explains spatial sensing of ligands by cells (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


    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

  13. Coordination chemistry of poly(thioether)borate ligands (United States)

    Riordan, Charles G.


    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

  14. Carbohydrate Analogue Microarrays for Identification of Lectin-Selective Ligands. (United States)

    Hyun, Ji Young; Park, Cheol Wan; Liu, Yanna; Kwon, Daeun; Park, Seong-Hyun; Park, Sungjin; Pai, Jaeyoung; Shin, Injae


    Fifty-five mono- and disaccharide analogues were prepared and used for the construction of microarrays to uncover lectin-selective ligands. The microarray study showed that two disaccharide analogues, 28' and 44', selectively bind to Solanum tuberosum lectin (STL) and wheat germ agglutinin (WGA), respectively. Cell studies indicated that 28' and 44' selectively block the binding of STL and WGA to mammalian cells, unlike the natural ligand LacNAc, which suppresses binding of both STL and WGA to cells. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Development of catalysts and ligands for enantioselective gold catalysis. (United States)

    Wang, Yi-Ming; Lackner, Aaron D; Toste, F Dean


    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

  16. Isothermal Titration Calorimetry: Assisted Crystallization of RNA-Ligand Complexes. (United States)

    Da Veiga, Cyrielle; Mezher, Joelle; Dumas, Philippe; Ennifar, Eric


    The success rate of nucleic acids/ligands co-crystallization can be significantly improved by performing preliminary biophysical analyses. Among suitable biophysical approaches, isothermal titration calorimetry (ITC) is certainly a method of choice. ITC can be used in a wide range of experimental conditions to monitor in real time the formation of the RNA- or DNA-ligand complex, with the advantage of providing in addition the complete binding profile of the interaction. Following the ITC experiment, the complex is ready to be concentrated for crystallization trials. This chapter describes a detailed experimental protocol for using ITC as a tool for monitoring RNA/small molecule binding, followed by co-crystallization.

  17. Synthesis of multifunctional polyvinylsaccharide containing controllable amounts of biospecific ligands. (United States)

    Korzhikov, V; Roeker, S; Vlakh, E; Kasper, C; Tennikova, T


    In the present study, the attempt to synthesize a multibiofunctional polymeric vector to be used for construction of composite scaffolds for bone tissue engineering has been undertaken. The polymers based on 2-deoxy-2-methacrylamido- d-glucose were functionalized by a growth factor (BMP-2), GRGDSP peptide, and poly( l-lysine) using aldehyde chemistry. The covalent modification process was quantitatively studied, and a polymer conjugate containing all these ligands was formed. In addition, the impacts of coupled ligands toward the adsorption of polymers on the commercial mineral macroporous matrix Sponceram used in cell culture applications were studied.

  18. Luminescent cyclometallated iridium(III) complexes having acetylide ligands (United States)

    Thompson, Mark E.; Bossi, Alberto; Djurovich, Peter Ivan


    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.

  19. Tear lipocalins bind a broad array of lipid ligands. (United States)

    Glasgow, B J; Abduragimov, A R; Farahbakhsh, Z T; Faull, K F; Hubbell, W L


    To identify the native ligands of tear lipocalins, tear proteins were separated by size exclusion chromatography and the lipid content in the major protein fractions identified. Lipids extracted from native tears and purified tear lipocalins comigrated with fatty acids, fatty alcohols, phospholipids, glycolipids, and cholesterol on thin layer chromatograms. Abundant stearic and palmitic acids as well as cholesterol, and lesser amounts of lauric acid were specifically identified in extracts of purified lipocalins by gas chromatography-mass spectroscopy. A preliminary study of the ligand-protein interaction was carried out using nitroxide spin-labeled lipids.

  20. 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.

  1. Ionic liquids with amino acids as cations: novel chiral ligands in chiral ligand-exchange capillary electrophoresis. (United States)

    Mu, Xiaoyu; Qi, Li; Zhang, Haizhi; Shen, Ying; Qiao, Juan; Ma, Huimin


    Ionic liquids (ILs) with L-proline (L-Pro) as cations have been developed for the novel chiral ligands coordinated with Cu(II) in chiral ligand exchange capillary electrophoresis (CLE-CE). Four kinds of amino acid ionic liquids (AAILs), including [L-Pro][CF(3)COO], [L-Pro][NO(3)], [L-Pro][BF(4)] and [L-Pro(2)][SO(4)], were successfully synthesized. Among them, [L-Pro][CF(3)COO] was selected as the model ligand to optimize the separation conditions. The influences of AAIL concentration, pH, and methanol concentration on efficiency of chiral separation were investigated. Then it has been testified that the optimal buffer solution consisted of 25.0mM Cu(Ac)(2), 50.0 mM AAIL and 20% (v/v) methanol at pH 4.0. The interesting thing is well enantioresolution could be observed with [L-Pro][CF(3)COO] as the new chiral ligand and nine pairs of labeled D,L-AAs were successfully separated with the resolution ranging from 0.93 to 6.72. Meanwhile, the baseline separation of labeled D,L-AAs could be achieved with the other three kinds of AAILs as ligands. The results have demonstrated the good applicability of AAILs with AAs as cations for chiral separation in CLE-CE system. In addition, comparative study was also conducted for exploring the mechanism of the AAILs as new ligands in CLE-CE. Copyright © 2012 Elsevier B.V. All rights reserved.

  2. Synthesis, structure and reactivity of rare-earth metal complexes containing anionic phosphorus ligands. (United States)

    Li, Tianshu; Kaercher, Sabrina; Roesky, Peter W


    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.

  3. Tunable Phosphoramidite Ligands for Asymmetric Hydrovinylation: Ligands par excellence for Generation of All-Carbon Quaternary Centers (United States)

    Smith, Craig R.; Lim, Hwan Jung; Zhang, Aibin; RajanBabu, T. V.


    1-Alkylstyrenes undergo efficient hydrovinylation (addition of ethylene) in the presence of a Ni-catalyst prepared from [(allyl)NiBr]2, Na+ [BAr4]− (Ar = 3,5-bis-trifluromethylphenyl), and a phosphoramidite ligand giving products in excellent yields and enantioselectivities. In many cases phosphoramidites derived from achiral 2,2′-biphenol are almost as good as ligands derived from the more expensive enantiopure 2,2′-binaphthols. The hydrovinylation products, which carry two versatile latent functionalities, an aryl and a vinyl group, are potentially useful for the synthesis of several important natural products containing benzylic all-carbon quaternary centers. PMID:19763244


    African Journals Online (AJOL)

    SALESP is a potentially hexadentate ligand and its reactions with copper (II) ... 1 12 Infrared and uv-vis studies of copper-(II) complexes. Table 1. Analytical data. % C % H % N % S. Compound. Cole. Found Calc. Found C alc. Found Cale. .... hydrogen bonding between the OH moiety and the imine nitrogen atom [23].

  5. Nigerian Journal of Chemical Research Vol.12, 2007 Synthesis and ...

    African Journals Online (AJOL)


    complex. The room temperature magnetic moments of the copper(II) complexes of tetra- and hexadentate ligands are paramagnetic with ~teef values of 1.3-. 2.29 B.M., corresponding to the presence of one unpaired electron. There is a small but significant increase in magnetic moment due to an increased D4h distortion26.

  6. Fas Ligand Expression in Lynch Syndrome-Associated Colorectal Tumours

    NARCIS (Netherlands)

    Koornstra, Jan J.; de Jong, Steven; Boersma-van Eck, Wietske; Zwart, Nynke; Hollema, Harry; de Vries, Elisabeth G. E.; Kleibeuker, Jan H.

    Fas Ligand (FasL) expression by cancer cells may contribute to tumour immune escape via the Fas counterattack against tumour-infiltrating lymphocytes (TILs). Whether this plays a role in colorectal carcinogenesis in Lynch syndrome was examined studying FasL expression, tumour cell apoptosis and

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

    Indian Academy of Sciences (India)

    Synthesis of meta-substituted phosphinite ligands 3,3' (methoxyphosphanediyl) bis (N,Ndiethylaniline) (4a) and methoxybis(3-methoxyphenyl)phosphane (4b), in high yields, has been demonstrated. Typical phosphorus chemical shift between 110–120 ppm, appearance of methoxy protons and corresponding carbon, ...

  8. Biosensors engineered from conditionally stable ligand-binding domains (United States)

    Church, George M.; Feng, Justin; Mandell, Daniel J.; Baker, David; Fields, Stanley; Jester, Benjamin Ward; Tinberg, Christine Elaine


    Disclosed is a biosensor engineered to conditionally respond to the presence of specific small molecules, the biosensors including conditionally stable ligand-binding domains (LBDs) which respond to the presence of specific small molecules, wherein readout of binding is provided by reporter genes or transcription factors (TFs) fused to the LBDs.


    African Journals Online (AJOL)


  10. Biscalix[4]arene ligands for dinuclear lanthanide ion complexation

    NARCIS (Netherlands)

    Oude Wolbers, M.P.; van Veggel, F.C.J.M.; Heeringa, Remco H.M.; Hofstraat, Johannes W.; Geurts, Frank A.J.; van Hummel, G.J.; Harkema, Sybolt; Reinhoudt, David


    Three types of lower-lower rim linked biscalix[4]arenes that contain carboxylic ester (1) and/or amide functions (2 and 3) at their remaining phenolic oxygen atoms were synthesized. The homo- and heterodinuclear lanthanide ion complexes based on these ligands were used to study the energy transfer

  11. Synthesis and spectra characterization of mixed ligand complexes ...

    African Journals Online (AJOL)

    The synthesized ligand and its metal complexes have been characterized by elemental analysis and spectroscopic (i.r. and electronic) methods. An octahedral geometric structure is proposed for the metal complexes. The six coordinate environment of the metals is composed of N5X core with thr ee nitrogen atoms from the ...

  12. Design and synthesis of multidentate ligands via metal promoted C ...

    Indian Academy of Sciences (India)


    The coordination chemistry of the HL1 ligand involving some 3d-metal ions is described. Two unusual low-spin complexes of manganese(II) and iron(III) are reported. The ferric complex displayed a rhombic EPR while, the corresponding manganese compound showed a complex pattern due to hyperfine coupling. All the.


    Retinoids and associated derivatives represent a class of endogenousr hormones that bind to and activate different families of retinoic acid receptors (RARs, RXRs), and control many aspects of normal vertebrate development. Identification of potential RAR and RXRs ligands is of i...

  14. Ligands that store and release electrons during catalysis

    NARCIS (Netherlands)

    Dzik, W.I.; van der Vlugt, J.I.; Reek, J.N.H.; de Bruin, B.


    First-row transition metals can be given a noble character by redox-active ligands, thus enabling two-electron oxidative addition and reductive elimination steps (see scheme). A recently reported cobalt-mediated Negishi-type cross-coupling reaction provides an illustrative example of this concept

  15. GluR2 ligand-binding core complexes

    DEFF Research Database (Denmark)

    Kasper, C; Lunn, M-L; Liljefors, T


    X-ray structures of the GluR2 ligand-binding core in complex with (S)-Des-Me-AMPA and in the presence and absence of zinc ions have been determined. (S)-Des-Me-AMPA, which is devoid of a substituent in the 5-position of the isoxazolol ring, only has limited interactions with the partly hydrophobic...

  16. Phenalenyl-based ligand for transition metal chemistry: Application ...

    Indian Academy of Sciences (India) Abstract. We report the synthesis and characterization of the first transition metal complex of a phenalenyl- based ligand. The reaction of Cu(OAc)2.H2O with 9-N-methylamino-1-N -methylimino-phenalene (LH) in 1:1.

  17. Synthesis and characterization of mixed ligand complexes of bio ...

    Indian Academy of Sciences (India)

    In these complexes, the nucleoside (uridine) acts as a monodentate ligand coordinating through O(4) under the conditions of investigation, whereas the amino acids coordinate through the carboxylate oxygen and the amino nitrogen. Distorted octahedral geometry for Cu(II) and octahedral geometries for both Ni(II) and ...

  18. Water-soluble diphosphadiazacyclooctanes as ligands for aqueous organometallic catalysis

    KAUST Repository

    Boulanger, Jérôme


    Two new water-soluble diphosphacyclooctanes been synthesized and characterized by NMR and surface tension measurements. Both phosphanes proved to coordinate rhodium in a very selective way as well-defined bidentates were obtained. When used in Rh-catalyzed hydroformylation of terminal alkenes, both ligands positively impacted the reaction chemoselectivity. © 2012 Elsevier B.V.

  19. Heteromultivalent ligand-decoration for actively targeted nanomedicine. (United States)

    Modery-Pawlowski, Christa L; Gupta, Anirban Sen


    Active targeting has become an important component of nanomedicine design where nanovehicles are surface-decorated with cell receptor-specific or disease matrix-specific ligands to enable site-selective binding, retention and delivery of theranostic cargo. In this context, there have been numerous reports regarding surface-modification of nanovehicles with antibodies, antibody fragments, carbohydrates, aptamers and peptides as targeting ligands. However, majority of these reports have focused on using a single type of targeting moiety on the vehicle surface. In any disease development and progression, multiple receptors and proteins are often spatio-temporally upregulated simultaneously and heterogeneously. Rationalizing from this, a significant advantage can be envisioned in targeting multiple entities simultaneously using vehicle co-decoration with multiple types of ligands, to enhance binding activity and targeting specificity. To this end, we present a comprehensive up-to-date review on research endeavors in heteromultivalent ligand-modification of nanovehicles and provide a mechanistic rationale as well as an insightful discussion of this promising area, including findings from our own research. Copyright © 2013 Elsevier Ltd. All rights reserved.

  20. Topological estimation of proton–ligand formation constants of ...

    Indian Academy of Sciences (India)

    Proton-ligand formation constants of salicylhydroxamic acids (SHA) and their nuclear substituted derivatives have been estimated topologically using the normalized Wiener index, referred to as mean square Wiener index (Wms). Regression analysis of the data indicates that Wms can be used successfully for estimating ...

  1. Assessing ligand efficiencies using template-based molecular ...

    Indian Academy of Sciences (India)

    Statistical modelling using artificial neural network (ANN: 2 = 0.922) and multiple linear regression method (MLR: 2 = 0.851) showed good correlation between the biological activity, binding affinity, and different ligand efficiencies of the compounds, which suggest the robustness of the template-based binding ...

  2. Dependence of the cone angles of phosphorus-containing ligands ...

    Indian Academy of Sciences (India)


    Dependence of the cone angles of phosphorus-containing ligands in the chemistry of hydride and dihydrogen complexes of ruthenium. NISHA MATHEW and BALAJI R JAGIRDAR. Department of Inorganic and Physical Chemistry, Indian Institute of Science,. Bangalore 560 012, India. A series of new hydride complexes of ...

  3. 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


    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

  4. Evidence for clustered mannose as a new ligand for hyaluronan ...

    Indian Academy of Sciences (India)

    Here, we show the affinity of rHABP1 towards D-mannosylated albumin (DMA) by overlay assay and purification using a DMA affinity column. Our data suggests that DMA is another ligand for HABP1. Furthermore, we have observed that DMA inhibits the binding of HA in a concentration-dependent manner, suggesting its ...

  5. Modeling of metal interaction geometries for protein-ligand docking. (United States)

    Seebeck, Birte; Reulecke, Ingo; Kämper, Andreas; Rarey, Matthias


    The accurate modeling of metal coordination geometries plays an important role for structure-based drug design applied to metalloenzymes. For the development of a new metal interaction model, we perform a statistical analysis of metal interaction geometries that are relevant to protein-ligand complexes. A total of 43,061 metal sites of the Protein Data Bank (PDB), containing amongst others magnesium, calcium, zinc, iron, manganese, copper, cadmium, cobalt, and nickel, were evaluated according to their metal coordination geometry. Based on statistical analysis, we derived a model for the automatic calculation and definition of metal interaction geometries for the purpose of molecular docking analyses. It includes the identification of the metal-coordinating ligands, the calculation of the coordination geometry and the superposition of ideal polyhedra to identify the optimal positions for free coordination sites. The new interaction model was integrated in the docking software FlexX and evaluated on a data set of 103 metalloprotein-ligand complexes, which were extracted from the PDB. In a first step, the quality of the automatic calculation of the metal coordination geometry was analyzed. In 74% of the cases, the correct prediction of the coordination geometry could be determined on the basis of the protein structure alone. Secondly, the new metal interaction model was tested in terms of predicting protein-ligand complexes. In the majority of test cases, the new interaction model resulted in an improved docking accuracy of the top ranking placements. 2007 Wiley-Liss, Inc.

  6. Effect of second ligand on the luminescence of Samarium (III ...

    Indian Academy of Sciences (India)

    Effect of second ligand on the luminescence of Samarium (III) dibenzoylmethane complexes: Syntheses, crystal structures, thermal analysis and luminescence study. MUHAMMAD IDIRIS SALEH, MIN YEE CHOO, TAI WEI CHAN and MOHD R RAZALI. ∗. School of Chemical Sciences, Universiti Sains Malaysia, Penang, ...

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

    Indian Academy of Sciences (India)

    ... Lecture Workshops · Refresher Courses · Symposia. Home; Journals; Journal of Chemical Sciences; Volume 119; Issue 1. Study of the spectroscopic characteristics of methyl (ligand) cobaloximes and their antibacterial activity. N Navaneetha P A Nagarjun S Satyanarayana. Volume 119 Issue 1 January 2007 pp 29-34 ...

  8. Chelating ligands: enhancers of quality and purity of biogas ...

    African Journals Online (AJOL)

    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. Experimental ...

  9. Synergistic Effects of PPARγ Ligands and Retinoids in Cancer Treatment

    Directory of Open Access Journals (Sweden)

    Masahito Shimizu


    Full Text Available Peroxisome proliferator-activated receptors (PPARs are members of the nuclear receptor superfamily. The activation of PPARs by their specific ligands is regarded as one of the promising strategies to inhibit cancer cell growth. However, recent clinical trials targeting several common cancers showed no beneficial effect when PPAR ligands are used as a monotherapy. Retinoid X receptors (RXRs, which play a critical role in normal cell proliferation as a master regulator for nuclear receptors, preferentially form heterodimers with PPARs. A malfunction of RXRα due to phosphorylation by the Ras/MAPK signaling pathway is associated with the development of certain types of human malignancies. The activation of PPARγ/RXR heterodimer by their respective ligands synergistically inhibits cell growth, while inducing apoptosis in human colon cancer cells when the phosphorylation of RXRα was inhibited. We herein review the synergistic antitumor effects produced by the combination of the PPAR, especially PPARγ, ligands plus other agents, especially retinoids, in a variety of human cancers. We also focus on the phosphorylation of RXRα because the inhibition of RXRα phosphorylation and the restoration of its physiological function may activate PPAR/RXR heterodimer and, therefore, be a potentially effective and critical strategy for the inhibition of cancer cell growth.

  10. Synthesis and characterization of mixed ligand complexes of Zn (II ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 117; Issue 3. Synthesis and characterization of mixed ligand complexes of Zn(II) and Co(II) with amino acids: Relevance to zinc binding sites in zinc fingers. P Rabindra Reddy M Radhika P Manjula. Volume 117 Issue 3 May 2005 pp 239-246 ...

  11. Nickel (II) complexes containing ONS donor ligands: Synthesis ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 127; Issue 4. Nickel(II) complexes containing ONS donor ligands: Synthesis, characterization, crystal structure and catalytic application towards C-C cross-coupling reactions. Panneerselvam Anitha Rajendran Manikandan Paranthaman Vijayan Govindan Prakash ...

  12. Quantifying ligand effects in high-oxidation-state metal catalysis (United States)

    Billow, Brennan S.; McDaniel, Tanner J.; Odom, Aaron L.


    Catalysis by high-valent metals such as titanium(IV) impacts our lives daily through reactions like olefin polymerization. In any catalysis, optimization involves a careful choice of not just the metal but also the ancillary ligands. Because these choices dramatically impact the electronic structure of the system and, in turn, catalyst performance, new tools for catalyst development are needed. Understanding ancillary ligand effects is arguably one of the most critical aspects of catalyst optimization and, while parameters for phosphines have been used for decades with low-valent systems, a comparable system does not exist for high-valent metals. A new electronic parameter for ligand donation, derived from experiments on a high-valent chromium species, is now available. Here, we show that the new parameters enable quantitative determination of ancillary ligand effects on catalysis rate and, in some cases, even provide mechanistic information. Analysing reactions in this way can be used to design better catalyst architectures and paves the way for the use of such parameters in a host of high-valent processes.

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

    KAUST Repository

    Tang, Jiang


    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. Some new IIB group complexes of an imidazolidine ligand ...

    Indian Academy of Sciences (India)

    inosa, Staphylococcus aureus and Bacillus subtillis bac- teria and also for their inhibitory effects on the growth of Candid albicans using disc diffusion and MIC meth- ods. The antibacterial activities of the ligand and its complexes as inhibition zone (mm) of the bacterial and fungal growth have been classified in table 5 and.

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

    Indian Academy of Sciences (India)

    The association equilibrium constant (KE) for the outer sphere complex formation has been evaluated together with rate constants for the two subsequent steps. The rate constants increase with increasing ligand concentration and the evaluated activation parameters for all reactions suggest an associative substitution ...

  16. synthesis and spectra characterization of mixed- ligand complexes ...

    African Journals Online (AJOL)


    “Let's Twist Again”-Double-Stranded,. Triple-Stranded, and Circular Helicates. Chemical Reviews 101(11): 3457-3498. Belfrekh, N., Dietrich-Buchecker, C. and Sauvage, J. P.. 2000. Synthesis and Characterization of Dinuclear Metal. Complexes Stabilized by Tetradentate Schiff base ligands.Inorganic Chemistry 39: 5169-.

  17. Structural basis for AMPA receptor activation and ligand selectivity

    DEFF Research Database (Denmark)

    Hogner, A; Kastrup, Jette Sandholm Jensen; Jin, R


    with Br-HIBO and ACPA have allowed us to explain the molecular mechanism behind this selectivity and to identify key residues for ligand recognition. The agonists induce the same degree of domain closure as AMPA, except for Br-HIBO, which shows a slightly lower degree of domain closure. An excellent...

  18. Selective Electrocatalytic Activity of Ligand Stabilized Copper Oxide Nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Kauffman, Douglas R; Ohodnicki, Paul R; Kail, Brian W; Matranga, Christopher


    Ligand stabilization can influence the surface chemistry of Cu oxide nanoparticles (NPs) and provide unique product distributions for electrocatalytic methanol (MeOH) oxidation and CO{sub 2} reduction reactions. Oleic acid (OA) stabilized Cu{sub 2}O and CuO NPs promote the MeOH oxidation reaction with 88% and 99.97% selective HCOH formation, respectively. Alternatively, CO{sub 2} is the only reaction product detected for bulk Cu oxides and Cu oxide NPs with no ligands or weakly interacting ligands. We also demonstrate that OA stabilized Cu oxide NPs can reduce CO{sub 2} into CO with a {approx}1.7-fold increase in CO/H{sub 2} production ratios compared to bulk Cu oxides. The OA stabilized Cu oxide NPs also show 7.6 and 9.1-fold increases in CO/H{sub 2} production ratios compared to weakly stabilized and non-stabilized Cu oxide NPs, respectively. Our data illustrates that the presence and type of surface ligand can substantially influence the catalytic product selectivity of Cu oxide NPs.

  19. Synthesis and evaluation of potential ligands for nuclear waste processing

    NARCIS (Netherlands)

    Iqbal, M.


    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

  20. Mixed-ligand complexes of ruthenium (II) incorporating a diazo ...

    Indian Academy of Sciences (India)

    Binding of these complexes with calf thymus DNA (CT-DNA) has been investigated by absorption spectroscopy, steady-state emission spectroscopy and viscosity measurements. The experimental results indicate that the size and shape of the intercalating ligands have marked effect on the binding affinity of the complexes ...

  1. Designer Ligands. Part 13. Synthesis and Catalytic Activity of ...

    African Journals Online (AJOL)

    Copper(I), copper(II), cobalt(II) and zinc(II) complexes of a macrocyclic, multidentate Schiff-base ligand have been prepared and, with the exception of the zinc(II) complex, have been shown to exhibit biomimetic catecholase activity. Keywords: Copper(II);Cobalt(II); Zinc(II); Biomimetic complexes; Catecholase activity

  2. SLATE : a method for the superposition of flexible ligands

    NARCIS (Netherlands)

    Mills, J.E.; de Esch, I J; Perkins, T.D.; Dean, P.M.

    A novel program for the superposition of flexible molecules, SLATE, is presented. It uses simulated annealing to minimise the difference between the distance matrices calculated from the hydrogen-bonding and aromaticring properties of two ligands. A method for generating a molecular stack using

  3. Ligand.Info small-molecule Meta-Database. (United States)

    von Grotthuss, Marcin; Koczyk, Grzegorz; Pas, Jakub; Wyrwicz, Lucjan S; Rychlewski, Leszek


    Ligand.Info is a compilation of various publicly available databases of small molecules. The total size of the Meta-Database is over 1 million entries. The compound records contain calculated three-dimensional coordinates and sometimes information about biological activity. Some molecules have information about FDA drug approving status or about anti-HIV activity. Meta-Database can be downloaded from the http://Ligand.Info web page. The database can also be screened using a Java-based tool. The tool can interactively cluster sets of molecules on the user side and automatically download similar molecules from the server. The application requires the Java Runtime Environment 1.4 or higher, which can be automatically downloaded from Sun Microsystems or Apple Computer and installed during the first use of Ligand.Info on desktop systems, which support Java (Ms Windows, Mac OS, Solaris, and Linux). The Ligand.Info Meta-Database can be used for virtual high-throughput screening of new potential drugs. Presented examples showed that using a known antiviral drug as query the system was able to find others antiviral drugs and inhibitors.

  4. Synthesis and Characterization of Metal Complexes with Schiff Base Ligands (United States)

    Wilkinson, Shane M.; Sheedy, Timothy M.; New, Elizabeth J.


    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…

  5. Ligand-targeted particulate nanomedicines undergoing clinical evaluations: current status

    NARCIS (Netherlands)

    van der Meel, Roy; Vehmeijer, Laurens J.C.; Kok, Robbert J.; Storm, Gerrit; van Gaal, Ethlinn V.B.


    Since the introduction of Doxil® on the market nearly 20 years ago, a number of nanomedicines have become part of treatment regimens in the clinic. With the exception of antibody–drug conjugates, these nanomedicines are all devoid of targeting ligands and rely solely on their physicochemical

  6. Synthesis and characterization of mixed ligand complexes of bio ...

    Indian Academy of Sciences (India)


    bio-metals with pyrimidine nucleoside (uridine) and amino acids. P RABINDRA REDDY* and A MOHAN REDDY. Department of Chemistry, Osmania University, Hyderabad 500 007, India. MS received 24 December 1999; revised 28 August 2000. Abstract. The mixed ligand complexes of Cu(II), Ni(II) and Co(II) with uridine ...

  7. : Recyclable, ligand free palladium(II) catalyst for Heck reaction

    Indian Academy of Sciences (India)

    Abstract. Palladium substituted in cerium dioxide in the form of a solid solution, Ce0·98 Pd0·02 O1·98 is a new heterogeneous catalyst which exhibits high activity and 100% trans-selectivity for the Heck reactions of aryl bromides including heteroaryls with olefins. The catalytic reactions work without any ligand. Nano-.

  8. Group 4 Metal Complexes of Chelating Cyclopentadienyl-ketimide Ligands

    Czech Academy of Sciences Publication Activity Database

    Večeřa, M.; Varga, Vojtěch; Císařová, I.; Pinkas, Jiří; Kucharczyk, P.; Sedlařík, V.; Lamač, Martin


    Roč. 35, č. 5 (2016), s. 785-798 ISSN 0276-7333 R&D Projects: GA ČR(CZ) GA14-08531S; GA MŠk(CZ) LO1504 Institutional support: RVO:61388955 Keywords : group 4 metal complexes * cyclopentadienyl-ketimide ligands * metallocenes Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.862, year: 2016

  9. Columnar phases exhibited by some polycatenar ligands and a few ...

    Indian Academy of Sciences (India)

    Home; Journals; Pramana – Journal of Physics; Volume 61; Issue 2. Columnar phases exhibited by some polycatenar ligands and a few related metal complexes. B K Sadashiva V A Raghunathan. Volume 61 Issue 2 August 2003 pp 219-229 ... Keywords. Columnar phase; cubic phase; polycatenar; metal complex.

  10. Structure-Based Rational Design of Adenosine Receptor Ligands. (United States)

    Gutiérrez-de-Terán, Hugo; Sallander, Jessica; Sotelo, Eddy


    The family of adenosine receptors (ARs) is focus of several medicinal chemistry programs aimed to find new potent and selective drugs. Each receptor subtype has been proposed as a relevant drug target in the treatment of, e.g., cardiovascular or inflammatory diseases, asthma or Parkinson's disease. Until recently, most of these efforts have been dominated by ligand-based or empirical approaches. However, the latest advances in G protein-coupled receptor (GPCR) crystallography allowed for a thorough structural characterization of the A2AAR subtype, which has been crystalized with a number of agonists and antagonists. Consequently, the ligand discovery of AR ligands has been enriched with a number of structure-based approaches. These include the generation of higher-confident homology models for the remaining AR subtypes, virtual screening identification of novel chemotypes, structure-based lead-optimization programs, rationalization of selectivity profiles, or the structural characterization of novel binding sites that enable the design of novel allosteric modulators. Computational methodologies have importantly contributed to the success of these structure-based approaches, and the recent advances in the field are also analyzed in this review. We conclude that the design of adenosine receptor ligands has improved dramatically with the consideration of structure- based approaches, which is paving the way to a better understanding of the biology and pharmacological modulation of this relevant family of receptors.

  11. Heterogenization of Some PNP Ligands for the Oligomerization of ...

    African Journals Online (AJOL)

    Bis(diphenylphosphino)amine ligands were supported on Merrifield's resin and tested in catalytic ethylene oligomerization reactions with a chromium source. The supported ... Oligomerization reactions were carried out in a Parr pressure reactor using Cr(acac)3 as the precursor and MMAO-3A as the activator. The system ...

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

    African Journals Online (AJOL)

    Neil Grimmer

    metal, ligand and bridge choice has on polymerisation activity and the physical properties of the polymer produced. A major ... The Effect of Bridge Choice. 146. 4. Metallocene Synthesis: Resolving the ...... Separation strategies: the employment of techniques that extract the desired compound from a product mixture. 4.1.

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

    African Journals Online (AJOL)



    Mar 3, 2009 ... 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 ...

  14. 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 ...

  15. Design, synthesis and evaluation of multivalent glycodendrimers as multivalent ligands

    NARCIS (Netherlands)

    Branderhorst, H.M.


    Carbohydrates are more and more of interest in drug design as they are important mediators in a whole range of biological processes. Because of the low affinity of carbohydrates for their receptors, multivalent ligand presentation was introduced. Multivalent compounds were shown to improve the

  16. Effect of second ligand on the luminescence of Samarium (III ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 127; Issue 12. Effect of second ligand on the luminescence of Samarium (III) dibenzoylmethane complexes: ... Muhammad Idiris Saleh1 Min Yee Choo1 Tai Wei Chan1 Mohd R Razali1. School of Chemical Sciences, Universiti Sains Malaysia, Penang, Malaysia ...

  17. Tissue distribution of the death ligand TRAIL and its receptors

    NARCIS (Netherlands)

    Spierings, DC; de Vries, EG; Vellenga, E; van den Heuvel, FA; Koornstra, JJ; Wesseling, J; Hollema, H; de Jong, S

    Recombinant human (rh) TNF-related apoptosis-inducing ligand (TRAIL) harbors potential as an anticancer agent. RhTRAIL induces apoptosis via the TRAIL receptors TRAIL-R1 and TRAIL-R2 in tumors and is non-toxic to nonhuman primates. Because limited data are available about TRAIL receptor

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

    African Journals Online (AJOL)

    The tridentate N4-type Schiff base was synthesized from the condensation reaction of 2-hydrazinopyridine and pyridine-2-carbaldehyde. Neodymium and Samarium complexes were isolated when the corresponding nitrate salt was added to the solution of the ligand. The isolated compounds were characterized by ...

  19. Assessing ligand efficiencies using template-based molecular ...

    Indian Academy of Sciences (India)


    on a series of 38 TIBO derivatives as HIV-1 reverse transcriptase (HIV-1 RT) inhibitors. Four different templates of the Cl-TIBO (1-REV) were created and used as reference templates for docking and align- ing. On the basis of the optimal conformation of the ligands, when fitting to the template, the respective scoring functions ...

  20. Lead Generation and Optimization Based on Protein-Ligand Complementarity

    Directory of Open Access Journals (Sweden)

    Koji Ogata


    Full Text Available This work proposes a computational procedure for structure-based lead generation and optimization, which relies on the complementarity of the protein-ligand interactions. This procedure takes as input the known structure of a protein-ligand complex. Retaining the positions of the ligand heavy atoms in the protein binding site it designs structurally similar compounds considering all possible combinations of atomic species (N, C, O, CH3, NH,etc. Compounds are ranked based on a score which incorporates energetic contributions evaluated using molecular mechanics force fields. This procedure was used to design new inhibitor molecules for three serine/threonine protein kinases (p38 MAP kinase, p42 MAP kinase (ERK2, and c-Jun N-terminal kinase 3 (JNK3. For each enzyme, the calculations produce a set of potential inhibitors whose scores are in agreement with IC50 data and Ki values. Furthermore, the native ligands for each protein target, scored within the five top-ranking compounds predicted by our method, one of the top-ranking compounds predicted to inhibit JNK3 was synthesized and his inhibitory activity confirmed against ATP hydrolysis. Our computational procedure is therefore deemed to be a useful tool for generating chemically diverse molecules active against known target proteins.

  1. Are there physicochemical differences between allosteric and competitive ligands? (United States)

    Lu, Jing; Carlson, Heather A.


    Previous studies have compared the physicochemical properties of allosteric compounds to non-allosteric compounds. Those studies have found that allosteric compounds tend to be smaller, more rigid, more hydrophobic, and more drug-like than non-allosteric compounds. However, previous studies have not properly corrected for the fact that some protein targets have much more data than other systems. This generates concern regarding the possible skew that can be introduced by the inherent bias in the available data. Hence, this study aims to determine how robust the previous findings are to the addition of newer data. This study utilizes the Allosteric Database (ASD v3.0) and ChEMBL v20 to systematically obtain large datasets of both allosteric and competitive ligands. This dataset contains 70,219 and 9,511 unique ligands for the allosteric and competitive sets, respectively. Physically relevant compound descriptors were computed to examine the differences in their chemical properties. Particular attention was given to removing redundancy in the data and normalizing across ligand diversity and varied protein targets. The resulting distributions only show that allosteric ligands tend to be more aromatic and rigid and do not confirm the increase in hydrophobicity or difference in drug-likeness. These results are robust across different normalization schemes. PMID:29125840

  2. Identification of VDR Antagonists among Nuclear Receptor Ligands Using Virtual Screening

    Directory of Open Access Journals (Sweden)

    Kelly Teske


    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.

  3. Organic ligand-induced dissolution kinetics of antimony trioxide. (United States)

    Hu, Xingyun; He, Mengchang


    The influence of low-molecular-weight dissolved organic matter (LMWDOM) on the dissolution rate of Sb2O3 was investigated. Some representative LMWDOMs with carboxyl, hydroxyl, hydrosulfuryl and amidogen groups occurring naturally in the solution were chosen, namely oxalic acid, citric acid, tartaric acid, EDTA, salicylic acid, phthalandione, glycine, thiolactic acid, xylitol, glucose and catechol. These LMWDOMs were dissolved in inert buffers at pH=3.7, 6.6 and 8.6 and added to powdered Sb2O3 in a stirred, thermostatted reactor (25°C). The addition of EDTA, tartaric acid, thiolactic acid, citric acid and oxalic acid solutions at pH3.7 and catechol at pH8.6 increased the rate of release of antimony. In the 10mmol/L thiolactic acid solution, up to 97% by mass of the antimony was released after 120min reaction. There was no effect on the dissolution of Sb2O3 for the other ligands. A weak correlation between dissolution rate with the dissociation constant of ligands and the stability of the dissolved complex was also found. All the results showed that the extent of the promoting effect of ligands on the dissolution of Sb2O3 was not determined by the stability of the dissolved complex, but by the dissociation constant of ligands and detachment rate of surface chelates from the mineral surface. This study can not only help in further understanding the effect of individual low-molecular-weight organic ligands, but also provides a reference to deduce the effect of natural organic matters with oxygen-bearing functional groups on the dissolution of antimony oxide minerals. Copyright © 2016. Published by Elsevier B.V.

  4. Ligand design for multidimensional magnetic materials: a metallosupramolecular perspective. (United States)

    Pardo, Emilio; Ruiz-García, Rafael; Cano, Joan; Ottenwaelder, Xavier; Lescouëzec, Rodrigue; Journaux, Yves; Lloret, Francesc; Julve, Miguel


    The aim and scope of this review is to show the general validity of the 'complex-as-ligand' approach for the rational design of metallosupramolecular assemblies of increasing structural and magnetic complexity. This is illustrated herein on the basis of our recent studies on oxamato complexes with transition metal ions looking for the limits of the research avenue opened by Kahn's pioneering research twenty years ago. The use as building blocks of mono-, di- and trinuclear metal complexes with a novel family of aromatic polyoxamato ligands allowed us to move further in the coordination chemistry-based approach to high-nuclearity coordination compounds and high-dimensionality coordination polymers. In order to do so, we have taken advantage of the new developments of metallosupramolecular chemistry and in particular, of the molecular-programmed self-assembly methods that exploit the coordination preferences of metal ions and specifically tailored ligands. The judicious choice of the oxamato metal building block (substitution pattern and steric requirements of the bridging ligand, as well as the electronic configuration and magnetic anisotropy of the metal ion) allowed us to control the overall structure and magnetic properties of the final multidimensional nD products (n = 0-3). These species exhibit interesting magnetic properties which are brand-new targets in the field of molecular magnetism, such as single-molecule or single-chain magnets, and the well-known class of molecule-based magnets. This unique family of molecule-based magnetic materials expands on the reported examples of nD species with cyanide and related oxalato and dithiooxalato analogues. Moreover, the development of new oxamato metal building blocks with potential photo or redox activity at the aromatic ligand counterpart will provide us with addressable, multifunctional molecular materials for future applications in molecular electronics and nanotechnology.

  5. Structural and Electrochemical Consequences of [Cp*] Ligand Protonation. (United States)

    Peng, Yun; Ramos-Garcés, Mario V; Lionetti, Davide; Blakemore, James D


    There are few examples of the isolation of analogous metal complexes bearing [η5-Cp*] and [η4-Cp*H] (Cp* = pentamethylcyclopentadienyl) complexes within the same metal/ligand framework, despite the relevance of such structures to catalytic applications. Recently, protonation of Cp*Rh(bpy) (bpy = 2,2'-bipyridyl) has been shown to yield a complex bearing the uncommon [η4-Cp*H] ligand, rather than generating a [RhIII-H] complex. We now report the purification and isolation of this protonated species, as well as characterization of analogous complexes of 1,10-phenanthroline (phen). Specifically, reaction of Cp*Rh(bpy) or Cp*Rh(phen) with 1 equiv of Et3NH+Br- affords rhodium compounds bearing endo-η4-pentamethylcyclopentadiene (η4-Cp*H) as a ligand. NMR spectroscopy and single-crystal X-ray diffraction studies confirm protonation of the Cp* ligand, rather than formation of metal hydride complexes. Analysis of new structural data and electronic spectra suggests that phen is significantly reduced in Cp*Rh(phen), similar to the case of Cp*Rh(bpy). Backbonding interactions with olefinic motifs are activated by formation of [η4-Cp*H]; protonation of [Cp*] stabilizes the low-valent metal center and results in loss of reduced character on the diimine ligands. In accord with these changes in electronic structure, electrochemical studies reveal a distinct manifold of redox processes that are accessible in the [Cp*H] complexes in comparison with their [Cp*] analogues; these processes suggest new applications in catalysis for the complexes bearing endo-η4-Cp*H.

  6. ALX receptor ligands define a biochemical endotype for severe asthma (United States)

    Ricklefs, Isabell; Barkas, Ioanna; Duvall, Melody G.; Grossman, Nicole L.; Israel, Elliot; Bleecker, Eugene R.; Castro, Mario; Erzurum, Serpil C.; Fahy, John V.; Gaston, Benjamin M.; Denlinger, Loren C.; Mauger, David T.; Wenzel, Sally E.; Comhair, Suzy A.; Coverstone, Andrea M.; Fajt, Merritt L.; Hastie, Annette T.; Johansson, Mats W.; Peters, Michael C.; Phillips, Brenda R.; Levy, Bruce D.


    BACKGROUND. In health, inflammation resolution is an active process governed by specialized proresolving mediators and receptors. ALX/FPR2 receptors (ALX) are targeted by both proresolving and proinflammatory ligands for opposing signaling events, suggesting pivotal roles for ALX in the fate of inflammatory responses. Here, we determined if ALX expression and ligands were linked to severe asthma (SA). METHODS. ALX expression and levels of proresolving ligands (lipoxin A4 [LXA4], 15-epi-LXA4, and annexin A1 [ANXA1]), and a proinflammatory ligand (serum amyloid A [SAA]) were measured in bronchoscopy samples collected in Severe Asthma Research Program-3 (SA [n = 69], non-SA [NSA, n = 51] or healthy donors [HDs, n = 47]). RESULTS. Bronchoalveolar lavage (BAL) fluid LXA4 and 15-epi-LXA4 were decreased and SAA was increased in SA relative to NSA. BAL macrophage ALX expression was increased in SA. Subjects with LXA4loSAAhi levels had increased BAL neutrophils, more asthma symptoms, lower lung function, increased relative risk for asthma exacerbation, sinusitis, and gastroesophageal reflux disease, and were assigned more frequently to SA clinical clusters. SAA and aliquots of LXA4loSAAhi BAL fluid induced IL-8 production by lung epithelial cells expressing ALX receptors, which was inhibited by coincubation with 15-epi-LXA4. CONCLUSIONS. Together, these findings have established an association between select ALX receptor ligands and asthma severity that define a potentially new biochemical endotype for asthma and support a pivotal functional role for ALX signaling in the fate of lung inflammation. TRIAL REGISTRATION. Severe Asthma Research Program-3 (SARP-3; NCT01606826) FUNDING Sources. National Heart, Lung and Blood Institute, the NIH, and the German Society of Pediatric Pneumology. PMID:28724795

  7. Scandium SALEN complexes bearing chloro, aryloxo, and hydroxo ligands. (United States)

    Meermann, Christian; Törnroos, Karl W; Anwander, Reiner


    Heteroleptic amide complexes (SALEN)Sc[N(SiHMe(2))(2)] (SALEN = Salen(tBu,tBu), Salcyc(tBu,tBu), or Salpren(tBu,tBu) if not stated differently) were examined as synthesis precursors according to silylamine elimination reactions. Treatment of (SALEN)Sc[N(SiHMe(2))(2)] with H(2)O or phenols (HOAr(R,R); R = tBu, iPr) afforded complexes [(SALEN)Sc(mu-OH)](2) and (SALEN)Sc(OAr(R,R)), while chloro exchange products were formed from the respective reactions with NH(4)Cl or AlMe(2)Cl. Such complexes [(SALEN)Sc(mu-Cl)](2) and (SALEN)ScCl(thf) were also obtained by utilizing alternative synthesis protocols, allowing for controlled donor absence and presence. Heteroleptic amide precursors [Sc(NiPr(2))(2)(mu-Cl)(thf)](2) and [Sc[N(SiHMe(2))(2)](2)(mu-Cl)(thf)](2) readily undergo amine elimination reactions with H(2)SALEN derivatives to form the corresponding chloride complexes. Spectroscopic and X-ray structural data of the heteroleptic scandium complexes revealed an exclusive intramolecular tetradentate coordination mode of the SALEN ligands independent of the SALEN ligand bite angle and the nature of the "second" ligand (chloro, amido, aryloxo, hydroxo). The coordination of the SALEN ligands is rationalized on the basis of (a) the displacement d of the metal center from the [N(2)O(2)] least-squares plane, (b) the dihedral angle alpha between the phenyl rings of the salicylidene moieties, and (c) the angle beta = Ct-Ln-Ct (Ct = centroid of the phenyl rings) in the case of strongly twisted ligands.

  8. Heterobifunctional crosslinkers for tethering single ligand molecules to scanning probes

    Energy Technology Data Exchange (ETDEWEB)

    Riener, Christian K.; Kienberger, Ferry; Hahn, Christoph D.; Buchinger, Gerhard M.; Egwim, Innocent O.C.; Haselgruebler, Thomas; Ebner, Andreas; Romanin, Christoph; Klampfl, Christian; Lackner, Bernd; Prinz, Heino; Blaas, Dieter; Hinterdorfer, Peter; Gruber, Hermann J


    Single molecule recognition force microscopy (SMRFM) is a versatile atomic force microscopy (AFM) method to probe specific interactions of cognitive molecules on the single molecule level. It allows insights to be gained into interaction potentials and kinetic barriers and is capable of mapping interaction sites with nm positional accuracy. These applications require a ligand to be attached to the AFM tip, preferably by a distensible poly(ethylene glycol) (PEG) chain between the measuring tip and the ligand molecule. The PEG chain greatly facilitates specific binding of the ligand to immobile receptor sites on the sample surface. The present study contributes to tip-PEG-ligand tethering in three ways: (i) a convenient synthetic route was found to prepare NH{sub 2}-PEG-COOH which is the key intermediate for long heterobifunctional crosslinkers; (ii) a variety of heterobifunctional PEG derivatives for tip-PEG-ligand linking were prepared from NH{sub 2}-PEG-COOH; (iii) in particular, a new PEG crosslinker with one thiol-reactive end and one terminal nitrilotriacetic acid (NTA) group was synthesized and successfully used to tether His{sub 6}-tagged protein molecules to AFM tips via noncovalent NTA-Ni{sup 2+}-His{sub 6} bridges. The new crosslinker was applied to link a recombinant His{sub 6}-tagged fragment of the very-low density lipoprotein receptor to the AFM tip whereupon specific docking to the capsid of human rhinovirus particles was observed by force microscopy. In a parallel study, the specific interaction of the small GTPase Ran with the nuclear import receptor importin {beta}1 was studied in detail by SMRFM, using the new crosslinker to link His{sub 6}-tagged Ran to the measuring tip [Nat. Struct. Biol. (2003), 10, 553-557].

  9. Efficient mapping of ligand migration channel networks in dynamic proteins. (United States)

    Lin, Tu-Liang; Song, Guang


    For many proteins such as myoglobin, the binding site lies in the interior, and there is no obvious route from the exterior to the binding site in the average structure. Although computer simulations for a limited number of proteins have found some transiently open channels, it is not clear if there exist more channels elsewhere or how the channels are regulated. A systematic approach that can map out the whole ligand migration channel network is lacking. Ligand migration in a dynamic protein resembles closely a well-studied problem in robotics, namely, the navigation of a mobile robot in a dynamic environment. In this work, we present a novel robotic motion planning inspired approach that can map the ligand migration channel network in a dynamic protein. The method combines an efficient spatial mapping of protein inner space with a temporal exploration of protein structural heterogeneity, which is represented by a structure ensemble. The spatial mapping of each conformation in the ensemble produces a partial map of protein inner cavities and their inter-connectivity. These maps are then merged to form a super map that contains all the channels that open dynamically. Results on the pathways in myoglobin for gaseous ligands demonstrate the efficiency of our approach in mapping the ligand migration channel networks. The results, obtained in a significantly less amount of time than trajectory-based approaches, are in agreement with previous simulation results. Additionally, the method clearly illustrates how and what conformational changes open or close a channel. Copyright © 2011 Wiley-Liss, Inc.

  10. Impact of glucocorticoid receptor density on ligand-independent dimerization, cooperative ligand-binding and basal priming of transactivation: a cell culture model. (United States)

    Robertson, Steven; Rohwer, Johann M; Hapgood, Janet P; Louw, Ann


    Glucocorticoid receptor (GR) levels vary between tissues and individuals and are altered by physiological and pharmacological effectors. However, the effects and implications of differences in GR concentration have not been fully elucidated. Using three statistically different GR concentrations in transiently transfected COS-1 cells, we demonstrate, using co-immunoprecipitation (CoIP) and fluorescent resonance energy transfer (FRET), that high levels of wild type GR (wtGR), but not of dimerization deficient GR (GRdim), display ligand-independent dimerization. Whole-cell saturation ligand-binding experiments furthermore establish that positive cooperative ligand-binding, with a concomitant increased ligand-binding affinity, is facilitated by ligand-independent dimerization at high concentrations of wtGR, but not GRdim. The down-stream consequences of ligand-independent dimerization at high concentrations of wtGR, but not GRdim, are shown to include basal priming of the system as witnessed by ligand-independent transactivation of both a GRE-containing promoter-reporter and the endogenous glucocorticoid (GC)-responsive gene, GILZ, as well as ligand-independent loading of GR onto the GILZ promoter. Pursuant to the basal priming of the system, addition of ligand results in a significantly greater modulation of transactivation potency than would be expected solely from the increase in ligand-binding affinity. Thus ligand-independent dimerization of the GR at high concentrations primes the system, through ligand-independent DNA loading and transactivation, which together with positive cooperative ligand-binding increases the potency of GR agonists and shifts the bio-character of partial GR agonists. Clearly GR-levels are a major factor in determining the sensitivity to GCs and a critical factor regulating transcriptional programs.

  11. Ligand flexibility and framework rearrangement in a new family of porous metal-organic frameworks

    DEFF Research Database (Denmark)

    Hawxwell, Samuel M; Espallargas, Guillermo Mínguez; Bradshaw, Darren


    Ligand flexibility permits framework rearrangement upon evacuation and gas uptake in a new family of porous MOFs.......Ligand flexibility permits framework rearrangement upon evacuation and gas uptake in a new family of porous MOFs....

  12. Switching of bacterial adhesion to a glycosylated surface by reversible reorientation of the carbohydrate ligand

    DEFF Research Database (Denmark)

    Weber, Theresa; Chrasekaran, Vijayan; Stamer, Insa


    The surface recognition in many biological systems is guided by the interaction of carbohydrate-specific proteins (lectins) with carbohydrate epitopes (ligands) located within the unordered glycoconjugate layer (glycocalyx) of cells. Thus, for recognition, the respective ligand has to reorient...

  13. Iron and Zinc Complexes of Bulky Bis-Imidazole Ligands : Enzyme Mimicry and Ligand-Centered Redox Activity

    NARCIS (Netherlands)

    Folkertsma, E.


    The research described in this thesis is directed to the development of cheap and non-toxic iron-based homogeneous catalysts, using enzyme models and redox non-innocent ligands. Inspired by nature, the first approach focuses on the synthesis of structural models of the active site of non-heme iron

  14. Dinuclear Palladium Complexes with Two Ligand-Centered Radicals and a Single Bridging Ligand: Subtle Tuning of Magnetic Properties

    NARCIS (Netherlands)

    Broere, D.L.J.; Demeshko, S.; de Bruin, B.; Pidko, E.A.; Reek, J.N.H.; Siegler, M.A.; Lutz, M.; van der Vlugt, J.I.


    The facile and tunable preparation of unique dinuclear [(L-center dot) Pd-X-Pd(L-center dot)] complexes (X = Cl or N-3), bearing a ligand radical on each Pd, is disclosed, as well as their magnetochemistry in solution and solid state is reported. Chloride abstraction from [PdCl(NNOISQ)] (NNOISQ =

  15. Metal ligand aromatic cation-pi interactions in metalloproteins: ligands coordinated to metal interact with aromatic residues. (United States)

    Zarić, S D; Popović, D M; Knapp, E W


    Cation-pi interactions between aromatic residues and cationic amino groups in side chains and have been recognized as noncovalent bonding interactions relevant for molecular recognition and for stabilization and definition of the native structure of proteins. We propose a novel type of cation-pi interaction in metalloproteins; namely interaction between ligands coordinated to a metal cation--which gain positive charge from the metal--and aromatic groups in amino acid side chains. Investigation of crystal structures of metalloproteins in the Protein Data Bank (PDB) has revealed that there exist quite a number of metalloproteins in which aromatic rings of phenylalanine, tyrosine, and tryptophan are situated close to a metal center interacting with coordinated ligands. Among these ligands are amino acids such as asparagine, aspartate, glutamate, histidine, and threonine, but also water and substrates like ethanol. These interactions play a role in the stability and conformation of metalloproteins, and in some cases may also be directly involved in the mechanism of enzymatic reactions, which occur at the metal center. For the enzyme superoxide dismutase, we used quantum chemical computation to calculate that Trp163 has an interaction energy of 10.09 kcal mol(-1) with the ligands coordinated to iron.

  16. Synthesis and ligand-based reduction chemistry of boron difluoride complexes with redox-active formazanate ligands

    NARCIS (Netherlands)

    Chang, M. -C.; Otten, E.


    Mono(formazanate) boron difluoride complexes (LBF2), which show remarkably facile and reversible ligand-based redox-chemistry, were synthesized by transmetallation of bis(formazanate) zinc complexes with boron trifluoride. The one-electron reduction product [LBF2](-)[Cp2Co](+) and a key intermediate

  17. Effects of size and ligand density on the chirality transfer from chiral-ligand-capped nanoparticles to nematic liquid crystals (United States)

    Mori, Taizo; Sharma, Anshul; Nemati, Ahlam; Bergquist, Leah; Hegmann, Torsten


    Studies of chiroptical effects of chiral ligand-capped gold nanoparticles (Au NPs) are a fascinating and rapidly evolving field in nanomaterial research with promising applications of such chiral metal NPs in catalysis and metamaterials as well as chiral sensing and separation. The aim of our studies was to seek out a system that not only allows the detection and understanding of Au NP chirality but also permits visualization and ranking — considering size, shape and nature as well as density of the ligand shell — of the extent of chirality transfer to a surrounding medium. Nematic liquid crystal (N-LC) phases are an ideal platform to examine these effects, exhibiting characteristic defect textures upon doping with a chiral additive. To test this, we synthesized series of Au NPs capped with two structurally different chiral ligands and studied well-dispersed mixtures in two nematic liquid crystal hosts. Induced circular dichroism (ICD) spectropolarimetry and polarized light optical microscopy (POM) confirmed that all Au NPs induce chiral nematic (N*-LC) phases, and measurements of the helical pitch as well as calculation of the helical twisting power (HTP) in various cell geometries allowed for an insightful ranking of the efficiency of chirality transfer of all Au NPs as well as their free ligands.

  18. The synthesis, structures and characterisation of new mixed-ligand manganese and iron complexes with tripodal, tetradentate ligands

    NARCIS (Netherlands)

    van Gorkum, R.; Berding, J.; Mills, A.M.; Kooijman, H.|info:eu-repo/dai/nl/091208610; Tooke, D.M.; Spek, A.L.|info:eu-repo/dai/nl/156517566; Mutikainen, I.; Turpeinen, U.; Reedijk, J.; Bouwman, E.


    The preparation of new manganese and iron complexes with the general formula [M(tripod)(anion)] is described, where M = FeIII or MnIII, “tripod” is a dianionic tetradentate tripodal ligand and the anion is a chelating β-diketonate, 8-oxyquinoline or acetate. The synthesis of this type of complexes

  19. Redesigning an FKBP–ligand interface to generate chemical dimerizers with novel specificity


    Clackson, Tim; Yang, Wu; Rozamus, Leonard W.; Hatada, Marcos; Amara, Jane F.; Rollins, Carl T.; Stevenson, Lauren F.; Magari, Shannon R.; Wood, Susan A.; Courage, Nancy L.; Lu, Xiaode; Cerasoli, Franklin; Gilman, Michael; Holt, Dennis A.


    FKBP ligand homodimers can be used to activate signaling events inside cells and animals that have been engineered to express fusions between appropriate signaling domains and FKBP. However, use of these dimerizers in vivo is potentially limited by ligand binding to endogenous FKBP. We have designed ligands that bind specifically to a mutated FKBP over the wild-type protein by remodeling an FKBP-ligand interface to introduce a specificity binding pocket. A compound bearing an ethyl substituen...



    habibie, habibie


    - TNF-related apoptosis-inducing ligand merupakan salah satu pilihan pengobatan kanker yang secara efektif dapat menginduksi apoptosis melalui aktivasi death receptor (DR4 dan DR5). Penggunaan TNF-related apoptosis-inducing ligand menyebabkan efek samping yang jauh lebih kecil dibandingkan dengan penggunaan kemoterapi. Namun saat ini beberapa jenis kanker menunjukkan resistensi terhadap TNF-related apoptosis-inducing ligand. Penggunaan TNF-related apoptosis-inducing ligand yang dikombinasi...

  1. New biphenol-based, fine-tunable monodentate phosphoramidite ligands for catalytic asymmetric transformations. (United States)

    Hua, Zihao; Vassar, Victor C; Choi, Hojae; Ojima, Iwao


    Monodentate phosphoramidite ligands have been developed based on enantiopure 6,6'-dimethylbiphenols with axial chirality. These chiral ligands are easy to prepare and flexible for modifications. The fine-tuning capability of these ligands plays a significant role in achieving high enantioselectivity in the asymmetric hydroformylation of allyl cyanide and the conjugate addition of diethylzinc to cycloalkenones.

  2. New biphenol-based, fine-tunable monodentate phosphoramidite ligands for catalytic asymmetric transformations


    Hua, Zihao; Vassar, Victor C.; Choi, Hojae; OJIMA, IWAO


    Monodentate phosphoramidite ligands have been developed based on enantiopure 6,6′-dimethylbiphenols with axial chirality. These chiral ligands are easy to prepare and flexible for modifications. The fine-tuning capability of these ligands plays a significant role in achieving high enantioselectivity in the asymmetric hydroformylation of allyl cyanide and the conjugate addition of diethylzinc to cycloalkenones.

  3. Redox non-innocent ligands: versatile new tools to control catalytic reactions

    NARCIS (Netherlands)

    Lyaskovskyy, V.; de Bruin, B.


    In this (tutorial overview) perspective we highlight the use of "redox non-innocent" ligands in catalysis. Two main types of reactivity in which the redox non-innocent ligand is involved can be specified: (A) The redox active ligand participates in the catalytic cycle only by accepting/donating

  4. Flow Cytometry-Based Bead-Binding Assay for Measuring Receptor Ligand Specificity

    NARCIS (Netherlands)

    Sprokholt, Joris K.; Hertoghs, Nina; Geijtenbeek, Teunis B. H.


    In this chapter we describe a fluorescent bead-binding assay, which is an efficient and feasible method to measure interaction between ligands and receptors on cells. In principle, any ligand can be coated on fluorescent beads either directly or via antibodies. Binding between ligand-coated beads

  5. Nickel speciation and complexation kinetics in freshwater by ligand exchange and DPCSV

    NARCIS (Netherlands)

    Han Bin Xue,; Jansen, S.; Prasch, A.; Sigg, L.


    A technique of ligand exchange with DMG (dimethylglyoxime) and DPCSV was applied to determine Ni speciation in lake, river, and groundwater samples. The working conditions related to ligand-exchange equilibrium were optimized, and the ligand-exchange kinetics were examined. The observed

  6. Amino acids as chiral anionic ligands for ruthenium based asymmetric olefin metathesis. (United States)

    Ivry, Elisa; Ben-Asuly, Amos; Goldberg, Israel; Lemcoff, N Gabriel


    Several amino acid ligands were introduced into the Hoveyda-Grubbs 2nd generation complex by a facile anionic ligand exchange. The chiral pre-catalysts obtained displayed enantioselectivity in asymmetric ring-closing and ring-opening cross-metathesis reactions. Reduction of the lability of the carboxylate ligands was found to be cardinal for improving the observed enantiomeric product enrichment.

  7. Olefin Metathesis Mediated By: - Schiff Base Ru-Alkylidenes -Ru-Alkylidenes Bearing Unsymmetrical NH Ligands (United States)

    Monsaert, Stijn; Voort, Pascal Van Der; Ledoux, Nele; Allaert, Bart; Drozdzak, Renata; Verpoort, Francis

    The classic Grubbs second-generation complex 2 was modified through 1. The introduction of a bidentate Schiff base ligand 2. Changes in the amino side groups of the NHC ligand Representative olefin metathesis test reactions show the effects induced by the ligand modifications and demonstrate some interesting new properties of the described catalysts. catalysts.

  8. Design, Testing and Kinetic Analysis of Bulky Monodentate Phosphorus Ligands in the Mizoroki-Heck Reaction

    NARCIS (Netherlands)

    Dodds, Deborah L.; Boele, Maarten D. K.; van Strijdonck, Gino P. F.; de Vries, Johannes G.; van Leeuwen, Piet W. N. M.; Kamer, Paul C. J.

    A series of new monodentate phosphane ligands 2 have been evaluated in the MizorokiHeck arylation reaction of iodobenzene and styrene and compared with our previously reported ligands, 1, 3 and 4. The concept of rational ligand design is discussed, and we describe how the performance of this new

  9. Design, testing and kinetic analysis of bulky monodentate phosphorus ligands in the Mizoroki-Heck reaction

    NARCIS (Netherlands)

    Dodds, D.L.; Boele, M.D.K.; van Strijdonck, G.P.F.; de Vries, J.G.; van Leeuwen, P.W.N.M.; Kamer, P.C.J.


    A series of new monodentate phosphane ligands 2 have been evaluated in the Mizoroki-Heck arylation reaction of iodobenzene and styrene and compared with our previously reported ligands, 1, 3 and 4. The concept of rational ligand design is discussed, and we describe how the performance of this new

  10. Balancing specificity, sensitivity, and speed of ligand discrimination by zero-order ultraspecificity (United States)

    Kajita, Masashi K.; Aihara, Kazuyuki; Kobayashi, Tetsuya J.


    Specific interactions between receptors and their target ligands in the presence of nontarget ligands are crucial for biological processes such as T cell ligand discrimination. To discriminate between the target and nontarget ligands, cells have to increase specificity to the target ligands by amplifying the small differences in affinity among ligands. In addition, sensitivity to the ligand concentration and quick discrimination are also important to detect low amounts of target ligands and facilitate fast cellular decision making after ligand recognition. In this work we propose a mechanism for nonlinear specificity amplification (ultraspecificity) based on zero-order saturating reactions, which was originally proposed to explain nonlinear sensitivity amplification (ultrasensitivity) to the ligand concentration. In contrast to the previously proposed proofreading mechanisms that amplify the specificity by a multistep reaction, our model can produce an optimal balance of specificity, sensitivity, and quick discrimination. Furthermore, we show that a model for insensitivity to a large number of nontarget ligands can be naturally derived from a model with the zero-order ultraspecificity. The zero-order ultraspecificity, therefore, may provide an alternative way to understand ligand discrimination from the viewpoint of nonlinear properties in biochemical reactions.

  11. Computational approaches to modeling receptor flexibility upon ligand binding: Application to interfacially activated enzymes

    DEFF Research Database (Denmark)

    Wade, R.C.; Sobolev, V.; Ortiz, A.R. .


    Receptors generally undergo conformational change upon ligand binding. We describe how fairly simple techniques may be used in docking and design studies to account for some of the changes in the conformations of proteins on ligand binding. Simulations of protein-ligand interactions that give a m...

  12. Mixed-ligand complex formation equilibria of Cu with biguanide in ...

    Indian Academy of Sciences (India)


    metric EDTA titration methods.23 Equilibrium study for the determination of proton-ligand and metal- ligand complex formation constants involved pH- metric titrations of series of solutions, each of initial volume 0⋅025 dm–3, containing known amounts. (0⋅001–0⋅002 mol dm–3) of the ligands, biguanide and/or glycine in ...

  13. DMPD: Endogenous ligands of Toll-like receptors. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 15178705 Endogenous ligands of Toll-like receptors. Tsan MF, Gao B. J Leukoc Biol. ...2004 Sep;76(3):514-9. Epub 2004 Jun 3. (.png) (.svg) (.html) (.csml) Show Endogenous ligands of Toll-like re...ceptors. PubmedID 15178705 Title Endogenous ligands of Toll-like receptors. Authors Tsan MF, Gao B. Publicat

  14. A Langmuir study of novel Schiff Base ligand for ion sensor application

    African Journals Online (AJOL)

    Two novel Schiff Base ligands are used in this work. These amphiphilic ligands were being chosen because of the suitability in forming Langmuir film by using Langmuir-Blodgett (LB) technique. Characterizations of these ligands were carried out through LB technique to obtain the surface pressure-mean molecular area ...

  15. Understanding ligand effects in gold clusters using mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Grant E.; Laskin, Julia


    This review summarizes recent research on the influence of phosphine ligands on the size, stability, and reactivity of gold clusters synthesized in solution. Sub-nanometer clusters exhibit size- and composition-dependent properties that are unique from those of larger nanoparticles. The highly tunable properties of clusters and their high surface-to-volume ratio make them promising candidates for a variety of technological applications. However, because “each-atom-counts” toward defining cluster properties it is critically important to develop robust synthesis methods to efficiently prepare clusters of predetermined size. For decades phosphines have been known to direct the size-selected synthesis of gold clusters. Despite the preparation of numerous species it is still not understood how different functional groups at phosphine centers affect the size and properties of gold clusters. Using electrospray ionization mass spectrometry (ESI-MS) it is possible to characterize the effect of ligand substitution on the distribution of clusters formed in solution at defined reaction conditions. In addition, ligand exchange reactions on preformed clusters may be monitored using ESI-MS. Collision induced dissociation (CID) may also be employed to obtain qualitative insight into the fragmentation of mixed ligand clusters and the relative binding energies of differently substituted phosphines. Quantitative ligand binding energies and cluster stability may be determined employing surface induced dissociation (SID) in a custom-built Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR-MS). Rice-Ramsperger-Kassel-Marcus (RRKM) based modeling of the SID data allows dissociation energies and entropy values to be extracted that may be compared with the results of high-level theoretical calculations. The charge reduction and reactivity of atomically precise gold clusters, including partially ligated species generated in the gas-phase by in source CID, on well

  16. Understanding ligand effects in gold clusters using mass spectrometry. (United States)

    Johnson, Grant E; Laskin, Julia


    This review summarizes recent research on the influence of phosphine ligands on the size, stability, and reactivity of gold clusters synthesized in solution. Sub-nanometer clusters exhibit size- and composition-dependent properties that are unique from those of larger nanoparticles. The highly tunable properties of clusters and their high surface-to-volume ratio make them promising candidates for a variety of technological applications. However, because "each-atom-counts" toward defining cluster properties it is critically important to develop robust synthesis methods to efficiently prepare clusters of predetermined size. For decades phosphines have been known to direct the size-selected synthesis of gold clusters. Despite the preparation of numerous species it is still not understood how different functional groups at phosphine centers affect the size and properties of gold clusters. Using electrospray ionization mass spectrometry (ESI-MS) it is possible to characterize the effect of ligand substitution on the distribution of clusters formed in solution at defined reaction conditions. In addition, ligand exchange reactions on preformed clusters may be monitored using ESI-MS. Collision induced dissociation (CID) may also be employed to obtain qualitative insight into the fragmentation of mixed ligand clusters and the relative binding energies of differently substituted phosphines. Quantitative ligand binding energies and cluster stability may be determined employing surface induced dissociation (SID) in a custom-built Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR-MS). Rice-Ramsperger-Kassel-Marcus (RRKM) based modeling of the SID data allows dissociation energies and entropy values to be extracted. The charge reduction and reactivity of atomically precise gold clusters, including partially ligated species generated in the gas-phase by in source CID, on well-defined surfaces may be explored using ion soft landing (SL) in a custom

  17. Frontal affinity chromatography with MS detection of the ligand binding domain of PPARγ receptor: ligand affinity screening and stereoselective ligand-macromolecule interaction. (United States)

    Calleri, E; Fracchiolla, G; Montanari, R; Pochetti, G; Lavecchia, A; Loiodice, F; Laghezza, A; Piemontese, L; Massolini, G; Temporini, C


    In this study we report the development of new chromatographic tools for binding studies based on the gamma isoform ligand binding domain (LBD) of peroxisome proliferator-activated receptor (PPARγ) belonging to the nuclear receptor superfamily of ligand-activated transcription factors. PPARγ subtype plays important roles in the functions of adipocytes, muscles, and macrophages with a direct impact on type 2 diabetes, dyslipidemia, atherosclerosis, and cardiovascular disease. In order to set up a suitable immobilization chemistry, the LBD of PPARγ receptor was first covalently immobilized onto the surface of aminopropyl silica particles to create a PPARγ-Silica column for zonal elution experiments and then onto the surface of open tubular (OT) capillaries to create PPARγ-OT capillaries following different immobilization conditions. The capillaries were used in frontal affinity chromatography coupled to mass spectrometry (FAC-MS) experiments to determine the relative binding affinities of a series of chiral fibrates. The relative affinity orders obtained for these derivatives were consistent with the EC(50) values reported in literature. The optimized PPARγ-OT capillary was validated by determining the K(d) values of two selected compounds. Known the role of stereoselectivity in the binding of chiral fibrates, for the first time a detailed study was carried out by analysing two enantioselective couples on the LBD-PPARγ capillary by FAC and a characteristic two-stairs frontal profile was derived as the result of the two saturation events. All the obtained data indicate that the immobilized form of PPARγ-LBD retained the ability to specifically bind ligands. Copyright © 2011 Elsevier B.V. All rights reserved.

  18. Age dependent accumulation patterns of advanced glycation end product receptor (RAGE) ligands and binding intensities between RAGE and its ligands differ in the liver, kidney, and skeletal muscle. (United States)

    Son, Myeongjoo; Chung, Wook-Jin; Oh, Seyeon; Ahn, Hyosang; Choi, Chang Hu; Hong, Suntaek; Park, Kook Yang; Son, Kuk Hui; Byun, Kyunghee


    Much evidence indicates receptor for advanced glycation end products (RAGE) related inflammation play essential roles during aging. However, the majority of studies have focused on advanced glycation end products (AGEs) and not on other RAGE ligands. In the present study, the authors evaluated whether the accumulation of RAGE ligands and binding intensities between RAGE and its ligands differ in kidney, liver, and skeletal muscle during aging. In C57BL/6 N mice aged 12 weeks, 12 months, and 22 months, ligands accumulation, binding intensities between RAGE and its ligands, activated macrophage infiltration, M1/M2 macrophage expression, glyoxalase-1expression, and signal pathways related to inflammation were evaluated. The RAGE ligands age-associated accumulation patterns were found to be organ dependent. Binding intensities between RAGE and its ligands in kidney and liver increased with age, but those in skeletal muscle were unchanged. Infiltration of activated macrophages in kidney and liver increased with age, but infiltration in the skeletal muscle was unchanged. M1 expression increased and M2 and glyoxalase-1 expression decreased with age in kidney and liver, but their expressions in skeletal muscle were not changed. These findings indicate patterns of RAGE ligands accumulation, RAGE/ligands binding intensities, or inflammation markers changes during aging are organs dependent.

  19. Ligand design for functional metal-organic frameworks. (United States)

    Paz, Filipe A Almeida; Klinowski, Jacek; Vilela, Sérgio M F; Tomé, João P C; Cavaleiro, José A S; Rocha, João


    Metal-organic frameworks (MOFs), also known as coordination polymers, are formed by the self-assembly of metallic centres and bridging organic linkers. In this critical review, we review the key advances in the field and discuss the relationship between the nature and structure of specifically designed organic linkers and the properties of the products. Practical examples demonstrate that the physical and chemical properties of the linkers play a decisive role in the properties of novel functional MOFs. We focus on target materials suitable for the storage of hydrogen and methane, sequestration of carbon dioxide, gas separation, heterogeneous catalysis and as magnetic and photoluminescent materials capable of both metal- and ligand-centred emission, ion exchangers and molecular sieves. The advantages of highly active discrete complexes as metal-bearing ligands in the construction of MOFs are also briefly reviewed (128 references). This journal is © The Royal Society of Chemistry 2012

  20. Old to new ligand-binding assay method modifications. (United States)

    Stouffer, Bruce; Stocker, Dennis


    This article aims to address approaches to ensuring method changes for regulated ligand-binding assays of biologics drugs from old to newer formats and technology are properly understood, characterized and validated to meet current industry expectations and regulatory requirements. Sections in the chapter will include descriptions of different formats of ligand-binding assays, reasons that may drive updating of methods and procedures for qualifying method changes for immunoassays that are designed to support PK and immunogenicity analyses for clinical and nonclinical applications. Case studies from the authors' experience, as well as literature references will be provided as examples of challenges, as well as providing guidance of when and how to provide smooth transitions of older methods to newer, more robust or sensitive methods as reagents or technology are available.

  1. The Role of Stress-Induced Ligands in Immune Response

    Directory of Open Access Journals (Sweden)

    G.Seyda Seydel


    Full Text Available Natural killer (NK cells which are a component of the immune system are capable of killing tumor cells and virally infected cells. The activation of NK cells is regulated by the balance of activating and inhibitory surface receptors. NKG2D is one of the these activating receptors. The ligands of NKG2D are the human class I like molecules MICA and MICB which are encoded within the human MHC. MICA and MICB are not expressed on normal cells but up-regulated under condition of stress such as heat schock and viral infection. Therefore, NKG2D ligands are defined as stress-induced antigens. [Archives Medical Review Journal 2011; 20(1.000: 1-19

  2. Programmed death-1 & its ligands: promising targets for cancer immunotherapy. (United States)

    Shrimali, Rajeev K; Janik, John E; Abu-Eid, Rasha; Mkrtichyan, Mikayel; Khleif, Samir N


    Novel strategies for cancer treatment involving blockade of immune inhibitors have shown significant progress toward understanding the molecular mechanism of tumor immune evasion. The preclinical findings and clinical responses associated with programmed death-1 (PD-1) and PD-ligand pathway blockade seem promising, making these targets highly sought for cancer immunotherapy. In fact, the anti-PD-1 antibodies, pembrolizumab and nivolumab, were recently approved by the US FDA for the treatment of unresectable and metastatic melanoma resistant to anticytotoxic T-lymphocyte antigen-4 antibody (ipilimumab) and BRAF inhibitor. Here, we discuss strategies of combining PD-1/PD-ligand interaction inhibitors with other immune checkpoint modulators and standard-of-care therapy to break immune tolerance and induce a potent antitumor activity, which is currently a research area of key scientific pursuit.

  3. Isothermal titration calorimetry for measuring macromolecule-ligand affinity. (United States)

    Duff, Michael R; Grubbs, Jordan; Howell, Elizabeth E


    Isothermal titration calorimetry (ITC) is a useful tool for understanding the complete thermodynamic picture of a binding reaction. In biological sciences, macromolecular interactions are essential in understanding the machinery of the cell. Experimental conditions, such as buffer and temperature, can be tailored to the particular binding system being studied. However, careful planning is needed since certain ligand and macromolecule concentration ranges are necessary to obtain useful data. Concentrations of the macromolecule and ligand need to be accurately determined for reliable results. Care also needs to be taken when preparing the samples as impurities can significantly affect the experiment. When ITC experiments, along with controls, are performed properly, useful binding information, such as the stoichiometry, affinity and enthalpy, are obtained. By running additional experiments under different buffer or temperature conditions, more detailed information can be obtained about the system. A protocol for the basic setup of an ITC experiment is given.

  4. Purification and characterization of a human brain galectin-1 ligand. (United States)

    Chadli, A; LeCaer, J P; Bladier, D; Joubert-Caron, R; Caron, M


    Our previous studies have characterized an endogenous lectin from human brain identified as galectin-1. A soluble ligand of galectin-1 was purified from human brain by affinity chromatography and preparative electrophoresis. The purified ligand (termed HBGp82, for human brain galectin-1-binding polypeptide of 82,000 daltons) has an apparent molecular mass of 82 kDa and is glycosylated by N-linked biantennary complex structures. HBGp82 was partially characterized by microsequencing of peptide fragments. Similar peptides were found in a heat shock of protein of 90,000 daltons, hsp90. However, comparison of apparent molecular weights and matrix-assisted laser desorption mass spectrometry clearly showed that HBGp82 differs to some degree from hsp90.

  5. Ligand regulation of a constitutively dimeric EGF receptor (United States)

    Freed, Daniel M.; Alvarado, Diego; Lemmon, Mark A.


    Ligand-induced receptor dimerization has traditionally been viewed as the key event in transmembrane signalling by epidermal growth factor receptors (EGFRs). Here we show that the Caenorhabditis elegans EGFR orthologue LET-23 is constitutively dimeric, yet responds to its ligand LIN-3 without changing oligomerization state. SAXS and mutational analyses further reveal that the preformed dimer of the LET-23 extracellular region is mediated by its domain II dimerization arm and resembles other EGFR extracellular dimers seen in structural studies. Binding of LIN-3 induces only minor structural rearrangements in the LET-23 dimer to promote signalling. Our results therefore argue that EGFR can be regulated by allosteric changes within an existing receptor dimer--resembling signalling by insulin receptor family members, which share similar extracellular domain compositions but form covalent dimers.

  6. Ligand effects in aluminum cluster basedEnergetic materials (United States)


    heard of the term DFT. Dr. Hooper channeled Mr. Miyagi from the Karate Kid to help me learn DFT. There was quite a bit of “ paint the fence” and “wax...been achieved in the area of self-assembled monolayers [16]. Jouet et al. successfully produced organic-coated, oxide-free aluminum nanoparticles the formation of nanoparticles , and AlCp* units have proven to be an efficient ligand in many transition metal complexes [22]–[25]. Larger

  7. Approaching the RNA ligand for RIG-I? (United States)

    Schlee, Martin; Hartmann, Evelyn; Coch, Christoph; Wimmenauer, Vera; Janke, Markus; Barchet, Winfried; Hartmann, Gunther


    Innate and antigen-specific antiviral immunity are triggered by immunorecognition of viral nucleic acids. The helicase retinoic acid-inducible gene I (RIG-I) (also known as DDX58) is the key sensor of negative strand RNA viruses in the cytosol of cells. RNA containing a triphosphate at the 5'-end was shown to activate RIG-I, but the exact structure of RNA supporting 5'-triphosphate recognition, the requirement of a 5'-triphosphate group, as well as the existence of RNA structures detected by RIG-I in the absence of 5'-triphosphate remain controversial. Here, we revisit the literature on RIG-I and RIG-I ligands. The literature proposes at least six different RIG-I ligands: (i) single strand with a 5'-triphosphate, (ii) double-stranded RNA with a 5'-triphosphate, (iii) 5'-triphosphate single-stranded RNA with A- and U-rich 3'-sequences, (iv) double-stranded RNA of intermediate length (>300 and <2000 bp) without 5'-triphosphate, (v) blunt-end short double-stranded RNA (23-30 bp) without 5'-triphosphate, and (vi) short double-stranded RNA (23-30 bp) with 5'-monophosphate. RIG-I thus seems promiscuous for a variety of different RNA molecules, very similar to the Toll-like receptors, of which 10 family members are sufficient for the safe detection of the microbial cosmos. In the light of these outstanding publications, it seems an unlikely possibility that there is a fundamental shortcoming in the design of all studies. Looking closely, the only issue that comes to mind is the in vitro transcription technique used by all investigators without confirming the identity of RNA products. This technique, together with the different biological systems used, the lack of dose responses and of proper comparison of different published ligands and controls leave us with more questions than answers as to what the exact RIG-I ligand is, if in fact it exists.

  8. Sampling and energy evaluation challenges in ligand binding protein design (United States)

    Dou, Jiayi; Doyle, Lindsey; Jr. Greisen, Per; Schena, Alberto; Park, Hahnbeom; Johnsson, Kai; Stoddard, Barry L.


    Abstract The steroid hormone 17α‐hydroxylprogesterone (17‐OHP) is a biomarker for congenital adrenal hyperplasia and hence there is considerable interest in development of sensors for this compound. We used computational protein design to generate protein models with binding sites for 17‐OHP containing an extended, nonpolar, shape‐complementary binding pocket for the four‐ring core of the compound, and hydrogen bonding residues at the base of the pocket to interact with carbonyl and hydroxyl groups at the more polar end of the ligand. Eight of 16 designed proteins experimentally tested bind 17‐OHP with micromolar affinity. A co‐crystal structure of one of the designs revealed that 17‐OHP is rotated 180° around a pseudo‐two‐fold axis in the compound and displays multiple binding modes within the pocket, while still interacting with all of the designed residues in the engineered site. Subsequent rounds of mutagenesis and binding selection improved the ligand affinity to nanomolar range, while appearing to constrain the ligand to a single bound conformation that maintains the same “flipped” orientation relative to the original design. We trace the discrepancy in the design calculations to two sources: first, a failure to model subtle backbone changes which alter the distribution of sidechain rotameric states and second, an underestimation of the energetic cost of desolvating the carbonyl and hydroxyl groups of the ligand. The difference between design model and crystal structure thus arises from both sampling limitations and energy function inaccuracies that are exacerbated by the near two‐fold symmetry of the molecule. PMID:28980354

  9. P-selectin glycoprotein ligand-1 in T cells. (United States)

    Abadier, Michael; Ley, Klaus


    We review P-selectin glycoprotein ligand-1 (PSGL-1) as a selectin and chemokine-binding adhesion molecule. PSGL-1 is widely studied in neutrophils. Here, we focus on T cells, because PSGL-1 was recently described as a major immunomodulatory molecule during viral infection. PSGL-1 also plays a crucial role in T-cell homeostasis by binding to lymphoid chemokines, and can induce tolerance by enhancing the functions of regulatory T cells. PSGL-1 was originally described as a leukocyte ligand for P-selectin, but it is actually a ligand for all selectins (P-, L- and E-selectin), binds chemokines, activates integrins and profoundly affects T-cell biology. It has been shown recently that PSGL-1 can modulate T cells during viral infection by acting as a negative regulator for T-cell functions. Absence of PSGL-1 promotes effector CD4 and CD8 T-cell differentiation and prevents T-cell exhaustion. Consistent with this, tumor growth was significantly reduced in PSGL-1-deficient mice because of an enhanced number of effector T cells together with reduced levels of inhibitory receptors that induce T-cell exhaustion. PSGL-1 is the best-studied selectin ligand and has become a posterchild of versatility in leukocyte adhesion, inflammation and immunology. The direct involvement of PSGL-1 in T-cell biology suggests that it might be a drug target. Indeed, PSGL-1 has been tested in some clinical trials and recently, PSGL-1 blockers were proposed as a potential cotherapy in cancer immunotherapy.


    African Journals Online (AJOL)

    suspension was allowed to cool to room temperature and then filtered off. The precipitate was ..... of the carbonyl, [O1-Ni-N1 154.32(6)o] and the equatorial plane is thus formed by one oxygen atom, two pyridyl ... molecule ligand and the two nitrogen atoms (equatorial plane: Cl1, N1, N2, O1; rms mean deviation of 0.082 and ...

  11. Sampling and energy evaluation challenges in ligand binding protein design. (United States)

    Dou, Jiayi; Doyle, Lindsey; Jr Greisen, Per; Schena, Alberto; Park, Hahnbeom; Johnsson, Kai; Stoddard, Barry L; Baker, David


    The steroid hormone 17α-hydroxylprogesterone (17-OHP) is a biomarker for congenital adrenal hyperplasia and hence there is considerable interest in development of sensors for this compound. We used computational protein design to generate protein models with binding sites for 17-OHP containing an extended, nonpolar, shape-complementary binding pocket for the four-ring core of the compound, and hydrogen bonding residues at the base of the pocket to interact with carbonyl and hydroxyl groups at the more polar end of the ligand. Eight of 16 designed proteins experimentally tested bind 17-OHP with micromolar affinity. A co-crystal structure of one of the designs revealed that 17-OHP is rotated 180° around a pseudo-two-fold axis in the compound and displays multiple binding modes within the pocket, while still interacting with all of the designed residues in the engineered site. Subsequent rounds of mutagenesis and binding selection improved the ligand affinity to nanomolar range, while appearing to constrain the ligand to a single bound conformation that maintains the same "flipped" orientation relative to the original design. We trace the discrepancy in the design calculations to two sources: first, a failure to model subtle backbone changes which alter the distribution of sidechain rotameric states and second, an underestimation of the energetic cost of desolvating the carbonyl and hydroxyl groups of the ligand. The difference between design model and crystal structure thus arises from both sampling limitations and energy function inaccuracies that are exacerbated by the near two-fold symmetry of the molecule. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

  12. Solid phase strategies for the preparation of phosphorus ligand libraries


    Samuels, Michiel C.


    Catalysis plays a key role in chemical conversions by making them faster and more selective. Despite its widespread use and decades of academic and industrial research, limited catalyst selectivity and stability still call for major improvements in catalyst performance to meet the demands of a sustainable society. Phosphine ligands are ubiquitous in transition metal chemistry and lead to extremely reactive and versatile homogeneous catalysts. Fast development of tailor-made catalysts and cata...

  13. Ligand pose and orientational sampling in molecular docking.

    Directory of Open Access Journals (Sweden)

    Ryan G Coleman

    Full Text Available Molecular docking remains an important tool for structure-based screening to find new ligands and chemical probes. As docking ambitions grow to include new scoring function terms, and to address ever more targets, the reliability and extendability of the orientation sampling, and the throughput of the method, become pressing. Here we explore sampling techniques that eliminate stochastic behavior in DOCK3.6, allowing us to optimize the method for regularly variable sampling of orientations. This also enabled a focused effort to optimize the code for efficiency, with a three-fold increase in the speed of the program. This, in turn, facilitated extensive testing of the method on the 102 targets, 22,805 ligands and 1,411,214 decoys of the Directory of Useful Decoys-Enhanced (DUD-E benchmarking set, at multiple levels of sampling. Encouragingly, we observe that as sampling increases from 50 to 500 to 2000 to 5000 to 20,000 molecular orientations in the binding site (and so from about 1×10(10 to 4×10(10 to 1×10(11 to 2×10(11 to 5×10(11 mean atoms scored per target, since multiple conformations are sampled per orientation, the enrichment of ligands over decoys monotonically increases for most DUD-E targets. Meanwhile, including internal electrostatics in the evaluation ligand conformational energies, and restricting aromatic hydroxyls to low energy rotamers, further improved enrichment values. Several of the strategies used here to improve the efficiency of the code are broadly applicable in the field.

  14. High-affinity benzodiazepine receptor ligands among benzodiazepines and betacarbolines with different intrinsic activity

    Energy Technology Data Exchange (ETDEWEB)

    Yliniemelae, A.; Gynther, J. (Univ. of Kuopio (Finland)); Konschin, H.; Tylli, H. (Univ. of Helsinki (Finland)); Rouvinen, J. (Univ. of Joensuu (Finland))


    Structural and electrostatic features of diazepam, flumazenil, and methyl betacarboline-3-carboxylate (BCCM) have been investigated using the molecular superimposition method. These high-affinity benzodiazepine (BZ) receptor ligands are structurally unrelated and they have different intrinsic activity. These ligands are superimposed in such a way that common structural and electrostatic features essential for the high receptor binding affinity overlap. In addition to this binding pharmacophore, there are roughly three separate binding zones in the BZ receptor, one for each class of ligands. The intrinsic activity of BZ receptor ligands depends on the molecular structures and the way the ligand approaches the receptor.

  15. Evolution of ligand specificity in vertebrate corticosteroid receptors

    Directory of Open Access Journals (Sweden)

    Deitcher David L


    Full Text Available Abstract Background Corticosteroid receptors include mineralocorticoid (MR and glucocorticoid (GR receptors. Teleost fishes have a single MR and duplicate GRs that show variable sensitivities to mineralocorticoids and glucocorticoids. How these receptors compare functionally to tetrapod MR and GR, and the evolutionary significance of maintaining two GRs, remains unclear. Results We used up to seven steroids (including aldosterone, cortisol and 11-deoxycorticosterone [DOC] to compare the ligand specificity of the ligand binding domains of corticosteroid receptors between a mammal (Mus musculus and the midshipman fish (Porichthys notatus, a teleost model for steroid regulation of neural and behavioral plasticity. Variation in mineralocorticoid sensitivity was considered in a broader phylogenetic context by examining the aldosterone sensitivity of MR and GRs from the distantly related daffodil cichlid (Neolamprologus pulcher, another teleost model for neurobehavioral plasticity. Both teleost species had a single MR and duplicate GRs. All MRs were sensitive to DOC, consistent with the hypothesis that DOC was the initial ligand of the ancestral MR. Variation in GR steroid-specificity corresponds to nine identified amino acid residue substitutions rather than phylogenetic relationships based on receptor sequences. Conclusion The mineralocorticoid sensitivity of duplicate GRs in teleosts is highly labile in the context of their evolutionary phylogeny, a property that likely led to neo-functionalization and maintenance of two GRs.

  16. Synthesis, spectroscopic, thermogravimetric and antimicrobial studies of mixed ligands complexes (United States)

    Mahmoud, Walaa H.; Mahmoud, Nessma F.; Mohamed, Gehad G.; El-Sonbati, Adel Z.; El-Bindary, Ashraf A.


    An interesting series of mixed ligand complexes have been synthesized by the reaction of metal chloride with guaifenesin (GFS) in the presence of 2-aminoacetic acid (HGly) (1:1:1 molar ratio). The elemental analysis, magnetic moments, molar conductance, spectral (UV-Vis, IR, 1H NMR and ESR) and thermal studies were used to characterize the isolated complexes. The molecular structure of GFS is optimized theoretically and the quantum chemical parameters are calculated. The IR showed that the ligand (GFS) acts as monobasic tridentate through the hydroxyl, phenoxy etheric and methoxy oxygen atoms and co-ligand (HGly) as monobasic bidentate through the deprotonated carboxylate oxygen atom and nitrogen atom of amino group. The molar conductivities showed that all the complexes are non-electrolytes except Cr(III) complex is electrolyte. Electronic and magnetic data proposed the octahedral structure for all complexes under investigation. ESR spectrum for Cu(II) revealed data which confirm the proposed structure. Antibacterial screening of the compounds were carried out in vitro on gram positive (Bacillus subtilis and Staphylococcus aureus), gram negative (Escherichia coli and Neisseria gonorrhoeae) bacteria and for in vitro antifungal activity against Candida albicans organism. However, some complexes showed more chemotherapeutic efficiency than the parent GFS drug. The complexes were also screened for their in vitro anticancer activity against the breast cell line (MFC7) and the results obtained showed that they exhibit a considerable anticancer activity.

  17. TYK2 activity promotes ligand-induced IFNAR1 proteolysis. (United States)

    Marijanovic, Zrinka; Ragimbeau, Josiane; Kumar, K G Suresh; Fuchs, Serge Y; Pellegrini, Sandra


    The type I IFNR (interferon receptor) is a heterodimer composed of two transmembrane chains, IFNAR1 (interferon-alpha receptor 1 subunit) and IFNAR2, which are associated with the tyrosine kinases Tyk2 and Jak1 (Janus kinase 1) respectively. Ligand-induced down-regulation of the type I IFNR is a major mechanism of negative regulation of cellular signalling and involves the internalization and lysosomal degradation of IFNAR1. IFNalpha promotes the phosphorylation of IFNAR1 on Ser535, followed by recruitment of the E3 ubiquitin ligase, beta-TrCP2 (beta-transducin repeats-containing protein 2), ubiquitination of IFNAR1 and proteolysis. The non-catalytic role of Tyk2 in sustaining the steady-state IFNAR1 level at the plasma membrane is well documented; however, little is known about the function of Tyk2 in the steps that precede and succeed serine phosphorylation and ubiquitination of IFNAR1 in response to ligand binding. In the present study, we show that catalytic activation of Tyk2 is not essential for IFNAR1 internalization, but is required for ligand-induced IFNAR1 serine phosphorylation, ubiquitination and efficient lysosomal proteolysis.

  18. Coupling of Ligands to the Liposome Surface by Click Chemistry. (United States)

    Spanedda, Maria Vittoria; De Giorgi, Marcella; Hassane, Fatouma Saïd; Schuber, Francis; Bourel-Bonnet, Line; Frisch, Benoît


    Click chemistry represents a new bioconjugation strategy that can be used to conveniently attach various ligands to the surface of preformed liposomes. This efficient and chemoselective reaction involves a Cu(I)-catalyzed azide-alkyne cycloaddition which can be performed under mild experimental conditions in aqueous media. Here we describe the application of a model click reaction to the conjugation, in a single step, of unprotected α-1-thiomannosyl ligands, functionalized with an azide group, to liposomes containing a terminal alkyne-functionalized lipid anchor. Excellent coupling yields have been obtained in the presence of bathophenanthroline disulfonate, a water soluble copper-ion chelator, acting as a catalyst. No vesicle leakage is triggered by this conjugation reaction and the coupled mannose ligands are exposed at the surface of the liposomes. The major limitation of Cu(I)-catalyzed click reactions is that this conjugation is restricted to liposomes made of saturated (phospho)lipids. To circumvent that constraint, an example of alternative copper-free azide-alkyne click reaction has been developed. Molecular tools and results are presented here.

  19. Electrophilic Metal Alkyl Chemistry in New Ligand Environments

    Energy Technology Data Exchange (ETDEWEB)

    Jordan, Richard F. [University of Chicago


    The goals of this project were to design new electrophilic metal alkyl complexes and to exploit these systems in fundamental studies of olefin polymerization and other important and new catalytic reactions. A key target reaction is insertion copolymerization of olefins and polar CH2=CHX vinyl monomers such as vinyl halides and vinyl ethers. During the period covered by this report we (i) investigated the properties of ortho-alkoxy-arylphosphine ligands in Ni-based olefin polymerization catalysts, (ii) studied the synthesis of double-end-capped polyethylene using group 4 metal catalysts that contain tris-pyrazolylborate ligands, (iii) explored the ethylene insertion reactivity of group 4 metal tris-pyrazolyl-borate complexes, (iv) showed that (α-diimine)PdMe{sup +} species undergo multiple insertion of silyl vinyl ethers, (v) synthesized and explored the reactivity of base-free Ni benzyl complexes that contain ortho-phosphino-arene sulfonate ligands, (vi) established the mechanism of the reaction of vinyl chloride with (α-diimine)PdMe{sup +} catalysts, (vii) explored the role of cationic polymerization and insertion chemistry in the reactions of vinyl ethers with (α-diimine)PdMe{sup +} species, (viii) discovered a new class of self-assembled tetranuclear Pd catalysts that produce high molecular weight linear polyethylene and copolymerize ethylene and vinyl fluoride, and (ix) developed model systems that enabled investigation of cis-trans isomerization of {phosphine-sulfonate}Pd(II) complexes.

  20. TLR ligands stimulation protects MSC from NK killing. (United States)

    Giuliani, Massimo; Bennaceur-Griscelli, Annelise; Nanbakhsh, Arash; Oudrhiri, Noufissa; Chouaib, Salem; Azzarone, Bruno; Durrbach, Antoine; Lataillade, Jean-Jacques


    Mesenchymal stem cells (MSCs) play a fundamental role in allograft rejection and graft-versus-host disease through their immunosuppressive abilities. Recently, Toll-like receptors (TLR) have been shown to modulate MSC functions. The aim of this study was to investigate the effects of several TLR ligands on the interaction between MSC and natural killer (NK) cells. Our results show that TLR-primed adult bone marrow and embryonic MSC are more resistant than unprimed MSC to IL-2-activated NK-induced killing. Such protection can be explained by the modulation of Natural Killer group 2D ligands major histocompatibility complex class I chain A and ULBP3 and DNAM-1 ligands by TLR-primed MSC. These results indicate that MSCs are able to adapt their immuno-behavior in an inflammatory context, decreasing their susceptibility to NK killing. In addition, TLR3 but not TLR4-primed MSC enhance their suppressive functions against NK cells. However, the efficiency of this response is heterogeneous, even if the phenotypes of different analyzed MSC are rather homogeneous. The consequences could be important in MSC-mediated cell therapy, since the heterogeneity of adult MSC responders may be explored in order to select the more efficient responders. © 2013 AlphaMed Press.

  1. Using inositol as a biocompatible ligand for efficient transgene expression (United States)

    Zhang, Lei; Bellis, Susan L; Fan, Yiwen; Wu, Yunkun


    Transgene transfection techniques using cationic polymers such as polyethylenimines (PEIs) and PEI derivatives as gene vectors have shown efficacy, although they also have shortcomings. PEIs have decent DNA-binding capability and good cell internalization performance, but they cannot deliver gene payloads very efficiently to cell nuclei. In this study, three hyperbranched polyglycerol-polyethylenimine (PG6-PEI) polymers conjugated with myo-inositol (INO) molecules were developed. The three resulting PG6-PEI-INO polymers have an increased number of INO ligands per molecule. PG6-PEI-INO 1 had only 14 carboxymethyl INO (CMINO) units per molecule. PG6-PEI-INO 2 had approximately 130 CMINO units per molecule. PG6-PEI-INO 3 had as high as 415 CMINO units approximately. Mixing PG6-PEI-INO polymers with DNA produced compact nanocomposites. We then performed localization studies using fluorescent microscopy. As the number of conjugated inositol ligands increased in PG6-PEI-INO polymers, there was a corresponding increase in accumulation of the polymers within 293T cell nuclei. Transfection performed with spherical 293T cells yielded 82% of EGFP-positive cells when using PG6-PEI-INO 3 as the vehicle. Studies further revealed that extracellular adenosine triphosphate (eATP) can inhibit the transgene efficiency of PG6-PEI-INO polymers, as compared with PEI and PG6-PEI that were not conjugated with inositol. Our work unveiled the possibility of using inositol as an effective ligand for transgene expression. PMID:25926732

  2. Nanopore force spectroscopy of aptamer-ligand complexes. (United States)

    Arnaut, Vera; Langecker, Martin; Simmel, Friedrich C


    The stability of aptamer-ligand complexes is probed in nanopore-based dynamic force spectroscopy experiments. Specifically, the ATP-binding aptamer is investigated using a backward translocation technique, in which the molecules are initially pulled through an α-hemolysin nanopore from the cis to the trans side of a lipid bilayer membrane, allowed to refold and interact with their target, and then translocated back in the trans-cis direction. From these experiments, the distribution of bound and unbound complexes is determined, which in turn allows determination of the dissociation constant Kd ≈ 0.1 mM of the aptamer and of voltage-dependent unfolding rates. The experiments also reveal differences in binding of the aptamer to AMP, ADP, or ATP ligands. Investigation of an aptamer variant with a stabilized ATP-binding site indicates fast conformational switching of the original aptamer before ATP binding. Nanopore force spectroscopy is also used to study binding of the thrombin-binding aptamer to its target. To detect aptamer-target interactions in this case, the stability of the ligand-free aptamer-containing G-quadruplexes-is tuned via the potassium content of the buffer. Although the presence of thrombin was detected, limitations of the method for aptamers with strong secondary structures and complexes with nanomolar Kd were identified. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  3. Nanopore Force Spectroscopy of Aptamer–Ligand Complexes (United States)

    Arnaut, Vera; Langecker, Martin; Simmel, Friedrich C.


    The stability of aptamer–ligand complexes is probed in nanopore-based dynamic force spectroscopy experiments. Specifically, the ATP-binding aptamer is investigated using a backward translocation technique, in which the molecules are initially pulled through an α-hemolysin nanopore from the cis to the trans side of a lipid bilayer membrane, allowed to refold and interact with their target, and then translocated back in the trans–cis direction. From these experiments, the distribution of bound and unbound complexes is determined, which in turn allows determination of the dissociation constant Kd ≈ 0.1 mM of the aptamer and of voltage-dependent unfolding rates. The experiments also reveal differences in binding of the aptamer to AMP, ADP, or ATP ligands. Investigation of an aptamer variant with a stabilized ATP-binding site indicates fast conformational switching of the original aptamer before ATP binding. Nanopore force spectroscopy is also used to study binding of the thrombin-binding aptamer to its target. To detect aptamer–target interactions in this case, the stability of the ligand-free aptamer—containing G-quadruplexes—is tuned via the potassium content of the buffer. Although the presence of thrombin was detected, limitations of the method for aptamers with strong secondary structures and complexes with nanomolar Kd were identified. PMID:24010663

  4. Formyl peptide receptor chimeras define domains involved in ligand binding. (United States)

    Perez, H D; Holmes, R; Vilander, L R; Adams, R R; Manzana, W; Jolley, D; Andrews, W H


    We have begun to study the structural requirements for the binding of formyl peptides to their specific receptors. As an initial approach, we constructed C5a-formyl peptide receptor chimeras. Unique (and identical) restriction sites were introduced within the transmembrane domains of these receptors that allowed for the exchange of specific areas. Four types of chimeric receptors were generated. 1) The C5a receptor was progressively substituted by the formyl peptide receptor. 2) The formyl peptide receptor was progressively substituted by the C5a receptor. 3) Specific domains of the C5a receptor were substituted by the corresponding domain of the formyl peptide receptor. 4) Specific domains of the formyl peptide receptor were replaced by the same corresponding domain of the C5a receptor. Wild type and chimeric receptors were transfected into COS 7 cells and their ability to bind formyl peptide determined, taking into account efficiency of transfection and expression of chimeric protein. Based on these results, a ligand binding model is presented in which the second, third, and fourth extracellular (and/or their transmembrane) domains together with the first transmembrane domain form a ligand binding pocket for formyl peptides. It is proposed that the amino-terminal domain plays a role by presumably providing a "lid" to the pocket. The carboxyl-terminal cytoplasmic tail appears to modulate ligand binding by regulating receptor affinity.

  5. Copper isotope fractionation during equilibration with natural and synthetic ligands. (United States)

    Ryan, Brooke M; Kirby, Jason K; Degryse, Fien; Scheiderich, Kathleen; McLaughlin, Mike J


    As copper (Cu) stable isotopes emerge as a tool for tracing Cu biogeochemical cycling, an understanding of how Cu isotopes fractionate during complexation with soluble organic ligands in natural waters and soil solutions is required. A Donnan dialysis technique was employed to assess the isotopic fractionation of Cu during complexation with the soluble synthetic ligands ethylenediaminetetraacetic acid (EDTA), nitrilotriacetic acid (NTA), iminodiacetic acid (IDA) and desferrioxamine B (DFOB), as well as with Suwannee River fulvic acid (SRFA). The results indicated enrichment of the heavy isotope ((65)Cu) in the complexes, with Δ(65)Cu complex-free values ranging from +0.14 to +0.84‰. A strong linear correlation was found between the logarithms of the stability constants of the Cu complexes and the magnitudes of isotopic fractionation. These results show that complexation of Cu by organic ligands can affect the isotopic signature of the free Cu ion. This free Cu is considered the most bioavailable species, and hence, our results highlight the importance of understanding fractionation processes in the uptake medium when using Cu isotopes to study the uptake mechanisms of organisms. These data contribute a vital piece to the emerging picture of Cu isotope cycling in the natural environment, as organic complexation plays a key role in the Cu cycle.

  6. CREDO: a protein-ligand interaction database for drug discovery. (United States)

    Schreyer, Adrian; Blundell, Tom


    Harnessing data from the growing number of protein-ligand complexes in the Protein Data Bank is an important task in drug discovery. In order to benefit from the abundance of three-dimensional structures, structural data must be integrated with sequence as well as chemical data and the protein-small molecule interactions characterized structurally at the inter-atomic level. In this study, we present CREDO, a new publicly available database of protein-ligand interactions, which represents contacts as structural interaction fingerprints, implements novel features and is completely scriptable through its application programming interface. Features of CREDO include implementation of molecular shape descriptors with ultrafast shape recognition, fragmentation of ligands in the Protein Data Bank, sequence-to-structure mapping and the identification of approved drugs. Selected analyses of these key features are presented to highlight a range of potential applications of CREDO. The CREDO dataset has been released into the public domain together with the application programming interface under a Creative Commons license at We believe that the free availability and numerous features of CREDO database will be useful not only for commercial but also for academia-driven drug discovery programmes.

  7. Novel sterically hindered cannabinoid CB1 receptor ligands. (United States)

    Urbani, Paolo; Cascio, Maria Grazia; Ramunno, Anna; Bisogno, Tiziana; Saturnino, Carmela; Di Marzo, Vincenzo


    In the present study, 11 novel N-(3,3-diphenyl)propyl-2,2-diphenylacetamide derivatives (4a-d and 9a-g) and six triphenylacetamides (10a-c and 11a-c) were synthesized and tested as ligands of cannabinoid CB(1) and CB(2) receptors. All compounds exhibited affinity for CB(1) and CB(2) receptors. Four compounds (4b, 9a, 9b, and 11a) showed selectivity for CB(1) versus CB(2) receptors, although only the N-(3,3-diphenyl)propyl-2,2-diphenylacetamide (4b) can be considered a potent CB(1) ligand (K(i)=58 nM). It was 140-fold selective over CB(2) receptors (K(i)=7800 nM) and behaved as an inverse agonist by stimulating forskolin-induced cAMP formation in mouse N18TG2 neuroblastoma cells. This compound is the first of a novel class of tetraphenyl CB(1) ligands that, in view of its easy synthesis and high affinity for CB(1) receptors and despite its sterical hindrance, will be useful for the design of new blockers of this therapeutically exploitable receptor type.

  8. A look at ligand binding thermodynamics in drug discovery. (United States)

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


    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.

  9. Conformational diversity and ligand tunnels of mammalian cytochrome P450s. (United States)

    Yu, Xiaofeng; Cojocaru, Vlad; Wade, Rebecca C


    The mammalian cytochrome P450 (CYP) enzymes play important roles in drug metabolism, steroid biosynthesis, and xenobiotic degradation. The active site of CYPs is buried in the protein and thus the ligands have to enter and exit the active site via ligand tunnels. Conformational changes of flexible parts of the protein usually accompany the entrance and exit of ligands. Comparison of the crystal structures of mammalian CYPs in closed, open, and partially open states reveals that the greatest conformational diversity associated with ligand tunnel opening is in the regions of the B-C and F-G loops. Some CYPs have been observed to adopt different open and closed conformations when bound to different ligands, suggesting that the ligand entrance and exit routes might differ according to the ligand properties. Mammalian CYPs are mostly membrane-bound enzymes, making them difficult to characterize structurally and dynamically. A range of molecular dynamics simulation techniques has been applied to investigate the dynamics and the ligand tunnels of these proteins both in the aqueous environment, and more recently, in lipid bilayers. These simulations not only reveal multiple tunnels through which ligands can pass but also show that different tunnels are preferred by different ligands and that the lipid bilayer can influence the protein dynamics and tunnel opening. The results indicate that not only the active site but also the ligand tunnels can contribute to the different substrate specificity profiles of the mammalian CYPs. © 2013 International Union of Biochemistry and Molecular Biology, Inc.

  10. Complex Relationship between Ligand Binding and Dimerization in the Epidermal Growth Factor Receptor

    Directory of Open Access Journals (Sweden)

    Nicholas J. Bessman


    Full Text Available The epidermal growth factor receptor (EGFR plays pivotal roles in development and is mutated or overexpressed in several cancers. Despite recent advances, the complex allosteric regulation of EGFR remains incompletely understood. Through efforts to understand why the negative cooperativity observed for intact EGFR is lost in studies of its isolated extracellular region (ECR, we uncovered unexpected relationships between ligand binding and receptor dimerization. The two processes appear to compete. Surprisingly, dimerization does not enhance ligand binding (although ligand binding promotes dimerization. We further show that simply forcing EGFR ECRs into preformed dimers without ligand yields ill-defined, heterogeneous structures. Finally, we demonstrate that extracellular EGFR-activating mutations in glioblastoma enhance ligand-binding affinity without directly promoting EGFR dimerization, suggesting that these oncogenic mutations alter the allosteric linkage between dimerization and ligand binding. Our findings have important implications for understanding how EGFR and its relatives are activated by specific ligands and pathological mutations.

  11. DNA-Based Nanostructures: Changes of Mechanical Properties of DNA upon Ligand Binding (United States)

    Nechipurenko, Yury; Grokhovsky, Sergey; Gursky, Georgy; Nechipurenko, Dmitry; Polozov, Robert

    The formation of DNA-based nanostructures involves the binding of different kinds of ligands to DNA as well as the interaction of DNA molecules with each other. Complex formation between ligand and DNA can alter physicochemical properties of the DNA molecule. In the present work, the accessibility of DNA-ligand complexes to cleavage by DNase I are considered, and the exact algorithms for analysis of diagrams of DNase I footprinting for ligand-DNA complexes are obtained. Changes of mechanical properties of the DNA upon ligand binding are also demonstrated by the cleavage patterns generated upon ultrasound irradiation of cis-platin-DNA complexes. Propagation of the mechanical perturbations along DNA in the presence of bound ligands is considered in terms of a string model with a heterogeneity corresponding to the position of a bound ligand on DNA. This model can reproduce qualitatively the cleavage patterns obtained upon ultrasound irradiation of cis-platin-DNA complexes.

  12. Fluorescent GPCR ligands as new tools in pharmacology-update, years 2008-early 2014. (United States)

    Kuder, Kamil J; Kieć-Kononowicz, Katarzyna


    The robust of fluorescent techniques to study the ligand-receptor interaction followed by rapidly developing fluorescence imaging techniques resulted in a burst of the novel fluorescent ligands development. Taking into consideration not only ligand's high affinity to the receptor, but also their fluorescent properties to visualize the interaction even in the single cell level, gives the researchers a strong impulse to investigate that field of GPCR ligands. Moreover, paying attention to the "non pharmacological" advantages of these ligands, as well as the techniques to be used, fluorescent ligands become commonly used pharmacological tools to study GPCRs. Herein we report on the results described in the literature since late 2007 in the field of the fluorescent GPCR small, non-peptide ligands according the receptor affinity, fluorophores that has been used to tag the molecules and their fluorescent properties as well as their application in GPCR research.

  13. One ligand capable of in situ reaction in a mixed-ligand system with two new different frameworks

    KAUST Repository

    Wang, Xiaofang


    The in situ ligand 2,3-pyrazinedicarboxylic acid (2,3-H2pzdc) mixed with 1,1′-(1,4-butanediyl)bis(benzimidazole) (bbbi) is used to form two coordination polymers ([Cd(2,3-pzdc)(bbbi)] (1) and [Cd2Cl3(2-pzc)(bbbi)2] (2)) under hydrothermal conditions. Complex 1 was obtained in the absence of in situ reaction and 2 was synthesized with 2,3-H2pzdc in situ generating 2-pyrazinecarboxylate (2-pzc−). The structural details reveal that 1 has a 3D framework with dia topology, and 2 is a 2D layer structure and develops a 3D supramolecular structure via strong π⋯π stacking interactions. The ligand effects were compared for the two frameworks. In addition, fluorescence properties and thermal stabilities of 1 and 2 in the solid were studied.

  14. Design and Formation of a Large, Tetrahedral, Metal-ligand Cluster Using 1,1'-Binaphthyl Ligands

    Energy Technology Data Exchange (ETDEWEB)

    Biros, Shannon M.; Yeh, Robert M.; Raymond, Kenneth N.


    Many chemists have been fascinated with the development of discrete supramolecular structures that encapsulate guest molecules. These structures can be assembled through covalent or hydrogen bonds, electrostatic or metal-ligand interactions. These host structures have provided valuable insight into the forces involved in small molecule recognition. Our work has focused on the design and study of metal-ligand clusters of varying sizes. The naphthalene [M{sub 4}L{sub 6}]{sup 12-} cluster 1, shown in Figure 1, has demonstrated diastereoselective guest binding and chiral induction properties as well as the ability to catalyze reactions carried out inside the cavity in an enzyme-like manner. However, the size of the cavity (ca. 300-500 {angstrom}{sup 3}) has often limited the scope of substrates for these transformations.

  15. Cellular trafficking of quantum dot-ligand bioconjugates and their induction of changes in normal routing of unconjugated ligands

    DEFF Research Database (Denmark)

    Tekle, Christina; van Deurs, Bo; Sandvig, Kirsten


    Can quantum dots (Qdots) act as relevant intracellular probes to investigate routing of ligands in live cells? The intracellular trafficking of Qdots that were coupled to the plant toxin ricin, Shiga toxin, or the ligand transferrin (Tf) was studied by confocal fluorescence microscopy. The Tf......:Qdots were internalized by clathrin-dependent endocytosis as fast as Tf, but their recycling was blocked. Unlike Shiga toxin, the Shiga:Qdot bioconjugate was not routed to the Golgi apparatus. The internalized ricin:Qdot bioconjugates localized to the same endosomes as ricin itself but could...... not be visualized in the Golgi apparatus. Importantly, we find that the endosomal accumulation of ricin:Qdots affects endosome-to-Golgi transport of both ricin and Shiga toxin: Transport of ricin was reduced whereas transport of Shiga toxin was increased. In conclusion, the data reveal that, although coupling...

  16. The Movable Type Method Applied to Protein-Ligand Binding. (United States)

    Zheng, Zheng; Ucisik, Melek N; Merz, Kenneth M


    Accurately computing the free energy for biological processes like protein folding or protein-ligand association remains a challenging problem. Both describing the complex intermolecular forces involved and sampling the requisite configuration space make understanding these processes innately difficult. Herein, we address the sampling problem using a novel methodology we term "movable type". Conceptually it can be understood by analogy with the evolution of printing and, hence, the name movable type. For example, a common approach to the study of protein-ligand complexation involves taking a database of intact drug-like molecules and exhaustively docking them into a binding pocket. This is reminiscent of early woodblock printing where each page had to be laboriously created prior to printing a book. However, printing evolved to an approach where a database of symbols (letters, numerals, etc.) was created and then assembled using a movable type system, which allowed for the creation of all possible combinations of symbols on a given page, thereby, revolutionizing the dissemination of knowledge. Our movable type (MT) method involves the identification of all atom pairs seen in protein-ligand complexes and then creating two databases: one with their associated pairwise distant dependent energies and another associated with the probability of how these pairs can combine in terms of bonds, angles, dihedrals and non-bonded interactions. Combining these two databases coupled with the principles of statistical mechanics allows us to accurately estimate binding free energies as well as the pose of a ligand in a receptor. This method, by its mathematical construction, samples all of configuration space of a selected region (the protein active site here) in one shot without resorting to brute force sampling schemes involving Monte Carlo, genetic algorithms or molecular dynamics simulations making the methodology extremely efficient. Importantly, this method explores the free

  17. MOST: most-similar ligand based approach to target prediction. (United States)

    Huang, Tao; Mi, Hong; Lin, Cheng-Yuan; Zhao, Ling; Zhong, Linda L D; Liu, Feng-Bin; Zhang, Ge; Lu, Ai-Ping; Bian, Zhao-Xiang


    Many computational approaches have been used for target prediction, including machine learning, reverse docking, bioactivity spectra analysis, and chemical similarity searching. Recent studies have suggested that chemical similarity searching may be driven by the most-similar ligand. However, the extent of bioactivity of most-similar ligands has been oversimplified or even neglected in these studies, and this has impaired the prediction power. Here we propose the MOst-Similar ligand-based Target inference approach, namely MOST, which uses fingerprint similarity and explicit bioactivity of the most-similar ligands to predict targets of the query compound. Performance of MOST was evaluated by using combinations of different fingerprint schemes, machine learning methods, and bioactivity representations. In sevenfold cross-validation with a benchmark Ki dataset from CHEMBL release 19 containing 61,937 bioactivity data of 173 human targets, MOST achieved high average prediction accuracy (0.95 for pKi ≥ 5, and 0.87 for pKi ≥ 6). Morgan fingerprint was shown to be slightly better than FP2. Logistic Regression and Random Forest methods performed better than Naïve Bayes. In a temporal validation, the Ki dataset from CHEMBL19 were used to train models and predict the bioactivity of newly deposited ligands in CHEMBL20. MOST also performed well with high accuracy (0.90 for pKi ≥ 5, and 0.76 for pKi ≥ 6), when Logistic Regression and Morgan fingerprint were employed. Furthermore, the p values associated with explicit bioactivity were found be a robust index for removing false positive predictions. Implicit bioactivity did not offer this capability. Finally, p values generated with Logistic Regression, Morgan fingerprint and explicit activity were integrated with a false discovery rate (FDR) control procedure to reduce false positives in multiple-target prediction scenario, and the success of this strategy it was demonstrated with a case of fluanisone

  18. Chiral ligand-protected gold nanoclusters: Considering the optical activity from a viewpoint of ligand dissymmetric field

    Directory of Open Access Journals (Sweden)

    Hiroshi Yao


    Full Text Available Chirality is a geometric property of a physical, chemical, or biological object, which is not superimposable on its mirror image. Its significant presence has led to a strong demand in the development of chiral drugs, sensors, catalysts, and photofunctional materials. In recent years, chirality of nanoscale organic/inorganic hybrids has received tremendous attention owing to potential applications in chiral nanotechnology. In particular, with the recent progress in the syntheses and characterizations of atomically precise gold nanoclusters protected by achiral thiolates, atomic level origins of their chirality have been unveiled. On the other hand, chirality or optical activity in metal nanoclusters can also be introduced via the surface chiral ligands, which should be universal for the nanosystems. This tutorial review presents some optically-active metal (gold nanoclusters protected by chiral thiolates or phosphines, and their chiroptical (or circular dichroism; CD properties are discussed mostly from a viewpoint of the ligand dissymmetric field scheme. The examples are the gold nanoclusters protected by (R-/(S-2-phenylpropane-1-thiol, (R-/(S-mercaptosuccinic acid, phenylboronate-D/L-fructose complexes, phosphine sulfonate-ephedrinium ion pairs, or glutathione. Some methodologies for versatile asymmetric transformation and chiroptical controls of the nanocluster compounds are also described. In the dissymmetric field model as the origin of optical activity, the chiroptical responses of the gold nanoclusters are strongly associated with coupled oscillator and/or CD stealing mechanisms based on the concept of induced CD (ICD derived from a perturbation theory, so on this basis, some characteristic features of the observed CD responses of chiral ligand-protected gold nanoclusters are presented in detail. We believe that various kinds of origins of chirality found in ligand-protected gold nanoclusters may provide models for understanding those of

  19. Iron-binding ligands in the southern California Current System: mechanistic studies

    Directory of Open Access Journals (Sweden)

    Randelle M Bundy


    Full Text Available The distributions of dissolved iron and organic iron-binding ligands were examined in water column profiles and deckboard incubation experiments in the southern California Current System (sCCS along a transition from coastal to semi-oligotrophic waters. Analysis of the iron-binding ligand pool by competitive ligand exchange-adsorptive cathodic stripping voltammetry (CLE-ACSV using multiple analytical windows (MAWs revealed three classes of iron-binding ligands present throughout the water column (L1-L3, whose distributions closely matched those of dissolved iron and nitrate. Despite significant biogeochemical gradients, ligand profiles were similar between stations, with surface minima in strong ligands (L1 and L2, and relatively constant concentrations of weaker ligands (L3 down to 500 m. A phytoplankton grow-out incubation, initiated from an iron-limited water mass, showed dynamic temporal cycling of iron-binding ligands. A biological iron model was able to capture the patterns of the strong ligands in the grow-out incubation relatively well with only the microbial community as a biological source. An experiment focused on remineralization of particulate organic matter showed production of both strong and weak iron-binding ligands by the heterotrophic community, supporting a mechanism for in-situ production of both strong and weak iron-binding ligands in the subsurface water column. Photochemical experiments showed a variable influence of sunlight on the degradation of natural iron-binding ligands, providing some evidence to explain differences in surface ligand concentrations between stations. Patterns in ligand distributions between profiles and in the incubation experiments were primarily related to macronutrient concentrations, suggesting microbial remineralization processes might dominate on longer time-scales over short-term changes associated with photochemistry or phytoplankton growth.

  20. A web server for analysis, comparison and prediction of protein ligand binding sites. (United States)

    Singh, Harinder; Srivastava, Hemant Kumar; Raghava, Gajendra P S


    One of the major challenges in the field of system biology is to understand the interaction between a wide range of proteins and ligands. In the past, methods have been developed for predicting binding sites in a protein for a limited number of ligands. In order to address this problem, we developed a web server named 'LPIcom' to facilitate users in understanding protein-ligand interaction. Analysis, comparison and prediction modules are available in the "LPIcom' server to predict protein-ligand interacting residues for 824 ligands. Each ligand must have at least 30 protein binding sites in PDB. Analysis module of the server can identify residues preferred in interaction and binding motif for a given ligand; for example residues glycine, lysine and arginine are preferred in ATP binding sites. Comparison module of the server allows comparing protein-binding sites of multiple ligands to understand the similarity between ligands based on their binding site. This module indicates that ATP, ADP and GTP ligands are in the same cluster and thus their binding sites or interacting residues exhibit a high level of similarity. Propensity-based prediction module has been developed for predicting ligand-interacting residues in a protein for more than 800 ligands. In addition, a number of web-based tools have been integrated to facilitate users in creating web logo and two-sample between ligand interacting and non-interacting residues. In summary, this manuscript presents a web-server for analysis of ligand interacting residue. This server is available for public use from URL .

  1. L-Lysine-derived ionic liquids as chiral ligands of Zn(II) complexes used in ligand-exchange CE. (United States)

    Zhang, Haizhi; Qi, Li; Shen, Ying; Qiao, Juan; Mao, Lanqun


    Amino acid ionic liquids (AAILs) with L-lysine (L-Lys) as anion were synthesized and applied as new chiral ligands in Zn(II) complexes for chiral ligand-exchange CE. After effective optimization, baseline enantioseparation of seven pairs of dansylated amino acids was achieved with a buffer of 100.0 mM boric acid, 5.0 mM ammonium acetate, 3.0 mM ZnSO4 , and 6.0 mM [C6 mim][L-Lys] at pH 8.2. To validate the unique behavior of AAILs, a comparative study between the performance of Zn(II)-L-Lys and Zn(II)-[C6 mim][L-Lys] systems was conducted. In Zn(II)-[C6 mim][L-Lys] system, it has been found that the improved chiral resolution could be obtained and the migration times of the three test samples were markedly prolonged. Then the separation mechanism was further discussed. The role of [C6 mim][L-Lys] indicated clearly that the synthesized AAILs could be used as chiral ligands and would have potential utilization in separation science in future. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Amino propynyl benzoic acid building block in rigid spacers of divalent ligands binding to the Syk SH2 domains with equally high affinity as the natural ligand

    NARCIS (Netherlands)

    Dekker, Frank J; de Mol, Nico J; Fischer, Marcel J E; Liskamp, Rob M J; Dekker, Frank


    The construction of rigid spacers composed of amino propynyl benzoic acid building blocks is described. These spacers were used to link two phosphopeptide ligand sites towards obtaining divalent ligands with a high affinity for Syk tandem SH2 domains, which are important in signal transduction. The

  3. High resolution crystal structures of unliganded and liganded human liver ACBP reveal a new mode of binding for the acyl-CoA ligand

    DEFF Research Database (Denmark)

    Taskinen, Jukka P; van Aalten, Daan M; Knudsen, Jens


    The acyl-CoA binding protein (ACBP) is essential for the fatty acid metabolism, membrane structure, membrane fusion, and ceramide synthesis. Here high resolution crystal structures of human cytosolic liver ACBP, unliganded and liganded with a physiological ligand, myristoyl-CoA are described...

  4. Magnetic ligand fishing as a targeting tool for HPLC-HRMS-SPE-NMR: α-glucosidase inhibitory ligands and alkylresorcinol glycosides from Eugenia catharinae

    DEFF Research Database (Denmark)

    Wubshet, Sileshi Gizachew; Brighente, Inês M. C.; Moaddel, Ruin


    A bioanalytical platform combining magnetic ligand fishing for α-glucosidase inhibition profiling and HPLC-HRMS-SPE-NMR for structural identification of α-glucosidase inhibitory ligands, both directly from crude plant extracts, is presented. Magnetic beads with N-terminus-coupled α-glucosidase we...

  5. Nuclear magnetic resonance studies of the solution chemistry of metal complexes. 26. Mixed ligand complexes of cadmium, nitrilotriacetic acid, glutathione, and related ligands. (United States)

    Kadima, W; Rabenstein, D L


    The complexation of glutathione and related ligands by the nitrilotriacetic acid complex of Cd2+ (Cd(NTA)-) has been investigated by 1H NMR as a model for the coordination chemistry of Cd2+ and GSH in biological systems. Related ligands included glycine, glutamic acid, cysteine, N-acetylcysteine, penicillamine, N-acetylpenicillamine, mercaptosuccinic acid, and the S-methyl derivative of glutathione. The nature of the complexes formed was deduced from 1H NMR spectra of Cd(NTA)- and the ligands. Mixed ligand complexes (Cd(NTA)L) and single ligand complexes (CdLx) are formed with the thiol ligands, whereas only mixed ligand complexes form with glycine, glutamic acid and S-methylglutathione. Formation constants of the mixed and the single ligand complexes were determined from NMR data. The results indicate that formation constants for binding of a thiolate donor group by Cd2+, either as the free ion or in a coordinately unsaturated complex, are in the range 10(5)-10(6).

  6. Estimation of affinities of ligands in mixtures via magnetic recovery of target-ligand complexes and chromatographic analyses: chemometrics and an experimental model

    Directory of Open Access Journals (Sweden)

    Yuan Huidong


    Full Text Available Abstract Background The combinatorial library strategy of using multiple candidate ligands in mixtures as library members is ideal in terms of cost and efficiency, but needs special screening methods to estimate the affinities of candidate ligands in such mixtures. Herein, a new method to screen candidate ligands present in unknown molar quantities in mixtures was investigated. Results The proposed method involves preparing a processed-mixture-for-screening (PMFS with each mixture sample and an exogenous reference ligand, initiating competitive binding among ligands from the PMFS to a target immobilized on magnetic particles, recovering target-ligand complexes in equilibrium by magnetic force, extracting and concentrating bound ligands, and analyzing ligands in the PMFS and the concentrated extract by chromatography. The relative affinity of each candidate ligand to its reference ligand is estimated via an approximation equation assuming (a the candidate ligand and its reference ligand bind to the same site(s on the target, (b their chromatographic peak areas are over five times their intercepts of linear response but within their linear ranges, (c their binding ratios are below 10%. These prerequisites are met by optimizing primarily the quantity of the target used and the PMFS composition ratio. The new method was tested using the competitive binding of biotin derivatives from mixtures to streptavidin immobilized on magnetic particles as a model. Each mixture sample containing a limited number of candidate biotin derivatives with moderate differences in their molar quantities were prepared via parallel-combinatorial-synthesis (PCS without purification, or via the pooling of individual compounds. Some purified biotin derivatives were used as reference ligands. This method showed resistance to variations in chromatographic quantification sensitivity and concentration ratios; optimized conditions to validate the approximation equation could be

  7. A Protein Data Bank survey reveals shortening of intermolecular hydrogen bonds in ligand-protein complexes when a halogenated ligand is an H-bond donor.

    Directory of Open Access Journals (Sweden)

    Jarosław Poznański

    Full Text Available Halogen bonding in ligand-protein complexes is currently widely exploited, e.g. in drug design or supramolecular chemistry. But little attention has been directed to other effects that may result from replacement of a hydrogen by a strongly electronegative halogen. Analysis of almost 30000 hydrogen bonds between protein and ligand demonstrates that the length of a hydrogen bond depends on the type of donor-acceptor pair. Interestingly, lengths of hydrogen bonds between a protein and a halogenated ligand are visibly shorter than those estimated for the same family of proteins in complexes with non-halogenated ligands. Taking into account the effect of halogenation on hydrogen bonding is thus important when evaluating structural and/or energetic parameters of ligand-protein complexes. All these observations are consistent with the concept that halogenation increases the acidity of the proximal amino/imino/hydroxyl groups and thus makes them better, i.e. stronger, H-bond donors.

  8. A Protein Data Bank Survey Reveals Shortening of Intermolecular Hydrogen Bonds in Ligand-Protein Complexes When a Halogenated Ligand Is an H-Bond Donor (United States)

    Poznański, Jarosław; Poznańska, Anna; Shugar, David


    Halogen bonding in ligand-protein complexes is currently widely exploited, e.g. in drug design or supramolecular chemistry. But little attention has been directed to other effects that may result from replacement of a hydrogen by a strongly electronegative halogen. Analysis of almost 30000 hydrogen bonds between protein and ligand demonstrates that the length of a hydrogen bond depends on the type of donor-acceptor pair. Interestingly, lengths of hydrogen bonds between a protein and a halogenated ligand are visibly shorter than those estimated for the same family of proteins in complexes with non-halogenated ligands. Taking into account the effect of halogenation on hydrogen bonding is thus important when evaluating structural and/or energetic parameters of ligand-protein complexes. All these observations are consistent with the concept that halogenation increases the acidity of the proximal amino/imino/hydroxyl groups and thus makes them better, i.e. stronger, H-bond donors. PMID:24933273

  9. Distinct Iron-binding Ligands in the Upper Water Column at Station ALOHA (United States)

    Bundy, R.; Boiteau, R.; Repeta, D.


    The distribution and chemical properties of iron-binding organic ligands at station ALOHA were examined using a combination of solid phase extraction (SPE) followed by high pressure liquid chromatography-inductively coupled plasma mass spectrometry (HPLC-ICPMS). HPLC-ICPMS ligand measurements were complemented by competitive ligand exchange adsorptive cathodic stripping voltammetry (CLE-ACSV) analysis using salicylaldoxime as the added ligand. By HPLC-ICPMS, we find enhanced concentrations of distinct naturally-occurring polar iron-binding ligands present at the surface and in the chlorophyll maximum. Lower concentrations were found in the subsurface, where a suite of non-polar ligands was detected. Siderophores were present at the deepest depths sampled at station ALOHA, down to 400m. Incubation studies provided evidence for the production of iron-binding ligands associated with nutrient amended phytoplankton growth in surface waters, and as a result of microbial particle remineralization in the subsurface water column. Ligands classes identified via SPE were then compared to CLE-ACSV ligand measurements, as well as the conditional stability constants measured from model polar and non-polar siderophores, yielding insight to the sources of iron-binding ligands throughout the water column at station ALOHA.

  10. Ligand-induced protein mobility in complexes of carbonic anhydrase II and benzenesulfonamides with oligoglycine chains.

    Directory of Open Access Journals (Sweden)

    Vijay M Krishnamurthy

    Full Text Available This paper describes a biophysical investigation of residual mobility in complexes of bovine carbonic anhydrase II (BCA and para-substituted benzenesulfonamide ligands with chains of 1-5 glycine subunits, and explains the previously observed increase in entropy of binding with chain length. The reported results represent the first experimental demonstration that BCA is not the rigid, static globulin that has been typically assumed, but experiences structural fluctuations upon binding ligands. NMR studies with (15N-labeled ligands demonstrated that the first glycine subunit of the chain binds without stabilization or destabilization by the more distal subunits, and suggested that the other glycine subunits of the chain behave similarly. These data suggest that a model based on ligand mobility in the complex cannot explain the thermodynamic data. Hydrogen/deuterium exchange studies provided a global estimate of protein mobility and revealed that the number of exchanged hydrogens of BCA was higher when the protein was bound to a ligand with five glycine subunits than when bound to a ligand with only one subunit, and suggested a trend of increasing number of exchanged hydrogens with increasing chain length of the BCA-bound ligand, across the series. These data support the idea that the glycine chain destabilizes the structure of BCA in a length-dependent manner, causing an increase in BCA mobility. This study highlights the need to consider ligand-induced mobility of even "static" proteins in studies of protein-ligand binding, including rational ligand design approaches.

  11. Radiochemical studies of 99mTc complexes of modified cysteine ligands and bifunctional chelating agents. (United States)

    Pillai, M R; Kothari, K; Banerjee, S; Samuel, G; Suresh, M; Sarma, H D; Jurisson, S


    The synthesis of four novel ligands using the amino-acid cysteine and its ethyl carboxylate derivative is described. The synthetic method involves a two-step procedure, wherein the intermediate Schiff base formed by the condensation of the amino group of the cysteine substrate and salicylaldehyde is reduced to give the target ligands. The intermediates and the final products were characterized by high resolution nuclear magnetic resonance spectroscopy. Complexation studies of the ligands with 99mTc were optimized using stannous tartrate as the reducing agent under varying reaction conditions. The complexes were characterized using standard quality control techniques such as thin layer chromatography, paper electrophoresis, and paper chromatography. Lipophilicities of the complexes were estimated by solvent extraction into chloroform. Substantial changes in net charge and lipophilicity of the 99mTc complexes were observed on substituting the carboxylic acid functionality in ligands I and II with the ethyl carboxylate groups (ligands II and IV). All the ligands formed 99mTc complexes in high yield. Whereas the complexes with ligands I and II were observed to be hydrophilic in nature and not extractable into CHCl3, ligands III and IV resulted in neutral and lipophilic 99mTc complexes. The 99mTc complex with ligand II was not stable and on storage formed a hydrophilic and nonextractable species. The biodistribution of the complexes of ligands I and II showed that they cleared predominantly through the kidneys, whereas the complexes with ligands III and IV were excreted primarily through the hepatobiliary system. No significant brain uptake was observed with the 99mTc complexes with ligands III and IV despite their favorable properties of neutrality, lipophilicity, and conversion into a hydrophilic species. These ligands offer potential for use as bifunctional chelating agents.

  12. bipyridine host: Synthesis, X-ray structure, DNA cleavage

    Indian Academy of Sciences (India) Before docking, the DNA structure was stimulated and modified following the previously described methods.24. The structures of the free ligand and ... necrotic as judged by the staining, nuclear morphology and membrane .... This feature of the complex drew our attention since polypyridyl ...

  13. Synthesis, photophysical and preliminary investigation of the dye ...

    Indian Academy of Sciences (India)

    transfer resistances (Rct) of the electrons on the TiO2 semiconductor. Keywords. Ruthenium(II), polypyridyl ligands, spectroscopy, electrochemistry, DSSCs. 1. Introduction. The quest for new materials that efficiently harvest solar light continues to be an important goal. Recently, considerable efforts have been focused on ...

  14. Synthesis of asymmetric supramolecular compounds using a Ni(0) catalysed homo-coupling approach

    NARCIS (Netherlands)

    Cassidy, Lynda; Horn, Sabine; Cleary, Laura; Halpin, Yvonne; Browne, Wesley R.; Vos, Johannes G.


    The synthesis and characterisation of a series of dinuclear ruthenium and osmium polypyridyl metal complexes based on the bridging ligands [5-(5'-bipyridin-2',2 ''-yl)-3-(pyridin-2-yl)]-1,2,4-triazole (Hpytr-bipy), 2,2 ''-bis(pyridin-2 '' yl)-5,5 ''-bis(pyridin-3 ''-yl) (bipy-bipy) and

  15. Distinctive responses of brain tumor cells to TLR2 ligands. (United States)

    Yoon, Hee Jung; Jeon, Sae-Bom; Koh, Han Seok; Song, Jae-Young; Kim, Sang Soo; Kim, In-Hoo; Park, Eun Jung


    Malignant brain tumor mass contains significant numbers of infiltrating glial cells that may intimately interact with tumor cells and influence cancer treatments. Understanding of characteristic discrepancies between normal GLIA and tumor cells would, therefore, be valuable for improving anticancer therapeutics. Here, we report distinct differences in toll-like receptors (TLR)-2-mediated responses between normal glia and primary brain tumor cell lines. We found that tyrosine phosphorylation of STAT1 by TLR2 ligands and its downstream events did not occur in mouse, rat, or human brain tumor cell lines, but were markedly induced in normal primary microglia and astrocytes. Using TLR2-deficient, interferon (IFN)-γ-deficient, and IFNγ-receptor-1-deficient mice, we revealed that the impaired phosphorylation of STAT1 might be linked with defective TLR2 system in tumor cells, and that a TLR2-dependent pathway, not IFNγ-receptor machinery, might be critical for tyrosine STAT1 phosphorylation by TLR2 ligands. We also found that TLR2 and its heterodimeric partners, TLR1 and 6, on brain tumor cells failed to properly respond to TLR2 ligands, and representative TLR2-dependent cellular events, such as inflammatory responses and cell death, were not detected in brain tumor cells. Similar results were obtained in in vitro and in vivo experiments using orthotopic mouse and rat brain tumor models. Collectively, these results suggest that primary brain tumor cells may exhibit a distinctive dysfunction of TLR2-associated responses, resulting in abnormal signaling and cellular events. Careful targeting of this distinctive property could serve as the basis for effective therapeutic approaches against primary brain tumors. © 2015 Wiley Periodicals, Inc.

  16. Discovery of Aptamer Ligands for Hepatic Stellate Cells Using SELEX. (United States)

    Chen, Zhijin; Liu, Hao; Jain, Akshay; Zhang, Li; Liu, Chang; Cheng, Kun


    Insulin like growth factor II receptor (IGFIIR) is a transmembrane protein overexpressed in activated hepatic stellate cells (HSCs), which are the major target for the treatment of liver fibrosis. In this study, we aim to discover an IGFIIR-specific aptamer that can be potentially used as a targeting ligand for the treatment and diagnosis of liver fibrosis. Systematic evolution of ligands by exponential enrichment (SELEX) was conducted on recombinant human IGFIIR to identify IGFIIR-specific aptamers. The binding affinity and specificity of the discovered aptamers to IGFIIR and hepatic stellate cells were studied using flow cytometry and Surface Plasmon Resonance (SPR). Aptamer-20 showed the highest affinity to recombinant human IGFIIR protein with a K d of 35.5 nM, as determined by SPR. Aptamer-20 also has a high affinity (apparent K d 45.12 nM) to LX-2 human hepatic stellate cells. Binding of aptamer-20 to hepatic stellate cells could be inhibited by knockdown of IGFIIR using siRNA, indicating a high specificity of the aptamer. The aptamer formed a chimera with an anti-fibrotic PCBP2 siRNA and delivered the siRNA to HSC-T6 cells to trigger silencing activity. In Vivo biodistribution study of the siRNA-aptamer chimera also demonstrated a high and specific uptake in the liver of the rats with CCl 4 -induced liver fibrosis. These data suggest that aptamer-20 is a high-affinity ligand for antifibrotic and diagnostic agents for liver fibrosis.

  17. Differential expression of VEGF ligands and receptors in prostate cancer. (United States)

    Woollard, David J; Opeskin, Kenneth; Coso, Sanja; Wu, Di; Baldwin, Megan E; Williams, Elizabeth D


    Prostate cancer disseminates to regional lymph nodes, however the molecular mechanisms responsible for lymph node metastasis are poorly understood. The vascular endothelial growth factor (VEGF) ligand and receptor family have been implicated in the growth and spread of prostate cancer via activation of the blood vasculature and lymphatic systems. The purpose of this study was to comprehensively examine the expression pattern of VEGF ligands and receptors in the glandular epithelium, stroma, lymphatic vasculature and blood vessels in prostate cancer. The localization of VEGF-A, VEGF-C, VEGF-D, VEGF receptor (VEGFR)-1, VEGFR-2, and VEGFR-3 was examined in cancerous and adjacent benign prostate tissue from 52 subjects representing various grades of prostate cancer. Except for VEGFR-2, extensive staining was observed for all ligands and receptors in the prostate specimens. In epithelial cells, VEGF-A and VEGFR-1 expression was higher in tumor tissue compared to benign tissue. VEGF-D and VEGFR-3 expression was significantly higher in benign tissue compared to tumor in the stroma and the endothelium of lymphatic and blood vessels. In addition, the frequency of lymphatic vessels, but not blood vessels, was lower in tumor tissue compared with benign tissue. These results suggest that activation of VEGFR-1 by VEGF-A within the carcinoma, and activation of lymphatic endothelial cell VEGFR-3 by VEGF-D within the adjacent benign stroma may be important signaling mechanisms involved in the progression and subsequent metastatic spread of prostate cancer. Thus inhibition of these pathways may contribute to therapeutic strategies for the management of prostate cancer. Copyright © 2012 Wiley Periodicals, Inc.

  18. Six-coordinate uranium complexes featuring a bidentate anilide ligand

    Energy Technology Data Exchange (ETDEWEB)

    Fox, A.R.; Silvia, J.S.; Townsend, E.M.; Cummins, Ch.C. [Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA (United States)


    The synthesis of a new bidentate anilide ligand and four uranium amide complexes utilizing the ligand are reported. The secondary aniline HN[R]Ar{sub Met} (R = C(CD{sub 3}){sub 2}CH{sub 3}, Ar{sub Met} = 2-NMe{sub 2}-5-MeC{sub 6}H{sub 3}) is prepared by condensation of H{sub 2}NAr{sub Met} and acetone-d6 followed by alkylation of the resulting imine with MeLi. The ligand precursors (Et{sub 2}O)Li(N[R]Ar{sub Met}) and K(N[R]Ar{sub Met}) are prepared through deprotonation of HN[R]Ar{sub Met} with n-BuLi and KH, respectively. Treatment of UI{sub 3}(THF){sub 4} with (Et{sub 2}O)Li(N[R]Ar{sub Met}) (2 equiv) provides the uranium(III) -ate complex Li[I{sub 2}U(N[R]Ar{sub Met}){sub 2}] (Li[1]), while treatment of UI{sub 3} with three equiv. of K(N[R]Ar{sub Met}) provides the neutral uranium(III) complex U(N[R]Ar{sub Met}){sub 3} (2). Both uranium(III) complexes are susceptible to 1e oxidation, as is demonstrated by the syntheses of the uranium(IV) derivatives I{sub 2}U(N[R]Ar{sub Met}){sub 2} (1) and [U(N[R]Ar{sub Met}){sub 3}][OTf] ([2][OTf]; OTf=CF{sub 3}SO{sub 3}). The spectroscopic and X-ray structural characterization of all four uranium complexes is described. The structures of 2 and [2][OTf] exhibit a large degree of steric pressure about the uranium center, effectively preventing the [2]{sup +} ion from achieving a seven-coordinate structure. (authors)

  19. Suitable ligands for homogeneous ruthenium-catalyzed hydrogenolysis of esters


    Engelen, Marcel Chr. van; Teunissen, Herman T.; Vries, Johannes G. de; Elsevier, Cornelis J.


    Effective hydrogenolysis of dimethyl oxalate to ethylene glycol has been obtained using a catalyst prepared in situ from Ru(acac)3 with the facially coordinating tridentate phosphine ligand CH3C(CH2PPh2)3. This catalyst enabled full and selective conversion in 16 h at [S]/[Ru] = 500 at 80–100 bar hydrogen pressure at 120 °C. This catalyst is far more active than any known homogeneous catalyst able to hydrogenate dimethyl oxalate to ethylene glycol. Several mono-, di- and tridentate P- and N-l...

  20. Structural basis for ligand recognition of incretin receptors

    DEFF Research Database (Denmark)

    Underwood, Christina Rye; Parthier, Christoph; Reedtz-Runge, Steffen


    The glucose-dependent insulinotropic polypeptide (GIP) receptor and the glucagon-like peptide-1 (GLP-1) receptor are homologous G-protein-coupled receptors (GPCRs). Incretin receptor agonists stimulate the synthesis and secretion of insulin from pancreatic β-cells and are therefore promising agents...... analysis of the ECDs of incretin receptors and related GPCRs has shed new light on the process of ligand recognition and binding and provided a basis to disclose some of the mechanisms underlying receptor activation at high resolution....

  1. Octahedral molybdenum cluster complexes with aromatic sulfonate ligands


    Efremova, Olga A.; Vorotnikov, Yuri A.; Brylev, Konstantin A.; Vorotnikova, Natalya A.; Novozhilov, Igor N.; Kuratieva, Natalia V.; Edeleva, Mariya V.; Benoit, David M.; Kitamura, Noboru; Mironov, Yuri V.; Shestopalov, Michael A.; Sutherland, Andrew J.


    This article describes the synthesis, structures and systematic study of the spectroscopic and redox properties of a series of octahedral molybdenum metal cluster complexes with aromatic sulfonate ligands (nBu4N)2[{Mo6X8}(OTs)6] and (nBu4N)2[{Mo6X8}(PhSO3)6] (where X- is Cl-, Br- or I-; OTs- is p-toluenesulfonate and PhSO3 - is benzenesulfonate). All the complexes demonstrated photoluminescence in the red region and an ability to generate singlet oxygen. Notably, the highest quantum yields (>...

  2. Imaging ligand-gated ion channels with quantum dots (United States)

    Tomlinson, I. D.; Orndorff, Rebecca L.; Gussin, Hélène; Mason, John N.; Blakely, Randy D.; Pepperberg, David R.; Rosenthal, Sandra J.


    In this paper we report two different methodologies for labeling ligand-gated receptors. The first of these builds upon our earlier work with serotonin conjugated quantum dots and our studies with pegilated quantum dots to reduce non specific binding. In this approach a pegilated derivative of muscimol was synthesized and attached via an amide linkage to quantum dots coated in an amphiphillic polymer derivative of poly acrylamide. These conjugates were used to image the GABA C receptor in oocytes. An alternative approach was used to image tissue sections to study nicotinic acetylcholine receptors in the neuro muscular junction with biotinylated Bungerotoxin and streptavidin coated quantum dots.

  3. Ligands specify estrogen receptor alpha nuclear localization and degradation

    Directory of Open Access Journals (Sweden)

    Caze-Subra Stéphanie


    Full Text Available Abstract Background The estrogen receptor alpha (ERα is found predominately in the nucleus, both in hormone stimulated and untreated cells. Intracellular distribution of the ERα changes in the presence of agonists but the impact of different antiestrogens on the fate of ERα is a matter of debate. Results A MCF-7 cell line stably expressing GFP-tagged human ERα (SK19 cell line was created to examine the localization of ligand-bound GFP-ERα. We combined digitonin-based cell fractionation analyses with fluorescence and immuno-electron microscopy to determine the intracellular distribution of ligand-bound ERα and/or GFP-ERα. Using fluorescence- and electron microscopy we demonstrate that both endogenous ERα and GFP-ERα form numerous nuclear focal accumulations upon addition of agonist, 17β-estradiol (E2, and pure antagonists (selective estrogen regulator disruptor; SERD, ICI 182,780 or RU58,668, while in the presence of partial antagonists (selective estrogen regulator modulator; SERM, 4-hydroxytamoxifen (OHT or RU39,411, diffuse nuclear staining persisted. Digitonin based cell fractionation analyses confirmed that endogenous ERα and GFP-ERα predominantly reside in the nuclear fraction. Overall ERα protein levels were reduced after estradiol treatment. In the presence of SERMs ERα was stabilized in the nuclear soluble fraction, while in the presence of SERDs protein levels decreased drastically and the remaining ERα was largely found in a nuclear insoluble fraction. mRNA levels of ESR1 were reduced compared to untreated cells in the presence of all ligands tested, including E2. E2 and SERDs induced ERα degradation occurred in distinct nuclear foci composed of ERα and the proteasome providing a simple explanation for ERα sequestration in the nucleus. Conclusions Our results indicate that chemical structure of ligands directly affect the nuclear fate and protein turnover of the estrogen receptor alpha independently of their impact on

  4. Overview of Stabilizing Ligands for Biocompatible Quantum Dot Nanocrystals

    Directory of Open Access Journals (Sweden)

    Aaron Clapp


    Full Text Available Luminescent colloidal quantum dots (QDs possess numerous advantages as fluorophores in biological applications. However, a principal challenge is how to retain the desirable optical properties of quantum dots in aqueous media while maintaining biocompatibility. Because QD photophysical properties are directly related to surface states, it is critical to control the surface chemistry that renders QDs biocompatible while maintaining electronic passivation. For more than a decade, investigators have used diverse strategies for altering the QD surface. This review summarizes the most successful approaches for preparing biocompatible QDs using various chemical ligands.

  5. Isothermal titration calorimetry for studying protein-ligand interactions. (United States)

    Damian, Luminita


    Isothermal titration calorimetry (ITC) is a biophysical technique that allows a thermodynamic characterization of an interactive system. It is a free in solution technique that requires no labeling, using heat as signal. ITC allows simultaneous determination of affinity K a, stoichiometry n, enthalpy change ΔH and calculation of free energy change ΔG and entropy change ΔS in one single experiment. It is the only technique that allows direct enthalpy change measurement. By accessing the enthalpy change, we get a step closer in estimating the driving forces that characterize the interaction of a protein with a ligand, information much needed in the drug discovery process.

  6. Engineering periplasmic ligand binding proteins as glucose nanosensors

    Directory of Open Access Journals (Sweden)

    Constance J. Jeffery


    Full Text Available Diabetes affects over 100 million people worldwide. Better methods for monitoring blood glucose levels are needed for improving disease management. Several labs have previously made glucose nanosensors by modifying members of the periplasmic ligand binding protein superfamily. This minireview summarizes recent developments in constructing new versions of these proteins that are responsive within the physiological range of blood glucose levels, employ new reporter groups, and/or are more robust. These experiments are important steps in the development of novel proteins that have the characteristics needed for an implantable glucose nanosensor for diabetes management: specificity for glucose, rapid response, sensitivity within the physiological range of glucose concentrations, reproducibility, and robustness.

  7. Ultrafast infrared studies of complex ligand rearrangements in solution

    Energy Technology Data Exchange (ETDEWEB)

    Payne, Christine K. [Univ. of California, Berkeley, CA (United States)


    The complete description of a chemical reaction in solution depends upon an understanding of the reactive molecule as well as its interactions with the surrounding solvent molecules. Using ultrafast infrared spectroscopy it is possible to observe both the solute-solvent interactions and the rearrangement steps which determine the overall course of a chemical reaction. The topics addressed in these studies focus on reaction mechanisms which require the rearrangement of complex ligands and the spectroscopic techniques necessary for the determination of these mechanisms. Ligand rearrangement is studied by considering two different reaction mechanisms for which the rearrangement of a complex ligand constitutes the most important step of the reaction. The first system concerns the rearrangement of a cyclopentadienyl ring as the response of an organometallic complex to a loss of electron density. This mechanism, commonly referred to as ''ring slip'', is frequently cited to explain reaction mechanisms. However, the ring slipped intermediate is too short-lived to be observed using conventional methods. Using a combination of ultrafast infrared spectroscopy and electronic structure calculations it has been shown that the intermediate exists, but does not form an eighteen-electron intermediate as suggested by traditional molecular orbital models. The second example examines the initial steps of alkyne polymerization. Group 6 (Cr, Mo, W) pentacarbonyl species are generated photolytically and used to catalyze the polymerization of unsaturated hydrocarbons through a series of coordination and rearrangement steps. Observing this reaction on the femto- to millisecond timescale indicates that the initial coordination of an alkyne solvent molecule to the metal center results in a stable intermediate that does not rearrange to form the polymer precursor. This suggests that polymerization requires the dissociation of additional carbonyl ligands before

  8. Doping Control Via Molecularly Engineered Surface Ligand Coordination

    KAUST Repository

    Yuan, Mingjian


    A means to control the net doping of a CQD solid is identified via the design of the bidentate ligand crosslinking the material. The strategy does not rely on implementing different atmospheres at different steps in device processing, but instead is a robust strategy implemented in a single processing ambient. We achieve an order of magnitude difference in doping that allows us to build a graded photovoltaic device and maintain high current and voltage at maximum power-point conditions. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Binding-Induced Fluorescence of Serotonin Transporter Ligands

    DEFF Research Database (Denmark)

    Wilson, James; Ladefoged, Lucy Kate; Babinchak, Michael


    The binding-induced fluorescence of 4-(4-(dimethylamino)-phenyl)-1-methylpyridinium (APP(+)) and two new serotonin transporter (SERT)-binding fluorescent analogues, 1-butyl-4-[4-(1-dimethylamino)phenyl]-pyridinium bromide (BPP(+)) and 1-methyl-4-[4-(1-piperidinyl)phenyl]-pyridinium (PPP(+)), has...... calculations reveal that the probes are able to access the nonpolar and conformationally restrictive binding pocket of SERT. As a result, the probes exhibit previously not identified binding-induced turn-on emission that is spectroscopically distinct from dyes that have accumulated intracellularly. Thus......, binding and transport dynamics of SERT ligands can be resolved both spatially and spectroscopically....

  10. Ligands specify estrogen receptor alpha nuclear localization and degradation


    Caze-Subra Stéphanie; Mazaheri Mahta; Kocanova Silvia; Bystricky Kerstin


    Abstract Background The estrogen receptor alpha (ERα) is found predominately in the nucleus, both in hormone stimulated and untreated cells. Intracellular distribution of the ERα changes in the presence of agonists but the impact of different antiestrogens on the fate of ERα is a matter of debate. Results A MCF-7 cell line stably expressing GFP-tagged human ERα (SK19 cell line) was created to examine the localization of ligand-bound GFP-ERα. We combined digitonin-based cell fractionation anal...

  11. Galaxy7TM: flexible GPCR-ligand docking by structure refinement. (United States)

    Lee, Gyu Rie; Seok, Chaok


    G-protein-coupled receptors (GPCRs) play important physiological roles related to signal transduction and form a major group of drug targets. Prediction of GPCR-ligand complex structures has therefore important implications to drug discovery. With previously available servers, it was only possible to first predict GPCR structures by homology modeling and then perform ligand docking on the model structures. However, model structures generated without explicit consideration of specific ligands of interest can be inaccurate because GPCR structures can be affected by ligand binding. The Galaxy7TM server, freely accessible at, improves an input GPCR structure by simultaneous ligand docking and flexible structure refinement using GALAXY methods. The server shows better performance in both ligand docking and GPCR structure refinement than commonly used programs AutoDock Vina and Rosetta MPrelax, respectively. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Improved Metathesis Lifetime: Chelating Pyridinyl-Alcoholato Ligands in the Second Generation Grubbs Precatalyst

    Directory of Open Access Journals (Sweden)

    Jean I. du Toit


    Full Text Available Hemilabile ligands can release a free coordination site “on demand” of an incoming nucleophilic substrate while occupying it otherwise. This is believed to increase the thermal stability and activity of catalytic systems and therefore prevent decomposition via free coordination sites. In this investigation chelating pyridinyl-alcoholato ligands were identified as possible hemilabile ligands for incorporation into the second generation Grubbs precatalyst. The O,N-alcoholato ligands with different steric bulk could be successfully incorporated into the precatalysts. The incorporation of the sterically hindered, hemilabile O,N-ligands improved the thermal stability, activity, selectivity and lifetime of these complexes towards the metathesis of 1-octene. A decrease in the activity of the second generation Grubbs precatalyst was additionally observed after incorporating a hemilabile O,N-ligand with two phenyl groups into the system, while increasing their lifetime.

  13. Targeting Protein-Protein Interactions with Trimeric Ligands: High Affinity Inhibitors of the MAGUK Protein Family

    DEFF Research Database (Denmark)

    Nissen, Klaus B; Kedström, Linda Maria Haugaard; Wilbek, Theis S


    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...

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

    KAUST Repository

    Choi, Joshua J.


    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.

  15. Lighting up G protein-coupled purinergic receptors with engineered fluorescent ligands (United States)

    Ciruela, Francisco; Fernández-Dueñas, Víctor; Jacobson, Kenneth A.


    The use of G protein-coupled receptors fluorescent ligands is undergoing continuous expansion. In line with this, fluorescent agonists and antagonists of high affinity for G protein-coupled adenosine and P2Y receptors have been shown to be useful pharmacological probe compounds. Fluorescent ligands for A1R, A2AR, and A3R (adenosine receptors) and P2Y2R, P2Y4R, P2Y6R, and P2Y14R (nucleotide receptors) have been reported. Such ligands have been successfully applied to drug discovery and to GPCR characterization by flow cytometry, fluorescence correlation spectroscopy, fluorescence microscopy, fluorescence polarization, fluorescence resonance energy transfer and scanning confocal microscopy. Here we summarize recently reported and readily available representative fluorescent ligands of purinergic receptors. In addition, we pay special attention on the use of this family of fluorescent ligands revealing two main aspects of purinergic receptor biology, namely ligand binding and receptor oligomerization. PMID:25890205

  16. Dinuclear palladium complexes with two ligand-centered radicals and a single bridging ligand: subtle tuning of magnetic properties. (United States)

    Broere, Daniël L J; Demeshko, Serhiy; de Bruin, Bas; Pidko, Evgeny A; Reek, Joost N H; Siegler, Maxime A; Lutz, Martin; van der Vlugt, Jarl Ivar


    The facile and tunable preparation of unique dinuclear [(L(⋅))Pd-X-Pd(L(⋅))] complexes (X = Cl or N3), bearing a ligand radical on each Pd, is disclosed, as well as their magnetochemistry in solution and solid state is reported. Chloride abstraction from [PdCl(NNO(ISQ))] (NNO(ISQ) = iminosemiquinonato) with TlPF6 results in an unusual monochlorido-bridged dinuclear open-shell diradical species, [{Pd(NNO(ISQ))}2(μ-Cl)](+), with an unusually small Pd-Cl-Pd angle (ca. 93°, determined by X-ray). This suggests an intramolecular d(8)-d(8) interaction, which is supported by DFT calculations. SQUID measurements indicate moderate antiferromagnetic spin exchange between the two ligand radicals and an overall singlet ground state in the solid state. VT EPR spectroscopy shows a transient signal corresponding to a triplet state between 20 and 60 K. Complex 2 reacts with PPh3 to generate [Pd(NNO(ISQ))(PPh3)](+) and one equivalent of [PdCl(NNO(ISQ))]. Reacting an 1:1 mixture of [PdCl(NNO(ISQ))] and [Pd(N3)(NNO(ISQ))] furnishes the 1,1-azido-bridged dinuclear diradical [{Pd(NNO(ISQ))}2(κ(1)-N;μ-N3](+), with a Pd-N-Pd angle close to 127° (X-ray). Magnetic and EPR measurements indicate two independent S = 1/2 spin carriers and no magnetic interaction in the solid state. The two diradical species both show no spin exchange in solution, likely because of unhindered rotation around the Pd-X-Pd core. This work demonstrates that a single bridging atom can induce subtle and tunable changes in structural and magnetic properties of novel dinuclear Pd complexes featuring two ligand-based radicals. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Functional Short-Bite Ligands: Synthesis, Coordination Chemistry, and Applications of N-Functionalized Bis(diaryl/dialkylphosphino)amine-type Ligands. (United States)

    Fliedel, Christophe; Ghisolfi, Alessio; Braunstein, Pierre


    The aim of this review is to highlight how the diversity generated by N-substitution in the well-known short-bite ligand bis(diphenylphosphino)amine (DPPA) allows a fine-tuning of the ligand properties and offers a considerable scope for tailoring the properties and applications of their corresponding metal complexes. The various N-substituents include nitrogen-, oxygen-, phosphorus-, sulfur-, halogen-, and silicon-based functionalities and directly N-bound metals. Multiple DPPA-type ligands linked through an organic spacer and N-functionalized DRPA-type ligands, in which the PPh2 substituents are replaced by PR2 (R = alkyl, benzyl) groups, are also discussed. Owing to the considerable diversity of N-functionalized DPPA-type ligands available, the applications of their mono- and polynuclear metal complexes are very diverse and range from homogeneous catalysis with well-defined or in situ generated (pre)catalysts to heterogeneous catalysis and materials science. In particular, sustained interest for DPPA-type ligands has been motivated, at least in part, by their ability to promote selective ethylene tri- or tetramerization in combination with chromium. Ligands and metal complexes where the N-substituent is a pure hydrocarbon group (as opposed to N-functionalization) are outside the scope of this review. However, when possible, a comparison between the catalytic performances of N-functionalized systems with those of their N-substituted analogs will be provided.

  18. IR and ESR studies on novel Cu(II) theophyllinato complexes containing mono- or bidentate ligands (United States)

    Forizs, Edit; David, L.; Cozar, O.; Chiş, V.; Damian, G.; Csibi, Jolán


    Three mixed-ligand copper(II) complexes containing theophylline and mono- or bidentate N-donor ligands (2,2'-bipyridine, 4-fluoraniline and 1,10-phenanthroline) were synthesized and characterized by elemental analysis, IR and ESR spectra. According to IR and ESR data the Cu(II) complexes exhibit a distorted tetrahedral coordination of copper by two nitrogen atoms of the monodentate or bidentate ligands and the two monodentate theophyllinate anion bonded through N(7) atom.

  19. Structure-activity relationships of constrained phenylethylamine ligands for the serotonin 5-ht2 receptors

    DEFF Research Database (Denmark)

    Isberg, Vignir; Paine, James; Leth-Petersen, Sebastian


    Serotonergic ligands have proven effective drugs in the treatment of migraine, pain, obesity, and a wide range of psychiatric and neurological disorders. There is a clinical need for more highly 5-HT2 receptor subtype-selective ligands and the most attention has been given to the phenethylamine......-activity relationships of constrained phenethylamines and contributes towards the development of 5-HT2 receptor subtype-selective ligands....

  20. Novel fluorinated ligands for gold nanoparticle labelling with application in 19F-MRI.


    Michelena Olatz; Padro Daniel; Carrillo-Carrión Carolina; del Pino Pablo; Blanco Jorge; Arnáiz Blanca; Parak Wolfgang J.; Carril Monica


    Novel fluorinated ligands for gold nanoparticle labelling have been designed and synthesised. Several types of gold nanoparticles have been prepared in the presence of these fluorinated ligands alone, or in combination with non-fluorinated ligands. Their colloidal stability in water and other solvents was tested and the magnetic resonance properties of the so-obtained nanoparticles were also assessed in detail. H-1 and F-19-NMR spectra were evaluated and MRI phantoms of the most promising nan...

  1. Conformational transitions upon ligand binding: holo-structure prediction from apo conformations.

    Directory of Open Access Journals (Sweden)

    Daniel Seeliger


    Full Text Available Biological function of proteins is frequently associated with the formation of complexes with small-molecule ligands. Experimental structure determination of such complexes at atomic resolution, however, can be time-consuming and costly. Computational methods for structure prediction of protein/ligand complexes, particularly docking, are as yet restricted by their limited consideration of receptor flexibility, rendering them not applicable for predicting protein/ligand complexes if large conformational changes of the receptor upon ligand binding are involved. Accurate receptor models in the ligand-bound state (holo structures, however, are a prerequisite for successful structure-based drug design. Hence, if only an unbound (apo structure is available distinct from the ligand-bound conformation, structure-based drug design is severely limited. We present a method to predict the structure of protein/ligand complexes based solely on the apo structure, the ligand and the radius of gyration of the holo structure. The method is applied to ten cases in which proteins undergo structural rearrangements of up to 7.1 A backbone RMSD upon ligand binding. In all cases, receptor models within 1.6 A backbone RMSD to the target were predicted and close-to-native ligand binding poses were obtained for 8 of 10 cases in the top-ranked complex models. A protocol is presented that is expected to enable structure modeling of protein/ligand complexes and structure-based drug design for cases where crystal structures of ligand-bound conformations are not available.

  2. Selective high-affinity polydentate ligands and methods of making such

    Energy Technology Data Exchange (ETDEWEB)

    Denardo, Sally J.; Denardo, Gerald L.; Balhorn, Rodney L.


    This invention provides novel polydentate selective high affinity ligands (SHALs) that can be used in a variety of applications in a manner analogous to the use of antibodies. SHALs typically comprise a multiplicity of ligands that each bind different region son the target molecule. The ligands are joined directly or through a linker thereby forming a polydentate moiety that typically binds the target molecule with high selectivity and avidity.

  3. Effect of ligand substitution on the exchange interactions in {Mn12}-type single-molecule magnets


    Boukhvalov, D. W.; Dobrovitski, V. V.; Kögerler, P.; Al-Saqer, M.; Katsnelson, M. I.; Lichtenstein, A. I.; Harmon, B. N.


    We investigate how the ligand substitution affects the intra-molecular spin exchange interactions, studying a prototypal family of single-molecule magnets comprising dodecanuclear cluster molecules [Mn12O12(COOR)16]. We identify a simple scheme based on accumulated Pauling electronegativity numbers (a.e.n.) of the carboxylate ligand groups (R). The redistribution of the electron density, controlled by a.e.n. of a ligand, changes the degree of hybridization between 3d electrons of manganese an...

  4. Size and ligand effects on the electrochemical and spectroelectrochemical responses of CdSe nanocrystals. (United States)

    Querner, Claudia; Reiss, Peter; Sadki, Said; Zagorska, Malgorzata; Pron, Adam


    The electrochemical properties of CdSe quantum dots with electrochemically inactive surface ligands (TOPO) have been investigated in comparison with the analogous nanocrystals containing electrochemically active oligoaniline ligands. The TOPO-capped nanocrystals have been studied in a wide size range (from 3 to 6.5 nm) with the goal to amplify the influence of the quantum confinement effect on the electrochemical response. The determined HOMO and LUMO levels have been found in good agreement with the ones obtained from photoluminescence studies and those predicted theoretically. Ligand exchange with aniline tetramer significantly influences the voltammetric peaks associated with the HOMO oxidation and the LUMO reduction of the quantum dots, which are shifted to higher and lower potentials, respectively. These shifts are interpreted in terms of the positive ligand charging which precedes the oxidation of the nanocrystals and the insulating nature of the ligand in the case of the nanocrystal reduction. The ligand-nanocrystal interactions have also been studied by UV-Vis-NIR and Raman spectroelectrochemistry in comparison with a specially prepared model compound which, apart from the anchoring function is identical to the grafted oligoaniline ligand. Both spectroelectrochemical techniques clearly indicate the same nature of the oxidation/reduction pathway for both the model compound and the grafted ligand. The influence of the grafting is manifested by a shift in the onset of the ligand oxidation as compared to the case of the "free" model compound. Since both components (ligands and nanocrystals) mutually influence their electrochemical and spectroelectrochemical properties, the newly developed system can be considered as a true molecular hybrid. Such hybrids are of interest because the potential zone of the ligand electroactivity is well separated from that of the nanocrystals and, as a result, the organic part can be electrochemically switched between the

  5. A ligand-reversible dimerization system for controlling protein–protein interactions


    Rollins, Carl T.; Rivera, Victor M.; Woolfson, Derek N.; Keenan, Terence; Hatada, Marcos; Adams, Susan E.; Andrade, Lawrence J.; Yaeger, David; van Schravendijk, Marie Rose; Holt, Dennis A.; Gilman, Michael; Clackson, Tim


    Chemically induced dimerization provides a general way to gain control over intracellular processes. Typically, FK506-binding protein (FKBP) domains are fused to a signaling domain of interest, allowing crosslinking to be initiated by addition of a bivalent FKBP ligand. In the course of protein engineering studies on human FKBP, we discovered that a single point mutation in the ligand-binding site (Phe-36 → Met) converts the normally monomeric protein into a ligand-reversible dimer. Two-hybri...

  6. Asymmetric Iron-Catalyzed C-H Alkylation Enabled by Remote Ligand meta-Substitution. (United States)

    Loup, Joachim; Zell, Daniel; Oliveira, João C A; Keil, Helena; Stalke, Dietmar; Ackermann, Lutz


    Highly enantioselective iron-catalyzed C-H alkylations by inner-sphere C-H activation were accomplished with ample scope. High levels of enantiocontrol proved viable through a novel ligand design that exploits a remote meta-substitution on N-heterocyclic carbenes within a facile ligand-to-ligand H-transfer C-H cleavage. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. New L-Serine Derivative Ligands as Cocatalysts for Diels-Alder Reaction (United States)

    Sousa, Carlos A. D.; Rodríguez-Borges, José E.; Freire, Cristina


    New L-serine derivative ligands were prepared and tested as cocatalyst in the Diels-Alder reactions between cyclopentadiene (CPD) and methyl acrylate, in the presence of several Lewis acids. The catalytic potential of the in situ formed complexes was evaluated based on the reaction yield. Bidentate serine ligands showed good ability to coordinate medium strength Lewis acids, thus boosting their catalytic activity. The synthesis of the L-serine ligands proved to be highly efficient and straightforward. PMID:24383009

  8. Probing interaction of a fluorescent ligand with HIV TAR RNA (United States)

    Qi, Liang; Zhang, Jing; He, Tian; Huo, Yuan; Zhang, Zhi-Qi


    Trans-activator of Transcription (Tat) antagonists could block the interaction between Tat protein and its target, trans-activation responsive region (TAR) RNA, to inhibit Tat function and prevent human immunodeficiency virus type 1 (HIV-1) replication. For the first time, a small fluorescence ligand, ICR 191, was found to interact with TAR RNA at the Tat binding site and compete with Tat. It was also observed that the fluorescence of ICR 191 could be quenched when binding to TAR RNA and recovered when discharged via competition with Tat peptide or a well-known Tat inhibitor, neomycin B. The binding parameters of ICR 191 to TAR RNA were determined through theoretical calculations. Mass spectrometry, circular dichroism and molecular docking were used to further confirm the interaction of ICR 191 with TAR RNA. Inspired by these discoveries, a primary fluorescence model for the discovery of Tat antagonists was built using ICR 191 as a fluorescence indicator and the feasibility of this model was evaluated. This ligand-RNA interaction could provide a new strategy for research aimed at discovering Tat antagonists.

  9. 01-ERD-111 - The Development of Synthetic High Affinity Ligands

    Energy Technology Data Exchange (ETDEWEB)

    Perkins, J; Balhorn, R; Cosman, M; Lightstone, F; Zeller, L


    The aim of this project was to develop Synthetic High-Affinity Ligands (SHALs), which bind with high affinity and specificity to proteins of interest for national security and cancer therapy applications. The aim of producing synthetic ligands for sensory devices as an alternative to antibody-based detection assays and therapeutic agents is to overcome the drawbacks associated with antibody-based in next-generation sensors and systems. The focus area of the project was the chemical synthesis of the SHALs. The project concentrated on two different protein targets. (a) The C fragment of tetanus and botulinum toxin, potential biowarfare agents. A SHAL for tetanus or botulinum toxin would be incorporated into a sensory device for the toxins. (b) HLA-DR10, a protein found in high abundance on the surface of Non-Hodgkins Lymphoma. A SHAL specific to a tumor marker, labeled with a radionuclide, would enable the targeted delivery of radiation therapy to metastatic disease. The technical approach used to develop a SHAL for each protein target will be described in more detail below. However, in general, the development of a SHAL requires a combination of computational modeling techniques, modern nuclear magnetic resonance spectroscopy (NMR) and synthetic chemistry.

  10. The role of KIR genes and ligands in leukemia surveillance

    Directory of Open Access Journals (Sweden)

    Florian eBabor


    Full Text Available The anti-leukemic potential of natural killer (NK cells has been of rising interest in recent years. Interactions between inhibitory killer immunoglobulin-like receptors (KIR and HLA class I ligands seem to be critically involved in the immunosurveillance process. It is also well established that mismatching of HLA class I-encoded KIR ligands in the setting of hematopoietic stem cell transplantation leads to allorecognition of leukemic cells by NK cells, which is in line with the concept of missing-self recognition. Recent data now suggest that KIR gene polymorphism constitutes another important parameter that needs to be taken into account for selection of suitable stem cell donors. Moreover, the role of KIR gene polymorphism for predisposition to leukemia is a current matter of debate. Here, we would like to review the role of KIR function and genetic polymorphism for recognition of leukemia and discuss the impact of these findings for developing novel concepts for NK cell-based immunotherapy strategies.

  11. Evolution of ligands, receptors and metabolizing enzymes of thyroid signaling. (United States)

    Holzer, Guillaume; Roux, Natacha; Laudet, Vincent


    Thyroid hormones (THs) play important roles in vertebrates such as the control of the metabolism, development and seasonality. Given the pleiotropic effects of thyroid disorders (developmental delay, mood disorder, tachycardia, etc), THs signaling is highly investigated, specially using mammalian models. In addition, the critical role of TH in controlling frog metamorphosis has led to the use of Xenopus as another prominent model to study THs action. Nevertheless, animals regarded as non-model species can also improve our understanding of THs signaling. For instance, studies in amphioxus highlighted the role of Triac as a bona fide thyroid hormone receptor (TR) ligand. In this review, we discuss our current understanding of the THs signaling in the different taxa forming the metazoans (multicellular animals) group. We mainly focus on three actors of the THs signaling: the ligand, the receptor and the deiodinases, enzymes playing a critical role in THs metabolism. By doing so, we also pinpoint many key questions that remain unanswered. How can THs accelerate metamorphosis in tunicates and echinoderms while their TRs have not been yet demonstrated as functional THs receptors in these species? Do THs have a biological effect in insects and cnidarians even though they do not have any TR? What is the basic function of THs in invertebrate protostomia? These questions can appear disconnected from pharmacological issues and human applications, but the investigation of THs signaling at the metazoans scale can greatly improve our understanding of this major endocrinological pathway. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. i-Motif DNA: structure, stability and targeting with ligands. (United States)

    Day, Henry A; Pavlou, Pavlos; Waller, Zoë A E


    i-Motifs are four-stranded DNA secondary structures which can form in sequences rich in cytosine. Stabilised by acidic conditions, they are comprised of two parallel-stranded DNA duplexes held together in an antiparallel orientation by intercalated, cytosine-cytosine(+) base pairs. By virtue of their pH dependent folding, i-motif forming DNA sequences have been used extensively as pH switches for applications in nanotechnology. Initially, i-motifs were thought to be unstable at physiological pH, which precluded substantial biological investigation. However, recent advances have shown that this is not always the case and that i-motif stability is highly dependent on factors such as sequence and environmental conditions. In this review, we discuss some of the different i-motif structures investigated to date and the factors which affect their topology, stability and dynamics. Ligands which can interact with these structures are necessary to aid investigations into the potential biological functions of i-motif DNA and herein we review the existing i-motif ligands and give our perspective on the associated challenges with targeting this structure. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. Structure-Specific Ligand Recognition of Multistranded DNA Structures. (United States)

    Kaushik, Mahima; Singh, Anju; Kumar, Mohan; Chaudhary, Swati; Ahmed, Saami; Kukreti, Shrikant


    Structural polymorphism is an extremely significant phenomenon of nucleic acids, in which DNA and RNA oligonucleotide sequences are able to adapt various canonical, alternative and multistranded structures. These alternative forms of DNA and RNA have an enormous potential of participating in various cellular processes by recognizing ligands such as proteins, drugs and metal ions in a sequence and structure-specific manner. Such DNA-ligand interactions prove to be highly beneficial when exploited for therapeutic purposes. Many of these DNA/ RNA structures recognizing drugs have already proved their potential as anticancer, antibacterial, anthelmintic and antiviral properties. Over the last 2-3 decades, many mechanisms of DNA-drug interactions have been documented, but still many other new mechanisms are being explored. Designing new drugs with improved efficacy and specificity is of prime concern for all researchers which not only deals with the experiments related to synthesizing drugs, but also takes care of searching novel routes or agents for administration or delivery of these therapeutic agents by increasing their nuclear and cellular uptake. This review aims at explaining the structural polymorphs/ multistranded DNA structures and their interactions with pharmaceutical drugs in a structure-specific manner, along with their modes of interactions and biological relevance. This detailed overview of multistranded DNA structures and interacting drugs might further facilitate our understanding about molecular targets and drug development in a more precise manner for the larger benefit of mankind.

  14. Molecular basis of ligand recognition and transport by glucose transporters. (United States)

    Deng, Dong; Sun, Pengcheng; Yan, Chuangye; Ke, Meng; Jiang, Xin; Xiong, Lei; Ren, Wenlin; Hirata, Kunio; Yamamoto, Masaki; Fan, Shilong; Yan, Nieng


    The major facilitator superfamily glucose transporters, exemplified by human GLUT1-4, have been central to the study of solute transport. Using lipidic cubic phase crystallization and microfocus X-ray diffraction, we determined the structure of human GLUT3 in complex with D-glucose at 1.5 Å resolution in an outward-occluded conformation. The high-resolution structure allows discrimination of both α- and β-anomers of D-glucose. Two additional structures of GLUT3 bound to the exofacial inhibitor maltose were obtained at 2.6 Å in the outward-open and 2.4 Å in the outward-occluded states. In all three structures, the ligands are predominantly coordinated by polar residues from the carboxy terminal domain. Conformational transition from outward-open to outward-occluded entails a prominent local rearrangement of the extracellular part of transmembrane segment TM7. Comparison of the outward-facing GLUT3 structures with the inward-open GLUT1 provides insights into the alternating access cycle for GLUTs, whereby the C-terminal domain provides the primary substrate-binding site and the amino-terminal domain undergoes rigid-body rotation with respect to the C-terminal domain. Our studies provide an important framework for the mechanistic and kinetic understanding of GLUTs and shed light on structure-guided ligand design.

  15. In Silico Docking of HNF-1a Receptor Ligands

    Directory of Open Access Journals (Sweden)

    Gumpeny Ramachandra Sridhar


    Full Text Available Background. HNF-1a is a transcription factor that regulates glucose metabolism by expression in various tissues. Aim. To dock potential ligands of HNF-1a using docking software in silico. Methods. We performed in silico studies using HNF-1a protein 2GYP·pdb and the following softwares: ISIS/Draw 2.5SP4, ARGUSLAB 4.0.1, and HEX5.1. Observations. The docking distances (in angstrom units: 1 angstrom unit (Å = 0.1 nanometer or  metres with ligands in decreasing order are as follows: resveratrol (3.8 Å, aspirin (4.5 Å, stearic acid (4.9 Å, retinol (6.0 Å, nitrazepam (6.8 Å, ibuprofen (7.9 Å, azulfidine (9.0 Å, simvastatin (9.0 Å, elaidic acid (10.1 Å, and oleic acid (11.6 Å. Conclusion. HNF-1a domain interacted most closely with resveratrol and aspirin

  16. Designing allosteric peptide ligands targeting a globular protein. (United States)

    Selz, Karen A; Samoylova, Tatiana I; Samoylov, Alexandre M; Vodyanoy, Vitaly J; Mandell, Arnold J


    Patented signal analytic algorithms applied to hydrophobically transformed, numerical amino acid sequences have previously been used to design short, protein-targeted, L or D retro-inverso peptides. These peptides have demonstrated allosteric and/or indirect agonist effects on a variety of G-protein and tyrosine kinase coupled membrane receptors with 30% to over 80% hit rates. Here we extend these approaches to a globular protein target. We designed eight peptide ligands targeting an ELISA antibody responsive protein, beta-galactosidase, betaGAL. Three of the eight 14mer peptides allosterically activated betaGAL with ELISA methodology. Using Bayesian statistics, this 38% hit rate would have occurred 2 x 10(-9) by chance. These peptides demonstrated binding site competitive or noncompetitive interactions, suggesting allosteric site multiplicity with respect to their betaGAL binding-mediated ELISA signal. Kinetic studies demonstrated the temperature dependence of the betaGAL peptide binding functions. Using the van't Hoff relation, we found evidence for enthalpy-entropy compensation. This relation is often found for hydrophobic interactions in aqueous media, and is consistent with the postulated hydrophobic series encoding underlying our protein-targeted, peptide design methods. It appears that our algorithmic, hydrophobic autocovariance eigenvector template approach to the design of allosteric peptides targeting membrane receptors may also be applicable to the design of peptide ligands targeting nonmembrane involved globular proteins. Copyright 2006 Wiley Periodicals, Inc.

  17. Modeling of ligand binding to dopamine D2 receptor

    Directory of Open Access Journals (Sweden)

    Ostopovici-Halip Liliana


    Full Text Available The dopaminic receptors have been for long time the major targets for developing new small molecules with high affinity and selectivity to treat psychiatric disorders, neurodegeneration, drug abuse, and other therapeutic areas. In the absence of a 3D structure for the human D2 dopamine (HDD2 receptor, the efforts for discovery and design of new potential drugs rely on comparative models generation, docking and pharmacophore development studies. To get a better understanding of the HDD2 receptor binding site and the ligand-receptor interactions a homology model of HDD2 receptor based on the X-ray structure of β2-adrenergic receptor has been built and used to dock a set of partial agonists of HDD2 receptor. The main characteristics of the binding mode for the HDD2 partial agonists set are given by the ligand particular folding and a complex network of contacts represented by stacking interactions, salt bridge and hydrogen bond formation. The characterization of the partial agonist binding mode at HDD2 receptor provide the needed information to generate pharmacophore models which represent essential information in the future virtual screening studies in order to identify new potential HDD2 partial agonists.

  18. Structure and function of the selectin ligand PSGL-1

    Directory of Open Access Journals (Sweden)

    R.D. Cummings


    Full Text Available P-selectin glycoprotein ligand-1 (PSGL-1 is a dimeric mucin-like 120-kDa glycoprotein on leukocyte surfaces that binds to P- and L-selectin and promotes cell adhesion in the inflammatory response. The extreme amino terminal extracellular domain of PSGL-1 is critical for these interactions, based on site-directed mutagenesis, blocking monoclonal antibodies, and biochemical analyses. The current hypothesis is that for high affinity interactions with P-selectin, PSGL-1 must contain O-glycans with a core-2 branched motif containing the sialyl Lewis x antigen (NeuAca2®3Galß1®4[Fuca1®3]GlcNAcß1®R. In addition, high affinity interactions require the co-expression of tyrosine sulfate on tyrosine residues near the critical O-glycan structure. This review addresses the biochemical evidence for this hypothesis and the evidence that PSGL-1 is an important in vivo ligand for cell adhesion.

  19. Portraying G Protein-Coupled Receptors with Fluorescent Ligands (United States)


    The thermodynamics of ligand–receptor interactions at the surface of living cells represents a fundamental aspect of G protein-coupled receptor (GPCR) biology; thus, its detailed elucidation constitutes a challenge for modern pharmacology. Interestingly, fluorescent ligands have been developed for a variety of GPCRs in order to monitor ligand–receptor binding in living cells. Accordingly, new methodological strategies derived from noninvasive fluorescence-based approaches, especially fluorescence resonance energy transfer (FRET), have been successfully developed to characterize ligand–receptor interactions. Importantly, these technologies are supplanting more hazardous and expensive radioactive binding assays. In addition, FRET-based tools have also become extremely powerful approaches for visualizing receptor–receptor interactions (i.e., GPCR oligomerization) in living cells. Thus, by means of the synthesis of compatible fluorescent ligands these novel techniques can be implemented to demonstrate the existence of GPCR oligomerization not only in heterologous systems but also in native tissues. Finally, there is no doubt that these methodologies would also be relevant in drug discovery in order to develop new high-throughput screening approaches or to identify new therapeutic targets. Overall, herein, we provide a thorough assessment of all technical and biological aspects, including strengths and weaknesses, of these fluorescence-based methodologies when applied to the study of GPCR biology at the plasma membrane of living cells. PMID:25010291

  20. Reactions of diiron m-aminocarbyne complexes containing nitrile ligands

    Directory of Open Access Journals (Sweden)

    Busetto Luigi


    Full Text Available The acetonitrile ligand in the mu-aminocarbyne complexes [Fe2{mu-CN(MeR}(mu-CO(CO(NCMe(Cp2][SO 3CF3] (R = Me, 2a, CH2Ph, 2b, Xyl, 2c (Xyl = 2,6-Me2C6H3 is readily displaced by halides and cyanide anions affording the corresponding neutral species [Fe2{mu-CN(MeR}(mu-CO(CO(X(Cp2 ] (X = Br, I, CN. Complexes 2 undergo deprotonation and rearrangement of the coordinated MeCN upon treatment with organolithium reagents. Trimethylacetonitrile, that does not contain acidic alpha hydrogens has been used in place of MeCN to form the complexes [Fe2{mu-CN(MeR}(mu-CO(CO(NCCMe3 (Cp2][SO3CF3] (7a-c. Attempts to replace the nitrile ligand in 3 with carbon nucleophiles (by reaction with RLi failed, resulting in decomposition products. However the reaction of 7c with LiCºCTol (Tol = C6H4Me, followed by treatment with HSO3CF3, yielded the imino complex [Fe2{mu-CN(MeXyl}(mu-CO(CO {N(HC(CºCC6H4Me-4CMe3}(Cp 2][SO3CF3 ] (8, obtained via acetilyde addition at the coordinated NCCMe3.

  1. Characterization of Selectin Ligands on Hematopoietic Stem Cells

    KAUST Repository

    Mahmood, Hanan


    Successful bone marrow (BM) transplantation requires the homing of the transplanted hematopoietic stem/progenitor cells (HSPCs) to their bone marrow niche, where they undergo differentiation to form mature cells that are eventually released into the peripheral blood. However, the survival rate of patients receiving BM transplants is poor since many of the transplanted HSPCs do not make it to their BM niches in the recipient’s body. Since the availability of HSPCs from traditional sources is limited, transplanting more number of HSPCs is not a solution to this problem. This study aims to characterize the adhesion molecules mediating cell migration in order to better understand the adhesion mechanisms of HSCs with the bone marrow endothelium. This will aid in developing future tools to improve the clinical transplantation of HSPCs. This study also aims to understand the factors that influence HSPC proliferation in the bone marrow niche. E-selectin plays an important role in the process of homing; however, its ligands on HSPCs are not well characterized. We used western blotting and immunoprecipitation to show that endomucin is expressed on HSPCs and plays a role in the binding of HSPCs to E-selectin. We also studied the effect of recombinant E-selectin on the expression of a newly characterized E-selectin ligand in our lab, CD34, in HSPCs. This will provide us insight into novel roles for endomucin and E-selectin and help us to understand the factors influencing HSPC migration to BM endothelium.

  2. Effect of urea on protein-ligand association. (United States)

    Stepanian, Lora; Son, Ikbae; Chalikian, Tigran V


    We combine experimental and theoretical approaches to investigate the influence of a cosolvent on a ligand-protein association event. We apply fluorescence measurements to determining the affinity of the inhibitor tri-N-acetylglucosamine [(GlcNAc)3] for lysozyme at urea concentrations ranging from 0 to 8M. Notwithstanding that, at room temperature and neutral pH, lysozyme retains its native conformation up to the solubility limit of urea, the affinity of (GlcNAc)3 for the protein steadily decreases as the concentration of urea increases. We analyze the urea dependence of the binding free energy within the framework of a simplified statistical thermodynamics-based model that accounts for the excluded volume effect and direct solute-solvent interactions. The analysis reveals that the detrimental action of urea on the inhibitor-lysozyme binding originates from competition between the free energy contributions of the excluded volume effect and direct solute-solvent interactions. The free energy contribution of direct urea-solute interactions narrowly overcomes the excluded volume contribution thereby resulting in urea weakening the protein-ligand association. More broadly, the successful application of the simple model employed in this work points to the possibility of its use in quantifying the stabilizing/destabilizing action of individual cosolvents on biochemical folding and binding reactions. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Synthesis of Copper Nanoparticles Coated with Nitrogen Ligands

    Directory of Open Access Journals (Sweden)

    Rubén Sierra-Ávila


    Full Text Available The synthesis of copper nanoparticles was studied by wet chemical methods using copper sulfate pentahydrate (CuSO4·5H2O and nitrogen ligands allylamine (AAm and polyallylamine (PAAm as stabilizers. The results suggest that the use of these ligands leads to the exclusive formation of metallic copper nanoparticles (Cu-NPs. The use of partially crosslinked polyallylamine (PAAmc leads to nanoparticles (NPs with low yields and high coating content, while linear PAAm leads to NPs with high yields and low coating content. The chemical composition of the particles was determined by XRD and average particle diameters were determined by the Debye-Scherrer equation. TGA analysis provided evidence of the content and thermal stability of the coating on the nanoparticles and PAAm. The morphology, particle size distribution, and presence of PAAm coating were observed through TEM. The use of AAm in the synthesis of NPs could be a good alternative to reduce costs. By using TGA, TEM, and DSC techniques, it was determined that synthesized NPs with AAm presented a coating with similar characteristics to NPs with PAAm, suggesting that AAm underwent polymerization during the synthesis.

  4. Synthesis, spectral, thermal and biological studies of mixed ligand complexes with newly prepared Schiff base and 1,10-phenanthroline ligands (United States)

    Abd El-Halim, Hanan F.; Mohamed, Gehad G.; Khalil, Eman A. M.


    A series of mixed ligand complexes were prepared from the Schiff base (L1) as a primary ligand, prepared by condensation of oxamide and furan-2-carbaldehyde, and 1,10-phenanthroline (1,10-phen) as a secondary ligand. The Schiff base ligand and its mixed ligand chelates were characterized based on elemental analysis, IR, 1H NMR, thermal analysis, UV-Visible, mass, molar conductance, magnetic moment. X-ray diffraction, solid reflectance and ESR also have been studied. The mixed ligand complexes were found to have the formulae of [M(L1) (1,10-phen)]Clm.nH2O (M = Cr(III) and Fe(III) (m = 3) (n = 0); M = Mn(II), Cu(II) and Cd(II) (m = 2) (n = 0); and M = Co(II) (m = 2) (n = 1), Ni(II) (m = 2) (n = 2) and Zn(II) (m = 2) (n = 3)) and that the geometrical structure of the complexes were octahedral. The parameters of thermodynamic using Coats-Redfern and Horowitz-Metzger equations were calculated. The synthesized Schiff base ligand, 1,10-phenanthroline ligand and Their mixed ligand complexes were also investigated for their antibacterial and antifungal activity against bacterial species (Gram-Ve bacteria: Pseudomonas aeruginosa and Escherichia coli) and (Gram + Ve bacteria: Bacillus subtilis and Streptococcus pneumonia) and fungi (Aspergillus fumigates and Candida albicans). The anticancer activity of the new compounds had been tested against breast (MFC7) and colon (HCT-116) cell lines. The results showed high activity for the synthesized compounds.

  5. Using robotics to fold proteins and dock ligands. (United States)

    Brutlag, Douglas; Apaydin, Serkan; Guestrin, Carlos; Hsu, David; Varma, Chris; Singh, Amit; Latombe, Jean-Claude


    The problems of protein folding and ligand docking have been explored largely using molecular dynamics or Monte Carlo methods. These methods are very compute intensive because they often explore a much wider range of energies, conformations and time than necessary. In addition, Monte Carlo methods often get trapped in local minima. We initially showed that robotic motion planning permitted one to determine the energy of binding and dissociation of ligands from protein binding sites (Singh et al., 1999). The robotic motion planning method maps complicated three-dimensional conformational states into a much simpler, but higher dimensional space in which conformational rearrangements can be represented as linear paths. The dimensionality of the conformation space is of the same order as the number of degrees of conformational freedom in three-dimensional space. We were able to determine the relative energy of association and dissociation of a ligand to a protein by calculating the energetics of interaction for a few thousand conformational states in the vicinity of the protein and choosing the best path from the roadmap. More recently, we have applied roadmap planning to the problem of protein folding (Apaydin et al., 2002a). We represented multiple conformations of a protein as nodes in a compact graph with the edges representing the probability of moving between neighboring states. Instead of using Monte Carlo simulation to simulate thousands of possible paths through various conformational states, we were able to use Markov methods to calculate the steady state occupancy of each conformation, needing to calculate the energy of each conformation only once. We referred to this Markov method of representing multiple conformations and transitions as stochastic roadmap simulation or SRS. We demonstrated that the distribution of conformational states calculated with exhaustive Monte Carlo simulations asymptotically approached the Markov steady state if the same Boltzman

  6. Self-assembly of heteroleptic dinuclear metallosupramolecular kites from multivalent ligands via social self-sorting

    Directory of Open Access Journals (Sweden)

    Christian Benkhäuser


    Full Text Available A Tröger's base-derived racemic bis(1,10-phenanthroline ligand (rac-1 and a bis(2,2'-bipyridine ligand with a central 1,3-diethynylbenzene unit 2 were synthesized. Each of these ligands acts as a multivalent entity for the binding of two copper(I ions. Upon coordination to the metal ions these two ligands undergo selective self-assembly into heteroleptic dinuclear metallosupramolecular kites in a high-fidelity social self-sorting manner as evidenced by NMR spectroscopy and mass spectrometry.

  7. Ligand-specific homology modeling of human cannabinoid (CB1) receptor. (United States)

    Ai, Rizi; Chang, Chia-en A


    Cannabinoid (CB1) receptor is a therapeutic drug target, and its structure and conformational changes after ligand binding are of great interest. To study the protein conformations in ligand bound state and assist in drug discovery, CB1 receptor homology models are needed for computer-based ligand screening. The known CB1 ligands are highly diverse structurally, so CB1 receptor may undergo considerable conformational changes to accept different ligands, which is challenging for molecular docking methods. To account for the flexibility of CB1 receptor, we constructed four CB1 receptor models based on four structurally distinct ligands, HU-210, ACEA, WIN55212-2 and SR141716A, using the newest X-ray crystal structures of human β₂ adrenergic receptor and adenosine A(2A) receptor as templates. The conformations of these four CB1-ligand complexes were optimized by molecular dynamics (MD) simulations. The models revealed interactions between CB1 receptor and known binders suggested by experiments and could successfully discriminate known ligands and non-binders in our docking assays. MD simulations were used to study the most flexible ligand, ACEA, in its free and bound states to investigate structural mobility achieved by the rearrangement of the fatty acid chain. Our models may capture important conformational changes of CB1 receptor to help improve accuracy in future CB1 drug screening. Copyright © 2012 Elsevier Inc. All rights reserved.

  8. Comprehensive analysis of MHC ligands in clinical material by immunoaffinity-mass spectrometry. (United States)

    Kasuga, Kie


    Major histocompatibility complexes (MHC) are expressed on antigen-presenting cells (APC) that display peptide antigens. This is a crucial step to activate a T-cell response. Since immunogenic ligand of MHC is closely related with autoimmunity, inflammatory diseases, and cancer, comprehensive analysis of MHC ligands (the so-called Ligandome) is essential to unveil disease pathogenesis. Recently, immunotherapies such as vaccination have been focused on as new therapies of cancer, HIV, and infectious diseases. Therefore, the importance of comprehensive analysis of MHC ligands is increasing. Mass spectrometry has been the core technology of ligand identification since the 1990s. The sensitivity of mass spectrometers has been improved dramatically in recent years; thus, it enables to identify MHC ligands in clinical materials. This chapter lays out the workflow of MHC ligand identification in clinical materials, especially human bronchoalveolar (BAL) cells. MHC-ligand complexes are enriched by immunoaffinity extraction and captured ligand peptides are identified by LC-MS/MS. MHC class II ligand in BAL cells is described in this text; however, this approach is applicable to MHC class I and other clinical materials such as tissues.

  9. Rational design of cyclopropane-based chiral PHOX ligands for intermolecular asymmetric Heck reaction

    Directory of Open Access Journals (Sweden)

    Marina Rubina


    Full Text Available A novel class of chiral phosphanyl-oxazoline (PHOX ligands with a conformationally rigid cyclopropyl backbone was synthesized and tested in the intermolecular asymmetric Heck reaction. Mechanistic modelling and crystallographic studies were used to predict the optimal ligand structure and helped to design a very efficient and highly selective catalytic system. Employment of the optimized ligands in the asymmetric arylation of cyclic olefins allowed for achieving high enantioselectivities and significantly suppressing product isomerization. Factors affecting the selectivity and the rate of the isomerization were identified. It was shown that the nature of this isomerization is different from that demonstrated previously using chiral diphosphine ligands.

  10. PPARγ and Its Ligands: Potential Antitumor Agents in the Digestive System. (United States)

    Shu, Linjing; Huang, Renhuan; Wu, Songtao; Chen, Zhaozhao; Sun, Ke; Jiang, Yan; Cai, Xiaoxiao


    Peroxisome proliferator-activated receptor γ (PPARγ) is a versatile member of the ligand-activated nuclear hormone receptor superfamily of transcription factors, with expression in several different cell lines, especially in the digestive system. After being activated by its ligand, PPARγ can suppress the growth of oral, esophageal, gastric, colorectal, liver, biliary, and pancreatic tumor cells, suggesting that PPARγ ligand is a potential anticancer agent in PPARγ-expressing tumors. This review highlights key advances in understanding the effects of PPARγ ligands in the treatment of tumors in the digestive system.

  11. Sorption of heavy metal ions on new metal-ligand complexes chemically derived from Lycopodium clavatum

    Energy Technology Data Exchange (ETDEWEB)

    Pehlivan, E.; Ersoz, M.; Yildiz, S. [Univ. of Selcuk, Konya (Turkey); Duncan, H.J. [Univ. of Glasgow, Scotland (United Kingdom)


    Sorption of heavy metal ions from aqueous solution has been investigated as a function of pH using a novel exchanger system whereby Lycopodium clavatum is functionalized with carboxylate and glyoxime metal-ligand complexes. The new ligand exchangers were prepared using a reaction of diaminosporopollenin with various metal-ligand complexes of glyoxime and monocarboxylic acid. The sorptive behavior of these metal-ligand exchangers and the possibilities to remove and to recover selectively heavy metal cations using these systems are discussed on the basis of their chemical natures and their complexing properties.

  12. Cd44 Is a Major E-Selectin Ligand on Human Hematopoietic Progenitor Cells


    Dimitroff, Charles J.; Lee, Jack Y.; Rafii, Shahin; Fuhlbrigge, Robert C.; Sackstein, Robert


    E-selectin plays a critical role in mediating tissue-specific homing of T cells into skin, and of primitive hematopoietic progenitor cells (HPCs) into bone marrow (BM). Though it is known that a glycoform of PSGL-1 (CLA) functions as the principal E-selectin ligand on human T lymphocytes, the E-selectin ligand(s) of human HPCs has not been identified. We used a shear-based adherence assay to analyze and define the E-selectin ligand activity of membrane proteins from human HPCs. Our data show ...

  13. Versatility or Promiscuity: The Estrogen Receptors, Control of Ligand Selectivity and an Update on Subtype Selective Ligands

    Directory of Open Access Journals (Sweden)

    Hui Wen Ng


    Full Text Available The estrogen receptors (ERs are a group of versatile receptors. They regulate an enormity of processes starting in early life and continuing through sexual reproduction, development, and end of life. This review provides a background and structural perspective for the ERs as part of the nuclear receptor superfamily and discusses the ER versatility and promiscuity. The wide repertoire of ER actions is mediated mostly through ligand-activated transcription factors and many DNA response elements in most tissues and organs. Their versatility, however, comes with the drawback of promiscuous interactions with structurally diverse exogenous chemicals with potential for a wide range of adverse health outcomes. Even when interacting with endogenous hormones, ER actions can have adverse effects in disease progression. Finally, how nature controls ER specificity and how the subtle differences in receptor subtypes are exploited in pharmaceutical design to achieve binding specificity and subtype selectivity for desired biological response are discussed. The intent of this review is to complement the large body of literature with emphasis on most recent developments in selective ER ligands.

  14. Stability Constants of Mixed Ligand Complexes of Transition Metal(II Ions with Salicylidene-4-methoxyaniline as Primary Ligand and 5-Bromosalicylidene-4-nitroaniline as Secondary Ligand

    Directory of Open Access Journals (Sweden)

    N. G. Nadkarni


    Full Text Available Binary and ternary complexes of the type M-Y and M-X-Y [M = Mn(II, Ni(II, Cu(II and Zn(II; X = salicylidene-4-methoxyaniline and Y=5-bromosalicylidene-4-nitroaniline] have been examined pH-metrically at 27±0.5 °C and at constant ionic strength, μ= 0.1 M (KCl in 75 : 25(v/v 1,4-dioxne-water medium. The stability constants for binary (M-Y and ternary (M-X-Y systems were calculated. The relative stability (Δ log KT values of the ternary complexes with corresponding binary complexes for all the metal(II ions in the present study found to be negative indicating that ternary 1:1:1 (M-X-Y complexes are less stable than binary 1:1 (M-Y complexes. In the ternary system studied, the order of stability constants of mixed ligand complexes with respect to the metal ions was found to be Cu(II > NI(II > Mn(II > Zn(II; which is same as in the corresponding binary (M-Y systems.

  15. Abundance of Flt3 and its ligand in astrocytic tumors

    Directory of Open Access Journals (Sweden)

    Eßbach C


    Full Text Available C Eßbach,1 N Andrae,1 D Pachow,1 J-P Warnke,2 A Wilisch-Neumann,1 E Kirches,1 C Mawrin11Department of Neuropathology, Otto-von-Guericke University, Magdeburg, 2Department of Neurosurgery, Paracelsus Hospital, Zwickau, GermanyBackground: Molecular targeted therapies for astrocytic tumors are the subject of growing research interest, due to the limited response of these tumors, especially glioblastoma multiforme, to conventional chemotherapeutic regimens. Several of these approaches exploit the inhibition of receptor tyrosine kinases. To date, it has not been elucidated if fms-like tyrosine kinase-3 (Flt3 and its natural ligand (Flt3L are expressed in astrocytic tumors, although some of the clinically intended small-molecule receptor tyrosine kinase inhibitors affect Flt3, while others do not. More importantly, the recent proof of principle for successful stimulation of the immune system against gliomas in preclinical models via local Flt3L application requires elucidation of this receptor tyrosine kinase pathway in these tumors in more detail. This therapy is based on recruitment of Flt3-positive dendritic cells, but may be corroborated by activity of this signaling pathway in glioma cells.Methods: Receptor and ligand expression was analyzed by real-time polymerase chain reaction in 31 astrocytic tumors (six diffuse and 11 anaplastic astrocytomas, 14 glioblastomas derived from patients of both genders and in glioblastoma cell lines. The two most common activating mutations of the Flt3 gene, ie, internal tandem duplication and D835 point mutation, were assessed by specific polymerase chain reaction.Results: A relatively high abundance of Flt3L mRNA (4%–6% of the reference, β2 microglobulin could be demonstrated in all tumor samples. Flt3 expression could generally be demonstrated by 40 specific polymerase chain reaction cycles and gel electrophoresis in 87% of the tumors, including all grades, although the small quantities of the receptor did

  16. Ligand Binding and Substrate Discrimination by UDP-Galactopyranose Mutase

    Energy Technology Data Exchange (ETDEWEB)

    Gruber, Todd D.; Borrok, M. Jack; Westler, William M.; Forest, Katrina T.; Kiessling, Laura L.; (UW)


    Galactofuranose (Galf) residues are present in cell wall glycoconjugates of numerous pathogenic microbes. Uridine 5{prime}-diphosphate (UDP) Galf, the biosynthetic precursor of Galf-containing glycoconjugates, is produced from UDP-galactopyranose (UDP-Galp) by the flavoenzyme UDP-galactopyranose mutase (UGM). The gene encoding UGM (glf) is essential for the viability of pathogens, including Mycobacterium tuberculosis, and this finding underscores the need to understand how UGM functions. Considerable effort has been devoted to elucidating the catalytic mechanism of UGM, but progress has been hindered by a lack of structural data for an enzyme-substrate complex. Such data could reveal not only substrate binding interactions but how UGM can act preferentially on two very different substrates, UDP-Galp and UDP-Galf, yet avoid other structurally related UDP sugars present in the cell. Herein, we describe the first structure of a UGM-ligand complex, which provides insight into the catalytic mechanism and molecular basis for substrate selectivity. The structure of UGM from Klebsiella pneumoniae bound to the substrate analog UDP-glucose (UDP-Glc) was solved by X-ray crystallographic methods and refined to 2.5 {angstrom} resolution. The ligand is proximal to the cofactor, a finding that is consistent with a proposed mechanism in which the reduced flavin engages in covalent catalysis. Despite this proximity, the glucose ring of the substrate analog is positioned such that it disfavors covalent catalysis. This orientation is consistent with data indicating that UDP-Glc is not a substrate for UGM. The relative binding orientations of UDP-Galp and UDP-Glc were compared using saturation transfer difference NMR. The results indicate that the uridine moiety occupies a similar location in both ligand complexes, and this relevant binding mode is defined by our structural data. In contrast, the orientations of the glucose and galactose sugar moieties differ. To understand the

  17. NH3-promoted ligand lability in eleven-vertex rhodathiaboranes. (United States)

    Calvo, Beatriz; Roy, Beatriz; Macías, Ramón; Artigas, Maria Jose; Lahoz, Fernando J; Oro, Luis A


    The reaction of the 11-vertex rhodathiaborane, [8,8-(PPh3)2-nido-8,7-RhSB9H10] (1), with NH3 affords inmediately the adduct, [8,8,8-(NH3)(PPh3)2-nido-8,7-RhSB9H10] (4). The NH3-Rh interaction induces the labilization of the PPh3 ligands leading to the dissociation product, [8,8-(NH3)(PPh3)-nido-8,7-RhSB9H10] (5), which can then react with another molecule of NH3 to give [8,8,8-(NH3)2(PPh3)-nido-8,7-RhSB9H10] (6). These clusters have been characterized in situ by multielement NMR spectroscopy at different temeperatures. The variable temperature behavior of the system demonstrates that the intermediates 4-6 are in equilibrium, involving ligand exchange processes. On the basis of low intensity signals present in the (1)H NMR spectra of the reaction mixture, some species are tentatively proposed to be the bis- and tris-NH3 ligated clusters, [8,8-(NH3)2-nido-8,7-RhSB9H10] (7) and [8,8,8-(NH3)3-nido-8,7-RhSB9H10] (8). After evaporation of the solvent and the excess of NH3, the system containing species 4-8 regenerates the starting reactant, 1, thus closing a stoichiometric cycle of ammonia addition and loss. After 40 h at room temperature, the reaction of 1 with NH3 gives the hydridorhodathiaborane, [8,8,8-(H)(PPh3)2-nido-8,7-RhSB9H9] (2), as a single product. The reported rhodathiaboranes show reversible H3N-promoted ligand lability, which implies weak Rh-N interactions, leading to a rare case of metal complexes that circumvent "classical" Werner chemistry.

  18. 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: [Department of Chemical Engineering, Stanford University, Stanford, CA 94305 (United States)


    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.

  19. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. (United States)

    Adams, Paul D; Aertgeerts, Kathleen; Bauer, Cary; Bell, Jeffrey A; Berman, Helen M; Bhat, Talapady N; Blaney, Jeff M; Bolton, Evan; Bricogne, Gerard; Brown, David; Burley, Stephen K; Case, David A; Clark, Kirk L; Darden, Tom; Emsley, Paul; Feher, Victoria A; Feng, Zukang; Groom, Colin R; Harris, Seth F; Hendle, Jorg; Holder, Thomas; Joachimiak, Andrzej; Kleywegt, Gerard J; Krojer, Tobias; Marcotrigiano, Joseph; Mark, Alan E; Markley, John L; Miller, Matthew; Minor, Wladek; Montelione, Gaetano T; Murshudov, Garib; Nakagawa, Atsushi; Nakamura, Haruki; Nicholls, Anthony; Nicklaus, Marc; Nolte, Robert T; Padyana, Anil K; Peishoff, Catherine E; Pieniazek, Susan; Read, Randy J; Shao, Chenghua; Sheriff, Steven; Smart, Oliver; Soisson, Stephen; Spurlino, John; Stouch, Terry; Svobodova, Radka; Tempel, Wolfram; Terwilliger, Thomas C; Tronrud, Dale; Velankar, Sameer; Ward, Suzanna C; Warren, Gregory L; Westbrook, John D; Williams, Pamela; Yang, Huanwang; Young, Jasmine


    Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic Data Center/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the PDB? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. Evaluation of Receptor-Ligand Mechanisms of Dual-Targeted Particles to an Inflamed Endothelium. (United States)

    Fromen, Catherine A; Fish, Margaret B; Zimmerman, Anthony; Adili, Reheman; Holinstat, Michael; Eniola-Adefeso, Omolola


    Vascular-targeted carriers (VTCs) are designed as leukocyte mimics, decorated with ligands that target leukocyte adhesion molecules (LAMs) and facilitate adhesion to diseased endothelium. VTCs require different design considerations than other targeted particle therapies; adhesion of VTCs in regions with dynamic blood flow requires multiple ligand-receptor (LR) pairs that provide particle adhesion and disease specificity. Despite the ultimate goal of leukocyte mimicry, the specificity of multiple LAM-targeted VTCs remains poorly understood, especially in physiological environments. Here, we investigate particle binding to an inflamed mesentery via intravital microscopy using a series of particles with well-controlled ligand properties. We find that the total number of sites of a single ligand can drive particle adhesion to the endothelium, however, combining ligands that target multiple LR pairs provides a more effective approach. Combining sites of sialyl Lewis A (sLeA) and anti-intercellular adhesion molecule-1 (aICAM), two adhesive molecules, resulted in ~3-7-fold increase of adherent particles at the endothelium over single-ligand particles. At a constant total ligand density, a particle with a ratio of 75% sLeA: 25% aICAM resulted in more than 3-fold increase over all over other ligand ratios tested in our in vivo model. Combined with in vitro and in silico data, we find the best dual-ligand design of a particle is heavily dependent on the surface expression of the endothelial cells, producing better adhesion with more particle ligand for the lesser-expressed receptor. These results establish the importance of considering LR-kinetics in intelligent VTC ligand design for future therapeutics.