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Sample records for 2-phenoxypyridyl dinucleating ligands

  1. A versatile dinucleating ligand containing sulfonamide groups

    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. Dinuclear first-row transition metal complexes with a naphthyridine-based dinucleating ligand.

    Davenport, T C; Tilley, T D

    2015-07-21

    A series of dinuclear and tetranuclear first-row transition metal complexes were synthesized with the dinucleating ligand 2,7-bis(di(2-pyridyl)fluoromethyl)-1,8-naphthyridine (DPFN). The coordination pocket and rigidity of the DPFN ligand enforces pseudo-octahedral geometries about the metal centers that contain chloro, hydroxo, and aqua bridging ligands forming a "diamond" shaped configuration with metal-metal distances varying from 2.7826(5) to 3.2410(11) Å. Each metal center in the dinuclear complexes has an additional open coordination site that accommodates terminal ligands in a syn geometry of particular interest in catalyst design. The complexes are characterized by electronic spectroscopy, electrochemistry and potentiometric titration methods. PMID:25420206

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

    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

    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. 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

    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.

  6. 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.

    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

  7. Synthesis and electronic properties of dinucleic octaethylporphyrin (OEP derivatives spaced with p-phenylene group [OEP-(p-Phenn-OEP].

    Naoto Hayashi et al

    2007-01-01

    Full Text Available The dinucleic octaethylporphyrin (OEP derivatives described as OEP-(p-Phenn-OEP (n=1–4 were synthesized, in each of which the porphyrin ring is spaced with p-phenylene group. Their electronic properties were studied, as compared with those of the corresponding dihexylbithiophene (DHBTh derivatives with head-to-head (HH and tail-to-tail (TT orientations. It proves that OEP-(p-Phenn-OEP possesses an in-between feature of OEP-(HH-DHBThn-OEP and OEP-(TT-DHBThn-OEP in electronic properties.

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

    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.

  9. Ylide Ligands

    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 ...

  10. Handling ligands with Coot

    Debreczeni, Judit É.; Emsley, Paul

    2012-01-01

    Coot is a molecular-graphics application primarily aimed to assist in model building and validation of biological macromolecules. Recently, tools have been added to work with small molecules. The newly incorporated tools for the manipulation and validation of ligands include interaction with PRODRG, subgraph isomorphism-based tools, representation of ligand chemistry, ligand fitting and analysis, and are described here.

  11. Metal-ligand cooperation.

    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

  12. Ligand modeling and design

    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.

  13. Ligand modeling and design

    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.

  14. Glutamate receptor ligands

    Guldbrandt, Mette; Johansen, Tommy N; Frydenvang, Karla Andrea; Bräuner-Osborne, Hans; Stensbøl, Tine B; Nielsen, Birgitte; Karla, Rolf; Santi, Flavio; Krogsgaard-Larsen, Povl; Madsen, Ulf

    2002-01-01

    Homologation and substitution on the carbon backbone of (S)-glutamic acid [(S)-Glu, 1], as well as absolute stereochemistry, are structural parameters of key importance for the pharmacological profile of (S)-Glu receptor ligands. We describe a series of methyl-substituted 2-aminoadipic acid (AA...

  15. AMPA receptor ligands

    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

    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

    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. Radiobiology with DNA ligands

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

  19. Imidazoline receptors ligands

    Agbaba Danica

    2012-01-01

    Full Text Available Extensive biochemical and pharmacological studies have determined three different subtypes of imidazoline receptors: I1-imidazoline receptors (I1-IR involved in central inhibition of sympathicus that produce hypotensive effect; I2-imidazoline receptors (I2-IR modulate monoamine oxidase B activity (MAO-B; I3-imidazoline receptors (I3-IR regulate insulin secretion from pancreatic β-cells. Therefore, the I1/I2/I3 imidazoline receptors are selected as new, interesting targets for drug design and discovery. Novel selective I1/I2/I3 agonists and antagonists have been recently developed. In the present review, we provide a brief update to the field of imidazoline research, highlighting some of the chemical diversity and progress made in the 2D-QSAR, 3D-QSAR and quantitative pharmacophore development studies of I1-IR and I2-IR imidazoline receptor ligands. Theoretical studies of I3-IR ligands are not yet performed because of insufficient number of synthesized I3-IR ligands.

  20. Molecular path for ligand search

    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

    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. Released ligand fluoroimmunoassay

    Radioimmunoassay (RIA) is one of the most sensitive and specific methods for analysis of proteins, drugs and other substances commonly found in biological fluids. Because of the limited stability and problems in handling radioisotopes (particularly 125I), there has been a continuous effort in recent years to develop non-isotopic immunoassays. Fluoroimmunoassay is one of the more promising alternatives to RIA, but has relatively low sensitivity due to background fluorescence from other substances in biological fluids. The authors have proposed an alternative type of fluoroimmunoassay, released ligand fluoroimmunoassay (RLFIA), wherein the fluorophore is released from the analyte and analyzed separately, thus reducing the problems of background fluorescence. 1-(4-(3-(2,3-dihydroxy-1-carboxyethyl))-phenyl)-3-(3-(7-diethylamino-4-methylcoumarinyl)) thiourea (IX), a fluorescent coumarin derivative with a periodate cleavable vic-glycol linkage, was synthesized and employed to demonstrate the principle of RLFIA. The principle of the RLFIA was tested by comparison with a commercially available kit Immuno-Fluor IgG Assay. Because of the lower quantum yield of the fluorophore used, the sensitivity of the resulting RLFIA was only one tenth that of the commercial kit. As an outgrowth of this project, a series of analogs of compound IX, having electron donating and withdrawing groups at the phenyl ring, were synthesized in order to study the effect of substituent on fluorescence yield. An interactive computer graphics system, Chemical Structure Drawing 2-Dimensional (CSD2D), developed by the author mainly for the generation of publication quality structure drawings is also described

  3. Nutraceuticals as Ligands of PPARγ

    Meera Penumetcha; Nalini Santanam

    2012-01-01

    Peroxisome proliferator-activated receptors (PPARs) are ligand-activated nuclear receptors that respond to several exogenous and endogenous ligands by modulating genes related to lipid, glucose, and insulin homeostasis. PPARγ, expressed in adipose tissue and liver, regulates lipid storage and glucose metabolism and is the target of type 2 diabetes drugs, thiazolidinediones (TZDs). Due to high levels of toxicity associated with the first generation TZDs, troglitazone (Rezulin), rosiglitazone (...

  4. Validity of Ligand Efficiency Metrics

    Murray, Christopher W; Erlanson, Daniel A.; Hopkins, Andrew L.; Keserü, György M; Leeson, Paul D.; Rees, David C.; Reynolds, Charles H.; Richmond, Nicola J.

    2014-01-01

    A recent viewpoint article (Improving the plausibility of success with inefficient metrics. ACS Med. Chem. Lett.2014, 5, 2–5) argued that the standard definition of ligand efficiency (LE) is mathematically invalid. In this viewpoint, we address this criticism and show categorically that the definition of LE is mathematically valid. LE and other metrics such as lipophilic ligand efficiency (LLE) can be useful during the multiparameter optimization challenge faced by med...

  5. Ligand Identification Scoring Algorithm (LISA)

    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

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

    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.

  7. Why mercury prefers soft ligands

    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.

  8. Polypharmacology of dopamine receptor ligands.

    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

  9. Crystallization of protein–ligand complexes

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

  10. Ligand chain length conveys thermochromism.

    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

  11. Presentation of Ligands on Hydroxylapatite

    Chu, Barbara C. F.; Orgel, Leslie E.

    1997-01-01

    Conjugates of biotin with the decamer of glutamic acid (glu(sub 10)) and the trimer of D,L-2-amino-5-phosphonovaleric acid (I) have been synthesized, and it has been shown that they mediate the binding of avidin to hydroxylapatite. In a similar way a conjugate of methotrexate with glu(sub 10) mediates the binding of dihydrofolate reductase to the mineral. The presentation of ligands on the hydroxylapatite component of bone may find applications in clinical medicine.

  12. Privileged chiral ligands and catalysts

    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.

  13. Tumor targeting via integrin ligands

    HorstKessler

    2013-08-01

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

  14. Radioiodinated ligands for dopamine receptors

    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

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

    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

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

    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.

  17. Ruthenium Cumulenylidene Complexes Bearing Heteroscorpionate Ligands

    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...

  18. Phenotypic spandrel: absolute discrimination and ligand antagonism

    François, Paul; Johnson, Kyle A.; Saunders, Laura N.

    2015-01-01

    We consider the general problem of absolute discrimination between categories of ligands irrespective of their concentration. An instance of this problem is immune discrimination between self and not-self. We connect this problem to biochemical adaptation, and establish that ligand antagonism - the ability of sub threshold ligands to negatively impact response - is a necessary consequence of absolute discrimination.Thus antagonism constitutes a "phenotypic spandrel": a phenotype existing as a...

  19. Clinical Use of PPARγ Ligands in Cancer

    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.

  20. Development of immobilized ligands for actinide separations

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

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

    Pless, Stephan Alexander; Lynch, Joseph W

    2009-01-01

    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...

  2. Macrocyclic ligands for uranium complexation

    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

  3. Synthesis and characterization of mixed ligand chiral nanoclusters

    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.

  4. Ligand-receptor Interactions by NMR Spectroscopy

    Novak. P.

    2008-04-01

    Full Text Available Today NMR spectroscopy is a method of choice for elucidation of interactions between biomolecules and the potential ligands. Knowledge on these interactions is an essential prerequisite for the rational drug design. The most important contribution of NMR to drug design a few years ago was the 3D structure determination of proteins. Besides delivering the 3D structures of the free proteins as a raw material for the modeling studies on ligand binding, NMR can directly yield valuable experimental data on the biologically important protein-ligand complexes. In addition to X-ray diffraction, NMR spectroscopy can provide information on the internal protein dynamics ordynamics of intermolecular interactions. Changes in NMR parameters allow us to detect ("SAR by NMR" and quantitatively determine binding affinities (titration, diffusion NMR experiments, etc. of potential ligands. Also, it is possible to determine the binding site and conformations of ligands, receptors and receptor-ligand complexes with the help of NMR methods such as tr-NOESY. Epitopes or functional groups responsible for binding of ligands to the receptor can be identified by employing STD or WaterLOGSY experiments. In this review are described some of the most frequent NMR methods for the characterization of the interactions between biomolecules and ligands, together with their advantages and disadvantages.

  5. Magnetic nanoparticles linked to a ligand

    Penadés, Soledad; Martín-Lomas, Manuel; Martínez de la Fuente, Jesús; Rademacher, Thomas W.

    2006-01-01

    Materials and methods for making small magnetic particles, e.g. clusters of metal atoms, which can be employed as a substrate for immobilising a plurality of ligands. Also disclosed are uses of these magnetic nanoparticles as therapeutic and diagnostic reagents, and in the study of ligand-mediated interactions.

  6. Electrochemistry of complex combinations with organic ligands

    The electrochemical behaviour of Cd(2), Ni(2), Fe(2), Fe(3), In(3), Pb(2) complexes with organic bi-and polydentate ligands have been studied by methods of classical and alternating current polarography. Cadmium and indium complexing depending on pH value and the nature of the ligands (bipyridyl isomers, phosphoric acid esters) is discussed

  7. Ligand sphere conversions in terminal carbide complexes

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

    2016-01-01

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

  8. Protein-ligand-based pharmacophores: generation and utility assessment in computational ligand profiling.

    Meslamani, Jamel; Li, Jiabo; Sutter, Jon; Stevens, Adrian; Bertrand, Hugues-Olivier; Rognan, Didier

    2012-04-23

    Ligand profiling is an emerging computational method for predicting the most likely targets of a bioactive compound and therefore anticipating adverse reactions, side effects and drug repurposing. A few encouraging successes have already been reported using ligand 2-D similarity searches and protein-ligand docking. The current study describes the use of receptor-ligand-derived pharmacophore searches as a tool to link ligands to putative targets. A database of 68,056 pharmacophores was first derived from 8,166 high-resolution protein-ligand complexes. In order to limit the number of queries, a maximum of 10 pharmacophores was generated for each complex according to their predicted selectivity. Pharmacophore search was compared to ligand-centric (2-D and 3-D similarity searches) and docking methods in profiling a set of 157 diverse ligands against a panel of 2,556 unique targets of known X-ray structure. As expected, ligand-based methods outperformed, in most of the cases, structure-based approaches in ranking the true targets among the top 1% scoring entries. However, we could identify ligands for which only a single method was successful. Receptor-ligand-based pharmacophore search is notably a fast and reliable alternative to docking when few ligand information is available for some targets. Overall, the present study suggests that a workflow using the best profiling method according to the protein-ligand context is the best strategy to follow. We notably present concrete guidelines for selecting the optimal computational method according to simple ligand and binding site properties. PMID:22480372

  9. Autocrine signal transmission with extracellular ligand degradation

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

  10. Improving protein-ligand docking with flexible interfacial water molecules using SWRosettaLigand.

    Li, Linqing; Xu, Weiwei; Lü, Qiang

    2015-11-01

    Computational protein-ligand docking is of great importance in drug discovery and design. Conformational changes greatly affect the results of protein-ligand docking, especially when water molecules take part in mediating protein ligand interactions or when large conformational changes are observed in the receptor backbone interface. We have developed an improved protocol, SWRosettaLigand, based on the RosettaLigand protocol. This approach incorporates the flexibility of interfacial water molecules and modeling of the interface of the receptor into the original RosettaLigand. In a coarse sampling step, SWRosettaLigand pre-optimizes the initial position of the water molecules, docks the ligand to the receptor with explicit water molecules, and minimizes the predicted structure with water molecules. The receptor backbone interface is treated as a loop and perturbed and refined by kinematic closure, or cyclic coordinate descent algorithm, with the presence of the ligand. In two cross-docking test sets, it was identified that for 8 out of 14, and 16 out of 22, test instances, the top-ranked structures by SWRosettaLigand achieved better accuracy than other protocols. PMID:26515196

  11. Ligand Exchange Processes on Solvated Lithium Cations

    Pasgreta, Ewa Maria

    2007-01-01

    In this work the solvation process of Li+ ion, as well as solvent and ligand exchange reactions on Li+ ion were studied. Li+ ions possess interesting properties and like other alkali metal ions are known to form complexes with macrocyclic ligands called cryptands. In this summary, an overview over the insights gained in the factors that control the reactivity of Li+ complexes with respect to the solvent and cryptand properties is presented. Three main questions were addressed: • How does the ...

  12. Chemistry of Marine Ligands and Siderophores

    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...

  13. Fas ligand deficiency in HIV disease

    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...

  14. Construction of dinuclear complexes using multidentate ligands

    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 to try and

  15. Visualizing ligand molecules in twilight electron density

    A software script is presented for facilitating the analysis and visual inspection of ligand molecules in the context of the electron-density maps calculated from experimental data associated with protein structures determined by X-ray crystallography. Three-dimensional models of protein structures determined by X-ray crystallography are based on the interpretation of experimentally derived electron-density maps. The real-space correlation coefficient (RSCC) provides an easily comprehensible, objective measure of the residue-based fit of atom coordinates to electron density. Among protein structure models, protein–ligand complexes are of special interest, given their contribution to understanding the molecular underpinnings of biological activity and to drug design. For consumers of such models, it is not trivial to determine the degree to which ligand-structure modelling is biased by subjective electron-density interpretation. A standalone script, Twilight, is presented for the analysis, visualization and annotation of a pre-filtered set of 2815 protein–ligand complexes deposited with the PDB as of 15 January 2012 with ligand RSCC values that are below a threshold of 0.6. It also provides simplified access to the visualization of any protein–ligand complex available from the PDB and annotated by the Uppsala Electron Density Server. The script runs on various platforms and is available for download at http://www.ruppweb.org/twilight//

  16. Designer TGFβ superfamily ligands with diversified functionality.

    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.

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

    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.

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

    DeLuca, Samuel; Khar, Karen; Meiler, Jens

    2015-01-01

    RosettaLigand has been successfully used to predict binding poses in protein-small molecule complexes. However, the RosettaLigand docking protocol is comparatively slow in identifying an initial starting pose for the small molecule (ligand) making it unfeasible for use in virtual High Throughput Screening (vHTS). To overcome this limitation, we developed a new sampling approach for placing the ligand in the protein binding site during the initial ‘low-resolution’ docking step. It combines the translational and rotational adjustments to the ligand pose in a single transformation step. The new algorithm is both more accurate and more time-efficient. The docking success rate is improved by 10–15% in a benchmark set of 43 protein/ligand complexes, reducing the number of models that typically need to be generated from 1000 to 150. The average time to generate a model is reduced from 50 seconds to 10 seconds. As a result we observe an effective 30-fold speed increase, making RosettaLigand appropriate for docking medium sized ligand libraries. We demonstrate that this improved initial placement of the ligand is critical for successful prediction of an accurate binding position in the ‘high-resolution’ full atom refinement step. PMID:26207742

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

    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.

  20. Organotellurium ligands - designing and complexation reactions

    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

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

    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.

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

    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.

  3. Impact of receptor clustering on ligand binding

    Caré Bertrand R

    2011-03-01

    Full Text Available Abstract Background Cellular response to changes in the concentration of different chemical species in the extracellular medium is induced by ligand binding to dedicated transmembrane receptors. Receptor density, distribution, and clustering may be key spatial features that influence effective and proper physical and biochemical cellular responses to many regulatory signals. Classical equations describing this kind of binding kinetics assume the distributions of interacting species to be homogeneous, neglecting by doing so the impact of clustering. As there is experimental evidence that receptors tend to group in clusters inside membrane domains, we investigated the effects of receptor clustering on cellular receptor ligand binding. Results We implemented a model of receptor binding using a Monte-Carlo algorithm to simulate ligand diffusion and binding. In some simple cases, analytic solutions for binding equilibrium of ligand on clusters of receptors are provided, and supported by simulation results. Our simulations show that the so-called "apparent" affinity of the ligand for the receptor decreases with clustering although the microscopic affinity remains constant. Conclusions Changing membrane receptors clustering could be a simple mechanism that allows cells to change and adapt its affinity/sensitivity toward a given stimulus.

  4. Ligand identification using electron-density map correlations

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

  5. Effects of PPARγ Ligands on Leukemia

    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.

  6. Flexible Ligand Docking Using Evolutionary Algorithms

    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...

  7. Flexible Ligand Docking Using Differential Evolution

    Thomsen, René

    2003-01-01

    Molecular docking of biomolecules is becoming an increasingly important part in the process of developing new drugs, as well as searching compound databases for promising drug candidates. The docking of ligands to proteins can be formulated as an optimization problem where the task is to find 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...... evolution algorithm (DE) is applied to the docking problem using the AutoDock program. The introduced DockDE algorithm is compared with the Lamarckian GA (LGA) provided with AutoDock, and the DockEA previously found to outperform the LGA. The comparison is performed on a suite of six commonly used docking...

  8. Supramolecular architectures constructed using angular bipyridyl ligands

    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)

  9. The first scorpionate ligand based on diazaphosphole.

    Mlateček, Martin; Dostál, Libor; Růžičková, Zdeňka; Honzíček, Jan; Holubová, Jana; Erben, Milan

    2015-12-14

    The reaction of PhBCl2 with 1H-1,2,4-λ(3)-diazaphosphole in the presence of NEt3 gives a new scorpionate ligand, phenyl-tris(1,2,4-diazaphospholyl)borate (PhTdap). The coordination behaviour of this ligand toward transition and non-transition metals has been comprehensively studied. In the thallium(I) complex, Tl(PhTdap), κ(2)-N,N bonding supported with intramolecular η(3)-phenyl coordination has been observed in the solid state. Tl(PhTdap) also shows unusual intermolecular π-interactions between five-membered diazaphosphole rings and the thallium atom giving infinite molecular chains in the crystal. In the square planar complex [Pd(C,N-C6H4CH2NMe2)(PhTdap)], κ(2)-bonded scorpionate has been detected in both solution and in the solid state. For other studied compounds with the central metal ion Ti(IV), Mo(II), Mn(I), Fe(II), Ru(II), Co(II), Co(III), Ni(II) and Cd(II), the κ(3)-N,N,N coordination pattern was observed. Electronic properties of PhTdap and its ligand-field strength were elucidated from UV-Vis spectra of transition-metal species. The CH/P replacement on going from tris(pyrazolyl)borate to the ligand PhTdap causes a slight increase in electronic density rendered to the central metal atom. The following order of ligand-field strength has been established: HB(3,5-Me2pz)3 PhB(pz)3 PhB(1,2,4-triazolyl) < PhTdap. The crystal structures of ten metal complexes bearing the new ligand are reported. The possibility of PhTdap coordination through the phosphorus atom is also briefly discussed. PMID:26537349

  10. Cationic ruthenium alkylidene catalysts bearing phosphine ligands

    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...

  11. Ligand Intermediates in Metal-Catalyzed Reactions

    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.

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

    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

  13. Supramolecular architectures constructed using angular bipyridyl ligands

    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...

  14. Constitutive and ligand-induced TCR degradation

    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...

  15. Ligand iron catalysts for selective hydrogenation

    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.

  16. Identification of ligands for bacterial sensor proteins.

    Fernández, Matilde; Morel, Bertrand; Corral-Lugo, Andrés; Rico-Jiménez, Miriam; Martín-Mora, David; López-Farfán, Diana; Reyes-Darias, José Antonio; Matilla, Miguel A; Ortega, Álvaro; Krell, Tino

    2016-02-01

    Bacteria have evolved a variety of different signal transduction mechanisms. However, the cognate signal molecule for the very large amount of corresponding sensor proteins is unknown and their functional annotation represents a major bottleneck in the field of signal transduction. The knowledge of the signal molecule is an essential prerequisite to understand the signalling mechanisms. Recently, the identification of signal molecules by the high-throughput protein screening of commercially available ligand collections using differential scanning fluorimetry has shown promise to resolve this bottleneck. Based on the analysis of a significant number of different ligand binding domains (LBDs) in our laboratory, we identified two issues that need to be taken into account in the experimental design. Since a number of LBDs require the dimeric state for ligand recognition, it has to be assured that the protein analysed is indeed in the dimeric form. A number of other examples demonstrate that purified LBDs can contain bound ligand which prevents further binding. In such cases, the apo-form can be generated by denaturation and subsequent refolding. We are convinced that this approach will accelerate the functional annotation of sensor proteins which will help to understand regulatory circuits in bacteria. PMID:26511375

  17. Circulating amounts of osteoprotegerin and RANK ligand

    Abrahamsen, Bo; Hjelmborg, Jacob Vb; Kostenuik, Paul;

    2005-01-01

    UNLABELLED: Osteoprotegerin (OPG) is a circulating receptor that inhibits osteoclastogenesis by binding to RANK ligand (RANKL). OPG knock-out animals develop severe osteoporosis. Treatment with OPG lowers bone resorption and increases BMD. OPG production is influenced by a wide range of hormones ...

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

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

    2011-07-01

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

  19. Substrate coated with receptor and labelled ligand for assays

    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.)

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

    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

  1. Ligand binding was acquired during evolution of nuclear receptors

    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...

  2. Leaching behavior of butanedionedioxime as gold ligand

    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

  3. Selective oxoanion separation using a tripodal ligand

    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.

  4. Polyfluoroalkylated tripyrazolylmethane ligands: Synthesis and complexes

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

    2011-01-01

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

  5. Targeting Selectins and Their Ligands in Cancer.

    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

  6. Quantification of ligand bias for clinically relevant β2-adrenergic receptor ligands: implications for drug taxonomy.

    van der Westhuizen, Emma T; Breton, Billy; Christopoulos, Arthur; Bouvier, Michel

    2014-03-01

    The concepts of functional selectivity and ligand bias are becoming increasingly appreciated in modern drug discovery programs, necessitating more informed approaches to compound classification and, ultimately, therapeutic candidate selection. Using the β2-adrenergic receptor as a model, we present a proof of concept study that assessed the bias of 19 β-adrenergic ligands, including many clinically used compounds, across four pathways [cAMP production, extracellular signal-regulated kinase 1/2 (ERK1/2) activation, calcium mobilization, and receptor endocytosis] in the same cell background (human embryonic kidney 293S cells). Efficacy-based clustering placed the ligands into five distinct groups with respect to signaling signatures. In some cases, apparent functional selectivity originated from off-target effects on other endogenously expressed adrenergic receptors, highlighting the importance of thoroughly assessing selectivity of the responses before concluding receptor-specific ligand-biased signaling. Eliminating the nonselective compounds did not change the clustering of the 10 remaining compounds. Some ligands exhibited large differences in potency for the different pathways, suggesting that the nature of the receptor-effector complexes influences the relative affinity of the compounds for specific receptor conformations. Calculation of relative effectiveness (within pathway) and bias factors (between pathways) for each of the compounds, using an operational model of agonism, revealed a global signaling signature for all of the compounds relative to isoproterenol. Most compounds were biased toward ERK1/2 activation over the other pathways, consistent with the notion that many proximal effectors converge on this pathway. Overall, we demonstrate a higher level of ligand texture than previously anticipated, opening perspectives for the establishment of pluridimensional correlations between signaling profiles, drug classification, therapeutic efficacy, and

  7. Landscape of protein-small ligand binding modes.

    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

  8. Tungsten acetonitrile complexes, containing nitrosyl ligand

    Synthesized are tungsten acetonitrile derivatives, containing nitrosyl ligand. In a course of boiling W(CO)4(NO)I-(1) at the excess of acetonitrile there is formed bis-(acetonitrile)-dicarbonilenitrosyltungsteniod-(2): W(CO)4(NO)I+2CH3CN → 2CO+(CH3CN)2W(CO)2(NO)I-(2). Investigation in reactionary ability of compound (2) is carried out. It is shown that at the reaction of acetonitrile complex (2) with two equivalents of triphenylphosphine depending on reaction conditions formed is a number of products

  9. Transmutable nanoparticles with reconfigurable surface ligands

    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.

  10. Scorpionates the coordination chemistry of polypyrazolylborate ligands

    Trofimenko, Swiatoslaw

    1999-01-01

    This book deals with polypyrazolylborates (scorpionates), a class of ligands known since 1966, but becoming rapidly popular with inorganic, organometallic and coordination chemists since 1986, because of their versatility and user-friendliness. They can be readily modified sterically and electronically through appropriate substitution on the pyrazole ring and on boron, and have led to a number of firsts in coordination chemistry (first stable CuCO complex, first monomeric MgR complex, and many other such firsts). Their denticity can range from two to four, their "Bite" can be adjusted, and add

  11. Metal mediated template synthesis of ligands

    Costisor, Otilia

    2004-01-01

    This book surveys the relatively new area of the synthesis of organic ligands when metal ions act as a template. In the last fifty years this field has undergone an explosive development, marked by a great amount of literature. The material in the book has been arranged according to the type of chemical reaction involved. In this frame, the basic principles of metal template reactions and the shape of the molecules are considered. Designed to satisfy the demands of students, young researchers doing their PhDs, and those working in the field of coordination chemistry, the book details the role

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

    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.

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

    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. The Dynamics of Ligand Barrier Crossing inside the Acetylcholinesterase Gorge

    Bui, Jennifer M.; Henchman, Richard H.; McCammon, J. Andrew

    2003-01-01

    The dynamics of ligand movement through the constricted region of the acetylcholinesterase gorge is important in understanding how the ligand gains access to and is released from the active site of the enzyme. Molecular dynamics simulations of the simple ligand, tetramethylammonium, crossing this bottleneck region are conducted using umbrella potential sampling and activated flux techniques. The low potential of mean force obtained is consistent with the fast reaction rate of acetylcholineste...

  15. Quasielastic neutron scattering study of POSS ligand dynamics

    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. Rapid flexible docking using a stochastic rotamer library of ligands

    Ding, Feng; Yin, Shuangye; Dokholyan, Nikolay V.

    2010-01-01

    Existing flexible docking approaches model the ligand and receptor flexibility either separately or in a loosely-coupled manner, which captures the conformational changes inefficiently. Here, we propose a flexible docking approach, MedusaDock, which models both ligand and receptor flexibility simultaneously with sets of discrete rotamers. We develop an algorithm to build the ligand rotamer library “on-the-fly” during docking simulations. MedusaDock benchmarks demonstrate a rapid sampling effi...

  17. Ligand Binding Analysis and Screening by Chemical Denaturation Shift

    Sch n, Arne; Brown, Richard K; Hutchins, Burleigh M.; Freire, Ernesto

    2013-01-01

    The identification of small molecule ligands is an important first step in drug development, especially drugs that target proteins with no intrinsic activity. Towards this goal, it is important to have access to technologies that are able to measure binding affinities for a large number of potential ligands in a fast and accurate way. Since ligand binding stabilizes the protein structure in a manner dependent on concentration and binding affinity, the magnitude of the protein stabilization ef...

  18. Dynamic Presentation of Immobilized Ligands Regulated through Biomolecular Recognition

    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...

  19. Do organic ligands affect calcite dissolution rates?

    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.

  20. The first nitro-substituted heteroscorpionate ligand.

    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

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

    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. Single-incubation immunoassay for a multivalent ligand

    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)

  3. The Dynamics of Ligand Barrier Crossing Inside the Acetylcholinesterase Gorge

    Bui, Jennifer M.(University of California, San Diego); Henchman, Richard H.(University of California, San Diego); Mccammon, Andy (University of California, San Diego)

    2003-10-01

    The dynamics of ligand movement through the constricted region of the acetylcholinesterase gorge is important in understanding how the ligand gains access to and is released from the active site of the enzyme. Molecular dynamics simulations of the simple ligand, tetramethylammonium, crossing this bottleneck region are conducted using umbrella potential sampling and activated .ux techniques. The low potential of mean force obtained is consistent with the fast reaction rate of acetylcholinesterase observed experimentally. From the results of the activated dynamics simulations, local conformational .uctuations of the gorge residues and larger scale collective motions of the protein are found to correlate highly with the ligand crossing.

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

    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

  5. Spectra of fluorinated rare earth. beta. -diketonates with added ligands

    Khomenko, V.S.; Lozinskij, M.O.; Fialkov, Yu.A.; Rasshinina, T.A.; Krasovskaya, L.I. (AN Belorusskoj SSR, Minsk. Inst. Fiziki; AN Ukrainskoj SSR, Kiev. Inst. Organicheskoj Khimii)

    1984-01-01

    Different-ligand rare earth complexes are synthesized. Fluorated ..beta..-diketones, triethylphosphine oxide and trifluoracetic acid are used as active ligands. Mass-spectra of low and high resolution are taken at the energy of ionizing electrons of 70 eV, as well as luminescence spectra of complexes. Fragmentation ways of complexes decomposition under electron shock are studied. A series of changing the bound strength of additional ligands with europium in mixed complexes is determined. It is shown that the introduction of additional ligands can purposefully change physical and chemical properties of complexes.

  6. Superior serum half life of albumin tagged TNF ligands

    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.

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

    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.

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

    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

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

    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

  10. Rational design of class I MHC ligands

    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.

  11. Ligand-directed trafficking of receptor stimulus.

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

    2014-12-01

    GPCRs are seven transmembrane-spanning receptors that convey specific extracellular stimuli to intracellular signalling. They represent the largest family of cell surface proteins that are therapeutically targeted. According to the traditional two-state model of receptor theory, GPCRs were considered as operating in equilibrium between two functional conformations, an active (R*) and inactive (R) state. Thus, it was assumed that a GPCR can exist either in an "off" or "on" conformation causing either no activation or equal activation of all its signalling pathways. Over the past several years it has become evident that this model is too simple and that GPCR signalling is far more complex. Different studies have presented a multistate model of receptor activation in which ligand-specific receptor conformations are able to differentiate between distinct signalling partners. Recent data show that beside G proteins numerous other proteins, such as β-arrestins and kinases, may interact with GPCRs and activate intracellular signalling pathways. GPCR activation may therefore involve receptor desensitization, coupling to multiple G proteins, Gα or Gβγ signalling, and pathway activation that is independent of G proteins. This latter effect leads to agonist "functional selectivity" (also called ligand-directed receptor trafficking, stimulus trafficking, biased agonism, biased signalling), and agonist intervention with functional selectivity may improve the therapy. Many commercially available drugs with beneficial efficacy also show various undesirable side effects. Further studies of biased signalling might facilitate our understanding of the side effects of current drugs and take us to new avenues to efficiently design pathway-specific medications. PMID:25443729

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

    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

  13. Organopalladium complexes with bidentate phosphorus and nitrogen containing ligands

    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

  14. Polymerization catalysts containing electron-withdrawing amide ligands

    Watkin, John G.; Click, Damon R.

    2002-01-01

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

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

    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

  16. Immobilisation of ligands by radio-derivatized polymers

    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

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

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

    2003-01-01

    -(phosphonomethoxy)-4-isoxazolyl]propionic acid (ATPO) in complex with the ligand-binding core of the receptor. Comparison with the only previous structure of the ligand-binding core in complex with an antagonist, 6,7-dinitro-2,3-quinoxalinedione (DNQX) (Armstrong, N.; Gouaux, E. Neuron 2000, 28, 165-181), reveals...

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

    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

  19. Mechanochemical synthesis of mixed-ligand europium β-diketonates with nitrogen-containing neutral ligands

    The solid-phase reaction between europium salts of β-diketones and nitrogen-containing neutral ligands in a planetary mill produces luminescent mixed-ligand compounds Eu(β-dic)3 · D, where β-dic stands for dibenzoylmethane, benzoylacetone, thenoyltrifluoroacetone, or benzoyltrifluoroacetone; and D stands for 1,10-phenanthroline, 2,2-dipyridyl, or diphenylguanidine. The mechanosynthesis and yield of lanthanide β-diketonates are studied as affected by the treatment parameters and the nature of the reagents. Powder X-ray diffraction demonstrates a staged course of the mechanochemical synthesis. Examination of formation-rate curves shows that grinding/stirring is the rate-controlling stage of the process. Thermogravimetric analysis shows that the mechanosynthesis can proceed in the self-propagation mode. The relative luminescence intensity is determined as a function of treatment time. Particles of the mechanically activated mixture have sizes of 10-100 μm

  20. A response calculus for immobilized T cell receptor ligands

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

    2001-01-01

    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 affini...... affinity in solution, are of optimal two-dimensional affinity thereby allowing effective TCR binding under physiological conditions, i.e. at low ligand densities in cellular interfaces....... 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 the...

  1. Labeling of amine ligands with sup(99m)Tc in aqueous solutions by ligand exchange

    Volkert, W.A.; Troutner, D.E.; Holmes, R.A. (Missouri Univ., Columbia (USA). Dept. of Radiology; Missouri Univ., Columbia (USA). Dept. of Chemistry; Harry S. Truman Memorial Veterans Hospital, Columbia, MO (USA). Nuclear Medicine Service)

    1982-10-01

    Cyclam, ethylenediamine (EN) and a linear tetraamine (TA) form structurally similar complexes in high yields when pertechnetate is reduced with Sn(II) in aqueous solutions. Efficient labeling of these amine ligands is also accomplished by transfer of sup(99m)Tc from its complexes with diethylenetriaminepentaacetate (DTPA) and citrate. The labeling yields of cyclam, TA and EN using (sup(99m)Tc)DTPA are greater than 95% after standing for 30 min at room temperature in 0.03 M solutions of the amine ligands at pH above 11, but less than 10% at pH below 9. Yields of greater than 90% are obtained using (sup(99m)Tc)citrate under similar conditions at pH 7 or greater. Ethylenediamine-N,N'-diacetic acid (ENDA) also forms a complex with sup(99m)Tc that exhibits pH dependent stability characteristics that are the same as those of (sup(99m)Tc)EN. The labeling efficiency of ENDA with sup(99m)Tc as a function of pH is nearly identical to that of the other amine ligands.

  2. Regulation mechanisms of the FLT3-ligand after irradiation

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

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

    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

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

    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.

  5. Metal-ligand cooperation in H2 activation with iron complexes bearing hemilabile bis(diphenylphosphino)amine ligands.

    Frank, Nicolas; Hanau, Katharina; Langer, Robert

    2014-10-20

    The octahedral transition-metal complex [(dppa)Fe(Ph2P-N-PPh2)2] (1) [dppa = bis(diphenylphosphino)amine] with homofunctional bidentate ligands is described. The ligand exhibits hemilability due to its small bite angle and the steric repulsion of the coordinated donor groups. As the {Ph2P-N-PPh2}(-) ligand can act as an internal base, heterolytic cleavage of dihydrogen by complex 1 leads to the formation of the hydride complex [(dppa)(Ph2P-N-PPh2)Fe(H)(κ(1)-Ph2P-NH-PPh2)2] (2), representing an example of cooperative bond activation with a homofunctional hemilabile ligand. This study demonstrates that hemilability of homofunctionalized ligands can be affected by careful adjustment of geometric parameters. PMID:25290535

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

    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.

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

    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

  8. Triazacyclononane Phosphinic Acids (TRAP) as ligands for 68Ga radiopharmaceuticals

    Gallium-68 radiopharmaceuticals are the most interesting alternatives to those based on 18-F. 68-Ga is produced in commercial 68-Ge/68-Ga generator for fraction of the 18-F price. As metal isotope, 68-Ga must be tightly complexed by a suitable ligand. Macrocyclic ligands are the most suitable ones as their Ga3+ complexes are thermodynamically stable and kinetically inert. Till now, 68-Ga radiopharmaceuticals have been based on DOTA and NOTA skeletons but these ligands exhibit non-optimal labelling properties (high excess of the ligand, long heating, narrow pH range etc.). 1,4,9-TRiAzacyclononane Phosphinic acids (TRAP ligands) have been suggested as ligands for the fast and efficient 68-Ga incorporation. Due to low basicity of the phosphinic acid moieties as well as the ring nitrogen atoms, full complexation is possible even in highly acidic solutions (down to pH 1, i.e. pH of the neat generator eluate). Presence of weakly complexing atoms outside the ligand cage (oxygen atoms e.g. in TRAP-Pr or TRAP-OH) facilitates metal isotope incorporation in highly diluted solutions (non-carrier-added conditions) due to increasing effective metal ion concentration close to the macrocyclic cage. As very low excess of the ligands/conjugates is necessary for complexation, very high specific activity can be obtained. Unusual out-of-cage complexes were observed in the Ga-TRAP-OH system where deprotonated P-CH2O- groups participate in the Ga3+ coordination. The efficiency of 68-Ga labelling is also govern by selectivity of the TRAP ligands for Ga3+ over the most common impurities, e.g. Zn2+ and Fe3+ ions. The article is illustrated by the molecular schemes of NOTA, DOTA, TRAP-Pr and TRAP-OH

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

    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

  10. Database of ligand-induced domain movements in enzymes

    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

  11. Niobium tetrahalide complexes with neutral diphosphine ligands.

    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

  12. Synthesis and study of new oxazoline-based ligands

    Tilliet, Mélanie

    2008-01-01

    This thesis deals with the study of oxazoline-based ligands in metal-catalyzed asymmetric reactions. The first part describes the synthesis of six new bifunctinal pyridine-bis(oxazoline) ligands and their applications in asymmetric metal-catalysis. These ligands, in addition to a Lewis acid coordination site, are equipped with a Lewis basic part in the 4-position of the oxazoline rings. Dual activation by means of this system was probed in cyanide addition to aldehydes. The second part is con...

  13. Quasielastic neutron scattering study of POSS ligand dynamics

    Poly-oligo-silsesquioxanes (POSS) are relatively large (1-2 nm diameter) molecules, that are composed of Si8O12 cages to which a wide variety of possible ligands can be attached. 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 (M-POSS, IBU-POSS, TMS-POSS and DMS-POSS) molecules that illustrate the presence of strong coupling between the ligand dynamics and the POSS crystal structures. (authors)

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

    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

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

    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

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

    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

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

    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.

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

    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

  19. Unique advantages of organometallic supporting ligands for uranium complexes

    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.

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

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

  1. Steered molecular dynamics simulations of protein-ligand interactions

    XU Yechun; SHEN Jianhua; LUO Xiaomin; SHEN Xu; CHEN Kaixian; JIANG Hualiang

    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.

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

    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.

  3. A new fullerene complexation ligand: N-pyridylfulleropyrrolidine.

    Tat, Fatma T; Zhou, Zhiguo; MacMahon, Shaun; Song, Fayi; Rheingold, Arnold L; Echegoyen, Luis; Schuster, David I; Wilson, Stephen R

    2004-07-01

    The subject of this paper is a new fullerene building block design with the potential for defined geometry and good electronic communication. The synthesis and characterization of a new pyridinofullerene ligand capable of forming axially symmetric complexes with metalloporphyrins is reported. X-ray structural and molecular modeling studies, (1)H NMR, UV-vis spectroscopy, electrochemistry studies, and fluorescence quenching data support the formation of a strong complex between the new ligand and the metal center of ZnTPP. On the basis of computational studies, the highest occupied molecular orbital (HOMO) of this ligand is significantly different from a model compound with insulating carbons between the pyridine and the fullerene. The N-pyridinium fulleropyrrolidine salts of the new ligand and model compound were also prepared and their spectral and electrochemical properties are reported. PMID:15230581

  4. Dysprosium complexes with the tetraphenylporphyrin macrocyclic ligand

    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)

  5. Increased CD40 ligand in patients with acute anterior uveitis

    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....

  6. Force History Dependence of Receptor-Ligand Dissociation

    Marshall, Bryan T.; Sarangapani, Krishna K.; Lou, Jizhong; McEver, Rodger P.; Zhu, Cheng

    2004-01-01

    Receptor-ligand bonds that mediate cell adhesion are often subjected to forces that regulate their dissociation via modulating off-rates. Off-rates control how long receptor-ligand bonds last and how much force they withstand. One should therefore be able to determine off-rates from either bond lifetime or unbinding force measurements. However, substantial discrepancies exist between the force dependence of off-rates derived from the two types of measurements even for the same interactions, e...

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

    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.

  8. Coordination chemistry of poly(thioether)borate ligands

    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...

  9. Designer ligands: The search for metal ion selectivity

    Perry T. Kaye

    2011-01-01

    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-s...

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

    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...

  11. Ligand assisted cleavage of uranium oxo-clusters

    Nocton, Gregory; Pecaut, Jacques; Mazzanti, Marinella [Laboratoire de Reconnaissance Ionique et Chimie de Coordination, Service de Chimie Inorganique et Biologique, UMR-E 3 CEA-UJF, CEA/DSM/INAC, CEA-Grenoble, 38054 Grenoble, Cedex 09 (France); Filinchuk, Yaroslav [Swiss Norwegian Beam Lines (SNBL) at the European Synchrotron Radiation Facility (ESRF), rue Jules Horowitz, 38043 Grenoble (France)

    2010-07-01

    Dibenzoylmethanate replaces the bridging triflate ligands in uranium triflate poly-oxo-clusters and cleaves the U{sub 12}O{sub 20} core yielding the new [U{sub 6}O{sub 4}(OH){sub 4}({eta}-dbm){sub 12}] dibenzoylmethanate (dbm{sup -}) cluster which slowly dissociates into a monomeric complex. This reactivity demonstrates the importance of bridging ligands in stabilizing uranium poly-oxo-clusters. (authors)

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

    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

  13. Ligand and interfacial dynamics in a homodimeric hemoglobin

    Gupta, Prashant Kumar; Meuwly, Markus

    2016-01-01

    The structural dynamics of dimeric hemoglobin (HbI) from Scapharca inaequivalvis in different ligand-binding states is studied from atomistic simulations on the μs time scale. The intermediates are between the fully ligand-bound (R) and ligand-free (T) states. Tertiary structural changes, such as rotation of the side chain of Phe97, breaking of the Lys96–heme salt bridge, and the Fe–Fe separation, are characterized and the water dynamics along the R-T transition is analyzed. All these properties for the intermediates are bracketed by those determined experimentally for the fully ligand-bound and ligand-free proteins, respectively. The dynamics of the two monomers is asymmetric on the 100 ns timescale. Several spontaneous rotations of the Phe97 side chain are observed which suggest a typical time scale of 50–100 ns for this process. Ligand migration pathways include regions between the B/G and C/G helices and, if observed, take place in the 100 ns time scale. PMID:26958581

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

    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.

  15. Extracellular interactions and ligand degradation shape the nodal morphogen gradient

    Wang, Yin; Wang, Xi; Wohland, Thorsten; Sampath, Karuna

    2016-01-01

    The correct distribution and activity of secreted signaling proteins called morphogens is required for many developmental processes. Nodal morphogens play critical roles in embryonic axis formation in many organisms. Models proposed to generate the Nodal gradient include diffusivity, ligand processing, and a temporal activation window. But how the Nodal morphogen gradient forms in vivo remains unclear. Here, we have measured in vivo for the first time, the binding affinity of Nodal ligands to their major cell surface receptor, Acvr2b, and to the Nodal inhibitor, Lefty, by fluorescence cross-correlation spectroscopy. We examined the diffusion coefficient of Nodal ligands and Lefty inhibitors in live zebrafish embryos by fluorescence correlation spectroscopy. We also investigated the contribution of ligand degradation to the Nodal gradient. We show that ligand clearance via degradation shapes the Nodal gradient and correlates with its signaling range. By computational simulations of gradient formation, we demonstrate that diffusivity, extra-cellular interactions, and selective ligand destruction collectively shape the Nodal morphogen gradient. DOI: http://dx.doi.org/10.7554/eLife.13879.001 PMID:27101364

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

    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. Serum albumin ligand binding volumes using high pressure denaturation

    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.

  18. Acetate binding induces fluorescence enhancement in tryptophan ligands

    Deka, Arup K.; Sarma, Rupam J., E-mail: rjs@gauhati.ac.in

    2014-03-15

    The anion coordination properties of bis-tryptophan dicarboxamide ligands 1–3 were investigated using fluorescence and {sup 1}H NMR spectroscopy. It was observed that the coordination of acetate anions to these ligands produced emissions at 381 nm with gradual enhancement of fluorescence. In comparison, fluoride produced minor enhancement, the addition of chloride, bromide and nitrate anions caused quenching of ligand fluorescence. {sup 1}H NMR studies revealed that the ligands coordinated to the acetate anions through the indole and amide NH groups. -- Highlights: • We have synthesized and characterized three tryptophan-based diamide ligands 1–3. • We have reported new polymorph of ligand 1 (Crystal structure) in this article. • The role of intramolecular hydrogen bonding (1 vs. 2) in anion binding was investigated. • We were able to identify the role amide/indole NH in anion binding using {sup 1}H NMR. • On the basis of {sup 1}H NMR, we have established role of aromatic CH–anion interactions during anion complexation.

  19. Narrow escape for a stochastically gated Brownian ligand.

    Reingruber, Jürgen; Holcman, David

    2010-02-17

    Molecular activation in cellular microdomains is usually characterized by a forward binding rate, which is the reciprocal of the arrival time of a ligand to a key target. Upon chemical interactions or conformational changes, a Brownian ligand may randomly switch between different states, and when target activation is possible in a specific state only, switching can significantly alter the activation process. The main goal of this paper is to study the mean time for a switching ligand to activate a small substrate, modelled as the time to exit a microdomain through a small absorbing window on the surface. We present the equations for the mean sojourn times the ligand spends in each state, and study the escape process with switching between two states in dimension one and three. When the ligand can exit in only one of the two states, we find that switching always decreases its sojourn time in the state where it can exit. Moreover, the fastest exit is obtained when the ligand diffuses most of the time in the state with the maximal diffusion coefficient, although this may imply that it spends most of the time 'hidden' in the state where it cannot exit. We discuss the physical mechanisms responsible for this apparent paradox. In dimension three we confirm our results with Brownian simulations. Finally, we suggest possible applications in cellular biology. PMID:21389363

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

    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

  1. Rule of five in 2015 and beyond: Target and ligand structural limitations, ligand chemistry structure and drug discovery project decisions.

    Lipinski, Christopher A

    2016-06-01

    The rule of five (Ro5), based on physicochemical profiles of phase II drugs, is consistent with structural limitations in protein targets and the drug target ligands. Three of four parameters in Ro5 are fundamental to the structure of both target and drug binding sites. The chemical structure of the drug ligand depends on the ligand chemistry and design philosophy. Two extremes of chemical structure and design philosophy exist; ligands constructed in the medicinal chemistry synthesis laboratory without input from natural selection and natural product (NP) metabolites biosynthesized based on evolutionary selection. Exceptions to Ro5 are found mostly among NPs. Chemistry chameleon-like behavior of some NPs due to intra-molecular hydrogen bonding as exemplified by cyclosporine A is a strong contributor to NP Ro5 outliers. The fragment derived, drug Navitoclax is an example of the extensive expertise, resources, time and key decisions required for the rare discovery of a non-NP Ro5 outlier. PMID:27154268

  2. LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters.

    Wolber, Gerhard; Langer, Thierry

    2005-01-01

    From the historically grown archive of protein-ligand complexes in the Protein Data Bank small organic ligands are extracted and interpreted in terms of their chemical characteristics and features. Subsequently, pharmacophores representing ligand-receptor interaction are derived from each of these small molecules and its surrounding amino acids. Based on a defined set of only six types of chemical features and volume constraints, three-dimensional pharmacophore models are constructed, which are sufficiently selective to identify the described binding mode and are thus a useful tool for in-silico screening of large compound databases. The algorithms for ligand extraction and interpretation as well as the pharmacophore creation technique from the automatically interpreted data are presented and applied to a rhinovirus capsid complex as application example. PMID:15667141

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

    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.

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

    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. - Graphical abstract: The structural differences show that the ancillary ligands have great effects on the spatial connective fashions, resulting in the formation of various dimensional compounds. - Highlights: • Five new Co(II) coordination polymers have been synthesized by solvothermal reactions based on 3,5-bis(pyridin-4-ylmethoxy)benzoic acid (HL). • The long-flexible ligand (HL) is a good candidate to produce interpenetrating architectures. • The secondary dicarboxylic acid ligands play important roles in the spatial connective fashions and the formation of various dimensional compounds. • The magnetism studies show that both 2 and 5 exhibit antiferromagnetic interactions

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

    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, ...

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

    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.

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

    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

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

    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.

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

    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.

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

    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

  11. Role of the T cell receptor ligand affinity in T cell activation by bacterial superantigens

    Andersen, P S; Geisler, C; Buus, S; Mariuzza, R A; Karjalainen, K

    2001-01-01

    the SEC3 variants correlated with enhanced binding without any optimum in the binding range covered by native TCR ligands. Comparable studies using anti-TCR antibodies of known affinity confirmed these observations. By comparing the biological potency of the two sets of ligands, we found a significant...... 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....

  12. Ligand Migration and Binding in Myoglobin Mutant L29W

    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

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

    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

  14. Predicting protein ligand binding motions with the conformation explorer

    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.

  15. Kinetics of Receptor-Ligand Interactions in Immune Responses

    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.

  16. NKG2D ligands mediate immunosurveillance of senescent cells.

    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

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

    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...

  18. Analytical developments for screening of lanthanides/ligands interactions

    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)

  19. Memetic algorithms for ligand expulsion from protein cavities

    Rydzewski, J.; Nowak, W.

    2015-09-01

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

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

    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...... 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...... 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. In the...

  1. Protecting Ligands Enhance Selective Targeting of Multivalent Nanoparticles

    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.

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

    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.

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

    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

  5. Docking Screens for Novel Ligands Conferring New Biology.

    Irwin, John J; Shoichet, Brian K

    2016-05-12

    It is now plausible to dock libraries of 10 million molecules against targets over several days or weeks. When the molecules screened are commercially available, they may be rapidly tested to find new leads. Although docking retains important liabilities (it cannot calculate affinities accurately nor even reliably rank order high-scoring molecules), it can often can distinguish likely from unlikely ligands, often with hit rates above 10%. Here we summarize the improvements in libraries, target quality, and methods that have supported these advances, and the open access resources that make docking accessible. Recent docking screens for new ligands are sketched, as are the binding, crystallographic, and in vivo assays that support them. Like any technique, controls are crucial, and key experimental ones are reviewed. With such controls, docking campaigns can find ligands with new chemotypes, often revealing the new biology that may be docking's greatest impact over the next few years. PMID:26913380

  6. Memetic algorithms for ligand expulsion from protein cavities

    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...

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

    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

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

    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.

  9. Conformational diversity of flexible ligand in metal-organic frameworks controlled by size-matching mixed ligands

    Hua, Xiu-Ni; Qin, Lan; Yan, Xiao-Zhi; Yu, Lei; Xie, Yi-Xin; Han, Lei

    2015-12-01

    Hydrothermal reactions of N-auxiliary flexible exo-bidentate ligand 1,3-bis(4-pyridyl)propane (bpp) and carboxylates ligands naphthalene-2,6-dicarboxylic acid (2,6-H2ndc) or 4,4‧-(hydroxymethylene)dibenzoic acid (H2hmdb), in the presence of cadmium(II) salts have given rise to two novel metal-organic frameworks based on flexible ligands (FL-MOFs), namely, [Cd2(2,6-ndc)2(bpp)(DMF)]·2DMF (1) and [Cd3(hmdb)3(bpp)]·2DMF·2EtOH (2) (DMF=N,N-Dimethylformamide). Single-crystal X-ray diffraction analyses revealed that compound 1 exhibits a three-dimensional self-penetrating 6-connected framework based on dinuclear cluster second building unit. Compound 2 displays an infinite three-dimensional 'Lucky Clover' shape (2,10)-connected network based on the trinuclear cluster and V-shaped organic linkers. The flexible bpp ligand displays different conformations in 1 and 2, which are successfully controlled by size-matching mixed ligands during the self-assembly process.

  10. New formamidine ligands and their mixed ligand palladium(II) oxalate complexes: Synthesis, characterization, DFT calculations and in vitro cytotoxicity

    Soliman, Ahmed A.; Alajrawy, Othman I.; Attabi, Fawzy A.; Shaaban, Mohamed R.; Linert, W.

    2016-01-01

    A series of new ternary palladium(II) complexes of the type [Pd(L1-4)ox]·xH2O where L = formamidine ligands and ox = oxalate, were synthesized and characterized by elemental analyses, magnetic susceptibility, UV-Vis, infrared (IR) and mass spectroscopy and thermal analysis. The spectroscopic data indicated that the formamidine ligands act as bidentate N2 donors and the oxalate as O2 ligand. The complexes (1-4) are diamagnetic and the optimization of their structures indicated that the geometry is distorted square planer with O-Pd-O and N-Pd-N bond angles ranged 82.70-83.87° and 88.21-95.02°; respectively which is acceptable for the heteroleptic complexes. The dipole moment of the complexes (13.97-18.77 Debye) indicating that the complexes are more polarized than the ligands (1.93-4.96 Debye). The complexes are thermally stable as shown from their relatively higher overall activation energies (441-688 kJ mol-1). The ligands and the complexes are proved to have good cytotoxicity with IC50 (μM) in the range of (0.011-0.168) against MCF-7, (0.012-0.150) against HCT-116, (0.042-0.094) against PC-3 and (0.006-0.222) against HepG-2 cell lines, which open the field for further application as antitumor compounds.

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

    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. Sequestering agent for uranyl chelation: new bi-naphtyl ligands

    The synthesis of phosphonate, sulfocatecholamide (CAMS) and hydroxy-pyridinone (HOPO) bi-naphtyl ligands is presented. Their binding abilities for uranyl cation were determined by UV spectrophotometry in aqueous media versus pH. These titrations showed that the efficiency of these chelating agents depends on the nature of the chelating group. Each ligand shows a more or less pronounced affinity towards uranium. While the bis-phosphonate compound did not show any affinity towards the uranyl ion, the BINHOPO derivative exhibits significant affinity at acidic and neutral pH while the BINCAMS is more efficient at basic pH. (authors)

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

    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.

  14. Complexation of neptunium(V) by polyaminocarboxylate ligands

    The stability constants of complexes of NpO2+ ion with a series of polyaminocarboxylate, oxydiacetate (ODA) and thiodiacetate (TDA) ligands were determined using spectrophotometric and potentiometric techniques. The measurements were conducted at an ionic strength of 0.50 M (NaClO4). By contrast to lanthanide complexation, the interaction of the ether oxygen of ODA with NpO2+ cation is very small whereas TDA acts only as a monodentate ligand via one of the carboxylate groups. (orig.)

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

    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.)

  16. Two ligands for a GPCR, proton vs lysolipid

    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.

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

    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.

  18. Ligand-assisted capillary electrophoresis separations of the lanthanides

    Capillary electrophoresis is used with simple organic ligands added to the electrolyte matrix to achieve separation of the individual lanthanide cations. Results for acetate (AC-) and malonate (MA-) yield good resolution for the lighter lanthanides, but not the heavier lanthanides. In contrast, α-hydroxyisobutyrate (HIB-) gives complete resolution for all of the lanthanide cations. These results are related to the complexation chemistry between the lanthanides and the ligands across the lanthanide series. In addition, preliminary results for lanthanide separations using AC- in mixed methanol:water solvent systems are provided. The presence of methanol improves resolution but slows the separation. (author)

  19. Identification of Physiologically Active Substances as Novel Ligands for MRGPRD

    Makiko Uno; Satoko Nishimura; Keisuke Fukuchi; Yasuyuki Kaneta; Yoko Oda; Hironobu Komori; Shigeki Takeda; Tatsuya Haga; Toshinori Agatsuma; Futoshi Nara

    2012-01-01

    Mas-related G-protein coupled receptor member D (MRGPRD) is a G protein-coupled receptor (GPCR) which belongs to the Mas-related GPCRs expressed in the dorsal root ganglia (DRG). In this study, we investigated two novel ligands in addition to beta-alanine: (1) beta-aminoisobutyric acid, a physiologically active substance, with which possible relation to tumors has been seen together with beta-alanine; (2) diethylstilbestrol, a synthetic estrogen hormone. In addition to the novel ligands, we f...

  20. Designer ligands: The search for metal ion selectivity

    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.

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

    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

  2. Predicting Electrophoretic Mobility of Protein-Ligand Complexes for Ligands from DNA-Encoded Libraries of Small Molecules.

    Bao, Jiayin; Krylova, Svetlana M; Cherney, Leonid T; Hale, Robert L; Belyanskaya, Svetlana L; Chiu, Cynthia H; Shaginian, Alex; Arico-Muendel, Christopher C; Krylov, Sergey N

    2016-05-17

    Selection of target-binding ligands from DNA-encoded libraries of small molecules (DELSMs) is a rapidly developing approach in drug-lead discovery. Methods of kinetic capillary electrophoresis (KCE) may facilitate highly efficient homogeneous selection of ligands from DELSMs. However, KCE methods require accurate prediction of electrophoretic mobilities of protein-ligand complexes. Such prediction, in turn, requires a theory that would be applicable to DNA tags of different structures used in different DELSMs. Here we present such a theory. It utilizes a model of a globular protein connected, through a single point (small molecule), to a linear DNA tag containing a combination of alternating double-stranded and single-stranded DNA (dsDNA and ssDNA) regions of varying lengths. The theory links the unknown electrophoretic mobility of protein-DNA complex with experimentally determined electrophoretic mobilities of the protein and DNA. Mobility prediction was initially tested by using a protein interacting with 18 ligands of various combinations of dsDNA and ssDNA regions, which mimicked different DELSMs. For all studied ligands, deviation of the predicted mobility from the experimentally determined value was within 11%. Finally, the prediction was tested for two proteins and two ligands with a DNA tag identical to those of DELSM manufactured by GlaxoSmithKline. Deviation between the predicted and experimentally determined mobilities did not exceed 5%. These results confirm the accuracy and robustness of our model, which makes KCE methods one step closer to their practical use in selection of drug leads, and diagnostic probes from DELSMs. PMID:27119259

  3. Glucagon-like peptide-1 receptor ligand interactions: structural cross talk between ligands and the extracellular domain.

    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.

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

    Cao, Ke-Li; Zhang, Yi-Ping; Cai, Yi-Ni; Xu, Xiao-Wei; Feng, Yun-Long, E-mail: sky37@zjnu.cn

    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 [CoL{sub 2}(H{sub 2}O){sub 2}]{sub n}·2nH{sub 2}O (1), which possesses a 1D chain structure. In the presence of ancillary ligands, namely, 1,3-adamantanedicarboxylic acid (H{sub 2}adbc), terephthalic acid (H{sub 2}tpa), thiophene-2,5-dicarboxylic acid (H{sub 2}tdc) and 1,4-benzenedithioacetic acid (H{sub 2}bdtc), four 3D structures [Co{sub 2}L{sub 2}(adbc)]{sub n}·nH{sub 2}O (2), [Co{sub 2}L{sub 2}(tpa)]{sub n} (3), [Co{sub 2}L{sub 2}(tdc)]{sub n} (4), [Co{sub 2}L{sub 2}(bdtc)(H{sub 2}O)]{sub n} (5) were obtained, respectively. It can be observed from the architectures of 1–5 that hydrogen bonds and secondary ligands both have great effects on the spatial connective fashions, resulting in the formation of various dimensional compounds. The XRPD, TGA data of title polymers and the magnetic properties for 2 and 5 have also been investigated. - Graphical abstract: The structural differences show that the ancillary ligands have great effects on the spatial connective fashions, resulting in the formation of various dimensional compounds. - Highlights: • Five new Co(II) coordination polymers have been synthesized by solvothermal reactions based on 3,5-bis(pyridin-4-ylmethoxy)benzoic acid (HL). • The long-flexible ligand (HL) is a good candidate to produce interpenetrating architectures. • The secondary dicarboxylic acid ligands play important roles in the spatial connective fashions and the formation of various dimensional compounds. • The magnetism studies show that both 2 and 5 exhibit antiferromagnetic interactions.

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

    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.

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

    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...

  7. The imidazoline receptors and ligands in pain modulation

    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.

  8. Fluorescent ligands for studying neuropeptide receptors by confocal microscopy

    A. Beaudet

    1998-11-01

    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.

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

    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. The imidazoline receptors and ligands in pain modulation.

    Bektas, Nurcan; Nemutlu, Dilara; Arslan, Rana

    2015-01-01

    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 I2 receptor 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 I2 receptor 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. PMID:26600633

  11. A Guided Inquiry Activity for Teaching Ligand Field Theory

    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…

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

    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. Ligand for neurotransmission SPECT in extra-pyramidal diseases

    It is now possible to study by scintigraphy some parameters of dopaminergic neurotransmission with iodinated ligands. Some clinical studies have shown the interest of this kind of exploration for the early diagnosis, the differential diagnosis and the follow-up of evolution and treatment of the different extra pyramidal pathologies. However, advances are still expected in several fields (tracers, cameras resolutions). (N.C.)

  14. Helquats as a new class of G-quadruplex ligands

    Devadig, Pradeep; Kozák, Jaroslav; Kužmová, Erika; Hubálková, Pavla; Novotná, J.; Komárková, Veronika; Císařová, I.; Šaman, David; Pohl, Radek; Bednárová, Lucie; Urbanová, M.; Hájek, Miroslav; Teplý, Filip

    Praha: Czech Chemical Society, 2015. s. 66. [Liblice 2015. Advances in Organic , Bioorganic and Pharmaceutical Chemistry /50./. 06.11.2015-08.11.2015, Olomouc] R&D Projects: GA ČR GA13-19213S Institutional support: RVO:61388963 Keywords : helquats * G-quadruplex ligands Subject RIV: CC - Organic Chemistry

  15. Dependence of acridine adsorption on ligand hydration enthalpy

    Matzner, R.; Bales, R.C. (Univ. of Arizona, Tucson, AZ (United States). Dept. of Hydrology and Water Resources)

    1994-11-01

    The environmental fate of acridine is of concern because of its toxic and teratogenic properties. It is found in tobacco smoke, air pollution source effluents, recent lake sediments, wood preservative wastewater, wastewater treatment plant biosludge, and contaminated groundwater. The effect of the aqueous solution pH and ligand type (H[sub 2]PO[sup [minus

  16. Selective Electrocatalytic Activity of Ligand Stabilized Copper Oxide Nanoparticles

    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.

  17. Ligand and ensemble effects in adsorption on alloy surfaces

    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....

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

    Kristensen, Thomas Greve; Pedersen, Christian Storm

    2009-01-01

    spatial alignment of a set of active ligands taking the flexibility of chemical bonds into account. We present two implementations of our method. One using Differential Evolution (DE) for numerical optimization, and one using the Nelder-Mead method for numerical optimization. We investigate the quality of...

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

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

    2016-01-01

    Roč. 35, č. 5 (2016), s. 785-798. ISSN 0276-7333 R&D Projects: GA ČR(CZ) GA14-08531S; GA MŠk(CZ) LO1504 Institutional support: RVO:61388955 Keywords : group 4 metal complexes * cyclopentadienyl-ketimide ligands * metallocenes Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.126, year: 2014

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

    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. GluR2 ligand-binding core complexes

    Kasper, C; Lunn, M-L; Liljefors, T; Gouaux, E; Egebjerg, J; Kastrup, Jette Sandholm Jensen

    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...

  2. Modeling of metal interaction geometries for protein-ligand docking.

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

    2008-05-15

    The accurate modeling of metal coordination geometries plays an important role for structure-based drug design applied to metalloenzymes. For the development of a new metal interaction model, we perform a statistical analysis of metal interaction geometries that are relevant to protein-ligand complexes. A total of 43,061 metal sites of the Protein Data Bank (PDB), containing amongst others magnesium, calcium, zinc, iron, manganese, copper, cadmium, cobalt, and nickel, were evaluated according to their metal coordination geometry. Based on statistical analysis, we derived a model for the automatic calculation and definition of metal interaction geometries for the purpose of molecular docking analyses. It includes the identification of the metal-coordinating ligands, the calculation of the coordination geometry and the superposition of ideal polyhedra to identify the optimal positions for free coordination sites. The new interaction model was integrated in the docking software FlexX and evaluated on a data set of 103 metalloprotein-ligand complexes, which were extracted from the PDB. In a first step, the quality of the automatic calculation of the metal coordination geometry was analyzed. In 74% of the cases, the correct prediction of the coordination geometry could be determined on the basis of the protein structure alone. Secondly, the new metal interaction model was tested in terms of predicting protein-ligand complexes. In the majority of test cases, the new interaction model resulted in an improved docking accuracy of the top ranking placements. PMID:18041759

  3. NMR-based screening of membrane protein ligands.

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

    2010-03-01

    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 ligands non-specifically, overlap with protein signals, modulate protein dynamics and conformational exchange and compromise sensitivity by adding highly intense background signals. In this article, we discuss the special considerations arising from these problems when conducting NMR-based ligand-binding studies with membrane proteins. While the use of (13)C and (15)N isotopes is becoming increasingly feasible, (19)F and (1)H NMR-based approaches are currently the most widely explored. By using suitable NMR parameter selection schemes independent of or exploiting the presence of detergent, (1)H-based approaches require least effort in sample preparation because of the high sensitivity and natural abundance of (1)H in both, ligand and protein. On the other hand, the (19)F nucleus provides an ideal NMR probe because of its similarly high sensitivity to that of (1)H and the lack of natural (19)F background in biologic systems. Despite its potential, the use of NMR spectroscopy is highly underdeveloped in the area of drug discovery for membrane proteins. PMID:20331645

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

    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

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

    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…

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

    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.

  7. Organoosmium complexes of imidazole-containing chelate acceptor ligands

    Sarper, O.; Sarkar, B.; Fiedler, Jan; Lissner, F.; Kaim, W.

    2010-01-01

    Roč. 363, č. 12 (2010), s. 3070-3077. ISSN 0020-1693 R&D Projects: GA MŠk OC09043 Institutional research plan: CEZ:AV0Z40400503 Keywords : arene ligand * electrochemistry * electronic structure Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.899, year: 2010

  8. NMR-based screening of membrane protein ligands

    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

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

    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

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

    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.

  11. Magnesium incorporation in calcite in the presence of organic ligands

    Mavromatis, Vasileios; Baldermann, Andre; Purgstaller, Bettina; Dietzel, Martin

    2015-04-01

    The formation of authigenic Mg-calcites in marine early diagenetic environments is commonly driven by a bio-induced process, the anaerobic oxidation of methane (AOM), which provides inorganic carbon required for the precipitation of such authigenic carbonates. In such settings the availability of major and/or trace divalent metal cations (Me2+) incorporated in calcite and their aqueous speciation are controlled by the presence of aqueous organic molecules that are produced either as (by-)products of biological activity (i.e. exopolymeric substances) or during degradation of allochthonous organic matter in the sediments. Despite the fact that the presence of aqueous organic ligands strongly affects the growth rates and the mineralogy of precipitating CaCO3 polymorphs, till now no study addresses the role of Me2+-ligand aqueous complexes on the extent of Mg and/or other trace element content of Mg-calcites. In order to shed light on this process, relevant to authigenic calcite formation in organic-rich marine sediments and continental soils, we precipitated calcite in the presence of aqueous Mg and a variety of low molecular weight carboxylic- and aminoacids. Our experimental data indicate that the presence of organic ligands augments significantly the saturation state of calcite in the parent fluid during its precipitation. Moreover, they suggest that the higher the ligand concentration, the higher the obtained distribution coefficient of Mg in calcite. The latter is directly proportional to the ratio of Mg2+/Ca2+ aqueous ions for all ligands used. Hydrogeochemical modelling of the aqueous fluids indicate that the observed correlation can be explained by the stronger complexation of Ca2+ with organic ligands compared to Mg2+, which results in higher availability of Mg2+ vs. Ca2+ aqueous ions. Overall the obtained results suggest that the higher the organic ligand aqueous concentration the higher the Mg content of calcite forming from this fluid. These findings are

  12. Specific uranyl binding by macrocyclic ligands attached to resins

    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

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

    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. PMID:23941661

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

    Hawxwell, Samuel M; Espallargas, Guillermo Mínguez; Bradshaw, Darren; Rosseinsky, Matthew J; Prior, Timothy J; Florence, Alastair J; van de Streek, Jacco; Brammer, Lee

    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....

  15. Covalent Coupling of Nanoparticles with Low-Density Functional Ligands to Surfaces via Click Chemistry

    Ina Rianasari; de Jong, Michel P.; Jurriaan Huskens; van der Wiel, Wilfred G.

    2013-01-01

    We demonstrate the application of the 1,3-dipolar cycloaddition (“click” reaction) to couple gold nanoparticles (Au NPs) functionalized with low densities of functional ligands. The ligand coverage on the citrate-stabilized Au NPs was adjusted by the ligand:Au surface atom ratio, while maintaining the colloidal stability of the Au NPs in aqueous solution. A procedure was developed to determine the driving forces governing the selectivity and reactivity of citrate-stabilized and ligand-functio...

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

    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...

  17. Development of high performance structure and ligand based virtual screening techniques

    Shave, Steven R.

    2010-01-01

    Virtual Sreening (VS) is an in silico technique for drug discovery. An overview of VS methods is given and is seen to be approachable from two sides: structure based and ligand based. Structure based virtual screening uses explicit knowledge of the target receptor to suggest candidate receptor-ligand complexes. Ligand based virtual screening can infer required characteristics of binders from known ligands. A consideration for all virtual screening techniques is the amount of co...

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

    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 m...... 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....

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

    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...

  20. A New Method for Ligand Docking to Flexible Receptors by Dual Alanine Scanning and Refinement (SCARE)

    Bottegoni, Giovanni; Kufareva, Irina; Totrov, Maxim; Abagyan, Ruben

    2008-01-01

    Protein binding sites undergo ligand specific conformational changes upon ligand binding. However, most docking protocols rely on a fixed conformation of the receptor, or on the prior knowledge of multiple conformations representing the variation of the pocket, or on a known bounding box for the ligand. Here we described a general induced fit docking protocol that requires only one initial pocket conformation and identifies most of the correct ligand positions as the lowest score. We expanded...

  1. Synthesis of Yttrium and Aluminum Complexes Supported by a Mono-Substituted Ferrocene Ligand

    Gao, Jun

    2015-01-01

    Ferrocene chelating ligands provide good stability of the resulting metal complexes and redox-switchable control in chemical processes catalyzed by those complexes. In comparison to traditional di-substituted ferrocene tetradentate ligands, mono-substituted tridentate ferrocene ligands may form metal complexes with a more open coordination sphere around the metal center that may allow an increased preference for substrate coordination. In addition, a mono-substituted ferrocene ligand allows t...

  2. O-fucosylation of the notch ligand mDLL1 by POFUT1 is dispensable for ligand function.

    Julia Müller

    Full Text Available Fucosylation of Epidermal Growth Factor-like (EGF repeats by protein O-fucosyltransferase 1 (POFUT1 in vertebrates, OFUT1 in Drosophila is pivotal for NOTCH function. In Drosophila OFUT1 also acts as chaperone for Notch independent from its enzymatic activity. NOTCH ligands are also substrates for POFUT1, but in Drosophila OFUT1 is not essential for ligand function. In vertebrates the significance of POFUT1 for ligand function and subcellular localization is unclear. Here, we analyze the importance of O-fucosylation and POFUT1 for the mouse NOTCH ligand Delta-like 1 (DLL1. We show by mass spectral glycoproteomic analyses that DLL1 is O-fucosylated at the consensus motif C²XXXX(S/TC³ (where C² and C³ are the second and third conserved cysteines within the EGF repeats found in EGF repeats 3, 4, 7 and 8. A putative site with only three amino acids between the second cysteine and the hydroxy amino acid within EGF repeat 2 is not modified. DLL1 proteins with mutated O-fucosylation sites reach the cell surface and accumulate intracellularly. Likewise, in presomitic mesoderm cells of POFUT1 deficient embryos DLL1 is present on the cell surface, and in mouse embryonic fibroblasts lacking POFUT1 the same relative amount of overexpressed wild type DLL1 reaches the cell surface as in wild type embryonic fibroblasts. DLL1 expressed in POFUT1 mutant cells can activate NOTCH, indicating that POFUT1 is not required for DLL1 function as a Notch ligand.

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

    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

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

    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

  5. Micro-flow synthesis and structural analysis of sterically crowded diimine ligands with five aryl rings

    Shinichiro Fuse

    2013-11-01

    Full Text Available Sterically crowded diimine ligands with five aryl rings were prepared in one step in good yields using a micro-flow technique. X-ray crystallographic analysis revealed the detailed structure of the bulky ligands. The nickel complexes prepared from the ligands exerted high polymerization activity in the ethylene homopolymerization and copolymerization of ethylene with polar monomers.

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

    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

  7. Understanding ligand effects in gold clusters using mass spectrometry.

    Johnson, Grant E; Laskin, Julia

    2016-06-21

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

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

    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. PMID:26250412

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

    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

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

    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.

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

    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.

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

    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. The cholinergic ligand binding material of axonal membranes

    Choline acetyltransferase and acetylcholinesterase, the enzymes responsible for the synthesis and hydrolysis of ACh, are present in nerve fibers. In crustacean peripheral nerves, release of ACh from cut nerve fibers has been demonstrated. Previously closed membrane vesicles have been prepared from lobster walking leg nerve plasma membrane and saturable binding of cholinergic agonsist and antagonists to such membranes have been demonstrated. This paper studies this axonal cholinergic binding material, and elucidates its functions. The binding of tritium-nicotine to lobster nerve plasma membranes was antagonized by a series of cholinergic ligands as well as by a series of local anesthetics. This preparation was capable of binding I 125-alpha-bungarotoxin, a ligand widely believed to be a specific label for nicotinic ACh receptor. The labelling of 50 K petide band with tritium-MBTA following disulfide reduction is illustrated

  14. Scintillation proximity radioimmunoassay utilizing 125I-labeled ligands

    A unique type of radioimmunoassay is described that does not require centrifugation or separation. Microbeads containing a fluorophor are covalently linked to antibody. When an 125I-labeled antigen is added it binds to the beads and, by its proximity, the emitted short-range electrons of the 125I excite the fluorophor in the beads. The light emitted can be measured in a standard scintillation counter. Addition of unlabeled antigen from tissue extracts displaces the labeled ligand and diminishes the fluorescent signal. Application of scintillation proximity immunoassay to tissue enkephalins, serum thyroxin, and urinary morphine is described. Applications of the principle to study the kinetics of interaction between receptors and ligands are discussed

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

    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

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

    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.

  17. Multidentate Terephthalamidate And Hydroxypyridonate Ligands: Towards New Orally Active Chelators

    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 59Fe, 238Pu, and 241Am 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.

  18. Stereochemical investigation of mixed-ligand complexes of neodymium

    Khomenko, V.S.; Lozinskii, M.O.; Fialkov, Yu.A.; Krasovskaya, L.I.; Rasshinina, T.A.

    1987-04-01

    A number of new adducts of the neodymium complexes with 1,1,1,5,5,5-hexafluoro-pentane-2,4-dione and 2-heptafluoropropoxy-1,1,1,2-tetrafluoro-5-phenylpentane-3,5-dione have been synthesized. Their fragmentation paths under electron impact have been established. The strength of the bonding of the additional ligands to the central atom in the complexes investigated has been evaluated. Data on the fragmentation paths of doubly charged ions have been obtained for the first time. The addition of the bis heterocycles to three-ligand complexes of neodymium alters the properties of the complexes, i.e., their thermal stability and photochemical stability increase, and in some cases, their volatility increases.

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

    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

  20. Advances in Computational Techniques to Study GPCR-Ligand Recognition.

    Ciancetta, Antonella; Sabbadin, Davide; Federico, Stephanie; Spalluto, Giampiero; Moro, Stefano

    2015-12-01

    G-protein-coupled receptors (GPCRs) are among the most intensely investigated drug targets. The recent revolutions in protein engineering and molecular modeling algorithms have overturned the research paradigm in the GPCR field. While the numerous ligand-bound X-ray structures determined have provided invaluable insights into GPCR structure and function, the development of algorithms exploiting graphics processing units (GPUs) has made the simulation of GPCRs in explicit lipid-water environments feasible within reasonable computation times. In this review we present a survey of the recent advances in structure-based drug design approaches with a particular emphasis on the elucidation of the ligand recognition process in class A GPCRs by means of membrane molecular dynamics (MD) simulations. PMID:26538318

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

    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...

  2. Screening and Optimization of Ligand Conjugates for Lysosomal Targeting

    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. METAL NANOPARTICLES FUNCTIONALIZED WITH METAL-LIGAND COVALENT BONDS

    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 ...

  4. Flexible Docking of Proteins and "Drug-like" Ligands.

    Tang, Hai-Xu; Ye, Yu-Zhen; Ding, Da-Fu

    1998-01-01

    By using "tabu search" algorithm and Gehlhaar potential function, a new approach is presented for flexible docking of protein and its "drug-like" ligand has been developed. Computational test for this method with a set of 100 complexes has been performed, which indicated that the deviation of 89% of the predicted complex conformation was less than 0.25 nm. Compared with GOLD, a program of genetic algorithm, our method has high accuracy, low limit and short computation time. PMID:12168000

  5. Proton-dependent zinc release from intracellular ligands

    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...

  6. Novel retinoic acid receptor ligands in Xenopus embryos.

    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...

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

    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...

  8. Synthesis and vibrational study of some polydentate ligands

    Esteban, M. F. Gargallo; Serrano, R. Vilaplana; Vilchez, F. González

    Sodium salts of iminodiacetic acid (IDA), ethylenediaminetetraacetic acid (EDTA), 1,2-propylenediaminetetraacetic acid (PDTA) and 1,2-diaminocyclohexanetetraacetic acid (DCTA) were prepared by modification of the literature methods and their i.r. and Raman spectra were studied. The results obtained by application of both techniques allowed a better characterization of these polydentate ligands. Raman spectroscopy was specially useful in elucidating structural aspects in compounds containing acetate groups.

  9. RANK-Ligand inhibitor associated osteonecrosis of the jaw

    Rashad, Ashkan

    2013-11-01

    Full Text Available Osteonecrosis of the jaw may be caused by many different triggers. One of them is described to be the drug or medication related osteonecrosis of the jaw. Since many years bisphosphonates induced the dreaded diagnosis. Recently a drug named denosumab is reported to show similar effects on the jaw. In this case report we present a RANK-Ligand inhibitor associated osteonecrosis of the lower jaw and discuss the lights and shadows of this newly introduced drug.

  10. Transition metal complexing with polymetric sulfur-containing fibrous ligand

    A study was made on interaction of Cr4, V5, Cu2 transition metals with thioamidated polymeric PVS-PAN-T ligand of fibrous structure. Sorption characteristics of PVS-PAN-T, depending on pH and temperature of solutions of copper, chromium and vanadium salts were determined. Parameters of ESR spectra of PVS-PAN-T compounds with transition metals enabled to determine the structure of formed coordination centers

  11. Modified nucleosides and oligonucleotides as ligands for asymmetric reactions

    Nuzzolo, Marzia

    2010-01-01

    Development of chiral ligands capable of achieving high selectivity for various asymmetric catalytic reactions has been an important aim of both academia and industry. Nature is capable to selectively catalyze chemical reactions by using enzymes. An ideal catalyst would combine the selectivity of nature and the reactivity of man-made catalysts based on transition metal complexes. The two biomolecules chosen to achieve this are DNA and PNA. DNA is a chiral molecule with high binding selectivit...

  12. Properties modification of nanopatterned surfaces functionalized with photo activated ligands

    Stoianov, Stefan Vladimirov

    2011-01-01

    This dissertation focuses on four research topics: self-assembly of colloidal nanoparticles, surface modifications of the properties of ionically self-assembled multilayer films, surface enhanced Raman spectroscopy of functionalized gold nanoparticles, and two photon uncaging in gel. Those techniques are used for development of novel nanofabrication methods for top-down and bottom-up assembly of nanostructures, by modifying the properties of nanopatterned surfaces with photoactive ligands, an...

  13. A streptavidin mutant with altered ligand-binding specificity

    Reznik, Gabriel O.; Vajda, Sandor; Sano, Takeshi; Cantor, Charles R.

    1998-01-01

    The biotin-binding site of streptavidin was modified to alter its ligand-binding specificity. In natural streptavidin, the side chains of N23 and S27 make two of the three hydrogen bonds with the ureido oxygen of biotin. These two residues were mutated to severely weaken biotin binding while attempting to maintain the affinity for two biotin analogs, 2-iminobiotin and diaminobiotin. Redesigning of the biotin-binding site used the difference in local electrostatic charge distribution between b...

  14. Predicting protein-ligand and protein-peptide interfaces

    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.

  15. Imaging Ligand-Dependent Activation of CXCR7

    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.

  16. Aerobic oxidation assisted by ligand-free palladium catalysts

    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.

  17. Ligand pose and orientational sampling in molecular docking.

    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.

  18. Synthesis and Coordination Chemistry of Ligands for Supramolecular Chemistry and Sensing Applications

    Clayton, Hayley J.

    2008-01-01

    A series of multidentate N-donor ligands have been synthesised all containing pyridyl and pyridyl/thiazole units and their coordination behaviour is described. The ligands are classified into four types; i) terpyridine containing pyridyl/thiazole ligands (L1-3); ii) pyridyl/thiazole ligands containing a 3,3′-disubstituted bipyridine core. (L4-8); iii) 2,2′-bipyridine containing a crown ether moiety (L9-11); and iv) a 2,2′- bipyridine derived ligand containing a urea functional ...

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

    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

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

    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

  1. Evolution of ligand specificity in vertebrate corticosteroid receptors

    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.

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

    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.

  3. Structure and ligand recognition of class C GPCRs

    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.

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

    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

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

    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

  6. Synthesis and characterisation of a mesocyclic tripodal triamine ligand.

    Ure, Andrew D; Lázaro, Isabel Abánades; Cotter, Michelle; McDonald, Aidan R

    2016-01-14

    Meso- and macrocyclic polydentate amine ligands have been widely explored in oxidation catalysis and for the stabilization of unstable metal-superoxide, -peroxide, and -oxo intermediates. Herein we report on the design and synthesis of a novel mesocyclic, tripodal, triamine ligand that we believe will be an excellent addition to this field. We explored a number of synthetic procedures towards the mesocyclic asymmetric tetraalkylated ligand 1. We expect that 1 will bind metals in a facially capping manner, yielding complexes that display pseudo-tetrahedral geometry, potentially providing access to unprecedented late transition metal-oxo complexes (metal = Co, Ni, Cu). We describe the preparation of a library of mesocyclic polyamine synthons (8, 16, 17, 18, 19) that are precursors in the synthesis of 1. These synthons will be used to tailor the electronic properties of metal complexes of 1 and derivatives thereof. The X-ray crystal structures of 19 and mono- and di-protonated forms of 1b show that the triamine crystalises in a boat–chair conformation which is undesirable for metal coordination. However, solution (1)H NMR studies show that in solution both 19 and the tetraalkylated derivative 1b are remarkably flexible. 1b reacted with [CuI(NCCH3)4](OTf) yielding a 1:1 copper(I) complex [CuI(NCCH3)(1b)](+). PMID:26488232

  7. Ligand Binding to Chlorite Dismutase from Magnetospirillum sp.

    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

  8. Electrophilic Metal Alkyl Chemistry in New Ligand Environments

    Jordan, Richard F. [University of Chicago

    2013-06-30

    The goals of this project were to design new electrophilic metal alkyl complexes and to exploit these systems in fundamental studies of olefin polymerization and other important and new catalytic reactions. A key target reaction is insertion copolymerization of olefins and polar CH2=CHX vinyl monomers such as vinyl halides and vinyl ethers. During the period covered by this report we (i) investigated the properties of ortho-alkoxy-arylphosphine ligands in Ni-based olefin polymerization catalysts, (ii) studied the synthesis of double-end-capped polyethylene using group 4 metal catalysts that contain tris-pyrazolylborate ligands, (iii) explored the ethylene insertion reactivity of group 4 metal tris-pyrazolyl-borate complexes, (iv) showed that (α-diimine)PdMe{sup +} species undergo multiple insertion of silyl vinyl ethers, (v) synthesized and explored the reactivity of base-free Ni benzyl complexes that contain ortho-phosphino-arene sulfonate ligands, (vi) established the mechanism of the reaction of vinyl chloride with (α-diimine)PdMe{sup +} catalysts, (vii) explored the role of cationic polymerization and insertion chemistry in the reactions of vinyl ethers with (α-diimine)PdMe{sup +} species, (viii) discovered a new class of self-assembled tetranuclear Pd catalysts that produce high molecular weight linear polyethylene and copolymerize ethylene and vinyl fluoride, and (ix) developed model systems that enabled investigation of cis-trans isomerization of {phosphine-sulfonate}Pd(II) complexes.

  9. 2 : 2 Fe(III): ligand and "adamantane core" 4 : 2 Fe(III): ligand (hydr)oxo complexes of an acyclic ditopic ligand

    Ghiladi, Morten; Larsen, Frank B.; McKenzie, Christine J.; Søtofte, Inger; Tuchagues, Jean-Pierre

    -ray structure of the dinuclear complex [{( Hbpbp) Fe(mu-OH)}(2)](ClO4)(4) center dot 2C(3)H(6)O ( 1 center dot 2C(3)H(6)O) shows that only one of the metal-binding cavities of each ligand is occupied by an iron( III) atom and two [Fe(Hbpbp)](3+) units are linked together by two hydroxo bridging groups to form a......A bis-hydroxo-bridged diiron(III) complex and a bis-mu-oxo-bis-mu-hydroxo-bridged tetrairon( III) complex are isolated from the reaction of 2,6-bis((N, N'-bis-(2-picolyl) amino) methyl)-4-tert-butylphenol (Hbpbp) with iron perchlorate in acidic and neutral solutions respectively. The X...... bond lengths of the two different octahedral iron sites: Fe -mu-OH, 1.953( 5), 2.013( 5) angstrom and Fe-mu-O, 1.803( 5), 1.802( 5) angstrom. The difference in ligand environment is too small for allowing Mossbauer spectroscopy to distinguish between the two crystallographically independent Fe sites...

  10. 125I-LSD: a high sensitivity ligand for serotonin receptors

    125I-labeled receptor ligands offer unique advantages over their 3H-labeled counterparts. Carrier-free 125I-labeled ligands can be synthesized with specific activities of up to 2170 Ci/mmol while (mono) tritium labeled ligands are limited to 29 Ci/mmol. Therefore, 125I-labeled ligands can be approximately 70-fold more sensitive than 3H-labeled ligands in detecting receptor sites. In addition, 125I-labeled ligands emit relatively energetic X-rays and γ-rays which are readily detected by gamma counting equipment. The authors report here the serotonergic binding properties of 125I-LSD the first reported 125I-labeled ligand for serotonin receptors. (Auth.)

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

    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.

  12. Design and Formation of a Large, Tetrahedral, Metal-ligand Cluster Using 1,1'-Binaphthyl Ligands

    Biros, Shannon M.; Yeh, Robert M.; Raymond, Kenneth N.

    2008-03-13

    Many chemists have been fascinated with the development of discrete supramolecular structures that encapsulate guest molecules. These structures can be assembled through covalent or hydrogen bonds, electrostatic or metal-ligand interactions. These host structures have provided valuable insight into the forces involved in small molecule recognition. Our work has focused on the design and study of metal-ligand clusters of varying sizes. The naphthalene [M{sub 4}L{sub 6}]{sup 12-} cluster 1, shown in Figure 1, has demonstrated diastereoselective guest binding and chiral induction properties as well as the ability to catalyze reactions carried out inside the cavity in an enzyme-like manner. However, the size of the cavity (ca. 300-500 {angstrom}{sup 3}) has often limited the scope of substrates for these transformations.

  13. Proton-dependent zinc release from intracellular ligands.

    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

  14. New functionalized β-diketiminate ligands and f elements

    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

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

    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

  16. Ligand fishing with functionalized magnetic nanoparticles coupled with mass spectrometry for herbal medicine analysis: Ligand fishing for herbal medicine analysis

    Qing, Lin-Sen; Xue, Ying; Deng, Wen-Long; Liao, Xun; Xu, Xue-Min; Li, Bo-Gang; Liu, Yi-Ming

    2010-01-01

    The chemical composition of herbal medicines is very complex, and their therapeutic effects are determined by multi-components with sophisticated synergistic and/or suppressive actions. Therefore, quality control of herbal medicines has been a formidable challenge. In this work, we describe a fast analytical method that can be used for quality assessment of herbal medicines. The method is based on ligand fishing using human-serum-albumin-functionalized magnetic nanoparticles (HSA-MNPs) and ma...

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

    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

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

    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.

  19. Elucidating ligand binding and channel gating mechanisms in pentameric ligand-gated ion channels by atomistic simulations.

    Comitani, Federico; Melis, Claudio; Molteni, Carla

    2015-04-01

    Pentameric ligand-gated ion channels (pLGICs) are important biomolecules that mediate fast synaptic transmission. Their malfunctions are linked to serious neuronal disorders and they are major pharmaceutical targets; in invertebrates, they are involved in insecticide resistance. The complexity of pLGICs and the limited crystallographic information available prevent a detailed understanding of how they function. State-of-the-art computational techniques are therefore crucial to build an accurate picture at the atomic level of the mechanisms which drive the activation of pLGICs, complementing the available experimental data. We have used a series of simulation methods, including homology modelling, ligand-protein docking, density functional theory, molecular dynamics and metadynamics, a powerful scheme for accelerating rare events, with the guidance of mutagenesis electrophysiology experiments, to explore ligand-binding mechanisms, the effects of mutations and the potential role of a proline molecular switch for the gating of the ion channels. Results for the insect RDL receptor, the GABAC receptor, the 5-HT3 receptor and the nicotinic acetylcholine receptor will be reviewed. PMID:25849909

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

    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.

  1. A Protein Data Bank survey reveals shortening of intermolecular hydrogen bonds in ligand-protein complexes when a halogenated ligand is an H-bond donor.

    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.

  2. Metal nanoparticles functionalized with metal-ligand covalent bonds

    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

  3. Six-coordinate uranium complexes featuring a bidentate anilide ligand

    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)

  4. Natural compounds in the synthesis of chiral organophosphorous ligands

    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.

  5. Natural compounds in the synthesis of chiral organophosphorous ligands

    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.

  6. Programmed cell death 1 ligand 1 expression in osteosarcoma

    Shen, Jacson K.; Cote, Gregory M.; Choy, Edwin; Yang, Pei; Harmon, David; Schwab, Joseph; Nielsen, G. Petur; Chebib, Ivan; Ferrone, Soldano; Wang, Xinhui; Wang, Yangyang; Mankin, Henry; Francis J. Hornicek; Duan, Zhenfeng

    2014-01-01

    Programmed cell death 1 ligand 1 (PD-L1, B7H1) is a cell-surface protein that suppresses the cytotoxic CD8+ T cell-mediated immune response. PD-L1 expression and its clinical relevance in sarcomas are not well understood. Therefore, we sought to measure RNA expression levels for PD-L1 in 38 clinically annotated osteosarcoma tumor samples, and aimed to determine if PD-L1 expression correlates with clinical features and tumor-infiltrating T-lymphocytes (TILs). Quantitative real-time RT-PCR for ...

  7. Hypoxic regulation of the NKG2D ligand, H60

    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...

  8. Engineering periplasmic ligand binding proteins as glucose nanosensors

    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.

  9. FES kinase participates in KIT-ligand induced chemotaxis

    Voisset, Edwige, E-mail: Edwige.Voisset@inserm.fr [INSERM U891, Centre de Recherche en Cancerologie de Marseille (CRCM) (France); Institut Paoli-Calmettes, Marseille (France); Universite de la Mediterranee, Aix-Marseille II (France); Lopez, Sophie, E-mail: Sophie.Lopez@inserm.fr [INSERM U891, Centre de Recherche en Cancerologie de Marseille (CRCM) (France); Institut Paoli-Calmettes, Marseille (France); Universite de la Mediterranee, Aix-Marseille II (France); Chaix, Amandine, E-mail: Amandine.Chaix@inserm.fr [INSERM U891, Centre de Recherche en Cancerologie de Marseille (CRCM) (France); Institut Paoli-Calmettes, Marseille (France); Universite de la Mediterranee, Aix-Marseille II (France); Vita, Marina, E-mail: Marina.Vita@inserm.fr [INSERM U891, Centre de Recherche en Cancerologie de Marseille (CRCM) (France); Institut Paoli-Calmettes, Marseille (France); Universite de la Mediterranee, Aix-Marseille II (France); George, Coralie, E-mail: Coralie.Georges@inserm.fr [INSERM U891, Centre de Recherche en Cancerologie de Marseille (CRCM) (France); Institut Paoli-Calmettes, Marseille (France); Universite de la Mediterranee, Aix-Marseille II (France); Dubreuil, Patrice, E-mail: Patrice.Dubreuil@inserm.fr [INSERM U891, Centre de Recherche en Cancerologie de Marseille (CRCM) (France); Institut Paoli-Calmettes, Marseille (France); Universite de la Mediterranee, Aix-Marseille II (France); De Sepulveda, Paulo, E-mail: Sepulveda@inserm.fr [INSERM U891, Centre de Recherche en Cancerologie de Marseille (CRCM) (France); Institut Paoli-Calmettes, Marseille (France); Universite de la Mediterranee, Aix-Marseille II (France)

    2010-02-26

    FES is a cytoplasmic tyrosine kinase activated by several membrane receptors, originally identified as a viral oncogene product. We have recently identified FES as a crucial effector of oncogenic KIT mutant receptor. However, FES implication in wild-type KIT receptor function was not addressed. We report here that FES interacts with KIT and is phosphorylated following activation by its ligand SCF. Unlike in the context of oncogenic KIT mutant, FES is not involved in wild-type KIT proliferation signal, or in cell adhesion. Instead, FES is required for SCF-induced chemotaxis. In conclusion, FES kinase is a mediator of wild-type KIT signalling implicated in cell migration.

  10. Ligands specify estrogen receptor alpha nuclear localization and degradation

    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

  11. Novel types of tripodal CMPO ligands: synthesis and extraction

    Novel tripodal CMPO ligands having either aryl groups at the N-atom or alkyl groups at the CMPO methylene bridge were prepared in good yields. In the latter case one alkyl group per CMPO moiety was selectively introduced. Extraction studies with Am3+ and Eu3+ show that there is an influence of the electronic character of the aryl groups on the extraction. Alkylation of the CMPO methylene group gives rise to a considerable decrease of the D-values (about 100-1000 times), dependent on the bulkiness of the alkyl substituent. (orig.)

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

    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

  13. Ligand-protected gold clusters: the structure, synthesis and applications

    Pichugina, D. A.; Kuz'menko, N. E.; Shestakov, A. F.

    2015-11-01

    Modern concepts of the structure and properties of atomic gold clusters protected by thiolate, selenolate, phosphine and phenylacetylene ligands are analyzed. Within the framework of the superatom theory, the 'divide and protect' approach and the structure rule, the stability and composition of a cluster are determined by the structure of the cluster core, the type of ligands and the total number of valence electrons. Methods of selective synthesis of gold clusters in solution and on the surface of inorganic composites based, in particular, on the reaction of Aun with RS, RSe, PhC≡C, Hal ligands or functional groups of proteins, on stabilization of clusters in cavities of the α-, β and γ-cyclodextrin molecules (Au15 and Au25) and on anchorage to a support surface (Au25/SiO2, Au20/C, Au10/FeOx) are reviewed. Problems in this field are also discussed. Among the methods for cluster structure prediction, particular attention is given to the theoretical approaches based on the density functional theory (DFT). The structures of a number of synthesized clusters are described using the results obtained by X-ray diffraction analysis and DFT calculations. A possible mechanism of formation of the SR(AuSR)n 'staple' units in the cluster shell is proposed. The structure and properties of bimetallic clusters MxAunLm (M=Pd, Pt, Ag, Cu) are discussed. The Pd or Pt atom is located at the centre of the cluster, whereas Ag and Cu atoms form bimetallic compounds in which the heteroatom is located on the surface of the cluster core or in the 'staple' units. The optical properties, fluorescence and luminescence of ligand-protected gold clusters originate from the quantum effects of the Au atoms in the cluster core and in the oligomeric SR(AuSR)x units in the cluster shell. Homogeneous and heterogeneous reactions catalyzed by atomic gold clusters are discussed in the context of the reaction mechanism and the nature of the active sites. The bibliography includes 345 references.

  14. Ultrafast infrared studies of complex ligand rearrangements in solution

    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

  15. Ligand-directed profiling of organelles with internalizing phage libraries

    Dobroff, Andrey S.; Rangel, Roberto; Guzman-Roja, Liliana; Salmeron, Carolina C.; Gelovani, Juri G.; Sidman, Richard L.; Bologa, Cristian G.; Oprea, Tudor I.; Brinker, C. Jeffrey; Pasqualini, Renata; Arap, Wadih

    2015-01-01

    Phage display is a resourceful tool to, in an unbiased manner, discover and characterize functional protein-protein interactions, to create vaccines, and to engineer peptides, antibodies, and other proteins as targeted diagnostic and/or therapeutic agents. Recently, our group has developed a new class of internalizing phage (iPhage) for ligand-directed targeting of organelles and/or to identify molecular pathways within live cells. This unique technology is suitable for applications ranging from fundamental cell biology to drug development. Here we describe the method for generating and screening the iPhage display system, and explain how to select and validate candidate internalizing homing peptide. PMID:25640897

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

    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...

  17. Doping Control Via Molecularly Engineered Surface Ligand Coordination

    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.

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

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

    2012-01-01

    commonly used capture step in mAb down stream processing; however, the use of Protein A chromatography is less attractive due to toxic ligand leakage as well as high cost. Whether used as an alternative to the Protein A chromatographic media or as a subsequent polishing step, small synthetic peptide...... the interaction is favorable and entropy-driven with an enthalpy penalty. Our results show that the binding of the Fc fragment of IgG is mediated by hydrophobic interactions and that elution at low pH is most likely due to electrostatic repulsion. Furthermore, we have separated aggregated IgG from non...

  19. Overview of Stabilizing Ligands for Biocompatible Quantum Dot Nanocrystals

    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.

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

    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

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

    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.

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

    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.

  3. Redox potential parameterization in coordination compounds with polydentate scorpionate and benzene ligands

    The Lever redox potential parameterization model is extended to half-sandwich type complexes bearing polydentate boron-based or carbon-based scorpionate-type or π-aromatic (benzene or p-cymene) ligands, allowing to estimate the electrochemical EL ligand parameter of a diversity of such polytopal ligands which, thus, are ordered according to their electron-donor character and compared with other ligands. Partial EL values assigned to each metal ligated arm (2-electron-donor) of the scorpionate ligand (i.e., pyrazolyl, indazolyl or carboxylate groups) and to each unsaturated C=C moiety of π-benzene (or π-p-cymene) are also proposed. The studied scorpionate ligands comprise the following basic ones and derivatives: tris(pyrazol-1-yl or indazol-1-yl)borate, tris(pyrazol-1-yl)methane and bis(pyrazol-1-yl)acetic acid.

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

    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

  5. Targeting Protein-Protein Interactions with Trimeric Ligands: High Affinity Inhibitors of the MAGUK Protein Family

    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...

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

    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

  7. New perspectives regarding β2-adrenoceptor ligands in the treatment of asthma

    Walker, JKL; Penn, RB; Hanania, NA; Dickey, BF; Bond, RA

    2011-01-01

    In the last two decades several significant changes have been proposed in the receptor theory that describes how ligands can interact with G protein-coupled receptors (GPCRs). Here we briefly summarize the evolution of receptor theory and detail recent prominent advances. These include: (i) the existence of spontaneously active GPCRs that are capable of signalling even though they are unoccupied by any ligand; (ii) the discovery of ligands that can inactivate these spontaneously active recept...

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

    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.

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

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

    2002-01-01

    is regulated by mechanisms distinct from those involved in constitutive internalization, whereas other studies have suggested that the ligand-induced TCR internalization pathway is identical with the constitutive pathway. To resolve this question, we first identified requirements for constitutive TCR...... ligand-induced internalization of the TCR. In conclusion, ligand-induced TCR internalization and constitutive cycling of the TCR represents two independent pathways regulated by different mechanisms....

  10. Epithelial Wnt ligand secretion is required for adult hair follicle growth and regeneration

    Myung, Peggy; Takeo, Makoto; Ito, Mayumi; Atit, Radhika

    2012-01-01

    β-catenin, a key transducer molecule of Wnt signaling, is required for adult hair follicle growth and regeneration. However, the cellular source of Wnt ligands required for Wnt/β-catenin activation during anagen induction is unknown. In this study, we genetically deleted Wntless, a gene required for Wnt ligand secretion by Wnt-producing cells, specifically in the hair follicle epithelium during telogen phase. We show that epithelial Wnt ligands are required for anagen, as loss of Wntless in t...

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

    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.

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

    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

  13. Novel Suicide Ligands of Tubulin Arrest Cancer Cells in S-Phase

    Ashley Davis; Jian-Dong Jiang; Middleton, Kim M; Yue Wang; Imre Weisz; Yi-He Ling; J. George Bekesi

    1999-01-01

    It is presently accepted that the mechanism of action for all anti-tumor tubulin ligands involves the perturbation of microtubule dynamics during the G2/M phase of cell division and subsequent entry into apoptosis 1]. In this report, we challenge the established dogma by describing a unique mechanism of action caused by a novel series of tubulin ligands, halogenated derivatives of acetamido benzoyl ethyl ester. We have developed a suicide ligand for tubulin, which covalently attaches to the t...

  14. Novel Suicide Ligands of Tubulin Arrest Cancer Cells in S-Phase1

    Davis, Ashley; Jiang, Jian-Dong; Middleton, Kim M; Wang, Yue; Weisz, Imre; Ling, Yi-He; Bekesi, J George

    1999-01-01

    It is presently accepted that the mechanism of action for all anti-tumor tubulin ligands involves the perturbation of microtubule dynamics during the G2/M phase of cell division and subsequent entry into apoptosis [1]. In this report, we challenge the established dogma by describing a unique mechanism of action caused by a novel series of tubulin ligands, halogenated derivatives of acetamido benzoyl ethyl ester. We have developed a suicide ligand for tubulin, which covalently attaches to the ...

  15. New chiral ligands in asymmetric catalysis. Application in stabilization of metal nanoparticles

    Axet Martí, M. Rosa

    2006-01-01

    Thesis M. Rosa AxetThis thesis deals with the development and application of diphosphite ligands derived from carbohydrates to rhodium-catalysed asymmetric hydroformylation and hydrogenation reactions. The use of various carbohydrate derivative ligands as stabilisers of metal nanoparticles is also studied. The synthesis and the characterisation of the series of diphosphite ligands are described in Chapter 2. The results of the asymmetric hydroformylation of styrene and related vinyl arenes ar...

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

    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

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

    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 ...

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

    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 ...

  19. Geometric filters for protein–ligand complexes based on phenomenological molecular models

    Sudakov O. O.; Balinskyi O. M.; Platonov M. O.; Kovalskyy D. B.

    2013-01-01

    Molecular docking is a widely used method of computer-aided drug design capable of accurate prediction of protein-ligand complex conformations. However, scoring functions used to estimate free energy of binding still lack accuracy. Aim. Development of computationally simple and rapid algorithms for ranking ligands based on docking results. Methods. Computational filters utilizing geometry of protein-ligand complex were designed. Efficiency of the filters was verified in a cross-docking study ...

  20. IDENTIFICATION OF VDR ANTAGONISTS AMONG NUCLEAR RECEPTOR LIGANDS USING VIRTUAL SCREENING

    Kelly Teske; Premchendar Nandhikonda; Bogart, Jonathan W.; Belaynesh Feleke; Preetpal Sidhu; Yuan, Nina Y.; Joshua Preston; Robin Goy; Lanlan Han; Silvaggi, Nicholas R; Singh, Rakesh K.; Bikle, Daniel D.; Cook, James M.; Arnold, Leggy A.

    2014-01-01

    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 ...

  1. A review of monoamine transporter-ligand interactions.

    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

  2. Modeling of ligand binding to dopamine D2 receptor

    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.

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

    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

  4. Ligand exchange in gold-coated FePt nanoparticles

    de la Presa, P; Morales, M P; Hernando, A; 10.1109/TMAG.2008.2002251

    2009-01-01

    In this work we present the magnetic properties of gold coated FePt nanoparticles and the study of stable aqueous dispersions of FePt@Au and FePt synthesized after ligand exchange with mercaptoundecanoic acid. The particle size determined from TEM micrographs goes from 4 nm for the uncoated nanoparticles to a maximum of 10 nm for the gold coated ones indicating that the thickness of the shell ranges from 1 to 3 nm. The magnetic characterization consists in hysteresis cycles at 10 and 300 K. The results show that, at low field and room temperature, the magnetic behavior of uncoated and coated nanoparticles are surprisingly quite similar. Since the gold coated nanoparticles keep the magnetic properties of FePt and the presence of gold improves the functionalization of nanoparticles, the system is suitable for biological application. Mercaptoundecanoic ligand transfer was used to render water stable nanoparticles in a wide pH range. Transmission electron microscopy and dynamic light scattering results show the n...

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

    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

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

    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.

  7. Organic ligands influence leaching kinetics of fixated FGD material

    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.

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

    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

  9. Characterization of Selectin Ligands on Hematopoietic Stem Cells

    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.

  10. Oxytocin receptor ligands induce changes in cytoskeleton in neuroblastoma cells.

    Bakos, Jan; Strbak, Vladimir; Paulikova, Helena; Krajnakova, Lucia; Lestanova, Zuzana; Bacova, Zuzana

    2013-07-01

    Aim of the present study was to evaluate effects of ligands of oxytocin receptors on gene expression of neurofilament proteins (nestin and microtubule-associated protein 2 (MAP2)) associated with neuronal differentiation and growth factors (brain-derived neurotrophic factor (BDNF) and nerve growth factor (NGF)) related to neuronal growth. Fluorescent staining of F-actin was used to observe morphology of cells. Co-treatment with oxytocin and oxytocin receptor antagonist--atosiban--resulted in significant increase of MAP2 gene expression in SK-N-SH cells. There was no effect of oxytocin on gene expression of growth factors BDNF and NGF. Surprisingly, oxytocin with atosiban significantly increased mRNA levels for both BDNF and NGF. Gene expression of vasopressin receptor (V1aR) significantly decreased in response to vasopressin. Atosiban decreased mRNA levels for oxytocin receptor (OXTR) and V1aR. Oxytocin significantly decreased OXTR and nestin mRNA levels and increased mRNA levels for BDNF and NGF in U-87 MG cells. The densest recruitment of F-actin filaments was observed in apical parts of filopodia in SK-N-SH cells incubated in oxytocin presence. Present data demonstrate complex role of ligands of oxytocin receptors in regulation of gene expression of intermediate filaments and thus, oxytocin might be considered as a growth factor in neuronal type of cells. PMID:23335033

  11. Cherry-picked ligands at histamine receptor subtypes.

    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

  12. Lipid A binding proteins in macrophages detected by ligand blotting

    Endotoxin (LPS) stimulates a variety of eukaryotic cells. These actions are involved in the pathogenesis of Gram-negative septicemia. The site of action of the LPS toxic moiety, lipid A (LA), is unclear. Their laboratory has previously identified a bioactive LA precursor lipid IV/sub A/, which can be enzymatically labeled with 32P/sub i/ (109 dpm/nmole) and purified (99%). They now show that this ligand binds to specific proteins immobilized on nitrocellulose (NC) from LPS-sensitive RAW 264.7 cultured macrophages. NC blots were incubated with [32P]-IV/sub A/ in a buffer containing BSA, NaCl, polyethylene glycol, and azide. Binding was assessed using autoradiography or scintillation counting. Dot blot binding of the radioligand was inhibited by excess cold IV/sub A/, LA, or ReLPS but not by phosphatidylcholine, cardiolipin, phosphatidylinositol, or phosphatidic acid. Binding was trypsin-sensitive and dependent on protein concentration. Particulate macrophage proteins were subjected to SDS-PAGE and then electroblotted onto NC. Several discrete binding proteins were observed. Identical treatment of fetal bovine serum or molecular weight standards revealed no detectable binding. By avoiding high nonspecific binding of intact membranes, this ligand blotting assay may be useful in elucidating the molecular actions of LPS

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

    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

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

    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

  15. Exploring Hydrophobic Binding Surfaces Using Comfa and Flexible Hydrophobic Ligands

    Thakkar, Shraddha; Sanchez, Rosa. I.; Bhuveneswaran, Chidambaram; Compadre, Cesar M.

    2011-06-01

    Cysteine proteinases are a very important group of enzymes involved in a variety of physiological and pathological processes including cancer metastasis and rheumatoid arthritis. In this investigation we used 3D-Quantitative Structure Activity Relationships (3D-QSAR) techniques to model the binding of a variety of substrates to two cysteine proteinases, papain, and cathepsin B. The analysis was performed using Comparative Molecular Field Analysis (CoMFA). The molecules were constructed using standard bond angles and lengths, minimized and aligned. Charges were calculated using the PM3 method in MOPAC. The CoMFA models derived for the binding of the studied substrates to the two proteinases were compared with the expected results from the experimental X-ray crystal structures of the same proteinases. The results showed the value of CoMFA modeling of flexible hydrophobic ligands to analyze ligand binding to protein receptors, and could also serve as the basis to design specific inhibitors of cysteine proteinases with potential therapeutic value.

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

    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. 01-ERD-111 - The Development of Synthetic High Affinity Ligands

    Perkins, J; Balhorn, R; Cosman, M; Lightstone, F; Zeller, L

    2004-02-05

    The aim of this project was to develop Synthetic High-Affinity Ligands (SHALs), which bind with high affinity and specificity to proteins of interest for national security and cancer therapy applications. The aim of producing synthetic ligands for sensory devices as an alternative to antibody-based detection assays and therapeutic agents is to overcome the drawbacks associated with antibody-based in next-generation sensors and systems. The focus area of the project was the chemical synthesis of the SHALs. The project concentrated on two different protein targets. (a) The C fragment of tetanus and botulinum toxin, potential biowarfare agents. A SHAL for tetanus or botulinum toxin would be incorporated into a sensory device for the toxins. (b) HLA-DR10, a protein found in high abundance on the surface of Non-Hodgkins Lymphoma. A SHAL specific to a tumor marker, labeled with a radionuclide, would enable the targeted delivery of radiation therapy to metastatic disease. The technical approach used to develop a SHAL for each protein target will be described in more detail below. However, in general, the development of a SHAL requires a combination of computational modeling techniques, modern nuclear magnetic resonance spectroscopy (NMR) and synthetic chemistry.

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

    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

  19. 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

    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

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

    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 ...

  1. THE STUDY OF ORIENTATION OF AXIAL AMINO-LIGANDS IN SOME Co(III DIOXIMATES

    Andrei Rija

    2013-12-01

    Full Text Available As a result of the comparative study of axial ligand orientation towards the equatorial plane in α - dioximates Co (III obtained by us and those described in the specialized literature (found in Cambridge Crystallographic Data Centre showed that the external anions and solvent molecules contribute to the orientation of axial ligands as selenourea and thiourea. For aniline and sulphanilamide ligands, is more convenient the parallel orientation to form π-π interactions between the aromatic rings of ligands and the metallocycle of equatorial plane.

  2. Modulation of keratinocyte gene expression and differentiation by PPAR-selective ligands and tetradecylthioacetic acid

    Westergaard, M; Henningsen, J; Svendsen, M L; Johansen, C; Jensen, Uffe Birk; Schrøder, H D; Kratchmarova - Blagoeva, Irina H; Berge, R K; Iversen, L; Bolund, L; Kragballe, K; Kristiansen, K

    2001-01-01

    nuclear receptor corepressor and silence mediator for retinoid and thyroid hormone receptors. We critically evaluated the effects of selective PPAR ligands and a synthetic fatty acid analog, tetradecylthioacetic acid. Tetradecylthioacetic acid activated all human PPAR subtypes in the ranking order...... PPARdelta >> PPARalpha > PPARgamma. All selective PPAR ligands marginally induced transglutaminase-1 expression with the PPARdelta-selective ligand L165041 being the most potent. The PPARalpha- and PPARgamma-selective ligands Wy14643 and BRL49653 had negligible effect on involucrin expression, whereas a...

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

    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.

  4. Single-Molecule Analysis of Human Telomere Sequence Interactions with G-quadruplex Ligand.

    Zhang, Ling; Zhang, Kaixiang; Rauf, Sana; Dong, Duo; Liu, Yang; Li, Jinghong

    2016-04-19

    Ligands that selectively promote the formation of G-quadruplexes in human telomeres have great potential for cancer treatment by inhibiting the telomere extension by telomerase. Thus, understanding the interactions of the G-quadruplex ligands with the telomere sequence at the single-molecule level is of significant importance. Here, human telomere sequence interactions with a small molecule ligand pyridostatin (PDS) were analyzed via α-hemolysin protein nanopore, and a nanopore thermodynamic analytical method was proposed. The prolonged unraveling time of the telomeric DNA G-quadruplex after PDS binding demonstrated the potent stabilization effect of ligand on G-quadruplex structure. The signature two-level electronic blocks generated by K(+)-PDS-G-quadruplex complexes suggested a two-state unraveling process, including the dissociation of the interquartet cation and the unraveling of the cation-free ligand-bound G-quadruplex. The translocation studies and the analysis of free-energy changes demonstrated a ligand-binding mode in which PDS molecule and K(+) were simultaneously bound to one G-quadruplex structure with the coordinated effect on G-quadruplex stabilization. The single-molecular nanopore platform permits the efficient and accurate determination of ligand affinity constants without the requirement for labeling, amplification, or ligand/receptor titration, which provides a general analytical tool for effectively monitoring and quantifying the G-quadruplex/ligand interactions, possessing important implications for the design and screen of anticancer drugs. PMID:27012789

  5. Nonsteroidal Bivalent Estrogen Ligands - An Application of the Bivalent Concept to the Estrogen Receptor

    Shan, Min; Carlson, Kathryn E.; Bujotzek, Alexander; Wellner, Anja; Gust, Ronald; Weber, Marcus; Katzenellenbogen, John A.; Haag, Rainer

    2013-01-01

    The estrogen receptor (ER) is a hormone-regulated transcription factor that binds, as a dimer, to estrogens and to specific DNA sequences. To explore at a fundamental level the geometric and topological features of bivalent-ligand binding to the ER dimer, dimeric ER crystal structures were used to rationally design nonsteroidal bivalent estrogen ligands. Guided by this structure-based ligand design, we prepared two series of bivalent ligands (agonists and antagonists) tethered by flexible spacers of varying lengths (7–47Å) and evaluated their ER-binding affinities for the two ER subtypes and their biological activities in cell lines. Bivalent ligands based on the agonist diethylstilbestrol (DES) proved to be poor candidates, but bivalent ligands based on the antagonist hydroxytamoxifen (OHT) were well suited for intensive study. Binding affinities of the OHT-based bivalent ligands were related to spacer length in a distinctive fashion, reaching two maximum values at 14 and 29Å in both ER subtypes. These results demonstrate that the bivalent concept can operate in determining ER-ligand binding affinity and suggest that two distinct modes operate for the binding of bivalent estrogen ligands to the ER dimers, an intermolecular as well as an intramolecular mode. Our insights, particularly the possibility of intramolecular bivalent binding on a single ER monomer, may provide an alternative strategy to prepare more selective and active ER antagonists for endocrine therapy of breast cancer. PMID:23312071

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

    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.

  7. Proton NMR studies of aliphatic ligand binding to human plasminogen kringle 4

    A detailed 1H NMR analysis of ligand binding to the human plasminogen kringle 4 domain has been carried out at 300 MHz. The ligands that were investigated are Nα-acetyl-L-lysine, L-lysine methyl ester, Nα-acetyl-L-lysine methyl ester, L-lysine hydroxamic acid, trans-(aminomethyl)cyclohexanecarboxylic acid (AMCHA), and 4-(aminomethyl)bicyclo[2.2.2]octane-1-carboxylic acid (AMBOC). Specific ligand-binding effects were detected via two-dimensional COSY experiments. The side chains that are the most perturbed by ligand presence are those from Trp62, Phe64, and Trp72. Ligand-kringle saturation transfer (Overhauser) experiments show that the aromatic rings from these three residues are in direct contact with the ligand. These results add support to a previously reported model of the kringle 4 lysine-binding site by which these aromatic groups are assigned a key role in establishing hydrophobic interactions with the ligand molecule. Equilibrium association constants (Ka) and kinetic rate constants (kon, koff) were determined for the binding of the various linear and cyclic ligands to kringle 4. The numerical data are discussed in terms of optimal ligand structure and requirements for fibrin binding in vivo

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

    Benkhäuser, Christian; Lützen, Arne

    2015-01-01

    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. PMID:26124873

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

    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

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

    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.

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

    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.

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

    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).

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

    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.

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

    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.

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

    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.

  16. Abundance of Flt3 and its ligand in astrocytic tumors

    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

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

    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.

  18. High Linear Energy Transfer Radiolysis of Solvent Extraction Ligands

    Pearson, Jeremy David

    The response to high linear energy transfer (LET) radiation of a variety of aqueous systems such as biological systems and the Fricke dosimeter has frequently been studied in the literature. Linear energy transfer is a unique property of radiation which describes the special distribution with which energy from radiation is deposited and concentrated as it travels through matter and can have implications on degradation within the matter itself. The four types of ionizing radiation alpha, beta, gamma, and neutrons have different LET, classified from low for gamma and beta, to high for alpha. All types of ionizing radiation are encountered in used nuclear fuel. This radiation induces damage to solvent extraction processes designed to recycle used nuclear fuel which results in impaired selectivity and reduced process efficiencies. While the effects of low LET radiation on organic solutions have been widely studied, the effects of high LET radiation have not due to difficulties in studying this type of radiation such as short radiation path lengths on the order of 50 mum. This study investigates the effects of high LET radiation deposited in situ from fission products lithium and helium emitted in the 10B(n,alpha)7Li reaction. The reaction, studied previously in aqueous systems, is applied here to organic solvents containing ligands used in solvent extraction. Ligands studied were TBP, CMPO, and TODGA utilized in the PUREX and TRUEX processes. Results demonstrate that high LET radiation has the tendency to reduce degradation to the parent compound due to reactive products being consumed within the radiation track, while encouraging secondary degradation products to occur within the radiation track. Products of these secondary degradation reactions may be more detrimental to the solvent extraction process than primary degradation products and are therefore important to understand and monitor. Results also demonstrate the utility of using the 10B(n,alpha) 7Li reaction to

  19. Transport regulation of two-dimensional receptor-ligand association.

    Ju, Lining; Qian, Jin; Zhu, Cheng

    2015-04-01

    The impact of flow disturbances on platelet adhesion is complex and incompletely understood. At the molecular scale, platelet glycoprotein Ibα (GPIbα) must associate with the von Willebrand factor A1 domain (VWF-A1) with a rapid on-rate under high hemodynamic forces, as occurs in arterial thrombosis, where various transport mechanisms are at work. Here, we theoretically modeled the coupled transport-reaction process of the two-dimensional (2D) receptor-ligand association kinetics in a biomembrane force probe to explicitly account for the effects of molecular length, confinement stiffness, medium viscosity, surface curvature, and separation distance. We experimentally verified the theoretical approach by visualizing association and dissociation of individual VWF-A1-GPIbα bonds in a real-time thermal fluctuation assay. The apparent on-rate, reciprocal of the average time intervals between sequential bonds, decreased with the increasing gap distance between A1- and GPIbα-bearing surfaces with an 80-nm threshold (beyond which bond formation became prohibitive) identified as the combined contour length of the receptor and ligand molecules. The biomembrane force probe spring constant and diffusivity of the protein-bearing beads also significantly influenced the apparent on-rate, in accordance with the proposed transport mechanisms. The global agreement between the experimental data and the model predictions supports the hypothesis that receptor-ligand association behaves distinctly in the transport- and reaction-limited scenarios. To our knowledge, our results represent the first detailed quantification of physical regulation of the 2D on-rate that allows platelets to sense and respond to local changes in their hemodynamic environment. In addition, they provide an approach for determining the intrinsic kinetic parameters that employs simultaneous experimental measurements and theoretical modeling of bond association in a single assay. The 2D intrinsic forward rate

  20. Ligand Binding and Substrate Discrimination by UDP-Galactopyranose Mutase

    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

  1. Coordination chemistry of lanthanides(III) ions with oxygen nitrogen tripodal ligands

    This work aims at demonstrating the great potentialities of flexible tripodal ligands in various fields of applications of the coordination chemistry of lanthanide(III) ions. The coordination properties of different tripodal ligands with Ln(III) ions are reported. The ligand trenphen acts as a nona-dentate ligand for the Ln(III) ions independently to the ion size. The solid-state crystal structure and the rigid solution structure of the isostructural [Ln(trenphen)](OTt)3 complexes have been determined. Solvent extraction studies of lanthanides(III) and actinides(III) shows that the ligand trenphen is a selective complexant of actinides(III), thus confirming the interest of tripodal ligand containing soft nitrogen atoms for the selective extraction of actinides(III). The high number of coordination sites and the likely presence of interstrand interactions in the potentially dodeca-dentate ligand trenterpy prevent the formation of mononuclear complexes. In presence of lanthanum triflate, this ligand leads to the self-assembly of a discrete trinuclear complex. The use of tripodal ligands is a possible way to generate polynuclear arrays. We also report the synthesis and the structural properties of the Ln(III) complexes of the hepta-dentate ligand tpaa. Three types of crystal structures have been found for these complexes along the series which differ in their nuclearity and in the coordination number of the metal (10, 9 and 8). This flexible podate leads to a Gd complex with a relaxivity remarkably higher than those of the currently used contrast agents for MRI based on complexes of octa-dentate ligands. A shorter water proton-Gd(III) bond distance associated with a probable water coordination equilibrium appear to be at the origin of the high relaxivity of the Gd complex. This complex also displays a fast exchange rate of the coordinated water. Renee, the use of carefully tailored podates could prove to be a very efficient way to achieve optimized relaxivity

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

    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.

  3. Preparation, Spectroscopic Investigation and Biological Activity of New Mixed Ligand Chelates

    Preparation and investigation of new Co(II), Ni(II), Zn(II) and Cr(III) chelates with mixed ligands including Schiff base (L1) formed from the condensation of 4-dimethylaminobenzaldehyde with 2-aminophenol and anthranilic acid (L2) were studied. The obtained Schiff base and mixed ligand chelates were subjected to several physiochemical techniques, in terms of CHN elemental analyses, molar conductivity, magnetic moment measurements, infrared, proton nuclear magnetic resonance, electronic and mass spectra. The analytical data showed the formation of the Schiff base compound and the ratio of metal to ligands of the chelates are 1:1:1(M:L1:L2). The infrared spectral data exhibited that the used ligands behaving as bidentate ligands towards the metal ions. The proton nuclear magnetic resonance spectral data showed the signals of the active groups in the ligands which entered in chelation with Zn(II) metal ion. The electronic spectral results showed the existence of pie (phenyl ring) and n = pie (C=N) of the ligands and suggested the geometrical structures of the chelates. Meanwhile, the mass spectral data revealed the fragmentations of the Schiff base, anthranilic acid and their Ni(II) mixed ligand chelate has been preformed the only chelate conducted for justification. All the prepared mixed chelates were non-electrolyte in nature. The antibacterial activity of the Schiff base, anthranilic acid, metal salts and mixed ligand chelates were studied and found to be that mixed ligand chelates have the most biological activity in comparison to the free ligands and salts. (author)

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

    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

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

    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

  6. Architecture effects on multivalent interactions by polypeptide-based multivalent ligands

    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

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

    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)

  8. Halogenated benzamides as ligands for cerebral dopamine receptors

    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

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

    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

  10. Characteristics of Tau and Its Ligands in PET Imaging

    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.

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

    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

  12. Selection of Genetic engineering peptide ligands for TNF receptor imaging

    Objective: To screen the peptide ligands of TNF receptor from phage 6-mer peptide library with the purpose of developing new peptides radiopharmaceuticals for TNF receptor imaging. Methods: The soluble protein of TNF receptor I (sTNFR I) was used to screen the TNF-specific epitopes from phage 6-mer peptide library. After four rounds of affinity screening, the peptides displayed on the selected phage were directly subjected to ELISA to determine their immunological activity to sTNFR. The amino acid sequences of the peptides with highest immunological activity were deduced through DNA sequencing. And their conserved sequences were further determined. Results: Peptides sequences mimicking TNF-specific epitopes were obtained. Conclusion: The short peptides sequences mimicking TNF -specific epitopes were successfully acquired. The method which was established in the present study may provide a feasible way in peptides radiopharmaceuticals development for TNF receptor imaging. (authors)

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

    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

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

    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.

  15. 3-Substituted phenylalanines as selective AMPA- and kainate receptor ligands

    Szymanska, Ewa; Pickering, Darryl S; Nielsen, Birgitte;

    2009-01-01

    On the basis of X-ray structures of ionotropic glutamate receptor constructs in complex with amino acid-based AMPA and kainate receptor antagonists, a series of rigid as well as flexible biaromatic alanine derivatives carrying selected hydrogen bond acceptors and donors have been synthesized in...... order to investigate the structural determinants for receptor selectivity between AMPA and the GluR5 subtype of kainate receptors. Compounds selective for either GluR5 or AMPA receptors were identified. One particular substituent position appeared to be of special importance for control of ligand...... selectivity. Using molecular modeling the observed structure-activity relationships at AMPA and GluR5 receptors were deduced....

  16. Structural basis for AMPA receptor activation and ligand selectivity

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

    2002-01-01

    structures reveal that AMPA agonists with an isoxazole moiety adopt different binding modes in the receptor, dependent on the substituents of the isoxazole. Br-HIBO displays selectivity among different AMPA receptor subunits, and the design and structure determination of the S1S2J-Y702F mutant in complex...... with Br-HIBO and ACPA have allowed us to explain the molecular mechanism behind this selectivity and to identify key residues for ligand recognition. The agonists induce the same degree of domain closure as AMPA, except for Br-HIBO, which shows a slightly lower degree of domain closure. An excellent...... the functional studies on the full-length receptor, form a powerful platform for the design of new selective agonists....

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

    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...

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

    Drachmann, Nikolaj Düring

    2015-01-01

    a from pig hearts is presented. The purified protein was used for X-ray crystallographic studies aiming at determining the three dimensional structure of the SERCA2a isoform in a Ca2+-free conformation. Crystals of the Ca2+ free state of SERCA2a stabilised by the inhibitor cyclopiazonic acid was...... obtained and a dataset was collected scaling to 3.26 Å resolution, allowing a preliminary structural analysis. The overall crystal structure is very similar to SERCA1a. Additionally, co-crystallisation studies have been initiated of SERCA2a and recombinantly expressed Phospholamban. Besides the above...... resolution of the proof-of-concept Ca2+ bound crystal form, indicated that the information content of SFX data is higher than synchrotron data, and ligands and ions can be detected with low redundant data. The data of the E2 stabilised form was processed to 5 Å resolution, and it was possible to extract...

  19. Structure and function of Toll receptors and their ligands.

    Gay, Nicholas J; Gangloff, Monique

    2007-01-01

    The Toll family of class I transmembrane receptors recognizes and responds to diverse structures associated with pathogenic microorganisms. These receptors mediate initial responses in innate immunity and are required for the development of the adaptive immune response. Toll receptor signaling pathways are also implicated in serious autoimmune diseases such as endotoxic shock and thus are important therapeutic targets. In this review we discuss how microbial structures as different as nucleic acids and lipoproteins can be recognized by the extracellular domains of Toll receptors. We review recent evidence that the mechanism of signal transduction is complex and involves sequential changes in the conformation of the receptor induced by binding of the ligand. Finally, we assess the emerging area of cross talk in the Toll pathways. Recent work suggests that signaling through TLR4 in response to endotoxin is modified by inputs from at least two other pathways acting through beta2 integrins and protein kinase Cepsilon. PMID:17362201

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

    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.

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

    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.

  2. 3'-Phosphoadenosine-5'-phosphosulfate: Photoaffinity ligand for sulfotransferase enzymes

    Sulfation is an important pathway in the biotransformation of many drugs, xenobiotic compounds, neurotransmitters, and hormones. The sulfate donor for these reactions is 3'-phosphoadenosine-5'-phosphosulfate (PAPS). We set out to determine whether PAPS might serve as a photoaffinity ligand for sulfotransferase enzymes. UV irradiation of [35S]PAPS with partially purified human liver thermostable (TS) phenol sulfotransferase (PST) radioactively labeled a protein with a molecular mass of 35 kDa, as estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Photoaffinity labeling of TS PST with [35S] PAPS did not require the presence of a phenolic substrate but rather was inhibited by p-nitrophenol, a sulfate acceptor substrate for TS PST. Inhibitors of TS PST enzymatic activity, including 3'-phosphoadenosine-5'-phosphate, ATP, ADP, and 2,6-dichloro-4-nitrophenol, also inhibited photoaffinity labeling of the 35-kDa protein with [35S]PAPS, in a concentration-dependent fashion, with IC50 values of 14 microM, 2.1 mM, 7.7 mM, and 91 microM, respectively. The 35-kDa protein that was radioactively labeled by [35S]PAPS in the presence of UV light coeluted with TS PST enzymatic activity during gel filtration high performance liquid chromatography. [35S]PAPS was then used to photoaffinity label another sulfotransferase enzyme, the thermolabile (TL) form of PST partially purified from human liver. Therefore, [35S]PAPS appears to be a photoaffinity ligand that could be used to study a variety of PAPS-dependent sulfotransferases. Photoaffinity labeling of TS and TL PST, as well as other PAPS-dependent sulfotransferases, should enhance our ability to purify this important group of enzymes and to determine amino acid sequences at or near their active sites

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

    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.

  4. Imaging of a glioma using peripheral benzodiazepine receptor ligands

    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.

  5. Imaging of a glioma using peripheral benzodiazepine receptor ligands

    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

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

    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

  7. Role of soluble Fas ligand in autoimmune diseases

    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.

  8. Facile ligand oxidation and ring nitration in ruthenium complexes derived from a ligand with dicarboxamide-N and phosphine-P donors.

    Fry, Nicole L; Rose, Michael J; Nyitray, Crystal; Mascharak, Pradip K

    2008-12-15

    The reaction of the tetradentate dicarboxamide ligand 1,2-bis-N-[2'(diphenylphosphanyl)benzoyl]diaminobenzene (dppbH(2)) with RuCl(3) in DMF or ethanol results in metal-mediated ligand oxidation and formation of the diamagnetic Ru(II) complex [(dppQ)Ru(Cl)(2)] (1) with N(2)P(2) chromophore. The o-phenylenedicarboxamide portion of the dppb(2-) ligand is oxidized to a o-benzoquinonediimine (bqdi) moiety in [(dppQ)Ru(Cl)(2)]. Presence of oxygen accelerates the ligand oxidation process. Unlike other tetradentate dicarboxamide ligands with pyridine-N, phenolato-O, or thiolato-S donors, dppb(2-) provides stability to the +2 oxidation state of ruthenium and facilitates oxidation of the coordinated ligand frame. Results of spectroscopic and redox studies strongly support the +2 oxidation state of Ru in 1. Exposure of 1 to NO(g) does not lead to formation of any metal nitrosyl; instead, the bqdi ring is nitrated to afford [(NO(2)dppQ)Ru(Cl)(2)] (2). PMID:19006289

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

    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.

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

    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.

  11. Molecular and electronic structure of chromium(V) nitrido complexes with azide and isothiocyanate ligands

    Bendix, Jesper; Birk, Torben; Weyhermüller, Thomas

    2005-01-01

    ligators. This absorption provides the spectrochemical series for the equatorial ligands, which is found to be numerically almost identical to that determined for chromium(III). DFT calculations reproduce the observed structures and corroborate the ligand field picture of the electronic structure of these...

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

    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.

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

    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

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

    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.

  15. Computer-aided design of a novel ligand for retinoic acid receptor in cancer chemotherapy

    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.

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

    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.

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

    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

  18. Functional phylogenetics reveals contributions of pleiotropic peptide action to ligand-receptor coevolution

    The evolution of peptidergic signaling has been accompanied by a significant degree of ligand-receptor coevolution. Closely related clusters of peptide signaling molecules are observed to activate related groups of receptors, implying that genes encoding these ligands may orchestrate an array of fu...

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

    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.

  20. Dynamic NMR study of ligand exchange reactions in U(VI)-phosphonic acid systems

    The rates of hydrogen ion exchange on phosphonic acid ligands and that of phosphonate ligand exchange on selected uranyl-phosphonate complexes have been investigated by dynamic NMR spectroscopy. The spin-spin relaxation time (ln(1/T2)) for H+ exchange on the fee ligands exhibits a parabolic dependence on reciprocal temperature (1/T (K-1)). The empirical fit parameters are correlated with the activation parameters (ΔH*, ΔS*, ΔCp*) by adapting the statistical mechanical framework developed by Braibanti et al. to the Eyring activated complex theory. The correlation of the apparent activation enthalpy with temperature indicates that 6--11 water molecules participate in the transition from reactants to activated complex for ligand proton exchange reactions, depending on the ligand. Mechanistic details of ligand exchange reactions of phosphonic acid complexants onto the corresponding uranium(VI) complexes are not fully developed, but the negative values for ΔS* imply increased order in the transition to the activated complex. Though ΔH* for ligand exchange covers a range of 15 kJ/mol, the free energy of activation (ΔG*) is nearly constant for the series of ligands, implying substantial entropy compensation in the activation process. Application of the Marcus relationship defines a correlation between ΔG* and the thermodynamic stability (ΔG degree) for the 1:2 uranyl complexes with methanediphosphonic acid and 1-hydroxyethane-1,1-diphosphonic acid

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

    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.

  2. Synthesis of silver nanoparticles: Effects of anionic ligands on formation and catalytic activity

    We report a facile method to synthesize water soluble Ag nanoparticles (NPs) using various anionic complexing ligands as reducing as well as stabilizing agents. The formation of the particles depends on the initial molar ratio of ligands to silver nitrate. Also, the alkaline condition of preparative solution is found to be necessary for the formation of Ag NPs. It has been important to mention here that the temperature of the reaction mixture plays an important factor on the rate of formation of the particles. The particles were characterized by UV–vis spectroscopy, transmission electron microscopy, dynamic light scattering and X-ray diffraction techniques. The formed particles were found to be stable for more than a month. Zeta potential measurements suggest that the negative potential created by the adsorbed complexing ligands contribute to the stability of the Ag NPs suspensions. The effect of the ligands on the formation, stability and catalytic activity of the Ag NPs was evaluated. The obtained Ag NPs exhibit a good catalytic activity toward reduction of o-nitroaniline. The results reveal that the presence of more coordination sites in the ligands affects the catalytic activity of the particles. - Highlights: • Formation of Ag nanoparticles using anionic ligands as reducing agents and stabilizers. • Number of –COOH groups in the ligands affect the formation of particles. • The formed nanoparticles show good catalytic activity. • Number of –COOH groups in the ligands affect the catalytic activity of the particles

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

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

    2013-01-01

    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...

  4. Copper-complexing ligands produced by an intact estuarine microbial community in response to copper stress.

    Bingham, J.; Dryden, C.; Gordon, A.

    2002-12-01

    Copper is both an important nutrient and a pollutant in the marine environment. By studying the interactions between microorganisms and copper in the Elizabeth River (VA), home to a major Naval Base, we field tested the hypothesis that picoplankton and/or bacterioplankton produce strong, copper-complexing ligands in response to elevated copper concentrations. A simple light/ dark test was used to distinguish between heterotrophic and phototrophic ligand production. Samples were bottled and moored, submerged one meter, for a week. Direct counts using DAPI stain and epiflourescence were conducted to find concentrations of picoplankton and bacterioplankton. Using cathodic stripping voltammetry, we found the total copper concentrations, and then from a titration of the ligands by copper, the ligand concentrations and conditional stability constants were obtained. The Elizabeth River naturally had between 10-20 nM total dissolved copper concentrations. However when copper complexation was considered we found that the levels of bio-available Cu(II) ions were much lower. In fact in the natural samples the levels were not high enough to affect the relative reproductive rates of several microorganisms. Naturally there was a 50 nM "buffer zone" of ligand to total dissolved copper concentration. Furthermore, when stressed with excess copper, healthy picoplankton produced enough ligand to alleviate toxicity, and rebuild the buffer zone. However bacterioplankton only produced enough ligand so that they were no longer affected. Therefore, intact estuarine communities regulate copper bioavailability and toxicity with ligand production.

  5. Non-innocent Redox Behavior of Amidinato Ligands: Spectroscopic Evidence for Amidinyl Complexes

    Ehret, F.; Bubrin, M.; Záliš, Stanislav; Kaim, W.

    2014-01-01

    Roč. 640, č. 14 (2014), s. 2781-2787. ISSN 0044-2313 Grant ostatní: COST(XE) CM1202 Institutional support: RVO:61388955 Keywords : Amidinato ligands * Non-innocent ligands * Ruthenium Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.160, year: 2014

  6. Modifying the properties of 4f single-ion magnets by peripheral ligand functionalisation

    Pedersen, Kasper Steen; Ungur, Liviu; Sigrist, Marc; Sundt, Alexander; Schau-Magnussen, Magnus; Vieru, Veacheslav; Mutka, Hannu; Rols, Stephane; Weihe, Høgni; Waldmann, Oliver; Chibotaru, Liviu F.; Bendix, Jesper; Dreiser, Jan

    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...

  7. A novel technique for modifier free delivery of ligands for supercritical fluid extraction

    A novel method has been developed for the controlled delivery of various ligands including solid extractants using supercritical carbon dioxide (Sc-CO2). A ligand delivery vessel with a restricted geometry where its inlet and outlet are located beside each other, accomplished the task of the controlled delivery of ligands. The proposed method eliminates the usage of modifier solvent such as methanol for the delivery of various ligands during the supercritical fluid extraction of metal ions. Using neat Sc-CO2, the delivery profiles for the various ligands such as octyl(phenyl)-N,N-diisobutylcarbamoylmethyl-phosphineoxide (CMPO), tri-n-butyl phosphate (TBP), tri-n-octyl phosphine oxide (TOPO), theonyltrifluroacetone (TTA) and di(2-ethylhexyl)isobutyramide (D2EHIBA) were established. The delivery profiles were optimised by investigating the influence of various extraction parameters such as ligand delivery vessel geometry, temperature, pressure, flow rate of Sc-CO2 and ligand content. Applications of these ligand delivery modes were demonstrated for the supercritical fluid extraction of uranium from tissue paper matrix and preferential extraction of uranium over thorium. These results are compared with the extraction studies involving methanol or hexane modifier under similar experimental conditions. The extraction of neodymium nitrate was also demonstrated using modifier free delivery mode. (orig.)

  8. Correlation between ligand density of states and 5f delocalization in uranium intermetallic compounds

    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

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

    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.

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

    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.

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

    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

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

    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…

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

    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.

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

    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

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

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

    2013-01-01

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

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

    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

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

    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

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

    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

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

    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, UO22+). 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, these

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

    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

  1. Equilibrium studies on mixed ligand complexes of some tripositive rare earth ions

    Interaction of the rare earth ions, La3+, Ce3+, Pr3+, Nd3+, Sm3+ and Eu3+ with the pair of ligands 1-amino-2-naphthol-4-sulphonic acid (an, H2A) and o-aminophenol (ap, HB) have been studied in aqueous solution at 25 degC (μ=0.1 M KNO3/NaCl). Equilibrium constants of the reactions involving the formations of the mixed ligand species MAB, MA2B2-, MB2A- (M = metal ion) and the binary complexes containing up to three ligand molecules have been evaluated from the pH-metric data, and coordinating behaviour of the ligands in the formation of the mixed ligand complexes has been discussed. (author). 10 refs., 1 tab., 1 fig

  2. Bioluminescent Ligand-Receptor Binding Assays for Protein or Peptide Hormones.

    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

  3. Surface-Bound Ligands Modulate Chemoselectivity and Activity of a Bimetallic Nanoparticle Catalyst

    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.

  4. Development of radioiodinated receptor ligands for cerebral single photon emission tomography

    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

  5. Surfactant Ligand Removal and Rational Fabrication of Inorganically Connected Quantum Dots

    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.

  6. Cloud computing approaches for prediction of ligand binding poses and pathways.

    Lawrenz, Morgan; Shukla, Diwakar; Pande, Vijay S

    2015-01-01

    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. PMID:25608737

  7. Small potent ligands to the insulin-regulated aminopeptidase (IRAP)/AT(4) receptor.

    Axén, Andreas; Andersson, Hanna; Lindeberg, Gunnar; Rönnholm, Harriet; Kortesmaa, Jarkko; Demaegdt, Heidi; Vauquelin, Georges; Karlén, Anders; Hallberg, Mathias

    2007-07-01

    Angiotensin IV analogs encompassing aromatic scaffolds replacing parts of the backbone of angiotensin IV have been synthesized and evaluated in biological assays. Several of the ligands displayed high affinities to the insulin-regulated aminopeptidase (IRAP)/AT(4) receptor. Displacement of the C-terminal of angiotensin IV with an o-substituted aryl acetic acid derivative delivered the ligand 4, which exhibited the highest binding affinity (K(i) = 1.9 nM). The high affinity of this ligand provides support to the hypothesis that angiotensin IV adopts a gamma-turn in the C-terminal of its bioactive conformation. Ligand (4) inhibits both human IRAP and aminopeptidase N-activity and induces proliferation of adult neural stem cells at low concentrations. Furthermore, ligand 4 is degraded considerably more slowly in membrane preparations than angiotensin IV. Hence, it might constitute a suitable research tool for biological studies of the (IRAP)/AT(4) receptor. PMID:17559064

  8. The influences of sensitivity of ligand in determination of fluors with LaF3

    The influences of acetate and carbonate ligand as a binder of uranium in uranium-tetra fluoride solution, with 0,1 M HNO3 acid condition was been studied. The aim of binding is to looses of uranium from UO2(F4)2- compound, so the free of fluoride were able detected with LaF3 membrane electrode on potentiometric method. Base on the free of Fluoride, acetate ligand was more sensitive than carbonate ligand. The addition method was able to prevented influent of HF species in high acidity was realized. The method was use to determination of Fluoride in Concentrated Uranium, and yield are 1,215x10-5 M±1,957x10-4 in acetate ligand and 3,957x10-5 M±2,57x10-4 in carbonate ligand. (author)

  9. Ligand-Free Noble Metal Nanocluster Catalysts on Carbon Supports via "Soft" Nitriding.

    Liu, Ben; Yao, Huiqin; Song, Wenqiao; Jin, Lei; Mosa, Islam M; Rusling, James F; Suib, Steven L; He, Jie

    2016-04-13

    We report a robust, universal "soft" nitriding method to grow in situ ligand-free ultrasmall noble metal nanocatalysts (UNMN; e.g., Au, Pd, and Pt) onto carbon. Using low-temperature urea pretreatment at 300 °C, soft nitriding enriches nitrogen-containing species on the surface of carbon supports and enhances the affinity of noble metal precursors onto these supports. We demonstrated sub-2-nm, ligand-free UNMNs grown in situ on seven different types of nitrided carbons with no organic ligands via chemical reduction or thermolysis. Ligand-free UNMNs supported on carbon showed superior electrocatalytic activity for methanol oxidation compared to counterparts with surface capping agents or larger nanocrystals on the same carbon supports. Our method is expected to provide guidelines for the preparation of ligand-free UNMNs on a variety of supports and, additionally, to broaden their applications in energy conversion and electrochemical catalysis. PMID:27014928

  10. Using RosettaLigand for small molecule docking into comparative models.

    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.

  11. Pyridylidene ligand facilitates gold-catalyzed oxidative C–H arylation of heterocycles

    Hata, Kazuhiro; Ito, Hideto

    2015-01-01

    Summary Triaryl-2-pyridylidene effectively facilitates the gold-catalyzed oxidative C–H arylation of heteroarenes with arylsilanes as a unique electron-donating ligand on gold. The employment of the 2-pyridylidene ligand, which is one of the strongest electron-donating N-heterocyclic carbenes, resulted in the rate acceleration of the C–H arylation reaction of heterocycles over conventional ligands such as triphenylphosphine and a classical N-heterocyclic carbene. In situ observation and isolation of the 2-pyridylidene-gold(III) species, as well as a DFT study, indicated unusual stability of gold(III) species stabilized by strong electron donation from the 2-pyridylidene ligand. Thus, the gold(I)-to-gold(III) oxidation process is thought to be facilitated by the highly electron-donating 2-pyridylidene ligand. PMID:26877796

  12. Heteroligand molecular "stirrups" using conformationally flexible ditopic pyridyl-pyrazolyl ligands.

    Lu, Jinzhen; Turner, David R; Harding, Lindsay P; Batten, Stuart R

    2009-08-17

    Heteroligand molecular "stirrups" form by the self-assembly of flexible ditopic ligands in combination with 4,4'-bipyridine and [(dppp)Pd)](2+). Crystallographic analysis shows that the ligands, bis[3-(4-pyridyl)pyrazolyl]-m-xylene (mXy(4py3pz)) and bis[4-(4-pyridyl)pyrazolyl]-p-xylene (pXy(4py4pz)) form complexes of the type [{(dppp)Pd}(2)(4,4'-bipy)(L)].4OTf (1.4OTf and 2.4OTf, respectively) in the solid state, with remarkably similar structures considering the differences in substitution patterns between the two ligands. The self-assembly of both 1(4+) and 2(4+) is assisted by face-to-face pi interactions on the exterior of the macrocycle between the phenyl rings of the dppp ligands and the pyridyl groups of the ditopic ligands. PMID:19594137

  13. Solvent fluctuations induce non-Markovian kinetics in hydrophobic pocket-ligand binding

    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...

  14. Nanoparticle Shape Anisotropy Dictates the Collective Behavior of Surface-Bound Ligands

    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.

  15. A feasibility study of unconventional planar ligand spacers in chalcogenide nanocrystals.

    Lukose, Binit; Clancy, Paulette

    2016-05-18

    The solar cell efficiency of chalcogenide nanocrystals (quantum dots) has been limited in the past by the insulation between neighboring quantum dots caused by intervening, often long-chain, aliphatic ligands. We have conducted a computationally based feasibility study to investigate the use of ultra-thin, planar, charge-conducting ligands as an alternative to traditional long passive ligands. Not only might these radically unconventional ligands decrease the mean distance between adjacent quantum dots, but, since they are charge-conducting, they have the potential to actively enhance charge migration. Our ab initio studies compare the binding energies, electronic energy gaps, and absorption characteristics for both conventional and unconventional ligands, such as phthalocyanines, porphyrins and coronene. This comparison identified these unconventional ligands with the exception of titanyl phthalocyanine, that bind to themselves more strongly than to the surface of the quantum dot, which is likely to be less desirable for enhancing charge transport. The distribution of finite energy levels of the bound system is sensitive to the ligand's binding site and the levels correspond to delocalized states. We also observed a trap state localized on a single Pb atom when a sulfur-containing phenyldithiocarbamate (PTC) ligand is attached to a slightly off-stoichiometric dot in a manner that the sulfur of the ligand completes stoichiometry of the bound system. Hence, this is indicative of the source of trap state when thio-based ligands are bound to chalcogenide nanocrystals. We also predict that titanyl phthalocyanine in a mix with chalcogenide dots of diameter ∼1.5 Å can form a donor-acceptor system. PMID:26918246

  16. Sensitive bioassay for detection of PPARα potentially hazardous ligands with gold nanoparticle probe

    Highlights: → We develop a sensitive and high throughput method to screen PPARα ligands. → This method is based on the ligand-receptor interaction on microplate. → The sensitivity is increased through sliver enhancement on captured gold nanoparticle probes. → There is a significant correlation between the bioassay and LC-MS for water spiked samples. - Abstract: There are so many kinds of peroxisome proliferator-activated receptor α (PPARα) ligands with hazardous effect for human health in the environment, such as certain herbicides, plasticizers and drugs. Among these agonists, perfluorooctane sulfonate (PFOS), perfluorooctanoic acid (PFOA), and mono-(2-ethylhexyl) phthalate (MEHP) are mostly investigated due to their persistence and accumulation in environment and their potential toxicity via PPARα. This investigation aims at developing a bioassay method to detect PPARα ligands based on the ligand-receptor interaction on microplate. PPARα, which formed heterodimers with retinoid X receptor-α (RXRα), were activated by PPARα ligands to form ligands-PPARα-RXRα complexes. Then the complexes were transferred into a microplate and captured via monoclonal anti-PPARα antibody. The PPARα responsive elements (PPRE) modified-gold nanoparticle probes were captured by the ligand-PPARα-RXRα complexes immobilized on the microplate, and then could be quantified through measuring the optical density after silver enhancement. The results showed that PFOS was quantified with a linear range from 100 pM to 1 μM and the detection limit was 10 pM. In addition to PFOS, PFOA and MEHP were also quantified within a proper range through the proposed bioassay. This bioassay was compared with that of liquid chromatography tandem-mass spectrometry (LC-MS) for water spiked samples with a significant correlation (r = 0.9893). This study provides a high-throughput detection method for PPARα ligands in microplate with high sensitivity and wide linear range. It may serve as

  17. Explicit all-atom modeling of realistically sized ligand-capped nanocrystals

    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.

  18. Investigation on critical structural motifs of ligands for triggering glucocorticoid receptor nuclear migration through molecular docking simulations.

    Liu, Ya-Lin; Jang, Soonmin; Wang, Shih-Min; Chen, Chiu-Hao; Li, Feng-Yin

    2016-06-01

    The glucocorticoid receptor (GR), a transcription factor regulating gene expression in a ligand-dependent fashion, is known for flexibility in adapting various ligands with their structures ranging from steroid to non-steroid. However, in our previous study, GR shows a stringent discrimination against a set of steroid ligands with highly similar structures for triggering its nuclear migration. In order to resolve this puzzle, we employed molecular docking simulations to investigate the origin of this structural discrimination. By analyzing the docking orientations and the related ligand-GR interaction patterns, we found that the hydrophilicity mismatch between the docking ligand and the GR ligand-binding site is the main cause combined with the steric hindrance and structural rigidness of these steroid ligands. Furthermore, we utilized this knowledge to rationalize how the structure-binding interaction of non-steroid ligands triggers GR nuclear migration with their structures available in Protein Data Bank. PMID:26198481

  19. Theoretical investigation on the diatomic ligand migration process and ligand binding properties in non-O2-binding H-NOX domain.

    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

  20. Prospects for three-electron donor boronyl (BO) ligands and dioxodiborene (B2O2) ligands as bridging groups in binuclear iron carbonyl derivatives.

    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

  1. The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation

    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...

  2. Influence of bidentate structure of an aryl phosphine oxide ligand on photophysical properties of its Eu~Ⅲ complex

    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...

  3. Synthesis and Application of Chiral Spiro Cp Ligands in Rhodium-Catalyzed Asymmetric Oxidative Coupling of Biaryl Compounds with Alkenes.

    Zheng, Jun; Cui, Wen-Jun; Zheng, Chao; You, Shu-Li

    2016-04-27

    The vastly increasing application of chiral Cp ligands in asymmetric catalysis results in growing demand for novel chiral Cp ligands. Herein, we report a new class of chiral Cp ligands based on 1,1'-spirobiindane, a privileged scaffold for chiral ligands and catalysts. The corresponding Rh complexes are shown to be excellent catalysts in asymmetric oxidative coupling reactions, providing axially chiral biaryls in 19-97% yields with up to 98:2 er. PMID:27070297

  4. Pharmacological profiles of the metabotropic glutamate receptor ligands.

    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

  5. Polarographic study of mixed-ligand complexes of cadmium(II) with L-amino acid and vitamin B5

    A survey of literature shows that ternary complexes of CdII with L-amino acids and vitamin B5 have not been studied so far. The present communication reports the formation of mixed-ligand complexes of CdII with L-amino acids as primary ligands and vitamin B5 as secondary ligand, studied by polarographic technique. (author)

  6. DMPD: Anti-inflammatory actions of PPAR ligands: new insights on cellular andmolecular mechanisms. [Dynamic Macrophage Pathway CSML Database

    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

  7. Ligand Exchange Reaction of Au(I) R-N-Heterocyclic Carbene Complexes with Cysteine.

    Dos Santos, H F; Vieira, M A; Sánchez Delgado, G Y; Paschoal, D

    2016-04-14

    The chemotherapy with gold complexes has been attempted since the 90s after the clinical success of auranofin, a gold(I) coordination complex. Currently, the organometallics compounds have shown promise in cancer therapy, mainly in those complexes containing N-heterocylic carbenes (NHC) as a ligand. The present study shows a kinetic analysis of the reaction of six alkyl-substituted NHC with cysteine (Cys), which is taken as an important bionucleophile representative. The first and second ligand exchange processes were analyzed with the complete description of the mechanism and energy profiles. For the first reaction step, which is the rate-limiting step of the whole substitution reaction, the activation enthalpy follows the order 1/Me2 order is correlated with the r(Au-S) calculated for the transition state structures where S is the sulfur ligand from the Cys entering group. This means that longer r(Au-S) leads to higher activation enthalpy and is consistent with the effectiveness of gold shielding from nucleophile attack by bulkier alkyl-substituted NHC ligand. When electronic effect was addressed we found that higher activation barrier was predicted for strongly electron-donating NHC ligand, represented by the eigenvalue of σ-HOMO orbital of the free ligands. The molecular interpretation of the electronic effects is that strong donating NHC forms strong metal-ligand bond. For the second reaction step, similar structure-reactivity relationships were obtained, however the activation energies are less sensitive to the structure. PMID:27010796

  8. PANP is a novel O-glycosylated PILRα ligand expressed in neural tissues

    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.

  9. Engineering and optimization of an allosteric biosensor protein for peroxisome proliferator-activated receptor γ ligands.

    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

  10. Synthesis and Characterization of Dinuclear Metal Complexes Stabilized by Tetradentate Schiff Base Ligands

    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.

  11. PANP is a novel O-glycosylated PILR{alpha} ligand expressed in neural tissues

    Kogure, Amane [Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871 (Japan); Laboratory of Immunochemistry, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871 (Japan); Shiratori, Ikuo [Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871 (Japan); Wang, Jing [Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871 (Japan); Laboratory of Immunochemistry, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871 (Japan); Lanier, Lewis L. [Department of Microbiology and Immunology and the Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143 (United States); Arase, Hisashi, E-mail: arase@biken.osaka-u.ac.jp [Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871 (Japan); Laboratory of Immunochemistry, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871 (Japan); JST CREST, Saitama 332-0012 (Japan)

    2011-02-18

    Research highlights: {yields} A Novel molecule, PANP, was identified to be a PILR{alpha} ligand. {yields} Sialylated O-glycan structures on PANP were required for PILR{alpha} recognition. {yields} Transcription of PANP was mainly observed in neural tissues. {yields} PANP seems to be involved in immune regulation as a ligand for PILR{alpha}. -- Abstract: PILR{alpha} 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 PILR{alpha} to its ligand CD99 is involved in immune regulation; however, whether there are other PILR{alpha} 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 PILR{alpha}. Transcription of PANP was mainly observed in neural tissues. PILR{alpha}-Ig fusion protein bound cells transfected with PANP and the transfectants stimulated PILR{alpha} 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 PILR{alpha}.

  12. Photostability of CdSe quantum dots functionalized with aromatic dithiocarbamate ligands.

    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

  13. Ligand substitution reactions of a phenolic quinolyl hydrazone; oxidovanadium (IV complexes

    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.

  14. Spectroscopic studies on the luminescence properties of ternary europium complexes with different ligands

    Zhang Xiao, E-mail: zhangx@simtech.a-star.edu.s [Singapore Institute of Manufacturing Technology, 71 Nanyang Drive, Singapore 638075 (Singapore)

    2010-06-15

    In this paper, ligand effect of several bi-dental oxygen (O) and nitrogen (N) ligands on the red luminescence properties of europium ion (Eu{sup 3+}) was studied comprehensively. Absorption, emission, and excitation spectral properties of ternary europium complexes with different combinations of ligands including thenoyl trifluoroacetone (TTA), naphthyl trifluoroacetone (NTA), 2,2'-bipyridyl (bpy) and phenanthroline (Phen) were investigated. Efficient Eu{sup 3+} red emission was observed with all the combinations of the above mentioned ligands. The most intense emission was found with the all nitrogen coordinated complex Eu(bpy){sub 2}(Phen){sub 2} while the longest wavelength excitation band was recorded with oxygen-nitrogen mixed NTA-bpy complex Eu(NTA){sub 1}(bpy){sub 3}. With change of the ligands combination and ratio, the Eu{sup 3+} emission peak changes slightly from 612 to 618 nm. The absorption and excitation spectra of the europium complexes were compared and analyzed referring to the individual absorption spectral properties of the ligands. The relation between ligand-to-metal charge transfer states and luminescence intensities for different complexes was studied.

  15. Structure-based analysis of the ultraspiracle protein and docking studies of putative ligands

    Souphatta Sasorith

    2002-12-01

    Full Text Available The ultraspiracle protein (USP is the insect ortholog of the mammalian retinoid X receptor (RXR. Fundamental questions concern the functional role of USP as the heterodimerization partner of insect nuclear receptors such as the ecdysone receptor. The crystallographic structures of the ligand binding domain of USPs of Heliothis virescens and Drosophila melanogaster solved recently show that helix 12 is locked in an antagonist conformation raising the question whether USPs could adopt an agonist conformation as observed in RXRalpha. In order to investigate this hypothesis, a homology model for USP is proposed that allows a structural analysis of the agonist conformation of helix 12 based on the sequence comparison with RXR. For USP, one of the main issues concerns its function and in particular whether its activity is ligand independent or not. The x-ray structures strongly suggest that USP can bind ligands. Putative ligands have therefore been docked in the USP homology model. Juvenile hormones and juvenile hormone analogs were chosen as target ligands for the docking study. The interaction between the ligand and the receptor are examined in terms of the pocket shape as well as in terms of the chemical nature of the residues lining the ligand binding cavity.

  16. Development of different types of novel ligands for nuclear waste treatment

    Partitioning of actinide (An(III)/lanthanide (Ln(III)) cations is an important step in nuclear waste treatment, which utilizes different types of ligands in different processes. Novel ligands, a sort of hybrids, were prepared by combining essential parts of different well-known classes of ligands, viz. malonamides and glycolamides. However, their extraction behavior turned out to be not as good as that of the original parent ligands. N,N,N',N'-Tetraoctyl-3-oxapentanediamide (TODGA) is currently one of the innovative-SANEX reference compounds due to its high distribution ratios for An(III) and Ln(III) from highly acidic media. TODGA was pre-organized on tripodal and Calix(4)arene platforms and the resulting ligands were evaluated for the extraction of various An(III) cations. The extraction results clearly showed the positive effect of bringing together ligating sites on a molecular platform. Water-soluble TODGA derivatives and tripodal ligands showed interesting back extraction properties. Many nitrogen-donor extractants are known to lose their complexation ability due to protonation of nitrogen under the highly acidic nuclear waste conditions. To possibly overcome this drawback a series of novel pyrazinc-based O,N,O-donor ligands was designed and synthesized, employing a newly developed methodology for palladium-catalyzed phosphorus-carbon coupling of chloropyrazines with various phosphorus pronucleophiles. Several appropriately functionalized pyrazines were grouped together on a Calix arene and their extraction behavior compared with that of the individual pyrazines

  17. Determinants governing ligand specificity of the Vibrio harveyi LuxN quorum-sensing receptor.

    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. PMID:25367076

  18. Binding affinity prediction of novel estrogen receptor ligands using receptor-based 3-D QSAR methods.

    Sippl, Wolfgang

    2002-12-01

    We have recently reported the development of a 3-D QSAR model for estrogen receptor ligands showing a significant correlation between calculated molecular interaction fields and experimentally measured binding affinity. The ligand alignment obtained from docking simulations was taken as basis for a comparative field analysis applying the GRID/GOLPE program. Using the interaction field derived with a water probe and applying the smart region definition (SRD) variable selection procedure, a significant and robust model was obtained (q(2)(LOO)=0.921, SDEP=0.345). To further analyze the robustness and the predictivity of the established model several recently developed estrogen receptor ligands were selected as external test set. An excellent agreement between predicted and experimental binding data was obtained indicated by an external SDEP of 0.531. Two other traditionally used prediction techniques were applied in order to check the performance of the receptor-based 3-D QSAR procedure. The interaction energies calculated on the basis of receptor-ligand complexes were correlated with experimentally observed affinities. Also ligand-based 3-D QSAR models were generated using program FlexS. The interaction energy-based model, as well as the ligand-based 3-D QSAR models yielded models with lower predictivity. The comparison with the interaction energy-based model and with the ligand-based 3-D QSAR models, respectively, indicates that the combination of receptor-based and 3-D QSAR methods is able to improve the quality of prediction. PMID:12413831

  19. Theoretical survey of the ligand tunability of poly(azolyl)borates.

    Lu, Dongmei; Tang, Huarong

    2015-07-14

    Using density functional calculations, we have systematically investigated a series of homoleptic poly(azolyl)borate ligands, which display unusual steadily declining bond strengths accompanied by bond contractions when the azolyl groups are sequentially substituted to the parent BH4(-). As ligands, their effects on the coordinated metal ions (Cu(i) and Mo(0)) are quantitatively represented by two ligand tunability descriptors: the vibration frequency (νCO) of the CO groups complexed to the metal ions and the charge of the metal-(CO)x moiety, between which a good linear correlation exists. For the same number of azolyl substitutions, the boundary of ligand tunability is always marked by the pyrazolyl and tetrazolyl groups at the two ends, which feature the lowest and the highest nitrogen content in the azolyl ring, respectively. With the increase of the azolyl substitution number in the borate ligands, the νCO range expands, indicating a higher tunability of the ligands. The type of metal ion and the charge they carry play minor roles in influencing the ligand tunability. PMID:26062889

  20. Induction of proliferation and monocytic differentiation of human CD34+ cells by CD137 ligand signaling.

    Jiang, Dongsheng; Yue, Pei Shan Eunice; Drenkard, Daniela; Schwarz, Herbert

    2008-09-01

    CD137 is a member of the tumor necrosis factor receptor family and is involved in the regulation of activation, proliferation, differentiation, and cell death of leukocytes. Bidirectional signaling exists for the CD137 receptor/ligand system, as CD137 ligand, which is expressed as a transmembrane protein, can also transduce signals into the cells on which it is expressed. In this study, we have identified expression of CD137 in human bone marrow and expression of CD137 ligand on a subset of CD34+ cells. Cross-linking of CD137 ligand on CD34+ cells by CD137 ligand agonists induces activation, prolongation of survival, proliferation, and colony formation. CD137 ligand agonists induce differentiation of early hematopoietic progenitor cells to colony-forming units-granulocyte/macrophage and subsequently to monocytes and macrophages but not to dendritic cells. These data uncover a novel function of CD137 and CD137 ligand by showing their participation in the growth and differentiation of hematopoietic progenitor cells. PMID:18566330

  1. Molecular dynamics simulation of ligand dissociation from liver fatty acid binding protein.

    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.

  2. Molecular dynamics simulation of ligand dissociation from liver fatty acid binding protein.

    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

  3. Natural ligand binding and transfer from liver fatty acid binding protein (LFABP) to membranes.

    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

  4. A comparative study of actinide complexation in three ligand systems with increasing complexity

    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.

  5. An approach to rational ligand-design based on a thermodynamic analysis.

    Ui, Mihoko; Tsumoto, Kouhei

    2010-11-01

    Thermodynamic analysis is an effective tool in screening of lead-compounds for development of potential drug candidates. In most cases, a ligand achieve high affinity and specificity to a target protein by means of both favorable enthalpy and entropy terms, which can be reflected in binding profiles of Isothermal Titration Calorimetry (ITC). A favorable enthalpy change suggests the contribution of noncovalent contacts such as hydrogen bonding and van der Waals interaction between a ligand and its target protein. In general, optimization of binding enthalpy is more difficult than that of entropies in ligand-design; therefore, it is desirable to choose firstly a lead-compound based on its binding enthalpic gain. In this paper, we demonstrate the utility of thermodynamic approach to ligand screening using anti-ciguatoxin antibody 10C9 as a model of a target protein which possesses a large hydrophobic pocket. As a result of this screening, we have identified three compounds that could bind to the antigen-binding pocket of 10C9 with a few kcal/mol of favorable binding enthalpy. Comparison of their structure with the proper antigen ciguatoxin CTX3C revealed that 10C9 rigorously identifies their cyclic structure and a characteristic hydroxyl group. ITC measurement might be useful and powerful for a rational ligand screening and the optimization of the ligand; the enthalpic gain is an effective index for ligand-design studies. PMID:21171955

  6. Direct Measure of Metal-Ligand Bonding Replacing the Tolman Electronic Parameter.

    Setiawan, Dani; Kalescky, Robert; Kraka, Elfi; Cremer, Dieter

    2016-03-01

    The Tolman electronic parameter (TEP) derived from the A1-symmetrical CO stretching frequency of nickel-tricarbonyl complexes L-Ni(CO)3 with varying ligands L is misleading as (i) it is not based on a mode decoupled CO stretching frequency and (ii) a generally applicable and quantitatively correct or at least qualitatively reasonable relationship between the TEP and the metal-ligand bond strength does not exist. This is shown for a set of 181 nickel-tricarbonyl complexes using both experimental and calculated TEP values. Even the use of mode-mode decoupled CO stretching frequencies (L(ocal)TEPs) does not lead to a reliable description of the metal-ligand bond strength. This is obtained by introducing a new electronic parameter that is directly based on the metal-ligand local stretching force constant. For the test set of 181 nickel complexes, a direct metal-ligand electronic parameter (MLEP) in the form of a bond strength order is derived, which reveals that phosphines and related ligands (amines, arsines, stibines, bismuthines) are bonded to Ni both by σ-donation and π-back-donation. The strongest Ni-L bonds are identified for carbenes and cationic ligands. The new MLEP quantitatively assesses electronic and steric factors. PMID:26900632

  7. Synthesis, crystal structures and properties of three new mixed-ligand d10 metal complexes constructed from pyridinecarboxylate and in situ generated amino-tetrazole ligand

    Three new metal-organic frameworks, [Zn(atz)(nic)]n(1), [Zn(atz)(isonic)]n.nHisonic(2) and [Cd(atz)(isonic)]n(3) (Hnic=nicotinic acid, Hisonic=isonicotinic acid), have been firstly synthesized by employing mixed-ligand of pyridinecarboxylate with the in situ generated ligand of 5-amino-tetrazolate(atz-), and characterized by elemental analysis, IR spectroscopy, TGA and single crystal X-ray diffraction. The results revealed that 1 presents a two-dimensional (2D) 'sql' topological network constructed from the linear chain subunit of Zn(nic)2 and atz- ligand. A remarkable feature of 2 is a 2-fold interpenetrated diamondoid network with free Hisonic molecules locating in the channels formed by the zigzag chain subunits of Zn(isonic)2. Complex 3 is a 3D non-interpenetrated pillared framework constructed from the double chain subunits of Cd-COO-Cd. It possesses a rarely observed (4,6)-connected 'fsc' topology. The thermal stabilities and fluorescent properties of the complexes were investigated. All of these complexes exhibited intense fluorescent emissions in the solid state at room temperature. - Graphical abstract: Three new mixed-ligand d10 metal complexes have been synthesized by employing mixed-ligand synthetic approach. Complex 1 presents a 2D 'sql' topological network. Complex 2 is a 2-fold interpenetrated diamondoid network with microporous channels. Rarely observed (4,6)-connected 'fsc' topological network was found in complex 3.

  8. 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

    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.

  9. SPOT-Ligand: Fast and effective structure-based virtual screening by binding homology search according to ligand and receptor similarity.

    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

  10. Are superhalogens without halogen ligand capable of transcending traditional halogen-based superhalogens? Ab initio case study of binuclear anions based on pseudohalogen ligand

    The superhalogen properties of polynuclear structures without halogen ligand are theoretically explored here for several [M2(CN)5]−1 (M =  Ca, Be) clusters. At CCSD(T) level, these clusters have been confirmed to be superhalogens due to their high vertical electron detachment energies (VDE). The largest one is 9.70 eV for [Ca2(CN)5]−1 which is even higher than those of corresponding traditional structures based on fluorine or chlorine ligands. Therefore the superhalogens stronger than the traditional halogen-based structures could be realized by ligands other than halogen atoms. Compared with CCSD(T), outer valence Green’s function (OVGF) method either overestimates or underestimates the VDEs for different structures while MP2 results are generally consistent in the aspect of relative values. The extra electrons of the highest VDE anions here aggregate on the bridging CN units with non-negligible distribution occurring on other CN units too. These two features lower both the potential and kinetic energies of the extra electron respectively and thus lead to high VDE. Besides superhalogen properties, the structures, relative stabilities and thermodynamic stabilities with respect to the detachment of cyanide ligand were also investigated. The sum of these results identifies the potential of polynuclear structures with pseudohalogen ligand as suitable candidates with enhanced superhalogens properties

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

    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.

  12. Influence of ligands in metal nanoparticle electrophoresis for the fabrication of biofunctional coatings

    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

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

    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

  14. Ligand-induced conformational changes in a thermophilic ribose-binding protein

    Hellinga Homme W

    2008-11-01

    Full Text Available Abstract Background Members of the periplasmic binding protein (PBP superfamily are involved in transport and signaling processes in both prokaryotes and eukaryotes. Biological responses are typically mediated by ligand-induced conformational changes in which the binding event is coupled to a hinge-bending motion that brings together two domains in a closed form. In all PBP-mediated biological processes, downstream partners recognize the closed form of the protein. This motion has also been exploited in protein engineering experiments to construct biosensors that transduce ligand binding to a variety of physical signals. Understanding the mechanistic details of PBP conformational changes, both global (hinge bending, twisting, shear movements and local (rotamer changes, backbone motion, therefore is not only important for understanding their biological function but also for protein engineering experiments. Results Here we present biochemical characterization and crystal structure determination of the periplasmic ribose-binding protein (RBP from the hyperthermophile Thermotoga maritima in its ribose-bound and unliganded state. The T. maritima RBP (tmRBP has 39% sequence identity and is considerably more resistant to thermal denaturation (appTm value is 108°C than the mesophilic Escherichia coli homolog (ecRBP (appTm value is 56°C. Polar ligand interactions and ligand-induced global conformational changes are conserved among ecRBP and tmRBP; however local structural rearrangements involving side-chain motions in the ligand-binding site are not conserved. Conclusion Although the large-scale ligand-induced changes are mediated through similar regions, and are produced by similar backbone movements in tmRBP and ecRBP, the small-scale ligand-induced structural rearrangements differentiate the mesophile and thermophile. This suggests there are mechanistic differences in the manner by which these two proteins bind their ligands and are an example of

  15. Influence of ligands in metal nanoparticle electrophoresis for the fabrication of biofunctional coatings

    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

  16. Ligand Field Theory: An ever-modern theory

    The Ligand Field (LF) model in molecular science or the Crystal Field model in condensed matter science has been introduced more than eighty years ago. Since then, this theory plays a central role each time that molecules containing d- and/or f-elements with open shells are adressed. No doubt, this fact is related to the dominant localisation of the frontier orbitals within the metal-sphere. This common feature enables us to describe approximately the electronic structure of these molecules using orbitals that are centred on a single atom and to treat their interaction with the chemical environment essentially as a perturbation. Another reason for the success of this simple theory is the fact that the more accurate molecular orbital theory does generally over-estimate covalence of transition metal atoms and thus yields wave functions that are too delocalized. We give here a survey of the development of LF theory since its introduction simultaneously by Hans Bethe and John Hasbrouck van Vleck more than eighty years ago. Over the years, LF theory was a semi-empirical model with adjustable parameter until the end of last century when we introduced non-empirical LF theory that is based on DFT calculations. The results of this first-principle prediction are in very good agreement with the experimental observations. Sample calculations of tetrahedral and octahedral Cr-complexes and hexa-acquo Ni(II)-complexes are used to validate the new model and to analyse the calculated parameters.

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

    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

  18. Monitoring ligand-receptor interactions by photonic force microscopy

    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.

  19. Interactions of rare earth elements with bacteria and organic ligands

    We investigated the interactions of rare earth elements (REEs) Eu(III) and/or Ce(III, IV) with the common soil bacterium Pseudomonas fluorescens and organic ligands, such as malic acid, citric acid, a siderophore (DFO), cellulose, chitin, and chitosan. Malic acid formed complexes with Eu(III), but degradation of malic acid was observed when the ratio of malic acid to Eu(III) was higher than 100. Citric acid formed a stoichiometric complex with Eu(III) that was not degraded by P. fluorescens. Adsorption of Eu(III) from the DFO complex occurred as a free ion dissociated from DFO and not as the Eu(III)-DFO complex. Cerium(III) was oxidized to Ce(IV) during complexation with DFO to form the Ce(IV)-DFO complex. Time-resolved laser-induced fluorescence spectroscopy (TRLFS) analysis showed that cellulose, chitin, and chitosan, respectively, formed a weak complex, an inner-spherical complex, and an outer-spherical complex with Eu(III). This method also demonstrated that the coordination environment of Eu(III) adsorbed on P. fluorescens possessed similar characteristics to that of chitin, and revealed that adsorption of Eu(III) on P. fluorescens was through a multidentate and predominantly inner-spherical coordination

  20. Tetrazoles: Unique Capping Ligands and Precursors for Nanostructured Materials.

    Voitekhovich, Sergei V; Lesnyak, Vladimir; Gaponik, Nikolai; Eychmüller, Alexander

    2015-11-18

    Capping agents play an important role in the colloidal synthesis of nanomaterials because they control the nucleation and growth of particles, as well as their chemical and colloidal stability. During recent years tetrazole derivatives have proven to be advanced capping ligands for the stabilization of semiconductor and metal nanoparticles. Tetrazole-capped nanoparticles can be prepared by solution-phase or solventless single precursor approaches using metal derivatives of tetrazoles. The solventless thermolysis of metal tetrazolates can produce both individual semiconductor nanocrystals and nanostructured metal monolithic foams displaying low densities and high surface areas. Alternatively, highly porous nanoparticle 3D assemblies are achieved through the controllable aggregation of tetrazole-capped particles in solutions. This approach allows for the preparation of non-ordered hybrid structures consisting of different building blocks, such as mixed semiconductor and metal nanoparticle-based (aero)gels with tunable compositions. Another unique property of tetrazoles is their complete thermal decomposition, forming only gaseous products, which is employed in the fabrication of organic-free semiconductor films from tetrazole-capped nanoparticles. After deposition and subsequent thermal treatment these films exhibit significantly improved electrical transport. The synthetic availability and advances in the functionalization of tetrazoles necessitate further design and study of tetrazole-capped nanoparticles for various applications. PMID:26395565