WorldWideScience

Sample records for 2-phenoxypyridyl dinucleating ligands

  1. A versatile dinucleating ligand containing sulfonamide groups

    DEFF Research Database (Denmark)

    Sundberg, Jonas; Witt, Hannes; Cameron, Lisa;

    2014-01-01

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

  2. Dinucleating Ligand Platforms Supporting Indium and Zinc Catalysts for Cyclic Ester Polymerization.

    Science.gov (United States)

    Kremer, Alexandre B; Osten, Kimberly M; Yu, Insun; Ebrahimi, Tannaz; Aluthge, Dinesh C; Mehrkhodavandi, Parisa

    2016-06-01

    The synthesis of the first alkoxide-bridged indium complex supported by a chiral dinucleating ligand platform (1), along with its zinc analogue (2), is reported. Both complexes are synthesized in a one-pot reaction starting from a chiral dinucleating bis(diamino)phenolate ligand platform, sodium ethoxide, and respective metal salts. The dinucleating indium analogue (7) based on an achiral ligand backbone is also reported. Indium complexes bearing either the chiral or achiral ligand catalyze the ring-opening polymerization of racemic lactide (rac-LA) to afford highly heterotactic poly(lactic acid) (PLA; Pr > 0.85). The indium complex bearing an achiral ligand affords essentially atactic PLA from meso-LA. The role of the dinucleating ligand structure in catalyst synthesis and polymerization activity is discussed. PMID:27187767

  3. Synthesis and Characterization of Porphyrin.Trisbenzimidazole Dinucleating Ligand and Its Heterodinuclear Complex as CcO Active Site Model

    Institute of Scientific and Technical Information of China (English)

    LuWei-bing; WangCun-xin; DengLi-zhi; ZhouXiao-hai; RenJian-guo

    2003-01-01

    A new dinucleating ligand having two metalbinding sites has been designed and synthesized as model ligand for Cytochrome c Oxidase. The corresponding heterodinuclear complex, as an active site model of Cytochrome c Oxidase, consisting of a porphyrinatocobalt compound covalently linked with a copper derivative of tris(2-benzimidazylmethyl)amine bearing three benzimidazole ligands for copper was synthesized and spectroscopically characterized. The spectra data suggest that there are interactions between the cobalt and copper coordination units. The cobalt is coordinated to four central nitrogens of the porphyrin and the copper has pentacoordinate geometry with the four tertiary amine nitrogens and a chloride.

  4. Synthesis and Characterization of Porphyrin- Trisbenzimidazole Dinucleating Ligand and Its Heterodinuclear Complex as CcO Active Site Model

    Institute of Scientific and Technical Information of China (English)

    Lu Wei-bing; Wang Cun-xin; Deng Li-zhi; Zhou Xiao-hai; Ren Jian-guo

    2003-01-01

    A new dinucleating ligand having two metal-binding sites has been designed and synthesized as model lig-and for Cytochrome c Oxidase. The corresponding heterodi-nuclear complex, as an active site model of Cytochrome c Oxi-dase, consisting of a porphyrinatocobalt compound covalently linked with a copper derivative of tris(2-benzimidazylmethyl)amine bearing three benzimidazole ligands for copper was syn-thesized and spectroscopically characterized. The spectra data suggest that there are interactions between the cobalt and copper coordination units. The cobalt is coordinated to four central nitrogens of the porphyrin and the copper has pentaeo-ordinate geometry with the four tertiary amine nitrogens and a chloride.

  5. Modeling dinuclear copper sites of biological relevance - synthesis, molecular-structure, magnetic-properties, and h-1- nmr spectroscopy of a nonsymmetric dinuclear copper(ii) complex - microcalorimetric determination of stepwise complexation of copper(ii) by a nonsymmetric dinucleating ligand

    NARCIS (Netherlands)

    Lubben, M; Hage, R.; Meetsma, A.; Bijma, Koos; Feringa, B.L.

    1995-01-01

    The new nonsymmetric dinuclear copper(II) complex [Cu(2)L(1)(OAcW(ClO4) (7) was synthesized by complexation of Cu(OAc). H2O with a new nonsymmetric dinucleating ligand (5) which' is formed in situ by condensation of 2-formyl-6-((4-methylpiperazin-1-yl)methyl)phenol (3a) with 2-(aminoethyl)pyridine.

  6. Kit for unsymmetric dinucleating double-Schiff-base ligands: facile access to a versatile new ligand system and its first heterobimetallic copper-zinc complex.

    Science.gov (United States)

    Roth, Arne; Spielberg, Eike T; Plass, Winfried

    2007-05-28

    The synthetic route toward new unsymmetric compartmental "end-off" Schiff-base ligands in a straightforward two-step reaction of 2,6-diformyl-4-methylphenol and two different amine components is presented. To demonstrate the versatility of this method, we have synthesized two different single-Schiff-base proligands, Hbpahmb and Hphmb, utilizing (2-aminoethyl)bis(2-pyridylmethyl)amine and (2-aminomethyl)pyridine, respectively. Subsequent reaction with thiosemicarbazide as the second amine component leads to the novel unsymmetric double-Schiff-base ligands {1-[3-[2-[bis(pyridin-2-ylmethyl)amino]ethyliminomethyl]-2-hydroxy-5-methylphenyl]methylidene}hydrazine carbothioamide (H2bpamptsc) and {1-[3-(pyridin-2-ylmethyliminomethyl)-2-hydroxy-5-methylphenyl]methylidene}hydrazine carbothioamide (H2pmptsc). Both ligands provide two distinctly different coordination pockets: a rigid tridentate N,O,S donor set of the hydrazide compartment versus a rather flexible pentadentate (H2bpamptsc) or tridentate (H2pmptsc) nitrogen-rich chelating side arm. The reaction of the ligand H2bpamptsc with zinc(II) acetate and copper(II) perchlorate yields the heterobinuclear Cu-Zn complex [CuZn(bpamptsc)(mu2,eta1-OAc)(MeCN)](ClO4) (1). PMID:17461577

  7. The Synthesis of a New Macrocyclic Dinucleating Ligand,3,6,9,17,20, 23-Hexaaza-29,30-Dihydroxy-13,27- Dimethyl-Tricyclo [23,3,1,111,15]Triaconta-1(28),11,13, 15(30),25,26-Hexaene

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A new dinucleating 24-membered hexaazadiphenol macrocyclic ligand, 3,6,9,17,20, 23-hexaaza-29,30- dihydroxy-13,27-dimethyl-tricyclo [23, 3, 1, 111, 15] triaconta -1(28), 11,13, 15(30),25, 26-hexaene, BDBPH, was synthesized by the NaBH4 reduction of the Schiff-base obtained from the [2+2] condensation between diethylenetriamine and diformyl -p-cresol. The structure was characterized by elemental analysis, 1HNMR and FAB-MS. The synthetic method was also discussed.

  8. Heterobridged dinuclear, tetranuclear, dinuclear-based 1-d, and heptanuclear-based 1-D complexes of copper(II) derived from a dinucleating ligand: syntheses, structures, magnetochemistry, spectroscopy, and catecholase activity.

    Science.gov (United States)

    Majumder, Samit; Sarkar, Sohini; Sasmal, Sujit; Sañudo, E Carolina; Mohanta, Sasankasekhar

    2011-08-15

    The work in this paper presents syntheses, characterization, crystal structures, variable-temperature/field magnetic properties, catecholase activity, and electrospray ionization mass spectroscopic (ESI-MS positive) study of five copper(II) complexes of composition [Cu(II)(2)L(μ(1,1)-NO(3))(H(2)O)(NO(3))](NO(3)) (1), [{Cu(II)(2)L(μ-OH)(H(2)O)}(μ-ClO(4))](n)(ClO(4))(n) (2), [{Cu(II)(2)L(NCS)(2)}(μ(1,3)-NCS)](n) (3), [{Cu(II)(2)L(μ(1,1)-N(3))(ClO(4))}(2)(μ(1,3)-N(3))(2)] (4), and [{Cu(II)(2)L(μ-OH)}{Cu(II)(2)L(μ(1,1)-N(3))}{Cu(II)(μ(1,1)-N(3))(4)(dmf)}{Cu(II)(2)(μ(1,1)-N(3))(2)(N(3))(4)}](n)·ndmf (5), derived from a new compartmental ligand 2,6-bis[N-(2-pyridylethyl)formidoyl]-4-ethylphenol, which is the 1:2 condensation product of 4-ethyl-2,6-diformylphenol and 2-(2-aminoethyl)pyridine. The title compounds are either of the following nuclearities/topologies: dinuclear (1), dinuclear-based one-dimensional (2 and 3), tetranuclear (4), and heptanuclear-based one-dimensional (5). The bridging moieties in 1-5 are as follows: μ-phenoxo-μ(1,1)-nitrate (1), μ-phenoxo-μ-hydroxo and μ-perchlorate (2), μ-phenoxo and μ(1,3)-thiocyanate (3), μ-phenoxo-μ(1,1)-azide and μ(1,3)-azide (4), μ-phenoxo-μ-hydroxo, μ-phenoxo-μ(1,1)-azide, and μ(1,1)-azide (5). All the five compounds exhibit overall antiferromagnetic interaction. The J values in 1-4 have been determined (-135 cm(-1) for 1, -298 cm(-1) for 2, -105 cm(-1) for 3, -119.5 cm(-1) for 4). The pairwise interactions in 5 have been evaluated qualitatively to result in S(T) = 3/2 spin ground state, which has been verified by magnetization experiment. Utilizing 3,5-di-tert-butyl catechol (3,5-DTBCH(2)) as the substrate, catecholase activity of all the five complexes have been checked. While 1 and 3 are inactive, complexes 2, 4, and 5 show catecholase activity with turn over numbers 39 h(-1) (for 2), 40 h(-1) (for 4), and 48 h(-1) (for 5) in dmf and 167 h(-1) (for 2) and 215 h(-1) (for 4) in acetonitrile

  9. Design, synthesis and physico-chemical investigation of a dinuclear zinc(II) complex with a novel ‘end-off’ compartmental ligand

    Indian Academy of Sciences (India)

    Anil D Naik; Vidyanand K Revankar

    2001-08-01

    A novel dinucleating pentadentate Schiff base, resulting from the condensation of 2,6-diformyl--cresol and N-methyl-indolyl-3-thiohydrazide, and its Zn complex have been prepared and characterized on the basis of elemental analysis, IR, UV-Visible, 1H NMR and 13C NMR studies. The ligand is acyclic and consists of a phenolate head unit, with two inbuilt azomethine shoulders and two indole thiohydrazide arms forming SNONS coordinating sites. NMR and IR spectral studies show that the ligand exists in thioketo form. Each Zn ion in the dinuclear core is in tetrahedral environment with endogenous phenolate bridging and exogenous acetate bridging. The zinc complex in DMF exhibits fluorescence.

  10. Establishing the Family of Diruthenium Water Oxidation Catalysts Based on the Bis(bipyridyl)pyrazolate Ligand System.

    Science.gov (United States)

    Neudeck, Sven; Maji, Somnath; López, Isidoro; Dechert, Sebastian; Benet-Buchholz, Jordi; Llobet, Antoni; Meyer, Franc

    2016-03-01

    A bis(bipyridyl)pyrazolate ((Me)bbp(-)) has recently been introduced as a rugged dinucleating, bis(tridentate) ligand for the formation of efficient diruthenium water oxidation catalysts (J. Am. Chem. Soc. 2014, 136, 24-27). Now, detailed protocols for the synthesis of a whole family of such dinuclear ruthenium complexes [{Ru(pyR(2))2}2(μ-(R1)bbp)(X,Y)](2+) based on the bis(bipyridyl)pyrazolate scaffold are reported. The isolation of a synthetic key intermediate allowed the straightforward introduction of different pyridines as axial ligands. Thereby, a set of complexes with different substituents at the pyrazolate backbone (R(1) = Br, H, Me), different pyridines as axial ligand (R(2) = H, NMe2, SO3), and different (non)bridging units in the in,in-position (X,Y = Cl, H2O, OAc) has been prepared and thoroughly characterized. Complexes of the type [{Ru(pyR(2))2}2(μ-(R1)bbp)(μ-OAc)](2+), with an exogenous acetato bridge, have been used as catalyst precursors in catalytic water oxidation experiments with a sacrificial oxidant. The effect of substitution on the pyrazole core of the (R1)bbp(-) ligand as well as on the pyridine ligands on both electrochemistry and catalytic activity has been systematically investigated. The catalyst stability, reflected by the turnover number, is crucially determined by the substituent at the pyrazolate ligand (R(1) = Me > H > Br). In contrast, the axial pyridine ligands modulate the rate of the catalytic process, expressed by the initial turnover frequency (R(2) = H > NMe2H(+)). PMID:26894408

  11. Ylide Ligands

    OpenAIRE

    Esteban P. Urriolabeitia

    2010-01-01

    The use of ylides of P, N, As, or S as ligands toward transition metals is still a very active research area in organometallic chemistry. This fact is mainly due to the nucleophilic character of the ylides and to their particular bonding properties and coordination modes. They can behave as monodentate or bidentate chelate or bridging species, they can be used as chiral auxiliary reagents, and they are interesting reaction intermediates or useful starting materials in a wide ...

  12. Metal-ligand cooperation.

    Science.gov (United States)

    Khusnutdinova, Julia R; Milstein, David

    2015-10-12

    Metal-ligand cooperation (MLC) has become an important concept in catalysis by transition metal complexes both in synthetic and biological systems. MLC implies that both the metal and the ligand are directly involved in bond activation processes, by contrast to "classical" transition metal catalysis where the ligand (e.g. phosphine) acts as a spectator, while all key transformations occur at the metal center. In this Review, we will discuss examples of MLC in which 1) both the metal and the ligand are chemically modified during bond activation and 2) bond activation results in immediate changes in the 1st coordination sphere involving the cooperating ligand, even if the reactive center at the ligand is not directly bound to the metal (e.g. via tautomerization). The role of MLC in enabling effective catalysis as well as in catalyst deactivation reactions will be discussed. PMID:26436516

  13. Ligand modeling and design

    Energy Technology Data Exchange (ETDEWEB)

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

    1997-10-01

    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.

  14. Ligand modeling and design

    Energy Technology Data Exchange (ETDEWEB)

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

    1996-10-01

    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.

  15. AMPA receptor ligands

    DEFF Research Database (Denmark)

    Strømgaard, Kristian; Mellor, Ian

    2004-01-01

    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...

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

    Science.gov (United States)

    Von Dreele, Robert B.

    2008-12-23

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

  17. Ligand-Receptor Interactions

    CERN Document Server

    Bongrand, Pierre

    2008-01-01

    The formation and dissociation of specific noncovalent interactions between a variety of macromolecules play a crucial role in the function of biological systems. During the last few years, three main lines of research led to a dramatic improvement of our understanding of these important phenomena. First, combination of genetic engineering and X ray cristallography made available a simultaneous knowledg of the precise structure and affinity of series or related ligand-receptor systems differing by a few well-defined atoms. Second, improvement of computer power and simulation techniques allowed extended exploration of the interaction of realistic macromolecules. Third, simultaneous development of a variety of techniques based on atomic force microscopy, hydrodynamic flow, biomembrane probes, optical tweezers, magnetic fields or flexible transducers yielded direct experimental information of the behavior of single ligand receptor bonds. At the same time, investigation of well defined cellular models raised the ...

  18. Ligand exclusion on acetylcholinesterase.

    Science.gov (United States)

    Berman, H A; Leonard, K

    1990-11-27

    This paper examines covalent reactivity of AchE with respect to cationic and uncharged methylphosphonates and substrates in the absence and presence of cationic ligands selective for the active center and the peripheral anionic site. The organophosphorus inhibitors are enantiomeric alkyl methylphosphonothioates (1-5) containing cycloheptyl and isopropyl phosphono ester groups and S-methyl, S-n-pentyl, and S-[beta-(trimethylammonio)ethyl] leaving groups; these agents differ in their configuration about phosphorus and their steric, hydrophobic, and electrostatic characteristics. The synthetic substrates examined are acetylthiocholine, p-nitrophenyl acetate, and 7-acetoxy-4-methylcoumarin (7AMC). Antagonism of the methylphosphonothioate reaction by cationic ligands is strongly dependent on the nature of both the cation and the methylphosphonate but independent of the configuration about phosphorus. While all cations cause linear mixed inhibition of acetylthiocholine hydrolysis, there are observed a variety of inhibition patterns of 7AMC and p-nitrophenyl acetate hydrolysis that are distinctly nonlinear, as well as patterns in which the reciprocal plots intersect in the upper right quadrant. Strong antagonism of cationic (methylphosphonyl)thiocholines correlates very well with linear inhibition of acetylthiocholine. Ligands that cause only negligible antagonism of the uncharged methylphosphonates display nonlinear inhibition of uncharged substrates. These relationships, since they are most pronounced for peripheral site ligands and are strongly dependent on the charge carried by the reactant, suggest that the peripheral anionic site alters enzyme reactivity through an electrostatic interaction with the net negative active center. Such behavior indicates a potential role for the peripheral anionic site in conserving AchE catalytic efficiency within a narrow range of values. PMID:2271673

  19. Bexarotene ligand pharmaceuticals.

    Science.gov (United States)

    Hurst, R E

    2000-12-01

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

  20. Molecular path for ligand search

    Institute of Scientific and Technical Information of China (English)

    Tao Lu; Yuan Yuan Qiao; Pan Wen Shen

    2011-01-01

    A ligand is a small molecule bind to several residues of a receptor. We adapt the concept of molecular path for effective ligand search with its contacting residues. Additionally, we allow wild type definitions on atoms and bonds of molecular paths for fuzzy algorithms on structural match. We choose hydrogen bond interactions to characterize the binding mode of a ligand by several proper molecular paths and use them to query the deposited ligands in PDBe that interact with their residues in the same way. Expression of molecular path and format of database entries are described with examples. Our molecular path provides a new approach to explore the ligand-receptor interactions and to provide structural framework reference on new ligand design.

  1. Macrocyclic G-quadruplex ligands

    DEFF Research Database (Denmark)

    Nielsen, M C; Ulven, Trond

    2010-01-01

    G-quadruplex stabilizing compounds have recently received increased interest due to their potential application as anticancer therapeutics. A significant number of structurally diverse G-quadruplex ligands have been developed. Some of the most potent and selective ligands currently known 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...

  2. Ligand Identification Scoring Algorithm (LISA)

    Science.gov (United States)

    Zheng, Zheng; Merz, Kenneth M.

    2011-01-01

    A central problem in de novo drug design is determining the binding affinity of a ligand with a receptor. A new scoring algorithm is presented that estimates the binding affinity of a protein-ligand complex given a three-dimensional structure. The method, LISA (Ligand Identification Scoring Algorithm), uses an empirical scoring function to describe the binding free energy. Interaction terms have been designed to account for van der Waals (VDW) contacts, hydrogen bonding, desolvation effects and metal chelation to model the dissociation equilibrium constants using a linear model. Atom types have been introduced to differentiate the parameters for VDW, H-bonding interactions and metal chelation between different atom pairs. A training set of 492 protein-ligand complexes was selected for the fitting process. Different test sets have been examined to evaluate its ability to predict experimentally measured binding affinities. By comparing with other well known scoring functions, the results show that LISA has advantages over many existing scoring functions in simulating protein-ligand binding affinity, especially metalloprotein-ligand binding affinity. Artificial Neural Network (ANN) was also used in order to demonstrate that the energy terms in LISA are well designed and do not require extra cross terms. PMID:21561101

  3. Visualization of Metal-to-Ligand and Ligand-to-Ligand Charge Transfer in Metal-Ligand Complexes

    Institute of Scientific and Technical Information of China (English)

    Yong Ding; Jian-xiu Guo; Xiang-si Wang; Sha-sha Liu; Feng-cai Ma

    2009-01-01

    Three methods including the atomic resolved density of state, charge difference density, and the transition density matrix are used to visualize metal to ligand charge transfer (MLCT) in ruthenium(Ⅱ) ammine complex. The atomic resolved density of state shows that there is density of Ru on the HOMOs. All the density is localized on the ammine, which reveals that the excited electrons in the Ru complex are delocalized over the ammine ligand. The charge difference density shows that all the holes are localized on the Ru and the electrons on the ammine. The localization explains the MLCT on excitation. The transition density matrix shows that there is electron-hole coherence between Ru and ammine. These methods are also used to examine the MLCT in Os(bpy)(p0p)Cl ("Osp0p"; bpy=2,2'-bipyridyl; p0p=4,4'-bipyridyl) and the ligand-to-ligand charge transfer (LLCT) in Alq3. The calculated results show that these methods are powerful to examine MLCT and LLCT in the metal-ligand system.

  4. 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

    2013-01-01

    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.

  5. A race for RAGE ligands.

    Science.gov (United States)

    Schleicher, Erwin D

    2010-08-01

    In experimental animals a causal involvement of the multiligand receptor for advanced glycation end products (RAGE) in the development of diabetic vascular complications has been demonstrated. However, the nature of RAGE ligands present in patients with diabetic nephropathy has not yet been defined; this leaves open the relevance of the RAGE system to the human disease.

  6. Polypharmacology of dopamine receptor ligands.

    Science.gov (United States)

    Butini, S; Nikolic, K; Kassel, S; Brückmann, H; Filipic, S; Agbaba, D; Gemma, S; Brogi, S; Brindisi, M; Campiani, G; Stark, H

    2016-07-01

    Most neurological diseases have a multifactorial nature and the number of molecular mechanisms discovered as underpinning these diseases is continuously evolving. The old concept of developing selective agents for a single target does not fit with the medical need of most neurological diseases. The development of designed multiple ligands holds great promises and appears as the next step in drug development for the treatment of these multifactorial diseases. Dopamine and its five receptor subtypes are intimately involved in numerous neurological disorders. Dopamine receptor ligands display a high degree of cross interactions with many other targets including G-protein coupled receptors, transporters, enzymes and ion channels. For brain disorders like Parkinsońs disease, schizophrenia and depression the dopaminergic system, being intertwined with many other signaling systems, plays a key role in pathogenesis and therapy. The concept of designed multiple ligands and polypharmacology, which perfectly meets the therapeutic needs for these brain disorders, is herein discussed as a general ligand-based concept while focusing on dopaminergic agents and receptor subtypes in particular. PMID:27234980

  7. Ligand chain length conveys thermochromism.

    Science.gov (United States)

    Ganguly, Mainak; Panigrahi, Sudipa; Chandrakumar, K R S; Sasmal, Anup Kumar; Pal, Anjali; Pal, Tarasankar

    2014-08-14

    Thermochromic properties of a series of non-ionic copper compounds have been reported. Herein, we demonstrate that Cu(II) ion with straight-chain primary amine (A) and alpha-linolenic (fatty acid, AL) co-jointly exhibit thermochromic properties. In the current case, we determined that thermochromism becomes ligand chain length-dependent and at least one of the ligands (A or AL) must be long chain. Thermochromism is attributed to a balanced competition between the fatty acids and amines for the copper(II) centre. The structure-property relationship of the non-ionic copper compounds Cu(AL)2(A)2 has been substantiated by various physical measurements along with detailed theoretical studies based on time-dependent density functional theory. It is presumed from our results that the compound would be a useful material for temperature-sensor applications. PMID:24943491

  8. Controlled-deactivation cannabinergic ligands.

    Science.gov (United States)

    Sharma, Rishi; Nikas, Spyros P; Paronis, Carol A; Wood, Jodianne T; Halikhedkar, Aneetha; Guo, Jason Jianxin; Thakur, Ganesh A; Kulkarni, Shashank; Benchama, Othman; Raghav, Jimit Girish; Gifford, Roger S; Järbe, Torbjörn U C; Bergman, Jack; Makriyannis, Alexandros

    2013-12-27

    We report an approach for obtaining novel cannabinoid analogues with controllable deactivation and improved druggability. Our design involves the incorporation of a metabolically labile ester group at the 2'-position on a series of (-)-Δ(8)-THC analogues. We have sought to introduce benzylic substituents α to the ester group which affect the half-lives of deactivation through enzymatic activity while enhancing the affinities and efficacies of individual ligands for the CB1 and CB2 receptors. The 1'-(S)-methyl, 1'-gem-dimethyl, and 1'-cyclobutyl analogues exhibit remarkably high affinities for both CB receptors. The novel ligands are susceptible to enzymatic hydrolysis by plasma esterases in a controllable manner, while their metabolites are inactive at the CB receptors. In further in vitro and in vivo experiments key analogues were shown to be potent CB1 receptor agonists and to exhibit CB1-mediated hypothermic and analgesic effects.

  9. Privileged chiral ligands and catalysts

    CERN Document Server

    Zhou, Qi-Lin

    2011-01-01

    This ultimate ""must have"" and long awaited reference for every chemist working in the field of asymmetric catalysis starts with the core structure of the catalysts, explaining why a certain ligand or catalyst is so successful. It describes in detail the history, the basic structural characteristics, and the applications of these ""privileged catalysts"". A novel concept that gives readers a much deeper insight into the topic.

  10. Radioiodinated ligands for dopamine receptors

    International Nuclear Information System (INIS)

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

  11. Ligand placement based on prior structures: the guided ligand-replacement method

    Energy Technology Data Exchange (ETDEWEB)

    Klei, Herbert E. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Bristol-Myers Squibb, Princeton, NJ 08543-4000 (United States); Moriarty, Nigel W., E-mail: nwmoriarty@lbl.gov; Echols, Nathaniel [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Terwilliger, Thomas C. [Los Alamos National Laboratory, Los Alamos, NM 87545-0001 (United States); Baldwin, Eric T. [Bristol-Myers Squibb, Princeton, NJ 08543-4000 (United States); Natural Discovery LLC, Princeton, NJ 08542-0096 (United States); Pokross, Matt; Posy, Shana [Bristol-Myers Squibb, Princeton, NJ 08543-4000 (United States); Adams, Paul D. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); University of California at Berkeley, Berkeley, CA 94720-1762 (United States)

    2014-01-01

    A new module, Guided Ligand Replacement (GLR), has been developed in Phenix to increase the ease and success rate of ligand placement when prior protein-ligand complexes are available. The process of iterative structure-based drug design involves the X-ray crystal structure determination of upwards of 100 ligands with the same general scaffold (i.e. chemotype) complexed with very similar, if not identical, protein targets. In conjunction with insights from computational models and assays, this collection of crystal structures is analyzed to improve potency, to achieve better selectivity and to reduce liabilities such as absorption, distribution, metabolism, excretion and toxicology. Current methods for modeling ligands into electron-density maps typically do not utilize information on how similar ligands bound in related structures. Even if the electron density is of sufficient quality and resolution to allow de novo placement, the process can take considerable time as the size, complexity and torsional degrees of freedom of the ligands increase. A new module, Guided Ligand Replacement (GLR), was developed in Phenix to increase the ease and success rate of ligand placement when prior protein–ligand complexes are available. At the heart of GLR is an algorithm based on graph theory that associates atoms in the target ligand with analogous atoms in the reference ligand. Based on this correspondence, a set of coordinates is generated for the target ligand. GLR is especially useful in two situations: (i) modeling a series of large, flexible, complicated or macrocyclic ligands in successive structures and (ii) modeling ligands as part of a refinement pipeline that can automatically select a reference structure. Even in those cases for which no reference structure is available, if there are multiple copies of the bound ligand per asymmetric unit GLR offers an efficient way to complete the model after the first ligand has been placed. In all of these applications, GLR

  12. 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.

  13. Ruthenium Cumulenylidene Complexes Bearing Heteroscorpionate Ligands

    OpenAIRE

    Strinitz, Frank

    2014-01-01

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

  14. Clinical Use of PPARγ Ligands in Cancer

    Directory of Open Access Journals (Sweden)

    Jennifer L. Hatton

    2008-01-01

    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.

  15. Macrocyclic ligands for uranium complexation

    International Nuclear Information System (INIS)

    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 Pd0 chemistry, this procedure should make a variety of substituted 4-vinylpyridines available for the first time. 3 refs

  16. Synthesis and characterization of mixed ligand chiral nanoclusters

    OpenAIRE

    Güven, Zekiye Pelin; Guven, Zekiye Pelin; Üstbaş, Burçin; Ustbas, Burcin; Harkness, Kellen M.; Coşkun, Hikmet; Coskun, Hikmet; Joshi, Chakra P.; Besong, Tabot M. D.; Stellacci, Francesco; Bakr, Osman M.; Akbulut, Özge; Akbulut, Ozge

    2015-01-01

    Chiral mixed ligand silver nanoclusters were synthesized in the presence of a chiral and an achiral ligand. The ratio of the ligands was changed to track the formation of these clusters. While the chiral ligand lead to nanoparticles, Presence of the achiral ligand induced the formation of nanoclusters with chiral properties.

  17. Rhodium olefin complexes of diiminate type ligands

    NARCIS (Netherlands)

    Willems, Sander Theodorus Hermanus

    2003-01-01

    The mono-anionic beta-diiminate ligand (ArNC(CH3)CHC(CH3)NAr) on several previous occasions proved useful in stabilising low coordination numbers for both early and late transition metals. In this thesis the reactivity of the rhodium olefin complexes of one of these beta-diiminate ligands (Ar = 2,6-

  18. Flexible Ligand Docking Using Differential Evolution

    DEFF Research Database (Denmark)

    Thomsen, René

    2003-01-01

    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 preferred methods for flexible ligand docking. The differential...

  19. 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)

    1993-12-31

    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.

  20. Ligand inducible assembly of a DNA tetrahedron.

    Science.gov (United States)

    Dohno, Chikara; Atsumi, Hiroshi; Nakatani, Kazuhiko

    2011-03-28

    Here we show that a small synthetic ligand can be used as a key building component for DNA nanofabrication. Using naphthyridinecarbamate dimer (NCD) as a molecular glue for DNA hybridization, we demonstrate NCD-triggered formation of a DNA tetrahedron.

  1. Chemistry of Marine Ligands and Siderophores

    OpenAIRE

    Vraspir, Julia M.; Butler, Alison

    2009-01-01

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

  2. Fas ligand deficiency in HIV disease

    OpenAIRE

    Sieg, Scott; Smith, Dawn; Yildirim, Zafer; Kaplan, David

    1997-01-01

    Apoptosis is postulated to be involved as an anti-viral immune mechanism by killing infected cells before viral replication has occurred. The Fas–Fas ligand interaction is a powerful regulator of T cell apoptosis and could potentially act as a potent anti-viral immune mechanism against T cell tropic virus such as human immunodeficiency virus (HIV). We investigated the status of Fas ligand in peripheral blood mononuclear cells (PBMCs) obtained from persons infected with HIV. We found that mono...

  3. 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.

  4. Construction of dinuclear complexes using multidentate ligands

    Energy Technology Data Exchange (ETDEWEB)

    Sampson, C.L

    2000-04-01

    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

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

    KAUST Repository

    Chen, Peng

    2014-12-03

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

  6. Synthesis and characterization of mixed ligand chiral nanoclusters

    KAUST Repository

    Guven, Zekiye P.

    2016-06-22

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Varga, J.M.; Fritsch, P.

    1995-01-30

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

  8. Organotellurium ligands - designing and complexation reactions

    Indian Academy of Sciences (India)

    Ajai K Singh

    2002-08-01

    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 several hybrid telluroethers is extensively studied in our laboratories. The ditelluroether ligand RTeCH2TeR (where R = 4-MeOC6H4) (1), similar to dppm [1,2-bis(diphenylphosphino) methane], has been synthesized in good yield (∼80 %) by reacting CHCl3 with RTe- (generated in situ by borohydride reduction of R2Te2). Iodine reacts with 1 to give tetra-iodo derivative, which has intermolecular Te$\\cdots$I interactions resulting in a macro structure containing rectangular Te-I$\\cdots$Te bridges. 1 readily forms four membered rings with Pd(II) and Ru(II). On the formation of this chelate ring, the signal in 125Te NMR spectra shifts significantly upfield (50-60 ppm). The bridging mode of 1 has been shown in [Ru(-cymene)Cl2](-1)[Ru(-cymene)Cl2]. The hybrid telluroether ligands explored are of the types (Te, S), (Te, N) and (Te, O). The tellurium donor site has strong trans influence, which is manifested more strongly in square planar complexes of palladium(II). The morpholine N-donor site has been found to have weaker donor characteristics in (Te, N) ligands than pyridine and alkylamine donor sites of analogous ligands. The singlet oxygen readily oxidises the coordinated Te. This oxidation follows first order kinetics. The complexation reaction of RuCl3.H2O with N-[2-(4-methoxyphenyltelluro)ethyl]phthalimide (2) results in a novel (Te, N, O)-heterocycle, Te-chloro,Te-anisyl-1a-aza-4-oxa-3-tellura-1H, 2H, 4aH-9 fluorenone. The (Te, O) ligands can be used as hemilabile ligands, the oxygen atom temporarily protects the vacant coordination site before the arrival of the substrate. The chelate shifts observed in 125Te NMR spectra of metal complexes of Te-ligands have

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

    KAUST Repository

    Li, Huaifeng

    2014-12-01

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

  10. Sliding tethered ligands add topological interactions to the toolbox of ligand-receptor design

    Science.gov (United States)

    Bauer, Martin; Kékicheff, Patrick; Iss, Jean; Fajolles, Christophe; Charitat, Thierry; Daillant, Jean; Marques, Carlos M.

    2015-09-01

    Adhesion in the biological realm is mediated by specific lock-and-key interactions between ligand-receptor pairs. These complementary moieties are ubiquitously anchored to substrates by tethers that control the interaction range and the mobility of the ligands and receptors, thus tuning the kinetics and strength of the binding events. Here we add sliding anchoring to the toolbox of ligand-receptor design by developing a family of tethered ligands for which the spacer can slide at the anchoring point. Our results show that this additional sliding degree of freedom changes the nature of the adhesive contact by extending the spatial range over which binding may sustain a significant force. By introducing sliding tethered ligands with self-regulating length, this work paves the way for the development of versatile and reusable bio-adhesive substrates with potential applications for drug delivery and tissue engineering.

  11. Ligand-specific conformational changes in the alpha1 glycine receptor ligand-binding domain

    DEFF Research Database (Denmark)

    Pless, Stephan Alexander; Lynch, Joseph W

    2009-01-01

    indicate that channel opening is accompanied by conformational rearrangements in both beta-sheets. In an attempt to resolve ligand-dependent movements in the ligand-binding domain, we employed voltage-clamp fluorometry on alpha1 glycine receptors to compare changes mediated by the agonist, glycine...... in the inner beta-sheet and pre-M1 domain that may be important for activation, desensitization, or both. In contrast, most labeled residues in loops C and F yielded fluorescence changes identical in magnitude for glycine and strychnine. A notable exception was H201C in loop C. This labeled residue responded...... differently to glycine and strychnine, thus underlining the importance of loop C in ligand discrimination. These results provide an important step toward mapping the domains crucial for ligand discrimination in the ligand-binding domain of glycine receptors and possibly other Cys loop receptors....

  12. Flexible Ligand Docking Using Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Thomsen, Rene

    2003-01-01

    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......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...... 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...

  13. Effects of PPARγ Ligands on Leukemia

    Directory of Open Access Journals (Sweden)

    Yoko Tabe

    2012-01-01

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

  14. Ligand sphere conversions in terminal carbide complexes

    DEFF Research Database (Denmark)

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

    2016-01-01

    Metathesis is introduced as a preparative route to terminal carbide complexes. The chloride ligands of the terminal carbide complex [RuC(Cl)2(PCy3)2] (RuC) can be exchanged, paving the way for a systematic variation of the ligand sphere. A series of substituted complexes, including the first...... example of a cationic terminal carbide complex, [RuC(Cl)(CH3CN)(PCy3)2]+, is described and characterized by NMR, MS, X-ray crystallography, and computational studies. The experimentally observed irregular variation of the carbide 13C chemical shift is shown to be accurately reproduced by DFT, which also...... 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...

  15. Supramolecular architectures constructed using angular bipyridyl ligands

    International Nuclear Information System (INIS)

    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(NO3)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(NO3)2 and Zn(NO3)2. Whereas Zn(NO3)2 compounds exhibit solvent mediated polymorphism, a range of structures were obtained for the reactions with Cd(NO3)2, including the first example of a doubly parallel interpenetrated 4.82 net. 4,7-phenanthroline, was reacted with various metal(ll) nitrates as well as cobalt(ll) and copper(ll) halides. The ability of 4,7-phenanthroline to act as both a N-donor ligand and a hydrogen bond acceptor has been discussed. Reactions of CuSCN with pyrimidine yield an unusual three-dimensional structure in which polymeric propagation is not a result of ligand bridging. The reaction of CuSCN with dpt yielded structural supramolecular isomers. (author)

  16. Cationic ruthenium alkylidene catalysts bearing phosphine ligands

    OpenAIRE

    Endo, Koji; Grubbs, Robert H.

    2016-01-01

    The discovery of highly active catalysts and the success of ionic liquid immobilized systems have accelerated attention to a new class of cationic metathesis catalysts. We herein report the facile syntheses of cationic ruthenium catalysts bear-ing bulky phosphine ligands. Simple ligand exchange using silver(I) salts of non-coordinating or weakly coordinating anions pro-vided either PPh3 or chelating Ph2P(CH2)nPPh2 (n = 2 or 3) ligated cationic catalysts. The structures of these newly reported...

  17. Ligand Intermediates in Metal-Catalyzed Reactions

    Energy Technology Data Exchange (ETDEWEB)

    Gladysz, John A.

    1999-07-31

    The longest-running goal of this project has been the synthesis, isolation, and physical chemical characterization of homogeneous transition metal complexes containing ligand types believed to be intermediates in the metal-catalyzed conversion of CO/H{sub 2}, CO{sub 2}, CH{sub 4}, and similar raw materials to organic fuels, feedstocks, etc. In the current project period, complexes that contain unusual new types of C{sub x}(carbide) and C{sub x}O{sub y} (carbon oxide) ligands have been emphasized. A new program in homogeneous fluorous phase catalysis has been launched as described in the final report.

  18. Efficient chemoenzymatic synthesis of chiral pincer ligands.

    Science.gov (United States)

    Felluga, Fulvia; Baratta, Walter; Fanfoni, Lidia; Pitacco, Giuliana; Rigo, Pierluigi; Benedetti, Fabio

    2009-05-01

    Chiral, nonracemic pincer ligands based on the 6-phenyl-2-aminomethylpyridine and 2-aminomethylbenzo[h]quinoline scaffolds were obtained by a chemoenzymatic approach starting from 2-pyridyl and 2-benzoquinolyl ethanone. In the enantiodifferentiating step, secondary alcohols of opposite absolute configuration were obtained by a baker's yeast reduction of the ketones and by lipase-mediated dynamic kinetic resolution of the racemic alcohols. Their transformation into homochiral 1-methyl-1-heteroarylethanamines occurred without loss of optical purity, giving access to pincer ligands used in enantioselective catalysis.

  19. Rosetta and the Design of Ligand Binding Sites.

    Science.gov (United States)

    Moretti, Rocco; Bender, Brian J; Allison, Brittany; Meiler, Jens

    2016-01-01

    Proteins that bind small molecules (ligands) can be used as biosensors, signal modulators, and sequestering agents. When naturally occurring proteins for a particular target ligand are not available, artificial proteins can be computationally designed. We present a protocol based on RosettaLigand to redesign an existing protein pocket to bind a target ligand. Starting with a protein structure and the structure of the ligand, Rosetta can optimize both the placement of the ligand in the pocket and the identity and conformation of the surrounding sidechains, yielding proteins that bind the target compound. PMID:27094285

  20. Self-assembly and photophysical properties of lanthanide dinuclear triple-helical complexes

    Energy Technology Data Exchange (ETDEWEB)

    Piguet, C.; Bernardinelli, G.; Williams, A.F. (Univ. of Geneva (Switzerland)); Buenzli, J.C.G. (Univ. of Lausanne (Switzerland)); Hopfgartner, G. (Hoffmann-La Roche, Basel (Switzerland))

    1993-09-08

    The dinucleating ligand bis[1-methyl-2-(6[prime]-[1[double prime]-(3,5-dimethoxybenzyl)benzimidazol-2[double prime]-yl]pyrid-2[prime]-yl)benzimidazol-5-yl]methane (L) reacts with lanthanide perchlorates to give dinuclear 2:3 complexes [Ln[sub 2](L)[sub 3

  1. Catalytic catechol oxidation by copper complexes : development of a structure-activity relationship

    NARCIS (Netherlands)

    Ording-Wenker, Erica C M; Siegler, Maxime A; Lutz, Martin; Bouwman, Elisabeth

    2015-01-01

    A large library of Cu(II) complexes with mononucleating and dinucleating ligands was synthesized to investigate their potential as catalysts for the catalytic oxidation of 3,5-di-tert-butylcatechol (3,5-DTBC). X-ray structure determination for a number of these complexes revealed relatively large Cu

  2. Constitutive and ligand-induced TCR degradation

    DEFF Research Database (Denmark)

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

    2004-01-01

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

  3. Ligand iron catalysts for selective hydrogenation

    Science.gov (United States)

    Casey, Charles P.; Guan, Hairong

    2010-11-16

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

  4. Metal speciation dynamics in colloidal ligand dispersions

    NARCIS (Netherlands)

    Pinheiro, J.P.; Minor, M.; Leeuwen, van H.P.

    2005-01-01

    In this work we propose a dynamic metal speciation theory for colloidal systems in which the complexing ligands are localized on the surface of the particles; i.e., there is spatial heterogeneity of binding sites within the sample volume. The differences between the complex formation and dissociatio

  5. Supramolecular architectures constructed using angular bipyridyl ligands

    CERN Document Server

    Barnett, S A

    2003-01-01

    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...

  6. Substrate coated with receptor and labelled ligand for assays

    International Nuclear Information System (INIS)

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

  7. Role of ligand-ligand vs. core-core interactions in gold nanoclusters.

    Science.gov (United States)

    Milowska, Karolina Z; Stolarczyk, Jacek K

    2016-05-14

    The controlled assembly of ligand-coated gold nanoclusters (NCs) into larger structures paves the way for new applications ranging from electronics to nanomedicine. Here, we demonstrate through rigorous density functional theory (DFT) calculations employing novel functionals accounting for van der Waals forces that the ligand-ligand interactions determine whether stable assemblies can be formed. The study of NCs with different core sizes, symmetry forms, ligand lengths, mutual crystal orientations, and in the presence of a solvent suggests that core-to-core van der Waals interactions play a lesser role in the assembly. The dominant interactions originate from combination of steric effects, augmented by ligand bundling on NC facets, and related to them changes in electronic properties induced by neighbouring NCs. We also show that, in contrast to standard colloidal theory approach, DFT correctly reproduces the surprising experimental trends in the strength of the inter-particle interaction observed when varying the length of the ligands. The results underpin the importance of understanding NC interactions in designing gold NCs for a specific function. PMID:27097887

  8. Ligand binding was acquired during evolution of nuclear receptors

    OpenAIRE

    Escriva, Hector; Safi, Rachid; Hänni, Catherine; Langlois, Marie-Claire; Saumitou-Laprade, Pierre; Stehelin, Dominique; Capron, André; Pierce, Raymond; Laudet, Vincent

    1997-01-01

    The nuclear receptor (NR) superfamily comprises, in addition to ligand-activated transcription factors, members for which no ligand has been identified to date. We demonstrate that orphan receptors are randomly distributed in the evolutionary tree and that there is no relationship between the position of a given liganded receptor in the tree and the chemical nature of its ligand. NRs are specific to metazoans, as revealed by a screen of NR-related sequences in early- and non-metazoan organism...

  9. Open-shell organometallics: reactivity at the ligand

    NARCIS (Netherlands)

    W.I. Dzik; B. de Bruin

    2011-01-01

    The purpose of this review is to show that (cooperative) ligand radical reactivity can be effectively employed in synthetic organometallic chemistry and catalysis to achieve selectivity in radical-type transformations. The ‘redox non-innocence’ of ligands, and the controlled reactivity of ‘ligand ra

  10. Triple Bioaffinity Mass Spectrometry Concept for Thyroid Transporter Ligands

    NARCIS (Netherlands)

    Aqai, P.; Fryganas, C.; Mizuguchi, M.; Haasnoot, W.; Nielen, M.W.F.

    2012-01-01

    For the analysis of thyroid transporter ligands, a triple bioaffinity mass spectrometry (BioMS) concept was developed, with the aim at three different analytical objectives: rapid screening of any ligand, confirmation of known ligands in accordance with legislative requirements, and identification o

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

    DEFF Research Database (Denmark)

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

    2016-01-01

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

  12. Gas-phase ligand loss and ligand substitution reactions of platinum(II) complexes of tridentate nitrogen donor ligands.

    Science.gov (United States)

    Wee, Sheena; O'Hair, Richard A J; McFadyen, W David

    2004-01-01

    The source of protons associated with the ligand loss channel of HX((n - 1)+) from [Pt(II)(dien)X](n+) (X = Cl, Br and I for n = 1 and X = NC(5)H(5) for n = 2) in the gas phase was investigated by deuterium-labelling studies. The results of these studies indicate that these protons originate from both the amino groups and the carbon backbone of the dien ligand. In some instances (e.g. X = Br and I), the protons lost from the carbon backbone can be even more abundant than the protons lost from the amino groups. The gas-phase substitution reactions of coordinatively saturated [Pt(II)(L(3))L(a)](2+) complexes (L(3) = tpy or dien) were also examined using ion-molecule reactions. The outcome of the ion-molecule reactions depends on both the ancillary ligand (L(3)) as well as the leaving group (L(a)). [Pt(II)(tpy)L(a)](2+) complexes undergo substitution reactions, with a faster rate when L(a) is a good leaving group, while the [Pt(II)(dien)L(a)](2+) complex undergoes a proton transfer reaction. PMID:15164352

  13. Leaching behavior of butanedionedioxime as gold ligand

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Butanedionedioxime, a small organic compound with low-toxicity and good chemical stability, has been proposed as an effective gold ligand in gold extraction. The result of experiment shows that: 1) highly effective gold lixiviantcan be composed of butanedionedioxime (BDM) with many oxidants, especially potassium permanganate; 2)in the leaching system of BD M- K M nO4 the suitable Ox/Lig(ratio of oxidants to gold ligands) tange is 0.20 ~ 0. 50, optimally 0.25 ~0.45 at the pH range of 7 ~ 11; 3) BDM-KMnO4 extraction of gold from an oxide ore is similar to cyanide(cyanide-O2)extraction, but the leaching rate of gold by BDM-KMnO4 is faster than that by cyanide-O2; 4) gold may readily be recov-ered by carbon adsorption and zinc precipitation

  14. Glycomimetic ligands for the human asialoglycoprotein receptor.

    Science.gov (United States)

    Mamidyala, Sreeman K; Dutta, Sanjay; Chrunyk, Boris A; Préville, Cathy; Wang, Hong; Withka, Jane M; McColl, Alexander; Subashi, Timothy A; Hawrylik, Steven J; Griffor, Matthew C; Kim, Sung; Pfefferkorn, Jeffrey A; Price, David A; Menhaji-Klotz, Elnaz; Mascitti, Vincent; Finn, M G

    2012-02-01

    The asialoglycoprotein receptor (ASGPR) is a high-capacity galactose-binding receptor expressed on hepatocytes that binds its native substrates with low affinity. More potent ligands are of interest for hepatic delivery of therapeutic agents. We report several classes of galactosyl analogues with varied substitution at the anomeric, C2-, C5-, and C6-positions. Significant increases in binding affinity were noted for several trifluoromethylacetamide derivatives without covalent attachment to the protein. A variety of new ligands were obtained with affinity for ASGPR as good as or better than that of the parent N-acetylgalactosamine, showing that modification on either side of the key C3,C4-diol moiety is well tolerated, consistent with previous models of a shallow binding pocket. The galactosyl pyranose motif therefore offers many opportunities for the attachment of other functional units or payloads while retaining low-micromolar or better affinity for the ASGPR.

  15. Selective oxoanion separation using a tripodal ligand

    Energy Technology Data Exchange (ETDEWEB)

    Custelcean, Radu; Moyer, Bruce A.; Rajbanshi, Arbin

    2016-02-16

    The present invention relates to urea-functionalized crystalline capsules self-assembled by sodium or potassium cation coordination and by hydrogen-bonding water bridges to selectively encapsulate tetrahedral divalent oxoanions from highly competitive aqueous alkaline solutions and methods using this system for selective anion separations from industrial solutions. The method involves competitive crystallizations using a tripodal tris(urea) functionalized ligand and, in particular, provides a viable approach to sulfate separation from nuclear wastes.

  16. Targeting Selectins and Their Ligands in Cancer.

    Science.gov (United States)

    Natoni, Alessandro; Macauley, Matthew S; O'Dwyer, Michael E

    2016-01-01

    Aberrant glycosylation is a hallmark of cancer cells with increased evidence pointing to a role in tumor progression. In particular, aberrant sialylation of glycoproteins and glycolipids has been linked to increased immune cell evasion, drug evasion, drug resistance, tumor invasiveness, and vascular dissemination, leading to metastases. Hypersialylation of cancer cells is largely the result of overexpression of sialyltransferases (STs). Differentially, humans express twenty different STs in a tissue-specific manner, each of which catalyzes the attachment of sialic acids via different glycosidic linkages (α2-3, α2-6, or α2-8) to the underlying glycan chain. One important mechanism whereby overexpression of STs contributes to an enhanced metastatic phenotype is via the generation of selectin ligands. Selectin ligand function requires the expression of sialyl-Lewis X and its structural isomer sialyl-Lewis A, which are synthesized by the combined action of alpha α1-3-fucosyltransferases, α2-3-sialyltransferases, β1-4-galactosyltranferases, and N-acetyl-β-glucosaminyltransferases. The α2-3-sialyltransferases ST3Gal4 and ST3Gal6 are critical to the generation of functional E- and P-selectin ligands and overexpression of these STs have been linked to increased risk of metastatic disease in solid tumors and poor outcome in multiple myeloma. Thus, targeting selectins and their ligands as well as the enzymes involved in their generation, in particular STs, could be beneficial to many cancer patients. Potential strategies include ST inhibition and the use of selectin antagonists, such as glycomimetic drugs and antibodies. Here, we review ongoing efforts to optimize the potency and selectivity of ST inhibitors, including the potential for targeted delivery approaches, as well as evaluate the potential utility of selectin inhibitors, which are now in early clinical development. PMID:27148485

  17. Targeting Selectins and Their Ligands in Cancer

    Directory of Open Access Journals (Sweden)

    Alessandro eNatoni

    2016-04-01

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

  18. Syntheses of oxysterol receptors'(LXRs) ligands

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    The LXRs' agonist, 24S,25-epoxycholesterol 1, was synthesized stereoselectively (100% d.e.) in 56% overall yield from methyl hyodeoxycholanate 4 in 9 steps with desmosterol acetate 11 as the key intermediate and the modified Sharpless asymmetric dihydroxylation as the key step. The LXR? subtype selective agonist 5α,6α:24S,25-diepoxycho- lesterol 2 and the novel LXRs' ligand 5β,6β:24S,25-diepo- xycholesterol 3 were also synthesized from 1.

  19. EXPRESSION OF Fas LIGAND IN HUMAN COLON CANCER CELL LINES

    Institute of Scientific and Technical Information of China (English)

    张建军; 丁尔迅; 王强; 陈学云; 付志仁

    2001-01-01

    To investigate the expression of Fas ligand in human colon carcinoma cell lines. Methods: A total of six human colon cancer cell lines were examined for the expression of Fas ligand mRNA and cell surface protein by using RT-PCR and flow cytometry respectively. Results: The results showed that Fas ligand mRNA was expressed in all of the six cancer cell lines and Fas ligand cell surface protein was expressed in part of them. Conclusion: These data suggest that Fas ligand was expressed, at least in part, in human colon cancer cell lines and might facilitate to escape from immune surveillance of the host.

  20. The Recognition of Identical Ligands by Unrelated Proteins.

    Science.gov (United States)

    Barelier, Sarah; Sterling, Teague; O'Meara, Matthew J; Shoichet, Brian K

    2015-12-18

    The binding of drugs and reagents to off-targets is well-known. Whereas many off-targets are related to the primary target by sequence and fold, many ligands bind to unrelated pairs of proteins, and these are harder to anticipate. If the binding site in the off-target can be related to that of the primary target, this challenge resolves into aligning the two pockets. However, other cases are possible: the ligand might interact with entirely different residues and environments in the off-target, or wholly different ligand atoms may be implicated in the two complexes. To investigate these scenarios at atomic resolution, the structures of 59 ligands in 116 complexes (62 pairs in total), where the protein pairs were unrelated by fold but bound an identical ligand, were examined. In almost half of the pairs, the ligand interacted with unrelated residues in the two proteins (29 pairs), and in 14 of the pairs wholly different ligand moieties were implicated in each complex. Even in those 19 pairs of complexes that presented similar environments to the ligand, ligand superposition rarely resulted in the overlap of related residues. There appears to be no single pattern-matching "code" for identifying binding sites in unrelated proteins that bind identical ligands, though modeling suggests that there might be a limited number of different patterns that suffice to recognize different ligand functional groups.

  1. A response calculus for immobilized T cell receptor ligands

    DEFF Research Database (Denmark)

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

    2001-01-01

    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......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...... the importance of receptor cross-linking density in determining TCR signaling. Moreover, it was found that the functional two-dimensional affinity of TCR ligands was affected by the chemical composition of the ligand-presenting surface. This makes it possible that cell-bound TCR ligands, despite their low...

  2. Redox-Active-Ligand-Mediated Formation of an Acyclic Trinuclear Ruthenium Complex with Bridging Nitrido Ligands.

    Science.gov (United States)

    Bagh, Bidraha; Broere, Daniël L J; Siegler, Maxime A; van der Vlugt, Jarl Ivar

    2016-07-11

    Coordination of a redox-active pyridine aminophenol ligand to Ru(II) followed by aerobic oxidation generates two diamagnetic Ru(III) species [1 a (cis) and 1 b (trans)] with ligand-centered radicals. The reaction of 1 a/1 b with excess NaN3 under inert atmosphere resulted in the formation of a rare bis(nitrido)-bridged trinuclear ruthenium complex with two nonlinear asymmetrical Ru-N-Ru fragments. The spontaneous reduction of the ligand centered radical in the parent 1 a/1 b supports the oxidation of a nitride (N(3-) ) to half an equivalent of N2 . The trinuclear omplex is reactive toward TEMPO-H, tin hydrides, thiols, and dihydrogen. PMID:27321547

  3. Interaction of calreticulin with CD40 ligand, TRAIL and Fas ligand

    DEFF Research Database (Denmark)

    Duus, K; Pagh, R T; Holmskov, U;

    2007-01-01

    found to bind calreticulin strongly. A low level or no binding was observed for adiponectin, tumour necrosis factor-alpha (TNF-alpha), CD30L, surfactant protein-A and -D and collagen VIII. The interaction with calreticulin required a conformational change in CD40L, TRAIL and FasL and showed the same...... is utilized by many other functionally diverse molecules and in this work the interaction of calreticulin with C1q and structurally similar molecules was investigated. In addition to C1q and MBL, CD40 ligand (CD40L), tumour necrosis factor-related apoptosis-inducing ligand (TRAIL) and Fas ligand (FasL) were...... characteristics as calreticulin's interaction with C1q and MBL: a time-dependent saturable binding to immobilized protein, which was initially sensitive to salt but gradually developed into a salt-insensitive interaction. Thus, the interaction requires a structural change in the interaction partner and leads...

  4. Landscape of protein-small ligand binding modes.

    Science.gov (United States)

    Kasahara, Kota; Kinoshita, Kengo

    2016-09-01

    Elucidating the mechanisms of specific small-molecule (ligand) recognition by proteins is a long-standing conundrum. While the structures of these molecules, proteins and ligands, have been extensively studied, protein-ligand interactions, or binding modes, have not been comprehensively analyzed. Although methods for assessing similarities of binding site structures have been extensively developed, the methods for the computational treatment of binding modes have not been well established. Here, we developed a computational method for encoding the information about binding modes as graphs, and assessing their similarities. An all-against-all comparison of 20,040 protein-ligand complexes provided the landscape of the protein-ligand binding modes and its relationships with protein- and chemical spaces. While similar proteins in the same SCOP Family tend to bind relatively similar ligands with similar binding modes, the correlation between ligand and binding similarities was not very high (R(2)  = 0.443). We found many pairs with novel relationships, in which two evolutionally distant proteins recognize dissimilar ligands by similar binding modes (757,474 pairs out of 200,790,780 pairs were categorized into this relationship, in our dataset). In addition, there were an abundance of pairs of homologous proteins binding to similar ligands with different binding modes (68,217 pairs). Our results showed that many interesting relationships between protein-ligand complexes are still hidden in the structure database, and our new method for assessing binding mode similarities is effective to find them.

  5. Landscape of protein-small ligand binding modes.

    Science.gov (United States)

    Kasahara, Kota; Kinoshita, Kengo

    2016-09-01

    Elucidating the mechanisms of specific small-molecule (ligand) recognition by proteins is a long-standing conundrum. While the structures of these molecules, proteins and ligands, have been extensively studied, protein-ligand interactions, or binding modes, have not been comprehensively analyzed. Although methods for assessing similarities of binding site structures have been extensively developed, the methods for the computational treatment of binding modes have not been well established. Here, we developed a computational method for encoding the information about binding modes as graphs, and assessing their similarities. An all-against-all comparison of 20,040 protein-ligand complexes provided the landscape of the protein-ligand binding modes and its relationships with protein- and chemical spaces. While similar proteins in the same SCOP Family tend to bind relatively similar ligands with similar binding modes, the correlation between ligand and binding similarities was not very high (R(2)  = 0.443). We found many pairs with novel relationships, in which two evolutionally distant proteins recognize dissimilar ligands by similar binding modes (757,474 pairs out of 200,790,780 pairs were categorized into this relationship, in our dataset). In addition, there were an abundance of pairs of homologous proteins binding to similar ligands with different binding modes (68,217 pairs). Our results showed that many interesting relationships between protein-ligand complexes are still hidden in the structure database, and our new method for assessing binding mode similarities is effective to find them. PMID:27327045

  6. Integrin receptors and ligand-gated channels.

    Science.gov (United States)

    Morini, Raffaella; Becchetti, Andrea

    2010-01-01

    Plastic expression of different integrin subunits controls the different stages of neural development, whereas in the adult integrins regulate synaptic stability. Evidence of integrin-channel crosstalk exists for ionotropic glutamate receptors. As is often the case in other tissues, integrin engagement regulates channel activity through complex signaling pathways that often include tyrosine phosphorylation cascades. The specific pathways recruited by integrin activation depend on cerebral region and cell type. In turn, ion channels control integrin expression onto the plasma membrane and their ligand binding affinity. The most extensive studies concern the hippocampus and suggest implications for neuronal circuit plasticity. The physiological relevance of these findings depends on whether adhesion molecules, aside from determining tissue stability, contribute to synaptogenesis and the responsiveness of mature synapses, thus contributing to long-term circuit consolidation. Little evidence is available for other ligand-gated channels, with the exception of nicotinic receptors. These exert a variety of functions in neurons and non neural tissue, both in development and in the adult, by regulating cell cycle, synaptogenesis and synaptic circuit refinement. Detailed studies in epidermal keratinocytes have shed some light on the possible mechanisms through which ACh can regulate cell motility, which may be of general relevance for morphogenetic processes. As to the control of mature synapses, most results concern the integrinic control of nicotinic receptors in the neuromuscular junction. Following this lead, a few studies have addressed similar topics in adult cerebral synapses. However, pursuing and interpreting these results in the brain is especially difficult because of the complexity of the nicotinic roles and the widespread contribution of nonsynaptic, paracrine transmission. From a pathological point of view, considering the well-known contribution of both

  7. Transmutable nanoparticles with reconfigurable surface ligands

    Science.gov (United States)

    Kim, Youngeun; Macfarlane, Robert J.; Jones, Matthew R.; Mirkin, Chad A.

    2016-02-01

    Unlike conventional inorganic materials, biological systems are exquisitely adapted to respond to their surroundings. Proteins and other biological molecules can process a complex set of chemical binding events as informational inputs and respond accordingly via a change in structure and function. We applied this principle to the design and synthesis of inorganic materials by preparing nanoparticles with reconfigurable surface ligands, where interparticle bonding can be programmed in response to specific chemical cues in a dynamic manner. As a result, a nascent set of “transmutable nanoparticles” can be driven to crystallize along multiple thermodynamic trajectories, resulting in rational control over the phase and time evolution of nanoparticle-based matter.

  8. Increased accuracy of ligand sensing by receptor internalization

    CERN Document Server

    Aquino, Gerardo

    2010-01-01

    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.

  9. Architectural repertoire of ligand-binding pockets on protein surfaces.

    Science.gov (United States)

    Weisel, Martin; Kriegl, Jan M; Schneider, Gisbert

    2010-03-01

    Knowledge of the three-dimensional structure of ligand binding sites in proteins provides valuable information for computer-assisted drug design. We present a method for the automated extraction and classification of ligand binding site topologies, in which protein surface cavities are represented as branched frameworks. The procedure employs a growing neural gas approach for pocket topology assignment and pocket framework generation. We assessed the structural diversity of 623 known ligand binding site topologies based on framework cluster analysis. At a resolution of 5 A only 23 structurally distinct topology groups were formed; this suggests an overall limited structural diversity of ligand-accommodating protein cavities. Higher resolution allowed for identification of protein-family specific pocket features. Pocket frameworks highlight potentially preferred modes of ligand-receptor interactions and will help facilitate the identification of druggable subpockets suitable for ligand affinity and selectivity optimization. PMID:20069621

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

    KAUST Repository

    Bealing, Clive R.

    2012-03-27

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

  11. SuperLigands – a database of ligand structures derived from the Protein Data Bank

    Directory of Open Access Journals (Sweden)

    Preissner Robert

    2005-05-01

    Full Text Available Abstract Background Currently, the PDB contains approximately 29,000 protein structures comprising over 70,000 experimentally determined three-dimensional structures of over 5,000 different low molecular weight compounds. Information about these PDB ligands can be very helpful in the field of molecular modelling and prediction, particularly for the prediction of protein binding sites and function. Description Here we present an Internet accessible database delivering PDB ligands in the MDL Mol file format which, in contrast to the PDB format, includes information about bond types. Structural similarity of the compounds can be detected by calculation of Tanimoto coefficients and by three-dimensional superposition. Topological similarity of PDB ligands to known drugs can be assessed via Tanimoto coefficients. Conclusion SuperLigands supplements the set of existing resources of information about small molecules bound to PDB structures. Allowing for three-dimensional comparison of the compounds as a novel feature, this database represents a valuable means of analysis and prediction in the field of biological and medical research.

  12. SuperLigands – a database of ligand structures derived from the Protein Data Bank

    Science.gov (United States)

    Michalsky, Elke; Dunkel, Mathias; Goede, Andrean; Preissner, Robert

    2005-01-01

    Background Currently, the PDB contains approximately 29,000 protein structures comprising over 70,000 experimentally determined three-dimensional structures of over 5,000 different low molecular weight compounds. Information about these PDB ligands can be very helpful in the field of molecular modelling and prediction, particularly for the prediction of protein binding sites and function. Description Here we present an Internet accessible database delivering PDB ligands in the MDL Mol file format which, in contrast to the PDB format, includes information about bond types. Structural similarity of the compounds can be detected by calculation of Tanimoto coefficients and by three-dimensional superposition. Topological similarity of PDB ligands to known drugs can be assessed via Tanimoto coefficients. Conclusion SuperLigands supplements the set of existing resources of information about small molecules bound to PDB structures. Allowing for three-dimensional comparison of the compounds as a novel feature, this database represents a valuable means of analysis and prediction in the field of biological and medical research. PMID:15943884

  13. Mixed ligand oxovanadium(IV) complexes with salicylic acid and N,N-bidentate ligands

    International Nuclear Information System (INIS)

    Two mixed-ligand oxovanadium(IV) complexes VO(A)(B) [where H2A=salicylic acid and B=2,2'-bipyridine or 1,10-phenanthroline (hereafter, bipy and phen respectively)] have been synthesized and characterized by magnetic moment and spectral (IR, UV/VIS and EPR) data. The A2- ion acts as a bidentate dinegative ligand while B ligands acts as a neutral bidentate. The magnetic susceptibility values indicate the existence of a small amount of antiferromagnetic interaction. The vanadium atoms in the complexes are hexacoordinated and the coordination sphere is of the type [VO(OO)(NN)], where O atoms are of oxo, carboxylic and phenolic type and N atoms are of pyridine type. The sixth coordination site is occupied by phenolic oxygen of the neighbouring molecule forming a bridge. The vv=o confirms the hexacoordination. All the complexes have dxy1 type axial EPR spectra and they exhibit two ligand field transitions at 740 and 440 nm. (author)

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

    Science.gov (United States)

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

    2008-01-01

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

  15. 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

    2015-01-01

    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.

  16. Dynamic Presentation of Immobilized Ligands Regulated through Biomolecular Recognition

    OpenAIRE

    Liu, Bo; Liu, Yang; Riesberg, Jeremiah J.; Shen, Wei

    2010-01-01

    To mimic the dynamic regulation of signaling ligands immobilized on extracellular matrices or on the surfaces of neighboring cells for guidance of cell behavior and fate selection, we have harnessed biomolecular recognition in combination with polymer engineering to create dynamic surfaces on which the accessibility of immobilized ligands to cell surface receptors can be reversibly interconverted under physiological conditions. The cell-adhesive RGD peptide is chosen as a model ligand. RGD is...

  17. The first nitro-substituted heteroscorpionate ligand.

    Science.gov (United States)

    Pellei, Maura; Benetollo, Franco; Lobbia, Giancarlo Gioia; Alidori, Simone; Santini, Carlo

    2005-02-21

    The new dihydridobis(3-nitro-1,2,4-triazolyl)borate ligand, [H2B(tzNO2)2]-, has been synthesized in dimethylacetamide solution, using 3-nitro-1,2,4-triazole and KBH4 through careful temperature control, and characterized as its potassium salt. The zinc(II) and cadmium(II) complexes, {M[H2B(tzNO2)2]Cl(H2O)2}, have been prepared by metathesis of [H2B(tzNO2)2]K with ZnCl2 and CdCl2, respectively. The complexes likely contain a metal core in which the ligand is coordinated to the metal ions in the K2-N,N' or K4-N,N',O,O' fashion. A single-crystal structural characterization is reported for the potassium dihydrobis(3-nitro-1,2,4-triazolyl)borate. The potassium salt is polymeric and shows several K...N and K...O interactions. PMID:15859260

  18. Do organic ligands affect calcite dissolution rates?

    Science.gov (United States)

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

    2011-04-01

    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 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.

  19. Continuous microfluidic assortment of interactive ligands (CMAIL)

    Science.gov (United States)

    Hsiao, Yi-Hsing; Huang, Chao-Yang; Hu, Chih-Yung; Wu, Yen-Yu; Wu, Chung-Hsiun; Hsu, Chia-Hsien; Chen, Chihchen

    2016-08-01

    Finding an interactive ligand-receptor pair is crucial to many applications, including the development of monoclonal antibodies. Biopanning, a commonly used technique for affinity screening, involves a series of washing steps and is lengthy and tedious. Here we present an approach termed continuous microfluidic assortment of interactive ligands, or CMAIL, for the screening and sorting of antigen-binding single-chain variable antibody fragments (scFv) displayed on bacteriophages (phages). Phages carrying native negative charges on their coat proteins were electrophoresed through a hydrogel matrix functionalized with target antigens under two alternating orthogonal electric fields. During the weak horizontal electric field phase, phages were differentially swept laterally depending on their affinity for the antigen, and all phages were electrophoresed down to be collected during the strong vertical electric field phase. Phages of different affinity were spatially separated, allowing the continuous operation. More than 105 CFU (colony forming unit) antigen-interacting phages were isolated with ~100% specificity from a phage library containing 3 × 109 individual members within 40 minutes of sorting using CMAIL. CMAIL is rapid, sensitive, specific, and does not employ washing, elution or magnetic beads. In conclusion, we have developed an efficient and cost-effective method for isolating and sorting affinity reagents involving phage display.

  20. Superior serum half life of albumin tagged TNF ligands

    International Nuclear Information System (INIS)

    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.

  1. Riboswitch Structure: an Internal Residue Mimicking the Purine Ligand

    Energy Technology Data Exchange (ETDEWEB)

    Delfosse, V.; Bouchard, P; Bonneau, E; Dagenais, P; Lemay, J; Lafontaine, D; Legault, P

    2009-01-01

    The adenine and guanine riboswitches regulate gene expression in response to their purine ligand. X-ray structures of the aptamer moiety of these riboswitches are characterized by a compact fold in which the ligand forms a Watson-Crick base pair with residue 65. Phylogenetic analyses revealed a strict restriction at position 39 of the aptamer that prevents the G39-C65 and A39-U65 combinations, and mutational studies indicate that aptamers with these sequence combinations are impaired for ligand binding. In order to investigate the rationale for sequence conservation at residue 39, structural characterization of the U65C mutant from Bacillus subtilis pbuE adenine riboswitch aptamer was undertaken. NMR spectroscopy and X-ray crystallography studies demonstrate that the U65C mutant adopts a compact ligand-free structure, in which G39 occupies the ligand-binding site of purine riboswitch aptamers. These studies present a remarkable example of a mutant RNA aptamer that adopts a native-like fold by means of ligand mimicking and explain why this mutant is impaired for ligand binding. Furthermore, this work provides a specific insight into how the natural sequence has evolved through selection of nucleotide identities that contribute to formation of the ligand-bound state, but ensures that the ligand-free state remains in an active conformation.

  2. Ligand Release Pathways Obtained with WExplore: Residence Times and Mechanisms.

    Science.gov (United States)

    Dickson, Alex; Lotz, Samuel D

    2016-06-23

    The binding of ligands with their molecular receptors is of tremendous importance in biology. Although much emphasis has been placed on characterizing binding sites and bound poses that determine the binding thermodynamics, the pathway by which a ligand binds importantly determines the binding kinetics. The computational study of entire unbiased ligand binding and release pathways is still an emerging field, made possible only recently by advances in computational hardware and sampling methodologies. We have developed one such method (WExplore) that is based on a weighted ensemble of trajectories, which we apply to ligand release for the first time, using a set of three previously characterized interactions between low-affinity ligands and the protein FKBP-12 (FK-506 binding protein). WExplore is found to be more efficient that conventional sampling, even for the nanosecond-scale unbinding events observed here. From a nonequilibrium ensemble of unbinding trajectories, we obtain ligand residence times and release pathways without using biasing forces or a Markovian assumption of transitions between regions. We introduce a set of analysis tools for unbinding transition pathways, including using von Mises-Fisher distributions to model clouds of ligand exit points, which provide a quantitative proxy for ligand surface diffusion. Differences between the transition pathway ensembles of the three ligands are identified and discussed. PMID:27231969

  3. Single-incubation immunoassay for a multivalent ligand

    International Nuclear Information System (INIS)

    In a two-site immunoassay method for a multivalent ligand using a single incubation, the ligand, labelled receptor for the ligand and unlabelled receptor for the ligand covalently bound to a solid-phase support are incubated as a stable suspension to produce a solid and liquid phase. The solid and liquid phases are separated from each other and the labelled receptor in either phase is quantified. The method has particular application as an assay for human thyroid stimulating hormone using purified, radioactively labelled antibodies and unlabelled antibodies covalently bound to hydrolyzed polyacrylamide particles. (author)

  4. 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: harald.wajant@mail.uni-wuerzburg.de [Division of Molecular Internal Medicine, Department of Internal Medicine II, University Hospital Wuerzburg, Roentgenring 11, 97070 Wuerzburg (Germany)

    2010-06-11

    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.

  5. Characterizing mixed phosphonic acid ligand capping on CdSe/ZnS quantum dots using ligand exchange and NMR spectroscopy.

    Science.gov (United States)

    Davidowski, Stephen K; Lisowski, Carmen E; Yarger, Jeffery L

    2016-03-01

    The ligand capping of phosphonic acid functionalized CdSe/ZnS core-shell quantum dots (QDs) was investigated with a combination of solution and solid-state (31) P nuclear magnetic resonance (NMR) spectroscopy. Two phosphonic acid ligands were used in the synthesis of the QDs, tetradecylphosphonic acid and ethylphosphonic acid. Both alkyl phosphonic acids showed broad liquid and solid-state (31) P NMR resonances for the bound ligands, indicative of heterogeneous binding to the QD surface. In order to quantify the two ligand populations on the surface, ligand exchange facilitated by phenylphosphonic acid resulted in the displacement of the ethylphosphonic acid and tetradecylphosphonic acid and allowed for quantification of the free ligands using (31) P liquid-state NMR. After washing away the free ligand, two broad resonances were observed in the liquids' (31) P NMR corresponding to the alkyl and aromatic phosphonic acids. The washed samples were analyzed via solid-state (31) P NMR, which confirmed the ligand populations on the surface following the ligand exchange process. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26639792

  6. Modification of diphenylamine-linked bis(oxazoline) ligands: Tuning of electronic effect and rigidity of ligand skeleton

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    The electronic effect of diphenylamine-linked bis(oxazoline) ligands was tuned through introduction of electron-withdrawing bromo and nitro substituents onto the 4 and 4′ position. The variation of the NH bond acidity was determined by the different chemical shifts of NH. The catalytic activity and enantioselectivity of the modified ligands were tested in the asymmetric Friedel-Crafts alkylation of indole with β-nitrostyrene. The effect of ligand skeleton rigidity was also investigated through the synthesis of iminodibenzyl-linked bis(oxazoline) ligands and evaluation of their catalytic activity in Friedel-Crafts alkylation.

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

    Science.gov (United States)

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

    2016-09-01

    We present here the calculation of the mean time to capture of a tethered ligand to the receptor. This calculation is then used to determine the shift in the partitioning between (1) free, (2) singly bound, and (3) doubly bound ligands in chemical equilibrium as a function of the length of the tether. These calculations are used in the research article Fibroblast Growth Factor 2 Dimer with Superagonist in vitro Activity Improves Granulation Tissue Formation During Wound Healing (Decker et al., in press [1]) to explain quantitatively how changes in polymeric linker length in the ligand dimers modifies the efficacy of these molecules relative to that of free ligands. PMID:27408925

  8. Functional metal-organic frameworks via ligand doping: influences of ligand charge and steric demand.

    Science.gov (United States)

    Wang, Cheng; Liu, Demin; Xie, Zhigang; Lin, Wenbin

    2014-02-01

    Doping a functional ligand into a known crystalline system built from ligands of similar shape and length provides a powerful strategy to construct functional metal-organic frameworks (MOFs) with desired functionality and structural topology. This mix-and-match approach mimics the widely applied metal ion doping (or solid solution formation) in traditional inorganic materials, such as metal oxides, wherein maintaining charge balance of the doped lattice and ensuring size match between doped metal ions and the parent lattice are key to successful doping. In this work, we prepared three sterically demanding dicarboxylate ligands based on Ir/Ru-phosphors with similar structures and variable charges (-2 to 0), [Ir(ppy)3]-dicarboxylate (L1, ppy is 2-phenylpyridine), [Ir(bpy)(ppy)2](+)-dicarboxylate (L2, bpy is 2,2'-bipyridine), and Ru(bpy)3](2+)-dicarboxylate (L3), and successfully doped them into the known IRMOF-9/-10 structures by taking advantage of matching length between 4,4'-biphenyl dicarboxylate (BPDC) and L1-L3. We systematically investigated the effects of size and charge of the doping ligand on the MOF structures and the ligand doping levels in these MOFs. L1 carries a -2 charge to satisfy the charge requirement of the parent Zn4O(BPDC)3 framework and can be mixed into the IRMOF-9/-10 structure in the whole range of H2L1/H2BPDC ratios from 0 to 1. The steric bulk of L1 induces a phase transition from the interpenetrated IRMOF-9 structure to the non-interpenetrated IRMOF-10 counterpart. L2 and L3 do not match the dinegative charge of BPDC in order to maintain the charge balance for a neutral IRMOF-9/-10 framework and can only be doped into the IRMOF-9 structure to a certain degree. L2 and L3 form a charge-balanced new phase with a neutral framework structure at higher doping levels (>8% For L2 and >6% For L3). This systematic investigation reveals the influences of steric demand and charge balance on ligand doping in MOFs, a phenomenon that has been well

  9. Rational design of class I MHC ligands

    Science.gov (United States)

    Rognan, D.; Scapozza, L.; Folkers, G.; Daser, Angelika

    1995-04-01

    From the knowledge of the three-dimensional structure of a class I MHC protein, several non natural peptides were designed in order to either optimize the interactions of one secondary anchor amino acid with its HLA binding pocket or to substitute the non interacting part with spacer residues. All peptides were synthesized and tested for binding to the class I MHC protein in an in vitro reconstitution assay. As predicted, the non natural peptides present an enhanced binding to the HLA-B27 molecule with respect to their natural parent peptides. This study constitutes the first step towards the rational design of non peptidic MHC ligands that should be very promising tools for the selective immunotherapy of autoimmune diseases.

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

    DEFF Research Database (Denmark)

    Kristensen, Thomas Greve; Pedersen, Christian Storm

    2009-01-01

    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 mi...

  11. Organopalladium complexes with bidentate phosphorus and nitrogen containing ligands

    NARCIS (Netherlands)

    Koten, G. van; Graaf, W. de; Harder, Sjoerd; Boersma, J.; Kanters, J.A.

    1988-01-01

    Organopalladium complexes containing the potentially P, N-bidentate ligands o-diphenylphosphino-N,N-dimethylbenzylamine (PN) and o-diphenylphosphino-@a-methyl-N,N-dimethylbenzylamine (PN}*{) have been studied. The palladium(0) complexes Pd(P@?N){3} (P@?N = PN or PN}*{) have been prepared: the ligand

  12. Death receptors and ligands in cervical carcinogenesis : an immunohistochemical study

    NARCIS (Netherlands)

    Reesink-Peters, N; Hougardy, B M T; van den Heuvel, F A J; Ten Hoor, K A; Hollema, H; Boezen, H M; de Vries, E G E; de Jong, S; van der Zee, A G J

    2005-01-01

    OBJECTIVE: Increasing imbalance between proliferation and apoptosis is important in cervical carcinogenesis. The death ligands FasL and tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) induce apoptosis by binding to their cognate cell-surface death receptors Fas or death receptor (DR)

  13. Functionalized pyrazines as ligands for minor actinide extraction and catalysis

    NARCIS (Netherlands)

    Nikishkin, N.

    2013-01-01

    The research presented in this thesis concerns the design of ligands for a wide range of applications, from nuclear waste treatment to catalysis. The strategies employed to design actinide-selective extractants, for instance, comprise the fine tuning of the ligand electronic properties as well as us

  14. Influence of the platform in multicoordinate ligands for actinide partitioning

    NARCIS (Netherlands)

    Dam, Henk H.; Reinhoudt, David N.; Verboom, Willem

    2007-01-01

    Multicoordinate ligands based on the trityl, C-pivot, and CTV platforms and the ligating groups CMPO, DGA, PICO, and MPMA were synthesized and studied for their extraction properties. The extraction efficiencies of these multicoordinate ligands are largely influenced by the properties of the platfor

  15. Immobilisation of ligands by radio-derivatized polymers

    International Nuclear Information System (INIS)

    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

  16. Improved ligand geometries in crystallographic refinement using AFITT in PHENIX.

    Science.gov (United States)

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

    2016-09-01

    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. PMID:27599738

  17. Polypharmacology: in silico methods of ligand design and development.

    Science.gov (United States)

    McKie, Samuel A

    2016-04-01

    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.

  18. Development of chiral sulfoxide ligands for asymmetric catalysis.

    Science.gov (United States)

    Trost, Barry M; Rao, Meera

    2015-04-20

    Nitrogen-, phosphorus-, and oxygen-based ligands with chiral backbones have been the historic workhorses of asymmetric transition-metal-catalyzed reactions. On the contrary, sulfoxides containing chirality at the sulfur atom have mainly been used as chiral auxiliaries for diastereoselective reactions. Despite several distinct advantages over traditional ligand scaffolds, such as the proximity of the chiral information to the metal center and the ability to switch between S and O coordination, these compounds have only recently emerged as a versatile class of chiral ligands. In this Review, we detail the history of the development of chiral sulfoxide ligands for asymmetric catalysis. We also provide brief descriptions of metal-sulfoxide bonding and strategies for the synthesis of enantiopure sulfoxides. Finally, insights into the future development of this underutilized ligand class are discussed.

  19. Regulation mechanisms of the FLT3-ligand after irradiation

    International Nuclear Information System (INIS)

    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

  20. Metrical oxidation states of 2-amidophenoxide and catecholate ligands: structural signatures of metal-ligand π bonding in potentially noninnocent ligands.

    Science.gov (United States)

    Brown, Seth N

    2012-02-01

    Catecholates and 2-amidophenoxides are prototypical "noninnocent" ligands which can form metal complexes where the ligands are best described as being in the monoanionic (imino)semiquinone or neutral (imino)quinone oxidation state instead of their closed-shell dianionic form. Through a comprehensive analysis of structural data available for compounds with these ligands in unambiguous oxidation states (109 amidophenolates, 259 catecholates), the well-known structural changes in the ligands with oxidation state can be quantified. Using these correlations, an empirical "metrical oxidation state" (MOS) which gives a continuous measure of the apparent oxidation state of the ligand can be determined based on least-squares fitting of its C-C, C-O, and C-N bond lengths to this single parameter (a simple procedure for doing so is provided via a spreadsheet in the Supporting Information). High-valent d(0) metal complexes, particularly those of vanadium(V) and molybdenum(VI), have ligands with unexpectedly positive, and generally nonintegral, MOS values. The structural effects in these complexes are attributed not to electron transfer, but rather to amidophenoxide- or catecholate-to-metal π bonding, an interpretation supported by the systematic variation of the MOS values as a function of the degree of competition with the other π-donating groups in the structures. PMID:22260321

  1. Ligand-size and ligand-chain hydrophilicity effects on the relaxometric properties of ultrasmall Gd2O3 nanoparticles

    Science.gov (United States)

    Tegafaw, Tirusew; Xu, Wenlong; Lee, Sang Hyup; Chae, Kwon Seok; Cha, Hyunsil; Chang, Yongmin; Lee, Gang Ho

    2016-06-01

    The relaxometric properties of ultrasmall Gd2O3 nanoparticles coated with various ligands were investigated. These ligands include small diacids with hydrophobic chains, namely, succinic acid (Mw = 118.09 amu), glutaric acid (Mw = 132.12 amu), and terephthalic acid (Mw = 166.13 amu), and large polyethylenimines (PEIs) with hydrophilic chains, namely, PEI-1300 ( M ¯ n = 1300 ) and PEI-10000 ( M ¯ n = 10000 ). Ligand-size and ligand-chain hydrophilicity effects were observed. The longitudinal (r1) and transverse (r2) water proton relaxivities generally decreased with increasing ligand-size (the ligand-size effect). The ligand-size effect was weaker for PEI because its hydrophilic chains allow water molecules to access the nanoparticle (the ligand-chain hydrophilicity effect). This result was explained on the basis of the magnetic dipole interaction between the dipoles of the nanoparticle and water proton. In addition, all samples were found to be non-toxic in cellular cytotoxicity tests.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    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...

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

    Science.gov (United States)

    Hupp, Joseph T.; Mulfort, Karen L.; Snurr, Randall Q.; Bae, Youn-Sang

    2011-01-04

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

  4. Electronic spectra and photophysics of platinum(II) complexes with alpha-diimine ligands - Solid-state effects. I - Monomers and ligand pi dimers

    Science.gov (United States)

    Miskowski, Vincent M.; Houlding, Virginia H.

    1989-01-01

    Two types of emission behavior for Pt(II) complexes containing alpha-diimine ligands have been observed in dilute solution. If the complex also has weak field ligands such as chloride, ligand field (d-d) excited states become the lowest energy excited states. If only strong field ligands are present, a diimine 3(pi-pi/asterisk/) state becomes the lowest. In none of the cases studied did metal-to-ligand charge transfer excited state lie lowest.

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

    Energy Technology Data Exchange (ETDEWEB)

    Prat-Lepesant, M

    2005-06-15

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

  6. Characterization of methacrylate chromatographic monoliths bearing affinity ligands.

    Science.gov (United States)

    Černigoj, Urh; Vidic, Urška; Nemec, Blaž; Gašperšič, Jernej; Vidič, Jana; Lendero Krajnc, Nika; Štrancar, Aleš; Podgornik, Aleš

    2016-09-16

    We investigated effect of immobilization procedure and monolith structure on chromatographic performance of methacrylate monoliths bearing affinity ligands. Monoliths of different pore size and various affinity ligands were prepared and characterized using physical and chromatographic methods. When testing protein A monoliths with different protein A ligand densities, a significant nonlinear effect of ligand density on dynamic binding capacity (DBC) for IgG was obtained and accurately described by Langmuir isotherm curve enabling estimation of protein A utilization as a function of ligand density. Maximal IgG binding capacity was found to be at least 12mg/mL exceeding theoretical monolayer adsorption value of 7.8mg/mL assuming hexagonal packing and IgG hydrodynamic diameter of 11nm. Observed discrepancy was explained by shrinkage of IgG during adsorption on protein A experimentally determined through calculated adsorbed IgG layer thickness of 5.4nm from pressure drop data. For monoliths with different pore size maximal immobilized densities of protein A as well as IgG dynamic capacity linearly correlates with monolith surface area indicating constant ligand utilization. Finally, IgGs toward different plasma proteins were immobilized via the hydrazide coupling chemistry to provide oriented immobilization. DBC was found to be flow independent and was increasing with the size of bound protein. Despite DBC was lower than IgG capacity to immobilized protein A, ligand utilization was higher. PMID:27554023

  7. Database of ligand-induced domain movements in enzymes

    Directory of Open Access Journals (Sweden)

    Hayward Steven

    2009-03-01

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

  8. Serum concentrations of Flt-3 ligand in rheumatic diseases.

    Science.gov (United States)

    Nakamura, Kayo; Nakatsuka, Noriko; Jinnin, Masatoshi; Makino, Takamitsu; Kajihara, Ikko; Makino, Katsunari; Honda, Noritoshi; Inoue, Kuniko; Fukushima, Satoshi; Ihn, Hironobu

    2015-10-01

    Fms-like tyrosine kinase 3 (Flt-3) is a cytokine receptor expressed on the surface of bone-marrow progenitor of hematopoietic cells. Flt-3 ligands are produced by peripheral blood mononuclear cells, and found in various human body fluids. Flt-3 signal is involved in the regulation of vessel formation as well as B cell differentiation, suggesting that Flt-3 signal contributes to the pathogenesis of vascular abnormalities and immune dysregulation in rheumatic diseases. The aim of the present study is to examine serum Flt-3 ligand levels in patients with various rheumatic diseases, and to evaluate the possibility that serum Flt-3 ligand levels can be a useful disease marker. Sera were obtained from 20 dermatomyositis (DM) patients, 36 systemic sclerosis (SSc) patients, 10 systemic lupus erythematosus (SLE) patients, 10 scleroderma spectrum disorder (SSD) patients, 4 mixed connective tissue disease (MCTD) patients, and 12 normal subjects. Flt-3 ligand levels were determined with ELISA. Serum Flt-3 ligand levels were significantly elevated in patients with DM, SSc, SSD and MCTD compared to those in normal subjects. DM patients with elevated Flt-3 ligand levels were accompanied with significantly increased CRP levels and increased frequency of heliotrope rash than those with normal levels. In addition, SSc patients with elevated Flt-3 ligand levels showed significantly reduced frequency of nailfold bleeding. Serum Flt-3 ligand levels can be a marker of cutaneous manifestation in DM and a marker of microangiopathy in SSc. Clarifying the role of Flt-3 ligand in rheumatic diseases may lead to further understanding of these diseases and new therapeutic approaches. PMID:26559027

  9. Ligand-based identification of environmental estrogens

    Energy Technology Data Exchange (ETDEWEB)

    Waller, C.L. [Environmental Protection Agency, Research Triangle Park, NC (United States); Oprea, T.I. [Los Alamos National Lab., NM (United States); Chae, K. [National Institute of Environmental Health Sciences, Research Triangle Park, NC (United States)] [and others

    1996-12-01

    Comparative molecular field analysis (CoMFA), a three-dimensional quantitative structure-activity relationship (3D-QSAR) paradigm, was used to examine the estrogen receptor (ER) binding affinities of a series of structurally diverse natural, synthetic, and environmental chemicals of interest. The CoMFA/3D-QSAR model is statistically robust and internally consistent, and successfully illustrates that the overall steric and electrostatic properties of structurally diverse ligands for the estrogen receptor are both necessary and sufficient to describe the binding affinity. The ability of the model to accurately predict the ER binding affinity of an external test set of molecules suggests that structure-based 3D-QSAR models may be used to supplement the process of endocrine disrupter identification through prioritization of novel compounds for bioassay. The general application of this 3D-QSAR model within a toxicological framework is, at present, limited only by the quantity and quality of biological data for relevant biomarkers of toxicity and hormonal responsiveness. 28 refs., 12 figs., 9 tabs.

  10. Niobium tetrahalide complexes with neutral diphosphine ligands.

    Science.gov (United States)

    Benjamin, Sophie L; Chang, Yao-Pang; Hector, Andrew L; Jura, Marek; Levason, William; Reid, Gillian; Stenning, Gavin

    2016-05-10

    The reactions of NbCl4 with diphosphine ligands o-C6H4(PMe2)2, Me2PCH2CH2PMe2 or Et2PCH2CH2PEt2 in a 1 : 2 molar ratio in MeCN solution produced eight-coordinate [NbCl4(diphosphine)2]. [NbBr4(diphosphine)2] (diphosphine = o-C6H4(PMe2)2 or Me2PCH2CH2PMe2) were made similarly from NbBr4. X-ray crystal structures show that [NbCl4{o-C6H4(PMe2)2}2] has a dodecahedral geometry, but the complexes with dimethylene-backboned diphosphines are distorted square antiprisms. The Nb-P distances and niobium tetrabromide, conveniently made from NbCl4 and BBr3, is a chain polymer with edge-linked NbBr6 octahedra and alternating long and short Nb-Nb distances, the latter ascribed to Nb-Nb bonds. PMID:27094082

  11. Effect of size and conformation of the ligand on asialoglycoprotein receptor-mediated ligand internalization and degradation in rat hepatocytes

    International Nuclear Information System (INIS)

    The rates of internalization and degradation of 125-I-labeled desialylated cyanogen bromide fragment I of orosomucoid (AS-CNBr-I) and its reduced and carboxymethylated derivative (AS-RC-CNBr-I) were compared with those of 125I-labeled asialoorosomucoid (ASOR) in rat hepatocytes. At 30 nM the rates of internalization and degradation of 125I-AS-CNBr-I were greater than those of 125I-ASOR. 125I-AS-RC-CNBr-I also had a lower rate of internalization and degradation. In contrast to 125I-ASOR, when degradation was inhibited by 5 μM colchicine there was a significant intracellular accumulation of the smaller ligands. At 40C the hepatocytes were found to bind the fragmented ligands more than 125I-ASOR. Incubation of the cells with bound ligand at 370 indicated that diacytosis of 125I-ASOR was greater than the smaller ligands. Colchincine markedly enhanced diacytosis of 125I-ASOR. On the other hand, there were marked accumulation of the smaller ligands by colchicine. These results suggest that the rates of internalization, degradation and diacytosis of the ligand are affected by the size and conformation of the ligand through different rates of receptor binding and intracellular transport

  12. HybridDock: A Hybrid Protein-Ligand Docking Protocol Integrating Protein- and Ligand-Based Approaches.

    Science.gov (United States)

    Huang, Sheng-You; Li, Min; Wang, Jianxin; Pan, Yi

    2016-06-27

    Structure-based molecular docking and ligand-based similarity search are two commonly used computational methods in computer-aided drug design. Structure-based docking tries to utilize the structural information on a drug target like protein, and ligand-based screening takes advantage of the information on known ligands for a target. Given their different advantages, it would be desirable to use both protein- and ligand-based approaches in drug discovery when information for both the protein and known ligands is available. Here, we have presented a general hybrid docking protocol, referred to as HybridDock, to utilize both the protein structures and known ligands by combining the molecular docking program MDock and the ligand-based similarity search method SHAFTS, and evaluated our hybrid docking protocol on the CSAR 2013 and 2014 exercises. The results showed that overall our hybrid docking protocol significantly improved the performance in both binding affinity and binding mode predictions, compared to the sole MDock program. The efficacy of the hybrid docking protocol was further confirmed using the combination of DOCK and SHAFTS, suggesting an alternative docking approach for modern drug design/discovery. PMID:26317502

  13. Biomimetic macroporous hydrogels: protein ligand distribution and cell response to the ligand architecture in the scaffold.

    Science.gov (United States)

    Savina, Irina N; Dainiak, Maria; Jungvid, Hans; Mikhalovsky, Sergey V; Galaev, Igor Yu

    2009-01-01

    Macroporous hydrogels (MHs), cryogels, are a new type of biomaterials for tissue engineering that can be produced from any natural or synthetic polymer that forms a gel. Synthetic MHs are rendered bioactive by surface or bulk modifications with extracellular matrix components. In this study, cell response to the architecture of protein ligands, bovine type-I collagen (CG) and human fibrinogen (Fg), immobilised using different methods on poly(2-hydroxyethyl methacrylate) (pHEMA) macroporous hydrogels (MHs) was analysed. Bulk modification was performed by cross-linking cryo-co-polymerisation of HEMA and poly(ethylene glycol)diacrylate (PEGA) in the presence of proteins (CG/pHEMA and Fg/pHEMA MHs). The polymer surface was modified by covalent immobilisation of the proteins to the active epoxy (ep) groups present on pHEMA after hydrogel fabrication (CG-epHEMA and Fg-epHEMA MHs). The concentration of proteins in protein/pHEMA and protein-epHEMA MHs was 80-85 and 130-140 mug/ml hydrogel, respectively. It was demonstrated by immunostaining and confocal laser scanning microscopy that bulk modification resulted in spreading of CG in the polymer matrix and spot-like distribution of Fg. On the contrary, surface modification resulted in spot-like distribution of CG and uniform spreading of Fg, which evenly coated the surface. Proliferation rate of fibroblasts was higher on MHs with even distribution of the ligands, i.e., on Fg-epHEMA and CG/pHEMA. After 30 days of growth, fibroblasts formed several monolayers and deposited extracellular matrix filling the pores of these MHs. The best result in terms of cell proliferation was obtained on Fg-epHEMA. The ligands displayed on surface of these scaffolds were in native conformation, while in bulk-modified CG/pHEMA MHs most of the proteins were buried inside the polymer matrix and were less accessible for interactions with specific antibodies and cells. The method used for MH modification with bioligands strongly affects spatial

  14. Ligand-based reactivity of a platinum bisdithiolene: double diene addition yields a new C2-chiral chelate ligand.

    Science.gov (United States)

    Kerr, Mitchell J; Harrison, Daniel J; Lough, Alan J; Fekl, Ulrich

    2009-10-01

    The reaction of Pt(tfd)(2) [tfd = S(2)C(2)(CF(3))(2)] with excess 2,3-dimethyl-1,3-butadiene initially yields the expected 1:1 adduct, in which the diene has added across two sulfur atoms on separate tfd ligands. However, within 1 day at 50 degrees C, this kinetic product quantitatively converts into a thermodynamic product where two dienes have added to one tfd ligand via unprecedented addition across the dithiolene CS bonds. The new reaction is highly selective for the C(2)-symmetric diastereomer. A new chiral bisthioether chelate ligand has formed in the product, which has been characterized crystallographically. PMID:19634863

  15. Modification of diphenylamine-linked bis(oxazoline)ligands:Tuning of electronic effect and rigidity of ligand skeleton

    Institute of Scientific and Technical Information of China (English)

    LIU Han; LI Wei; DU DaMing

    2009-01-01

    The electronic effect of diphenylamine-linked bis(oxazoline) ligands was tuned through introduction of electron-withdrawing bromo and nitro substituents onto the 4 and 4' position.The variation of the NH bond acidity was determined by the different chemical shifts of NH.The catalytic activity and enantioselectivity of the modified ligands were tested in the asymmetric FriedeI-Crafts alkylation of indole with β-nitrostyrene.The effect of iigand skeleton rigidity was also investigated through the synthesis of iminodibenzyl-linked bis(oxazoline) ligands and evaluation of their catalytic activity in Friedel-Crafts alkylation.

  16. Capacity of Diffusion-based Molecular Communication with Ligand Receptors

    CERN Document Server

    Einolghozati, Arash; Fekri, Faramarz

    2012-01-01

    A diffusion-based molecular communication system has two major components: the diffusion in the medium, and the ligand-reception. Information bits, encoded in the time variations of the concentration of molecules, are conveyed to the receiver front through the molecular diffusion in the medium. The receiver, in turn, measures the concentration of the molecules in its vicinity in order to retrieve the information. This is done via ligand-reception process. In this paper, we develop models to study the constraints imposed by the concentration sensing at the receiver side and derive the maximum rate by which a ligand-receiver can receive information. Therefore, the overall capacity of the diffusion channel with the ligand receptors can be obtained by combining the results presented in this paper with our previous work on the achievable information rate of molecular communication over the diffusion channel.

  17. Structural basis for ligand recognition of incretin receptors

    DEFF Research Database (Denmark)

    Underwood, Christina Rye; Parthier, Christoph; Reedtz-Runge, Steffen

    2010-01-01

    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...... for the treatment of type 2 diabetes. It is well established that the N-terminal extracellular domain (ECD) of incretin receptors is important for ligand binding and ligand specificity, whereas the transmembrane domain is involved in receptor activation. Structures of the ligand-bound ECD of incretin receptors have...... appear to be the main driving force for ligand binding to the ECD of incretin receptors. Obviously, the-still missing-structures of full-length incretin receptors are required to construct a complete picture of receptor function at the molecular level. However, the progress made recently in structural...

  18. Unique advantages of organometallic supporting ligands for uranium complexes

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-05-31

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

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

    Directory of Open Access Journals (Sweden)

    Burkhard König

    2003-05-01

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

  20. Steered molecular dynamics simulations of protein-ligand interactions

    Institute of Scientific and Technical Information of China (English)

    XU; Yechun; SHEN; Jianhua; LUO; Xiaomin; SHEN; Xu; CHEN; Ka

    2004-01-01

    Studies of protein-ligand interactions are helpful to elucidating the mechanisms of ligands, providing clues for rational drug design. The currently developed steered molecular dynamics (SMD) is a complementary approach to experimental techniques in investigating the biochemical processes occurring at microsecond or second time scale, thus SMD may provide dynamical and kinetic processes of ligand-receptor binding and unbinding, which cannot be accessed by the experimental methods. In this article, the methodology of SMD is described, and the applications of SMD simulations for obtaining dynamic insights into protein-ligand interactions are illustrated through two of our own examples. One is associated with the simulations of binding and unbinding processes between huperzine A and acetylcholinesterase, and the other is concerned with the unbinding process of α-APA from HIV-1 reverse transcriptase.

  1. Dysprosium complexes with the tetraphenylporphyrin macrocyclic ligand

    International Nuclear Information System (INIS)

    In this report, the results obtained on the synthesis, characterization and study of the chemical behavior of dysprosium complex with the acetylacetone chelating agent (Hacac) and the tetraphenylporphyrin macrocyclic ligand (H2TFP) are given. Based on the literature but according to our necessities and interest, the appropriate methodology settled down from the synthesis of prime matters until the obtaining and characterization of the products. The acetyl acetonate complex was obtained of mono hydrated dysprosium [Dy(acac)3. H20] and trihydrated [Dy(acac)3 .3 H20], the mono tetra phenyl porphyrinate [Dy(TFP)(acac). 2 ac] the double sandwich of the dysprosium porphyrinate [Dy(TFP)2] and the triple sandwich of the dysprosium porphyrinate [Dy(TFP)3. 2 TCB] (TCB = trichlorobenzene). Its were characterized by their melting points, solubility, IR, UV, TGA and DTA both first and besides the techniques already mentioned for NMR'H, RPE and Magnetic susceptibility the three last complexes. From the spectroscopic point of view, IR and RPE its suggested the existence of a complex of inverse mixed valence [Dy(TFP)2- (TFP) 1-] for the Dy(TFP)2 as a result of the existence of the free radical (TFP' 1- and that it was not in none of the other porphyrin compounds. In the NMR'H spectra of the compounds were not observed signals in the region from 0 to 10 ppm that which shows that the dysprosium complexes in special those of the porphyrin type are highly paramagnetic and its could be used as displacement reagents, creators of images and contrast agents of great utility in these days in studies of NMR, technique today by today used in medical diagnoses. (Author)

  2. Increased CD40 ligand in patients with acute anterior uveitis

    DEFF Research Database (Denmark)

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

    2005-01-01

    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....

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

    KAUST Repository

    Bootharaju, Megalamane Siddaramappa

    2015-05-21

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

  4. Coordination chemistry of poly(thioether)borate ligands

    OpenAIRE

    Riordan, Charles G.

    2010-01-01

    This review traces the development and application of the tris(thioether)borate ligands, tripodal ligands with highly polarizable thioether donors. Areas of emphasis include the basic coordination chemistry of the mid-to-late first row transition metals (Fe, Ni, Co, Cu), and the role of the thioether substituent in directing complex formation, the modeling of zinc thiolate protein active sites, high-spin organo-iron and organo-cobalt chemistry, the preparation of monovalent complexes of Fe, C...

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

    Science.gov (United States)

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

    2016-08-01

    Terpyridine based ligands 1 and 2, decorated with a C8F17 perfluorinated tag, are able to form stable thermoreversible gels in the presence of several d-block metal chloride salts. The gel systems obtained have been characterized by NMR, X-ray diffraction, electron microscopies and Tgel experiments in order to gain insights into the observed different behaviour of the two similar ligands, also in terms of the effect of additional common anionic species. PMID:27460754

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

    OpenAIRE

    Iqbal, M.

    2012-01-01

    The research presented in this thesis deals with the synthesis and evaluation of new potential ligands for the complexation of actinide and lanthanide ions either for their extraction from bulk radioactive waste or their stripping from an extracted organic phase for final processing of the waste. In particular, the aim of the work described here is the development of new ligands with improved separation and extraction efficiency. Separation of actinides (An) and lanthanides (Ln) is a challeng...

  7. Heterobifunctional PEG Ligands for Bioconjugation Reactions on Iron Oxide Nanoparticles

    OpenAIRE

    Maarten Bloemen; Thomas Van Stappen; Pieter Willot; Jeroen Lammertyn; Guy Koeckelberghs; Nick Geukens; Ann Gils; Thierry Verbiest

    2014-01-01

    Ever since iron oxide nanoparticles have been recognized as promising scaffolds for biomedical applications, their surface functionalization has become even more important. We report the synthesis of a novel polyethylene glycol-based ligand that combines multiple advantageous properties for these applications. The ligand is covalently bound to the surface via a siloxane group, while its polyethylene glycol backbone significantly improves the colloidal stability of the particle in complex envi...

  8. Analysis of cell locomotion on ligand gradient substrates.

    Science.gov (United States)

    Sarvestani, Alireza S; Jabbari, Esmaiel

    2009-06-01

    Directional cell motility plays a key role in many biological processes like morphogenesis, inflammation, wound repair, angiogenesis, immune response, and tumor metastasis. Cells respond to the gradient in surface ligand density by directed locomotion towards the direction of higher ligand density. Theoretical models which address the physical basis underlying the regulatory effect of ligand gradient on cell motility are highly desirable. Predictive models not only contribute to a better understanding of biological processes, but they also provide a quantitative interconnection between cell motility and biophysical properties of the extracellular matrix (ECM) for rational design of biomaterials as scaffolds in tissue engineering. In this work, we consider a one-dimensional (1D) continuum viscoelastic model to predict the cell velocity in response to linearly increasing density of surface ligands on a substrate. The cell is considered as a 1D linear viscoelastic object with position dependent elasticity due to the variation in actin network density. The cell-substrate interaction is characterized by a frictional force, controlled by the density of ligand-receptor pairs. The generation of contractile stresses is described in terms of kinetic equations for the reactions between actins, myosins, and guanine nucleotide regulatory proteins. The model predictions show a reasonable agreement with experimentally measured cell speeds, considering biologically relevant values for the model parameters. The model predicts a biphasic relationship between cell speed and slope of gradient as well as a maximum limiting speed after a finite migration time. For a given slope of ligand gradient, the onset of the limiting speed appears at longer times for substrates with lower ligand gradients. The model can be applied to the design of biomaterials as scaffolds for guided tissue regeneration as it predicts an optimum range for the slope of ligand gradient. PMID:19205048

  9. Delivering carbide ligands to sulfide-rich clusters.

    Science.gov (United States)

    Reinholdt, Anders; Herbst, Konrad; Bendix, Jesper

    2016-02-01

    The propensity of the terminal ruthenium carbide Ru(C)Cl2(PCy3)2 (RuC) to form carbide bridges to electron-rich transition metals enables synthetic routes to metal clusters with coexisting carbide and sulfide ligands. Electrochemical experiments show the Ru≡C ligand to exert a relatively large electron-withdrawing effect compared with PPh3, effectively shifting redox potentials.

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

    Science.gov (United States)

    Veenman, Leo; Vainshtein, Alex; Yasin, Nasra; Azrad, Maya; Gavish, Moshe

    2016-01-01

    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. PMID:27271616

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

    Directory of Open Access Journals (Sweden)

    Leo Veenman

    2016-06-01

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

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

    Science.gov (United States)

    Veenman, Leo; Vainshtein, Alex; Yasin, Nasra; Azrad, Maya; Gavish, Moshe

    2016-01-01

    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.

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

    Science.gov (United States)

    Veenman, Leo; Vainshtein, Alex; Yasin, Nasra; Azrad, Maya; Gavish, Moshe

    2016-01-01

    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. PMID:27271616

  14. Serum albumin ligand binding volumes using high pressure denaturation

    International Nuclear Information System (INIS)

    Highlights: ► We use pressure shift assay to study the thermodynamics of decanoate and dodecanoate ligand binding to human serum albumin. ► Pressure shift assay provides information on ligand binding volumes. ► The ligands stabilized human serum albumin against both pressure and temperature denaturation. ► ANS is a strong human serum albumin stabilizer and competes with lipids for the same binding sites. - Abstract: The pressure shift assay (PSA, also termed either PressureFluor or differential pressure fluorimetry) was used to study the thermodynamics of decanoate and dodecanoate lipid binding to human serum albumin (HSA) in the temperature range from 25 °C to 80 °C and the pressure range from 0.1 MPa to 400 MPa. The ligands stabilized HSA against both pressure and temperature denaturation. The P–T phase diagram for HSA bound to saturated fatty acids is shown. Pressure induced HSA denaturation reversibility is demonstrated via either intrinsic tryptophan or extrinsic probe 1,8-anilinonaphthalene sulfonate (ANS) fluorescence. The effect of guanidinium in a PSA was studied. PSA provides information on ligand binding volumes. The volume changes from protein–ligand binding are thermodynamically important and could be used in designing compounds with specific volumetric binding properties.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-10-06

    A series of highly luminescent Tb(III) complexes of para-substituted 2-hydroxyisophthalamide ligands (5LI-IAM-X) has been prepared (X = H, CH{sub 3}, (C=O)NHCH{sub 3}, SO{sub 3}{sup -}, NO{sub 2}, OCH{sub 3}, F, Cl, Br) to probe the effect of substituting the isophthalamide ring on ligand and Tb(III) emission in order to establish a method for predicting the effects of chromophore modification on Tb(III) luminescence. The energies of the ligand singlet and triplet excited states are found to increase linearly with the {pi}-withdrawing ability of the substituent. The experimental results are supported by time-dependent density functional theory (TD-DFT) calculations performed on model systems, which predict ligand singlet and triplet energies within {approx}5% of the experimental values. The quantum yield ({Phi}) values of the Tb(III) complex increases with the triplet energy of the ligand, which is in part due to the decreased non-radiative deactivation caused by thermal repopulation of the triplet. Together, the experimental and theoretical results serve as a predictive tool that can be used to guide the synthesis of ligands used to sensitize lanthanide luminescence.

  16. Porphyrin-based design of bioinspired multitarget quadruplex ligands.

    Science.gov (United States)

    Laguerre, Aurélien; Desbois, Nicolas; Stefan, Loic; Richard, Philippe; Gros, Claude P; Monchaud, David

    2014-09-01

    Secondary nucleic acid structures, such as DNA and RNA quadruplexes, are potential targets for cancer therapies. Ligands that interact with these targets could thus find application as anticancer agents. Synthetic G-quartets have recently found numerous applications, including use as bioinspired G-quadruplex ligands. Herein, the design, synthesis and preliminary biophysical evaluation of a new prototype multitarget G-quadruplex ligand, (PNA)PorphySQ, are reported, where peptidic nucleic acid guanine ((PNA)G) was incorporated in the porphyrin-templated synthetic G-quartet (PorphySQ). Using fluorescence resonance energy transfer (FRET)-melting experiments, PorphySQ was shown to possess enhanced quadruplex-interacting properties thanks to the presence of four positively charged (PNA)G residues that improve its electrostatic interactions with the binding site of both DNA and RNA quadruplexes (i.e., their negatively charged and accessible G-quartets), thereby making (PNA)PorphySQ an interesting prototype of a multitarget ligand. Both the chemical stability and water solubility of (PNA)PorphySQ are improved over the non-PNA derivative (PorphySQ), which are desirable properties for drug development, and while improvements remain to be made, this ligand is a promising lead for the further development of multitarget G-quadruplex ligands. PMID:24678052

  17. Agonists and Antagonists of TGF-β Family Ligands.

    Science.gov (United States)

    Chang, Chenbei

    2016-08-01

    The discovery of the transforming growth factor β (TGF-β) family ligands and the realization that their bioactivities need to be tightly controlled temporally and spatially led to intensive research that has identified a multitude of extracellular modulators of TGF-β family ligands, uncovered their functions in developmental and pathophysiological processes, defined the mechanisms of their activities, and explored potential modulator-based therapeutic applications in treating human diseases. These studies revealed a diverse repertoire of extracellular and membrane-associated molecules that are capable of modulating TGF-β family signals via control of ligand availability, processing, ligand-receptor interaction, and receptor activation. These molecules include not only soluble ligand-binding proteins that were conventionally considered as agonists and antagonists of TGF-β family of growth factors, but also extracellular matrix (ECM) proteins and proteoglycans that can serve as "sink" and control storage and release of both the TGF-β family ligands and their regulators. This extensive network of soluble and ECM modulators helps to ensure dynamic and cell-specific control of TGF-β family signals. This article reviews our knowledge of extracellular modulation of TGF-β growth factors by diverse proteins and their molecular mechanisms to regulate TGF-β family signaling.

  18. Ligands turning around in the midst of protein conformers: the origin of ligand-protein mating. A NMR view.

    Science.gov (United States)

    Pertinhez, T A; Spisni, A

    2011-01-01

    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. PMID:20939791

  19. A Ferrocene-Based Catecholamide Ligand: the Consequences of Ligand Swivel for Directed Supramolecular Self-Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Mugridge, Jeffrey; Fiedler, Dorothea; Raymond, Kenneth

    2010-02-04

    A ferrocene-based biscatecholamide ligand was prepared and investigated for the formation of metal-ligand supramolecular assemblies with different metals. Reaction with Ge(IV) resulted in the formation of a variety of Ge{sub n}L{sub m} coordination complexes, including [Ge{sub 2}L{sub 3}]{sup 4-} and [Ge{sub 2}L{sub 2}({mu}-OMe){sub 2}]{sup 2-}. The ligand's ability to swivel about the ferrocenyl linker and adopt different conformations accounts for formation of many different Ge{sub n}L{sub m} species. This study demonstrates why conformational ligand rigidity is essential in the rational design and directed self-assembly of supramolecular complexes.

  20. electronic Ligand Builder and Optimisation Workbench (eLBOW): A tool for ligand coordinate and restraint generation

    Energy Technology Data Exchange (ETDEWEB)

    Moriarty, Nigel; Grosse-Kunstleve, Ralf; Adams, Paul

    2009-07-01

    The electronic Ligand Builder and Optimisation Workbench (eLBOW) is a program module of the PHENIX suite of computational crystallographic software. It's designed to be a flexible procedure using simple and fast quantum chemical techniques to provide chemically accurate information for novel and known ligands alike. A variety of input formats and options allow for the attainment of a number of diverse goals including geometry optimisation and generation of restraints.

  1. Integration of screening and identifying ligand(s) from medicinal plant extracts based on target recognition by using NMR spectroscopy

    OpenAIRE

    sprotocols

    2015-01-01

    Authors: Yalin Tang, Qian Shang, Junfeng Xiang, Qianfan Yang, Qiuju Zhou, Lin Li, Hong Zhang, Qian Li, Hongxia Sun, Aijiao Guan, Wei Jiang & Wei Gai ### Abstract This protocol presents the screening of ligand(s) from medicinal plant extracts based on target recognition by using NMR spectroscopy. A detailed description of sample preparation and analysis process is provided. NMR spectroscopies described here are 1H NMR, diffusion-ordered spectroscopy (DOSY), relaxation-edited NMR, ...

  2. A thermal responsive affinity ligand for precipitation of sialylated proteins

    Directory of Open Access Journals (Sweden)

    Lindsay Arnold

    2016-01-01

    Full Text Available We report here the development of a thermal responsive affinity ligand specific to sialic acid, sialic acid containing oligosaccharides, glycoproteins, and other sialylated glycoconjugates. The ligand is a fusion protein of 40 repeats of pentapeptide of an elastin like polymer (ELP and the 21 kD sialic acid binding domain of a Vibrio cholera neuraminidase (VCNA. For cost-effective synthesis, the fusion protein was targeted to the periplasmic space of an E. coli lpp deletion mutant, resulting in its secretion to the growth medium. A pre-induction heat-shock step at 42 ˚C for 20 minutes was necessary to achieve high level expression of the ligand. Under optimized induction condition (18 ˚C, 0.1 mM IPTG and 48 hours of post-induction cultivation, the ligand was produced to about 100 mg/L. The ligand exhibited a transition temperature of 52 ˚C, which could be depressed to 37 ˚C with the addition of 0.5 M NaCl. Using fetuin as a model sialylated protein, the ligand was applied in an affinity precipitation process to illustrate its potential application in glycoprotein isolation. The ligand captured 100% fetuin from an aqueous solution when the molar ratio of ligand to fetuin was 10 to 1, which was lower than the expected for full titration of sialic acid on the glycoprotein by the lectin. Elution of fetuin from ligand was achieved with PBS buffer containing 2 mM sialic acid. To evaluate how protein and other contaminants influence the recovery of sialylated proteins, CHO medium was spiked into the fetuin solution. The predominant protein species in CHO medium was found to be albumin. Although its removal of over 94% was evident, purified fetuin contained some albumin due to its over-abundance. Additional experiments with albumin contaminant of varying concentrations showed that below 1 mg/L, albumin had no impact on the affinity precipitation, whereas above 10 mg/L, some albumin was co-purified with fetuin. However, even at 50 mg/ml, fetuin

  3. Biotechnological Fluorescent Ligands of the Bradykinin B1 Receptor: Protein Ligands for a Peptide Receptor.

    Directory of Open Access Journals (Sweden)

    Xavier Charest-Morin

    Full Text Available The bradykinin (BK B1 receptor (B1R is a peculiar G protein coupled receptor that is strongly regulated to the point of being inducible in immunopathology. Limited clinical evidence suggests that its expression in peripheral blood mononuclear cells is a biomarker of active inflammatory states. In an effort to develop a novel imaging/diagnostic tool, we report the rational design and testing of a fusion protein that is a ligand of the human B1R but not likely to label peptidases. This ligand is composed of a fluorescent protein (FP (enhanced green FP [EGFP] or mCherry prolonged at its N-terminus by a spacer peptide and a classical peptide agonist or antagonist (des-Arg9-BK, [Leu8]des-Arg9-BK, respectively. The design of the spacer-ligand joint peptide was validated by a competition assay for [3H]Lys-des-Arg9-BK binding to the human B1R applied to 4 synthetic peptides of 18 or 19 residues. The labeling of B1R-expressing cells with EGFP or mCherry fused with 7 of such peptides was performed in parallel (microscopy. Both assays indicated that the best design was FP-(Asn-Glyn-Lys-des-Arg9-BK; n = 15 was superior to n = 5, suggesting benefits from minimizing steric hindrance between the FP and the receptor. Cell labeling concerned mostly plasma membranes and was inhibited by a B1R antagonist. EGFP-(Asn-Gly15-Lys-des-Arg9-BK competed for the binding of [3H]Lys-des-Arg9-BK to human recombinant B1R, being only 10-fold less potent than the unlabeled form of Lys-des-Arg9-BK to do so. The fusion protein did not label HEK 293a cells expressing recombinant human BK B2 receptors or angiotensin converting enzyme. This study identifies a modular C-terminal sequence that can be adapted to protein cargoes, conferring high affinity for the BK B1R, with possible applications in diagnostic cytofluorometry, histology and drug delivery (e.g., in oncology.

  4. Synthesis and enzymatic cleavage of dual-ligand quantum dots

    Energy Technology Data Exchange (ETDEWEB)

    Sewell, Sarah L. [Department of Biomedical Engineering, Vanderbilt University, Nashville, TN (United States); Giorgio, Todd D., E-mail: todd.d.giorgio@vanderbilt.edu [Department of Biomedical Engineering, Vanderbilt University, Nashville, TN (United States); Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN (United States)

    2009-05-05

    Site directed therapy promises to minimize treatment-limiting systemic effects associated with cytotoxic agents that have no specificity for pathologic tissues. One general strategy is to target cell surface receptors uniquely presented on particular tissues. Highly specific in vivo targeting of an emerging neoplasm through a single molecular recognition mechanism has not generally been successful. Nonspecific binding and specific binding to non-target cells compromise the therapeutic index of small molecule, ubiquitous cancer targeting ligands. In this work, we have designed and fabricated a nanoparticle (NP) construct that could potentially overcome the current limitations of targeted in vivo delivery. Quantum dots (QDs) were functionalized with a poly(ethylene glycol) (PEG) modified to enable specific cleavage by matrix metalloprotease-7 (MMP-7). The QDs were further functionalized with folic acid, a ligand for a cell surface receptor that is overexpressed in many tumors, but also expressed in some normal tissues. The nanomolecular construct is designed so that the PEG initially conceals the folate ligand and construct binding to cells is inhibited. MMP-7 activated peptide cleavage and subsequent unmasking of the folate ligand occurs only near tumor tissue, resulting in a proximity activated (PA) targeting system. QDs functionalized with both the MMP-7 cleavable substrate and folic acid were successfully synthesized and characterized. The proteolytic capability of the dual ligand QD construct was quantitatively assessed by fluorometric analysis and compared to a QD construct functionalized with only the PA ligand. The dual ligand PA nanoparticles studied here exhibit significant susceptibility to cleavage by MMP-7 at physiologically relevant conditions. The capacity to autonomously convert a biopassivated nanostructure to a tissue-specific targeted delivery agent in vivo represents a paradigm change for site-directed therapies.

  5. Synthesis and enzymatic cleavage of dual-ligand quantum dots

    International Nuclear Information System (INIS)

    Site directed therapy promises to minimize treatment-limiting systemic effects associated with cytotoxic agents that have no specificity for pathologic tissues. One general strategy is to target cell surface receptors uniquely presented on particular tissues. Highly specific in vivo targeting of an emerging neoplasm through a single molecular recognition mechanism has not generally been successful. Nonspecific binding and specific binding to non-target cells compromise the therapeutic index of small molecule, ubiquitous cancer targeting ligands. In this work, we have designed and fabricated a nanoparticle (NP) construct that could potentially overcome the current limitations of targeted in vivo delivery. Quantum dots (QDs) were functionalized with a poly(ethylene glycol) (PEG) modified to enable specific cleavage by matrix metalloprotease-7 (MMP-7). The QDs were further functionalized with folic acid, a ligand for a cell surface receptor that is overexpressed in many tumors, but also expressed in some normal tissues. The nanomolecular construct is designed so that the PEG initially conceals the folate ligand and construct binding to cells is inhibited. MMP-7 activated peptide cleavage and subsequent unmasking of the folate ligand occurs only near tumor tissue, resulting in a proximity activated (PA) targeting system. QDs functionalized with both the MMP-7 cleavable substrate and folic acid were successfully synthesized and characterized. The proteolytic capability of the dual ligand QD construct was quantitatively assessed by fluorometric analysis and compared to a QD construct functionalized with only the PA ligand. The dual ligand PA nanoparticles studied here exhibit significant susceptibility to cleavage by MMP-7 at physiologically relevant conditions. The capacity to autonomously convert a biopassivated nanostructure to a tissue-specific targeted delivery agent in vivo represents a paradigm change for site-directed therapies.

  6. Microassay for measurement of binding of radiolabelled ligands to cell surface molecules

    International Nuclear Information System (INIS)

    An improved technique for measuring the binding of radiolabelled ligands to cell surface molecules has been developed by modification of a procedure using centrifugation through a water-immiscible oil to separate free and cell-bound ligand. It maximises the percentage of ligand bound since cell-bound and free ligand can be separated easily and reproducibly even when very small reaction volumes are used. This permits low levels of ligand radiolabelling and relatively low numbers of cells to be used

  7. Coarse-grained molecular dynamics simulations of protein-ligand binding.

    Science.gov (United States)

    Negami, Tatsuki; Shimizu, Kentaro; Terada, Tohru

    2014-09-30

    Coarse-grained molecular dynamics (CGMD) simulations with the MARTINI force field were performed to reproduce the protein-ligand binding processes. We chose two protein-ligand systems, the levansucrase-sugar (glucose or sucrose), and LinB-1,2-dichloroethane systems, as target systems that differ in terms of the size and shape of the ligand-binding pocket and the physicochemical properties of the pocket and the ligand. Spatial distributions of the Coarse-grained (CG) ligand molecules revealed potential ligand-binding sites on the protein surfaces other than the real ligand-binding sites. The ligands bound most strongly to the real ligand-binding sites. The binding and unbinding rate constants obtained from the CGMD simulation of the levansucrase-sucrose system were approximately 10 times greater than the experimental values; this is mainly due to faster diffusion of the CG ligand in the CG water model. We could obtain dissociation constants close to the experimental values for both systems. Analysis of the ligand fluxes demonstrated that the CG ligand molecules entered the ligand-binding pockets through specific pathways. The ligands tended to move through grooves on the protein surface. Thus, the CGMD simulations produced reasonable results for the two different systems overall and are useful for studying the protein-ligand binding processes.

  8. Aluminum complexes of the redox-active [ONO] pincer ligand.

    Science.gov (United States)

    Szigethy, Géza; Heyduk, Alan F

    2012-07-14

    A series of aluminum complexes containing the tridentate, redox-active ligand bis(3,5-di-tert-butyl-2-phenol)amine ([ONO]H(3)) in three different oxidation states were synthesized. The aluminum halide salts AlCl(3) and AlBr(3) were reacted with the doubly deprotonated form of the ligand to afford five-coordinate [ONHO(cat)]AlX(solv) complexes (1a, X = Cl, solv = OEt(2); 1b, X = Br, solv = THF), each having a trigonal bipyramidal coordination geometry at the aluminum and containing the [ONHO(cat)](2-) ligand with a protonated, sp(3)-hybridized nitrogen donor. The [ONO] ligand platform may also be added to aluminum through the use of the oxidized ligand salt [ONO(q)]K, which was reacted with AlCl(3) in the presence of either diphenylacetylacetonate (acacPh(2)(-)) or 8-oxyquinoline (quinO(-)) to afford [ONO(q)]Al(acacPh(2))Cl (2) or [ONO(q)]Al(quinO)Cl (3), respectively, with well-defined [ONO(q)](-) ligands. Quinonate complexes 2 and 3 were reduced by one electron to afford the corresponding complexes K{[ONO(sq)]Al(acacPh(2))(py)} (4) and K{[ONO(sq)]Al(quinO)(py)} (5), respectively, containing well-defined [ONO(sq)](2-) ligands. The addition of tetrachloro-1,2-quinone to 1a in the presence of pyridine resulted in the expulsion of HCl and the formation of an aluminum complex with two different redox active ligands, [ONO]Al(o-O(2)C(6)Cl(4))(py) (6). Similar results were obtained when 1a was reacted with 9,10-phenanthrenequinone to afford [ONO]Al(o-O(2)C(14)H(8))(py) (7) or with pyrene-4,5-dione to afford [ONO]Al(o-O(2)C(16)H(8))(py) (8). Structural, spectroscopic and preliminary magnetic measurements on 6-8 suggest ligand non-innocent redox behavior in these complexes. PMID:22669327

  9. Ligand Migration and Binding in Myoglobin Mutant L29W

    Science.gov (United States)

    Nienhaus, G. Ulrich; Waschipky, Robert; Nienhaus, Karin; Minkow, Oleksandr; Ostermann, Andreas; Parak, Fritz G.

    2001-09-01

    Myoglobin, a small globular heme protein that binds gaseous ligands such as O2, CO, and NO reversibly at the heme iron, has for many years been a paradigm for studying the effects of structure and dynamics on protein reactions. Time-resolved spectroscopic measurements after photodissociation of the ligand reveal a complex ligand binding reaction with multiple kinetic intermediates, resulting from protein relaxation and movements of the ligand within the protein. To observe structural changes induced by ligand dissociation, we have investigated carbonmonoxy myoglobin (MbCO) mutant L29W using time-resolved infrared spectroscopy in combination with x-ray crystallography. The presence of two distinct infrared stretch bands of the bound CO, AI at 1945 cm-1 and AII at 1955 cm-1, implies that L29W MbCO assumes two different conformations at neutral pH. Low-temperature flash photolysis experiments with monitoring of the absorption changes in the individual CO lines reveal markedly different rebinding properties. While recombination in AII is conceptually simple and well described by a two-state transition involving a distribution of enthalpy barriers, recombination in AI is more complicated: Besides a fast kinetic component, a second, slower kinetic component appears; its population grows with increasing temperature. X-ray crystallography of crystals illuminated below 180 K to photodissociate the CO reveals that the slow component arises from ligands that have migrated from their initial docking site to a remote site within the distal heme pocket. This process occurs in an essentially immobilized, frozen protein. Subsequently, ligands rebind by thermal activation over a barrier that is much higher than the barrier for recombination from the initial docking site. Upon photodissociation above 180 K, ligands escape from the distal pocket, aided by protein fluctuations that transiently open exit channels. The x-ray structure shows a large proportion of ligands in a cavity on

  10. Cloud computing for protein-ligand binding site comparison.

    Science.gov (United States)

    Hung, Che-Lun; Hua, Guan-Jie

    2013-01-01

    The proteome-wide analysis of protein-ligand binding sites and their interactions with ligands is important in structure-based drug design and in understanding ligand cross reactivity and toxicity. The well-known and commonly used software, SMAP, has been designed for 3D ligand binding site comparison and similarity searching of a structural proteome. SMAP can also predict drug side effects and reassign existing drugs to new indications. However, the computing scale of SMAP is limited. We have developed a high availability, high performance system that expands the comparison scale of SMAP. This cloud computing service, called Cloud-PLBS, combines the SMAP and Hadoop frameworks and is deployed on a virtual cloud computing platform. To handle the vast amount of experimental data on protein-ligand binding site pairs, Cloud-PLBS exploits the MapReduce paradigm as a management and parallelizing tool. Cloud-PLBS provides a web portal and scalability through which biologists can address a wide range of computer-intensive questions in biology and drug discovery.

  11. Kinetics of Receptor-Ligand Interactions in Immune Responses

    Institute of Scientific and Technical Information of China (English)

    Mian Long; Shouqin Lü; Ganyun Sun

    2006-01-01

    Receptor-ligand interactions in blood flow are crucial to initiate the biological processes as inflammatory cascade,platelet thrombosis, as well as tumor metastasis. To mediate cell adhesions, the interacting receptors and ligands must be anchored onto two apposing surfaces of two cells or a cell and a substratum, i.e., the two-dimensional (2D) binding, which is different from the binding of a soluble ligand in fluid phase to a receptor, i.e., three-dimensional (3D) binding. While numerous works have been focused on 3D kinetics of receptor-ligand interactions in immune systems, 2D kinetics and its regulations have less been understood, since no theoretical framework and experimental assays have been established until 1993. Not only does the molecular structure dominate 2D binding kinetics, but the shear force in blood flow also regulates cell adhesions mediated by interacting receptors and ligands. Here we provided the overview of current progresses in 2D bindings and regulations. Relevant issues of theoretical frameworks, experimental measurements, kinetic rates and binding affinities, and force regulations,were discussed.

  12. Cloud computing for protein-ligand binding site comparison.

    Science.gov (United States)

    Hung, Che-Lun; Hua, Guan-Jie

    2013-01-01

    The proteome-wide analysis of protein-ligand binding sites and their interactions with ligands is important in structure-based drug design and in understanding ligand cross reactivity and toxicity. The well-known and commonly used software, SMAP, has been designed for 3D ligand binding site comparison and similarity searching of a structural proteome. SMAP can also predict drug side effects and reassign existing drugs to new indications. However, the computing scale of SMAP is limited. We have developed a high availability, high performance system that expands the comparison scale of SMAP. This cloud computing service, called Cloud-PLBS, combines the SMAP and Hadoop frameworks and is deployed on a virtual cloud computing platform. To handle the vast amount of experimental data on protein-ligand binding site pairs, Cloud-PLBS exploits the MapReduce paradigm as a management and parallelizing tool. Cloud-PLBS provides a web portal and scalability through which biologists can address a wide range of computer-intensive questions in biology and drug discovery. PMID:23762824

  13. Predicting protein ligand binding motions with the conformation explorer

    Directory of Open Access Journals (Sweden)

    Flores Samuel C

    2011-10-01

    Full Text Available Abstract Background Knowledge of the structure of proteins bound to known or potential ligands is crucial for biological understanding and drug design. Often the 3D structure of the protein is available in some conformation, but binding the ligand of interest may involve a large scale conformational change which is difficult to predict with existing methods. Results We describe how to generate ligand binding conformations of proteins that move by hinge bending, the largest class of motions. First, we predict the location of the hinge between domains. Second, we apply an Euler rotation to one of the domains about the hinge point. Third, we compute a short-time dynamical trajectory using Molecular Dynamics to equilibrate the protein and ligand and correct unnatural atomic positions. Fourth, we score the generated structures using a novel fitness function which favors closed or holo structures. By iterating the second through fourth steps we systematically minimize the fitness function, thus predicting the conformational change required for small ligand binding for five well studied proteins. Conclusions We demonstrate that the method in most cases successfully predicts the holo conformation given only an apo structure.

  14. NKG2D ligands mediate immunosurveillance of senescent cells.

    Science.gov (United States)

    Sagiv, Adi; Burton, Dominick G A; Moshayev, Zhana; Vadai, Ezra; Wensveen, Felix; Ben-Dor, Shifra; Golani, Ofra; Polic, Bojan; Krizhanovsky, Valery

    2016-02-01

    Cellular senescence is a stress response mechanism that limits tumorigenesis and tissue damage. Induction of cellular senescence commonly coincides with an immunogenic phenotype that promotes self-elimination by components of the immune system, thereby facilitating tumor suppression and limiting excess fibrosis during wound repair. The mechanisms by which senescent cells regulate their immune surveillance are not completely understood. Here we show that ligands of an activating Natural Killer (NK) cell receptor (NKG2D), MICA and ULBP2 are consistently up-regulated following induction of replicative senescence, oncogene-induced senescence and DNA damage - induced senescence. MICA and ULBP2 proteins are necessary for efficient NK-mediated cytotoxicity towards senescent fibroblasts. The mechanisms regulating the initial expression of NKG2D ligands in senescent cells are dependent on a DNA damage response, whilst continuous expression of these ligands is regulated by the ERK signaling pathway. In liver fibrosis, the accumulation of senescent activated stellate cells is increased in mice lacking NKG2D receptor leading to increased fibrosis. Overall, our results provide new insights into the mechanisms regulating the expression of immune ligands in senescent cells and reveal the importance of NKG2D receptor-ligand interaction in protecting against liver fibrosis. PMID:26878797

  15. Oxamato-based dicopper(II) metallacyclophanes as prototypes of magnetic devices for molecular spintronics : A joint experimental and computational study

    OpenAIRE

    Castellano Sanz, María

    2013-01-01

    The work presented in this thesis constitutes a successful extension of our group’s research on the chemistry of dinuclear copper(II) metallacyclic complexes with dinucleating aromatic dioxamato ligands containing potential redox- and photoactive, extended -conjugated aromatic spacers. Using simple dicopper(II) metallacyclophanes as dynamic multifunctional magnetic systems to perform specific and selective tasks under the control of an external stimulus that switches “ON” and “OFF” their ele...

  16. Analytical developments for screening of lanthanides/ligands interactions

    International Nuclear Information System (INIS)

    This work investigates the potential of hyphenated capillary electrophoresis and inductively coupled mass spectrometry to classify different ligands according to their europium binding affinity in a hydro-organic medium. On the one hand, this method enables to evaluate the affinity of phosphorus-containing ligands in less than two hours and using less than 15 ng of ligand. On the other hand, complexation constants could be determined. The results are in excellent agreement with the values obtained by spectrophotometric titrations.Moreover, a library of copolymers for solid/liquid extraction of europium is investigated. The extraction protocol enables to classify copolymers according to their europium affinity in a hydro-organic medium. This screening requires 60 mg of copolymers. For the most promising recognition properties and selectivity La3+/Eu3+/Lu3+ are evaluated. (author)

  17. Ligand Binding Thermodynamics in Drug Discovery: Still a Hot Tip?

    Science.gov (United States)

    Geschwindner, Stefan; Ulander, Johan; Johansson, Patrik

    2015-08-27

    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.

  18. Coordination chemistry of N-heterocyclic nitrenium-based ligands.

    Science.gov (United States)

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

    2015-05-01

    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.

  19. Memetic algorithms for ligand expulsion from protein cavities

    CERN Document Server

    Rydzewski, Jakub

    2015-01-01

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

  20. Lanthanide and actinide complexation studies with tetradentate 'N' donor ligands

    International Nuclear Information System (INIS)

    Because of their similar charge and chemical behaviour separation of trivalent actinides and lanthanides is an important and challenging task in nuclear fuel cycle. Soft (S,N) donor ligands show selectivity towards the trivalent actinides over the lanthanides. Out of various 'N' donor ligands studied, bis(1,2,4)triazinyl bipyridine (BTBP) and bis(1,2,4)triazinyl phenanthroline (BTPhen) were found to be most promising. In order to understand the separation behaviour of these ligands, their complexation studies with these 'f' block elements are essential. In the present work, complexation studies of various lanthanide ions (La3+, Eu3+ and Er3+) was studied with ethyl derivatives of BTBP (C2BTBP) and BTBPhen (C2BTPhen) and pentyl derivative of BTBP (C5BTBP) in acetonitrile medium using UV-Vis spectrophotometry, fluorescence spectroscopy and solution calorimetry. Computational studies were also carried out to understand the experimental results

  1. Protecting Ligands Enhance Selective Targeting of Multivalent Nanoparticles

    CERN Document Server

    Angioletti-Uberti, Stefano

    2016-01-01

    Nanoparticles functionalized with multiple ligands can be programmed to bind biological targets, e.g. cells, depending on the receptors they express, providing a general platform for the development of different technologies, from selective drug-delivery to biosensing. In order to be highly selective ligands should exclusively bind to specific targeted receptors, since formation of bonds with other, untargeted ones would lead to non-specific binding and potentially harmful behaviour. This poses a particular problem for multivalent nanoparticles, because even very weak bonds can collectively lead to strong binding. A statistical mechanical model is presented here to describe the extent to which bond strength and nanoparticle valency can induce non-selective adsorption. The same model is used to describe a possible solution: functionalization of the nanoparticles with "protective" receptors. The latter compete with cell receptors for the targeting ligands, and can be optimized to strongly reduce the effect of u...

  2. Chiroptical activity in colloidal quantum dots coated with achiral ligands.

    Science.gov (United States)

    Melnikau, Dzmitry; Savateeva, Diana; Gaponik, Nikolai; Govorov, Alexander O; Rakovich, Yury P

    2016-01-25

    We studied the chiroptical properties of colloidal solution of CdSe and CdSe/ZnS quantum dots (QDs) with a cubic lattice structure which were initially prepared without use of any chiral molecules and coated with achiral ligands. We demonstrate circular dichroism (CD) activity around first and second excitonic transition of these CdSe based nanocrystals. We consider that this chiroptical activity is caused by imbalance in racemic mixtures of QDs between the left and right handed nanoparticles, which appears as a result of the formation of various defects or incorporation of impurities into crystallographic structure during their synthesis. We demonstrate that optical activity of colloidal solution of CdSe QDs with achiral ligands weakly depends on the QDs size and number of ZnS monolayers, but does not depend on the nature of achiral ligands or polarity of the solution. PMID:26832599

  3. Mononuclear and Oligonuclear Manganese Complexes with Organic Multidentate Ligands

    Science.gov (United States)

    Mikuriya, Masahiro

    The crystal structures of manganese complexes with tridentate, tetradentate, pentadentate, hexadentate, and dodecadentate ligands with oxygen and nitrogen donors are described. Reactions of these ligands with manganese salts afforded mononuclear (MnII, MnIII, and MnIV), dinuclear (MnII2, MnIII2, and MnIIMnIII), trinuclear (MnIII3), and tetranuclear (MnII2MnIII2 and MnIII4) complexes. As for MnII complexes, octahedral, trigonal prismatic, capped trigonal prismatic, and square antiprismatic geometries were found depending on the combination of the organic and anionic ligands. In the case of MnIII complexes, the Jahn-Teller distortions due to the high-spin d4 electronic configuration were observed as elongated or compressed octahedral geometries. An octahedral geometry was confirmed for the Mn (IV) complexes.

  4. Heterobifunctional PEG ligands for bioconjugation reactions on iron oxide nanoparticles.

    Directory of Open Access Journals (Sweden)

    Maarten Bloemen

    Full Text Available Ever since iron oxide nanoparticles have been recognized as promising scaffolds for biomedical applications, their surface functionalization has become even more important. We report the synthesis of a novel polyethylene glycol-based ligand that combines multiple advantageous properties for these applications. The ligand is covalently bound to the surface via a siloxane group, while its polyethylene glycol backbone significantly improves the colloidal stability of the particle in complex environments. End-capping the molecule with a carboxylic acid introduces a variety of coupling chemistry possibilities. In this study an antibody targeting plasminogen activator inhibitor-1 was coupled to the surface and its presence and binding activity was assessed by enzyme-linked immunosorbent assay and surface plasmon resonance experiments. The results indicate that the ligand has high potential towards biomedical applications where colloidal stability and advanced functionality is crucial.

  5. Advances Towards The Discovery of GPR55 Ligands.

    Science.gov (United States)

    Morales, Paula; Jagerovic, Nadine

    2016-01-01

    The G-protein-coupled receptor 55 (GPR55) was identified in 1999. It was proposed as a novel member of the endocannabinoid system due to the fact that some endogenous, plant-derived and synthetic cannabinoid ligands act on GPR55. However, the complexity of the cellular downstream signaling pathways related to GPR55 activation delayed the discovery of selective GPR55 ligands. It was only a few years ago that the high throughput screening of libraries of pharmaceutical companies and governmental organizations allowed to identify selective GPR55 agonists and antagonists. Since then, several GPR55 modulator scaffolds have been reported. The relevance of GPR55 has been explored in diverse physiological and pathological processes revealing its role in inflammation, neuropathic pain, bone physiology, diabetes and cancer. Considering GPR55 as a new promising therapeutic target, there is a clear need for new selective and potent GPR55 modulators. This review will address a current structural update of GPR55 ligands.

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

    Energy Technology Data Exchange (ETDEWEB)

    Krishnan, V V

    2005-04-26

    NMR based methods to screen for high-affinity ligands have become an indispensable tool for designing rationalized drugs, as these offer a combination of good experimental design of the screening process and data interpretation methods, which together provide unprecedented information on the complex nature of protein-ligand interactions. These methods rely on measuring direct changes in the spectral parameters, that are often simpler than the complex experimental procedures used to study structure and dynamics of proteins. The goal of this review article is to provide the basic details of NMR based ligand-screening methods, with particular focus on the saturation transfer difference (STD) experiment. In addition, we provide an overview of other NMR experimental methods and a practical guide on how to go about designing and implementing them.

  7. Aryl hydrocarbon receptor ligands in cancer: friend and foe.

    Science.gov (United States)

    Murray, Iain A; Patterson, Andrew D; Perdew, Gary H

    2014-12-01

    The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that is best known for mediating the toxicity and tumour-promoting properties of the carcinogen 2,3,7,8-tetrachlorodibenzo-p-dioxin, commonly referred to as ‘dioxin’. AHR influences the major stages of tumorigenesis — initiation, promotion, progression and metastasis — and physiologically relevant AHR ligands are often formed during disease states or during heightened innate and adaptive immune responses. Interestingly, ligand specificity and affinity vary between rodents and humans. Studies of aggressive tumours and tumour cell lines show increased levels of AHR and constitutive localization of this receptor in the nucleus. This suggests that the AHR is chronically activated in tumours, thus facilitating tumour progression. This Review discusses the role of AHR in tumorigenesis and the potential for therapeutic modulation of its activity in tumours. PMID:25568920

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

    DEFF Research Database (Denmark)

    Mollerup, Jørgen

    2007-01-01

    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...... 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...... 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....

  9. Secondary ligand-directed assembly of Co(II) coordination polymers based on a pyridine carboxylate ligand

    Science.gov (United States)

    Cao, Ke-Li; Zhang, Yi-Ping; Cai, Yi-Ni; Xu, Xiao-Wei; Feng, Yun-Long

    2014-07-01

    To investigate the influence of hydrogen bonds and secondary ligands on the structures and properties of the resulting frameworks, five new Co(II) compounds have been synthesized by the reactions of Co(II) salts and 3,5-bis(pyridin-4-ylmethoxy)benzoic acid (HL) with four rationally selected dicarboxylic acid ligands. Without secondary ligand, we got one compound [CoL2(H2O)2]n·2nH2O (1), which possesses a 1D chain structure. In the presence of ancillary ligands, namely, 1,3-adamantanedicarboxylic acid (H2adbc), terephthalic acid (H2tpa), thiophene-2,5-dicarboxylic acid (H2tdc) and 1,4-benzenedithioacetic acid (H2bdtc), four 3D structures [Co2L2(adbc)]n·nH2O (2), [Co2L2(tpa)]n (3), [Co2L2(tdc)]n (4), [Co2L2(bdtc)(H2O)]n (5) were obtained, respectively. It can be observed from the architectures of 1-5 that hydrogen bonds and secondary ligands both have great effects on the spatial connective fashions, resulting in the formation of various dimensional compounds. The XRPD, TGA data of title polymers and the magnetic properties for 2 and 5 have also been investigated.

  10. The OECD/NEA TDB review of selected organic ligands

    Energy Technology Data Exchange (ETDEWEB)

    Hummel, W. [Paul Scherrer Institut, Laboratory for Waste Management, 5232 Villigen PSI (Switzerland); Anderegg, G. [Swiss Federal Institute of Technology - ETH, Zuerich, 8092 Zuerich (Switzerland); Puigdomenech, I. [Swedish Nuclear Fuel and Waste Management Co. - SKB, Box 5864, 10240 Stockholm (Sweden); Rao, L. [Glenn T. Seaborg Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Tochiyama, O. [Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai (Japan)

    2005-07-01

    Within the scope of the OECD Nuclear Energy Agency (NEA) Thermochemical Data Base (TDB) Project a comprehensive review of selected organic ligands has been carried out by an international team of experts. The selected ligands are oxalate, citrate, ethylenediamine-tetra-acetate (EDTA) and {alpha}- iso-saccharinate (isa), and the elements considered in the review are U, Np, Pu, Am, Tc, Ni, Se and Zr, as well as the necessary basic data concerning protonation of the ligands and interactions with the major competing cations Na, K, Mg and Ca. As a remarkable result, this review on organic ligands showed that the pragmatic ionic strength correction procedure, the Specific ion Interaction Theory (SIT), chosen as the default method for all NEA TDB reviews, can be applied successfully also to organic ligands. The SIT interaction parameters derived from ligand protonation data for different media, e.g. NaCl and KCl, pass the consistency test when applied to other systems evaluated in the organics review, e.g. solubility data. Hence, the thermodynamic constants selected in this NEA TDB organics review can be used in real world applications, provided that SIT is used in the speciation calculations. Figure: Weighted multi-dimensional least squares SIT regression plot for the first protonation equilibrium of oxalate, ox{sup 2-} + H{sup +} {r_reversible} Hox{sup -}, in Li{sup +}, Na{sup +}, K{sup +} and Et{sub 4}N{sup +} (tetraethylammonium) media. All data can be fitted with a common parameter log{sub 10}K{sub 1}{sup 0} = (4.25 {+-} 0.01). (authors)

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

    KAUST Repository

    Jiang, Jing

    2015-03-19

    Ligand stabilized metal oxide nanoparticle resists are promising candidates for EUV lithography due to their high sensitivity for high-resolution patterning and high etching resistance. As ligand exchange is responsible for the patterning mechanism, we systematically studied the influence of ligand structures of metal oxide EUV nanoparticles on their sensitivity and dissolution behavior. ZrO2 nanoparticles were protected with various aromatic ligands with electron withdrawing and electron donating groups. These nanoparticles have lower sensitivity compared to those with aliphatic ligands suggesting the structures of these ligands is more important than their pka on resist sensitivity. The influence of ligand structure was further studied by comparing the nanoparticles’ solubility for a single type ligand to mixtures of ligands. The mixture of nanoparticles showed improved pattern quality. © (2015) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.

  12. Structural Basis of Cooperative Ligand Binding by the Glycine Riboswitch

    Energy Technology Data Exchange (ETDEWEB)

    E Butler; J Wang; Y Xiong; S Strobel

    2011-12-31

    The glycine riboswitch regulates gene expression through the cooperative recognition of its amino acid ligand by a tandem pair of aptamers. A 3.6 {angstrom} crystal structure of the tandem riboswitch from the glycine permease operon of Fusobacterium nucleatum reveals the glycine binding sites and an extensive network of interactions, largely mediated by asymmetric A-minor contacts, that serve to communicate ligand binding status between the aptamers. These interactions provide a structural basis for how the glycine riboswitch cooperatively regulates gene expression.

  13. Development of catalysts and ligands for enantioselective gold catalysis.

    Science.gov (United States)

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

    2014-03-18

    During the past decade, the use of Au(I) complexes for the catalytic activation of C-C π-bonds has been investigated intensely. Over this time period, the development of homogeneous gold catalysis has been extraordinarily rapid and has yielded a host of mild and selective methods for the formation of carbon-carbon and carbon-heteroatom bonds. The facile formation of new bonds facilitated by gold naturally led to efforts toward rendering these transformations enantioselective. In this Account, we survey the development of catalysts and ligands for enantioselective gold catalysis by our research group as well as related work by others. We also discuss some of our strategies to address the challenges of enantioselective gold(I) catalysis. Early on, our work with enantioselective gold-catalyzed transformations focused on bis(phosphinegold) complexes derived from axially chiral scaffolds. Although these complexes were highly successful in some reactions like cyclopropanation, the careful choice of the weakly coordinating ligand (or counterion) was necessary to obtain high levels of enantioselectivity for the case of allene hydroamination. These counterion effects led us to use the anion itself as a source of chirality, which was successful in the case of allene hydroalkoxylation. In general, these tactics enhance the steric influence around the reactive gold center beyond the two-coordinate ligand environment. The use of binuclear complexes allowed us to use the second gold center and its associated ligand (or counterion) to exert a further steric influence. In a similar vein, we employed a chiral anion (in place of or in addition to a chiral ligand) to move the chiral information closer to the reactive center. In order to expand the scope of reactions amenable to enantioselective gold catalysis to cycloadditions and other carbocyclization processes, we also developed a new class of mononuclear phosphite and phosphoramidite ligands to supplement the previously widely

  14. Spectroscopic study of cadmium (II) complexes with heterocyclic dithiocarbamate ligands

    Energy Technology Data Exchange (ETDEWEB)

    Garcia-Fontan, S. (Departamento de Quimica Pura y Aplicada, Universidad de Vigo (Spain)); Rodriguez-Seoane, P. (Departamento de Quimica Pura y Aplicada, Universidad de Vigo (Spain)); Casas, J.S. (Departamento de Quimica Inorganica, Universidad de Santiago de Compostela (Spain)); Sordo, J. (Departamento de Quimica Inorganica, Universidad de Santiago de Compostela (Spain)); Jones, M.M. (Department of Chemistry and Center in Molecular Toxicology, Vanderbilt University, Nashville, TN (United States))

    1993-09-15

    Cadmium(II) dithiocarbamates Cd(dtc)[sub 2] (dtc=4-carboxamidopiperidine-1-carbodithioate, morpholine-1-carbodithioate or 4-(2-hydroxyethyl)piperazine-1-carbodithioate) and Cd(dtc)[sub 2].H[sub 2]O (dtc=4-hydroxypiperidine-1-carbodithioate)[r brace] have been prepared and characterized by thermal analysis and IR and NMR ([sup 13]C, [sup 113]Cd) spectrometry. Two of these ligands have previously been shown capable of removing cadmium from its aged in vivo storage sites. The use of solid state [sup 13]C NMR measurements to establish the coordination mode of the dithiocarbomate ligands is also examined and the difficulties which arise are discussed. (orig.)

  15. Coordination chemistry of poly(thioether)borate ligands.

    Science.gov (United States)

    Riordan, Charles G

    2010-08-01

    This review traces the development and application of the tris(thioether)borate ligands, tripodal ligands with highly polarizable thioether donors. Areas of emphasis include the basic coordination chemistry of the mid-to-late first row transition metals (Fe, Ni, Co, Cu), and the role of the thioether substituent in directing complex formation, the modeling of zinc thiolate protein active sites, high-spin organo-iron and organo-cobalt chemistry, the preparation of monovalent complexes of Fe, Co and Ni, and dioxygen and sulfur activation by monovalent nickel complexes. PMID:20607091

  16. Isothermal Titration Calorimetry: Assisted Crystallization of RNA-Ligand Complexes.

    Science.gov (United States)

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

    2016-01-01

    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. Aluminum Dimer Containing Bulky 1,2,3-Triazolate Ligand

    Directory of Open Access Journals (Sweden)

    Issam Kobrsi

    2014-01-01

    Full Text Available The first molecular aluminum 1,2,3-triazolato complex was synthesized bearing a bulky 1,2,3-triazolate ligand. Oligomers and polymers were avoided due to the bulkiness and noncoordinating nature of the substituents. The novel Al2N4 ring formed contains symmetrical Al-N bond distances unexpectedly having asymmetric Al-N-N angles of 144.55(15° and 115.83(14°. This asymmetry demonstrates the effect of the steric hindrance of the ligand.

  18. Designer ligands: The search for metal ion selectivity

    Directory of Open Access Journals (Sweden)

    Perry T. Kaye

    2011-03-01

    Full Text Available The paper reviews research conducted at Rhodes University towards the development of metal-selective ligands. The research has focused on the rational design, synthesis and evaluation of novel ligands for use in the formation of copper complexes as biomimetic models of the metalloenzyme, tyrosinase, and for the selective extraction of silver, nickel and platinum group metal ions in the presence of contaminating metal ions. Attention has also been given to the development of efficient, metal-selective molecular imprinted polymers.

  19. Two ligands for a GPCR, proton vs lysolipid

    Institute of Scientific and Technical Information of China (English)

    Dong-soon IM

    2005-01-01

    Recently, two different chemicals have been matched as ligands with the same Gprotein-coupled receptor (GPCR). Double-pairing of OGR1 family GPCRs with proton and lysolipid raises several questions. First, whether both are the real ligands for the GPCRs. Second, whether modulation of a GPCR by two chemicals could be possible. Third, one of the chemicals is proton. Proton-sensing not only is a new action mode of GPCR activation, but also it could be generalized in other GPCRs.In this review, I'd like to summarize the issue and discuss questions with pharmacological criteria.

  20. 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.

  1. 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.

  2. Gut microbiota regulates NKG2D ligand expression on intestinal epithelial cells

    DEFF Research Database (Denmark)

    Hansen, Camilla Hartmann Friis; Holm, Thomas L.; Krych, Lukasz;

    2013-01-01

    Intestinal epithelial cells (IECs) are one of a few cell types in the body with constitutive surface expression of natural killer group 2 member D (NKG2D) ligands, although the magnitude of ligand expression by IECs varies. Here, we investigated whether the gut microbiota regulates the NKG2D ligand...... that the constitutive levels of NKG2D ligand expression on IECs are regulated by microbial signaling in the gut and further disfavor the intuitive notion that IEC NKG2D ligand expression is caused by low-grade immune reaction against commensal bacteria. It is more likely that constitutively high IEC NKG2D ligand...

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

    KAUST Repository

    Tang, Jiang

    2011-09-18

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

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

    DEFF Research Database (Denmark)

    Pedersen, Christian Storm; Kristensen, Thomas Greve

    When designing novel drugs, the need arise to screen databases for structures resembling active ligands, e.g. by generating a query meta-structure which summarizes these. We propose a flexible bond method for making a meta-structure and present Monte Carlo, Nelder-Mead and Differential Evolution ...

  5. Local Innate Responses to TLR Ligands in the Chicken Trachea

    Directory of Open Access Journals (Sweden)

    Neda Barjesteh

    2016-07-01

    Full Text Available The chicken upper respiratory tract is the portal of entry for respiratory pathogens, such as avian influenza virus (AIV. The presence of microorganisms is sensed by pathogen recognition receptors (such as Toll-like receptors (TLRs of the innate immune defenses. Innate responses are essential for subsequent induction of potent adaptive immune responses, but little information is available about innate antiviral responses of the chicken trachea. We hypothesized that TLR ligands induce innate antiviral responses in the chicken trachea. Tracheal organ cultures (TOC were used to investigate localized innate responses to TLR ligands. Expression of candidate genes, which play a role in antiviral responses, was quantified. To confirm the antiviral responses of stimulated TOC, chicken macrophages were treated with supernatants from stimulated TOC, prior to infection with AIV. The results demonstrated that TLR ligands induced the expression of pro-inflammatory cytokines, type I interferons and interferon stimulated genes in the chicken trachea. In conclusion, TLR ligands induce functional antiviral responses in the chicken trachea, which may act against some pathogens, such as AIV.

  6. Synthesis and structure of trialkyltantalum complexes stabilized by aminopyridinato ligands

    NARCIS (Netherlands)

    Noor, Awal; Kretschmer, Winfried; Kempe, Rhett

    2006-01-01

    (4-Methylpyridin-2-yl)(trimethylsilyl)amine (1), (6-methylpyridin-2-yl)(trimethylsilyl)amine (2), and (2,6-diisopropylphenyl)(pyridin-2-yl)amine (3) were deprotonated and used as ligands to synthesize trialkyltantalum complexes. The reaction of 2 equiv. of 1 or 2 with pentabenzyltantalum afforded tr

  7. GluR2 ligand-binding core complexes

    DEFF Research Database (Denmark)

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

    2002-01-01

    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...

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

    DEFF Research Database (Denmark)

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

    2003-01-01

    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-(ph...

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

    Directory of Open Access Journals (Sweden)

    Masahito Shimizu

    2008-01-01

    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. Spin-transition frameworks based on bistetrazole and triazine ligands

    NARCIS (Netherlands)

    Quesada Vilar, Manuel

    2007-01-01

    The present thesis deals with the synthesis and characterisation of new spin-transition materials based on tetrazole and triazine chemistry. The thesis is thus divided in two main parts. The first part examines the iron(II) coordination chemistry with bistetrazoles, which are well-known ligands in t

  11. Synthesis and Characterization of Heteropoly Coordination Compounds Containing Optical Ligands

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@Introduction   The heteropolyanion phase transfer chemistry created by Pope M. T. In 1984 has opened up a new field for heteropoly compound research[1-3]. But substituting coordination water molecules by organic optically active ligand has not been reported in literatures until 1997[4].

  12. Ligand Induced Spin Crossover in Penta-Coordinated Ferric Dithiocarbamates

    Science.gov (United States)

    Ganguli, P.; Iyer, R. M.

    1981-09-01

    On addition of lewis bases to Fe(dtc)2X, ligand exchange takes place through a SN2 mechanism, with a parallel spin crossover in the ferric ion. The two species (S = 3/2 and S = 5/2) formed are in dynamic chemical equilibrium, and a slow decomposition is then initiated.

  13. Synthesis and Characterization of Metal Complexes with Schiff Base Ligands

    Science.gov (United States)

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

    2016-01-01

    In order for undergraduate laboratory experiments to reflect modern research practice, it is essential that they include a range of elements, and that synthetic tasks are accompanied by characterization and analysis. This intermediate general chemistry laboratory exercise runs over 2 weeks, and involves the preparation of a Schiff base ligand and…

  14. Titanium complex formation of organic ligands in titania gels.

    Science.gov (United States)

    Nishikiori, Hiromasa; Todoroki, Kenta; Setiawan, Rudi Agus; Teshima, Katsuya; Fujii, Tsuneo; Satozono, Hiroshi

    2015-01-27

    Thin films of organic ligand-dispersing titania gels were prepared from titanium alkoxide sols containing ligand molecules by steam treatment without heating. The formation of the ligand-titanium complex and the photoinduced electron transfer process in the systems were investigated by photoelectrochemical measurements. The complex was formed between the 8-hydroxyquinoline (HQ) and titanium species, such as the titanium ion, on the titania nanoparticle surface through the oxygen and nitrogen atoms of the quinolate. A photocurrent was observed in the electrodes containing the complex due to the electron injection from the LUMO of the complex into the titania conduction band. A bidentate ligand, 2,3-dihydroxynaphthalene (DHN), formed the complex on the titania surface through dehydration between its two hydroxyl groups of DHN and two TiOH groups of the titania. The electron injection from the HOMO of DHN to the titania conduction band was observed during light irradiation. This direct electron injection was more effective than the two-step electron injection.

  15. Ligand and ensemble effects in adsorption on alloy surfaces

    DEFF Research Database (Denmark)

    Liu, Ping; Nørskov, Jens Kehlet

    2001-01-01

    Density functional theory is used to study the adsorption of carbon monoxide, oxygen and nitrogen on various Au/Pd(111) bimetallic alloy surfaces. By varying the Au content in the surface we are able to make a clear separation into geometrical (or ensemble) effects and electronic (or ligand......) effects determining the adsorption properties....

  16. A Guided Inquiry Activity for Teaching Ligand Field Theory

    Science.gov (United States)

    Johnson, Brian J.; Graham, Kate J.

    2015-01-01

    This paper will describe a guided inquiry activity for teaching ligand field theory. Previous research suggests the guided inquiry approach is highly effective for student learning. This activity familiarizes students with the key concepts of molecular orbital theory applied to coordination complexes. Students will learn to identify factors that…

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

    NARCIS (Netherlands)

    Iqbal, M.

    2012-01-01

    The research presented in this thesis deals with the synthesis and evaluation of new potential ligands for the complexation of actinide and lanthanide ions either for their extraction from bulk radioactive waste or their stripping from an extracted organic phase for final processing of the waste. In

  18. NMR-based screening of membrane protein ligands

    NARCIS (Netherlands)

    Yanamala, Naveena; Dutta, Arpana; Beck, Barbara; Van Fleet, Bart; Hay, Kelly; Yazbak, Ahmad; Ishima, Rieko; Doemling, Alexander; Klein-Seetharaman, Judith

    2010-01-01

    Membrane proteins pose problems for the application of NMR-based ligand-screening methods because of the need to maintain the proteins in a membrane mimetic environment such as detergent micelles: they add to the molecular weight of the protein, increase the viscosity of the solution, interact with

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

    KAUST Repository

    Boulanger, Jérôme

    2012-12-01

    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.

  20. Ultrafast Electron Trapping in Ligand-Exchanged Quantum Dot Assemblies

    Science.gov (United States)

    Kikkawa, J. M.; Turk, M. E.; Vora, P. M.; Fafarman, A. T.; Diroll, B. T.; Murray, C. B.; Kagan, C. R.

    2015-03-01

    We use time-integrated and time-resolved photoluminescence and absorption to characterize the low-temperature (10 K) optical properties of CdSe quantum dot (QD) solids with different ligand and annealing preparation. Close-packed CdSe quantum dot solids are prepared with native aliphatic ligands and with thiocyanate with and without thermal annealing. Using sub-picosecond, broadband time-resolved photoluminescence and absorption, we find that ligand exchange increases the rate of carrier surface trapping. We further determine that holes within the QD core, rather than electrons, can bleach the band-edge transition in these samples at low temperature, a finding that comes as a surprise given what is known about the surface treatment in these QDs. We find that our ligand treatments lead to faster electron trapping to the quantum dot surface, a greater proportion of surface photoluminescence, and an increased rate of nonradiative decay due to enhanced interparticle coupling upon exchange and annealing. All aspects of this work supported by the U.S. Department of Energy Office of Basic Energy Sciences, Division of Materials Science and Engineering, under Award No. DE-SC0002158.

  1. The imidazoline receptors and ligands in pain modulation

    Directory of Open Access Journals (Sweden)

    Nurcan Bektas

    2015-01-01

    Full Text Available Pain is an unpleasant experience and effects daily routine negatively. Although there are various drugs, many of them are not entirely successful in relieving pain, since pain modulation is a complex process involving numerous mediators and receptors. Therefore, it is a rational approach to identify the factors involved in the complex process and develop new agents that act on these pain producing mechanisms. In this respect, the involvement of the imidazoline receptors in pain modulation has drawn attention in recent years. In this review, it is aimed to focus on the imidazoline receptors and their ligands which contribute to the pain modulation. It is demonstrated that imidazoline-2 (I2 receptors are steady new drug targets for analgesics. Even if the mechanism of I2receptor is not well known in the modulation of pain, it is known that it plays a role in tonic and chronic pain but not in acute phasic pain. Moreover, the I2receptor ligands increase the analgesic effects of opioids in both acute and chronic pain and prevent the development of opioid tolerance. So, they are valuable for the chronic pain treatment and also therapeutic coadjuvants in the management of chronic pain with opiate drugs due to the attenuation of opioid tolerance and addiction. Thus, the use of the ligands which bind to the imidazoline receptors is an effective strategy for relieving pain. This educational forum exhibits the role of imidazoline receptors and ligands in pain process by utilizing experimental studies.

  2. Solvent-induced desorption of alkanethiol ligands from Au nanoparticles.

    Science.gov (United States)

    Huang, Yuanyuan; Liu, Wei; Cheng, Hao; Yao, Tao; Yang, Lina; Bao, Jie; Huang, Ting; Sun, Zhihu; Jiang, Yong; Wei, Shiqiang

    2016-06-21

    Removing surfactants from a colloidal metal nanoparticle surface is necessary for their realistic applications, and how they could be stripped is a subject of active investigation. Here, we report a solvent-induced desorption of dodecanethiol ligands from the gold nanoparticle surface, and traced this desorption process using a combination of in situ X-ray absorption fine structure (XAFS) and Raman spectroscopic techniques. In situ analysis results reveal that the solvent exchange of ethanol with tetrahydrofuran (THF) can effectively remove dodecanethiol ligands while keeping the particle morphology unchanged. Upon increasing the THF/ethanol ratio from 0 : 1 to 5 : 1, the surface coverage of thiol on the Au surface is reduced from 0.47 to 0.07, suggesting the depletion of ligands first from the nanoparticle facet sites, then from the edge sites, while the ligands at the corner sites are intact. This work enriches our knowledge on surfactant removal and may pave the way towards preparing surface-clean nanoparticles for practical applications. PMID:27241025

  3. 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

    2011-01-01

    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.

  4. Fluorescent ligands for studying neuropeptide receptors by confocal microscopy

    Directory of Open Access Journals (Sweden)

    Beaudet A.

    1998-01-01

    Full Text Available This paper reviews the use of confocal microscopy as it pertains to the identification of G-protein coupled receptors and the study of their dynamic properties in cell cultures and in mammalian brain following their tagging with specific fluorescent ligands. Principles that should guide the choice of suitable ligands and fluorophores are discussed. Examples are provided from the work carried out in the authors' laboratory using custom synthetized fluoresceinylated or BODIPY-tagged bioactive peptides. The results show that confocal microscopic detection of specifically bound fluorescent ligands permits high resolution appraisal of neuropeptide receptor distribution both in cell culture and in brain sections. Within the framework of time course experiments, it also allows for a dynamic assessment of the internalization and subsequent intracellular trafficking of bound fluorescent molecules. Thus, it was found that neurotensin, somatostatin and mu- and delta-selective opioid peptides are internalized in a receptor-dependent fashion and according to receptor-specific patterns into their target cells. In the case of neurotensin, this internalization process was found to be clathrin-mediated, to proceed through classical endosomal pathways and, in neurons, to result in a mobilization of newly formed endosomes from neural processes to nerve cell bodies and from the periphery of cell bodies towards the perinuclear zone. These mechanisms are likely to play an important role for ligand inactivation, receptor regulation and perhaps also transmembrane signaling.

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

    Directory of Open Access Journals (Sweden)

    Kelly Teske

    2014-04-01

    Full Text Available Herein, we described the development of two virtual screens to identify new vitamin D receptor (VDR antagonists among nuclear receptor (NR ligands. Therefore, a database of 14330 nuclear receptor ligands and their NR affinities was assembled using the online available “Binding Database.” Two different virtual screens were carried out in conjunction with a reported VDR crystal structure applying a stringent and less stringent pharmacophore model to filter docked NR ligand conformations. The pharmacophore models were based on the spatial orientation of the hydroxyl functionalities of VDR's natural ligands 1,25(OH2D3 and 25(OH2D3. The first virtual screen identified 32 NR ligands with a calculated free energy of VDR binding of more than -6.0 kJ/mol. All but nordihydroguaiaretic acid (NDGA are VDR ligands, which inhibited the interaction between VDR and coactivator peptide SRC2-3 with an IC50 value of 15.8 μM. The second screen identified 162 NR ligands with a calculated free energy of VDR binding of more than -6.0 kJ/mol. More than half of these ligands were developed to bind VDR followed by ERα/β ligands (26%, TRα/β ligands (7%, and LxRα/β ligands (7%. The binding between VDR and ERα ligand H6036 as well as TRα/β ligand triiodothyronine and a homoserine analog thereof was confirmed by fluorescence polarization.

  6. Docking validation resources: protein family and ligand flexibility experiments.

    Science.gov (United States)

    Mukherjee, Sudipto; Balius, Trent E; Rizzo, Robert C

    2010-11-22

    A database consisting of 780 ligand-receptor complexes, termed SB2010, has been derived from the Protein Databank to evaluate the accuracy of docking protocols for regenerating bound ligand conformations. The goal is to provide easily accessible community resources for development of improved procedures to aid virtual screening for ligands with a wide range of flexibilities. Three core experiments using the program DOCK, which employ rigid (RGD), fixed anchor (FAD), and flexible (FLX) protocols, were used to gauge performance by several different metrics: (1) global results, (2) ligand flexibility, (3) protein family, and (4) cross-docking. Global spectrum plots of successes and failures vs rmsd reveal well-defined inflection regions, which suggest the commonly used 2 Å criteria is a reasonable choice for defining success. Across all 780 systems, success tracks with the relative difficulty of the calculations: RGD (82.3%) > FAD (78.1%) > FLX (63.8%). In general, failures due to scoring strongly outweigh those due to sampling. Subsets of SB2010 grouped by ligand flexibility (7-or-less, 8-to-15, and 15-plus rotatable bonds) reveal that success degrades linearly for FAD and FLX protocols, in contrast to RGD, which remains constant. Despite the challenges associated with FLX anchor orientation and on-the-fly flexible growth, success rates for the 7-or-less (74.5%) and, in particular, the 8-to-15 (55.2%) subset are encouraging. Poorer results for the very flexible 15-plus set (39.3%) indicate substantial room for improvement. Family-based success appears largely independent of ligand flexibility, suggesting a strong dependence on the binding site environment. For example, zinc-containing proteins are generally problematic, despite moderately flexible ligands. Finally, representative cross-docking examples, for carbonic anhydrase, thermolysin, and neuraminidase families, show the utility of family-based analysis for rapid identification of particularly good or bad

  7. Benchmarking the Predictive Power of Ligand Efficiency Indices in QSAR.

    Science.gov (United States)

    Cortes-Ciriano, Isidro

    2016-08-22

    Compound physicochemical properties favoring in vitro potency are not always correlated to desirable pharmacokinetic profiles. Therefore, using potency (i.e., IC50) as the main criterion to prioritize candidate drugs at early stage drug discovery campaigns has been questioned. Yet, the vast majority of the virtual screening models reported in the medicinal chemistry literature predict the biological activity of compounds by regressing in vitro potency on topological or physicochemical descriptors. Two studies published in this journal showed that higher predictive power on external molecules can be achieved by using ligand efficiency indices as the dependent variable instead of a metric of potency (IC50) or binding affinity (Ki). The present study aims at filling the shortage of a thorough assessment of the predictive power of ligand efficiency indices in QSAR. To this aim, the predictive power of 11 ligand efficiency indices has been benchmarked across four algorithms (Gradient Boosting Machines, Partial Least Squares, Random Forest, and Support Vector Machines), two descriptor types (Morgan fingerprints, and physicochemical descriptors), and 29 data sets collected from the literature and ChEMBL database. Ligand efficiency metrics led to the highest predictive power on external molecules irrespective of the descriptor type or algorithm used, with an R(2)test difference of ∼0.3 units and a this difference ∼0.4 units when modeling small data sets and a normalized RMSE decrease of >0.1 units in some cases. Polarity indices, such as SEI and NSEI, led to higher predictive power than metrics based on molecular size, i.e., BEI, NBEI, and LE. LELP, which comprises a polarity factor (cLogP) and a size parameter (LE) constantly led to the most predictive models, suggesting that these two properties convey a complementary predictive signal. Overall, this study suggests that using ligand efficiency indices as the dependent variable might be an efficient strategy to model

  8. Specific uranyl binding by macrocyclic ligands attached to resins

    International Nuclear Information System (INIS)

    Macrocyclic polydentates have attracted enormous attention from chemists because of their unique and significant characteristics of the strong and selective binding of a variety of metal ions. The metal binding is governed mostly by the size of the macroring and the nature of heteroatoms involved. The most important role of the macrocyclic structure is, in general, the so-called macrocyclic effect - to increase (making less negative) a large negative entropy change involved in the polydentate chelation. Basic strategy of uranium binding, is to design a ligand of very strong metal binding to take advantage of this macrocyclic effect, where number of chelating heteroatoms and their spatial arrangement is designed to be most appropriate for uranyl (UO22+) binding, since in natural sea water uranium is dissolved mostly in a form of uranyl carbonate. The following macrocylic ligands, hexamine, hexaketone, hexacarboxylic acid, were prepared and tested. The macrocyclic hexacarboxylic ligand was the most promising. The addition of hexacarboxylic acid to a uranyl tricarbonate solution gave a change of visible absorption due to the competitive formation of the uranyl complex. From this competitive binding, a relative formation constant was estimated to be 10-5, giving a log K/sub f/ value of 16.4 at 250C for the uranyl complex. This value is the largest among the hosts ever reported to bind uranyl ion.The selectivity of the macrocyclic hexacarboxylic ligand was also ascertained by testing with other metal cations. Results indicate that uranyl ions can be extracted efficiently from sea water using the hexacarboxylic acid ligands which are attached to a polymer insoluble in water

  9. KLIFS: a knowledge-based structural database to navigate kinase-ligand interaction space.

    Science.gov (United States)

    van Linden, Oscar P J; Kooistra, Albert J; Leurs, Rob; de Esch, Iwan J P; de Graaf, Chris

    2014-01-23

    Protein kinases regulate the majority of signal transduction pathways in cells and have become important targets for the development of designer drugs. We present a systematic analysis of kinase-ligand interactions in all regions of the catalytic cleft of all 1252 human kinase-ligand cocrystal structures present in the Protein Data Bank (PDB). The kinase-ligand interaction fingerprints and structure database (KLIFS) contains a consistent alignment of 85 kinase ligand binding site residues that enables the identification of family specific interaction features and classification of ligands according to their binding modes. We illustrate how systematic mining of kinase-ligand interaction space gives new insights into how conserved and selective kinase interaction hot spots can accommodate the large diversity of chemical scaffolds in kinase ligands. These analyses lead to an improved understanding of the structural requirements of kinase binding that will be useful in ligand discovery and design studies.

  10. 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;

    2007-01-01

    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....

  11. Alkali metal salts of formazanate ligands : diverse coordination modes as a result of the nitrogen-rich [NNCNN] ligand backbone

    NARCIS (Netherlands)

    Travieso-Puente, Raquel; Chang, Mu-Chieh; Otten, Edwin

    2014-01-01

    Alkali metal salts of redox-active formazanate ligands were prepared, and their structures in the solid-state and in solution are determined. The nitrogen-rich [NNCNN] backbone of formazanates results in a varied coordination chemistry, with both the internal and terminal nitrogen atoms available fo

  12. Measurement of solubilities for rhodium complexes and phosphine ligands in supercritical carbon dioxide

    OpenAIRE

    Shimoyama, Yusuke; Sonoda, Masanori; Miyazaki, Kaoru; Higashi, Hidenori; Iwai, Yoshio; ARAI, Yasuhiko

    2008-01-01

    The solubilities of phosphine ligands and rhodium (Rh) complexes in supercritical carbon dioxide were measured with Fourier transform infrared (FT-IR) spectroscopy at 320 and 333 K and several pressures. Triphenylphosphine (TPP) and tris(p-trifluoromethylphenyl)-phosphine (TTFMPP) were selected as ligands for the Rh complex. The solubilities of the fluorinated ligands and complexes were compared with those of the non-fluorinated compounds. The solubilities of ligand increased up to 10 times b...

  13. Heteroskorpionate Ligands In Coordination Chemistry – Complexes Relevant To Hydrogenation Catalysis, Olefine Epoxidation, And Inhibitor Studies

    OpenAIRE

    Tampier, Stefan

    2012-01-01

    This work focuses on (i) the syntheses and characterisations of various ruthenium(II) complexes bearing the bdmpza ligand, (ii) complexes based on the new bis(3,5-di-tert-butylpyrazol-1-yl)dithioacetato ligand, (iii) complexes based on bispyrazolylacetate esters, and (iv) the syntheses and characteristics of ferrocenyl-substituted ligands derived from bispyrazolylacetic acid and related chelating ligands. Chapter 3.1.2 outlines principle substitution reactions of [Ru(bdmpza)Cl(PPh3)2] (1) [bd...

  14. 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. .;

    1998-01-01

    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 more complete description of the dynamics important for ligand binding are then discussed. These methods are illustrated for phospholipase A(2) and lipase, enzymes that both undergo interfacial activation....

  15. Gene Duplication of the zebrafish kit ligand and partitioning of melanocyte development functions to kit ligand a.

    Directory of Open Access Journals (Sweden)

    Keith A Hultman

    2007-01-01

    Full Text Available The retention of particular genes after the whole genome duplication in zebrafish has given insights into how genes may evolve through partitioning of ancestral functions. We examine the partitioning of expression patterns and functions of two zebrafish kit ligands, kit ligand a (kitla and kit ligand b (kitlb, and discuss their possible coevolution with the duplicated zebrafish kit receptors (kita and kitb. In situ hybridizations show that kitla mRNA is expressed in the trunk adjacent to the notochord in the middle of each somite during stages of melanocyte migration and later expressed in the skin, when the receptor is required for melanocyte survival. kitla is also expressed in other regions complementary to kita receptor expression, including the pineal gland, tail bud, and ear. In contrast, kitlb mRNA is expressed in brain ventricles, ear, and cardinal vein plexus, in regions generally not complementary to either zebrafish kit receptor ortholog. However, like kitla, kitlb is expressed in the skin during stages consistent with melanocyte survival. Thus, it appears that kita and kitla have maintained congruent expression patterns, while kitb and kitlb have evolved divergent expression patterns. We demonstrate the interaction of kita and kitla by morpholino knockdown analysis. kitla morphants, but not kitlb morphants, phenocopy the null allele of kita, with defects for both melanocyte migration and survival. Furthermore, kitla morpholino, but not kitlb morpholino, interacts genetically with a sensitized allele of kita, confirming that kitla is the functional ligand to kita. Last, we examine kitla overexpression in embryos, which results in hyperpigmentation caused by an increase in the number and size of melanocytes. This hyperpigmentation is dependent on kita function. We conclude that following genome duplication, kita and kitla have maintained their receptor-ligand relationship, coevolved complementary expression patterns, and that

  16. Secondary interactions or ligand scrambling? Subtle steric effects govern the iridium(I) coordination chemistry of phosphoramidite ligands.

    Science.gov (United States)

    Osswald, Tina; Rüegger, Heinz; Mezzetti, Antonio

    2010-01-25

    The like and unlike isomers of phosphoramidite (P*) ligands are found to react differently with iridium(I), which is a key to explaining the apparently inconsistent results obtained by us and other research groups in a variety of catalytic reactions. Thus, the unlike diastereoisomer (aR,S,S)-[IrCl(cod)(1 a)] (2 a; cod=1,5-cyclooctadiene, 1 a=(aR,S,S)-(1,1'-binaphthalene)-2,2'-diyl bis(1-phenylethyl)phosphoramidite) forms, upon chloride abstraction, the monosubstituted complex (aR,S,S)-[Ir(cod)(1,2-eta-1 a,kappaP)](+) (3 a), which contains a chelating P* ligand that features an eta(2) interaction between a dangling phenyl group and iridium. Under analogous conditions, the like analogue (aR,R,R)-1 a' gives the disubstituted species (aR,R,R)-[Ir(cod)(1 a',kappaP)(2)](+) (4 a') with monodentate P* ligands. The structure of 3 a was assessed by a combination of X-ray and NMR spectroscopic studies, which indicate that it is the configuration of the binaphthol moiety (and not that of the dangling benzyl N groups) that determines the configuration of the complex. The effect of the relative configuration of the P* ligand on its iridium(I) coordination chemistry is discussed in the context of our preliminary catalytic results and of apparently random results obtained by other groups in the iridium(I)-catalyzed asymmetric allylic alkylation of allylic acetates and in rhodium(I)-catalyzed asymmetric cycloaddition reactions. Further studies with the unlike ligand (aS,R,R)-(1,1'-binaphthalene)-2,2'-diyl bis{[1-(1-naphthalene-1-yl)ethyl]phosphoramidite} (1 b) showed a yet different coordination mode, that is, the eta(4)-arene-metal interaction in (aS,R,R)-[Ir(cod)(1,2,3,4-eta-1 b,kappaP)](+) (3 b).

  17. Novel bispidine ligands with a possible application in nuclear medicine

    International Nuclear Information System (INIS)

    Due to our current way of life and the environmental influences we are exposed in the industrial nations, cancer diseases turn out to be a more and more serious threat to our civilization. The ongoing research during the last decades leads to a better insight in cancer diseases and enables an earlier recognition of developing carcinoma. The detection of pathological tissue changes at an early stage increases the patients' chances of cure. Magnetic resonance tomography (MRT) and computed tomography (CT) as well as radiopharmaceutically assisted imaging techniques, like positron emission tomography (PET) and scintigraphy are an indispensable clinical tool in the oncological early diagnosis. By the development of multimodality imaging agents that combine the benefits of several imaging techniques, the early recognition of tumors can be more efficient and in consequence a matching therapy can be applied. This thesis deals with the synthesis of novel bispidine based ligands and their transition metal complexes as potential mono- and bimodal imaging agents for a 64Cu-assisted radiopharmaceutical application in positron emission tomography (PET) and optical imaging (OI). The synthesized ligands L and LOH are offering the opportunity to build up a ruthenium(II) polypyridine complex by one of the ligand's donor sets, to act as a fluorescence dye for optical imaging (OI), and to coordinate 64CuII by the ligand's vacant cavity for positron emission tomography (PET). The RuII complex exhibits two different fluorescence activities with two different lifetimes and only one of the two fluorescences is quenched by subsequent complexation of CuII. The calculated CuII stability constant of L and LOH is similar to that of the isomeric ligand N2py2 which has been already evaluated as a 64Cu-radiotracer. Further transition metal complexes of FeII, FeIII and MnII are dealing with interesting structural properties like pentagonal bipyramidal geometries. For the development of stable and

  18. 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

  19. Synthesis and Reactivity of Chiral, Wide-Bite-Angle, Hybrid Diphosphorus Ligands

    NARCIS (Netherlands)

    C.F. Czauderna; D.B. Cordes; A.M.Z. Slawin; C. Müller; J.I. van der Vlugt; D. Vogt; P.C.J. Kamer

    2014-01-01

    Effective and modular synthetic approaches toward phosphine-phosphite ligands and phosphine-phosphonite ligands featuring a diphenyl ether backbone have been developed. The phosphine-phosphite ligands are obtained by a two-step protocol from 2-bromo-2-methoxydiphenyl ether. The phosphine-phosphonite

  20. Olefin Metathesis Mediated By: - Schiff Base Ru-Alkylidenes -Ru-Alkylidenes Bearing Unsymmetrical NH Ligands

    Science.gov (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.

  1. Amino acids as chiral anionic ligands for ruthenium based asymmetric olefin metathesis.

    Science.gov (United States)

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

    2015-03-01

    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.

  2. Influence of bulky yet flexible N-heterocyclic carbene ligands in gold catalysis.

    Science.gov (United States)

    Collado, Alba; Patrick, Scott R; Gasperini, Danila; Meiries, Sebastien; Nolan, Steven P

    2015-01-01

    Three new Au(I) complexes of the formula [Au(NHC)(NTf2)] (NHC = N-heterocyclic carbene) bearing bulky and flexible ligands have been synthesised. The ligands studied are IPent, IHept and INon which belong to the 'ITent' ('Tent' for 'tentacular') family of NHC derivatives. The effect of these ligands in gold-promoted transformations has been investigated.

  3. Carborane phosphorus-derivatives as ligands for Pd-catalyzed cross-coupling reactions

    International Nuclear Information System (INIS)

    Synthesis of carborane-containing phosphine ligands possessing different steric and electronic properties has been considered. Testing of the given ligands in Pd-catalyzed Suzuki-Miyaura reaction demonstrated that sterically volume phosphine ligands with acceptor carborane substitutes possessed the most catalytic activity

  4. Amino acids as chiral anionic ligands for ruthenium based asymmetric olefin metathesis.

    Science.gov (United States)

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

    2015-03-01

    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. PMID:25656548

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

    NARCIS (Netherlands)

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

    2012-01-01

    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 li

  6. Understanding Ligand Effects in Gold Clusters using Mass Spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Grant E.; Laskin, Julia

    2016-06-16

    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

  7. Photoluminescent copper(I) complexes with amido-triazolato ligands.

    Science.gov (United States)

    Manbeck, Gerald F; Brennessel, William W; Eisenberg, Richard

    2011-04-18

    A series of heteroleptic copper(I) complexes incorporating amido-triazole and diphosphine ligands, [Cu(I)(N-phenyl-2-(1-phenyl-1H-1,2,3-triazol-4-yl)aniline)(dppb)] (1), [Cu(I)(N-(4-methylphenyl)-2-(1-phenyl-1H-1,2,3-triazol-4-yl)aniline)(dppb)] (2), [Cu(I)(N-(4-methoxyphenyl)-2-(1-phenyl-1H-1,2,3-triazol-4-yl)aniline)(dppb)] (3), [Cu(I)(N-(4-chlorophenyl)-2-(1-phenyl-1H-1,2,3-triazol-4-yl)aniline)(dppb)] (4), [Cu(I)(2,6-dimethyl-N-[2-(1-phenyl-1H-1,2,3-triazol-4-yl)phenyl]aniline)(dppb)] (5), [Cu(I)(2,6-dimethyl-N-[2-(1-benzyl-1H-1,2,3-triazol-4-yl)phenyl]aniline)(dppb)] (6), (dppb = 1,2-bis(diphenylphosphino)benzene), have been prepared. The complexes adopt a distorted tetrahedral geometry in the solid state with the amido-triazole ligand forming a six-member ring with the Cu(I) ion. The complexes exhibit long-lived photoluminescence with colors ranging from yellow to red-orange in the solid state, in frozen glass at 77 K, and in fluid solution with modest quantum yields of up to 0.022. Electrochemically, complexes 1-4 show irreversible oxidation waves while 5 and 6 are characterized by quasi-reversible oxidations as determined by cyclic voltammetry. For 1-4, the emission energy and oxidation potential are found to vary linearly with the Hammett parameter σ(p) of the substituent in the para position of the amido ligand, while in 5 and 6, large differences in emission are observed because of the nature of N3 substitution in the triazole ring. Density functional theory calculations have been performed on the singlet ground states (S(o)) of all complexes at the BP86/6-31G(d) level to assist in assignment of the excited states. On the basis of both experimental and computational results, we have assigned the excited states as intraligand + metal-to-ligand charge transfer (3)(ILCT+MLCT) or ligand-to-ligand charge transfer mixed with MLCT (3)(MLCT +LLCT) in these complexes. PMID:21417454

  8. PDB ligand conformational energies calculated quantum-mechanically.

    Science.gov (United States)

    Sitzmann, Markus; Weidlich, Iwona E; Filippov, Igor V; Liao, Chenzhong; Peach, Megan L; Ihlenfeldt, Wolf-Dietrich; Karki, Rajeshri G; Borodina, Yulia V; Cachau, Raul E; Nicklaus, Marc C

    2012-03-26

    We present here a greatly updated version of an earlier study on the conformational energies of protein-ligand complexes in the Protein Data Bank (PDB) [Nicklaus et al. Bioorg. Med. Chem. 1995, 3, 411-428], with the goal of improving on all possible aspects such as number and selection of ligand instances, energy calculations performed, and additional analyses conducted. Starting from about 357,000 ligand instances deposited in the 2008 version of the Ligand Expo database of the experimental 3D coordinates of all small-molecule instances in the PDB, we created a "high-quality" subset of ligand instances by various filtering steps including application of crystallographic quality criteria and structural unambiguousness. Submission of 640 Gaussian 03 jobs yielded a set of about 415 successfully concluded runs. We used a stepwise optimization of internal degrees of freedom at the DFT level of theory with the B3LYP/6-31G(d) basis set and a single-point energy calculation at B3LYP/6-311++G(3df,2p) after each round of (partial) optimization to separate energy changes due to bond length stretches vs bond angle changes vs torsion changes. Even for the most "conservative" choice of all the possible conformational energies-the energy difference between the conformation in which all internal degrees of freedom except torsions have been optimized and the fully optimized conformer-significant energy values were found. The range of 0 to ~25 kcal/mol was populated quite evenly and independently of the crystallographic resolution. A smaller number of "outliers" of yet higher energies were seen only at resolutions above 1.3 Å. The energies showed some correlation with molecular size and flexibility but not with crystallographic quality metrics such as the Cruickshank diffraction-component precision index (DPI) and R(free)-R, or with the ligand instance-specific metrics such as occupancy-weighted B-factor (OWAB), real-space R factor (RSR), and real-space correlation coefficient

  9. Tetrahedral nickel nitrosyl complexes with tripodal [N3] and [Se3] donor ancillary ligands: structural and computational evidence that a linear nitrosyl is a trivalent ligand.

    Science.gov (United States)

    Landry, Victoria K; Pang, Keliang; Quan, Stephanie M; Parkin, Gerard

    2007-02-28

    Linear nickel nitrosyl compounds supported by tridentate nitrogen and selenium ligands, namely the tris(3,5-dimethylpyrazolyl)hydroborato and tris(2-seleno-1-mesitylimidazolyl)hydroborato complexes, [TpMe2]NiNO and [TseMes]NiNO, have been synthesized and structurally characterized by X-ray diffraction. Computational studies demonstrate that the linear nitrosyl ligand behaves as a trivalent X3 ligand such that the Ni-N interaction has multiple bond character. PMID:17297507

  10. Comparison of the electronic properties of diarylamido-based PNZ pincer ligands: redox activity at the ligand and donor ability toward the metal.

    Science.gov (United States)

    Davidson, Jillian J; DeMott, Jessica C; Douvris, Christos; Fafard, Claudia M; Bhuvanesh, Nattamai; Chen, Chun-Hsing; Herbert, David E; Lee, Chun-I; McCulloch, Billy J; Foxman, Bruce M; Ozerov, Oleg V

    2015-03-16

    This paper presents the synthesis and characterization of a series of pincer ligands and their Ni, Pd, Pt, and Rh complexes. The ligands under examination are based on a diarylamine which is modified either by two phosphino (-PR2) substituents in the ortho-positions (PNP ligands) or by a combination of a phosphino and an iminyl (-CH═NX) substituent (PNN ligands). The ligands can be broken down into three groups: (a) C2v-symmetric PNP ligands with identical side -PR2 donors, (b) Cs-symmetric PNP' ligands with different -PR2 side donors, and (c) PNN ligands containing a -P(i)Pr2 side donor. All of the ligands under study readily formed square-planar complexes of the types (PNZ)PdCl, (PNZ)Pd(OAc), and (PNZ)RhCO, where PNZ is the corresponding anionic tridentate pincer ligand. For select PNP ligands, (PNP)NiCl and (PNP)PtCl were also studied. The (PNZ)MCl complexes (M = Ni, Pd, Pt) underwent quasireversible oxidation in cyclic voltammetry experiments. Based on the close similarity of formal potentials for Ni, Pd, and Pt analogs, and based on the previous literature evidence, these oxidation events are ascribed primarily to the PNZ ligand, and the E1/2 values can be used to compare the ease of oxidation of different ligands. A (PNP)PdCl complex containing methoxy substituents para- to the central nitrogen underwent two quasireversible oxidations. Two mono-oxidized complexes were isolated and structurally characterized in comparison to their neutral analog, revealing minimal changes in the bond distances and angles. Several other neutral complexes were also structurally characterized. The carbonyl stretching frequency in (PNZ)RhCO complexes was used to gauge the donating ability of the various pincer ligands toward the metal. Comparison of E1/2 values for (PNZ)PdCl and νCO values for (PNZ)RhCO revealed that the two are not consistently correlated across all the studied ligands and can be tuned to different degrees through judicious ligand alteration. PMID:25714352

  11. Topological Analyses of Protein-Ligand Binding: a Network Approach.

    Science.gov (United States)

    Costanzi, Stefano

    2016-01-01

    Proteins can be conveniently represented as networks of interacting residues, thus allowing the study of several network parameters that can shed light onto several of their structural and functional aspects. With respect to the binding of ligands, which are central for the function of many proteins, network analysis may constitute a possible route to assist the identification of binding sites. As the bulk of this review illustrates, this has generally been easier for enzymes than for non-enzyme proteins, perhaps due to the different topological nature of the binding sites of the former over those of the latter. The article also illustrates how network representations of binding sites can be used to search PDB structures in order to identify proteins that bind similar molecules and, lastly, how codifying proteins as networks can assist the analysis of the conformational changes consequent to ligand binding.

  12. Surface deformation and shear flow in ligand mediated cell adhesion

    Science.gov (United States)

    Sircar, Sarthok; Roberts, Anthony; Sarthok Sircar / Anthony Roberts Collaboration

    We present a unified, multiscale model to study the attachment/detachment dynamics of two deforming, near spherical cells, coated with binding ligands and subject to a slow, homogeneous shear flow in a viscous fluid medium. The binding ligands on the surface of the cells experience attractive and repulsive forces in an ionic medium and exhibit finite resistance to rotation via bond tilting. The microscale drag forces and couples describing the fluid flow inside the small separation gap between the cells, are calculated using a combination of methods in lubrication theory and previously published numerical results. For a select range of material and fluid parameters, a hysteretic transition of the sticking probability curves (i.e., the function g*) between the adhesion phase (when g*>0.5) and the fragmentation phase (when g*University startup funds and AR is supported by the Australian Research Council Discovery Grant DP150102385.

  13. Inside job: ligand-receptor pharmacology beneath the plasma membrane

    Science.gov (United States)

    Babcock, Joseph J; Li, Min

    2013-01-01

    Most drugs acting on the cell surface receptors are membrane permeable and thus able to engage their target proteins in different subcellular compartments. However, these drugs' effects on cell surface receptors have historically been studied on the plasma membrane alone. Increasing evidence suggests that small molecules may also modulate their targeted receptors through membrane trafficking or organelle-localized signaling inside the cell. These additional modes of interaction have been reported for functionally diverse ligands of GPCRs, ion channels, and transporters. Such intracellular drug-target engagements affect cell surface expression. Concurrent intracellular and cell surface signaling may also increase the complexity and therapeutic opportunities of small molecule modulation. Here we discuss examples of ligand-receptor interactions that are present in both intra- and extracellular sites, and the potential therapeutic opportunities presented by this phenomenon. PMID:23685953

  14. Inside job: ligand-receptor pharmacology beneath the plasma membrane

    Institute of Scientific and Technical Information of China (English)

    Joseph J BABCOCK; Min LI

    2013-01-01

    Most drugs acting on the cell surface receptors are membrane permeable and thus able to engage their target proteins in different subcellular compartments.However,these drugs' effects on cell surface receptors have historically been studied on the plasma membrane alone.Increasing evidence suggests that small molecules may also modulate their targeted receptors through membrane trafficking or organelle-localized signaling inside the cell.These additional modes of interaction have been reported for functionally diverse ligands of GPCRs,ion channels,and transporters.Such intracellular drug-target engagements affect cell surface expression.Concurrent intracellular and cell surface signaling may also increase the complexity and therapeutic opportunities of small molecule modulation.Here we discuss examples of ligand-receptor interactions that are present in both intra- and extracellular sites,and the potential therapeutic opportunities presented by this phenomenon.

  15. Immunotoxins, ligand-toxin conjugates and molecular targeting.

    Science.gov (United States)

    Soria, M

    1989-01-01

    Biotechnology provides tools for therapeutic exploitation following advances in the elucidation of protein-to-cell and cell-to-cell interactions. Molecular targeting of bacterial and plant toxins to the desired district of action can be achieved through effector molecules like monoclonal antibodies or protein ligands. Biochemical conjugation of these effectors to SO-6, a single-chain Ribosome Inactivating Protein from Saponaria officinalis, yielded powerful cytotoxic agents that are attractive candidates for therapeutic evaluation. Cloning of the gene for this plant toxin has been achieved. Technologies for expression of protein ligands, such as apolipoproteins or several growth factors, are available in recombinant microorganisms, providing adequate partners for the assembly of targeted chimaeras. Domain engineering of structural and functional regions in effector proteins is now possible and will be carried out with the available technologies to improve existing therapy. PMID:2698471

  16. Biophysics of selectin-ligand interactions in inflammation and cancer

    Science.gov (United States)

    Siu-Lun Cheung, Luthur; Raman, Phrabha S.; Balzer, Eric M.; Wirtz, Denis; Konstantopoulos, Konstantinos

    2011-02-01

    Selectins (l-, e- and p-selectin) are calcium-dependent transmembrane glycoproteins that are expressed on the surface of circulating leukocytes, activated platelets, and inflamed endothelial cells. Selectins bind predominantly to sialofucosylated glycoproteins and glycolipids (e-selectin only) present on the surface of apposing cells, and mediate transient adhesive interactions pertinent to inflammation and cancer metastasis. The rapid turnover of selectin-ligand bonds, due to their fast on- and off-rates along with their remarkably high tensile strengths, enables them to mediate cell tethering and rolling in shear flow. This paper presents the current body of knowledge regarding the role of selectins in inflammation and cancer metastasis, and discusses experimental methodologies and mathematical models used to resolve the biophysics of selectin-mediated cell adhesion. Understanding the biochemistry and biomechanics of selectin-ligand interactions pertinent to inflammatory disorders and cancer metastasis may provide insights for developing promising therapies and/or diagnostic tools to combat these disorders.

  17. Programmed death-1 & its ligands: promising targets for cancer immunotherapy.

    Science.gov (United States)

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

    2015-01-01

    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.

  18. Photomechanical actuation of ligand geometry in enantioselective catalysis.

    Science.gov (United States)

    Kean, Zachary S; Akbulatov, Sergey; Tian, Yancong; Widenhoefer, Ross A; Boulatov, Roman; Craig, Stephen L

    2014-12-22

    A catalyst that couples a photoswitch to the biaryl backbone of a chiral bis(phosphine) ligand, thus allowing photochemical manipulation of ligand geometry without perturbing the electronic structure is reported. The changes in catalyst activity and selectivity upon switching can be attributed to intramolecular mechanical forces, thus laying the foundation for a new class of catalysts whose selectivity can be varied smoothly and in situ over a useful range by controlling molecular stress experienced by the catalyst during turnover. Forces on the order of 100 pN are generated, thus leading to measurable changes in the enantioselectivities of asymmetric Heck arylations and Trost allylic alkylations. The differential coupling between applied force and competing stereochemical pathways is quantified and found to be more efficient for the Heck arylations.

  19. MULTIDENTATE TEREPHTHALAMIDATE AND HYDROXYPYRIDONATE LIGANDS: TOWARDS NEW ORALLY ACTIVE CHELATORS

    Energy Technology Data Exchange (ETDEWEB)

    Abergel, Rebecca J.; Raymond, Kenneth N.

    2011-07-13

    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. Silver, Gold, Palladium Nanoparticles: Ligand Design, Synthesis and Polymer Composites

    Science.gov (United States)

    Iqbal, Muhammad

    Metal nanoparticles, especially gold nanoparticles (AuNPs), have been extensively studied due to their interesting optical properties and potential applications in emerging technologies like drug delivery, cancer therapy, catalysis, chemical and bio-sensing and microelectronics devices. Alkyl thiol ligands in the form of self assembled monolayers are often used to stabilize and functionalize the gold nanoparticles while other types of ligands have been rarely employed and the properties of AuNPs protected by different types of ligands have not been studied comprehensively and comparatively. This dissertation reports the first comparative studies on the thermal and chemical stability of AuNPs protected by alkyl thiolates, alkyl selenolates, dialkyl dithiophosphinates, and dialkyl dithiophosphates (Chapters 2 and 3). AuNPs protected by dialkyl dithiophosphinates and dialkyl dithiophosphates are unprecedented. All AuNPs were prepared from amine protected precursor AuNPs by ligand exchange to ensure similar size, size distribution, and chemical composition. They were extensively characterized by solution 1H-NMR and UV-VIS spectroscopy, transmission electron microscopy (TEM), thermal analysis, X-ray photoelectron spectroscopy (XPS), and X-ray diffraction (XRD) analysis. For the first time, thermal stability was investigated by differential scanning calorimetry (DSC) that provided more accurate decomposition temperatures and enthalpies, whereas chemical stability was tested as the availability of the gold surface towards etching with cyanide in different solvents. Surprisingly, alkyl selenolate protected AuNPs are thermally less stable than alkyl thiolate protected AuNPs despite their proposed stronger binding to the gold surface and a much more crystalline monolayer, which suggests that different decomposition mechanisms apply to alkyl thiolate and alkyl selenolate protected AuNPs. Dialkyl dithiophosphinates and dialkyl dithiophosphates protected AuNPs are thermally

  1. Highly selective ligand binding by Methylophilus methylotrophus cytochrome c''.

    Science.gov (United States)

    Quintas, Pedro O; Catarino, Teresa; Todorovic, Smilja; Turner, David L

    2011-06-28

    Cytochrome c'' (cyt c'') from Methylophilus methylotrophus is unusual insofar as the heme has two axial histidine ligands in the oxidized form but one is detached when the protein is reduced. Despite cyt c'' having an axial site available for binding small ligands, we show here that only NO binds readily to the ferrous cyt c''. Binding of CO, as well as CN(-), on the other hand requires considerable structural reorganization, or reduction of the disulfide bridge close to the heme. Standard free energies for the binding of NO and CO reveal high selectivity of the ferrous cyt c'' for NO, indicating its putative physiological role. In this work, we characterize in detail the kinetics of NO binding and the structural features of the Fe(2+)-NO adduct by stopped-flow and resonance Raman spectroscopy, respectively.

  2. Screening and Optimization of Ligand Conjugates for Lysosomal Targeting

    OpenAIRE

    Meerovich, Igor; Koshkaryev, Alexander; Thekkedath, Ritesh; Torchilin, Vladimir P.

    2011-01-01

    The use of lysosome-targeted liposomes may significantly improve the delivery of therapeutic enzymes and chaperones into lysosomes for the treatment of lysosomal storage disorders. The aim of this research was to synthesize new potentially lysosomotropic ligands on a base of Neutral Red and rhodamine B and to study their ability to enhance specific lysosomal delivery of surface-modified liposomes loaded with a model compound, fluorescein isothiocyanate-dextran (FD). The delivery of these lipo...

  3. Multi-target-directed ligands: application to the Alzheimer's disease

    OpenAIRE

    Simoni, Elena

    2010-01-01

    The MTDL (multi-target-directed ligand) design strategy is used to develop single chemical entities that are able to simultaneously modulate multiple targets. The development of such compounds might disclose new avenues for the treatment of a variety of pathologies (e.g. cancer, AIDS, neurodegenerative diseases), for which an effective cure is urgently needed. This strategy has been successfully applied to Alzheimer’s disease (AD) due to its multifactorial nature, involving cholinergic dysfun...

  4. METAL NANOPARTICLES FUNCTIONALIZED WITH METAL-LIGAND COVALENT BONDS

    OpenAIRE

    Kang, Xiongwu

    2012-01-01

    Metal-organic contact has been recognized to play important roles in regulation of optical and electronic properties of nanoparticles. In this thesis, significant efforts have been devoted into synthesis of ruthenium nanoparticles with various metal-ligand interfacial linkages and investigation of their electronic and optical properties. Ruthenium nanoparticles were prepared by the self-assembly of functional group onto bare Ru colloid surface. As to Ru-alkyne nanoparticles, the formation of ...

  5. Novel retinoic acid receptor ligands in Xenopus embryos.

    OpenAIRE

    Blumberg, B; Bolado, J; Derguini, F; Craig, A G; Moreno, T A; Chakravarti, D; Heyman, R A; Buck, J.; Evans, R M

    1996-01-01

    Retinoids are a large family of natural and synthetic compounds related to vitamin A that have pleiotropic effects on body physiology, reproduction, immunity, and embryonic development. The diverse activities of retinoids are primarily mediated by two families of nuclear retinoic acid receptors, the RARs and RXRs. Retinoic acids are thought to be the only natural ligands for these receptors and are widely assumed to be the active principle of vitamin A. However, during an unbiased, bioactivit...

  6. Predicting protein-ligand and protein-peptide interfaces

    Science.gov (United States)

    Bertolazzi, Paola; Guerra, Concettina; Liuzzi, Giampaolo

    2014-06-01

    The paper deals with the identification of binding sites and concentrates on interactions involving small interfaces. In particular we focus our attention on two major interface types, namely protein-ligand and protein-peptide interfaces. As concerns protein-ligand binding site prediction, we classify the most interesting methods and approaches into four main categories: (a) shape-based methods, (b) alignment-based methods, (c) graph-theoretic approaches and (d) machine learning methods. Class (a) encompasses those methods which employ, in some way, geometric information about the protein surface. Methods falling into class (b) address the prediction problem as an alignment problem, i.e. finding protein-ligand atom pairs that occupy spatially equivalent positions. Graph theoretic approaches, class (c), are mainly based on the definition of a particular graph, known as the protein contact graph, and then apply some sophisticated methods from graph theory to discover subgraphs or score similarities for uncovering functional sites. The last class (d) contains those methods that are based on the learn-from-examples paradigm and that are able to take advantage of the large amount of data available on known protein-ligand pairs. As for protein-peptide interfaces, due to the often disordered nature of the regions involved in binding, shape similarity is no longer a determining factor. Then, in geometry-based methods, geometry is accounted for by providing the relative position of the atoms surrounding the peptide residues in known structures. Finally, also for protein-peptide interfaces, we present a classification of some successful machine learning methods. Indeed, they can be categorized in the way adopted to construct the learning examples. In particular, we envisage three main methods: distance functions, structure and potentials and structure alignment.

  7. Structural basis for AMPA receptor activation and ligand selectivity

    DEFF Research Database (Denmark)

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

    2002-01-01

    and binding experiments, has been used to increase our knowledge concerning the ionotropic glutamate receptor GluR2 at the molecular level. Five high-resolution X-ray structures of the ligand-binding domain of GluR2 (S1S2J) complexed with the three agonists (S)-2-amino-3-[3-hydroxy-5-(2-methyl-2H-tetrazol-5...

  8. Zwitterionic Group VIII transition metal initiators supported by olefin ligands

    Science.gov (United States)

    Bazan, Guillermo C.; Chen, Yaofeng

    2011-10-25

    A zwitterionic Group VIII transition metal complex containing the simple and relatively small 3-(arylimino)-but-1-en-2-olato ligand that catalyzes the formation of polypropylene and high molecular weight polyethylene. A novel feature of this catalyst is that the active species is stabilized by a chelated olefin adduct. The present invention also provides methods of polymerizing olefin monomers using zwitterionic catalysts, particularly polypropylene and high molecular weight polyethylene.

  9. 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.

  10. Rational design of metal coordination compounds with azomethine ligands

    Energy Technology Data Exchange (ETDEWEB)

    Garnovskii, Alexander D; Vasil' chenko, Igor S [Institute of Physical and Organic Chemistry, Rostov State University, Rostov-on-Don (Russian Federation)

    2002-11-30

    This review surveys the state of art in the coordination chemistry of chelating azomethine systems, viz., amino(hydroxy)-azomethines, {beta}-aminovinyl ketones, {beta}-aminovinylimines and their sulfur- and selenium-containing analogues. Variations in the fine structure of azomethine ligands allow one to perform the targeted synthesis of chelate and molecular, mono-, bi- and polynuclear, homo- and heterometallic structures. The bibliography includes 425 reference000.

  11. Proton-dependent zinc release from intracellular ligands

    OpenAIRE

    Kiedrowski, Lech

    2014-01-01

    In cultured cortical and hippocampal neurons when intracellular pH drops from 6.6 to 6.1, yet unclear intracellular stores release micromolar amounts of Zn2+ into the cytosol. Mitochondria, acidic organelles, and/or intracellular ligands could release this Zn2+. Although exposure to the protonophore FCCP precludes re-loading of the mitochondria and acidic organelles with Zn2+, FCCP failed to compromise the ability of the intracellular stores to repeatedly release Zn2+. There...

  12. Aerobic oxidation assisted by ligand-free palladium catalysts

    Institute of Scientific and Technical Information of China (English)

    Jia Rui Wang; Chu Ting Yang; Lei Liu; Qing Xiang Guo

    2007-01-01

    Aerobic oxidation of electron-rich benzylic and phenyl allylic alcohols was achieved with high yields with only 0.1 mol.% ofPd(OAc)2 catalyst in the absence of any ligand. This procedure was expected to be valuable for realistic industrial-scale applications from both economic as well as environmental points of view.(C) 2006 Qing Xiang Guo. Published by Elsevier B.V. on behalf of Chinese Chemical Society. All rights reserved.

  13. Probing heterotrimeric G protein activation: applications to biased ligands.

    OpenAIRE

    Denis, Colette; Saulière, Aude; Galandrin, Ségolène; Sénard, Jean-Michel; Galés, Céline

    2012-01-01

    Cell surface G protein-coupled receptors (GPCRs) drive numerous signaling pathways involved in the regulation of a broad range of physiologic processes. Today, they represent the largest target for modern drugs development with potential application in all clinical fields. Recently, the concept of “ligand-directed trafficking” has led to a conceptual revolution in pharmacological theory, thus opening new avenues for drug discovery. Accordingly, GPCRs do not function as simple on-off switch bu...

  14. Imaging Ligand-Dependent Activation of CXCR7

    Directory of Open Access Journals (Sweden)

    Kathryn E. Luker

    2009-10-01

    Full Text Available Chemokine CXCL12 is proposed to promote multiple steps in growth of primary tumors and progression to metastatic disease in more than 20 different cancers. Functions of CXCL12 previously were believed to be controlled only by receptor CXCR4, but CXCR7 was recently identified as a second receptor for this chemokine. CXCR7 increases tumor formation and metastasis in mouse models, suggesting that this receptor may also be a key target for blocking effects of CXCL12 in cancer. To image activation of CXCR7 in intact cells and living mice, we tested the hypothesis that binding of chemokine ligands to CXCR7 recruits β-arrestins, a family of cytosolic adapter proteins that interact with many activated chemokine and related seven-transmembrane receptors. Using firefly luciferase protein fragment complementation, we established that chemokine ligands CXCL12 and CXCL11 significantly increase association of CXCR7 and β-arrestins with preferential interaction of the receptor with β-arrestin 2. The magnitude of interactions between CXCR7 and β-arrestin 2 increased over time after treatment with ligands, contrasting with transient association of β-arrestin 2 and CXCR4. β-Arrestin 2 increased uptake of CXCL12 in cells expressing CXCR7, emphasizing the functional relevance of the interaction between CXCR7 and β-arrestin 2. In an orthotopic xenograft model of human breast cancer, we used bioluminescence imaging to quantify changes in the association of CXCR7 and β-arrestin 2. These studies demonstrate ligand-dependent interactions of CXCR7 with β-arrestin 2 that promote accumulation of chemokines and establish an imaging assay for the dynamic regulation of CXCR7 by chemokines and candidate therapeutic agents in cell-based assays and living mice.

  15. Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove

    DEFF Research Database (Denmark)

    McMurtrey, Curtis; Trolle, Thomas; Sansom, Tiffany;

    2016-01-01

    HLA class I presentation of pathogen-derived peptide ligands is essential for CD8+ T cell recognition of Toxoplasma gondii infected cells. Currently, little data exist pertaining to peptides that are presented after T. gondii infection. Herein we purify HLA-A*02:01 complexes from T. gondii infected...... cells and characterize the peptide ligands using LCMS. We identify 195 T. gondii encoded ligands originating from both secreted and cytoplasmic proteins. Surprisingly, T. gondii ligands are significantly longer than uninfected host ligands, and these longer pathogen derived peptides maintain a canonical...

  16. Ligand-protein docking using a quantum stochastic tunneling optimization method.

    Science.gov (United States)

    Mancera, Ricardo L; Källblad, Per; Todorov, Nikolay P

    2004-04-30

    A novel hybrid optimization method called quantum stochastic tunneling has been recently introduced. Here, we report its implementation within a new docking program called EasyDock and a validation with the CCDC/Astex data set of ligand-protein complexes using the PLP score to represent the ligand-protein potential energy surface and ScreenScore to score the ligand-protein binding energies. When taking the top energy-ranked ligand binding mode pose, we were able to predict the correct crystallographic ligand binding mode in up to 75% of the cases. By using this novel optimization method run times for typical docking simulations are significantly shortened.

  17. Conformational Changes and Ligand Recognition of Escherichia coli d-Xylose Binding Protein Revealed

    OpenAIRE

    Sooriyaarachchi, Sanjeewani; Ubhayasekera, Wimal; Park, Chankyu; Mowbray, Sherry

    2010-01-01

    ABC transport systems account for most import of necessary nutrients in bacteria. The periplasmic binding component (or an equivalent membrane-anchored protein) is critical to recognizing the cognate ligand and directing it to the appropriate membrane permease. Here we report X-ray structures of D-xylose-binding protein from Escherichia coli in ligand-free open, ligand-bound open and ligand-bound closed forms, at 2.15, 2.2, and 2.2-Å resolution, respectively. The ligand-bound open form is the...

  18. Microassay for measurement of binding of radiolabelled ligands to cell surface molecules.

    Science.gov (United States)

    Woof, J M; Burton, D R

    1988-07-22

    An improved technique for measuring the binding of radiolabelled ligands to cell surface molecules has been developed by modification of a procedure using centrifugation through a water-immiscible oil to separate free and cell-bound ligand. It maximises the percentage of ligand bound since cell-bound and free ligand can be separated easily and reproducibly even when very small reaction volumes are used. This permits low levels of ligand radiolabelling and relatively low numbers of cells to be used. PMID:2840465

  19. Ligand Promiscuity of Aryl Hydrocarbon Receptor Agonists and Antagonists Revealed by Site-Directed Mutagenesis

    OpenAIRE

    Soshilov, Anatoly A; DENISON, Michael S.

    2014-01-01

    The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that can be activated by structurally diverse chemicals. To examine the mechanisms responsible for the promiscuity in AhR ligand binding, we determined the effects of mutations within the AhR ligand-binding domain (LBD) on the activity of diverse AhR ligands. Site-directed mutagenesis identified Ile319 of the mouse AhR and, to a lesser extent, Phe318 as residues involved in ligand-selective modulation of AhR transf...

  20. Ligand Binding to Chlorite Dismutase from Magnetospirillum sp.

    Science.gov (United States)

    De Schutter, Amy; Correia, Hugo D; Freire, Diana M; Rivas, María G; Rizzi, Alberto; Santos-Silva, Teresa; González, Pablo J; Van Doorslaer, Sabine

    2015-10-29

    Chlorite dismutase (Cld) catalyzes the reduction of chlorite to chloride and dioxygen. Here, the ligand binding to Cld of Magnetospirillum sp. (MaCld) is investigated with X-ray crystallography and electron paramagnetic resonance (EPR). EPR reveals a large heterogeneity in the structure of wild-type MaCld, showing a variety of low- and high-spin ferric heme forms. Addition of an axial ligand, such as azide or imidazole, removes this heterogeneity almost entirely. This is in line with the two high resolution crystal structures of MaCld obtained in the presence of azide and thiocyanate that show the coordination of the ligands to the heme iron. The crystal structure of the MaCld-azide complex reveals a single well-defined orientation of the azide molecule in the heme pocket. EPR shows, however, a pH-dependent heme structure, probably due to acid-base transitions of the surrounding amino-acid residues stabilizing azide. For the azide and imidazole complex of MaCld, the hyperfine and nuclear quadrupole interactions with the close-by (14)N and (1)H nuclei are determined using pulsed EPR. These values are compared to the corresponding data for the low-spin forms observed in the ferric wild-type MaCld and to existing EPR data on azide and imidazole complexes of other heme proteins. PMID:26287794

  1. Structure and ligand recognition of class C GPCRs

    Institute of Scientific and Technical Information of China (English)

    Lei CHUN; Wen-hua ZHANG; Jian-feng LIU

    2012-01-01

    The G-protein-coupled receptors (GPCRs) are one of the largest super families of cell-surface receptors and play crucial roles in virtu-ally every organ system.One particular family of GPCRs,the class C GPCRs,is distinguished by a characteristically large extracellular domain and constitutive dimerization.The structure and activation mechanism of this family result in potentially unique ligand recognition sites,thereby offering a variety of possibilities by which receptor activity might be modulated using novel compounds.In the present article,we aim to provide an overview of the exact sites and structural features involved in ligand recognition of the class C GPCRs.Furthermore,we demonstrate the precise steps that occur during the receptor activation process,which underlie the possibilities by which receptor function may be altered by different approaches.Finally,we use four typical family members to illustrate orthosteric and allosteric sites with representative ligands and their corresponding therapeutic potential.

  2. Selective Chromium(VI) Ligands Identified Using Combinatorial Peptoid Libraries

    Science.gov (United States)

    Knight, Abigail S.; Zhou, Effie Y.; Pelton, Jeffrey G.; Francis, Matthew B.

    2013-01-01

    Hexavalent chromium (Cr(VI)) is a world-wide water contaminant that is currently without cost-effective and efficient remediation strategies. This is in part due to a lack of ligands that can bind it amid an excess of innocuous ions in aqueous solution. We present herein the design and application of a peptoid-based library of ligand candidates for toxic metal ions. A selective screening process was used to identify members of the library that can bind to Cr(VI) species at neutral pH and in the presence of a large excess of spectator ions. Eleven sequences were identified, and their affinities were compared using titrations monitored with UV-Vis spectroscopy. To identify the interactions involved in coordination and specificity, we evaluated the effects of sequence substitutions and backbone variation in the highest affinity structure. Additional characterization of the complex formed between this sequence and Cr(VI) was performed using NMR spectroscopy. To evaluate the ability of the developed sequences to remediate contaminated solutions, the structures were synthesized on a solid-phase resin and incubated with environmental water samples that contained simulated levels of chromium contamination. The synthetic structures demonstrated the ability to reduce the amount of toxic chromium to levels within the range of the EPA contamination guidelines. In addition to providing some of the first selective ligands for Cr(VI), these studies highlight the promise of peptoid sequences as easily-prepared components of environmental remediation materials. PMID:24195610

  3. Recent advances in the synthesis of endocannabinoid related ligands.

    Science.gov (United States)

    Razdan, R K; Mahadevan, A

    2002-12-31

    The chemical strategies used for the synthesis of various ligands related to the endocannabinoid system namely anandamide (AEA), 2-arachidonylglycerol (2-Ara-Gl), CB1/(vanilloid receptors) VR1, anandamide membrane transporter (AMT) and fatty acid amide hydrolase (FAAH) are described in this review. In general, the chemical synthesis of analogs with changes in the head group of AEA was quite straightforward involving the conversion of an acid to an amide or an ester. Analogs which had modifications in the end pentyl chain were more difficult to synthesize and required multistep synthetic sequences to prepare the target compounds. A facile total synthesis of 2-Ara-Gl was reported and an HPLC procedure for its identification and quantification was developed, but because of the instability of 2-Ara-Gl another synthesis was developed so that it can be stored as the more stable phenylboronate ester. Similarly the chemical synthesis of various ligands in the remaining areas of CB1/VR1, AMT and FAAH are described. A summary of the present state of knowledge about the SAR in each area is presented to help in the design and synthesis of novel ligands for the future. PMID:12505687

  4. Synthesis, spectroscopic, thermogravimetric and antimicrobial studies of mixed ligands complexes

    Science.gov (United States)

    Mahmoud, Walaa H.; Mahmoud, Nessma F.; Mohamed, Gehad G.; El-Sonbati, Adel Z.; El-Bindary, Ashraf A.

    2015-09-01

    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.

  5. Evolution of ligand specificity in vertebrate corticosteroid receptors

    Directory of Open Access Journals (Sweden)

    Deitcher David L

    2011-01-01

    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.

  6. Copper isotope fractionation during equilibration with natural and synthetic ligands.

    Science.gov (United States)

    Ryan, Brooke M; Kirby, Jason K; Degryse, Fien; Scheiderich, Kathleen; McLaughlin, Mike J

    2014-01-01

    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. PMID:24992660

  7. Mixed-ligand complexes of ruthenium(II) incorporating a diazo ligand: Synthesis, characterization and DNA binding

    Indian Academy of Sciences (India)

    Megha S Deshpande; Avinash S Kumbhar

    2005-03-01

    Mixed-ligand complexes of the type [Ru(N-N)2(dzdf)]Cl2, where N-N is 2,2'-bipyridine (bpy), 1,10-phenanthroline (phen) and 9-diazo-4,5-diazafluorene (dzdf), have been synthesized and characterized by elemental analysis, UV-Vis, IR and NMR spectroscopy. 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 to CT-DNA. The complex [Ru(phen)2(dzdf)]Cl2 binds with CT-DNA through an intercalative binding mode, while the complex [Ru(bpy)2(dzdf)]Cl2 binds electrostatically.

  8. New functionalized β-diketiminate ligands and f elements

    International Nuclear Information System (INIS)

    β-diketiminate ligands have received increased interest in coordination chemistry, especially for homogeneous catalysis. Their successful applications arise from an easy and fine tuning of the ligand electronic and geometric properties. However, these modifications are limited to the introduction of neutral donors (ethers or amines), on the nitrogen substituents of the β-diketiminate skeleton. The main focus of this research project is to overcome this limitation by synthesizing new β-diketiminate ligands functionalized by one or two anionic aryl-oxide groups, and to study their coordination chemistry with lanthanide and actinide ions. Access to these species relies on a fine understanding of the mechanism underlying their formation, and the sensitivity of the β-di-iminium skeleton towards nucleophiles (phenols) has been identified as the limiting side reaction in the synthetic route. Addition of reactants in well defined order allowed the formation of two new N-aryl-oxy-β-diketiminate dianions on a multi-gram scale. The two ligands differ by their steric bulk and exhibit different coordination behaviors towards lanthanides and actinide ions, which were rationalized on geometric considerations. The reactivity of three of these new complexes has been investigated. A Ce(III) N-aryl-oxy-β-diketiminate complex exhibits interesting reduction properties, due to the shift of its oxidation potential to negative values by its coordination environment. A Th(IV) complex presents a vacant coordination site, which has been probed with different Lewis bases, emphasizing two spatial arrangements ruled by inter-ligand repulsion. It has been compared to its U(IV) analogue, which can be oxidized to a rare terminal mono-oxo uranium(VI) species. The latter was reversibly reduced to its U(V) and U(IV) derivatives, creating the first series of terminal mono-oxo uranium complexes with three successive oxidation states. These compounds represent an opportunity to better understand

  9. The Movable Type Method Applied to Protein-Ligand Binding

    Science.gov (United States)

    Zheng, Zheng; Ucisik, Melek N.; Merz, Kenneth M.

    2013-01-01

    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

  10. Proton-dependent zinc release from intracellular ligands.

    Science.gov (United States)

    Kiedrowski, Lech

    2014-07-01

    In cultured cortical and hippocampal neurons when intracellular pH drops from 6.6 to 6.1, yet unclear intracellular stores release micromolar amounts of Zn(2+) into the cytosol. Mitochondria, acidic organelles, and/or intracellular ligands could release this Zn(2+) . Although exposure to the protonophore FCCP precludes reloading of the mitochondria and acidic organelles with Zn(2+) , FCCP failed to compromise the ability of the intracellular stores to repeatedly release Zn(2+) . Therefore, Zn(2+) -releasing stores were not mitochondria or acidic organelles but rather intracellular Zn(2+) ligands. To test which ligands might be involved, the rate of acid-induced Zn(2+) release from complexes with cysteine, glutathione, histidine, aspartate, glutamate, glycine, and carnosine was investigated; [Zn(2+) ] was monitored in vitro using the ratiometric Zn(2+) -sensitive fluorescent probe FuraZin-1. Carnosine failed to chelate Zn(2+) but did chelate Cu(2+) ; the remaining ligands chelated Zn(2+) and upon acidification were releasing it into the medium. However, when pH was decreasing from 6.6 to 6.1, only zinc-cysteine complexes rapidly accelerated the rate of Zn(2+) release. The zinc-cysteine complexes also released Zn(2+) when a histidine-modifying agent, diethylpyrocarbonate, was applied at pH 7.2. Since the cytosolic zinc-cysteine complexes can contain micromolar amounts of Zn(2+) , these complexes may represent the stores responsible for an acid-induced intracellular Zn(2+) release. This study aimed at identifying intracellular stores which release Zn(2+) when pHi drops from 6.6 to 6.1. It was found that these stores are not mitochondria or acidic organelles, but rather intracellular Zn(2+) ligands. When the pH was decreasing from 6.6 to 6.1, only zinc-cysteine complexes showed a rapid acceleration in the rate of Zn(2+) release. Therefore, the stores responsible for an acid-induced intracellular Zn(2+) release in neurons may be the cytosolic zinc-cysteine complexes

  11. Mixed-ligand complex formation equilibria of CuII with biguanide in presence of glycine as the auxiliary ligand

    Indian Academy of Sciences (India)

    Tannistha Roy Barman; G N Mukherjee

    2006-09-01

    Equilibrium study on the mixed ligand complex formation of CuII with biguanide(Bg) and glycine (HG), indicated the formation of the complexes: Cu(Bg)2+, Cu(Bg)$_{2}^{2+}$, Cu(Bg-H)(Bg)+, Cu(Bg-H)2, Cu(Bg)(OH)+, Cu(Bg-H)(OH); Cu(G)+, Cu(G)(OH), Cu(G)2; Cu(G)(Bg)+, Cu(G)(Bg-H); (G)Cu(Bg)Cu(G)2+, (G)Cu(Bg-H)Cu(G)+, and (G)Cu(Bg-2H)Cu(G). From the deprotonation constants of coordinated biguanide (Bg) in the complexes Cu(Bg)(OH)+, Cu(Bg-H)(Bg)+ and Cu(G)(Bg)+, the Lewis basicities of the coordinated ligand species (Bg-H)-, OH- and glycinate (G-) were found to be of the order: (Bg-H)- >> OH- > G-. Bridging (N1-N4, N2-N5) tetradentate mode of coordination by biguanide species Bg, (Bg-H)- and (Bg-2H)2- was indicated from the occurrence of biguanide-bridged dinuclear mixed ligand complexes (G)Cu(Bg)Cu(G)2+, (G)Cu(Bg-H)Cu(G)+, (G)Cu(Bg-2H)Cu(G) in the complexation equilibria.

  12. Demonstration of ligand decoration, and ligand-induced perturbation, of G-quadruplexes in a plasmid using atomic force microscopy.

    Science.gov (United States)

    Mela, Ioanna; Kranaster, Ramon; Henderson, Robert M; Balasubramanian, Shankar; Edwardson, J Michael

    2012-01-17

    G-Quadruplexes are nucleic acid secondary structures consisting of a planar arrangement of four guanine residues. Potential G-quadruplex-forming sequences are widely distributed throughout the genome. Significantly, they are present in telomeres and are enriched in gene promoters and first introns, raising the possibility that perturbation of G-quadruplex stability might have therapeutic potential, for example in the treatment of cancer. Ligands that interact selectively with G-quadruplexes include both proteins and small molecules, although the interactions between ligands and their G-quadruplex targets have been monitored using indirect methods. In addition, the G-quadruplex targets have often been short DNA fragments. Here, we have used atomic force microscopy imaging to examine directly at the single-molecule level the interaction of ligands with G-quadruplexes generated during transcription of a plasmid containing a G-rich insert. We show that the structures produced during transcription are decorated specifically by the single-chain antibody HF1 and by the nuclear protein PARP-1, both of which are known to recognize G-quadruplexes. Our results provide clear structural evidence of G-quadruplex formation in a transcription-dependent case and demonstrate directly how small-molecule stabilizers and destabilizers can manipulate these structures in a biochemically functional system. PMID:22225525

  13. Analysis of ligand-protein exchange by Clustering of Ligand Diffusion Coefficient Pairs (CoLD-CoP)

    Science.gov (United States)

    Snyder, David A.; Chantova, Mihaela; Chaudhry, Saadia

    2015-06-01

    NMR spectroscopy is a powerful tool in describing protein structures and protein activity for pharmaceutical and biochemical development. This study describes a method to determine weak binding ligands in biological systems by using hierarchic diffusion coefficient clustering of multidimensional data obtained with a 400 MHz Bruker NMR. Comparison of DOSY spectrums of ligands of the chemical library in the presence and absence of target proteins show translational diffusion rates for small molecules upon interaction with macromolecules. For weak binders such as compounds found in fragment libraries, changes in diffusion rates upon macromolecular binding are on the order of the precision of DOSY diffusion measurements, and identifying such subtle shifts in diffusion requires careful statistical analysis. The "CoLD-CoP" (Clustering of Ligand Diffusion Coefficient Pairs) method presented here uses SAHN clustering to identify protein-binders in a chemical library or even a not fully characterized metabolite mixture. We will show how DOSY NMR and the "CoLD-CoP" method complement each other in identifying the most suitable candidates for lysozyme and wheat germ acid phosphatase.

  14. 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.

  15. Copper binding ligands: production by marine plankton and characterization by ESI-MS

    Science.gov (United States)

    Orians, K.; Ross, A.; Lawrence, M.; Ikonomou, M.

    2003-04-01

    Organic complexation affects the bioavailability and distribution of copper in the surface ocean. The cyanobacterium Synechococcus sp. PCC 7002 was cultured in the lab and subjected to near-toxic Cu concentrations. Strong Cu-binding ligands were produced under these conditions, as found for other species of Synechococcus. The copper-binding ligand produced had a log K'cond. (log conditional stability constant) of 12.2, similar to the natural ligands found in the surface ocean. The amount of ligand produced was proportional to the amount of copper present. Isolation and concentration of these compounds for characterization by electrospray mass spectrometry (ESI-MS) provides information about the structure of the organic ligands and their metal-ion complexes. Using model ligands, we'll show that ligands can be characterized by ESI-MS and that the location of the copper binding site can be determined in complex molecules. We'll also present results of copper-complexing ligands extracted from the coastal waters of British Columbia. Ligand concentrations are higher at low salinity and in surface waters, indicating that these ligands are produced in surface waters and/or delivered to the region via the Fraser River. Analysis of the extracts with highest UV absorbance identified two Cu2+ ligands of molecular weight 259 and 264. The mass and isotopic distributions are consistent with dipeptides and tripeptides containing two metal-binding amino groups. This result is consistent with the findings of other studies attempting to characterize Cu2+ ligands in seawater. The structure of the identified ligand is similar to that of rhodotorulic acid (a microbial siderophore), glutathione, and phytochelatins, indicating that small peptides and related compounds can act as strong, specific metal chelators in natural waters

  16. Metal nanoparticles functionalized with metal-ligand covalent bonds

    Science.gov (United States)

    Kang, Xiongwu

    Metal-organic contact has been recognized to play important roles in regulation of optical and electronic properties of nanoparticles. In this thesis, significant efforts have been devoted into synthesis of ruthenium nanoparticles with various metal-ligand interfacial linkages and investigation of their electronic and optical properties. Ruthenium nanoparticles were prepared by the self-assembly of functional group onto bare Ru colloid surface. As to Ru-alkyne nanoparticles, the formation of a Ru-vinylidene (Ru=C=CH--R) interfacial bonding linkage was confirmed by the specific reactivity of the nanoparticles with imine derivatives and olefin at the metal-ligand interface, as manifested in NMR, photoluminescence, and electrochemical measurements. Interestingly, it was found the electronic coupling coefficient (beta)for strongly depend upon such metal-ligand interfacial bonding. Next, such metal-ligand interfacial bonding was extended to ruthenium-nitrene pi bonds on ruthenium colloids, which were investigated by XPS. The nanoparticles exhibited a 1:1 atomic ratio of nitrogen to sulfur, consistent with that of sulfonyl nitrene fragments. In addition, the nanoparticle-bound nitrene moieties behaved analogously to azo derivatives, as manifested in UV-vis and fluorescence measurements. Further testimony of the formation of Ru=N interfacial linkages was highlighted in the unique reactivity of the nanoparticles with alkenes by imido transfer. Extensive conjugation between metal-ligand interfacial bond results in remarkable intraparticle charge delocalization on Ru-alkynide nanoparticles, which was manipulated by simple chemical reduction or oxidation. Charging of extra electrons into the nanoparticle cores led to an electron-rich metal core and hence red-shift of the triple bond stretching mode, lower binding energy of sp hybridized C 1s and dimmed fluorescence of nanoparticles. Instead, chemical oxidation resulted in the opposite impacts on these properties. By taking

  17. 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)

    2010-06-15

    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)

  18. Screening and Optimization of Ligand Conjugates for Lysosomal Targeting

    Science.gov (United States)

    Meerovich, Igor; Koshkaryev, Alexander; Thekkedath, Ritesh; Torchilin, Vladimir P.

    2011-01-01

    The use of lysosome-targeted liposomes may significantly improve the delivery of therapeutic enzymes and chaperones into lysosomes for the treatment of lysosomal storage disorders. The aim of this research was to synthesize new potentially lysosomotropic ligands on a base of Neutral Red and rhodamine B and to study their ability to enhance specific lysosomal delivery of surface-modified liposomes loaded with a model compound, fluorescein isothiocyanate-dextran (FD). The delivery of these liposomes and their content to lysosomes in HeLa cells was investigated by confocal immunofluorescent microscopy, subcellular fractionation and flow cytometry. Confocal microscopy demonstrated that liposomes modified with derivatives of rhodamine B provide good rate of co-localization well the specific lysosomal markers. The comparison of fluorescence of FD in lysosomes isolated by subcellular fractionation also showed that the efficiency of lysosomal delivery of liposomal load by liposomes modified with some of synthesized ligands was significantly higher compared with plain liposomes. These results were additionally confirmed by the flow cytometry of the intact cells treated with liposomes loaded with with 5-dodecanoylaminofluorescein di-β-D-galactopyranoside, a specific substrate for the intralysosomal β-galactosidase, using a number of cell lines, including macrophages with induced phenotype of lysosomal enzyme deficiency; two of the synthesized ligands – rhodamine B DSPE-PEG2k-amide and 6-(3-(DSPE-PEG2k)-thioureido) rhodamine B – demonstrated enhanced lysosomal delivery, in some cases, higher than that for commercially available rhodamine B octadecyl ester, with the best results (the enhancement of the lysosomal delivery up to 75% greater in comparison to plain liposomes) shown for the cells with induced lysosomal enzyme deficiency phenotype. Use of liposomes modified with rhodamine B derivatives may be advantageous for the development of drug delivery systems for the

  19. Immunostimulation by OX40 Ligand Transgenic Ewing Sarcoma Cells.

    Science.gov (United States)

    Reuter, Dajana; Staege, Martin S; Kühnöl, Caspar D; Föll, Jürgen

    2015-01-01

    Interleukin-2 (IL-2) transgenic Ewing sarcoma cells can induce tumor specific T and NK cell responses and reduce tumor growth in vivo and in vitro. Nevertheless, the efficiency of this stimulation is not high enough to inhibit tumor growth completely. In addition to recognition of the cognate antigen, optimal T-cell stimulation requires signals from so-called co-stimulatory molecules. Several members of the tumor necrosis factor superfamily have been identified as co-stimulatory molecules that can augment antitumor immune responses. OX40 (CD134) and OX40 ligand (OX40L = CD252; also known as tumor necrosis factor ligand family member 4) is one example of such receptor/ligand pair with co-stimulatory function. In the present investigation, we generated OX40L transgenic Ewing sarcoma cells and tested their immunostimulatory activity in vitro. OX40L transgenic Ewing sarcoma cells showed preserved expression of Ewing sarcoma-associated (anti)gens including lipase member I, cyclin D1 (CCND1), cytochrome P450 family member 26B1 (CYP26B1), and the Ewing sarcoma breakpoint region 1-friend leukemia virus integration 1 (EWSR1-FLI1) oncogene. OX40L-expressing tumor cells showed a trend for enhanced immune stimulation against Ewing sarcoma cells in combination with IL-2 and stimulation of CD137. Our data suggest that inclusion of the OX40/OX40L pathway of co-stimulation might improve immunotherapy strategies for the treatment of Ewing sarcoma. PMID:26579494

  20. Engineering periplasmic ligand binding proteins as glucose nanosensors

    Directory of Open Access Journals (Sweden)

    Constance J. Jeffery

    2011-01-01

    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.

  1. Overview of Stabilizing Ligands for Biocompatible Quantum Dot Nanocrystals

    Directory of Open Access Journals (Sweden)

    Aaron Clapp

    2011-11-01

    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.

  2. Ligands specify estrogen receptor alpha nuclear localization and degradation

    Directory of Open Access Journals (Sweden)

    Caze-Subra Stéphanie

    2010-12-01

    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

  3. Single-Channel Recording of Ligand-Gated Ion Channels.

    Science.gov (United States)

    Plested, Andrew J R

    2016-01-01

    Single-channel recordings reveal the microscopic properties of individual ligand-gated ion channels. Such recordings contain much more information than measurements of ensemble behavior and can yield structural and functional information about the receptors that participate in fast synaptic transmission in the brain. With a little care, a standard patch-clamp electrophysiology setup can be adapted for single-channel recording in a matter of hours. Thenceforth, it is a realistic aim to record single-molecule activity with microsecond resolution from arbitrary cell types, including cell lines and neurons. PMID:27480725

  4. Coordination Chemistry of Europium(III) Ion Towards Acylpyrazolone Ligands.

    Science.gov (United States)

    Atanassova, Maria; Kurteva, Vanya; Billard, Isabelle

    2015-01-01

    Two Eu(III) complexes were synthesized using 4-acylpyrazolone ligands: 3-methyl-4-(4-methylbenzoyl)-1-phenyl-pyrazol-5-one (HPMMBP) and 3-methyl-1-phenyl-4-(4-phenylbenzoyl)-pyrazol-5-one (HPPMBP). The composition of the obtained solid complexes was determined as Eu(PMMBP)3·C2H5OH and Eu(PPMBP)3·3H2O based on elemental analysis and was further studied by IR, NMR and TG-TSC data. The lanthanoid complexation in solid state and in solution during liquid-liquid extraction (molecular diluent and ionic liquid) is discussed.

  5. Hypoxic regulation of the NKG2D ligand, H60

    OpenAIRE

    Krishnamurthy, Siddharth Ravindran

    2009-01-01

    Hypoxia in the context of cancer has been well studied as it has been shown that tumors that are in hypoxic conditions tend to become malignant or metastatic. There is evidence that hypoxia is able to modulate tumor immunogenicity, however this phenomenon has not been well characterized. Here, we look at the effects of hypoxia on tumor immunogenicity from the perspective of NK cell recognition. We find that hypoxia decreases the expression of the NKG2D ligand, H60 post-transcriptionally but n...

  6. Ligand-induced formation of nucleic acid triple helices.

    OpenAIRE

    Pilch, D S; Breslauer, K J

    1994-01-01

    We demonstrate that ligand binding can be used to induce the formation of triplex structures that would not otherwise form. Specifically, we show that binding of berenil or 4',6-diamidino-2-phenylindole DAPI) induces formation of the poly(rA).poly(rA).poly(dT) triplex, providing an example of an RNA(purine).RNA(purine).DNA(pyrimidine) triplex. We also show that binding of berenil, DAPI, ethidium, or netropsin can induce formation of the poly(dT).poly(rA).poly(dT) triplex, thereby overcoming a...

  7. From Toxins Targeting Ligand Gated Ion Channels to Therapeutic Molecules

    Directory of Open Access Journals (Sweden)

    Antoine Taly

    2011-03-01

    Full Text Available Ligand-gated ion channels (LGIC play a central role in inter-cellular communication. This key function has two consequences: (i these receptor channels are major targets for drug discovery because of their potential involvement in numerous human brain diseases; (ii they are often found to be the target of plant and animal toxins. Together this makes toxin/receptor interactions important to drug discovery projects. Therefore, toxins acting on LGIC are presented and their current/potential therapeutic uses highlighted.

  8. Ultrafast infrared studies of complex ligand rearrangements in solution

    Energy Technology Data Exchange (ETDEWEB)

    Payne, Christine K.

    2003-05-31

    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

  9. The Search for Covalently Ligandable Proteins in Biological Systems.

    Science.gov (United States)

    Badshah, Syed Lal; Mabkhot, Yahia Nasser

    2016-01-01

    This commentary highlights the recent article published in Nature, June 2016, titled: "Proteome-wide covalent ligand discovery in native biological systems". They screened the whole proteome of different human cell lines and cell lysates. Around 700 druggable cysteines in the whole proteome were found to bind the electrophilic fragments in both active and inactive states of the proteins. Their experiment and computational docking results agreed with one another. The usefulness of this study in terms of bringing a change in medicinal chemistry is highlighted here. PMID:27598117

  10. Doping Control Via Molecularly Engineered Surface Ligand Coordination

    KAUST Repository

    Yuan, Mingjian

    2013-08-05

    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.

  11. Iron-Catalyzed Hydroboration: Unlocking Reactivity through Ligand Modulation.

    Science.gov (United States)

    Espinal-Viguri, Maialen; Woof, Callum R; Webster, Ruth L

    2016-08-01

    Iron-catalyzed hydroboration (HB) of alkenes and alkynes is reported. A simple change in ligand structure leads to an extensive change in catalyst activity. Reactions proceed efficiently over a wide range of challenging substrates including activated, unactivated and sterically encumbered motifs. Conditions are mild and do not require the use of reducing agents or other additives. Large excesses of borating reagent are not required, allowing control of chemo- and regioselectivity in the presence of multiple double bonds. Mechanistic insight reveals that the reaction is likely to proceed via a highly reactive iron hydride intermediate. PMID:27321704

  12. Natural compounds in the synthesis of chiral organophosphorous ligands

    Science.gov (United States)

    Tolstikov, Alexander G.; Khlebnikova, Tatiana B.; Tolstikova, Olga V.; Tolstikov, Genrikh A.

    2003-09-01

    Methods for the synthesis of chiral organophosphorus compounds based on natural optically active compounds (hydroxy acids, amino acids and their derivatives, mono- and disaccharides, mono- and diterpenoids, steroids) are discussed. Particular attention is given to the synthesis of bisphosphines and bisphosphinites. These compounds serve as ligands for transition metal complexes, which catalyse asymmetric hydrogenation. Data on the enantioselectivity of hydrogenation of unsaturated precursors of amino acids and unsaturated prochiral acids as well as on information on the enantioselectivity of hydrosilylation of ketones are surveyed.

  13. Natural compounds in the synthesis of chiral organophosphorous ligands

    Energy Technology Data Exchange (ETDEWEB)

    Tolstikov, Alexander G; Khlebnikova, Tatiana B; Tolstikov, Genrikh A [G.K. Boreskov Institute of Catalysis, Siberian Branch of the Russian Academy of Sciences, Novosibirsk (Russian Federation); Tolstikova, Olga V [Institute of Technical Chemistry, Urals Branch of the Russian Academy of Sciences, Perm (Russian Federation)

    2003-09-30

    Methods for the synthesis of chiral organophosphorus compounds based on natural optically active compounds (hydroxy acids, amino acids and their derivatives, mono- and disaccharides, mono- and diterpenoids, steroids) are discussed. Particular attention is given to the synthesis of bisphosphines and bisphosphinites. These compounds serve as ligands for transition metal complexes, which catalyse asymmetric hydrogenation. Data on the enantioselectivity of hydrogenation of unsaturated precursors of amino acids and unsaturated prochiral acids as well as on information on the enantioselectivity of hydrosilylation of ketones are surveyed.

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

    Science.gov (United States)

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

    2016-01-14

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

  15. Galaxy7TM: flexible GPCR-ligand docking by structure refinement.

    Science.gov (United States)

    Lee, Gyu Rie; Seok, Chaok

    2016-07-01

    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 http://galaxy.seoklab.org/7TM, 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. PMID:27131365

  16. Improved Metathesis Lifetime: Chelating Pyridinyl-Alcoholato Ligands in the Second Generation Grubbs Precatalyst

    Directory of Open Access Journals (Sweden)

    Jean I. du Toit

    2014-04-01

    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.

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

    Science.gov (United States)

    Comba, Peter; Rudolf, Henning; Wadepohl, Hubert

    2015-02-14

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

  18. The connection between metal ion affinity and ligand affinity in integrin I domains

    DEFF Research Database (Denmark)

    Vorup-Jensen, Thomas; Waldron, TT; Astrof, N;

    2007-01-01

    Integrins are cell-surface heterodimeric proteins that mediate cell-cell, cell-matrix, and cell-pathogen interactions. Half of the known integrin alpha subunits contain inserted domains (I domains) that coordinate ligand through a metal ion. Although the importance of conformational changes within...... isolated I domains in regulating ligand binding has been reported, the relationship between metal ion binding affinity and ligand binding affinity has not been elucidated. Metal and ligand binding by several I domain mutants that are stabilized in different conformations are investigated using isothermal...... titration calorimetry and surface plasmon resonance studies. This work suggests an inverse relationship between metal ion affinity and ligand binding affinity (i.e. constructs with a high affinity for ligand exhibit a low affinity for metal). This trend is discussed in the context of structural studies...

  19. 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;

    2015-01-01

    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...

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

    KAUST Repository

    Choi, Joshua J.

    2011-03-09

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

  1. New avenues for ligand-mediated processes--expanding metal reactivity by the use of redox-active catechol, o-aminophenol and o-phenylenediamine ligands.

    Science.gov (United States)

    Broere, Daniël L J; Plessius, Raoul; van der Vlugt, Jarl Ivar

    2015-10-01

    Redox-active ligands have evolved from being considered spectroscopic curiosities - creating ambiguity about formal oxidation states in metal complexes - to versatile and useful tools to expand on the reactivity of (transition) metals or to even go beyond what is generally perceived possible. This review focusses on metal complexes containing either catechol, o-aminophenol or o-phenylenediamine type ligands. These ligands have opened up a new area of chemistry for metals across the periodic table. The portfolio of ligand-based reactivity invoked by these redox-active entities will be discussed. This ranges from facilitating oxidative additions upon d(0) metals or cross coupling reactions with cobalt(iii) without metal oxidation state changes - by functioning as an electron reservoir - to intramolecular ligand-to-substrate single-electron transfer to create a reactive substrate-centered radical on a Pd(ii) platform. Although the current state-of-art research primarily consists of stoichiometric and exploratory reactions, several notable reports of catalysis facilitated by the redox-activity of the ligand will also be discussed. In conclusion, redox-active ligands containing catechol, o-aminophenol or o-phenylenediamine moieties show great potential to be exploited as reversible electron reservoirs, donating or accepting electrons to activate substrates and metal centers and to enable new reactivity with both early and late transition as well as main group metals.

  2. New avenues for ligand-mediated processes--expanding metal reactivity by the use of redox-active catechol, o-aminophenol and o-phenylenediamine ligands.

    Science.gov (United States)

    Broere, Daniël L J; Plessius, Raoul; van der Vlugt, Jarl Ivar

    2015-10-01

    Redox-active ligands have evolved from being considered spectroscopic curiosities - creating ambiguity about formal oxidation states in metal complexes - to versatile and useful tools to expand on the reactivity of (transition) metals or to even go beyond what is generally perceived possible. This review focusses on metal complexes containing either catechol, o-aminophenol or o-phenylenediamine type ligands. These ligands have opened up a new area of chemistry for metals across the periodic table. The portfolio of ligand-based reactivity invoked by these redox-active entities will be discussed. This ranges from facilitating oxidative additions upon d(0) metals or cross coupling reactions with cobalt(iii) without metal oxidation state changes - by functioning as an electron reservoir - to intramolecular ligand-to-substrate single-electron transfer to create a reactive substrate-centered radical on a Pd(ii) platform. Although the current state-of-art research primarily consists of stoichiometric and exploratory reactions, several notable reports of catalysis facilitated by the redox-activity of the ligand will also be discussed. In conclusion, redox-active ligands containing catechol, o-aminophenol or o-phenylenediamine moieties show great potential to be exploited as reversible electron reservoirs, donating or accepting electrons to activate substrates and metal centers and to enable new reactivity with both early and late transition as well as main group metals. PMID:26148803

  3. Investigation of some novel ligands of pyruvaldehyde bis(thiosemicarbazone) as pet radiopharmaceuticals

    International Nuclear Information System (INIS)

    Three novel ligands of pyruvaldehyde bis (thiosemicarbazone) have been synthesized. These ligands are labelled with 64Cu. The factors that affect labelling yield are also investigated. The biodistribution of three 64Cu ligand complexes in mice are determined. The higher brain uptake with a prolonged retention time is found in case of 64Cu-PTSP. The results suggested that 62Cu-PTSP may be used as a PET tracer for cerebral perfusion and it needs more research

  4. Recent advances in catalytic asymmetric hydrogenation:Renaissance of the monodentate phosphorus ligands

    Institute of Scientific and Technical Information of China (English)

    GUO Hongchao; DING Kuiling; DAI Lixin

    2004-01-01

    The history for the development of chiral phosphorus ligands in catalytic asymmetric hydrogenation is briefly highlighted. This review focuses on the recent advances in the synthesis of the monodentate phosphorus ligands and their applications in catalytic asymmetric hydrogenation. The examples highlighted in this article clearly demonstrated the importance and advantages of monodentate phosphorus ligands, which had been ignored for 30 a and experienced a renaissance at the very beginning of this millennium, particularly in the area of asymmetric hydrogenation.

  5. Synthesis of optically active half-sandwich complexes with bidentate and tridentate ligands

    OpenAIRE

    Tsuno, Takashi

    2007-01-01

    PN ligands 1 and 2, derived from 2-diphenylphosphanylmethylpyridine, were synthesized, to which in the backbone a tether to a cyclopentadiene system and for comparison an iPr substituent were attached. The chiral compounds were resolved by introduction of a menthoxy substituent into the 2-position of the pyridine system. The tripod ligand 1 contains three different binding sites (Cp, P, and N) connected by a resolved chiral carbon atom. (SC)-Configuration of this tripod ligand enforces (RRh)-...

  6. A modular approach to neutral P,N-ligands: synthesis and coordination chemistry

    Science.gov (United States)

    Blasius, Clemens K; Intorp, Sebastian N; Wadepohl, Hubert

    2016-01-01

    Summary We report the modular synthesis of three different types of neutral κ2-P,N-ligands comprising an imine and a phosphine binding site. These ligands were reacted with rhodium, iridium and palladium metal precursors and the structures of the resulting complexes were elucidated by means of X-ray crystallography. We observed that subtle changes of the ligand backbone have a significant influence on the binding geometry und coordination properties of these bidentate P,N-donors. PMID:27340475

  7. Abnormal carbenes as ligands in transition metal chemistry: curiosities with exciting perspectives

    OpenAIRE

    Albrecht, Martin

    2009-01-01

    This review compiles the advances achieved in our laboratories using abnormal and less heteroatom-stabilized carbenes as ligands for transition metal chemistry. Fundamental studies allowed the evaluation of the impact of this new class of ligands both electronically and sterically. Based on these results, initial catalytic applications have been devised in the area of H-H and C-H bond activation, demonstrating the potential of abnormal carbenes as unique ligands for transition metals.

  8. Reversible self-assembly of gels through metal-ligand interactions

    OpenAIRE

    Yuichiro Kobayashi; Yoshinori Takashima; Akihito Hashidzume; Hiroyasu Yamaguchi; Akira Harada

    2013-01-01

    Metal-ligand interactions with various proteins form in vivo metal assemblies. In recent years, metallosupramolecular approaches have been utilized to forge an assortment of fascinating two- and three-dimensional nano-architectures, and macroscopic materials, such as metal-ligand coordination polymeric materials, have promise in artificial systems. However to the best of our knowledge, the self-assembly of macroscopic materials through metal-ligand interactions has yet to be reported. Herein ...

  9. Ligand-based reduction of CO2 and release of CO on iron(II).

    Science.gov (United States)

    Thammavongsy, Zachary; Seda, Takele; Zakharov, Lev N; Kaminsky, Werner; Gilbertson, John D

    2012-09-01

    A synthetic cycle for the CO(2)-to-CO conversion (with subsequent release of CO) based on iron(II), a redox-active pydridinediimine ligand (PDI), and an O-atom acceptor is reported. This conversion is a passive-type ligand-based reduction, where the electrons for the CO(2) conversion are supplied by the reduced PDI ligand and the ferrous state of the iron is conserved.

  10. Structural and functional characterization of a novel type of ligand-independent RXR-USP receptor

    OpenAIRE

    Iwema, Thomas; Billas, Isabelle ML; Beck, Yannick; Bonneton, François; Nierengarten, Hélène; Chaumot, Arnaud; Richards, Geoff; Laudet, Vincent; Moras, Dino

    2007-01-01

    Retinoid X receptor (RXR) and Ultraspiracle (USP) play a central role as ubiquitous heterodimerization partners of many nuclear receptors. While it has long been accepted that a wide range of ligands can activate vertebrate/mollusc RXRs, the existence and necessity of specific endogenous ligands activating RXR-USP in vivo is still matter of intense debate. Here we report the existence of a novel type of RXR-USP with a ligand-independent functional conformation. Our studies involved Tribolium ...

  11. FGO: A novel ontology for identification of ligand functional group

    Science.gov (United States)

    Varadwaj, Pritish Kumar; Lahiri, Tapobrata

    2007-01-01

    Small molecules play crucial role in the modulation of biological functions by interacting with specific macromolecules. Hence small molecule interactions are captured by a variety of experimental methods to estimate and propose correlations between molecular structures to their biological activities. The tremendous expanse in publicly available small molecules is also driving new efforts to better understand interactions involving small molecules particularly in area of drug docking and pharmacogenomics. We have studied and designed a functional group identification system with the associated ontology for it. The functional group identification system can detect the functional group components from given ligand structure with specific coordinate information. Functional group ontology (FGO) proposed by us is a structured classification of chemical functional group which acts as an important source of prior knowledge that may be automatically integrated to support identification, categorization and predictive data analysis tasks. We have used a new annotation method which can be used to construct the original structure from given ontological expression using exact coordinate information. Here, we also discuss about ontology-driven similarity measure of functional groups and uses of such novel ontology for pharmacophore searching and de-novo ligand designing. PMID:18288335

  12. A review of monoamine transporter-ligand interactions.

    Science.gov (United States)

    Immadisetty, Kalyan; Madura, Jeffry D

    2013-12-01

    Transporters of the monoamines serotonin, dopamine, and norepinephrine are plasma membrane proteins belonging to the neurotransmitter sodium symporter family (NSS). Monoamine transporters (MATs) by facilitating reuptake of neurotransmitters from the synapse into the presynaptic nerve terminal, regulate neurotransmitter chemical signaling and maintain homeostasis. MATs are targets for several psychostimulants such as cocaine and amphetamine; and also for drugs treating several psychiatric disorders such as depression, attention deficit hyperactivity disorder, Parkinson's disease, and schizophrenia. Since, currently available treatment has several limitations and side effects, novel treatment is highly desired. Efforts to develop better treatment have been hampered by the lack of crystal structures for MATs. However, leucine transporter (LeuTAa), a bacterial protein from Aquifex aeolicus, belonging to the same NSS family as MATs has recently been crystallized. LeuTAa is used as a template to develop homology models of MATs, which facilitates understanding of the structure, function and pharmacology of MATs. Experimental methods for drug discovery demand a significant amount of time, effort and money. Efficient utilization of computational techniques hastens the process of drug discovery and also significantly reduces the cost. Assessing the binding affinity of drugs to the receptors is a key aspect of drug design. Free energy calculations compliment the experiment by quantitatively assessing the affinity of ligands to receptors. These methods are highly beneficial in the lead identification and optimization stages of rational drug design. We review the currently available free energy methods to treat protein-ligand interactions along with several free energy studies performed on MATs. PMID:24138394

  13. Chiral benzamidinate ligands in rare-earth-metal coordination chemistry.

    Science.gov (United States)

    Benndorf, Paul; Kratsch, Jochen; Hartenstein, Larissa; Preuss, Corinna M; Roesky, Peter W

    2012-11-01

    The treatment of the recently reported potassium salt (S)-N,N'-bis-(1-phenylethyl)benzamidinate ((S)-KPEBA) and its racemic isomer (rac-KPEBA) with anhydrous lanthanide trichlorides (Ln = Sm, Er, Yb, Lu) afforded mostly chiral complexes. The tris(amidinate) complex [{(S)-PEBA}(3)Sm], bis(amidinate) complexes [{Ln(PEBA)(2)(μ-Cl)}(2)] (Ln = Sm, Er, Yb, Lu), and mono(amidinate) compounds [Ln(PEBA)(Cl)(2)(thf)(n)] (Ln = Sm, Yb, Lu) were isolated and structurally characterized. As a result of steric effects, the homoleptic 3:1 complexes of the smaller lanthanide atoms Yb and Lu were not accessible. Furthermore, chiral bis(amidinate)-amido complexes [{(S)-PEBA}(2)Ln{N(SiMe(3))(2)}] (Ln = Y, Lu) were synthesized by an amine-elimination reaction and salt metathesis. All of these chiral bis- and tris(amidinate) complexes had additional axial chirality and they all crystallized as diastereomerically pure compounds. By using rac-PEBA as a ligand, an achiral meso arrangement of the ligands was observed. The catalytic activities and enantioselectivities of [{(S)-PEBA}(2)Ln{N(SiMe(3))(2)}] (Ln = Y, Lu) were investigated in hydroamination/cyclization reactions. A clear dependence of the rate of reaction and enantioselectivity on the ionic radius was observed, which showed higher reaction rates but poorer enantioselectivities for the yttrium compound. PMID:23015310

  14. Organic ligands influence leaching kinetics of fixated FGD material

    Energy Technology Data Exchange (ETDEWEB)

    Chin-Min Cheng; Yu Sik Hwang; John J. Lenhart; Harold W. Walker [Ohio State University, Columbus, OH (United States). Department of Civil and Environmental Engineering and Geodetic Science

    2008-10-15

    The presence of organic ligands, including oxalate, citrate, maleate and Pahokee peat humic acid (PPHA), influenced the leaching kinetics of fixated flue gas desulfurization (FGD) material in acidic solution (pH 2.9-5.0). In the presence of oxalate, the leaching was inhibited at all pH values examined. XRD and SEM analyses demonstrated that formation of a calcium oxalate mineral phase on the fixated FGD material surface created a surface layer which reduced the extent of leaching. Maleate and PPHA inhibited leaching at pH 2.9, but either promoted, inhibited, or had no effect on leaching, depending on the particular element, at pH 5.0. ATR-FTIR analysis indicated maleate and PPHA formed both inner- and outer-spherically bound species at pH 2.9, whereas at pH 5.0 only outer-sphere complexes seemed evident. These surface species likely inhibited the leaching process at pH 2.9 through a surface blocking mechanism. At pH 5.0, the ligand surface complexes either promoted or inhibited leaching, depending on the element, through a combination of direct and indirect mechanisms. Citrate significantly promoted the leaching process at all pH values examined. 43 refs., 6 figs., 3 tabs.

  15. Modeling of ligand binding to dopamine D2 receptor

    Directory of Open Access Journals (Sweden)

    Ostopovici-Halip Liliana

    2014-01-01

    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.

  16. Gold(I) catalysts with bifunctional P, N ligands.

    Science.gov (United States)

    Wetzel, Corinna; Kunz, Peter C; Thiel, Indre; Spingler, Bernhard

    2011-08-15

    A series of phosphanes with imidazolyl substituents were prepared as hemilabile PN ligands. The corresponding gold(I) complexes were tested as bifunctional catalysts in the Markovnikov hydration of 1-octyne, as well as in the synthesis of propargylamines by the three component coupling reaction of piperidine, benzaldehyde, and phenylacetylene. While the activity in the hydration of 1-octyne was low, the complexes are potent catalysts for the three component coupling reaction. In homogeneous solution the conversions to the respective propargylamine were considerably higher than under aqueous biphasic conditions. The connectivity of the imidazolyl substituents to the phosphorus atom, their substitution pattern, as well as the number of heteroaromatic substituents have pronounced effects on the catalytic activity of the corresponding gold(I) complexes. Furthermore, formation of polymetallic species with Au(2), Au(3), and Au(4) units has been observed and the solid-state structures of the compounds [(5)(2)Au(3)Cl(2)]Cl and [(3c)(2)Au(4)Cl(2)]Cl(2) (3c = tris(2-isopropylimidazol-4(5)-yl phosphane, 5 = 2-tert-butylimidazol-4(5)-yldiphenyl phosphane) were determined. The gold(I) complexes of imidazol-2-yl phosphane ligands proved to be a novel source for bis(NHC)gold(I) complexes (NHC = N-heterocyclic carbene). PMID:21761834

  17. Cherry-picked ligands at histamine receptor subtypes.

    Science.gov (United States)

    Sadek, Bassem; Stark, Holger

    2016-07-01

    Histamine, a biogenic amine, is considered as a principle mediator of multiple physiological effects through binding to its H1, H2, H3, and H4 receptors (H1-H4Rs). Currently, the HRs have gained attention as important targets for the treatment of several diseases and disorders ranging from allergy to Alzheimer's disease and immune deficiency. Accordingly, medicinal chemistry studies exploring histamine-like molecules and their physicochemical properties by binding and interacting with the four HRs has led to the development of a diversity of agonists and antagonists that display selectivity for each HR subtype. An overview on H1-R4Rs and developed ligands representing some key steps in development is provided here combined with a short description of structure-activity relationships for each class. Main chemical diversities, pharmacophores, and pharmacological profiles of most innovative H1-H4R agonists and antagonists are highlighted. Therefore, this overview should support the rational choice for the optimal ligand selection based on affinity, selectivity and efficacy data in biochemical and pharmacological studies. This article is part of the Special Issue entitled 'Histamine Receptors'. PMID:26581501

  18. Characterization of Selectin Ligands on Hematopoietic Stem Cells

    KAUST Repository

    Mahmood, Hanan

    2013-05-18

    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.

  19. Small-molecule PSMA ligands. Current state, SAR and perspectives.

    Science.gov (United States)

    Machulkin, Alexey E; Ivanenkov, Yan A; Aladinskaya, Anastasia V; Veselov, Mark S; Aladinskiy, Vladimir A; Beloglazkina, Elena K; Koteliansky, Victor E; Shakhbazyan, Artem G; Sandulenko, Yuri B; Majouga, Alexander G

    2016-09-01

    Prostate cancer (PC) is the prevalent malignancy widespread among men in the Western World. Prostate specific membrane antigen (PSMA) is an established PC marker and has been considered as a promising biological target for anti-PC drug delivery and diagnostics. The protein was found to be overexpressed in PC cells, including metastatic, and the neovasculature of solid tumors. These properties make PSMA-based approach quite appropriate for effective PC imaging and specific drug therapy. Through the past decade, a variety of PSMA-targeted agents has been systematically evaluated. Small-molecule compounds have several advantages over other classes, such as improved pharmacokinetics and rapid blood clearance. These low-weight ligands have similar structure and can be divided into three basic categories in accordance with the type of their zinc-binding core-head. Several PSMA binders are currently undergoing clinical trials generally for PC imaging. The main goal of the present review is to describe the recent progress achieved within the title field and structure activity relationships (SAR) disclosed for different PSMA ligands. Recent in vitro and in vivo studies for each type of the compounds described have also been briefly summarized. PMID:26887438

  20. Adapting Document Similarity Measures for Ligand-Based Virtual Screening

    Directory of Open Access Journals (Sweden)

    Mubarak Himmat

    2016-04-01

    Full Text Available Quantifying the similarity of molecules is considered one of the major tasks in virtual screening. There are many similarity measures that have been proposed for this purpose, some of which have been derived from document and text retrieving areas as most often these similarity methods give good results in document retrieval and can achieve good results in virtual screening. In this work, we propose a similarity measure for ligand-based virtual screening, which has been derived from a text processing similarity measure. It has been adopted to be suitable for virtual screening; we called this proposed measure the Adapted Similarity Measure of Text Processing (ASMTP. For evaluating and testing the proposed ASMTP we conducted several experiments on two different benchmark datasets: the Maximum Unbiased Validation (MUV and the MDL Drug Data Report (MDDR. The experiments have been conducted by choosing 10 reference structures from each class randomly as queries and evaluate them in the recall of cut-offs at 1% and 5%. The overall obtained results are compared with some similarity methods including the Tanimoto coefficient, which are considered to be the conventional and standard similarity coefficients for fingerprint-based similarity calculations. The achieved results show that the performance of ligand-based virtual screening is better and outperforms the Tanimoto coefficients and other methods.

  1. Cage Opening of a Carborane Ligand by Metal Cluster Complexes.

    Science.gov (United States)

    Adams, Richard D; Kiprotich, Joseph; Peryshkov, Dmitry V; Wong, Yuen Onn

    2016-05-01

    The reaction of Os3 (CO)10 (NCMe)2 with closo-o-C2 B10 H10 has yielded two interconvertible isomers Os3 (CO)9 (μ3 -4,5,9-C2 B10 H8 )(μ-H)2 (1 a) and Os3 (CO)9 (μ3 -3,4,8-C2 B10 H8 )(μ-H)2 (1 b) formed by the loss of the two NCMe ligands and one CO ligand from the Os3 cluster. Two BH bonds of the o-C2 B10 H10 were activated in its addition to the osmium cluster. A second triosmium cluster was added to the 1 a/1 b mixture to yield the complex Os3 (CO)9 (μ-H)2 (μ3 -4,5,9-μ3 -7,11,12-C2 B10 H7 )Os3 (CO)9 (μ-H)3 (2) that contains two triosmium triangles attached to the same carborane cage. When heated, 2 was transformed to the complex Os3 (CO)9 (μ-H)(μ3 -3,4,8-μ3 -7,11,12-C2 B10 H8 )Os3 (CO)9 (μ-H) (3) by a novel opening of the carborane cage with loss of H2 . PMID:26971388

  2. Integration of Ligand Field Molecular Mechanics in Tinker.

    Science.gov (United States)

    Foscato, Marco; Deeth, Robert J; Jensen, Vidar R

    2015-06-22

    The ligand field molecular mechanics (LFMM) method for transition-metal complexes has been integrated in Tinker, an easily available and popular molecular modeling software package. The capability to calculate LFMM potentials has been provided by extending the functional forms of the Tinker package as well as by integrating routines for calculating the ligand field stabilization energy (LFSE), which is central to LFMM. The capabilities of the implementation are illustrated by both static calculations on the two spin states of [Fe(NH3)6](2+) and on [Cu(NH3)m](2+) (m = 4, 5, 6) and dynamic (LFMD) simulations of an FeN6-type spin-crossover compound. In addition to showing that results obtained with the Tinker-LFMM implementation are consistent with those of experiment and other computational methods and programs, we note that whereas LFMM is able to handle the conventional tetragonal Jahn-Teller distortion of the bond distances in [Cu(NH3)6](2+), the LFSE term is also necessary in order to obtain even qualitatively correct coordination geometries for the two lower-coordinate copper complexes. PMID:25970002

  3. Ligand Specific Efficiency (LSE) Index for PET Tracer Optimization.

    Science.gov (United States)

    Auberson, Yves P; Briard, Emmanuelle; Sykes, David; Reilly, John; Healy, Mark

    2016-07-01

    Ligand efficiency indices are widely used to guide chemical optimization in drug discovery, due to their predictive value in the early steps of optimization. At later stages, however, as more complex properties become critical for success, indices relying on calculated, rather than experimental, parameters become less informative. This problem is particularly acute when developing positron emission tomography (PET) imaging agents, for which nonspecific binding (NSB) to membranes and non-target proteins is a frequent cause of failure. NSB cannot be predicted using in silico parameters. To address this gap, we explored the use of the experimentally determined chromatographic hydrophobicity index on immobilized artificial membranes, CHI(IAM), to guide the optimization of NSB. The ligand specific efficiency (LSE) index was defined as the ratio between affinity (pIC50 or pKd ) and the logarithmic value of CHI(IAM). It allows for quantification of binding affinity to the target of interest, relative to NSB. Its use was illustrated by the optimization of PET tracer candidates for the prostacyclin receptor. PMID:27193393

  4. Mimicking nature: Phosphopeptide enrichment using combinatorial libraries of affinity ligands.

    Science.gov (United States)

    Batalha, Iris L; Zhou, Houjiang; Lilley, Kathryn; Lowe, Christopher R; Roque, Ana C A

    2016-07-29

    Phosphorylation is a reversible post-translational modification of proteins that controls a plethora of cellular processes and triggers specific physiological responses, for which there is a need to develop tools to characterize phosphorylated targets efficiently. Here, a combinatorial library of triazine-based synthetic ligands comprising 64 small molecules has been rationally designed, synthesized and screened for the enrichment of phosphorylated peptides. The lead candidate (coined A8A3), composed of histidine and phenylalanine mimetic components, showed high binding capacity and selectivity for binding mono- and multi-phosphorylated peptides at pH 3. Ligand A8A3 was coupled onto both cross-linked agarose and magnetic nanoparticles, presenting higher binding capacities (100-fold higher) when immobilized on the magnetic support. The magnetic adsorbent was further screened against a tryptic digest of two phosphorylated proteins (α- and β-caseins) and one non-phosphorylated protein (bovine serum albumin, BSA). The MALDI-TOF mass spectra of the eluted peptides allowed the identification of nine phosphopeptides, comprising both mono- and multi-phosphorylated peptides. PMID:27345211

  5. Efficient synthesis of hexahydroindenopyridines and their potential as melatoninergic ligands.

    Science.gov (United States)

    Párraga, Javier; Moreno, Laura; Diaz, Amelia; El Aouad, Noureddine; Galán, Abraham; Sanz, María Jesús; Caignard, Daniel-Henri; Figadère, Bruno; Cabedo, Nuria; Cortes, Diego

    2014-10-30

    Hexahydroindenopyridine (HHIP) is an interesting tricyclic piperidine nucleus that is structurally related to melatonin, a serotonin-derived neurohormone. Melatonin receptor ligands have applications in several cellular, neuroendocrine and neurophysiological disorders, including depression and/or insomnia. We report herein an efficient two-step method to prepare new HHIP via enamine C-alkylation-cyclization. The influence of substituents on the benzene ring and the nitrogen atom on melatoninergic receptors has been studied. Among the 25 synthesized HHIPs, some of them containing methylenedioxy (series 2) and 8-chloro-7-methoxy substituents (series 4) on the benzene ring revealed affinity for the MT1 and/or the MT2 receptors within the nanomolar range or low micromolar. Similar activities were also encountered for those presenting urea (4g), N-aryl (2e) and N-alkyl (2f) acetamide functions. Therefore, new synthesized compounds with a HHIP nucleus have emerged as new promising leads towards the discovery of melatoninergic ligands which could provide new therapeutic agents. PMID:25232966

  6. Cell adhesion on ligand gradient substrates: a thermodynamic study.

    Science.gov (United States)

    Sarvestani, Alireza S

    2010-01-01

    Gradient distribution of bio-adhesive proteins can regulate multiple cellular processes, including adhesion, growth, and migration. The ability to control the cell function by changing the surface density of immobilized ligands has become increasingly important in design of implantable medical devices and tissue regenerating scaffolds. Recent techniques in fabrication of substrates with controlled surface properties allow the examination of cell sensitivity to a wide range of adhesion gradients. Understanding the mechanisms by which cells sense and respond to these directional cues warrants a quantitative assessment of macroscopic cellular response to the surface gradients, supported by predictive theoretical models. This article presents a theoretical basis to examine the effect of ligand gradients on cellular adhesion, using an equilibrium thermodynamic model. The model facilitates a systematic investigation of the complex interplay of cell-substrate specific adhesions, non-specific repulsions, and membrane elasticity. This purely mechanistic model predicts a biphasic dependence between the extent of cell spreading and its position across the gradient substrate. PMID:19701944

  7. In Silico Docking of HNF-1a Receptor Ligands

    Directory of Open Access Journals (Sweden)

    Gumpeny Ramachandra Sridhar

    2012-01-01

    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

  8. Quantitation of species differences in albumin–ligand interactions for bovine, human and rat serum albumins using fluorescence spectroscopy: A test case with some Sudlow's site I ligands

    International Nuclear Information System (INIS)

    Albumin, the most abundant plasma protein is an approximately 67 kDa sized water-soluble macromolecule. Since several drugs and xenobiotics circulate in the blood at least partially in albumin-bound form, albumin plays a key role in the pharmacokinetics/toxicokinetics of these chemicals. Most of the drugs and xenobiotics are Sudlow's site I ligands. In numerous studies, bovine serum albumin (BSA) is used for modeling albumin–ligand interactions and the results are extrapolated to human serum albumin (HSA). Furthermore, only limited information is available related to albumin–ligand interactions of different albumin species. Therefore, in our study, we have focused on the quantification of differences between bovine, human and rat serum albumin (RSA) using four Sudlow's site I ligands (luteolin, ochratoxin A, phenylbutazone and warfarin). Interactions were analyzed by fluorescence spectroscopy. Stability constants as well as competing capacities of the ligands were determined, and thermodynamic study was also performed. Our results highlight that there could be major differences between BSA, HSA and RSA in their ligand binding properties. Based on our observations we emphasize that in molecular aspects BSA behaves considerably differently from HSA or from albumins of other species therefore, it is strongly recommended to apply at least some confirmatory measurements when data obtained from other species are attempted to be extrapolated to HSA. -- Highlights: • Albumin–ligand interactions of human, bovine and rat albumins were studied. • Four Sudlow's site I ligands were tested by fluorescence spectroscopy. • Substantial differences were found in stability constants among albumin complexes. • Competing capacity of ligands showed major differences in the studied species. • Data obtained for BSA cannot be directly extrapolated to human albumin

  9. Synthesis, Spectral study of Ni (II) and CU (II) metal ions with Heterocyclic Ligands

    OpenAIRE

    Sachin R Joshi; Seema I. Habib

    2014-01-01

    Four Complexes of Cu (II) and Ni (II) Schiff bases have been prepared. The Schiff bases are derived by the reaction of Salisylaldoxime primary ligand with heterocyclic compounds such as 2-aminopyridine (S-L2), 2-2- bipyridine (S-L4) to form the secondary ligand, which than react with the metal halides to form corresponding complexes. The elemental analysis data shows that the metal to ligand ratio in all Ni(II) and Cu(II) simple complexes are 1:2 while for mixed ligand complexes having ratio ...

  10. Self-assembly of heteroleptic dinuclear metallosupramolecular kites from multivalent ligands via social self-sorting

    Directory of Open Access Journals (Sweden)

    Christian Benkhäuser

    2015-05-01

    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.

  11. CLE Peptides in Plants: Proteolytic Processing,Structure-Activity Relationship, and Ligand-Receptor Interaction

    Institute of Scientific and Technical Information of China (English)

    Xiaoming Gao; Yongfeng Guo

    2012-01-01

    Ligand-receptor signaling initiated by the CLAVATA3/ENDOSPERM SURROUNDING REGION (CLE) family peptides is critical in regulating cell division and differentiation in meristematic tissues in plants.Biologically active CLE peptides are released from precursor proteins via proteolytic processing.The mature form of CLE ligands consists of 12-13 amino acids with several post-translational modifications.This review summarizes recent progress toward understanding the proteolytic activities that cleave precursor proteins to release CLE peptides,the molecular structure and function of mature CLE ligands,and interactions between CLE ligands and corresponding leucine-rich repeat (LRR) receptor-like kinases (RLKs).

  12. Preparation of New Chiral Ferroceny Phosphine Ligands and Their Application to Organic Synthesis

    Institute of Scientific and Technical Information of China (English)

    S.Fukuzawa

    2007-01-01

    1 Results The unique structure of chiral ferrocenes allows one to design a variety of chiral phosphine ligands,which are useful tools for metal catalyzed asymmetric reactions.Although some useful chiral ferrocenyl phosphine ligands have already been reported,it is still an challenging subject tocreate new ferrocenyl phosphine ligands in order to cover asymmetric reactions in which conventional ligands do not effectively work[1].We happned to discover that 1,5-dilithiation of o-TMS blocked ferrocene 1 pr...

  13. Study of the spectroscopic characteristics of methyl (ligand) cobaloximes and their antibacterial activity

    Indian Academy of Sciences (India)

    N Navaneetha; P A Nagarjun; S Satyanarayana

    2007-01-01

    Spectroscopic characterization (IR, NMR and electronic spectra) of methyl (ligand) cobaloxime was done, where ligand = pyrazole, dimethyl pyrazole, alanine and alanine methyl ester. The frequency changes in the IR spectra and shifts in the NMR were explained on the basis of basicity of the ligand, steric hindrance, HSAB principle and - back-bonding from metal to ligand. Alanine and alanine methyl ester form more stable complexes than pyrazole and dimethyl pyrazole. Based on their IR and 1H NMR spectra it is inferred that pyrazole and dimethylpyrazole bind to Co (III) via N-2 ring nitrogen, i.e. monodentate coordination.

  14. Water networks contribute to enthalpy/entropy compensation in protein-ligand binding.

    Science.gov (United States)

    Breiten, Benjamin; Lockett, Matthew R; Sherman, Woody; Fujita, Shuji; Al-Sayah, Mohammad; Lange, Heiko; Bowers, Carleen M; Heroux, Annie; Krilov, Goran; Whitesides, George M

    2013-10-16

    The mechanism (or mechanisms) of enthalpy-entropy (H/S) compensation in protein-ligand binding remains controversial, and there are still no predictive models (theoretical or experimental) in which hypotheses of ligand binding can be readily tested. Here we describe a particularly well-defined system of protein and ligands--human carbonic anhydrase (HCA) and a series of benzothiazole sulfonamide ligands with different patterns of fluorination--that we use to define enthalpy/entropy (H/S) compensation in this system thermodynamically and structurally. The binding affinities of these ligands (with the exception of one ligand, in which the deviation is understood) to HCA are, despite differences in fluorination pattern, indistinguishable; they nonetheless reflect significant and compensating changes in enthalpy and entropy of binding. Analysis reveals that differences in the structure and thermodynamic properties of the waters surrounding the bound ligands are an important contributor to the observed H/S compensation. These results support the hypothesis that the molecules of water filling the active site of a protein, and surrounding the ligand, are as important as the contact interactions between the protein and the ligand for biomolecular recognition, and in determining the thermodynamics of binding.

  15. Ultrafast dynamics of ligand and substrate interaction in endothelial nitric oxide synthase under Soret excitation.

    Science.gov (United States)

    Hung, Chih-Chang; Yabushita, Atsushi; Kobayashi, Takayoshi; Chen, Pei-Feng; Liang, Keng S

    2016-01-01

    Ultrafast transient absorption spectroscopy of endothelial NOS oxygenase domain (eNOS-oxy) was performed to study dynamics of ligand or substrate interaction under Soret band excitation. Photo-excitation dissociates imidazole ligand in 4ps. The eNOS-oxy without additive is partially bound with water molecule, thus its photoexcited dynamics also shows ligand dissociation in <800fs. Then it followed by vibrational cooling coupled with charge transfer in 4.8ps, and recombination of ligand to distal side of heme in 12ps.

  16. Ligand-induced TCR down-regulation is not dependent on constitutive TCR cycling

    DEFF Research Database (Denmark)

    Dietrich, Jes; Menné, Charlotte; Lauritsen, Jens Peter H;

    2002-01-01

    , we next studied ligand-induced internalization in cells with abolished constitutive TCR cycling. We found that ligand-induced TCR internalization was not dependent on constitutive TCR internalization. Likewise, constitutive internalization and recycling of the TCR were independent of an intact ligand......TCR internalization takes place both in resting T cells as part of constitutive TCR cycling, after PKC activation, and during TCR triggering. It is still a matter of debate whether these pathways represent distinct pathways. Thus, some studies have indicated that ligand-induced TCR internalization...

  17. Rational design of cyclopropane-based chiral PHOX ligands for intermolecular asymmetric Heck reaction

    Directory of Open Access Journals (Sweden)

    Marina Rubina

    2014-07-01

    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.

  18. Narcissistic self-sorting in self-assembled cages of rare Earth metals and rigid ligands.

    Science.gov (United States)

    Johnson, Amber M; Wiley, Calvin A; Young, Michael C; Zhang, Xing; Lyon, Yana; Julian, Ryan R; Hooley, Richard J

    2015-05-01

    Highly selective, narcissistic self-sorting can be achieved in the formation of self-assembled cages of rare earth metals with multianionic salicylhydrazone ligands. The assembly process is highly sensitive to the length of the ligand and the coordination geometry. Most surprisingly, high-fidelity sorting is possible between ligands of identical coordination angle and geometry, differing only in a single functional group on the ligand core, which is not involved in the coordination. Supramolecular effects allow discrimination between pendant functions as similar as carbonyl or methylene groups in a complex assembly process. PMID:25784462

  19. Semiconductor Nanocrystals Hybridized with Functional Ligands: New Composite Materials with Tunable Properties

    Directory of Open Access Journals (Sweden)

    Nathan I. Hammer

    2010-01-01

    Full Text Available Semiconductor nanocrystals hybridized with functional ligands represent an important new class of composite nanomaterials. The development of these new nanoscale building blocks has intensified over the past few years and offer significant advantages in a wide array of applications. Functional ligands allow for incorporation of nanocrystals into areas where their unique photophysics can be exploited. Energy and charge transfer between the ligands and the nanocrystal also result in enhanced physical properties that can be tuned by the choice of ligand architecture. Here, progress in the development and applications involving this new class of composite materials will be discussed.

  20. Origin and evolution of the ligand-binding ability of nuclear receptors.

    Science.gov (United States)

    Markov, Gabriel V; Laudet, Vincent

    2011-03-01

    The origin of the ligand-binding ability of nuclear receptors is still a matter of discussion. Current opposing models are the early evolution of an ancestral receptor that would bind a specific ligand with high affinity and the early evolution of an ancestral orphan that was a constitutive transcription factor. Here we review the arguments in favour or against these two hypotheses, and we discuss an alternative possibility that the ancestor was a ligand sensor, which would be able to explain the apparently contradictory data generated in previous models for the evolution of ligand binding in nuclear receptors. PMID:21055443

  1. 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;

    2007-01-01

    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...... are filled by other ligand fragments. This novel binding mode shows that the acyl moiety can flip out of its classical binding pocket and bind elsewhere, suggesting a mechanism for the acyl-CoA transfer between ACBP and the active site of a target enzyme. This mechanism is of possible relevance...

  2. Equilibrium and kinetic studies on ligand substitution reactions of chloromethyl(aquo)cobaloxime with aromatic and aliphatic N-donor ligands

    Indian Academy of Sciences (India)

    D Sudarshan Reddy; S Satyanarayana

    2003-06-01

    Equilibria and kinetics of the reactions of chloromethyl(aquo)cobaloxime with histamine, histidine, glycine and ethyl glycine ester were studied as a function of pH at 25°C, 1.0 M ionic strength (KCl) by spectrophotometric techniques. Comparison of equilibrium constants and rate constants tells that the order is Hisdn > Hiamn > Gly > EtGlyest. The rate of substitution of H2O varies with the p of the incoming ligand and nucleophilic participation of the ligand in the transition state. The rate constants and equilibrium constants are correlated to the hardness and softness of the ligands and the Co(III) of cobaloxime.

  3. Modelling tyrosinase monooxygenase activity. Activation of dioxygen by dicopper(I) complexes and characterisation of dicopper(II) complexes

    Indian Academy of Sciences (India)

    Rajeev Gupta; Debalina Ghosh; Rabindranath Mukherjee

    2000-06-01

    Activation of dioxygen on dicopper(I) centres was systematically investigated using a group of open-chain and a macrocyclic -xylyl-based dinucleating ligand from a bioinorganic viewpoint. Even though intermediate peroxodicopper(II) species was not detected (even at -80°C for the open-chain system), the putative intermediate reacted with C-H groups in ligands giving oxygenated products (C-OH groups). Absorption, spectroscopic and magnetic properties of the final dicopper(II) complexes have been investigated.

  4. Synthesis, Characterization and Solvatochromism Investigation of Mixed Ligand Chelate Copper(Ⅱ) Complexes with Acetyleacetonate and Three Diamine Ligands

    Institute of Scientific and Technical Information of China (English)

    Golchoubian Hamid; Afshar Zahra Mohseni; Moayyedi Golasa; Bruno Giuseppe; Rudbari Hadi Amiri

    2012-01-01

    The syntheses of three mixed ligand chelate copper(II) complexes of the type [Cu(L)(acac)(H2O)]BPh4 where acac=acetyleacetonate; L=N,N-dimethyl,N′-benzylethane-1,2-diamine (L1), N,N-dimethyl, N′-2-methylbenzylethane-1,2-diamine (L2) or N,N-dimethyl,N′-2-chlorobenzylethane-1,2-diamine (L3) are reported and characterized by elemental analyses, spectroscopic and molar conductance measurements. The X-ray structure of complex 1 shows that the central copper atom is placed in a distorted square pyramidal geometry made by acac and diamine chelate in the base and a H2O molecule on the apex. The prepared complexes are fairly soluble in a large number of organic solvents and show positive solvatochromism. Calculations of SMLR (stepwise multiple linear regression) method was utilized to find the best model explaining the observed solvatochromic behavior and showed that among different solvent parameters, donor number (DN) is a dominant factor responsible for the shift in the d-d absorption band of the complexes to the lower wavenumber with increasing its values. The importance of substituent effect in diamine ligand on the spectral and SMLR measurements is also discussed.

  5. Thermodynamic, kinetic and structural studies on the mixed ligand complexes of palladium(II) with tridentate and monodentate ligands.

    Science.gov (United States)

    Nagy, Zoltán; Fábián, István; Bényei, Attila; Sóvágó, Imre

    2003-03-01

    Stability constants of the complexes formed in the reaction of [Pd(bpma)](2+) [bpma=bis(pyridin-2-ylmethyl)amine] with monodentate nitrogen and thioether ligands including uridine, MeUH, cytidine, MeC, EtGH, AcHis, AcHm, AcLys and AcMet were determined by potentiometric method. The coordination chemistry of [Pd(bpma)](2+) shows a significant similarity to that of [Pd(terpy)](2+), but it is different from [Pd(dien)](2+). The formation of hydroxo and dinuclear complexes is especially enhanced in the case of [Pd(bpma)](2+) and [Pd(terpy)](2+), but the affinity of palladium(II) ions for the coordination of thioether residues is reduced in the presence of pyridine nitrogen atoms. Stopped-flow kinetic measurements reveal that the substitution reactions of the thioether ligand AcMet are much faster than those of the N-donor cytidine. The presence of the two pyridyl residues significantly enhances the kinetic reactivity of [Pd(bpma)](2+) as compared to that of [Pd(dien)](2+). The Pd-S(thioether) bonded species can be important intermediates in multicomponent systems, but the equilibrium state is characterised by the formation of Pd-N bonded species. The complex [Pd(bpma)NO(3)]NO(3) has been prepared in solid state and its structure was elucidated by single crystal X-ray diffraction method. PMID:12628710

  6. Organometallic chemistry of chiral diphosphazane ligands: Synthesis and structural characterisation

    Indian Academy of Sciences (India)

    Kannan Raghuraman; Swadhin K Mandal; T S Venkatakrishnan; Setharampattu S Krishnamurthy; Munirathinam Nethaji

    2002-08-01

    The diphosphazane ligands of the type, (C20H12O2)PN(R)P(E)Y2 (R = CHMe2 or ()-∗CHMePh; E = lone pair or S; Y2 = O2C20H12 or Y = OC6H5 or OC6H4Me-4 or OC6H4OMe-4 or OC6H4Bu-4 or C6H5) bearing axially chiral 1,1'-binaphthyl-2,2'-dioxy moiety have been synthesised. The structure and absolute configuration of a diastereomeric palladium complex, [PdCl2{2-((O2C20H12)PN(()-∗CHMePh)PPh2}] has been determined by X-ray crystallography. The reactions of [CpRu(PPh3)2Cl] with various symmetrical and unsymmetrical diphosphazanes of the type, X2PN(R)PYY' (R = CHMe2 or ()-∗CHMePh; X = C6H5 or X2 = O2C20H12; Y = Y' = C6H5 or Y = C6H5, Y' = OC6H4Me-4 or OC6H3Me2-3,5 or N2C3HMe2-3,5) yield several diastereomeric neutral or cationic half-sandwich ruthenium complexes which contain a stereogenic metal center. In one case, the absolute configuration of a trichiral ruthenium complex, viz. [Cp∗Ru{2-Ph2PN(()-∗CHMePh)∗PPh (N2C3HMe2-3,5)}Cl] is established by X-ray diffraction. The reactions of Ru3(CO)12 with the diphosphazanes (C20H12O2)PN(R)PY2 (R = CHMe2 or Me; Y2=O2C20H12 or Y = OC6H5 or OC6H4Me-4 or OC6H4OMe-4 or OC6H4Bu-4 or C6H5) yield the triruthenium clusters [Ru3(CO)10{-(O2C20H12)PN(R)PY2}], in which the diphosphazane ligand bridges two metal centres. Palladium allyl chemistry of some of these chiral ligands has been investigated. The structures of isomeric 3-allyl palladium complexes, [Pd(3-1,3-R'2-C3H3){2-(rac)-(O2C20H12)PN(CHMe2)PY2}](PF6) (R' = Me or Ph; Y = C6H5 or OC6H5) have been elucidated by high field twodimensional NMR spectroscopic and X-ray crystallographic studies.

  7. Abundance of Flt3 and its ligand in astrocytic tumors

    Directory of Open Access Journals (Sweden)

    Eßbach C

    2013-05-01

    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

  8. 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)

    2009-07-31

    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

  9. An ontology for pharmaceutical ligands and its application for in silico screening and library design.

    Science.gov (United States)

    Schuffenhauer, Ansgar; Zimmermann, Jürg; Stoop, Ruedi; van der Vyver, Jan-Jan; Lecchini, Steffano; Jacoby, Edgar

    2002-01-01

    Annotation efforts in biosciences have focused in past years mainly on the annotation of genomic sequences. Only very limited effort has been put into annotation schemes for pharmaceutical ligands. Here we propose annotation schemes for the ligands of four major target classes, enzymes, G protein-coupled receptors (GPCRs), nuclear receptors (NRs), and ligand-gated ion channels (LGICs), and outline their usage for in silico screening and combinatorial library design. The proposed schemes cover ligand functionality and hierarchical levels of target classification. The classification schemes are based on those established by the EC, GPCRDB, NuclearDB, and LGICDB. The ligands of the MDL Drug Data Report (MDDR) database serve as a reference data set of known pharmacologically active compounds. All ligands were annotated according to the schemes when attribution was possible based on the activity classification provided by the reference database. The purpose of the ligand-target classification schemes is to allow annotation-based searching of the ligand database. In addition, the biological sequence information of the target is directly linkable to the ligand, hereby allowing sequence similarity-based identification of ligands of next homologous receptors. Ligands of specified levels can easily be retrieved to serve as comprehensive reference sets for cheminformatics-based similarity searches and for design of target class focused compound libraries. Retrospective in silico screening experiments within the MDDR01.1 database, searching for structures binding to dopamine D2, all dopamine receptors and all amine-binding class A GPCRs using known dopamine D2 binding compounds as a reference set, have shown that such reference sets are in particular useful for the identification of ligands binding to receptors closely related to the reference system. The potential for ligand identification drops with increasing phylogenetic distance. The analysis of the focus of a tertiary

  10. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.

    Science.gov (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

    2016-04-01

    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.

  11. Fe-binding dissolved organic ligands in the oxic and suboxic waters of the Black Sea

    Directory of Open Access Journals (Sweden)

    Loes J.A. Gerringa

    2016-05-01

    Full Text Available In the oxygen-rich layer of the Black Sea, above the permanent halocline, the Fe and nitrate concentrations are low where fluorescence is relatively high , indicating uptake by phytoplankton. In this study we used ligand exchange adsorptive cathodic stripping voltammetry (CLE-aCSV, using 2-(2-Thiazolylazo-p-cresol (TAC as measuring ligand, to investigate the role of Fe-binding dissolved organic ligands in keeping Fe in the dissolved phase and potentially biologically available. The conditional stability constant, logK´, was between 21 and 22 in most samples, which is on average lower than in ocean water. The Fe-binding dissolved organic ligand concentrations varied between 0.35 and 4.81 nEq of M Fe, which was higher than the dissolved concentration of Fe (DFe as found in most samples. At two stations ligands were saturated in the surface. At one station ligands were saturated near the oxycline, where ligand concentrations seemed to increase, indicating that they play a role in keeping Fe in the dissolved phase across the redox gradient. At the fluorescence maximum (between 40 and 50 m, the dissolved organic ligand binding capacity (alphaFeL=K´*[L´] of Fe was at its highest while the concentration DFe was at its lowest. Here, we find a statistically significant, positive relationship between fluorescence and the logarithm of alphaFeL, along with fluorescence and the ratio of the total ligand concentration over DFe. These relationships are best explained by phytoplankton utilizing Fe from Fe-binding organic ligands, resulting in an increase in free Fe-binding ligands.

  12. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.

    Science.gov (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

    2016-04-01

    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. PMID:27050687

  13. Four homochiral coordination polymers contain N-acetyl-L-tyrosine and different N-donor ligand: Influence of metal cations, ancillary ligands and coordination modes

    International Nuclear Information System (INIS)

    Using the chiral ligand N-acetyl-L-tyrosine (Hacty) and maintaining identical reaction conditions, Zn(II), Co(II), and Cd(II) salts provided four novel homochiral coordination polymers ([Zn(acty)(bipy)2(H2O)2]·NO3·2H2O)n1, ([Co(acty)(bipy)2(H2O)2]·NO3·2H2O)n2, ([Cd(acty)2(bipy)H2O]·H2O)n3, and ([Cd(acty)(bpe)2(Ac)]·6H2O)n4 (bipy=4,4′-bipyridine; bpe=1,2-di(4-pyridyl)ethane) in the presence of ancillary ligands. Compounds 1 and 2 are isostructural 1D chain structures. The neighboring chains are further linked into a 3D supramolecular structure via π⋯π stacking and hydrogen bond interactions. Compound 3 shows a 2D network and 4 generates 1D infinite chains along the c-axis. Compounds 3 and 4 are further connected into 3D supramolecular network by hydrogen bond interactions. More importantly, coordination in acyl oxygen atoms and ancillary ligands (bpe) as monodentate decorating ligands in 4 are rarely reported. Ancillary ligands and metal cations significantly influence the structure of the complexes. The photoluminescence properties of 1, 3, and 4 were studied at room temperature. Circular dichroism (CD) of the complexes have been investigated. - Graphical abstract: Four new homochiral coordination polymers were prepared and structurally characterized, which investigate the influence of the ancillary ligands and metal ions on the design and synthesis of coordination polymers. Display Omitted - Highlights: • It is rarely reported that the chiral coordination polymers prepared with N-acetyl-L-tyrosine ligands. • The alkalescent acetyl oxygen atom is difficult to participate in coordination but it is happened in the N-acetyl-L-tyrosine ligands. • The ancillary ligands (4,4′-bipy and bpe) are present in an unusual coordination modes, monodentate decorating ligands in 1, 2 and 4. • Structure comparative analyses results indicate that the secondary ligands and metal ions influence the fabrication of these inorganic–organic arrangements

  14. Structural studies of Ca2+-ATPase ligand and regulatory complexes

    DEFF Research Database (Denmark)

    Drachmann, Nikolaj Düring

    2015-01-01

    against their concentration gradient upon ATP hydrolysis. The ion gradients are used to drive several key cellular processes, like the action potential in nerve tissue, acidification of the gastric juice, cell signalling and muscle contraction. The Ca2+-ATPase is an important part of mammalian cells...... choline lipids with different aliphatic chain length and saturation show three specific lipid binding sites. The four different lipids analysed bind to the same binding sites with varying degrees of disorder. The study contributes to understanding the complex interplay between the surrounding membrane......-of-concept Ca2+ bound crystal form, indicated that the information content of SFX data is higher than synchrotron data, and ligands and ions can be detected with low redundant data. The data of the E2 stabilised form was processed to 5 Å resolution, and it was possible to extract useful anomalous data showing...

  15. Tuning the spin state of iron phthalocyanine by ligand adsorption

    Energy Technology Data Exchange (ETDEWEB)

    Isvoranu, C; Ataman, E; Knudsen, J; Andersen, J N; Schnadt, J [Division of Synchrotron Radiation Research, Department of Physics, Lund University, Box 118, SE-221 00 Lund (Sweden); Wang, B; Bocquet, M L [Laboratoire de chimie, Ecole normale superieure de Lyon, 46 Allee d' Italie, F-69364 Lyon Cedex 07 (France); Schulte, K, E-mail: joachim.schnadt@sljus.lu.s [MAX-lab, Lund University, Box 118, SE-221 00 Lund (Sweden)

    2010-12-01

    The future use of single-molecule magnets in applications will require the ability to control and manipulate the spin state and magnetization of the magnets by external means. There are different approaches to this control, one being the modification of the magnets by adsorption of small ligand molecules. In this paper we use iron phthalocyanine supported by an Au(111) surface as a model compound and demonstrate, using x-ray photoelectron spectroscopy and density functional theory, that the spin state of the molecule can be tuned to different values (S {approx} 0, 1/2, 1) by adsorption of ammonia, pyridine, carbon monoxide or nitric oxide on the iron ion. The interaction also leads to electronic decoupling of the iron phthalocyanine from the Au(111) support. (fast track communication)

  16. Confined-but-Connected Quantum Solids via Controlled Ligand Displacement

    KAUST Repository

    Baumgardner, William J.

    2013-07-10

    Confined-but-connected quantum dot solids (QDS) combine the advantages of tunable, quantum-confined energy levels with efficient charge transport through enhanced electronic interdot coupling. We report the fabrication of QDS by treating self-assembled films of colloidal PbSe quantum dots with polar nonsolvents. Treatment with dimethylformamide balances the rates of self-assembly and ligand displacement to yield confined-but-connected QDS structures with cubic ordering and quasi-epitaxial interdot connections through facets of neighboring dots. The QDS structure was analyzed by a combination of transmission electron microscopy and wide-angle and small-angle X-ray scattering. Excitonic absorption signatures in optical spectroscopy confirm that quantum confinement is preserved. Transport measurements show significantly enhanced conductivity in treated films. © 2013 American Chemical Society.

  17. Toll-Like Receptors, Their Ligands, and Atherosclerosis

    Directory of Open Access Journals (Sweden)

    Conrad P. Hodgkinson

    2011-01-01

    Full Text Available Atherosclerosis is a disease characterized by inflammation in the arterial wall. Atherogenesis is dependent on the innate immune response involving activation of Toll-like receptors (TLRs and the expression of inflammatory proteins. TLRs, which recognize various pathogen-associated molecular patterns, are expressed in various cell types within the atherosclerotic plaque. Microbial agents are associated with an increased risk of atherosclerosis and this is, in part, due to activation of TLRs. Recently considerable evidence has been provided suggesting that endogenous proteins promote atherosclerosis by binding to TLRs. In this review, we describe the role of TLRs in atherosclerosis with particular emphasis on those atherogenic endogenous proteins that have been implicated as TLR ligands.

  18. How wet should be the reaction coordinate for ligand unbinding?

    CERN Document Server

    Tiwary, Pratyush

    2016-01-01

    We use a recently proposed method called Spectral Gap Optimization of Order Parameters (SGOOP) (Tiwary and Berne, Proc. Natl. Acad. Sci 2016, 113, 2839 (2016)), to determine an optimal 1-dimensional reaction coordinate (RC) for the unbinding of a bucky-ball from a pocket in explicit water. This RC is estimated as a linear combination of the multiple available order parameters that collectively can be used to distinguish the various stable states relevant for unbinding. We pay special attention to determining and quantifying the degree to which water molecules should be included in the RC. Using SGOOP with under-sampled biased simulations, we predict that water plays a distinct role in the reaction coordinate for unbinding in the case when the ligand is sterically constrained to move along an axis of symmetry. This prediction is validated through extensive calculations of the unbinding times through metadynamics, and by comparison through detailed balance with unbiased molecular dynamics estimate of the bindin...

  19. Metal ion separations using hydrophobic anions: Aspects of ligand design

    International Nuclear Information System (INIS)

    Metal ion extraction using hydrophobic anions has been investigated by several researchers for remediation of Cs-137 and Sr-90 in nuclear waste. The rich derivative chemistry of the cobalt bis-dicarbollide anion makes it amendable to systematic studies of the relative importance of anion structure, solvent, and synergists on the extraction selectivity and efficiency. Halogenation or alkylation of cobalt dicarbollide strongly influences the anion's solubility and stability but has little effect on extraction properties. Alkali metal selectivity depends primarily on solvent, while alkaline earth selectivity is driven by the concentration and molecular weight of polyethylene glycol synergists. Additional aspects of ligand design, including a simple extraction and recovery cycle based on redox-active metal centers, will be discussed

  20. Exhaustive proteome mining for functional MHC-I ligands.

    Science.gov (United States)

    Koch, Christian P; Perna, Anna M; Weissmüller, Sabrina; Bauer, Stefanie; Pillong, Max; Baleeiro, Renato B; Reutlinger, Michael; Folkers, Gerd; Walden, Peter; Wrede, Paul; Hiss, Jan A; Waibler, Zoe; Schneider, Gisbert

    2013-09-20

    We present the development and application of a new machine-learning approach to exhaustively and reliably identify major histocompatibility complex class I (MHC-I) ligands among all 20(8) octapeptides and in genome-derived proteomes of Mus musculus , influenza A H3N8, and vesicular stomatitis virus (VSV). Focusing on murine H-2K(b), we identified potent octapeptides exhibiting direct MHC-I binding and stabilization on the surface of TAP-deficient RMA-S cells. Computationally identified VSV-derived peptides induced CD8(+) T-cell proliferation after VSV-infection of mice. The study demonstrates that high-level machine-learning models provide a unique access to rationally designed peptides and a promising approach toward "reverse vaccinology". PMID:23772559

  1. [Ligands of cholinesterases of ephedrine and pseudoephedrine structure].

    Science.gov (United States)

    Basova, N E; Kormilitsin, B N; Perchenok, A Yu; Rozengatt, E V; Saakov, V S; Suvorov, A A

    2013-01-01

    The paper is a review of literature data on interaction of the mammalian erythrocyte acetylcholinesterase and blood serum butyrylcholinesterase with a group of isomer complex ester derivatives (acetates, propionates, butyrates, valerates, and isobutyrates) of bases and iodomethylates of ephedrine and its enantiomer pseudoephedrine. For 20 alkaloid monoesters, parameters of enzymatic hydrolysis are determined and their certain specificity toward acetylcholinesterase is revealed, whereas 5 diesters of iodomethylates of pseudoephedrine were hydrolyzed only by butyrylcholinesterase. The studied 20 aklaloid diesters and 10 trimethylammonium derivatives turned out to be non-competitive reversible inhibitors of acetylcholinesterase and competitive inhibitors of butyrylcholinesterase. The performed for the first time isomer and enantiomer analysis "structure-efficiency" has shown that in most cases it is possible to state the greater comlementarity of the catalytical surface of enzymes for ligands of the pseudoephedrine structure, such differentiation being realized more often at the reversible inhibition of enzymes. pseudoephedrine.

  2. [Ligands of cholinesterases of ephedrine and pseudoephedrine structure].

    Science.gov (United States)

    2013-01-01

    The paper is a review of literature data on interaction of the mammalian erythrocyte acetylcholinesterase and blood serum butyrylcholinesterase with a group of isomer complex ester derivatives (acetates, propionates, butyrates, valerates, and isobutyrates) of bases and iodomethylates of ephedrine and its enantiomer pseudoephedrine. For 20 alkaloid monoesters, parameters of enzymatic hydrolysis are determined and their certain specificity toward acetylcholinesterase is revealed, whereas 5 diesters of iodomethylates of pseudoephedrine were hydrolyzed only by butyrylcholinesterase. The studied 20 aklaloid diesters and 10 trimethylammonium derivatives turned out to be non-competitive reversible inhibitors of acetylcholinesterase and competitive inhibitors of butyrylcholinesterase. The performed for the first time isomer and enantiomer analysis "structure-efficiency" has shown that in most cases it is possible to state the greater comlementarity of the catalytical surface of enzymes for ligands of the pseudoephedrine structure, such differentiation being realized more often at the reversible inhibition of enzymes. pseudoephedrine. PMID:25509044

  3. Halogenated benzamides as ligands for cerebral dopamine receptors

    International Nuclear Information System (INIS)

    In the past several years the authors' has synthesized a series of high affinity iodine-123 and fluorine-18 labeled substituted benzamide ligands for SPECT and PET visualization of the dopamine D-2 receptors in brain regions with low receptor density outside the striatum. Radioiodination and radiofluorination in high yield and high specific activity was achieved by using the tributyltin precursor and nucleophilic displacement of the saturation analysis revealed that the optimal striatum-to-cerebellum uptake ratio in the rat brain is highly correlated with the product of Kw and KD. The authors have used [125I] and [123I] epidepride to detect extra striatal dopamine D2 receptors in vitro by saturation analysis and in vivo with high resolution SPECT imaging

  4. Motion of Elastic Microcapsules on Compliant Surfaces with Adhesive Ligands

    Science.gov (United States)

    Maresov, Egor; Kolmakov, German; Balazs, Anna

    2011-03-01

    By integrating mesoscale models for hydrodynamics, micromechanics and adhesion, we examine the fluid driven motion of elastic microcapsules on compliant surfaces. The capsules, modeled as three-dimensional fluid-filled elastic shells, represent polymeric microcapsules or biological cells. Our combined integrated Lattice Boltzmann model/Lattice spring model (LBM/LSM) approach allows for a dynamic interaction between the elastic capsule's wall and surrounding fluid. To capture the interaction between the shell and the surface, we adopt the Bell model, used previously to describe the interaction of biological cell like leukocytes rolling on surfaces under the influence of an imposed shear. The surface of the microcapsule contains receptors with an affinity to adhesive ligands of the substrate. We examine how the parameters of adhesion and rigidity of the capsules and the substrate affect movement of the capsules. The findings provide guidelines for creating smart surfaces that could regulate the microcapsules' motion.

  5. Chemistry of dihydrogen complexes containing only phosphorus co-ligands

    Indian Academy of Sciences (India)

    Balaji R Jagirdar; Nisha Mathew

    2002-08-01

    A series of new dicationic dihydrogen complexes of ruthenium of the type cis-[(dppm)2Ru(2-H2)(L)][BF4]2 (dppm = Ph2PCH2PPh2; L = phosphite) have been prepared by protonating the precursor hydride complexes cis-[(dppm)2Ru(H)(L)][BF4] using HBF4$\\cdot$Et2O. The precursor hydride complexes have been obtained from trans-[(dppm)2Ru(H)(L)][BF4] (L = phosphite) via a rare acidcatalysed isomerization reaction in six coordinate species. The trans-[(dppm)2Ru(H)(L)][BF4] complexes (L = phosphine) upon protonation gave the isomerized derivatives, however, further addition of acid resulted in a five-coordinate species, [(dppm)2RuCl]+ presumably via an intermediate phosphine dihydrogen complex. The electronic as well as the steric properties of the co-ligands seem to strongly influence the structure-reactivity behaviour of this series of complexes.

  6. Characteristics of Tau and Its Ligands in PET Imaging

    Directory of Open Access Journals (Sweden)

    Ryuichi Harada

    2016-01-01

    Full Text Available Tau deposition is one of the neuropathological hallmarks in Alzheimer’s disease as well as in other neurodegenerative disorders called tauopathies. Recent efforts to develop selective tau radiopharmaceuticals have allowed the visualization of tau deposits in vivo. In vivo tau imaging allows the assessment of the regional distribution of tau deposits in a single human subject over time for determining the pathophysiology of tau accumulation in aging and neurodegenerative conditions as well as for application in drug discovery of anti-dementia drugs as surrogate markers. However, tau deposits show complicated characteristics because of different isoform composition, histopathology, and ultrastructure in various neurodegenerative conditions. In addition, since tau radiopharmaceuticals possess different chemotype classes, they may show different binding characteristics with heterogeneous tau deposits. In this review, we describe the characteristics of tau deposits and their ligands that have β-sheet binding properties, and the status of tau imaging in clinical studies.

  7. Catalytic hydrogenation using complexes of base metals with tridentate ligands

    Energy Technology Data Exchange (ETDEWEB)

    Vasudevan, Kalyan V.; Zhang, Guoqi; Hanson, Susan K.

    2016-09-06

    Complexes of cobalt and nickel with tridentate ligand PNHP.sup.R are effective for hydrogenation of unsaturated compounds. Cobalt complex [(PNHP.sup.Cy)Co(CH.sub.2SiMe.sub.3)]BAr.sup.F.sub.4 (PNHP.sup.Cy=bis[2-(dicyclohexylphosphino)ethyl]amine, BAr.sup.F.sub.4=B(3,5-(CF.sub.3).sub.2C.sub.6H.sub.3).sub.4)) was prepared and used with hydrogen for hydrogenation of alkenes, aldehydes, ketones, and imines under mild conditions (25-60.degree. C., 1-4 atm H.sub.2). Nickel complex [(PNHP.sup.Cy)Ni(H)]BPh.sub.4 was used for hydrogenation of styrene and 1-octene under mild conditions. (PNP.sup.Cy)Ni(H) was used for hydrogenating alkenes.

  8. Galactose as Broad Ligand for Multiple Tumor Imaging and Therapy.

    Science.gov (United States)

    Ma, Yuxiang; Chen, Haiyan; Su, Shanyuhan; Wang, Tong; Zhang, Congying; Fida, Guissi; Cui, Sisi; Zhao, Juan; Gu, Yueqing

    2015-01-01

    Galactose residues could be specifically recognized by the asialoglycoprotein receptor (ASGPR) which is highly exhibited on liver tissues. However, ASGPR has not been widely investigated on different tumor cell lines except for hepatoma carcinoma cells, which motivates us to investigate the possibility of galactose serving as a board tumor ligand. In this study, a galactose (Gal)-based probe conjugated with fluorescence dye MPA (Gal-MPA) was constructed for the evaluation of tumor affinities/targeted ability on different tumor cell lines. In the vitro cell study, it was indicated that the fluorescence probe Gal-MPA displayed higher cell affinity to tumor cells (HepG2, MCF-7 and A549) than that of the normal liver cells l02. In the vivo dynamic study of Gal-MPA in tumor-bearing mice (HepG2, MCF-7, A549, HCT116, U87, MDA-MB-231 and S180), it was shown that its high tumor targeted ability with the maximal tumor/normal tissue ratio reached up to 6.8. Meanwhile, the fast tumor-targeted ability within 2 hours and long retention on tumor site up to 120 hours were observed. Our results demonstrated that galactose should be a promising broad ligand for multiple tumor imaging and targeted therapy. Subsequently, Gal was covalently conjugated to doxorubicin (DOX) to form prodrug Gal-DOX for tumor targeted therapy. The therapeutic results of Gal-DOX than DOX being better suggested that galactosylated prodrugs might have the prospective potential in tumor targeted therapy.

  9. Biotinylated recombinant human erythropoietins: Bioactivity and utility as receptor ligand

    Energy Technology Data Exchange (ETDEWEB)

    Wojchowski, D.M.; Caslake, L. (Pennsylvania State Univ., University Park (USA))

    1989-08-15

    Recombinant human erythropoietin labeled covalently with biotin at sialic acid moieties has been prepared, and has been shown to possess high biological activity plus utility as a receptor ligand. Initially, the effects on biological activity of covalently attaching biotin to erythropoietin alternatively at carboxylate, amino, or sialic acid groups were compared. Biotinylation of erythropoietin at carboxylate groups using biotin-amidocaproyl hydrazide plus 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide led to substantial biological inactivation, although biotinylated molecules retained detectable activity when prepared at low stoichiometries. Biotinylation at amino groups using sulfosuccinimidyl 6-(biotinamido) hexanoate resulted in a high level of biological inactivation with little, if any, retention of biological activity, regardless of labeling stoichiometries. Biotinylation at sialic acid moieties using periodate and biotinamidocaproyl hydrazide proceeded efficiently (greater than 95% and 80% labeling efficiencies for human urinary and recombinant erythropoietin, respectively) and yielded stably biotinylated erythropoietin molecules possessing comparably high biological activity (ie, 45% of the activity of unmodified hormone). Utility of recombinant biotin-(sialyl)-erythropoietin (in combination with 125I-streptavidin) in the assay of cell surface receptors was demonstrated using two distinct murine erythroleukemia cell lines, Friend 745 and Rauscher Red 1. The densities and affinities of specific hormone binding sites were 116 +/- 4 sites, 3.3 +/- 0.4 nmol/L kd and 164 +/- 5 sites, 2.7 +/- 0.4 nmol/L kd, respectively. It is predicted that the present development of biotin-(sialyl)-erythropoietin as a chemically and biologically stable, bioactive ligand will assist in advancing an understanding of the regulated expression and physicochemistry of the human and murine erythropoietin receptors.

  10. Role of soluble Fas ligand in autoimmune diseases

    Institute of Scientific and Technical Information of China (English)

    Ning-Li Li; Tong Zhou; Dong-Qing Zhang; Hong Nie; Qi-Wen Yu; Ji-Ying Zhang; An-Lun Ma; Bai-Hua Shen; Li Wang; Jun Bai; Xue-Hua Chen

    2004-01-01

    AIM: To investigate the role of soluble Fas ligand in autoimmune diseases.METHODS: RT-PCR was performed to amplify sFasL cDNA from the total RNA extracted from activated human peripheral blood lymphocytes. DNA fragments were cloned into PCR vector. After sequenced, sFasL gene fragments were inserted into pQE-31 vector and expressed in E. Coli M15respectively. Proteins were purified through affinity chromatography column with ligand of 6xHis tag and identified by SDS-PAGE and Western blot. Mice were immunized with sFasL protein and specific anti-serum was harvested 6 wk after immunization. Monoclonal anti-human FasL antibody was made from the immunized mice. Serum level of sFasL in different patients was detected using antiFasL antibodies from the immunized mice.RESULTS: The protein expressed was 24 ku by SDS-PAGE electrophrosis. The protein was specially bound to antihuman FasL antibody by Western blot analysis. The sFasL protein could induce Jurket cell apoptosis in vitro. The concentration of serum sFasL in patients with autoimmune diseases was higher than that in normal individuals. sFasL could reduce arthritis in collagen induced arthritis (CIA)mice model by subcutaneous injection.CONCLUSION: sFasL may be involved in either induction of apoptosis or autoimmune diseases. Furthermore, sFasL may have potential application in treatment of autoimmune diseases.

  11. Imaging of a glioma using peripheral benzodiazepine receptor ligands

    Energy Technology Data Exchange (ETDEWEB)

    Starosta-Rubinstein, S.; Ciliax, B.J.; Penney, J.B.; McKeever, P.; Young, A.B.

    1987-02-01

    Two types of benzodiazepine receptors have been demonstrated in mammalian tissues, one which is localized on neuronal elements in brain and the other, on glial cells and in peripheral tissues such as kidney. In vivo administration of /sup 3/H-labeled PK 11195 (1-(2-chlorophenyl-N-methyl-N-(1-methylpropyl)-3-isoquinoline carboxamide) or (/sup 3/H)flunitrazepam with 5 mg of clonazepam per kg to rats with intracranial C6 gliomas resulted in high levels of tritiated-drug binding to the tumor as shown by quantitative autoradiography. Pharmacological studies indicated that the bound drugs labeled the peripheral benzodiazepine binding site. Binding to the peripheral benzodiazepine site was confirmed primarily to malignant cells with little binding to adjacent normal brain tissue or to necrotic tissue. Tumor cell binding was completely inhibited by preadministration of the peripheral benzodiazepine blocking agent PK 11195 at 5 mg/kg. The centrally selective benzodiazepine ligand clonazepam had no effect on PK 11195 binding to the tumor cells. When binding to other tumor cell lines grown in nude mice and nude athymic rats was evaluated, little or no peripheral benzodiazepine binding was detected on human pheochromocytoma (RN1) and neuroblastoma (SK-N-MC, SK-N-SH) tumor cells, respectively. However, high densities of peripheral benzodiazepine binding sites were observed on tumors derived from a human glioma cell line (ATCC HTB 14, U-87 MG). The presence of high concentrations of specific peripheral benzodiazepine receptors on glial tumors suggests that human primary central nervous system tumors could be imaged and diagnosed using peripheral benzodiazepine ligands labeled with positron- or gamma-emitting isotopes.

  12. Imaging of a glioma using peripheral benzodiazepine receptor ligands

    International Nuclear Information System (INIS)

    Two types of benzodiazepine receptors have been demonstrated in mammalian tissues, one which is localized on neuronal elements in brain and the other, on glial cells and in peripheral tissues such as kidney. In vivo administration of 3H-labeled PK 11195 [1-(2-chlorophenyl-N-methyl-N-(1-methylpropyl)-3-isoquinoline carboxamide] or [3H]flunitrazepam with 5 mg of clonazepam per kg to rats with intracranial C6 gliomas resulted in high levels of tritiated-drug binding to the tumor as shown by quantitative autoradiography. Pharmacological studies indicated that the bound drugs labeled the peripheral benzodiazepine binding site. Binding to the peripheral benzodiazepine site was confirmed primarily to malignant cells with little binding to adjacent normal brain tissue or to necrotic tissue. Tumor cell binding was completely inhibited by preadministration of the peripheral benzodiazepine blocking agent PK 11195 at 5 mg/kg. The centrally selective benzodiazepine ligand clonazepam had no effect on PK 11195 binding to the tumor cells. When binding to other tumor cell lines grown in nude mice and nude athymic rats was evaluated, little or no peripheral benzodiazepine binding was detected on human pheochromocytoma (RN1) and neuroblastoma (SK-N-MC, SK-N-SH) tumor cells, respectively. However, high densities of peripheral benzodiazepine binding sites were observed on tumors derived from a human glioma cell line (ATCC HTB 14, U-87 MG). The presence of high concentrations of specific peripheral benzodiazepine receptors on glial tumors suggests that human primary central nervous system tumors could be imaged and diagnosed using peripheral benzodiazepine ligands labeled with positron- or gamma-emitting isotopes

  13. Design principles for ligand-sensing, conformation-switching ribozymes.

    Directory of Open Access Journals (Sweden)

    Xi Chen

    2009-12-01

    Full Text Available Nucleic acid sensor elements are proving increasingly useful in biotechnology and biomedical applications. A number of ligand-sensing, conformational-switching ribozymes (also known as allosteric ribozymes or aptazymes have been generated by some combination of directed evolution or rational design. Such sensor elements typically fuse a molecular recognition domain (aptamer with a catalytic signal generator (ribozyme. Although the rational design of aptazymes has begun to be explored, the relationships between the thermodynamics of aptazyme conformational changes and aptazyme performance in vitro and in vivo have not been examined in a quantitative framework. We have therefore developed a quantitative and predictive model for aptazymes as biosensors in vitro and as riboswitches in vivo. In the process, we have identified key relationships (or dimensionless parameters that dictate aptazyme performance, and in consequence, established equations for precisely engineering aptazyme function. In particular, our analysis quantifies the intrinsic trade-off between ligand sensitivity and the dynamic range of activity. We were also able to determine how in vivo parameters, such as mRNA degradation rates, impact the design and function of aptazymes when used as riboswitches. Using this theoretical framework we were able to achieve quantitative agreement between our models and published data. In consequence, we are able to suggest experimental guidelines for quantitatively predicting the performance of aptazyme-based riboswitches. By identifying factors that limit the performance of previously published systems we were able to generate immediately testable hypotheses for their improvement. The robust theoretical framework and identified optimization parameters should now enable the precision design of aptazymes for biotechnological and clinical applications.

  14. Screening Investigations of Novel Nitrogen Donor Ligands for Solvent Extraction

    International Nuclear Information System (INIS)

    It is important to have a concept on how to take care of spent nuclear fuel. Several options exist, such as the once-through cycle or reprocessing. Both these methods produce a residue that must be disposed of and isolated for a very long time. Transmutation of the spent nuclear fuel is a technique that may reduce the amount and the storage time of the spent nuclear fuel by converting the long lived radionuclides into short lived or stable nuclides. Successful transmutation must be accompanied with an effective separation, or partitioning, of the elements in the spent fuel since only a few elements are the target for transmutation. Solvent extraction is one of the preferred techniques for this partitioning. Special consideration is given to the separation of trivalent actinides and trivalent lanthanides in the waste since these groups of elements have similar chemical properties and hence may be difficult to separate. This work is focused on the separation of actinides from lanthanides using novel nitrogen containing extracting reagents for solvent extraction. These nitrogen bearing reagents has been investigated using mainly solvent extraction techniques to find chemical and extraction properties for these reagents and to optimize the system in order to use these reagents in a future process. Methods for making screening test of these ligands are discussed where certain properties of the reagents are investigated, such as solubility, radiolytic and hydrolytic stability and extraction capacity. The ligands were found to be able to specifically separate actinides from lanthanides. Further on, a model based on Hansen's solubility parameter concept, which can predict the outcome of an extraction experiment is presented. The model was found to work quite well

  15. Macrocyclic effects upon isomeric CuIIMII and MIICuII cores. Formation with unsymmetric phenol-based macrocyclic ligands

    Indian Academy of Sciences (India)

    Masami Yonemura; Yuuki Nakamura; Naoki Usuki; Hisashi Okawa

    2000-06-01

    This paper discusses coordination-position isomeric MIICuII and CuIIMII complexes, using unsymmetric dinucleating macrocycles (Lm;n)2- ((L2;2)2-, (L2;3)2- and (L2;4)2- that comprise two 2-(N-methyl)-aminomethyl-6-iminomethyl-4-bromophenonate entities, combined through the ethylene chain ( = 2) between the two amine nitrogens and through the ethylene, trimethylene or tetramethylene chain ( = 2, 3 or 4) between the two imine nitrogens. The macrocycles have dissimilar N(amine)2O2 and N(imine)2O2 metal-binding sites sharing the phenolic oxygens. The reaction of the mononuclear CuII precursors, [Cu(L2;2)], [Cu(L2;2)] and [Cu(L2;2)], with a MII perchlorate and a MII acetate salt formed (acetato)MII CuII complexes:[CoCu(L2;2)(AcO)]ClO4 0 5H2O] (1), [NiCu(L2;2) (AcO)]ClO4 (2), [ZnCu(L2;2((AcO)]ClO4 (3), [CoCu(L2;3)(AcO)]ClO4 0 5H2O (4), [NiCu(L2;3)(AcO)]ClO4 (5), [ZnCu(L2;3)(AcO)]ClO4 0 5H2O (6), [CoCu(L2;4)(AcO)(DMF)]ClO4 (7), [NiCu(L2;4)(AcO)]ClO4 2DMF (8) and [ZnCu(L2;4)(AcO)]ClO4 (9) (the formulation [MM (Lm;n)]2+ means that M resides in the aminic site and M in the iminic site). The site selectivity of the metal ions is demonstrated by X-ray crystallographic studies for 2 MeOH, 3, 5, 7, and 9. An (acetato)CuIIZnII complex, [CuZn(L2;3)(AcO)]ClO4 (10), was obtained by the reaction of [PbCu(L2;3)]-(ClO4)2 with ZnSO4 4H2O, in the presence of sodium acetate. Other complexes of the CuIIMII type were thermodynamically unstable to cause a scrambling of metal ions. The Cu migration from the iminic site to the aminic site in the synthesis of 10 is explained by the `kinetic macrocyclic effect’. The coordination-position isomers, 6 and 10, are differentiated by physicochemical properties.

  16. Synthesis and spectroscopic studies of mixed-ligand and polymeric dinuclear transition metal complexes with bis-acylhydrazone tetradentate ligands and 1,10-phenanthroline

    Science.gov (United States)

    Gup, Ramazan; Kırkan, Bülent

    2006-06-01

    Two types of dinuclear copper(II) and nickel(II) complexes with two tetradentate N 2O 2 donor ligands 1,4-bis(1-anthranoylhydrazonoethyl)benzene (L 1), 1,4-bis(1-salicyloylhydrazonoethyl)benzene (L 2) and N, N'-bidentate heterocyclic base [1,10-phenonthroline (phen)] have been synthesized and characterized by elemental analysis, infrared spectra, UV-vis electronic absorption spectra and magnetic susceptibility measurements. The reaction of metal(II) acetates with the solution containing ligand and 1,10-phenonthroline in methanol gives mixed-ligand dinuclear metal(II) complexes with general formula [M 2L(phen) 2]Cl 2 (L = L 1 or L 2), whereas, the ligands react with metal(II) acetates to form polymeric dinuclear complexes with general formula [(M 2L 2) n] (L = L 1 or L 2). In the complexes, the ligands act as dianionic tetradentate and coordination takes place in the enol tautomeric form with the enolic oxygen and azomethine nitrogen atoms while the phenolic hydroxyl and amino groups of aroylhydrazone moiety do not participate in coordination. The effect of varying pH and solvent on the absorption behavior of both ligands and complexes has been investigated.

  17. Synthesis, characterization and antimicrobial activities of mixed ligand transition metal complexes with isatin monohydrazone Schiff base ligands and heterocyclic nitrogen base

    Science.gov (United States)

    Devi, Jai; Batra, Nisha

    2015-01-01

    Mixed ligand complexes of Co(II), Ni(II), Cu(II) and Zn(II) with various uninegative tridentate ligands derived from isatin monohydrazone with 2-hydroxynapthaldehyde/substituted salicylaldehyde and heterocyclic nitrogen base 8-hydroxyquinoline have been synthesized and characterized by elemental analysis, conductometric studies, magnetic susceptibility and spectroscopic techniques (IR, UV-VIS, NMR, mass and ESR). On the basis of these characterizations, it was revealed that Schiff base ligands existed as monobasic tridentate ONO bonded to metal ion through oxygen of carbonyl group, azomethine nitrogen and deprotonated hydroxyl oxygen and heterocyclic nitrogen base 8-hydroxyquinoline existed as monobasic bidentate ON bonded through oxygen of hydroxyl group and nitrogen of quinoline ring with octahedral or distorted octahedral geometry around metal ion. All the compounds have been tested in vitro against various pathogenic Gram positive bacteria, Gram negative bacteria and fungi using different concentrations (25, 50, 100, 200 μg/mL) of ligands and their complexes. Comparative study of antimicrobial activity of ligands, and their mixed complexes indicated that complexes exhibit enhanced activity as compared to free ligands and copper(II) Cu(LIV)(Q)ṡH2O complex was found to be most potent antimicrobial agent.

  18. Ligand efficiency-based support vector regression models for predicting bioactivities of ligands to drug target proteins.

    Science.gov (United States)

    Sugaya, Nobuyoshi

    2014-10-27

    The concept of ligand efficiency (LE) indices is widely accepted throughout the drug design community and is frequently used in a retrospective manner in the process of drug development. For example, LE indices are used to investigate LE optimization processes of already-approved drugs and to re-evaluate hit compounds obtained from structure-based virtual screening methods and/or high-throughput experimental assays. However, LE indices could also be applied in a prospective manner to explore drug candidates. Here, we describe the construction of machine learning-based regression models in which LE indices are adopted as an end point and show that LE-based regression models can outperform regression models based on pIC50 values. In addition to pIC50 values traditionally used in machine learning studies based on chemogenomics data, three representative LE indices (ligand lipophilicity efficiency (LLE), binding efficiency index (BEI), and surface efficiency index (SEI)) were adopted, then used to create four types of training data. We constructed regression models by applying a support vector regression (SVR) method to the training data. In cross-validation tests of the SVR models, the LE-based SVR models showed higher correlations between the observed and predicted values than the pIC50-based models. Application tests to new data displayed that, generally, the predictive performance of SVR models follows the order SEI > BEI > LLE > pIC50. Close examination of the distributions of the activity values (pIC50, LLE, BEI, and SEI) in the training and validation data implied that the performance order of the SVR models may be ascribed to the much higher diversity of the LE-based training and validation data. In the application tests, the LE-based SVR models can offer better predictive performance of compound-protein pairs with a wider range of ligand potencies than the pIC50-based models. This finding strongly suggests that LE-based SVR models are better than pIC50-based

  19. Thiopyridazine-Based Copper Boratrane Complexes Demonstrating the Z-type Nature of the Ligand.

    Science.gov (United States)

    Holler, Stefan; Tüchler, Michael; Belaj, Ferdinand; Veiros, Luis F; Kirchner, Karl; Mösch-Zanetti, Nadia C

    2016-05-16

    In Z-type ligands the electrons for the coordination bond are formally provided by the metal. They represent an important addition to the much more extensively used L- and X-type σ-donor ligands for the development of transition metal complexes with new reactivities. We report here a new boron Z-type ligand with three tethering thiopyridazinyl donors forming exclusively complexes that feature a metal boron bond. Rational substitution pattern in the backbone of the pyridazinyl heterocycle led to a well-behaved ligand system that allowed preparation of a series of copper boratrane complexes in high yields. They are found to be more soluble in common organic solvents allowing reactivity studies in contrast to previous complexes with this type of ligand. Thus, copper complexes [Cu{B(Pn(Me,tBu))3}X] with X = Cl, OTf, N3, and κN-NCS are reported. Solution behavior was explored, and the molecular structures were determined by single-crystal X-ray diffraction analyses. The thiocyanate ligand is found to coordinate via its nitrogen atom pointing to a high oxidation state of the copper. Density functional theory calculations indicate a high positive charge on copper and a strong copper-boron interaction. Thus, here reported complexes deliver synthetic evidence for the Z-type nature of the ligand. These findings are important for further dissemination of these types of ligands in coordination chemistry. PMID:27110725

  20. Salan ligands assembled around chiral bipyrrolidine: predetermination of chirality around octahedral Ti and Zr centres.

    Science.gov (United States)

    Sergeeva, Ekaterina; Kopilov, Jacob; Goldberg, Israel; Kol, Moshe

    2009-06-01

    The first synthesis of Salan ligands assembled around the chiral 2,2'-bipyrrolidine backbone is described; as chelation to a metal can only occur via specific faces of the two pyrrolidine nitrogens, these ligands lead to predetermined chirality at metal centres of octahedral titanium and zirconium complexes. PMID:19462084

  1. Ureaphosphanes as hybrid, anionic or supramolecular bidentate ligands for asymmetric hydrogenation reactions

    NARCIS (Netherlands)

    Meeuwissen, J.; Detz, R.; Sandee, A. J.; de Bruin, B.; Siegler, M. A.; Spek, A.L.; Reek, J.N.H.

    2010-01-01

    We report the coordination behavior of ureaphosphane ligand 1-[2-(diphenylphosphanyl)ethyl]-3-phenylurea (L1) towards different rhodium precursor complexes. Depending on the nature of the anion and the ligand/metal ratio, L1 acts either as a hybrid P,O-coordinating chelate, as an anionic P,N-coordin

  2. MODIFICATION OF PALLADIUM METALLIC CATALYST WITH POLYMER-ANCHORED THIOETHER LIGANDS

    Institute of Scientific and Technical Information of China (English)

    LIU Hanfan; MAO Guoping

    1993-01-01

    A well-dispersed metallic palladium catalyst modified by polymer-anchored thioether ligands was used for the hydrogenation of cyclopentadiene to cyclopentene with high activity and selectivity in ambient condition. The evidences to show the modification of catalytic properties by polymer anchored ligands were given.

  3. SiteComp: a server for ligand binding site analysis in protein structures

    OpenAIRE

    Lin, Yingjie; Yoo, Seungyeul; Sanchez, Roberto

    2012-01-01

    Motivation: Computational characterization of ligand-binding sites in proteins provides preliminary information for functional annotation, protein design and ligand optimization. SiteComp implements binding site analysis for comparison of binding sites, evaluation of residue contribution to binding sites and identification of sub-sites with distinct molecular interaction properties.

  4. Topological estimation of proton-ligand formation constants of potential antitumour agents: Salicylhydroxamic acids

    Indian Academy of Sciences (India)

    Sneha Karmarkar; P V Khadikar; Vijay K Agrawal; Keshav C Mathur; Manorama Mandloi; Shobha Joshi

    2000-02-01

    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 and monitoring proton-ligand formation constants.

  5. Aryl hydrocarbon receptor ligand effects in RBL2H3 cells

    DEFF Research Database (Denmark)

    Maaetoft-Udsen, Kristina; Shimoda, Lori M. N.; Frøkiær, Hanne;

    2012-01-01

    (KA), Resveratrol, indolmycin, and violacein, affect mast cell activation and signaling. These ligands were tested on calcium signaling, degranulation, and gene expression. The data show that AHR is present in three model mast cell lines, and that various known and putative AHR ligands regulate gene...

  6. A convenient microwave-assisted synthesis of cinchona alkaloid-derived ligands

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    An efficient synthesis of cinchona alkaloid-derived ligands based on solvent-free microwave-assisted reaction was described. The coupling of 1,4-dichlorophthalazine or 3,6-dichloropyridazine with quinine, cinchonine or cinchonidine provide bis- or mono-cinchona alkaloid-derived ligands in moderate to good yields (52-89%) within 15 rain under optimum microwave conditions.

  7. The saccharinate anion: a versatile and fascinating ligand in coordination chemistry

    Directory of Open Access Journals (Sweden)

    Enrique J. Baran

    2005-03-01

    Full Text Available The saccharinate anion, obtained by deprotonation of the N-H moiety of saccharin (o-sulfobenzimide is a very versatile and polyfunctional ligand in coordination chemistry. In this review the different forms of metal-to-ligand interactions involving this anion and some other coordination peculiarities are briefly discussed on the basis of some selected examples.

  8. Multiparameter flow cytometry of a pH sensitive ligand bound to receptors and inside cells

    Energy Technology Data Exchange (ETDEWEB)

    Fay, S.P.; Habbersett, R.; Posner, R.G.; Domalewski, M.D.; Freer, R.J.; Pierson, E.; Whittaker, J.; Haugland, R.P.; Sklar, L.A. (Univ. of New Mexico, Albuquerque (United States) Los Alamos National Lab., NM (United States))

    1993-01-01

    Because fluoresceinated ligands of the neutrophil formyl peptide receptor can be protonated either upon binding to the receptor on the cell surface or in acidified intracellular compartments, the authors synthesized a ligand conjugated to the pH sensitive fluorescent probe SNAFL (CHO-Met-Leu-Phe-Phe-Lys-SNAFL). In the three laser flow cytometer at LANL, protonated dye is excited at 488 nm and emits at 530 nm; unprotonated dye is excited at 568 nm and emits at 650 nm. Detection at the isobestic and isoemissive points at 528 and 600 nm is used to keep track of variations in ligand concentration from sample to sample. The SNAFL-ligand bound to HL-60 cells (which overexpress the formyl peptide receptor) was compared to the free ligand in solution over a pH range from 6.5 to 9.0. The results suggest that the ligand bound to cell surface receptors was protonated in the binding pocket, possibly by virtue of its proximity to His 90, based on sequence data. When the cells were raised from 4[degrees] to 37[degrees], they also observed a time-dependent acidification of the ligand, indicative of ligand-receptor processing beginning 3-4 minutes after internalization.

  9. Design and Application of Latent Olefin Metathesis Catalysts Featuring S-Chelating Alkylidene Ligands

    Science.gov (United States)

    Szadkowska, Anna; Grela, Karol

    This review article is devoted to recent advances in the design and application of so-called “dormant” or “latent” ruthenium olefin metathesis catalysts bearing S-chelating alkylidene ligands. Selected ruthenium complexes containing S-donor ligands, which possess controllable initiation behaviour are presented. Applications of these complexes in olefin metathesis are described.

  10. Driving Oxygen Coordinated Ligand Exchange at Nanocrystal Surfaces using Trialkylsilylated Chalcogenides

    Energy Technology Data Exchange (ETDEWEB)

    Caldwell, Marissa A.; Albers, Aaron E.; Levy, Seth C.; Pick, Teresa E.; Cohen, Bruce E.; Helms, Brett A.; Milliron, Delia J.

    2010-11-11

    A general, efficient method is demonstrated for exchanging native oxyanionic ligands on inorganic nanocrystals with functional trimethylsilylated (TMS) chalcogenido ligands. In addition, newly synthesized TMS mixed chalcogenides leverage preferential reactivity of TMS-S bonds over TMS-O bonds, enabling efficient transfer of luminescent nanocrystals into aqueous media with retention of their optical properties.

  11. Computational Exploration of a Protein Receptor Binding Space with Student Proposed Peptide Ligands

    Science.gov (United States)

    King, Matthew D.; Phillips, Paul; Turner, Matthew W.; Katz, Michael; Lew, Sarah; Bradburn, Sarah; Andersen, Tim; McDougal, Owen M.

    2016-01-01

    Computational molecular docking is a fast and effective "in silico" method for the analysis of binding between a protein receptor model and a ligand. The visualization and manipulation of protein to ligand binding in three-dimensional space represents a powerful tool in the biochemistry curriculum to enhance student learning. The…

  12. Understanding the shape effect on the plasmonic response of small ligand coated nanoparticles

    Science.gov (United States)

    Chen, Xing; Jensen, Lasse

    2016-07-01

    The plasmonic properties of metallic nanoparticles typically depend strongly on their shapes and local environment. However, not much is known about the shape effects on the plasmonic response in small metallic nanoparticles when quantum size effects become important. In this work, we use atomistic electrodynamics models incorporated with quantum size effects to study the optical properties of both bare and ligand coated Ag nanoparticles in different shapes. Using classical electrodynamics, we find that the plasmonic response of bare metallic nanoparticles depends strongly on the morphology of the nanoparticles due to the presence of higher-order plasmon modes. By including quantum size effects in the simulations, we find a significant blue-shift of the dipole plasmon as well as the smearing-out of the multipole plasmon modes, and both lead to a weak shape dependence. The ligand effects on the nanoparticles cause a significant red-shift of the plasmon resonance arising from the reduction of the conductivity of the Ag atoms where the ligands bind. In contrast to the bare nanoparticles, we find several higher-order plasmon modes in the ligand coated nanoparticles, that are likely caused by the weak electron spill-out effect and the symmetry breaking at the surface in the presence of the ligands. Furthermore, we show that the ligand layer strongly modify the near-field distribution due to the screening of the ligands. This work highlights the importance of quantum size and ligand effects on the optical properties of small metallic nanoparticles.

  13. Synthesis of New Chiral Phosphine Ligands and Their Application in Asymmetric Hydrogenation of Ketones

    Institute of Scientific and Technical Information of China (English)

    XIE Jian-Hua; FU Yu; WANG Li-Xin; ZHOU Qi-Lin

    2004-01-01

    The design of new chiral ligands is the key in the development of transition metal catalyzed asymmetric synthesis. Many chiral diphosphine ligands have been prepared and applied in asymmetric catalytic reactions with excellent enantioselectivities. Among the chiral diphosphine ligands that have been reported, the atropisomeric C2-symmetric phosphines with a biaryl scaffold initiated by Noyori and co-workers with BINAP were found to have the widest application in the transition metal catalyzed reactions. Planar chiral diphosphines based on ferrocene or paracyclophane backbones have also been applied to a number of reactions with a remarkable degree of success. However, the spiro diphosphine compounds, another type of axially chiral ligands, have not been synthesized yet. Recently, we designed chiral phosphoramidite ligands (SIPHOS)containing a 1, 1′-spirobiindane backbone and demonstrated that these ligands can be highly efficient for the Rh-catalyzed asymmetric hydrogenation of functionalized olefins. Especially, in the case of asymmetric hydrogenation of α-arylethenylamines, the spiro monophosphoramidite ligands provided a significantly higher level of enantiocontrol compared to that of the monophosphoramidite ligands derived from BINOL. Herein we present the synthesis of spiro diphosphines (SDP) containing 1,1′-spirobiindane as a new chiral scaffold and their application in the ruthenium-catalyzed asymmetric hydrogenation of simple ketones with high activity (S/C up to 100 000) and excellent enantioselectivity (ee up to 99.5%).

  14. Aminotroponiminates as tunable, redox-active ligands: reversible single electron transfer and reductive dimerisation.

    Science.gov (United States)

    Lichtenberg, C; Krummenacher, I

    2016-08-21

    Aminotroponiminates (atis) are shown to be redox-active ligands. Under strongly reducing conditions, the result of electron transfer can be controlled by the choice of the metal bound to the ati ligand. Either reversible electron transfer or a reductively induced dimerisation is observed. The latter reaction is (regio- and diastereo-) selective and chemically reversible. PMID:27452905

  15. The complex interplay between ligand binding and conformational structure of the folate binding protein (folate receptor)

    DEFF Research Database (Denmark)

    Holm, Jan; Bruun, Susanne Wrang; Hansen, Steen I.

    2015-01-01

    , and the binding induces a conformational change with formation of hydrophilic and stable holo-FBP. Holo-FBP exhibits a ligand-mediated concentration-dependent self-association into multimers of great thermal and chemical stability due to strong intermolecular forces. Both ligand and FBP are thus protected against...

  16. Student-Directed Explorations to Learn about Ligands in an Inorganic Chemistry Course

    Science.gov (United States)

    Cass, Marion E.

    2004-01-01

    The student-directed explorations for learning various ligands and their impacts on the field of inorganic chemistry are discussed. Various themes can be adopted by the instructors, like ligand-of-the-week theme, while teaching inorganic chemistry to their students.

  17. Non-heme iron catalysts for the benzylic oxidation : a parallel ligand screening approach

    NARCIS (Netherlands)

    Klopstra, M; Hage, R; Kellogg, R.M.; Feringa, B.L.

    2003-01-01

    Ethylbenzene and 4-ethylanisole were used as model substrates for benzylic oxidation with H2O2 or O-2 using a range of non-heme iron catalysts following a parallel ligand screening approach. Effective oxidation was found for Fe complexes based on tetra- and pentadentate nitrogen ligands affording th

  18. Impact of ligand protonation on higher-order metal complexation kinetics in aqueous systems

    NARCIS (Netherlands)

    Town, R.M.; Leeuwen, van H.P.

    2008-01-01

    The impact of ligand protonation on the complexation kinetics of higher-order complexes is quantitatively described. The theory is formulated on the basis of the usual situation for metal complex formation in aqueous systems in which the exchange of water for the ligand in the inner coordination sph

  19. A Quantitative Measure of Conformational Changes in Apo, Holo and Ligand-Bound Forms of Enzymes.

    Science.gov (United States)

    Singh, Satendra; Singh, Atul Kumar; Wadhwa, Gulshan; Singh, Dev Bukhsh; Dwivedi, Seema; Gautam, Budhayash; Ramteke, Pramod W

    2016-06-01

    Determination of the native geometry of the enzymes and ligand complexes is a key step in the process of structure-based drug designing. Enzymes and ligands show flexibility in structural behavior as they come in contact with each other. When ligand binds with active site of the enzyme, in the presence of cofactor some structural changes are expected to occur in the active site. Motivation behind this study is to determine the nature of conformational changes as well as regions where such changes are more pronounced. To measure the structural changes due to cofactor and ligand complex, enzyme in apo, holo and ligand-bound forms is selected. Enzyme data set was retrieved from protein data bank. Fifteen triplet groups were selected for the analysis of structural changes based on selection criteria. Structural features for selected enzymes were compared at the global as well as local region. Accessible surface area for the enzymes in entire triplet set was calculated, which describes the change in accessible surface area upon binding of cofactor and ligand with the enzyme. It was observed that some structural changes take place during binding of ligand in the presence of cofactor. This study will helps in understanding the level of flexibility in protein-ligand interaction for computer-aided drug designing. PMID:26260067

  20. Synthesis of Novel Bisoxazoline Ligands for the Enantioselective Diels-Alder Reaction

    Institute of Scientific and Technical Information of China (English)

    Qing Hua BIAN; Jun LIU; Ming Ming YIN; Min WANG

    2006-01-01

    Four novel bisoxazoline ligands 8a-d were synthesized from (S)-amino alcohols and could be formed effective catalysts (up to 77% ee for endo isomer) with Cu(OTf)2 for enantioselective Diels-Alder addition. The facility of the reaction was dependent on the nature of the substituent R in the bisoxazoline ligand.

  1. Comparison of ligand migration and binding in heme proteins of the globin family

    Science.gov (United States)

    Karin, Nienhaus; Ulrich Nienhaus, G.

    2015-12-01

    The binding of small diatomic ligands such as carbon monoxide or dioxygen to heme proteins is among the simplest biological processes known. Still, it has taken many decades to understand the mechanistic aspects of this process in full detail. Here, we compare ligand binding in three heme proteins of the globin family, myoglobin, a dimeric hemoglobin, and neuroglobin. The combination of structural, spectroscopic, and kinetic experiments over many years by many laboratories has revealed common properties of globins and a clear mechanistic picture of ligand binding at the molecular level. In addition to the ligand binding site at the heme iron, a primary ligand docking site exists that ensures efficient ligand binding to and release from the heme iron. Additional, secondary docking sites can greatly facilitate ligand escape after its dissociation from the heme. Although there is only indirect evidence at present, a preformed histidine gate appears to exist that allows ligand entry to and exit from the active site. The importance of these features can be assessed by studies involving modified proteins (via site-directed mutagenesis) and comparison with heme proteins not belonging to the globin family.

  2. Unique Ligand-Based Oxidative DNA Cleavage by Zinc(II) Complexes of Hpyramol and Hpyrimol

    NARCIS (Netherlands)

    Maheswari, P.U.; Barends, S.; Özalp-Yaman, S.; de Hoog, P.; Casellas, H.; Teat, S.J.; Massera, C.; Lutz, M.; Spek, A.L.; van Wezel, G.P.; Gamez, P.; Reedijk, J.

    2007-01-01

    The zinc(II) complexes reported here have been synthesised from the ligand 4-methyl-2-N-(2-pyridylmethyl)aminophenol (Hpyramol) with chloride or acetate counterions. All the five complexes have been structurally characterised, and the crystal structures reveal that the ligand Hpyramol gradually unde

  3. Enabling Ligand Screening for Palladium-Catalysed Enantioselective Aza-Michael Addition Reactions

    NARCIS (Netherlands)

    Phua, Pim Huat; White, Andrew J.P.; Vries, Johannes G. de; Hii, King Kuok

    2006-01-01

    The bis(trifluoromethanesulfonate)palladium(II) dihydrate complex, Pd(OTf)2 · 2 H2O (1), is an active palladium(II) precursor for the generation of dicationic palladium(II) catalysts. Parallel ligand screening is enabled for the first time, and twenty-four chiral ligands were evaluated for the asymm

  4. Discriminating agonist and antagonist ligands of the nuclear receptors using 3D-pharmacophores.

    Science.gov (United States)

    Lagarde, Nathalie; Delahaye, Solenne; Zagury, Jean-François; Montes, Matthieu

    2016-01-01

    Nuclear receptors (NRs) constitute an important class of therapeutic targets. We evaluated the performance of 3D structure-based and ligand-based pharmacophore models in predicting the pharmacological profile of NRs ligands using the NRLiSt BDB database. We could generate selective pharmacophores for agonist and antagonist ligands and we found that the best performances were obtained by combining the structure-based and the ligand-based approaches. The combination of pharmacophores that were generated allowed to cover most of the chemical space of the NRLiSt BDB datasets. By screening the whole NRLiSt BDB on our 3D pharmacophores, we demonstrated their selectivity towards their dedicated NRs ligands. The 3D pharmacophores herein presented can thus be used as a predictor of the pharmacological activity of NRs ligands.Graphical AbstractUsing a combination of structure-based and ligand-based pharmacophores, agonist and antagonist ligands of the Nuclear Receptors included in the NRLiSt BDB database could be separated.

  5. Computer-aided design of a novel ligand for retinoic acid receptor in cancer chemotherapy

    Science.gov (United States)

    Silva, Carlos H. T. P.; Leopoldino, Andreia M.; Silva, Eloiza H. T.; Espinoza, V. A. A.; Taft, C. A.

    The isotypes of RAR and RXR are retinoic acid and retinoid X acid receptors, respectively, whose ligand-binding domain contains the ligand-dependent activation function, with distinct pharmacological targets for retinoids, involved in the treatment of various cancers and skin diseases. Due to the major challenge which cancer treatment and cure still imposes after many decades to the international scientific community, there is actually considerable interest in new ligands with increased bioactivity. We have focused on the retinoid acid receptor, which is considered an interesting target for drug design. In this work, we carried out density functional geometry optimizations and different docking procedures. We performed screening in a large database (hundreds of thousands of molecules which we optimized at the AM1 level) yielding a set of potential bioactive ligands. A new ligand was selected and optimized at the B3LYP/6-31G* level. A flexible docking program was used to investigate the interactions between the receptor and the new ligand. The result of this work is compared with several crystallographic ligands of RAR. Our theoretically more bioactive new ligand indicates stronger and more hydrogen bonds as well as hydrophobic interactions with the receptor.

  6. Thiopyridazine-Based Copper Boratrane Complexes Demonstrating the Z-type Nature of the Ligand.

    Science.gov (United States)

    Holler, Stefan; Tüchler, Michael; Belaj, Ferdinand; Veiros, Luis F; Kirchner, Karl; Mösch-Zanetti, Nadia C

    2016-05-16

    In Z-type ligands the electrons for the coordination bond are formally provided by the metal. They represent an important addition to the much more extensively used L- and X-type σ-donor ligands for the development of transition metal complexes with new reactivities. We report here a new boron Z-type ligand with three tethering thiopyridazinyl donors forming exclusively complexes that feature a metal boron bond. Rational substitution pattern in the backbone of the pyridazinyl heterocycle led to a well-behaved ligand system that allowed preparation of a series of copper boratrane complexes in high yields. They are found to be more soluble in common organic solvents allowing reactivity studies in contrast to previous complexes with this type of ligand. Thus, copper complexes [Cu{B(Pn(Me,tBu))3}X] with X = Cl, OTf, N3, and κN-NCS are reported. Solution behavior was explored, and the molecular structures were determined by single-crystal X-ray diffraction analyses. The thiocyanate ligand is found to coordinate via its nitrogen atom pointing to a high oxidation state of the copper. Density functional theory calculations indicate a high positive charge on copper and a strong copper-boron interaction. Thus, here reported complexes deliver synthetic evidence for the Z-type nature of the ligand. These findings are important for further dissemination of these types of ligands in coordination chemistry.

  7. Activation profiles of opioid ligands in HEK cells expressing δ opioid receptors

    Directory of Open Access Journals (Sweden)

    Clark J

    2002-11-01

    Full Text Available Abstract Background The aim of the present study was to characterize the activation profiles of 15 opioid ligands in transfected human embryonic kidney cells expressing only δ opioid receptors. Activation profiles of most of these ligands at δ opioid receptors had not been previously characterized in vitro. Receptor activation was assessed by measuring the inhibition of forskolin-stimulated cAMP production. Results Naltrexone and nalorphine were classified as antagonists at δ opioid receptor. The other ligands studied were agonists at δ opioid receptors and demonstrated IC50 values of 0.1 nM to 2 μM, maximal inhibition of 39–77% and receptor binding affinities of 0.5 to 243 nM. The rank order of efficacy of the ligands tested was metazocine = xorphanol ≥ fentanyl = SKF 10047 = etorphine = hydromorphone = butorphanol = lofentanil > WIN 44,441 = Nalbuphine = cyclazocine ≥ met-enkephalin >> morphine = dezocine. For the first time these data describe and compare the function and relative efficacy of several ligands at δ opioid receptors. Conclusions The data produced from this study can lead to elucidation of the complete activation profiles of several opioid ligands, leading to clarification of the mechanisms involved in physiological effects of these ligands at δ opioid receptors. Furthermore, these data can be used as a basis for novel use of existing opioid ligands based on their pharmacology at δ opioid receptors.

  8. Microwave assisted, ligand free, copper catalyzed reaction of aryl halides with phenyl urea

    Institute of Scientific and Technical Information of China (English)

    Sandip N. Gavade; Ravi S. Balaskar; Madhav S. Mane; Pramod N. Pabrekar; Murlidhar S. Shingare; Dhananjay V. Mane

    2011-01-01

    The ligand free coupling reaction of phenyl urea with different functionalized aryl halides in the presence of air stable Cu2O and t-BuOK as a base gives symmetrical and unsymmetrical diarylureas in relatively high yields. This method is milder than the palladium catalyzed arylation and avoids the use of toxic phosphine ligand.

  9. Correlation between ligand density of states and 5f delocalization in uranium intermetallic compounds

    International Nuclear Information System (INIS)

    We report spectra of the unoccupied state of uranium intermetallic compounds which contain both localized and delocalized final states. The intensity of the delocalized final states scales with the density of ligand states in the region of the occupied 5f state. The density of ligand states is an important factor influencing the detailed nature of the 5f states in U intermetallic compounds

  10. Enantioselective Addition of Organolithium Reagents to Imines Mediated by C2-Symmetric Bis(aziridine) Ligands

    DEFF Research Database (Denmark)

    Johansson, F.; Tanner, David Ackland

    1998-01-01

    The C-2-symmetric bis(aziridine) ligands 1 - 5 have been screened in the enantioselective addition of organolithium reagents to imines. Ligand 1 (used in stoichiometric amounts) was found to be superior in terms of chemical yield and enantioselectivity, the best result being 90% yield and 89% e.e...

  11. Modifying the properties of 4f single-ion magnets by peripheral ligand functionalisation

    DEFF Research Database (Denmark)

    Pedersen, Kasper Steen; Ungur, Liviu; Sigrist, Marc;

    2014-01-01

    We study the ligand-field splittings and magnetic properties of three ErIII single-ion magnets which differ in the peripheral ligand sphere but exhibit similar first coordination spheres by inelastic neutron scattering (INS) and SQUID magnetometry. The INS spectra of the three compounds are profo...

  12. Catalytic dioxygen activation by Co(II) complexes employing a coordinatively versatile ligand scaffold.

    Science.gov (United States)

    Sharma, Savita K; May, Philip S; Jones, Matthew B; Lense, Sheri; Hardcastle, Kenneth I; MacBeth, Cora E

    2011-02-14

    The ligand bis(2-isobutyrylamidophenyl)amine has been prepared and used to stabilize both mononuclear and dinuclear cobalt(II) complexes. The nuclearity of the cobalt product is regulated by the deprotonation state of the ligand. Both complexes catalytically oxidize triphenylphosphine to triphenylphosphine oxide in the presence of O(2).

  13. Co-variance of dissolved Fe-binding ligands with phytoplankton characteristics in the Canary Basin

    NARCIS (Netherlands)

    Gerringa, L. J. A.; Veldhuis, M. J. W.; Timmermans, K. R.; Sarthou, G.; de Baar, H. J. W.

    2006-01-01

    Dissolved Fe and ligand concentrations and the Fe-binding strength of the organic ligands were measured in samples from the upper water column (150 m) of the oligotrophic waters of the Canary Basin (eastern North Atlantic Ocean). Concentrations of major nutrients, phytoplankton abundance and photosy

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

    Energy Technology Data Exchange (ETDEWEB)

    Szigethy, Geza

    2009-08-12

    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, UO{sub 2}{sup 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 saturation

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

    Science.gov (United States)

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

    2016-07-27

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-08-12

    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

  17. Cloud computing approaches for prediction of ligand binding poses and pathways.

    Science.gov (United States)

    Lawrenz, Morgan; Shukla, Diwakar; Pande, Vijay S

    2015-01-22

    We describe an innovative protocol for ab initio prediction of ligand crystallographic binding poses and highly effective analysis of large datasets generated for protein-ligand dynamics. We include a procedure for setup and performance of distributed molecular dynamics simulations on cloud computing architectures, a model for efficient analysis of simulation data, and a metric for evaluation of model convergence. We give accurate binding pose predictions for five ligands ranging in affinity from 7 nM to > 200 μM for the immunophilin protein FKBP12, for expedited results in cases where experimental structures are difficult to produce. Our approach goes beyond single, low energy ligand poses to give quantitative kinetic information that can inform protein engineering and ligand design.

  18. Solvent fluctuations induce non-Markovian kinetics in hydrophobic pocket-ligand binding

    CERN Document Server

    Weiß, R Gregor; Dzubiella, Joachim

    2016-01-01

    We investigate the impact of water fluctuations on the key-lock association kinetics of a hydrophobic ligand (key) binding to a hydrophobic pocket (lock) by means of a minimalistic stochastic model system. It describes the collective hydration behavior of the pocket by bimodal fluctuations of a water-pocket interface that dynamically couples to the diffusive motion of the approaching ligand via the hydrophobic interaction. This leads to a set of overdamped Langevin equations in 2D-coordinate-space, that is Markovian in each dimension. Numerical simulations demonstrate locally increased friction of the ligand, decelerated binding kinetics, and local non-Markovian (memory) effects in the ligand's reaction coordinate as found previously in explicit-water molecular dynamics studies of model hydrophobic pocket-ligand binding [1,2]. Our minimalistic model elucidates the origin of effectively enhanced friction in the process that can be traced back to long-time decays in the force-autocorrelation function induced by...

  19. Architecture effects on multivalent interactions by polypeptide-based multivalent ligands

    Science.gov (United States)

    Liu, Shuang

    Multivalent interactions are characterized by the simultaneous binding between multiple ligands and multiple binding sites, either in solutions or at interfaces. In biological systems, most multivalent interactions occur between protein receptors and carbohydrate ligands through hydrogen-bonding and hydrophobic interactions. Compared with weak affinity binding between one ligand and one binding site, i.e. monovalent interaction, multivalent interactioins provide greater avidity and specificity, and therefore play unique roles in a broad range of biological activities. Moreover, the studies of multivalent interactions are also essential for producing effective inhibitors and effectors of biological processes that could have important therapeutic applications. Synthetic multivalent ligands have been designed to mimic the biological functions of natural multivalent interactions, and various types of scaffolds have been used to display multiple ligands, including small molecules, linear polymers, dendrimers, nanoparticle surfaces, monolayer surfaces and liposomes. Studies have shown that multivalent interactions can be highly affected by various architectural parameters of these multivalent ligands, including ligand identities, valencies, spacing, ligand densities, nature of linker arms, scaffold length and scaffold conformation. Most of these multivalent ligands are chemically synthesized and have limitations of controlling over sequence and conformation, which is a barrier for mimicking ordered and controlled natural biological systems. Therefore, multivalent ligands with precisely controlled architecture are required for improved structure-function relationship studies. Protein engineering methods with subsequent chemical coupling of ligands provide significant advantages of controlling over backbone conformation and functional group placement, and therefore have been used to synthesize recombinant protein-based materials with desired properties similar to natural

  20. Bioluminescent Ligand-Receptor Binding Assays for Protein or Peptide Hormones.

    Science.gov (United States)

    Liu, Ya-Li; Guo, Zhan-Yun

    2016-01-01

    Bioluminescence has been widely used in biomedical research due to its high sensitivity, low background, and broad linear range. In recent studies, we applied bioluminescence to ligand-receptor binding assays for some protein or peptide hormones based on a newly developed small monomeric Nanoluciferase (NanoLuc) reporter that has the so far brightest bioluminescence. The conventional ligand-receptor binding assays rely on radioligands that have drawbacks, such as radioactive hazards and short shelf lives. In contrast, the novel bioluminescent binding assays use the NanoLuc-based protein or peptide tracers that are safe, stable, and ultrasensitive. Thus, the novel bioluminescent ligand-receptor binding assay would be applied to more and more protein or peptide hormones for ligand-receptor interaction studies in future. In the present article, we provided detailed protocols for setting up the novel bioluminescent ligand-receptor binding assays using two representative protein hormones as examples. PMID:27424896

  1. Conformation and dynamics of the ligand shell of a water-soluble Au102 nanoparticle

    Science.gov (United States)

    Salorinne, Kirsi; Malola, Sami; Wong, O. Andrea; Rithner, Christopher D.; Chen, Xi; Ackerson, Christopher J.; Häkkinen, Hannu

    2016-01-01

    Inorganic nanoparticles, stabilized by a passivating layer of organic molecules, form a versatile class of nanostructured materials with potential applications in material chemistry, nanoscale physics, nanomedicine and structural biology. While the structure of the nanoparticle core is often known to atomic precision, gaining precise structural and dynamical information on the organic layer poses a major challenge. Here we report a full assignment of 1H and 13C NMR shifts to all ligands of a water-soluble, atomically precise, 102-atom gold nanoparticle stabilized by 44 para-mercaptobenzoic acid ligands in solution, by using a combination of multidimensional NMR methods, density functional theory calculations and molecular dynamics simulations. Molecular dynamics simulations augment the data by giving information about the ligand disorder and visualization of possible distinct ligand conformations of the most dynamic ligands. The method demonstrated here opens a way to controllable strategies for functionalization of ligated nanoparticles for applications.

  2. Using RosettaLigand for small molecule docking into comparative models.

    Directory of Open Access Journals (Sweden)

    Kristian W Kaufmann

    Full Text Available Computational small molecule docking into comparative models of proteins is widely used to query protein function and in the development of small molecule therapeutics. We benchmark RosettaLigand docking into comparative models for nine proteins built during CASP8 that contain ligands. We supplement the study with 21 additional protein/ligand complexes to cover a wider space of chemotypes. During a full docking run in 21 of the 30 cases, RosettaLigand successfully found a native-like binding mode among the top ten scoring binding modes. From the benchmark cases we find that careful template selection based on ligand occupancy provides the best chance of success while overall sequence identity between template and target do not appear to improve results. We also find that binding energy normalized by atom number is often less than -0.4 in native-like binding modes.

  3. Role of the T cell receptor ligand affinity in T cell activation by bacterial superantigens

    DEFF Research Database (Denmark)

    Andersen, P S; Geisler, C; Buus, S;

    2001-01-01

    (SEC3) with up to a 150-fold increase in TCR affinity. By stimulating T cells with SEC3 molecules immobilized onto plastic surfaces, we demonstrate that increasing the affinity of the SEC3/TCR interaction caused a proportional increase in the ability of SEC3 to activate T cells. Thus, the potency......Similar to native peptide/MHC ligands, bacterial superantigens have been found to bind with low affinity to the T cell receptor (TCR). It has been hypothesized that low ligand affinity is required to allow optimal TCR signaling. To test this, we generated variants of Staphylococcus enterotoxin C3...... correlation between ligand affinity and ligand potency indicating that it is the density of receptor-ligand complexes in the T cell contact area that determines TCR signaling strength....

  4. A simple competition assay to probe pentacopper(I)-thiolato cluster ligand exchange.

    Science.gov (United States)

    Chen, Yi-Hsun; Lin, Troy T Y; Chen, Hsuan-Ying; Kao, Chai-Lin; Chen, Hsing-Yin; Hsu, Sodio C N; Carey, James R; Chiang, Michael Y

    2013-03-01

    Two pentanuclear copper(I) thiolato clusters of the formula [Cu(5)(L)(3)](-) (L = pyridine-2,6-dimethanethiolate (L1), (1); 4-methylpyridine-2,6-dimethanethiolate (L2), (2)) were synthesized utilizing a single-step procedure, and their structures were characterized by X-ray crystallography. The aforementioned pentanuclear complexes possess an interesting propeller-like Cu(5)S(6) core where all Cu centers are three-coordinate. Electrospray ionization mass spectrometry (ESI-MS) investigation of the pentanuclear copper(I) thiolato clusters with added hetero-ligands demonstrated interesting ligand exchange behavior. The product distribution resulting from ligand exchange not only depended on the quantity of added ligand, but also was sensitive to the coordination ability of the ligand. The ESI-MS method used in this study can serve as a useful tool for probing exchange behavior in coordination metal complexes that cannot otherwise be determined by NMR.

  5. Development of radioiodinated receptor ligands for cerebral single photon emission tomography

    International Nuclear Information System (INIS)

    In the last decade the use of radiolabeled ligands for the imaging of cerebral receptors by emission computed tomography (ECT) has seen rapid growth. The opportunity to routinely perform cerebral single photon emission tomography (SPET) with iodine-123-labeled ligands depends on the availability of receptor ligands into which iodine can be introduced without decreasing the required high target receptor specificity. The use of iodine-123-labeled receptor-specific ligands also depends on the availability of high purity iodine-123 at reasonable costs and the necessary imaging instrumentation. In this paper, the development and current stage of evaluation of various iodine-123-labeled ligands for SPET imaging of dopaminergic, serotonergic and muscarinic acetylcholinergic receptor classes are discussed

  6. Nanoparticle Shape Anisotropy Dictates the Collective Behavior of Surface-Bound Ligands

    Energy Technology Data Exchange (ETDEWEB)

    Jones, Matthew R.; Macfarlane, Robert J.; Prigodich, Andrew E.; Patel, Pinal C.; Mirkin, Chad A. (NWU)

    2012-11-14

    We report on the modification of the properties of surface-confined ligands in nanoparticle systems through the introduction of shape anisotropy. Specifically, triangular gold nanoprisms, densely functionalized with oligonucleotide ligands, hybridize to complementary particles with an affinity that is several million times higher than that of spherical nanoparticle conjugates functionalized with the same amount of DNA. In addition, they exhibit association rates that are 2 orders of magnitude greater than those of their spherical counterparts. This phenomenon stems from the ability of the flat, extended facets of nonspherical nanoparticles to (1) support more numerous ligand interactions through greater surface contact with complementary particles, (2) increase the effective local concentration of terminal DNA nucleotides that mediate hybridization, and (3) relieve the conformational stresses imposed on nanoparticle-bound ligands participating in interactions between curved surfaces. Finally, these same trends are observed for the pH-mediated association of nanoparticles functionalized with carboxylate ligands, demonstrating the generality of these findings.

  7. Surfactant Ligand Removal and Rational Fabrication of Inorganically Connected Quantum Dots

    KAUST Repository

    Zhang, Haitao

    2011-12-14

    A novel method is reported to create inorganically connected nanocrystal (NC) assemblies for both II-VI and IV-VI semiconductors by removing surfactant ligands using (NH 4) 2S. This surface modification process differs from ligand exchange methods in that no new surfactant ligands are introduced and the post-treated NC surfaces are nearly bare. The detailed mechanism study shows that the high reactivity between (NH 4) 2S and metal-surfactant ligand complexes enables the complete removal of surfactant ligands in seconds and converts the NC metal-rich shells into metal sulfides. The post-treated NCs are connected through metal-sulfide bonding and form a larger NCs film assembly, while still maintaining quantum confinement. Such "connected but confined" NC assemblies are promising new materials for electronic and optoelectronic devices. © 2011 American Chemical Society.

  8. Surface-Bound Ligands Modulate Chemoselectivity and Activity of a Bimetallic Nanoparticle Catalyst

    KAUST Repository

    Vu, Khanh B.

    2015-04-03

    "Naked" metal nanoparticles (NPs) are thermodynamically and kinetically unstable in solution. Ligands, surfactants, or polymers, which adsorb at a particle\\'s surface, can be used to stabilize NPs; however, such a mode of stabilization is undesirable for catalytic applications because the adsorbates block the surface active sites. The catalytic activity and the stability of NPs are usually inversely correlated. Here, we describe an example of a bimetallic (PtFe) NP catalyst stabilized by carboxylate surface ligands that bind preferentially to one of the metals (Fe). NPs stabilized by fluorous ligands were found to be remarkably competent in catalyzing the hydrogenation of cinnamaldehyde; NPs stabilized by hydrocarbon ligands were significantly less active. The chain length of the fluorous ligands played a key role in determining the chemoselectivity of the FePt NP catalysts. (Chemical Presented). © 2015 American Chemical Society.

  9. Size-dependent ligand layer dynamics in semiconductor nanocrystals probed by anisotropy measurements.

    Science.gov (United States)

    Hadar, Ido; Abir, Tsafrir; Halivni, Shira; Faust, Adam; Banin, Uri

    2015-10-12

    Colloidal semiconductor nanocrystals (NC) have reached a high level of synthetic control allowing the tuning of their properties, and their use in various applications. However, the surface of NCs and in particular their size-dependent capping organic ligand behavior, which play an important role in the NC synthesis, dispersibility, and optoelectronic properties, is still not well understood. We study the size-dependent properties of the ligand shell on the surface of NCs, by embedding surface bound dyes as a probe within the ligand shell. The reorientation times for these dyes show a linear dependence on the NC surface curvature indicating size-dependent change in viscosity, which is related to a change in the density of the ligand layer because of the geometry of the surface, a unique feature of NCs. Understanding the properties of the ligand shell will allow rational design of the surface to achieve the desired properties, providing an additional important knob for tuning their functionality.

  10. Explicit all-atom modeling of realistically sized ligand-capped nanocrystals

    KAUST Repository

    Kaushik, Ananth P.

    2012-01-01

    We present a study of an explicit all-atom representation of nanocrystals of experimentally relevant sizes (up to 6 nm), capped with alkyl chain ligands, in vacuum. We employ all-atom molecular dynamics simulation methods in concert with a well-tested intermolecular potential model, MM3 (molecular mechanics 3), for the studies presented here. These studies include determining the preferred conformation of an isolated single nanocrystal (NC), pairs of isolated NCs, and (presaging studies of superlattice arrays) unit cells of NC superlattices. We observe that very small NCs (3 nm) behave differently in a superlattice as compared to larger NCs (6 nm and above) due to the conformations adopted by the capping ligands on the NC surface. Short ligands adopt a uniform distribution of orientational preferences, including some that lie against the face of the nanocrystal. In contrast, longer ligands prefer to interdigitate. We also study the effect of changing ligand length and ligand coverage on the NCs on the preferred ligand configurations. Since explicit all-atom modeling constrains the maximum system size that can be studied, we discuss issues related to coarse-graining the representation of the ligands, including a comparison of two commonly used coarse-grained models. We find that care has to be exercised in the choice of coarse-grained model. The data provided by these realistically sized ligand-capped NCs, determined using explicit all-atom models, should serve as a reference standard for future models of coarse-graining ligands using united atom models, especially for self-assembly processes. © 2012 American Institute of Physics.

  11. Lipoteichoic acid induces unique inflammatory responses when compared to other toll-like receptor 2 ligands.

    Directory of Open Access Journals (Sweden)

    Elizabeth M Long

    Full Text Available Toll-like receptors (TLRs recognize evolutionarily-conserved molecular patterns originating from invading microbes. In this study, we were interested in determining if microbial ligands, which use distinct TLR2-containing receptor complexes, represent unique signals to the cell and can thereby stimulate unique cellular responses. Using the TLR2 ligands, R-FSL1, S-FSL1, Pam2CSK4, Pam3CSK4, and lipoteichoic acid (LTA, we demonstrate that these ligands activate NF-kappaB and MAP Kinase pathways with ligand-specific differential kinetics in murine macrophages. Most strikingly, LTA stimulation of these pathways was substantially delayed when compared with the other TLR2 ligands. These kinetics differences were associated with a delay in the LTA-induced expression of a subset of genes as compared with another TLR2 ligand, R-FSL1. However, this did not translate to overall differences in gene expression patterns four hours following stimulation with different TLR2 ligands. We extended this study to evaluate the in vivo responses to distinct TLR2 ligands using a murine model of acute inflammation, which employs intravital microscopy to monitor leukocyte recruitment into the cremaster muscle. We found that, although R-FSL1, S-FSL1, Pam2CSK4, and Pam3CSK4 were all able to stimulate robust leukocyte recruitment in vivo, LTA remained functionally inert in this in vivo model. Therefore distinct TLR2 ligands elicit unique cellular responses, as evidenced by differences in the kinetic profiles of signaling and gene expression responses in vitro, as well as the physiologically relevant differences in the in vivo responses to these ligands.

  12. DMPD: Toll-like receptors, Notch ligands, and cytokines drive the chronicity of lunginflammation. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 18073395 Toll-like receptors, Notch ligands, and cytokines drive the chronicity of lunginflammation. Raymond...ors, Notch ligands, and cytokines drive the chronicity of lunginflammation. Authors Raymond T, Schaller M, H

  13. The Role of PPAR Ligands in Controlling Growth-Related Gene Expression and their Interaction with Lipoperoxidation Products

    Directory of Open Access Journals (Sweden)

    Giuseppina Barrera

    2008-01-01

    Full Text Available Peroxisome proliferators-activated receptors (PPARs are ligand-activated transcription factors that belong to the nuclear hormone receptor superfamily. The three PPAR isoforms (, and / have been found to play a pleiotropic role in cell fat metabolism. Furthermore, in recent years, evidence has been found regarding the antiproliferative, proapoptotic, and differentiation-promoting activities displayed by PPAR ligands, particularly by PPAR ligands. PPAR ligands affect the expression of different growth-related genes through both PPAR-dependent and PPAR-independent mechanisms. Moreover, an interaction between PPAR ligands and other molecules which strengthen the effects of PPAR ligands has been described. Here we review the action of PPAR on the control of gene expression with particular regard to the effect of PPAR ligands on the expression of genes involved in the regulation of cell-cycle, differentiation, and apoptosis. Moreover, the interaction between PPAR ligands and 4-hydroxynonenal (HNE, the major product of the lipid peroxidation, has been reviewed.

  14. Theoretical investigation on the diatomic ligand migration process and ligand binding properties in non-O2-binding H-NOX domain.

    Science.gov (United States)

    Zhang, Yuebin; Liu, Li; Wu, Lei; Li, Shuai; Li, Fei; Li, Zhengqiang

    2013-08-01

    The Nostoc sp (Ns) H-NOX (heme-nitric oxide or OXygen-binding) domain shares 35% sequence identity with soluble guanylate cyclase (sGC) and exhibits similar ligand binding property with the sGC. Previously, our molecular dynamic (MD) simulation work identified that there exists a Y-shaped tunnel system hosted in the Ns H-NOX interior, which servers for ligand migration. The tunnels were then confirmed by Winter et al. [PNAS 2011;108(43):E 881-889] recently using x-ray crystallography with xenon pressured conditions. In this work, to further investigate how the protein matrix of Ns H-NOX modulates the ligand migration process and how the distal residue composition affects the ligand binding prosperities, the free energy profiles for nitric oxide (NO), carbon monooxide (CO), and O2 migration are explored using the steered MDs simulation and the ligand binding energies are calculated using QM/MM schemes. The potential of mean force profiles suggest that the longer branch of the tunnel would be the most favorable route for NO migration and a second NO trapping site other than the distal heme pocket along this route in the Ns H-NOX was identified. On the contrary, CO and O2 would prefer to diffuse via the shorter branch of the tunnel. The QM/MM (quantum mechanics/molecular mechanics) calculations suggest that the hydrophobic distal pocket of Ns H-NOX would provide an approximately vacuum environment and the ligand discrimination would be determined by the intrinsic binding properties of the diatomic gas ligand to the heme group. PMID:23504767

  15. Prospects for three-electron donor boronyl (BO) ligands and dioxodiborene (B2O2) ligands as bridging groups in binuclear iron carbonyl derivatives.

    Science.gov (United States)

    Chang, Yu; Li, Qian-Shu; Xie, Yaoming; King, R Bruce

    2012-08-20

    Recent experimental work (2010) on (Cy(3)P)(2)Pt(BO)Br indicates that the oxygen atom of the boronyl (BO) ligand is more basic than that in the ubiquitous CO ligand. This suggests that bridging BO ligands in unsaturated binuclear metal carbonyl derivatives should readily function as three-electron donor bridging ligands involving both the oxygen and the boron atoms. In this connection, density functional theory shows that three of the four lowest energy singlet Fe(2)(BO)(2)(CO)(7) structures have such a bridging η(2)-μ-BO group as well as a formal Fe-Fe single bond. In addition, all four of the lowest energy singlet Fe(2)(BO)(2)(CO)(6) structures have two bridging η(2)-μ-BO groups and formal Fe-Fe single bonds. Other Fe(2)(BO)(2)(CO)(n) (n = 7, 6) structures are found in which the two BO groups have coupled to form a bridging dioxodiborene (B(2)O(2)) ligand with B-B bonding distances of ~1.84 Å. All of these Fe(2)(μ-B(2)O(2))(CO)(n) structures have long Fe···Fe distances indicating a lack of direct iron-iron bonding. One of the singlet Fe(2)(BO)(2)(CO)(7) structures has such a bridging dioxodiborene ligand with cis stereochemistry functioning as a six-electron donor to the pair of iron atoms. In addition, the lowest energy triplet structures for both Fe(2)(BO)(2)(CO)(7) and Fe(2)(BO)(2)(CO)(6) have bridging dioxodiborene ligands with trans stereochemistry functioning as a four-electron donor to the pair of iron atoms. PMID:22862812

  16. Influence of bidentate structure of an aryl phosphine oxide ligand on photophysical properties of its Eu~Ⅲ complex

    Institute of Scientific and Technical Information of China (English)

    许辉; 魏莹; 赵保敏; 黄维

    2010-01-01

    The bidentate phosphine oxide ligand 1,8-bis(diphenylphosphino) naphthalene oxide (NAPO) and its EuⅢ complex 1 Eu(TTA)3(NAPO) (TTA=2-thenoyltrifluoroacetonate) were chosen to study the effect of bidentate phosphine oxide ligand on the photophysical properties of the corresponding complex. The intramolecular energy transfer processes of 1 were studied. The investigation showed that with bidentate structure NAPO could suppress solvent-induced quenching by enforcing the ligand-ligand interaction and the rigidi...

  17. The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation

    OpenAIRE

    Gao, Mu; Skolnick, Jeffrey

    2012-01-01

    Protein-protein and protein-ligand interactions are ubiquitous in a biological cell. Here, we report a comprehensive study of the distribution of protein-ligand interaction sites, namely ligand-binding pockets, around protein-protein interfaces where protein-protein interactions occur. We inspected a representative set of 1,611 representative protein-protein complexes and identified pockets with a potential for binding small molecule ligands. The majority of these pockets are within a 6 Å dis...

  18. Pharmacological profiles of the metabotropic glutamate receptor ligands.

    Science.gov (United States)

    Naples, M A; Hampson, D R

    2001-01-01

    Metabotropic glutamate receptors (mGluRs) are a family of G-protein coupled receptors that are expressed in the central and peripheral nervous systems. The purpose of this study was to compare the ligand binding selectivity profiles of the mGluR agonist [(3)H]L-AP4 and the novel radiolabeled phenylglycine antagonist [(3)H]CPPG at all eight rat mGluR subtypes expressed in transfected human embryonic kidney cells. At a concentration of 30 nM [(3)H]L-AP4, no specific binding was detected in membranes expressing the group I receptors mGluR1a or mGluR5a, or in membranes expressing the group II mGluRs, mGluR2 and mGluR3. Among the group III mGluRs, specific [(3)H]L-AP4 binding was detected in cells expressing mGluR4a and mGluR8a but not in cells expressing mGluR6 or mGluR7a. The binding of [(3)H]CPPG showed an exceptional pattern of selectivity amongst the mGluR subtypes; at a concentration of 20 nM [(3)H]CPPG, a high level of specific binding was seen in membranes containing mGluR8a but not in any of the other mGluR subtypes. The affinity constant (K(D)) calculated for [(3)H]CPPG binding to mGluR8a was 183 nM. In competition experiments, the phosphono-substituted phenylglycine congeners including MPPG, (RS)-PPG, and unlabeled CPPG were the most potent inhibitors of [(3)H]CPPG binding while non-phosphonated compounds such as L-glutamate and MCPG were substantially less potent. These results demonstrate that [(3)H]L-AP4 and [(3)H]CPPG can be used as probes to selectively label group III mGluRs and that CPPG and related phenylglycine derivatives are useful for studying differences in the ligand recognition sites of highly homologous mGluRs. PMID:11114395

  19. Saturation-Transfer Difference (STD) NMR: A Simple and Fast Method for Ligand Screening and Characterization of Protein Binding

    Science.gov (United States)

    Viegas, Aldino; Manso, Joao; Nobrega, Franklin L.; Cabrita, Eurico J.

    2011-01-01

    Saturation transfer difference (STD) NMR has emerged as one of the most popular ligand-based NMR techniques for the study of protein-ligand interactions. The success of this technique is a consequence of its robustness and the fact that it is focused on the signals of the ligand, without any need of processing NMR information about the receptor…

  20. DMPD: Anti-inflammatory actions of PPAR ligands: new insights on cellular andmolecular mechanisms. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 17981503 Anti-inflammatory actions of PPAR ligands: new insights on cellular andmol...) (.html) (.csml) Show Anti-inflammatory actions of PPAR ligands: new insights on cellular andmolecular mech...anisms. PubmedID 17981503 Title Anti-inflammatory actions of PPAR ligands: new in

  1. Synthesis and Characterization of Dinuclear Metal Complexes Stabilized by Tetradentate Schiff Base Ligands

    Directory of Open Access Journals (Sweden)

    Eid A. Abdalrazaq

    2010-01-01

    Full Text Available Problem statement: The synthesis, spectroscopic properties and theoretical calculations of acetylacetonimine and acetylacetanilidimine Schiff-base ligands, L1H and L2H, respectively and their dinuclear complexes of the type [M2LnCl2(H2O2], where n = 1 or 2, M = Co(II, Ni(II, Cu(II, Zn(II and Cd(II are described. Approach: The new tetradentate dianion Schiff base ligand which was used as stabilizers for the complexes were prepared by condensation of hydrazine with acetylacetone or acetylacetanilide. The dinuclear complexes of theses ligands were synthesized by treating an ethanolic solution of the prepared ligand with hydrated metal salts in molar ratio of 1:2 (L:M. Results: The ligand and their dinuclear metal complexes were characterized by CHN elemental analysis, FT-IR, UV-Vis, 1HNMR (for the ligands, conductivity, magnetic susceptibility and theoretical calculation by using MM2 modeling program. Conclusion: The reaction of these ligands in a 1:2 (L:M afford dinuclear M(II metal complexes with tetrahedral arrangement around Co(II, Zn(II and Cd(II and square planar around Ni(II and Cu(II.

  2. Impact of killer immunoglobulin-like receptor-human leukocyte antigens ligand incompatibility among renal transplantation.

    Science.gov (United States)

    Alam, S; Rangaswamy, D; Prakash, S; Sharma, R K; Khan, M I; Sonawane, A; Agrawal, S

    2015-01-01

    Killer immunoglobulin-like receptor (KIR) gene shows a high degree of polymorphism. Natural killer cell receptor gets activated once they bind to self-human leukocyte antigens (HLAs) with specific ligand. KIR gene and HLA ligand incompatibility due to the presence/absence of KIR in the recipient and the corresponding HLA ligand in the allograft may impact graft survival in solid organ transplantation. This study evaluates the effect of matches between KIR genes and known HLA ligands. KIR genotypes were determined using sequence specific primer polymerase chain reaction. Presence of certain KIR in a recipient, where the donor lacked the corresponding HLA ligand was considered a mismatch. The allograft was considered matched when both KIR receptor and HLA alloantigen reveald compatibility among recipient and donor. The data revealed better survival among individuals with matched inhibitory KIR receptors and their corresponding HLA ligands (KIR2DL2/DL3-HLAC2, KIR3DL1-HLABw4). On the contrary, no adverse effect was seen for matched activating KIR receptors and their corresponding HLA ligands. One of the activating gene KIR2DS4 showed risk (P = 0.0413, odds ratio = 1.91, 95% confidence interval = 1.02-3.57) association with renal allograft rejection. We conclude that the presence of inhibitory KIR gene leads to better survival; whereas activating motifs show no significant role in renal allograft survival.

  3. Ligand substitution reactions of a phenolic quinolyl hydrazone; oxidovanadium (IV complexes

    Directory of Open Access Journals (Sweden)

    Seleem Hussein S

    2011-08-01

    Full Text Available Abstract Background Quinoline ring has therapeutic and biological activities. Quinolyl hydrazones constitute a class of excellent chelating agents. Recently, the physiological and biological activities of quinolyl hydrazones arise from their tendency to form metal chelates with transition metal ions. In this context, we have aimed to study the competency effect of a phenolic quinolyl hydrazone (H2L; primary ligand with some auxiliary ligands (Tmen, Phen or Oxine; secondary ligands towards oxidovanadium (IV ions. Results Mono- and binuclear oxidovanadium (IV - complexes were obtained from the reaction of a phenolic quinolyl hydrazone with oxidovanadium (IV- ion in absence and presence of N,N,N',N'- tetramethylethylenediamine (Tmen, 1,10-phenanthroline (Phen or 8-hydroxyquinoline (Oxine. The phenolic quinolyl hydrazone ligand behaves as monobasic bidentate (NO- donor with O- bridging. All the obtained complexes have the preferable octahedral geometry except the oxinato complex (2 which has a square pyramid geometry with no axial interaction; the only homoleptic complex in this study. Conclusion The ligand exchange (substitution/replacement reactions reflect the strong competency power of the auxiliary aromatic ligands (Phen/Oxine compared to the phenolic quinolyl hydrazone (H2L towards oxidovanadium (IV ion; (complexes 2 and 3. By contrast, in case of the more flexible aliphatic competitor (Tmen, an adduct was obtained (4. The obtained complexes reflect the strength of the ligand field towards the oxidovanadium (IV- ion; Oxine or Phen >> phenolic hydrazone (H2L > Tmen.

  4. VS-APPLE: A Virtual Screening Algorithm Using Promiscuous Protein-Ligand Complexes.

    Science.gov (United States)

    Okuno, Tatsuya; Kato, Koya; Terada, Tomoki P; Sasai, Masaki; Chikenji, George

    2015-06-22

    As the number of structurally resolved protein-ligand complexes increases, the ligand-binding pockets of many proteins have been found to accommodate multiple different compounds. Effective use of these structural data is important for developing virtual screening (VS) methods that identify bioactive compounds. Here, we introduce a VS method, VS-APPLE (Virtual Screening Algorithm using Promiscuous Protein-Ligand complExes), based on promiscuous protein-ligand binding structures. In VS-APPLE, multiple ligands bound to a pocket are combined into a query template for screening. Both the structural match between a test compound and the multiple-ligand template and the possible collisions between the test compound and the target protein are evaluated by an efficient geometric hashing method. The performance of VS-APPLE was examined on a filtered, clustered version of the Directory of Useful Decoys data set. In Area Under the Curve analyses of this data set, VS-APPLE outperformed several popular screening programs. Judging from the performance of VS-APPLE, the structural data of promiscuous protein-ligand bindings could be further analyzed and exploited for developing VS methods.

  5. A new test set for validating predictions of protein-ligand interaction.

    Science.gov (United States)

    Nissink, J Willem M; Murray, Chris; Hartshorn, Mike; Verdonk, Marcel L; Cole, Jason C; Taylor, Robin

    2002-12-01

    We present a large test set of protein-ligand complexes for the purpose of validating algorithms that rely on the prediction of protein-ligand interactions. The set consists of 305 complexes with protonation states assigned by manual inspection. The following checks have been carried out to identify unsuitable entries in this set: (1) assessing the involvement of crystallographically related protein units in ligand binding; (2) identification of bad clashes between protein side chains and ligand; and (3) assessment of structural errors, and/or inconsistency of ligand placement with crystal structure electron density. In addition, the set has been pruned to assure diversity in terms of protein-ligand structures, and subsets are supplied for different protein-structure resolution ranges. A classification of the set by protein type is available. As an illustration, validation results are shown for GOLD and SuperStar. GOLD is a program that performs flexible protein-ligand docking, and SuperStar is used for the prediction of favorable interaction sites in proteins. The new CCDC/Astex test set is freely available to the scientific community (http://www.ccdc.cam.ac.uk).

  6. Molecular dynamics simulation of ligand dissociation from liver fatty acid binding protein.

    Directory of Open Access Journals (Sweden)

    Dong Long

    Full Text Available The mechanisms of how ligands enter and leave the binding cavity of fatty acid binding proteins (FABPs have been a puzzling question over decades. Liver fatty acid binding protein (LFABP is a unique family member which accommodates two molecules of fatty acids in its cavity and exhibits the capability of interacting with a variety of ligands with different chemical structures and properties. Investigating the ligand dissociation processes of LFABP is thus a quite interesting topic, which however is rather difficult for both experimental approaches and ordinary simulation strategies. In the current study, random expulsion molecular dynamics simulation, which accelerates ligand motions for rapid dissociation, was used to explore the potential egress routes of ligands from LFABP. The results showed that the previously hypothesized "portal region" could be readily used for the dissociation of ligands at both the low affinity site and the high affinity site. Besides, one alternative portal was shown to be highly favorable for ligand egress from the high affinity site and be related to the unique structural feature of LFABP. This result lends strong support to the hypothesis from the previous NMR exchange studies, which in turn indicates an important role for this alternative portal. Another less favored potential portal located near the N-terminal end was also identified. Identification of the dissociation pathways will allow further mechanistic understanding of fatty acid uptake and release by computational and/or experimental techniques.

  7. Molecular dynamics simulation of ligand dissociation from liver fatty acid binding protein.

    Science.gov (United States)

    Long, Dong; Mu, Yuguang; Yang, Daiwen

    2009-01-01

    The mechanisms of how ligands enter and leave the binding cavity of fatty acid binding proteins (FABPs) have been a puzzling question over decades. Liver fatty acid binding protein (LFABP) is a unique family member which accommodates two molecules of fatty acids in its cavity and exhibits the capability of interacting with a variety of ligands with different chemical structures and properties. Investigating the ligand dissociation processes of LFABP is thus a quite interesting topic, which however is rather difficult for both experimental approaches and ordinary simulation strategies. In the current study, random expulsion molecular dynamics simulation, which accelerates ligand motions for rapid dissociation, was used to explore the potential egress routes of ligands from LFABP. The results showed that the previously hypothesized "portal region" could be readily used for the dissociation of ligands at both the low affinity site and the high affinity site. Besides, one alternative portal was shown to be highly favorable for ligand egress from the high affinity site and be related to the unique structural feature of LFABP. This result lends strong support to the hypothesis from the previous NMR exchange studies, which in turn indicates an important role for this alternative portal. Another less favored potential portal located near the N-terminal end was also identified. Identification of the dissociation pathways will allow further mechanistic understanding of fatty acid uptake and release by computational and/or experimental techniques. PMID:19564911

  8. Natural ligand binding and transfer from liver fatty acid binding protein (LFABP) to membranes.

    Science.gov (United States)

    De Gerónimo, Eduardo; Hagan, Robert M; Wilton, David C; Córsico, Betina

    2010-09-01

    Liver fatty acid-binding protein (LFABP) is distinctive among fatty acid-binding proteins because it binds more than one molecule of long-chain fatty acid and a variety of diverse ligands. Also, the transfer of fluorescent fatty acid analogues to model membranes under physiological ionic strength follows a different mechanism compared to most of the members of this family of intracellular lipid binding proteins. Tryptophan insertion mutants sensitive to ligand binding have allowed us to directly measure the binding affinity, ligand partitioning and transfer to model membranes of natural ligands. Binding of fatty acids shows a cooperative mechanism, while acyl-CoAs binding presents a hyperbolic behavior. Saturated fatty acids seem to have a stronger partition to protein vs. membranes, compared to unsaturated fatty acids. Natural ligand transfer rates are more than 200-fold higher compared to fluorescently-labeled analogues. Interestingly, oleoyl-CoA presents a markedly different transfer behavior compared to the rest of the ligands tested, probably indicating the possibility of specific targeting of ligands to different metabolic fates. PMID:20541621

  9. Photostability of CdSe quantum dots functionalized with aromatic dithiocarbamate ligands.

    Science.gov (United States)

    Tan, Yizheng; Jin, Song; Hamers, Robert J

    2013-12-26

    Organic ligands are widely used to enhance the ability of CdSe quantum dots (QDs) to resist photodegradation processes such as photo-oxidation. Because long alkyl chains may adversely affect the performance of QD devices that require fast and efficient charge transfer, shorter aromatic ligands are of increasing interest. In this work, we characterize the formation of phenyl dithiocarbamate (DTC) adducts on CdSe surfaces and the relative effectiveness of different para-substituted phenyl dithiocarbamates to enhance the aqueous photostability of CdSe QDs on TiO2. Optical absorption and photoluminescence measurements show that phenyl DTC ligands can be highly effective at reducing QD photocorrosion in water, and that ligands bearing electron-donating substituents are the most effective. A comparison of the QD photostability resulting from use of ligands bearing DTC versus thiol surface-binding groups shows that the DTC group provides greater QD photostability. Density functional calculations with natural bond order analysis show that the effectiveness of substituted phenyl DTC results from the ability of these ligands to remove positive charge away from the CdSe and to delocalize positive charge on the ligand. PMID:24256318

  10. A python-based docking program utilizing a receptor bound ligand shape: PythDock.

    Science.gov (United States)

    Chung, Jae Yoon; Cho, Seung Joo; Hah, Jung-Mi

    2011-09-01

    PythDock is a heuristic docking program that uses Python programming language with a simple scoring function and a population based search engine. The scoring function considers electrostatic and dispersion/repulsion terms. The search engine utilizes a particle swarm optimization algorithm. A grid potential map is generated using the shape information of a bound ligand within the active site. Therefore, the searching area is more relevant to the ligand binding. To evaluate the docking performance of PythDock, two well-known docking programs (AutoDock and DOCK) were also used with the same data. The accuracy of docked results were measured by the difference of the ligand structure between x-ray structure, and docked pose, i.e., average root mean squared deviation values of the bound ligand were compared for fourteen protein-ligand complexes. Since the number of ligands' rotational flexibility is an important factor affecting the accuracy of a docking, the data set was chosen to have various degrees of flexibility. Although PythDock has a scoring function simpler than those of other programs (AutoDock and DOCK), our results showed that PythDock predicted more accurate poses than both AutoDock4.2 and DOCK6.2. This indicates that PythDock could be a useful tool to study ligand-receptor interactions and could also be beneficial in structure based drug design.

  11. Engineering and optimization of an allosteric biosensor protein for peroxisome proliferator-activated receptor γ ligands.

    Science.gov (United States)

    Li, Jingjing; Gierach, Izabela; Gillies, Alison R; Warden, Charles D; Wood, David W

    2011-11-15

    The peroxisome proliferator-activated receptor gamma (PPARγ or PPARG) belongs to the nuclear receptor superfamily, and is a potential drug target for a variety of diseases. In this work, we constructed a series of bacterial biosensors for the identification of functional PPARγ ligands. These sensors entail modified Escherichia coli cells carrying a four-domain fusion protein, comprised of the PPARγ ligand binding domain (LBD), an engineered mini-intein domain, the E. coli maltose binding protein (MBD), and a thymidylate synthase (TS) reporter enzyme. E. coli cells expressing this protein exhibit hormone ligand-dependent growth phenotypes. Unlike our published estrogen (ER) and thyroid receptor (TR) biosensors, the canonical PPARγ biosensor cells displayed pronounced growth in the absence of ligand. They were able to distinguish agonists and antagonists, however, even in the absence of agonist. To improve ligand sensitivity of this sensor, we attempted to engineer and optimize linker peptides flanking the PPARγ LBD insertion point. Truncation of the original linkers led to decreased basal growth and significantly enhanced ligand sensitivity of the PPARγ sensor, while substitution of the native linkers with optimized G(4)S (Gly-Gly-Gly-Gly-Ser) linkers further increased the sensitivity. Our studies demonstrate that the properties of linkers, especially the C-terminal linker, greatly influence the efficiency and fidelity of the allosteric signal induced by ligand binding. Our work also suggests an approach to increase allosteric behavior in this multidomain sensor protein, without modification of the functional LBD. PMID:21893405

  12. Gold Nanoparticle Monolayers from Sequential Interfacial Ligand Exchange and Migration in a Three-Phase System

    Science.gov (United States)

    Yang, Guang; Hallinan, Daniel T.

    2016-01-01

    Using a three-phase system, centimeter-scale monolayer gold nanoparticle (Au NP) films have been prepared that have long-range order and hydrophobic ligands. The system contains an interface between an aqueous phase containing Au NPs and an oil phase containing one of various types of amine ligands, and a water/air interface. As the Au NPs diffuse to the water/oil interface, ligand exchange takes place which temporarily traps them at the water/oil interface. The ligand-exchanged particles then spontaneously migrate to the air/water interface, where they self-assemble, forming a monolayer under certain conditions. The spontaneous formation of the NP film at the air/water interface was due to the minimization of the system Helmholtz free energy. However, the extent of surface functionalization was dictated by kinetics. This decouples interfacial ligand exchange from interfacial self-assembly, while maintaining the simplicity of a single system. The interparticle center-to-center distance was dictated by the amine ligand length. The Au NP monolayers exhibit tunable surface plasma resonance and excellent spatial homogeneity, which is useful for surface-enhanced Raman scattering. The “air/water/oil” self-assembly method developed here not only benefits the fundamental understanding of NP ligand conformations, but is also applicable to the manufacture of plasmonic nanoparticle devices with precisely designed optical properties. PMID:27762394

  13. Computational protocol for predicting the binding affinities of zinc containing metalloprotein-ligand complexes.

    Science.gov (United States)

    Jain, Tarun; Jayaram, B

    2007-06-01

    Zinc is one of the most important metal ions found in proteins performing specific functions associated with life processes. Coordination geometry of the zinc ion in the active site of the metalloprotein-ligand complexes poses a challenge in determining ligand binding affinities accurately in structure-based drug design. We report here an all atom force field based computational protocol for estimating rapidly the binding affinities of zinc containing metalloprotein-ligand complexes, considering electrostatics, van der Waals, hydrophobicity, and loss in conformational entropy of protein side chains upon ligand binding along with a nonbonded approach to model the interactions of the zinc ion with all the other atoms of the complex. We examined the sensitivity of the binding affinity predictions to the choice of Lennard-Jones parameters, partial atomic charges, and dielectric treatments adopted for system preparation and scoring. The highest correlation obtained was R2 = 0.77 (r = 0.88) for the predicted binding affinity against the experiment on a heterogenous dataset of 90 zinc containing metalloprotein-ligand complexes consisting of five unique protein targets. Model validation and parameter analysis studies underscore the robustness and predictive ability of the scoring function. The high correlation obtained suggests the potential applicability of the methodology in designing novel ligands for zinc-metalloproteins. The scoring function has been web enabled for free access at www.scfbio-iitd.res.in/software/drugdesign/bapplz.jsp as BAPPL-Z server (Binding Affinity Prediction of Protein-Ligand complexes containing Zinc metal ions).

  14. A comparative study of actinide complexation in three ligand systems with increasing complexity

    Science.gov (United States)

    Jeanson, A.; Dahou, S.; Guillaumont, D.; Moisy, P.; Den Auwer, C.; Scheinost, A.; Hennig, C.; Vidaud, C.; Subra, G.; Solari, P. L.

    2009-11-01

    The complexation of thorium, neptunium and plutonium at oxidation state +IV with three ligands of increasing complexity has been investigated. These ligands are relevant for bio inorganic systems. The first ligand is the small nitrilotriacetic acid that often play the role of protecting ligands against hydrolysis. EXAFS results for the Th to Pu series have been correlated to quantum chemical calculations and show an homogeneous behavior of the actinide at oxidation state +IV. For larger ligands, steric effects may become significant and one can ask how the ligand may accommodate the large actinide cation coordination sphere. Model pentapeptides have been synthesized and tested as complexing agents. Comparison with NTA shows that the molecular arrangements are radically different. The third ligand system is transferrin, a diferric metalloptrotein that is well known to coordinate a large variety of cations from transition metals of f-elements. Metalloproteins bear primary, secondary and tertiary structures that all play a crucial role in bonding. At a given oxidation state (+IV), but for various atomic numbers (Th, Np, Pu) EXAFS data at the cation LIII edge exhibit significant coordination discrepancies that are related to a changes in protein geometry. In that sense, the metalloprotein may be viewed as a complex system.

  15. A comparative study of actinide complexation in three ligand systems with increasing complexity

    Energy Technology Data Exchange (ETDEWEB)

    Jeanson, A; Dahou, S; Guillaumont, D; Moisy, P; Auwer, C Den [CEA Marcoule, DEN/DRCP/SCPS, 30207 Bagnols sur Ceze (France); Scheinost, A; Hennig, C [Forschungszentrum Dresden-Rossendorf, 01314 Dresden (Germany); Vidaud, C [CEA Marcoule DSV/iBEB/SBTN, 30207 Bagnols sur Ceze (France); Subra, G [Institut des Biomolecules Max Mousseron, CNRS UMR-5247, Universite Montpellier I-II, 34093 Montpellier (France); Solari, P L, E-mail: Christophe.denauwer@cea.f [Synchrotron SOLEIL, MARS beam line, 91192 Gif sur Yvette (France)

    2009-11-15

    The complexation of thorium, neptunium and plutonium at oxidation state +IV with three ligands of increasing complexity has been investigated. These ligands are relevant for bio inorganic systems. The first ligand is the small nitrilotriacetic acid that often play the role of protecting ligands against hydrolysis. EXAFS results for the Th to Pu series have been correlated to quantum chemical calculations and show an homogeneous behavior of the actinide at oxidation state +IV. For larger ligands, steric effects may become significant and one can ask how the ligand may accommodate the large actinide cation coordination sphere. Model pentapeptides have been synthesized and tested as complexing agents. Comparison with NTA shows that the molecular arrangements are radically different. The third ligand system is transferrin, a diferric metalloptrotein that is well known to coordinate a large variety of cations from transition metals of f-elements. Metalloproteins bear primary, secondary and tertiary structures that all play a crucial role in bonding. At a given oxidation state (+IV), but for various atomic numbers (Th, Np, Pu) EXAFS data at the cation L{sub III} edge exhibit significant coordination discrepancies that are related to a changes in protein geometry. In that sense, the metalloprotein may be viewed as a complex system.

  16. PANP is a novel O-glycosylated PILRα ligand expressed in neural tissues

    International Nuclear Information System (INIS)

    Research highlights: → A Novel molecule, PANP, was identified to be a PILRα ligand. → Sialylated O-glycan structures on PANP were required for PILRα recognition. → Transcription of PANP was mainly observed in neural tissues. → PANP seems to be involved in immune regulation as a ligand for PILRα. -- Abstract: PILRα is an immune inhibitory receptor possessing an immunoreceptor tyrosine-based inhibitory motif (ITIM) in its cytoplasmic domain enabling it to deliver inhibitory signals. Binding of PILRα to its ligand CD99 is involved in immune regulation; however, whether there are other PILRα ligands in addition to CD99 is not known. Here, we report that a novel molecule, PILR-associating neural protein (PANP), acts as an additional ligand for PILRα. Transcription of PANP was mainly observed in neural tissues. PILRα-Ig fusion protein bound cells transfected with PANP and the transfectants stimulated PILRα reporter cells. Specific O-glycan structures on PANP were found to be required for PILR recognition of this ligand. These results suggest that PANP is involved in immune regulation as a ligand of the PILRα.

  17. Determinants governing ligand specificity of the Vibrio harveyi LuxN quorum-sensing receptor.

    Science.gov (United States)

    Ke, Xiaobo; Miller, Laura C; Bassler, Bonnie L

    2015-01-01

    Quorum sensing is a process of bacterial cell-cell communication that relies on the production, release and receptor-driven detection of extracellular signal molecules called autoinducers. The quorum-sensing bacterium Vibrio harveyi exclusively detects the autoinducer N-((R)-3-hydroxybutanoyl)-L-homoserine lactone (3OH-C4 HSL) via the two-component receptor LuxN. To discover the principles underlying the exquisite selectivity LuxN has for its ligand, we identified LuxN mutants with altered specificity. LuxN uses three mechanisms to verify that the bound molecule is the correct ligand: in the context of the overall ligand-binding site, His210 validates the C3 modification, Leu166 surveys the chain-length and a strong steady-state kinase bias imposes an energetic hurdle for inappropriate ligands to elicit signal transduction. Affinities for the LuxN kinase on and kinase off states underpin whether a ligand will act as an antagonist or an agonist. Mutations that bias LuxN to the agonized, kinase off, state are clustered in a region adjacent to the ligand-binding site, suggesting that this region acts as the switch that triggers signal transduction. Together, our analyses illuminate how a histidine sensor kinase differentiates between ligands and exploits those differences to regulate its signaling activity.

  18. Fringe-mediated extension of O-linked fucose in the ligand-binding region of Notch1 increases binding to mammalian Notch ligands.

    Science.gov (United States)

    Taylor, Paul; Takeuchi, Hideyuki; Sheppard, Devon; Chillakuri, Chandramouli; Lea, Susan M; Haltiwanger, Robert S; Handford, Penny A

    2014-05-20

    The Notch signaling pathway is essential for many aspects of development, cell fate determination, and tissue homeostasis. Notch signaling can be modulated by posttranslational modifications to the Notch receptor, which are known to alter both ligand binding and receptor activation. We have modified the ligand-binding region (EGF domains 11-13) of human Notch1 (hN1) with O-fucose and O-glucose glycans and shown by flow cytometry and surface plasmon resonance that the Fringe-catalyzed addition of GlcNAc to the O-fucose at T466 in EGF12 substantially increases binding to Jagged1 and Delta-like 1 (DLL1) ligands. We have subsequently determined the crystal structures of EGF domains 11-13 of hN1 modified with either the O-fucose monosaccharide or the GlcNAc-fucose disaccharide at T466 of EGF12 and observed no change in backbone structure for each variant. Collectively, these data demonstrate a role for GlcNAc in modulating the ligand-binding site in hN1 EGF12, resulting in an increased affinity of this region for ligands Jagged1 and DLL1. We propose that this finding explains the Fringe-catalyzed enhancement of Notch-Delta signaling observed in flies and humans, but suggest that the inhibitory effect of Fringe on Jagged/Serrate mediated signaling involves other regions of Notch.

  19. SPOT-Ligand: Fast and effective structure-based virtual screening by binding homology search according to ligand and receptor similarity.

    Science.gov (United States)

    Yang, Yuedong; Zhan, Jian; Zhou, Yaoqi

    2016-07-01

    Structure-based virtual screening usually involves docking of a library of chemical compounds onto the functional pocket of the target receptor so as to discover novel classes of ligands. However, the overall success rate remains low and screening a large library is computationally intensive. An alternative to this "ab initio" approach is virtual screening by binding homology search. In this approach, potential ligands are predicted based on similar interaction pairs (similarity in receptors and ligands). SPOT-Ligand is an approach that integrates ligand similarity by Tanimoto coefficient and receptor similarity by protein structure alignment program SPalign. The method was found to yield a consistent performance in DUD and DUD-E docking benchmarks even if model structures were employed. It improves over docking methods (DOCK6 and AUTODOCK Vina) and has a performance comparable to or better than other binding-homology methods (FINDsite and PoLi) with higher computational efficiency. The server is available at http://sparks-lab.org. © 2016 Wiley Periodicals, Inc. PMID:27074979

  20. Mixed ligand ruthenium(III) complexes of benzaldehyde 4-methyl-3-thiosemicarbazones with triphenylphosphine/triphenylarsine co-ligands: Synthesis, DNA binding, DNA cleavage, antioxidative and cytotoxic activity

    Science.gov (United States)

    Sampath, K.; Sathiyaraj, S.; Raja, G.; Jayabalakrishnan, C.

    2013-08-01

    The new ruthenium(III) complexes with 4-methyl-3-thiosemicarbazone ligands, (E)-2-(2-chlorobenzylidene)-N-methylhydrazinecarbothioamide (HL1) and (E)-2-(2-nitrobenzylidene)-N-methylhydrazinecarbothioamide (HL2), were prepared and characterized by various physico-chemical and spectroscopic methods. The title compounds act as bidentate, monobasic chelating ligands with S and N as the donor sites and are preferably found in the thiol form in all the complexes studied. The molecular structure of HL1 and HL2 were determined by single crystal X-ray diffraction method. DNA binding of the ligands and complexes were investigated by absorption spectroscopy and IR spectroscopy. It reveals that the compounds bind to nitrogenous bases of DNA via intercalation. The oxidative cleavage of the complexes with CT-DNA inferred that the effects of cleavage are dose dependent. Antioxidant study of the ligands and complexes showed the significant antioxidant activity against DPPH radical. In addition, the in vitro cytotoxicity of the ligands and complexes against MCF-7 cell line was assayed which showed higher cytotoxic activity with the lower IC50 values indicating their efficiency in killing the cancer cells even at low concentrations.

  1. Influence of ligands in metal nanoparticle electrophoresis for the fabrication of biofunctional coatings

    Energy Technology Data Exchange (ETDEWEB)

    Streich, Carmen; Koenen, Sven [Technical Chemistry I, University of Duisburg-Essen and Center for Nanointegration Duisburg-Essen (CENIDE), Universitaetsstr. 7, 45141 Essen (Germany); Lelle, Marco; Peneva, Kalina [Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany); Barcikowski, Stephan, E-mail: stephan.barcikowski@uni-due.de [Technical Chemistry I, University of Duisburg-Essen and Center for Nanointegration Duisburg-Essen (CENIDE), Universitaetsstr. 7, 45141 Essen (Germany)

    2015-09-01

    Graphical abstract: - Highlights: • Particle mobility measurements quantify how ligand size and charge influence particle electrophoresis. • Although negatively-charged ligands enhance particle mobility, ultimate deposition is suppressed. • Laser-generated metal nanoparticles can serve as model materials in electrophoretic deposition because they are ligand-free, hard colloidal spheres. • Only bare nanoparticles feature a high electrophoretic mobility and a constant deposition rate with no barrier formation. • Bioactive implant coatings may result from depositing nanoparticles functionalized with cell-penetrating peptides. - Abstract: Electrophoretic deposition of colloidal nanoparticles shows great promise for the fabrication of nanostructured surfaces, especially relevant for the surface modification of three dimensional medical implants. Here, the role of small and bulky, chemisorbent and physisorbent ligands on metal (gold, platinum) nanoparticle deposition dynamics are systematically investigated. To be able to compare ligand-coated to ligand-free nanoparticles, pulsed laser ablation in liquid is employed as nanoparticle fabrication method. Nanoparticles’ electrophoretic properties are assessed via zeta potential measurements and nanoparticle tracking analysis, while online-UV–vis spectroscopy provides information about the deposition dynamics. Electron micrographs and contact angle measurements are employed to characterize the deposit. We show that ligand-free nanoparticles feature a high electrophoretic mobility and linear deposition kinetics, representing an excellent model material for controlled electrophoretic deposition. In contrast, the electrophoretic mobility of surface-modified nanoparticles is altered due to the surrounding ligand layer, resulting in less efficient deposition. Notably, electrophoretic mobility is not solely governed by the ligand's charge and does not correlate to the zeta potential values directly. Finally

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

    Science.gov (United States)

    Kumar Mishra, Subodh; Kumar, Amit

    2016-01-01

    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 formula, molecular weight, net-formal charge, AlogP, number of rings, number of hydrogen bond donor and acceptor, potential energy along with their Ki, Kd, IC50 values. All these details at single platform would be helpful for the development and betterment of novel ligands targeting nucleic acids that could serve as a potential target in different diseases including cancers and neurological disorders. With maximum 255 conformers for each ligand entry, our database is a multi-conformer database and can facilitate the virtual screening process. NALDB provides powerful web-based search tools that make database searching efficient and simplified using option for text as well as for structure query. NALDB also provides multi-dimensional advanced search tool which can screen the database molecules on the basis of molecular properties of ligand provided by database users. A 3D structure visualization tool has also been included for 3D structure representation of ligands. NALDB offers an inclusive pharmacological information and the structurally flexible set of small molecules with their three-dimensional conformers that can accelerate the virtual screening and other modeling processes and eventually complement the nucleic acid-based drug discovery research. NALDB can be routinely updated and freely available on bsbe.iiti.ac.in/bsbe/naldb/HOME.php. Database URL: http://bsbe.iiti.ac.in/bsbe/naldb/HOME.php. PMID:26896846

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-01-01

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

  4. Directed evolution of estrogen receptor proteins with altered ligand-binding specificities.

    Science.gov (United States)

    Islam, Kazi Mohammed Didarul; Dilcher, Meik; Thurow, Corinna; Vock, Carsten; Krimmelbein, Ilga Kristine; Tietze, Lutz Friedjan; Gonzalez, Victor; Zhao, Huimin; Gatz, Christiane

    2009-01-01

    Transcriptional activators that respond to ligands with no cellular targets are powerful tools that can confer regulated expression of a transgene in almost all biological systems. In this study, we altered the ligand-binding specificity of the human estrogen receptor alpha (hER alpha) so that it would recognize a non-steroidal synthetic compound with structural similarities to the phytoestrogen resveratrol. For this purpose, we performed iterative rounds of site-specific saturation mutagenesis of a fixed set of ligand-contacting residues and subsequent random mutagenesis of the entire ligand-binding domain. Selection of the receptor mutants and quantification of the interaction were carried out by exploiting a yeast two-hybrid system that reports the ligand-dependent interaction between hER alpha and steroid receptor coactivator-1 (SRC-1). The screen was performed with a synthetic ligand (CV3320) that promoted growth of the reporter yeast strain to half maximal levels at a concentration of 3.7 microM. The optimized receptor mutant (L384F/L387M/Y537S) showed a 67-fold increased activity to the synthetic ligand CV3320 (half maximal yeast growth at 0.055 microM) and a 10-fold decreased activity to 17beta-estradiol (E2; half maximal yeast growth at 4 nM). The novel receptor-ligand pair partially fulfills the requirements for a specific 'gene switch' as it responds to concentrations of the synthetic ligand which do not activate the wildtype receptor. Due to its residual responsiveness to E2 at concentrations (4 nM) that might occur in vivo, further improvements have to be performed to render the system applicable in organisms with endogenous E2 synthesis.

  5. Monitoring ligand-receptor interactions by photonic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Jeney, Sylvia [M E Mueller Institute for Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, Basel, 4056 (Switzerland); Mor, Flavio; Forro, Laszlo [Laboratory of Complex Matter Physics (LPMC), Ecole Polytechnique Federale de Lausanne (EPFL), CH-1015 Lausanne (Switzerland); Koszali, Roland [Institute for Information and Communication Technologies (IICT), University of Applied Sciences of Western Switzerland (HEIG-VD), Rue Galilee 15, CH 1401 Yverdon-les-bains (Switzerland); Moy, Vincent T, E-mail: sylvia.jeney@unibas.ch, E-mail: vmoy@miami.edu [Department of Physiology and Biophysics, University of Miami Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136 (United States)

    2010-06-25

    We introduce a method for the acquisition of single molecule force measurements of ligand-receptor interactions using the photonic force microscope (PFM). Biotin-functionalized beads, manipulated with an optical trap, and a streptavidin-functionalized coverslip were used to measure the effect of different pulling forces on the lifetime of individual streptavidin-biotin complexes. By optimizing the design of the optical trap and selection of the appropriate bead size, pulling forces in excess of 50 pN were achieved. Based on the amplitude of three-dimensional (3D) thermal position fluctuations of the attached bead, we were able to select for a bead-coverslip interaction that was mediated by a single streptavidin-biotin complex. Moreover, the developed experimental system was greatly accelerated by automation of data acquisition and analysis. In force-dependent kinetic measurements carried out between streptavidin and biotin, we observed that the streptavidin-biotin complex exhibited properties of a catch bond, with the lifetime increasing tenfold when the pulling force increased from 10 to 20 pN. We also show that silica beads were more appropriate than polystyrene beads for the force measurements, as tethers, longer than 200 nm, could be extracted from polystyrene beads.

  6. Cyclic porphyrin dimers as hosts for coordinating ligands

    Indian Academy of Sciences (India)

    G Vaijayanthimala; V Krishnan; S K Mandal

    2008-01-01

    Bicovalently linked tetraphenylporphyrins bearing dioxypentane groups at the opposite (transoid, H4A) and adjacent (cisoid, H4B) aryl groups have been synthesised. Protonation of the free-base porphyrins leads to fully protonated species H8A4+/H8A4+ accompanied by expansion of cavity size of the bisporphyrins. The electrochemical redox studies of these porphyrins and their Zinc(II) derivatives revealed that the first ring oxidation proceeds through a two-electron process while the second ring oxidation occurs at two distinct one-electron steps indicating unsymmetrical charge distribution in the oxidized intermediate. The axial ligation properties of the Zinc(Il) derivatives of H4A/H4B with DABCO and PMDA investigated by spectroscopic and single crystal X-ray diffraction studies showed predominant existence of 1 : I complex. The Zn2A.DABCO complex assumes an interesting eclipsed structure wherein DABCO is located inside the cavity between the two porphyrin planes with Zn-N distances at 2.08 and 2.22 Å. The Zn atoms are pulled into the cavity due to coordination towards nitrogen atoms of DABCO and deviate from the mean porphyrin plane by 0.35 Å. The electrochemical redox potentials of the axially ligated metal derivatives are found to be sensitive function of the relative coordinating ability of the ligands and the conformation of the hosts.

  7. Somatostatin receptor ligands and resistance to treatment in pituitary adenomas.

    Science.gov (United States)

    Cuevas-Ramos, Daniel; Fleseriu, Maria

    2014-06-01

    Somatostatin (SST), an inhibitory polypeptide with two biologically active forms SST14 and SST28, inhibits GH, prolactin (PRL), TSH, and ACTH secretion in the anterior pituitary gland. SST also has an antiproliferative effect inducing cell cycle arrest and apoptosis. Such actions are mediated through five G-protein-coupled somatostatin receptors (SSTR): SSTR1-SSTR5. In GH-secreting adenomas, SSTR2 expression predominates, and somatostatin receptor ligands (SRLs; octreotide and lanreotide) directed to SSTR2 are presently the mainstays of medical therapy. However, about half of patients show incomplete biochemical remission, but the definition of resistance per se remains controversial. We summarize here the determinants of SRL resistance in acromegaly patients, including clinical, imaging features as well as molecular (mutations, SSTR variants, and polymorphisms), and histopathological (granulation pattern, and proteins and receptor expression) predictors. The role of SSTR5 may explain the partial responsiveness to SRLs in patients with adequate SSTR2 density in the cell membrane. In patients with ACTH-secreting pituitary adenomas, i.e. Cushing's disease (CD), SSTR5 is the most abundant receptor expressed and tumors show low SSTR2 density due to hypercortisolism-induced SSTR2 down-regulation. Clinical studies with pasireotide, a multireceptor-targeted SRL with increased SSTR5 activity, lead to approval of pasireotide for treatment of patients with CD. Other SRL delivery modes (oral octreotide), multireceptor-targeted SRL (somatoprim) or chimeric compounds targeting dopamine D2 receptors and SSTR2 (dopastatin), are briefly discussed. PMID:24647046

  8. Studies on mixed ligand complexes of lanthanide (III) ions

    International Nuclear Information System (INIS)

    As part of our research programme, we have prepared and characterized a few nitrato, thiocyanato and perchlorato complexes of lanthanide(III) ions with ligands, viz., a Schiff base derived from p-anisidine and vanillin and diphenyl sulphoxide. The complexes were characterized by the measurement of electrical conductances and magnetic susceptibilities, molecular mass and metal percentage and spectral analysis. The thermal decompositions were studied by TG and DTG techniques. The thiocyanato complexes were prepared by substitution method from nitrato complexes. p-Anisidine-vanillin (HDDA) and diphenyl sulphoxide (DPSO) are coordinated to the metal ion in unidentate fashion. All the anions were involved in coordination in these complexes. Thus they were found to have non- electrolytic behaviour with composition [Ln(HDDA)2 (DPSO)X3] where X = NO3) or SCN perchlorato complexes were prepared from metal perchlorate as done in the case of nitrato complexes. They were found to have electrical conductance which corresponds to 1 : 1 electrolyte. Hence one of the perchlorate ions is outside the coordination sphere. The composition of this complex is found to be [Ln(HDDA)3(DPSO)(ClO4)2]ClO4. (author)

  9. Coenzyme-like ligands for affinity isolation of cholesterol oxidase.

    Science.gov (United States)

    Xin, Yu; Lu, Liushen; Wang, Qing; Zhang, Ling; Tong, Yanjun; Wang, Wu

    2016-05-15

    Two coenzyme-like chemical ligands were designed and synthesized for affinity isolation of cholesterol oxidase (COD). To simulate the structure of natural coenzyme of COD (flavin adenine dinucleotide (FAD)), on Sepharose beads, 5-aminouracil, cyanuric chloride and 1, 4-butanediamine were composed and then modified. The COD gene from Brevibacterium sp. (DQ345780) was expressed in Escherichia coli BL21 (DE3), and then the sorbents were applied to adsorption analysis with the pure enzyme. Subsequently, the captured enzyme was applied to SDS-PAGE and activity analysis. As calculated, the theoretical maximum adsorption (Qmax) of the two affinity sorbents (RL-1 and RL-2) were ∼83.5 and 46.3mg/g wet gel; and the desorption constant Kd of the two sorbents were ∼6.02×10(-4) and 1.19×10(-4)μM. The proteins after cell lysis were applied to affinity isolation, and then after one step of affinity binding on the two sorbents, the protein recoveries of RL-1 and RL-2 were 9.2% and 9.7%; the bioactivity recoveries were 92.7% and 91.3%, respectively. SDS-PAGE analysis revealed that the purities of COD isolated with the two affinity sorbents were approximately 95%. PMID:26856529

  10. Mutual inactivation of Notch receptors and ligands facilitates developmental patterning.

    Directory of Open Access Journals (Sweden)

    David Sprinzak

    2011-06-01

    Full Text Available Developmental patterning requires juxtacrine signaling in order to tightly coordinate the fates of neighboring cells. Recent work has shown that Notch and Delta, the canonical metazoan juxtacrine signaling receptor and ligand, mutually inactivate each other in the same cell. This cis-interaction generates mutually exclusive sending and receiving states in individual cells. It generally remains unclear, however, how this mutual inactivation and the resulting switching behavior can impact developmental patterning circuits. Here we address this question using mathematical modeling in the context of two canonical pattern formation processes: boundary formation and lateral inhibition. For boundary formation, in a model motivated by Drosophila wing vein patterning, we find that mutual inactivation allows sharp boundary formation across a broader range of parameters than models lacking mutual inactivation. This model with mutual inactivation also exhibits robustness to correlated gene expression perturbations. For lateral inhibition, we find that mutual inactivation speeds up patterning dynamics, relieves the need for cooperative regulatory interactions, and expands the range of parameter values that permit pattern formation, compared to canonical models. Furthermore, mutual inactivation enables a simple lateral inhibition circuit architecture which requires only a single downstream regulatory step. Both model systems show how mutual inactivation can facilitate robust fine-grained patterning processes that would be difficult to implement without it, by encoding a difference-promoting feedback within the signaling system itself. Together, these results provide a framework for analysis of more complex Notch-dependent developmental systems.

  11. Progesterone in pregnancy; receptor-ligand interaction and signaling pathways.

    Science.gov (United States)

    Szekeres-Bartho, Julia; Halasz, Melinda; Palkovics, Tamas

    2009-12-01

    Progesterone is indispensable in creating a suitable endometrial environment for implantation, and also for the maintenance of pregnancy. Successful pregnancy depends on an appropriate maternal immune response to the fetus. Along with its endocrine effects, progesterone also acts as an "immunosteroid", by contributing to the establishment of a pregnancy protective immune milieu. Progesterone plays a role in uterine homing of NK cells and upregulates HLA-G gene expression, the ligand for NK inhibitory and activating receptors. At high concentrations, progesterone is a potent inducer of Th2-type cytokines as well as of LIF and M-CSF production by T cells. A protein called progesterone-induced blocking factor (PIBF), by inducing a Th2-dominant cytokine production mediates the immunological effects of progesterone. PIBF binds to a novel type of the IL-4 receptor and signals via the Jak/STAT pathway, to induce a number of genes, that not only affect the immune response, but might also play a role in trophoblast invasiveness. PMID:19880194

  12. A dodecanuclear Zn cluster sandwiched by polyoxometalate ligands.

    Science.gov (United States)

    Zhu, Guibo; Geletii, Yurii V; Zhao, Chongchao; Musaev, Djamaladdin G; Song, Jie; Hill, Craig L

    2012-09-01

    A dodecazinc silicotungstate K(20)Na(2)[Zn(6)(OH)(7)(H(2)O)(Si(2)W(18)O(66))](2)·34H(2)O (1) has been synthesized and characterized by X-ray crystallography, elemental analysis, infrared, UV-vis spectroscopy, cyclic voltammetry, acid-base titration, and DFT calculations. The twelve zinc atoms between the two [Si(2)W(18)O(66)](16-) frameworks make this complex more stable hydrolytically than the heteropolytungstate ligands, [Si(2)W(18)O(66)](16-), themselves. The structurally unique central Zn(12) core is formed by the fusion of two [Zn(6)(OH)(7)(H(2)O)](5+) units through two edge-sharing Zn6 atoms. DFT B3LYP calculations give HOMO-LUMO and (HOMO - 1)-LUMO energy gaps of ∼3.65 and 3.91 eV, respectively, as compared to the band gap in ZnO of 3.35 eV. PMID:22825397

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

    Science.gov (United States)

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

    2016-01-01

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

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

    International Nuclear Information System (INIS)

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

  15. How reliable are ligand-centric methods for Target Fishing?

    Science.gov (United States)

    Peon, Antonio; Dang, Cuong; Ballester, Pedro

    2016-04-01

    Computational methods for Target Fishing (TF), also known as Target Prediction or Polypharmacology Prediction, can be used to discover new targets for small-molecule drugs. This may result in repositioning the drug in a new indication or improving our current understanding of its efficacy and side effects. While there is a substantial body of research on TF methods, there is still a need to improve their validation, which is often limited to a small part of the available targets and not easily interpretable by the user. Here we discuss how target-centric TF methods are inherently limited by the number of targets that can possibly predict (this number is by construction much larger in ligand-centric techniques). We also propose a new benchmark to validate TF methods, which is particularly suited to analyse how predictive performance varies with the query molecule. On average over approved drugs, we estimate that only five predicted targets will have to be tested to find two true targets with submicromolar potency (a strong variability in performance is however observed). In addition, we find that an approved drug has currently an average of eight known targets, which reinforces the notion that polypharmacology is a common and strong event. Furthermore, with the assistance of a control group of randomly-selected molecules, we show that the targets of approved drugs are generally harder to predict.

  16. A sequence-based dynamic ensemble learning system for protein ligand-binding site prediction

    KAUST Repository

    Chen, Peng

    2015-12-03

    Background: Proteins have the fundamental ability to selectively bind to other molecules and perform specific functions through such interactions, such as protein-ligand binding. Accurate prediction of protein residues that physically bind to ligands is important for drug design and protein docking studies. Most of the successful protein-ligand binding predictions were based on known structures. However, structural information is not largely available in practice due to the huge gap between the number of known protein sequences and that of experimentally solved structures

  17. Luminescence of a europium (III) complex containing 4-n-octyloxydibenzoylmethane ligands doped poly(methylmethacrylate)

    Energy Technology Data Exchange (ETDEWEB)

    Liang Hao, E-mail: lianghao@ustc.ed [Department of Chemical Engineering, Huizhou University, Guangdong 516007 (China); Xie Fang [Department of Chemical Engineering, Huizhou University, Guangdong 516007 (China); Xu Jie [Key Lab of Green Processing and Functional Textiles of New Textile Materials, Ministry of Education, Wuhan University of Science and Engineering, Hubei 430073 (China); Chen Biao [Department of History of Science and Technology and Archaeometry, University of Science and Technology of China, Anhui 230026 (China); Bian Shi [School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangdong 510275 (China)

    2009-07-01

    A europium (III) complex containing 4-n-octyloxydibenzoylmethane (ODBM) ligands doped poly(methylmethacrylate) (PMMA) was synthesized. Its luminescence properties have been investigated by fluorescence emission spectra and lifetime measurements. According to the fluorescence emission spectra, the Judd-Ofelt parameters OMEGA{sub 2}, OMEGA{sub 4} of Eu(ODBM){sub 3}Phen doped PMMA have been calculated and the radiative properties were presented also. It showed that the long alkyloxy in ligand in the ODBM ligand can improve the radiative properties. The evaluation of the radiative properties showed that Eu(ODBM){sub 3}Phen doped PMMA has potential to be used for applications in amplifiers and lasers.

  18. Systematic Characterisation of Cellular Localisation and Expression Profiles of Proteins Containing MHC Ligands

    DEFF Research Database (Denmark)

    Juncker, Agnieszka; Larsen, Mette Voldby; Weinhold, Nils;

    2009-01-01

    -scale study, we used a large data set of proteins containing experimentally identified MHC class I or II ligands and examined the proteins according to their expression profiles at the mRNA level and their Gene Ontology (GO) classification within the cellular component ontology. Proteins encoded by highly...... the nature of MHC ligand-containing proteins and can be used to extend the existing methods for MHC ligand predictions by including the source protein's localisation and expression profile. Improving the current methods is important in the growing quest for epitopes that can be used for vaccine or diagnostic...

  19. Dioxouranium (VI) complexes of macrocyclic ligands derived from 2.6-diacetyl pyridine-bis(thiosemicarbazone)

    International Nuclear Information System (INIS)

    The dioxouranium(VI) complex of 2.6-diacetylpyridine-bis(thiosemicarbazone), (DAPTC), [UO2(DAPTC) (NO3)2] and its reactions with diketones are described. The complexes so obtained have been characterized on the basis of elemental analyses, electrical conductance and spectral (i.r. and electronic) data. The parent complex reacts with β-diketones to form a complex of the type [UO2(mac)(NO3)2], where mac is a macrocyclic ligand derived by the condensation of DAPTC and a β-diketone. The ligand, DAPTC, acts as a neutral, terdentate ligand having coordination sites at pyridine nitrogen and two azomethine nitrogens. 27 refs

  20. Following a TRAIL:Update on a ligand and its five receptors

    Institute of Scientific and Technical Information of China (English)

    Fiona C. KIMBERLEY; Gavin R. SCREATON

    2004-01-01

    Identification of tumour necrosis factor apoptosis inducing ligand (TRAIL), a TNF family ligand, sparked a torrent of research, following an initial observation that it could kill tumour cells, but spare normal cells. Almost a decade after its discovery, and with five known receptors, the true physiological role of TRAIL is still debated and its anti-tumorigenic properties limited by potential toxicity. This review takes a comprehensive look at the story of this enigmatic ligand,addressing its remaining potential as a therapeutic and providing an overview of the TRAIL receptors themselves.