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Sample records for base ligands derived

  1. Integrated ligand based pharmacophore model derived from diverse FAAH covalent ligand classes.

    PubMed

    Shen, Lingling; Huang, Hongwei; Makriyannis, Alexandros; Fisher, Luke S

    2012-12-01

    3D pharmacophore modeling is an important computational methodology for ligand-enzyme binding interactions in drug discovery. More specifically, a consensus pharmacophore model derived from diverse ligands is a key determinant upon which the prediction power of computational models is based for designing novel ligands. In this work, by merging the important pharmacophore features based on four classes of covalent FAAH ligands, and then integrating the exclusion volume spheres derived from the crystal structure, we created for the first time an integrated FAAH pharmacophore model to describe the ligand-enzyme binding interactions. This new integrated FAAH pharmacophore model can correctly predict the covalent ligand binding mode, which correlates with the SAR data. The study is expected to provide insights into novel covalent ligand-FAAH binding interactions, and facilitate the design of covalent ligands against FAAH.

  2. Synthesis and Characterization of Transition Metal complexes with pyrimidine based ligand derivative

    NASA Astrophysics Data System (ADS)

    Awate, Ruchita; Mishra, Ashutosh; Mansuri, A.

    2016-10-01

    The article deals with a study of Synthesis Transition Metal Complexes Like copper and iron with Pyrimidine based ligand derivatives. The synthesized complex were characterized by XRD, SEM, FTIR. Mossbauer Spectra of Iron complex has also taken out to find oxidation state of iron after complexation.The aim of this study is to preparation and characterization with Transition Metal complexes by different physical and chemical characterization techniques.

  3. Synthesis, spectroscopic, coordination and biological activities of some organometallic complexes derived from thio-Schiff base ligands

    PubMed Central

    Abou-Hussein, Azza A.; Linert, Wolfgang

    2014-01-01

    Two series of mono- and binuclear complexes cyclic or acyclic thio-ferocine Schiff base ligands, derived from the condensation of 2-aminobenzenthiol (L) with monoacetyl ferrocene in the molar ratio 1:1 or in the molar ratio 1:2 for diacetyl ferocine have been prepared. The condensation reactions yield the corresponding Schiff Base ligands, HLa-Maf and H2Lb-Daf. The chelation of the ligands to metal ions occurs through the sulfur of the thiol group as well as the nitrogen atoms of the azomethine group of the ligands. HLa-Maf acts as monobasic bidentate or dibasic tetradentate, while H2Lb-Daf behaves as twice negatively cargend tetradentate ligand. The structures of these ligands were elucidated by elemental analysis, infrared, ultraviolet–visible spectra, as well as 1H NMR spectra. Reactions of the Schiff bases ligands with ruthenium(III), oxovanadium(IV) and dioxouranium(VI) afforded the corresponding transition metal complexes. The properties of the newly prepared complexes were analyse by elemental analyses, infrared, electronic spectra, 1H NMR as well as the magnetic susceptibility and conductivity measurement. The metal complexes exhibits different geometrical arrangements such as octahedral and square pyramidal coordination. Schiff base ligands and their metal complexes were tested against two pathogenic bacteria as Gram-positive and Gram-negative bacteria as well as one kind of fungi to study their biological activity. All the complexes exhibit antibacterial and antifungal activities against these organisms. PMID:24070648

  4. Synthesis, spectroscopic, coordination and biological activities of some organometallic complexes derived from thio-Schiff base ligands

    NASA Astrophysics Data System (ADS)

    Abou-Hussein, Azza A.; Linert, Wolfgang

    2014-01-01

    Two series of mono- and binuclear complexes cyclic or acyclic thio-ferocine Schiff base ligands, derived from the condensation of 2-aminobenzenthiol (L) with monoacetyl ferrocene in the molar ratio 1:1 or in the molar ratio 1:2 for diacetyl ferocine have been prepared. The condensation reactions yield the corresponding Schiff Base ligands, HLa-Maf and H2Lb-Daf. The chelation of the ligands to metal ions occurs through the sulfur of the thiol group as well as the nitrogen atoms of the azomethine group of the ligands. HLa-Maf acts as monobasic bidentate or dibasic tetradentate, while H2Lb-Daf behaves as twice negatively cargend tetradentate ligand. The structures of these ligands were elucidated by elemental analysis, infrared, ultraviolet-visible spectra, as well as 1H NMR spectra. Reactions of the Schiff bases ligands with ruthenium(III), oxovanadium(IV) and dioxouranium(VI) afforded the corresponding transition metal complexes. The properties of the newly prepared complexes were analyse by elemental analyses, infrared, electronic spectra, 1H NMR as well as the magnetic susceptibility and conductivity measurement. The metal complexes exhibits different geometrical arrangements such as octahedral and square pyramidal coordination. Schiff base ligands and their metal complexes were tested against two pathogenic bacteria as Gram-positive and Gram-negative bacteria as well as one kind of fungi to study their biological activity. All the complexes exhibit antibacterial and antifungal activities against these organisms.

  5. Natural-product-derived fragments for fragment-based ligand discovery

    NASA Astrophysics Data System (ADS)

    Over, Björn; Wetzel, Stefan; Grütter, Christian; Nakai, Yasushi; Renner, Steffen; Rauh, Daniel; Waldmann, Herbert

    2013-01-01

    Fragment-based ligand and drug discovery predominantly employs sp2-rich compounds covering well-explored regions of chemical space. Despite the ease with which such fragments can be coupled, this focus on flat compounds is widely cited as contributing to the attrition rate of the drug discovery process. In contrast, biologically validated natural products are rich in stereogenic centres and populate areas of chemical space not occupied by average synthetic molecules. Here, we have analysed more than 180,000 natural product structures to arrive at 2,000 clusters of natural-product-derived fragments with high structural diversity, which resemble natural scaffolds and are rich in sp3-configured centres. The structures of the cluster centres differ from previously explored fragment libraries, but for nearly half of the clusters representative members are commercially available. We validate their usefulness for the discovery of novel ligand and inhibitor types by means of protein X-ray crystallography and the identification of novel stabilizers of inactive conformations of p38α MAP kinase and of inhibitors of several phosphatases.

  6. Spectral, Magnetic and Biological Studie on Some Bivalent 3d Metal Complexes of Hydrazine Derived Schiff-Base Ligands

    PubMed Central

    Sherazi, Syed K. A.

    1997-01-01

    Metal(II) complexes of hydrazine derived Schiff-base ligands of the type M(L)2Cl2 where M = Co, Cu, Ni and Zn and L = L1 and L2 have been prepared and characterised by molar conductance, magnetic moment, elemental analysis and electronic, IR, H-NMR and 13C spectral data.The different modes of chelation of the ligands and their comparative biological properties against different bacterial species are reported. PMID:18475770

  7. Tunable emissive lanthanidomesogen derived from a room-temperature liquid-crystalline Schiff-base ligand.

    PubMed

    Pramanik, Harun A R; Das, Gobinda; Bhattacharjee, Chira R; Paul, Pradip C; Mondal, Paritosh; Prasad, S Krishna; Rao, D S Shankar

    2013-09-23

    A novel photoluminescent room-temperature liquid-crystalline salicylaldimine Schiff base with a short alkoxy substituent and a series of lanthanide(III) complexes of the type [Ln(LH)3(NO3)3] (Ln = La, Pr, Sm, Gd, Tb, Dy; LH = (E)-5-(hexyloxy)-2-[{2-(2-hydroxyethylamino)ethylimino]methyl}phenol) have been synthesized and characterized by FTIR, (1)H and (13)C NMR, UV/Vis, and FAB-MS analyses. The ligand coordinates to the metal ions in its zwitterionic form. The thermal behavior of the compounds was investigated by polarizing optical microscopy (POM) and differential scanning calorimetry (DSC). The ligand exhibits an enantiotropic hexagonal columnar (Col(h)) mesophase at room temperature and the complexes show an enantiotropic lamellar columnar (Col(L)) phase at around 120 °C with high thermal stability. Based on XRD results, different space-filling models have been proposed for the ligand and complexes to account for the columnar mesomorphism. The ligand exhibits intense blue emission both in solution and in the condensed state. The most intense emissions were observed for the samarium and terbium complexes, with the samarium complex glowing with a bright-orange light (ca. 560-644 nm) and the terbium complex emitting green light (ca. 490-622 nm) upon UV irradiation. DFT calculations performed by using the DMol3 program at the BLYP/DNP level of theory revealed a nine-coordinate structure for the lanthanide complexes.

  8. Synthesis, Characterization, DNA Interaction, and Antitumor Activities of La (III) Complex with Schiff Base Ligand Derived from Kaempferol and Diethylenetriamine

    PubMed Central

    Wang, Qin; Huang, Yu; Zhang, Jin-Sheng; Yang, Xin-Bin

    2014-01-01

    A novel La (III) complex, [LaL(H2O)3]NO3·3H2O, with Schiff base ligand L derived from kaempferol and diethylenetriamine, has been synthesized and characterized by elemental analysis, IR, UV-visible, 1H NMR, thermogravimetric analysis, and molar conductance measurements. The fluorescence spectra, circular dichroism spectra, and viscosity measurements and gel electrophoresis experiments indicated that the ligand L and La (III) complex could bind to CT-DNA presumably via intercalative mode and the La (III) complex showed a stronger ability to bind and cleave DNA than the ligand L alone. The binding constants (Kb) were evaluated from fluorescence data and the values ranged from 0.454 to 0.659 × 105 L mol−1 and 1.71 to 17.3 × 105 L mol−1 for the ligand L and La (III) complex, respectively, in the temperature range of 298–310 K. It was also found that the fluorescence quenching mechanism of EB-DNA by ligand L and La (III) complex was a static quenching process. In comparison to free ligand L, La (III) complex exhibited enhanced cytotoxic activities against tested tumor cell lines HL-60 and HepG-2, which may correlate with the enhanced DNA binding and cleaving abilities of the La (III) complex. PMID:25371657

  9. Synthesis and characterization of metal complexes of Schiff base ligand derived from imidazole-2-carboxaldehyde and 4-aminoantipyrine

    NASA Astrophysics Data System (ADS)

    Selwin Joseyphus, R.; Shiju, C.; Joseph, J.; Justin Dhanaraj, C.; Arish, D.

    2014-12-01

    The Co(II), Ni(II), Cu(II) and Zn(II) complexes of the Schiff base derived from imidazole-2-carboxaldehyde and 4-aminoantipyrine were synthesized. These compounds were characterized by elemental analysis, IR, mass, 1H NMR, electronic spectra, magnetic moment, molar conductance, thermal analysis, powder XRD and SEM. The analytical data show that the metal to ligand ratio is 1:1. The IR results show that the ligand acts as a bidentate donor coordinating through the azomethine nitrogen and imidazole nitrogen atoms. From the electronic spectra and magnetic moment value predicts the geometry of the complexes. The surface morphology of the compounds was studied by SEM. The compounds were screened for their antibacterial activity and antifungal activity using Kirby Bayer disc diffusion method. The DNA cleavage and superoxide dismutase activities of the compounds were investigated. The anticancer activities of the complexes have been carried out towards HeLa and HCT116 cancer cells.

  10. Discovery, synthesis, biological evaluation and structure-based optimization of novel piperidine derivatives as acetylcholine-binding protein ligands

    PubMed Central

    Shen, Jian; Yang, Xi-cheng; Yu, Ming-cheng; Xiao, Li; Zhang, Xun-jie; Sun, Hui-jiao; Chen, Hao; Pan, Guan-xin; Yan, Yu-rong; Wang, Si-chen; Li, Wei; Zhou, Lu; Xie, Qiong; Yu, Lin-qian; Wang, Yong-hui; Shao, Li-ming

    2017-01-01

    The homomeric α7 nicotinic receptor (α7 nAChR) is widely expressed in the human brain that could be activated to suppress neuroinflammation, oxidative stress and neuropathic pain. Consequently, a number of α7 nAChR agonists have entered clinical trials as anti-Alzheimer's or anti-psychotic therapies. However, high-resolution crystal structure of the full-length α7 receptor is thus far unavailable. Since acetylcholine-binding protein (AChBP) from Lymnaea stagnalis is most closely related to the α-subunit of nAChRs, it has been used as a template for the N-terminal domain of α-subunit of nAChR to study the molecular recognition process of nAChR-ligand interactions, and to identify ligands with potential nAChR-like activities. Here we report the discovery and optimization of novel acetylcholine-binding protein ligands through screening, structure-activity relationships and structure-based design. We manually screened in-house CNS-biased compound library in vitro and identified compound 1, a piperidine derivative, as an initial hit with moderate binding affinity against AChBP (17.2% inhibition at 100 nmol/L). During the 1st round of optimization, with compound 2 (21.5% inhibition at 100 nmol/L) as the starting point, 13 piperidine derivatives with different aryl substitutions were synthesized and assayed in vitro. No apparent correlation was demonstrated between the binding affinities and the steric or electrostatic effects of aryl substitutions for most compounds, but compound 14 showed a higher affinity (Ki=105.6 nmol/L) than nicotine (Ki=777 nmol/L). During the 2nd round of optimization, we performed molecular modeling of the putative complex of compound 14 with AChBP, and compared it with the epibatidine-AChBP complex. The results suggested that a different piperidinyl substitution might confer a better fit for epibatidine as the reference compound. Thus, compound 15 was designed and identified as a highly affinitive acetylcholine-binding protein ligand. In

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

    PubMed

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

    2013-01-14

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

  12. New Cu(II) complexes with pyrazolyl derived Schiff base ligands: Synthesis and biological evaluation.

    PubMed

    Ribeiro, Nádia; Roy, Somnath; Butenko, Nataliya; Cavaco, Isabel; Pinheiro, Teresa; Alho, Irina; Marques, Fernanda; Avecilla, Fernando; Costa Pessoa, João; Correia, Isabel

    2017-09-01

    Since the discovery of cisplatin there has been a continuous pursuit for new metallodrugs showing higher efficacies and lower side effects. In this work, new copper(II) complexes (C1-C6) of Schiff bases derived from pyrazolyl were developed. Through condensation of 5-methyl-1H-pyrazole-3-carbohydrazide with different aromatic aldehydes - pyridoxal, salicylaldehyde, 3-methoxy-2-hydroxybenzaldehyde, 3-ethoxy-2-hydroxybenzaldehyde and 2-hydroxynaphthene-1-carbaldehyde - a set of new pyrazole based "ONO" tridentate Schiff bases were obtained in moderate to good yields - L1-L6, as well as their Cu(II)-complexes. All compounds were characterized by analytical techniques and their molecular formulae established. The antioxidant potential of all compounds was tested, yielding low activity in most cases, with the exception of L1 and C5. The Cu(II) complexes were tested for their aqueous stability, and for their interaction with biological molecules, namely DNA and HSA (human serum albumin), through fluorescence quenching experiments (and electrophoresis for DNA). With the exception of C3, all the synthesized complexes were able to interact with DNA and HSA. Their cytotoxic activity against two cancer cell lines (MCF7 - breast and PC3 - prostate) was also evaluated. Complexes C5 and C6, with larger aromatic systems, showed much higher cytotoxicity (in the low μM range), than C1-C4, as well as IC50 values much lower than cisplatin. For C6 the results suggest that the mechanisms of cell death do not seem to be mediated by apoptosis, through caspases 3/7 activation, but by involving membrane potential and imbalance in physiological elements such as P, K and Ca. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Application of ligand- and receptor-based approaches for prediction of the HIV-RT inhibitory activity of fullerene derivatives

    NASA Astrophysics Data System (ADS)

    Yilmaz, Hayriye; Ahmed, Lucky; Rasulev, Bakhtiyor; Leszczynski, Jerzy

    2016-05-01

    Fullerene and its derivatives have potential to be utilized in many biomedical applications. In the present study, we investigated the role of fullerene derivatives as inhibitors of HIV-RT by combined protein-ligand docking approach and QSAR methods. The study shows the best predictive QSAR model that represents a two-variable model. It has a good ratio of the number of descriptors and predictive ability. The main contributions to the inhibitory activity are provided by signal JhetZ descriptor and μ (dipole moment, as a measure of the polarity of a compound). The developed GA-MLRA-based model demonstrates a good performance, confirmed by statistics ( {R2_{{training}} = 0.867,Q2 = 0.788,R2_{{test}} = 0.902} ). The structure-activity analysis of these fullerene analogues allowed us to design and suggest for synthesis a set of new potentially active fullerenes. Finally, the molecular docking analysis was carried out to understand the details of interactions between HIV-RT and fullerene-C60 derivatives.

  14. Ligand-based design, synthesis, and experimental evaluation of novel benzofuroxan derivatives as anti-Trypanosoma cruzi agents.

    PubMed

    Jorge, Salomão Dória; Palace-Berl, Fanny; Mesquita Pasqualoto, Kerly Fernanda; Ishii, Marina; Ferreira, Adilson Kleber; Berra, Carolina Maria; Bosch, Rosemary Viola; Maria, Durvanei Augusto; Tavares, Leoberto Costa

    2013-06-01

    A set of substituted-[N'-(benzofuroxan-5-yl)methylene]benzohydrazides (4a-t), previously designed and synthesized, was experimentally assayed against Trypanosoma cruzi, the etiological agent of Chagas' disease, one of the most neglected tropical diseases. Exploratory data analysis, Hansch approach and VolSurf formalism were applied to aid the ligand-based design of novel anti-T. cruzi agents. The best 2D-QSAR model showed suitable statistical measures [n = 18; s = 0.11; F = 42.19; R(2) = 0.90 and Q(2) = 0.77 (SDEP = 0.15)], and according to the optimum 3D-QSAR model [R(2) = 0.98, Q(2) = 0.93 (SDEP = 0.08)], three latent variables explained 62% of the total variance from original data. Steric and hydrophobic properties were pointed out as the key for biological activity. Based upon the findings, six novel benzofuroxan derivatives (4u-z) were designed, synthesized, and in vitro assayed to perform the QSAR external prediction. Then, the predictability for the both models, 2D-QSAR (Rpred(2) = 0.91) and 3D-QSAR (Rpred(2) = 0.77), was experimentally validated, and compound 4u was identified as the most active anti-T. cruzi hit (IC50 = 3.04 μM). Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  15. A Chromone-Derived Schiff-Base Ligand as Al(3+) "Turn on" Fluorescent Sensor: Synthesis and Spectroscopic Properties.

    PubMed

    Li, Chao-rui; Qin, Jing-can; Wang, Bao-dui; Fan, Long; Yan, Jun; Yang, Zheng-yin

    2016-01-01

    In this study, a novel chromone-derived Schiff-base ligand called 6-Hydroxy-3-formylchromone (2'-furan formyl) hydrazone (HCFH) has been designed and synthesized as a "turn on" fluorescent sensor for Al(3+). This sensor HCFH showed high selectivity and sensitivity towards Al(3+) over other metal ions investigated, and most metal ions had nearly no influences on the fluorescence response of HCFH to Al(3+). Additionally, the significant enhancement by about 171-fold in fluorescence emission intensity at 502 nm was observed in the presence of Al(3+) in ethanol, and it was due to the chelation-enhanced fluorescence (CHEF) effect upon complexation of HCFH with Al(3+) which inhibited the photoinduced electron transfer (PET) phenomenon from the Schiff-base nitrogen atom to chromone group. Moreover, this sensor formed a 1 : 1 complex with Al(3+) and the fluorescence response of HCFH to Al(3+) was nearly completed within 1 min. Thus, this sensor HCFH could be used to detect and recognize Al(3+) for real-time detection.

  16. Binding mode of triazole derivatives as aromatase inhibitors based on docking, protein ligand interaction fingerprinting, and molecular dynamics simulation studies

    PubMed Central

    Mojaddami, Ayyub; Sakhteman, Amirhossein; Fereidoonnezhad, Masood; Faghih, Zeinab; Najdian, Atena; Khabnadideh, Soghra; Sadeghpour, Hossein; Rezaei, Zahra

    2017-01-01

    Aromatase inhibitors (AIs) as effective candidates have been used in the treatment of hormone-dependent breast cancer. In this study, we have proposed 300 structures as potential AIs and filtered them by Lipinski's rule of five using DrugLito software. Subsequently, they were subjected to docking simulation studies to select the top 20 compounds based on their Gibbs free energy changes and also to perform more studies on the protein-ligand interaction fingerprint by AuposSOM software. In this stage, anastrozole and letrozole were used as positive control to compare their interaction fingerprint patterns with our proposed structures. Finally, based on the binding energy values, one active structure (ligand 15) was selected for molecular dynamic simulation in order to get information for the binding mode of these ligands within the enzyme cavity. The triazole of ligand 15 pointed to HEM group in aromatase active site and coordinated to Fe of HEM through its N4 atom. In addition, two π-cation interactions was also observed, one interaction between triazole and porphyrin of HEM group, and the other was 4-chloro phenyl moiety of this ligand with Arg115 residue. PMID:28255310

  17. On the conditions for enhanced transport through molecular junctions based on metal centres ligated by pairs of pyridazino-derived ligands

    SciTech Connect

    Ding, Bei; Washington, Victoria; Dunietz, Barry D

    2010-10-10

    Transport properties of a Ni bis-η{sup 2} complex ligated by a pair of bi-pyridazino derivative are considered. This complex provides the opportunity to avoid perpendicular alignment of the ligand π planes. We study the effects of π-bonding and of intramolecular hydrogen bonding between the ligands as mediated by the metal centre on electron transport. The complicated effect of the electronic structure equilibration with the electrodes on the transport is discussed. The analysis at the electronic structure level provides guidelines to design a molecular bridge that is based on metal complexation with effective electronic transport.

  18. Synthesis, spectroscopic characterization and DNA nuclease activity of Cu(II) complexes derived from pyrazolone based NSO-donor Schiff base ligands

    NASA Astrophysics Data System (ADS)

    Vyas, Komal M.; Joshi, Rushikesh G.; Jadeja, R. N.; Ratna Prabha, C.; Gupta, Vivek K.

    2011-12-01

    Two neutral mononuclear Cu(II) complexes have been prepared in EtOH using Schiff bases derived from 4-toluoyl pyrazolone and thiosemicarbazide. Both the ligands have been characterized on the basis of elemental analysis, IR, 1H NMR, 13C NMR and mass spectral data. The molecular geometry of one of these ligands has been determined by single crystal X-ray study. It reveals that these ligands exist in amine-one tautomeric form in the solid state. Microanalytical data, Cu-estimation, molar conductivity, magnetic measurements, IR, UV-Visible, FAB-Mass, TG-DTA data and ESR spectral studies were used to confirm the structures of the complexes. Electronic absorption and IR spectra of the complexes suggest a square-planar geometry around the central metal ion. The interaction of complexes with pET30a plasmid DNA was investigated by spectroscopic measurements. Results suggest that the copper complexes bind to DNA via an intercalative mode and can quench the fluorescence intensity of EB bound to DNA. The interaction between the complexes and DNA has also been investigated by agarose gel electrophoresis, interestingly, we found that the copper(II) complexes can cleave circular plasmid DNA to nicked and linear forms.

  19. Palladium(II) and zinc(II) complexes of neutral [N2O2] donor Schiff bases derived from furfuraldehyde: synthesis, characterization, fluorescence and corrosion inhibitors of ligands.

    PubMed

    Ali, Omyma A M

    2014-11-11

    Metal complexes of Schiff bases derived from furfuraldehyde and 4,5-dimethyl-1,2-phenylendiamine (L1) or 4,5-dichloro-1,2-phenylendiamine (L2) have been reported and characterized based on elemental analyses, IR, 1H NMR, UV-Vis, magnetic moment, molar conductance and thermal analysis. The complexes are found to have the formulae [PdL1-2]Cl2 and [ZnL1-2](AcO)2·H2O. The molar conductance data reveal that Pd(II) and Zn(II) chelates are ionic in nature and are of the type 2:1 electrolytes. The spectral data are consistent with a square planar and tetrahedral geometry around Pd(II) and Zn(II), respectively, in which the ligands act as tetradentate ligands. The thermal behavior of some chelates is studied and the activation thermodynamic parameters are calculated using Coats-Redfern method. The corrosion inhibition of stainless steel types 410 and 304 in 1 M HCl using the synthesized Schiff bases as inhibitors have been studied by weight loss method. The obtained data considered these ligands as efficient corrosion inhibitors. The ligands and their metal complexes exhibited considerable antibacterial activity against Staphylococcusaureus, and Escherichiacoli and antifungal activity against Candida albicans. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Palladium(II) and zinc(II) complexes of neutral [N2O2] donor Schiff bases derived from furfuraldehyde: Synthesis, characterization, fluorescence and corrosion inhibitors of ligands

    NASA Astrophysics Data System (ADS)

    Ali, Omyma A. M.

    2014-11-01

    Metal complexes of Schiff bases derived from furfuraldehyde and 4,5-dimethyl-1,2-phenylendiamine (L1) or 4,5-dichloro-1,2-phenylendiamine (L2) have been reported and characterized based on elemental analyses, IR, 1H NMR, UV-Vis, magnetic moment, molar conductance and thermal analysis. The complexes are found to have the formulae [PdL1-2]Cl2 and [ZnL1-2](AcO)2·H2O. The molar conductance data reveal that Pd(II) and Zn(II) chelates are ionic in nature and are of the type 2:1 electrolytes. The spectral data are consistent with a square planar and tetrahedral geometry around Pd(II) and Zn(II), respectively, in which the ligands act as tetradentate ligands. The thermal behavior of some chelates is studied and the activation thermodynamic parameters are calculated using Coats-Redfern method. The corrosion inhibition of stainless steel types 410 and 304 in 1 M HCl using the synthesized Schiff bases as inhibitors have been studied by weight loss method. The obtained data considered these ligands as efficient corrosion inhibitors. The ligands and their metal complexes exhibited considerable antibacterial activity against Staphylococcusaureus, and Escherichiacoli and antifungal activity against Candida albicans.

  1. Synthesis, structure and reactivity of Pd and Ir complexes based on new lutidine-derived NHC/phosphine mixed pincer ligands.

    PubMed

    Sánchez, Práxedes; Hernández-Juárez, Martín; Álvarez, Eleuterio; Paneque, Margarita; Rendón, Nuria; Suárez, Andrés

    2016-11-14

    Coordination studies of new lutidine-derived hybrid NHC/phosphine ligands (CNP) to Pd and Ir have been performed. Treatment of the square-planar [Pd(CNP)Cl](AgCl2) complex 2a with KHMDS produces the selective deprotonation at the CH2P arm of the pincer to yield the pyridine-dearomatised complex 3a. A series of cationic [Ir(CNP)(cod)](+) complexes 4 has been prepared by reaction of the imidazolium salts 1 with Ir(acac)(cod). These derivatives exhibit in the solid state, and in solution, a distorted trigonal bipyramidal structure in which the CNP ligands adopt an unusual C(axial)-N(equatorial)-P(equatorial) coordination mode. Reactions of complexes 4 with CO and H2 yield the carbonyl species 5a(Cl) and 6a(Cl), and the dihydrido derivatives 7, respectively. Furthermore, upon reaction of complex 4b(Br) with base, selective deprotonation at the methylene CH2P arms is observed. The, thus formed, deprotonated Ir complex 8b reacts with H2 in a ligand-assisted process leading to the trihydrido complex 9b, which can also be obtained by reaction of 7b(Cl) with H2 in the presence of KO(t)Bu. Finally, the catalytic activity of Ir-CNP complexes in the hydrogenation of ketones has been briefly assessed.

  2. Synthesis, characterization, crystal structure and HSA binding of two new N,O,O-donor Schiff-base ligands derived from dihydroxybenzaldehyde and tert-butylamine

    NASA Astrophysics Data System (ADS)

    Khosravi, Iman; Hosseini, Farnaz; Khorshidifard, Mahsa; Sahihi, Mehdi; Rudbari, Hadi Amiri

    2016-09-01

    Two new o-hydroxy Schiff-bases compounds, L1 and L2, were derived from the 1:1 M condensation of 2,3-dihydroxybenzaldehyde and 2,4-dihydroxybenzaldehyde with tert-butylamine and were characterized by elemental analysis, FT-IR, 1H and 13C NMR spectroscopies. The crystal structure of L2 was also determined by single crystal X-ray analysis. The crystal structure of L2 showed that the compound exists as a zwitterionic form in the solid state, with the H atom of the phenol group being transferred to the imine N atom. It adopts an E configuration about the central Cdbnd N double bond. Furthermore, binding of these Schiff base ligands to Human Serum Albumin (HSA) was investigated by fluorescence quenching, absorption spectroscopy, molecular docking and molecular dynamics (MD) simulation methods. The fluorescence emission of HSA was quenched by ligands. Also, suitable models were used to analyze the UV-vis absorption spectroscopy data for titration of HSA solution by various amounts of Schiff bases. The spectroscopic studies revealed that these Schiff bases formed 1:1 complex with HSA. Energy transfer mechanism of quenching was discussed and the values of 3.35 and 1.57 nm as the mean distances between the bound ligands and the HSA were calculated for L1 and L2, respectively. Molecular docking results indicated that the main active binding site for these Schiff bases ligands is in subdomain IB. Moreover, MD simulation results suggested that this Schiff base complex can interact with HSA, with a slight modification of its tertiary structure.

  3. Synthesis, structure and stability of a chiral imine-based Schiff-based ligand derived from L-glutamic acid and its [Cu4] complex

    NASA Astrophysics Data System (ADS)

    Muche, Simon; Levacheva, Irina; Samsonova, Olga; Biernasiuk, Anna; Malm, Anna; Lonsdale, Richard; Popiołek, Łukasz; Bakowsky, Udo; Hołyńska, Małgorzata

    2017-01-01

    Studies of the stability of a ligand derived from L-glutamic acid and ortho-vanillin and its new [Cu4] complex are presented. The [Cu4] complex contains a heterocubane [CuII4O4] core and pendant carboxylic groups increasing its solubility in water, also under basic conditions. The stability of the complex in different solvents is confirmed with ESI-MS studies and such experiments as successful recrystallization. The complex is stable also under physiological conditions whereas the ligand is partly decomposed to L-glutamic acid and ortho-vanillin.

  4. Seven phenoxido-bridged complexes encapsulated by 8-hydroxyquinoline Schiff base derivatives and β-diketone ligands: single-molecule magnet, magnetic refrigeration and luminescence properties.

    PubMed

    Wang, Shi-Yu; Wang, Wen-Min; Zhang, Hong-Xia; Shen, Hai-Yun; Jiang, Li; Cui, Jian-Zhong; Gao, Hong-Ling

    2016-02-28

    Seven dinuclear complexes based on 8-hydroxyquinoline Schiff base derivatives and β-diketone ligands, [RE2(hfac)4L2] (RE = Y (1), Gd (2), Tb (3), Dy (4), Ho (5), Er (6) and Lu (7); hfac(-) = hexafluoroacetylacetonate; HL = 2-[(4-chloro-phenylimino)-methyl]-8-hydroxyquinoline), have been synthesized, and structurally and magnetically characterized. Complexes 1-7 have similar dinuclear structures, in which each RE(III) ion is eight coordinated by two L(-) and two hfac(-) ligands in a distorted dodecahedron geometry. The luminescence spectra indicate that complex 3 exhibits characteristic Tb(III) ion luminescence, while 1 and 7 show HL ligand luminescence. The magnetic studies reveal that 2 features a magnetocaloric effect with the magnetic entropy change of -ΔSm = 16.83 J kg(-1) K(-1) at 2 K for ΔH = 8 T, and 4 displays slow magnetic relaxation behavior with the anisotropic barrier of 6.7 K and pre-exponential factor τ0 = 5.3 × 10(-6) s.

  5. Deriving structural and functional insights from a ligand-based hierarchical classification of G protein-coupled receptors.

    PubMed

    Attwood, T K; Croning, M D R; Gaulton, A

    2002-01-01

    G protein-coupled receptors (GPCRs) constitute the largest known family of cell-surface receptors. With hundreds of members populating the rhodopsin-like GPCR superfamily and many more awaiting discovery in the human genome, they are of interest to the pharmaceutical industry because of the opportunities they afford for yielding potentially lucrative drug targets. Typical sequence analysis strategies for identifying novel GPCRs tend to involve similarity searches using standard primary database search tools. This will reveal the most similar sequence, generally without offering any insight into its family or superfamily relationships. Conversely, searches of most 'pattern' or family databases are likely to identify the superfamily, but not the closest matching subtype. Here we describe a diagnostic resource that allows identification of GPCRs in a hierarchical fashion, based principally upon their ligand preference. This resource forms part of the PRINTS database, which now houses approximately 250 GPCR-specific fingerprints (http://www.bioinf.man.ac.uk/dbbrowser/gpcrPRINTS/). This collection of fingerprints is able to provide more sensitive diagnostic opportunities than have been realized by related approaches and is currently the only diagnostic tool for assigning GPCR subtypes. Mapping such fingerprints on to three-dimensional GPCR models offers powerful insights into the structural and functional determinants of subtype specificity.

  6. Chiral manganese (IV) complexes derived from Schiff base ligands: Synthesis, characterization, in vitro cytotoxicity and DNA/BSA interaction.

    PubMed

    Li, Zhen; Niu, Meiju; Chang, Guoliang; Zhao, Changqiu

    2015-12-01

    Two new couples of chiral manganese (IV) complexes with Schiff-base ligands, Λ-[Mn(R-L(1))2]·2(CH3OH) (Λ-1) and Δ-[Mn(S-L(1))2]·2(CH3OH) (Δ-1), Λ-[Mn(R-L(2))2]·(H2O)2 (Λ-2) and Δ-[Mn(S-L(2))2]·(H2O)2 (Δ-2), {H2L(1)=(R/S)-(±)-1-[(1-hydroxymethyl-propylimino)-methyl]-naphthalen-2-ol, H2L(2)=(R/S)-(±)-1-[(1-Hydroxymethyl-2-phenyl-ethylimino)-methyl]-naphthalen-2-ol} have been synthesized, and fully characterized by elemental analyses, UV-Vis spectrum, circular dichroism spectrum, FT-IR spectrum, mass spectrum, and single crystal X-ray diffraction (SXRD). The interaction of the four chiral Mn (IV) complexes with CT-DNA and BSA were also investigated by various spectroscopic techniques (UV-visible, fluorescence spectroscopic). The results show that the Δ-complexes exhibit more efficient CT-DNA interaction with respect to the Λ-complexes. All the complexes could quench the intrinsic fluorescence of BSA by a static quenching process. In addition, the vitro cytotoxicity of these complexes toward four kinds of cancerous cell lines (A549, HeLa, HL-60, and Caco-2) was assayed by the MTT method, which exhibited to be selectively active against certain cell lines.

  7. Antioxidation and DNA-binding properties of binuclear Er(III) complexes with Schiff-base ligands derived from 8-hydroxyquinoline-2-carboxaldehyde and four aroylhydrazines.

    PubMed

    Liu, Yong-Chun; Yang, Zheng-Yin

    2010-03-01

    The Er(III) complexes are prepared from Er(NO(3))(3).6H(2)O and Schiff-base ligands derived from 8-hydroxyquinoline-2-carboxaldehyde with four aroylhydrazines, including benzoylhydrazine, 2-hydroxybenzoylhydrazine, 4-hydroxybenzoylhydrazine and isonicotinylhydrazine, respectively. X-ray crystal and other structural analyses indicate that Er(III) and every ligand can form a binuclear Er(III) complex with nine-coordination and 1: 1 metal-to-ligand stoichiometry at the Er(III) centre. All the Er(III) complexes can bind to calf thymus DNA through intercalation with the binding constants at the order of magnitude 10(6) M(-1), and they may be used as potential anticancer drugs. All the Er(III) complexes have strong scavenging effects for hydroxyl radicals and superoxide radicals; however, complex containing active phenolic hydroxyl group shows stronger scavenging effects for hydroxyl radicals and complex containing N-heteroaromatic substituent shows stronger scavenging effects for superoxide radicals.

  8. Ligand- and structure-based virtual screening for clathrodin-derived human voltage-gated sodium channel modulators.

    PubMed

    Tomašić, Tihomir; Hartzoulakis, Basil; Zidar, Nace; Chan, Fiona; Kirby, Robert W; Madge, David J; Peigneur, Steve; Tytgat, Jan; Kikelj, Danijel

    2013-12-23

    Voltage-gated sodium channels (VGSC) are attractive targets for drug discovery because of the broad therapeutic potential of their modulators. On the basis of the structure of marine alkaloid clathrodin, we have recently discovered novel subtype-selective VGSC modulators I and II that were used as starting points for two different ligand-based virtual screening approaches for discovery of novel VGSC modulators. Similarity searching in the ZINC database of drug-like compounds based on compound I resulted in five state-dependent Na(v)1.3 and Na(v)1.7 modulators with improved activity compared to I (IC₅₀ < 20 μM). Compounds 2 and 16 that blocked sodium permeation in Na(v)1.7 with IC₅₀ values of 7 and 9 μM, respectively, are among the most potent clathrodin analogs discovered so far. In the case of compound II, 3D similarity searching in the same database was followed by docking of an enriched compound library into our human Na(v)1.4 open-pore homology model. Although some of the selected compounds, e.g., 31 and 32 displayed 21% and 22% inactivated state I(peak) block of Na(v)1.4 at 10 μM, respectively, none showed better Na(v)1.4 modulatory activity than compound II. Taken together, virtual screening yielded compounds 2 and 16, which represent novel scaffolds for the discovery of human Na(v)1.7 modulators.

  9. A new bioactive Schiff base ligands derived from propylazo-N-pyrimidin-2-yl-benzenesulfonamides Mn(II) and Cu(II) complexes: synthesis, thermal and spectroscopic characterization biological studies and 3D modeling structures.

    PubMed

    Tawfik, Abdelrazak M; El-Ghamry, Mosad A; Abu-El-Wafa, Samy M; Ahmed, Naglaa M

    2012-11-01

    New series of Schiff base ligand H(2)L and their Cu(II) and Mn(II) complexes derived from azosulfapyrimidine were synthesized and characterized by elemental and thermal studies conductance measurements IR, electronic and EPR spectra. 3D modeling of the ligand indicate that azo group does not participate in complex formation and surface potential on one of the ligand under study indicate that electron density around azomethine groups are much higher than the azo group therefore coordination takes place around azomethine groups. The variety in the geometrical structures depends on the nature of both the metal ions and the Schiff base ligands. The thermo kinetic parameters are calculated and discussed. The biological activities of the ligands and complexes have been screened in vitro against some bacteria and fungi to study their capacity to inhibit their growth and to study the toxicity of the compounds.

  10. A new bioactive Schiff base ligands derived from propylazo-N-pyrimidin-2-yl-benzenesulfonamides Mn(II) and Cu(II) complexes: Synthesis, thermal and spectroscopic characterization biological studies and 3D modeling structures

    NASA Astrophysics Data System (ADS)

    Tawfik, Abdelrazak M.; El-ghamry, Mosad A.; Abu-El-Wafa, Samy M.; Ahmed, Naglaa M.

    2012-11-01

    New series of Schiff base ligand H2L and their Cu(II) and Mn(II) complexes derived from azosulfapyrimidine were synthesized and characterized by elemental and thermal studies conductance measurements IR, electronic and EPR spectra. 3D modeling of the ligand indicate that azo group does not participate in complex formation and surface potential on one of the ligand under study indicate that electron density around azomethine groups are much higher than the azo group therefore coordination takes place around azomethine groups. The variety in the geometrical structures depends on the nature of both the metal ions and the Schiff base ligands. The thermo kinetic parameters are calculated and discussed. The biological activities of the ligands and complexes have been screened in vitro against some bacteria and fungi to study their capacity to inhibit their growth and to study the toxicity of the compounds.

  11. A Piezochromic Dysprosium(III) Single-Molecule Magnet Based on an Aggregation-Induced-Emission-Active Tetraphenylethene Derivative Ligand.

    PubMed

    Chen, Wen-Bin; Chen, Yan-Cong; Liu, Jun-Liang; Jia, Jian-Hua; Wang, Long-Fei; Li, Quan-Wen; Tong, Ming-Liang

    2017-08-07

    A bifunctional dysprosium(III) dimer, [Dy2(HTPEIP(OMe))2(OAc)4(NO3)2] (1), comprising an AIE-active (AIE = aggregation-induced emission) ligand of 2-methoxy-6-[[[4-(1,2,2-triphenylvinyl)phenyl]imino]methyl]phenol (HTPEIP(OMe)), was successfully synthesized. It not only behaves as a single-molecule magnet (SMM) with an energy barrier of 168(15) K at zero field but also exhibits piezochromism during the pressing-fuming cycle with switchable color, photoluminescence, and magnetic response.

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

    PubMed

    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.

  13. Synthesis, Characterization, Antimicrobial, DNA Cleavage, and In Vitro Cytotoxic Studies of Some Metal Complexes of Schiff Base Ligand Derived from Thiazole and Quinoline Moiety

    PubMed Central

    Yernale, Nagesh Gunvanthrao; Bennikallu Hire Mathada, Mruthyunjayaswamy

    2014-01-01

    A novel Schiff base ligand N-(4-phenylthiazol-2yl)-2-((2-thiaxo-1,2-dihydroquinolin-3-yl)methylene)hydrazinecarboxamide (L) obtained by the condensation of N-(4-phenylthiazol-2-yl)hydrazinecarboxamide with 2-thioxo-1,2-dihydroquinoline-3-carbaldehyde and its newly synthesized Cu(II), Co(II), Ni(II), and Zn(II) complexes have been characterized by elemental analysis and various spectral studies like FT-IR, 1H NMR, ESI mass, UV-Visible, ESR, TGA/DTA, and powder X-ray diffraction studies. The Schiff base ligand (L) behaves as tridentate ONS donor and forms the complexes of type [ML(Cl)2] with square pyramidal geometry. The Schiff base ligand (L) and its metal complexes have been screened in vitro for their antibacterial and antifungal activities by minimum inhibitory concentration (MIC) method. The DNA cleavage activity of ligand and its metal complexes were studied using plasmid DNA pBR322 as a target molecule by gel electrophoresis method. The brine shrimp bioassay was also carried out to study the in vitro cytotoxicity properties for the ligand and its metal complexes against Artemia salina. The results showed that the biological activities of the ligand were found to be increased on complexation. PMID:24729778

  14. Ligand-based CoMFA and CoMSIA studies on chromone derivatives as radical scavengers.

    PubMed

    Phosrithong, Narumol; Ungwitayatorn, Jiraporn

    2013-08-01

    The antioxidant activity for a series of chromone compounds, evaluated by DPPH free radical scavenging assay, were subjected to 3D-QSAR studies using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). All 48 chromone derivatives were geometry optimized by AM1 and HF/6-31G(*) calculations. The CoMFA and CoMSIA results were compared between different alignment strategies. The best CoMFA model obtained from HF/6-31G(*) optimization with field fit alignment gave cross-validated r(2) (q(2))=0.821, noncross-validated r(2)=0.987, S=0.095, and F=388.255. The best CoMSIA model derived from AM1 optimized structures and superimposition alignment gave q(2)=0.876, noncross-validated r(2)=0.976, S=0.129, and F=208.073, including electrostatic, hydrophobic, hydrogen bond donor and acceptor fields. The contour maps provide the fruitful structure-radical scavenging activity relationships which are useful for designing new compounds with higher activity. Copyright © 2013 Elsevier Inc. All rights reserved.

  15. New L-Serine Derivative Ligands as Cocatalysts for Diels-Alder Reaction

    PubMed Central

    Sousa, Carlos A. D.; Rodríguez-Borges, José E.; Freire, Cristina

    2013-01-01

    New L-serine derivative ligands were prepared and tested as cocatalyst in the Diels-Alder reactions between cyclopentadiene (CPD) and methyl acrylate, in the presence of several Lewis acids. The catalytic potential of the in situ formed complexes was evaluated based on the reaction yield. Bidentate serine ligands showed good ability to coordinate medium strength Lewis acids, thus boosting their catalytic activity. The synthesis of the L-serine ligands proved to be highly efficient and straightforward. PMID:24383009

  16. Coordination behavior of new bis Schiff base ligand derived from 2-furan carboxaldehyde and propane-1,3-diamine. Spectroscopic, thermal, anticancer and antibacterial activity studies

    NASA Astrophysics Data System (ADS)

    Mohamed, Gehad G.; Zayed, Ehab M.; Hindy, Ahmed M. M.

    2015-06-01

    Novel bis Schiff base ligand, [N1,N3-bis(furan-2-ylmethylene)propane-1,3-diamine], was prepared by the condensation of furan-2-carboxaldehyde with propane-1,3-diamine. Its conformational changes on complexation with transition metal ions [Co(II), Ni(II), Cu(II), Mn(II), Cd(II), Zn(II) and Fe(III)] have been studied on the basis of elemental analysis, conductivity measurements, spectral (infrared, 1H NMR, electronic), magnetic and thermogravimetric studies. The conductance data of the complexes revealed their electrolytic nature suggesting them as 1:2 (for bivalent metal ions) and 1:3 (for Fe(III) ion) electrolytes. The complexes were found to have octahedral geometry based on magnetic moment and solid reflectance measurements. Thermal analysis data revealed the decomposition of the complexes in successive steps with the removal of anions, coordinated water and bis Schiff base ligand. The thermodynamic parameters were calculated using Coats-Redfern equation. The Anticancer screening studies were performed on human colorectal cancer (HCT), hepatic cancer (HepG2) and breast cancer (MCF-7) cell lines. The antimicrobial activity of all the compounds was studied against Gram negative (Escherichia coli and Proteus vulgaris) and Gram positive (Bacillus vulgaris and Staphylococcus pyogones) bacteria. It was observed that the coordination of metal ion has a pronounced effect on the microbial activities of the bis Schiff base ligand. All the metal complexes have shown higher antimicrobial effect than the free bis Schiff base ligand.

  17. Weakly-bridged dimeric diorganotin(IV) compounds derived from pyruvic acid hydrazone Schiff base ligands: Synthesis, characterization and crystal structures

    NASA Astrophysics Data System (ADS)

    Hong, Min; Yin, Han-Dong; Cui, Ji-Chun

    2011-03-01

    We report the synthesis of four diorganotin(IV) compounds of Schiff base pyruvic acid hydrazone derivatives formulated as [R 2SnLY] 2, where L 1 is 2-SC 4H 3CON 2C(CH 3)CO 2 with Y = CH 3CH 2CH 2CH 2OH, R = n-Bu ( 1); L 2 is C 6H 5CON 2C(CH 3)CO 2 with Y = CH 3CH 2OH, R = p-F-Bz ( 2); L 3 is 2-HOC 6H 4CON 2C(CH 3)CO 2 with Y dbnd H 2O, R = p-CN -Bz ( 3); and L 4 is 4-NO 2-C 6H 4CON 2C(CH 3)CO 2 with Y dbnd CH 3CH 2OH, R = Bz ( 4). The structures of all compounds have been established by a combination of single-crystal X-ray diffraction analysis, 1H and 119Sn NMR spectroscopy, IR spectroscopy, and elemental analysis. Studies reveal that four ligands present the same coordination mode with tin center, which all present tridentate ONO donor Schiff bases and coordinate to the tin center in an enolic form. In compounds 1- 4, each tin atom is seven-coordinated and exhibits a distorted pentagonal bipyramid with a planar SnO 4N unit and two apical alkyl carbon atoms, thus forming a weakly-bridged dimeric molecule. Additionally, the distance of Sn⋯O bridge in each compound is obviously affected by the choice of different alkyl groups and coordination solvent molecules, which fluctuates in the range of 2.571(5)-2.839(4) Å. Furthermore, the supramolecular structure analysis show that there are two types of supramolecular infrastructures, 1D chain or 2D network, which are formed by intermolecular O-H···N or C-H⋯X (X = O, N or F) hydrogen bonds.

  18. Self-assembled copper(II) metallacycles derived from asymmetric Schiff base ligands: efficient hosts for ADP/ATP in phosphate buffer.

    PubMed

    Kumar, Amit; Pandey, Rampal; Kumar, Ashish; Gupta, Rakesh Kumar; Dubey, Mrigendra; Mohammed, Akbar; Mobin, Shaikh M; Pandey, Daya Shankar

    2015-10-21

    Novel asymmetric Schiff base ligands 2-{[3-(3-hydroxy-1-methyl-but-2-enylideneamino)-2,4,6-trimethylphenylimino]-methyl}-phenol (H2L(1)) and 1-{[3-(3-hydroxy-1-methyl-but-2-enylideneamino)-2,4,6-trimethylphenylimino]-methyl}-naphthalen-2-ol (H2L(2)) possessing dissimilar N,O-chelating sites and copper(ii) metallacycles (CuL(1))4 (1) and (CuL(2))4 (2) based on these ligands have been described. The ligands and complexes have been thoroughly characterized by satisfactory elemental analyses, and spectral (IR, (1)H, (13)C NMR, ESI-MS, UV/vis) and electrochemical studies. Structures of H2L(2) and 1 have been unambiguously determined by X-ray single crystal analyses. The crystal structure of H2L(2) revealed the presence of two distinct N,O-chelating sites on dissimilar cores (naphthalene and β-ketoaminato groups) offering a diverse coordination environment. Metallacycles 1 and 2 having a cavity created by four Cu(ii) centres coordinated in a homo- and heteroleptic fashion with respective ligands act as efficient hosts for adenosine-5'-diphosphate (ADP) and adenosine-5'-triphosphate (ATP) respectively, over other nucleoside polyphosphates (NPPs). The disparate sensitivity of these metallacycles toward ADP and ATP has been attributed to the size of the ligands assuming diverse dimensions and spatial orientations. These are attuned for π-π stacking and electrostatic interactions suitable for different guest molecules under analogous conditions, metallacycle 1 offers better orientation for ADP, while 2 for ATP. The mechanism of the host-guest interaction has been investigated by spectral and electrochemical studies and supported by molecular docking studies.

  19. Synthesis, characterization and biological relevance of some metal (II) complexes with oxygen, nitrogen and oxygen (ONO) donor Schiff base ligand derived from thiazole and 2-hydroxy-1-naphthaldehyde

    NASA Astrophysics Data System (ADS)

    Nagesh, G. Y.; Mruthyunjayaswamy, B. H. M.

    2015-04-01

    The novel Schiff base ligand 2-((2-hydroxynaphthalen-1-yl)methylene)-N-(4-phenylthiazol-2-yl)hydrazinecarboxamide (L) obtained by the condensation of N-(4-phenylthiazol-2-yl)hydrazinecarboxamide with 2-hydroxy-1-naphthaldehyde and its newly synthesized Cu(II), Co(II), Ni(II), Zn(II) and Cd(II) complexes have been characterized by microanalysis, molar conductance, IR, 1H NMR, ESI-mass, UV-Visible, TGA/DTA, ESR and powder X-ray diffraction data to explicate their structures. The IR results confirmed the tridentate binding of the ligand involving oxygen atom of amide carbonyl, azomethine nitrogen and naphthol oxygen. 1H NMR spectral data of the ligand (L) and its Zn(II) complex agreed well with the proposed structures. Thermogravimetric studies for Cu(II) and Ni(II) complexes indicated the presence of coordinated water molecules and the final product is the metal oxide. In order to appraise the effect of antimicrobial activity of metal ions upon chelation, the newly synthesized ligand and its metal complexes were screened for their antimicrobial activity by minimum inhibitory concentration (MIC) method. The DNA cleavage activities were studied using plasmid DNA pBR322 (Bangal re Genei, Bengaluru, Cat. No 105850) as a target molecule by agarose gel electrophoresis method. The brine shrimp bioassay was also carried out to study the in vitro cytotoxicity properties against Artemia salina. Furthermore, the antioxidant activity were determined in vitro by reduction of 1,1-diphenyl-2-picryl hydrazyl (DPPH). The ligand exhibited better in vitro-antioxidant activity than its metal complexes.

  20. Metal-pyrazolyl diazine interaction: synthesis, structure and electrochemistry of binuclear transition metal(II) complexes derived from an 'end-off' compartmental Schiff base ligand.

    PubMed

    Budagumpi, Srinivasa; Revankar, Vidyanand K

    2010-09-15

    Pyrazolyl diazine (mu-NN) bridged late first row transition metal(II) complexes have been prepared by the interaction of metal(II) chlorides with an 'end-off' compartmental Schiff base ligand. The ligand system has a strong diazine bridging component and obtained as a condensation product between 1H-pyrazole-3,5-dicarbohydrazide and 3-acetylcoumarin in absolute ethanol. All synthesized compounds are characterized on the basis of various spectral and analytical techniques. Complexes are found to be non-electrolytes and monomeric in nature. The magnetic exchange interactions are very weak because of the more electronegative exogenous chloride, though diazine bridging group bring metal centers in a close proximity.

  1. Ligating behaviour of Schiff base ligands derived from heterocyclic β-diketone and ethanol or propanol amine with oxovanadium (IV) metal ion

    NASA Astrophysics Data System (ADS)

    Thaker, B. T.; Barvalia, R. S.

    2009-12-01

    Synthesis and evaluation of six new oxovanadium (IV) complexes, formed by the interaction of vanadyl sulphate pentahydrate and the Schiff base, viz.; (HL 1)-(HL 3) and (HL 4)-(HL 6) such as 5-hydroxy-3-methyl-1(2-chloro)phenyl-1H-pyrazolone-4-carbaldehyde (I), 5-hydroxy-3-methyl-1(3-chloro)phenyl-1H-pyrazolone-4-carbaldehyde (II) and 5-hydroxy-3-methyl-1(3-sulphoamido)phenyl-1H-pyrazolone-4-carbaldehyde (III) with ethanol amine and propanol amine, respectively, in aqueous ethanol medium. The ligands and their Schiff base ligands have been characterized by elemental analyses, IR and 1H NMR. The resulting complexes have been characterized by elemental analyses, IR, 1H NMR, mass, electronic, electron spin resonance spectra, magnetic susceptibility measurement, molar conductance and thermal studies. The IR spectral data suggest that the ligand behaves as a dibasic bidentate with ON donor sequence towards metal ion. The molar conductivity data show them to be non-electrolytes. From the electronic, magnetic and ESR spectral data suggest that all the oxovanadium (IV) complexes have distorted octahedral geometry.

  2. Ligating behaviour of Schiff base ligands derived from heterocyclic beta-diketone and ethanol or propanol amine with oxovanadium (IV) metal ion.

    PubMed

    Thaker, B T; Barvalia, R S

    2009-12-01

    Synthesis and evaluation of six new oxovanadium (IV) complexes, formed by the interaction of vanadyl sulphate pentahydrate and the Schiff base, viz.; (HL(1))-(HL(3)) and (HL(4))-(HL(6)) such as 5-hydroxy-3-methyl-1(2-chloro)phenyl-1H-pyrazolone-4-carbaldehyde (I), 5-hydroxy-3-methyl-1(3-chloro)phenyl-1H-pyrazolone-4-carbaldehyde (II) and 5-hydroxy-3-methyl-1(3-sulphoamido)phenyl-1H-pyrazolone-4-carbaldehyde (III) with ethanol amine and propanol amine, respectively, in aqueous ethanol medium. The ligands and their Schiff base ligands have been characterized by elemental analyses, IR and (1)H NMR. The resulting complexes have been characterized by elemental analyses, IR, (1)H NMR, mass, electronic, electron spin resonance spectra, magnetic susceptibility measurement, molar conductance and thermal studies. The IR spectral data suggest that the ligand behaves as a dibasic bidentate with ON donor sequence towards metal ion. The molar conductivity data show them to be non-electrolytes. From the electronic, magnetic and ESR spectral data suggest that all the oxovanadium (IV) complexes have distorted octahedral geometry.

  3. Syntheses, characterisation and crystal structures of ferrocenyl β-diketones and their Schiff base Nsbnd Nsbnd O ligand derivatives with 2-picolylamine

    NASA Astrophysics Data System (ADS)

    Artigas, Vania; González, Deborah; Fuentealba, Mauricio

    2017-02-01

    Ferrocenyl β-diketones compounds β3-4 were synthesised by Claisen condensation reaction between acetylferrocene and ethyl benzoate or 4-bromoethyl benzoate. We also synthesised four new Schiff base ligands L1-4 by condensation reaction between β1-4 and 2-picolylamine. Identities of all these compounds were confirmed by satisfactory elemental analysis, 1H nuclear magnetic resonance (NMR) correlation and infrared (IR) spectroscopy. In addition, all these compounds were authenticated by a single-crystal X-ray diffraction analysis. In solution, 1H NMR spectra of β3 and β4 exhibit a mixture of keto:enol tautomer ratios of 12:88 and 8:92, respectively, calculated by the integration of the free cyclopentadienyl ring. In contrast, the proton NMR spectra of L1-4 showed only the keto-enamine tautomer displacements. In addition, decoupled 13C NMR spectrum clearly confirmed the existence of these tautomers. These results are in accordance with X-ray crystallographic studies, in which the enol and keto-enamine forms were elucidated for β-diketones and Schiff base ligands, respectively.

  4. Synthesis and novel fluorescence phenomenon of terbium complex with a new Schiff base ligand derived from condensation of triaminotriethylamine and 3-indolemethanal.

    PubMed

    Yang, Tian-Lin; Qin, Wen-Wu

    2007-06-01

    A new Schiff base ligand with tripodal structure, N,N',N''-tri-(3-indolemethanal)-triaminotriethylamine (L), and its complex with terbium was synthesized. The complex was characterized by element analysis, IR spectra, mass spectra, thermal analysis and molar conductivity. The terbium ion was found to coordinate to the Schiff base nitrogen atoms and the bridgehead nitrogen atom. The fluorescence properties of the complex in aqueous solutions were studied. Under the excitation of UV light, the complex exhibits characteristic fluorescence of terbium ion. H(+) concentration could strongly enhance the luminescence of terbium complex with L in aqueous solutions. This phenomenon will make the new complex favorable to be used in the fluorescence switches and sensors. The mechanism of the fluorescence enhancement by protonation of the indole nitrogen atoms is due to the suppressed photoinduced electron transfer (PIET) fluorescence quenching when adding acid.

  5. A New Ligand-Based Method for Purifying Active Human Plasma-Derived Ficolin-3 Complexes Supports the Phenomenon of Crosstalk between Pattern-Recognition Molecules and Immunoglobulins

    PubMed Central

    Man-Kupisinska, Aleksandra; Michalski, Mateusz; Maciejewska, Anna; Swierzko, Anna S.; Cedzynski, Maciej; Lugowski, Czeslaw; Lukasiewicz, Jolanta

    2016-01-01

    Despite recombinant protein technology development, proteins isolated from natural sources remain important for structure and activity determination. Ficolins represent a class of proteins that are difficult to isolate. To date, three methods for purifying ficolin-3 from plasma/serum have been proposed, defined by most critical step: (i) hydroxyapatite absorption chromatography (ii) N-acetylated human serum albumin affinity chromatography and (iii) anti-ficolin-3 monoclonal antibody-based affinity chromatography. We present a new protocol for purifying ficolin-3 complexes from human plasma that is based on an exclusive ligand: the O-specific polysaccharide of Hafnia alvei PCM 1200 LPS (O-PS 1200). The protocol includes (i) poly(ethylene glycol) precipitation; (ii) yeast and l-fucose incubation, for depletion of mannose-binding lectin; (iii) affinity chromatography using O-PS 1200-Sepharose; (iv) size-exclusion chromatography. Application of this protocol yielded average 2.2 mg of ficolin-3 preparation free of mannose-binding lectin (MBL), ficolin-1 and -2 from 500 ml of plasma. The protein was complexed with MBL-associated serine proteases (MASPs) and was able to activate the complement in vitro. In-process monitoring of MBL, ficolins, and total protein content revealed the presence of difficult-to-remove immunoglobulin G, M and A, in some extent in agreement with recent findings suggesting crosstalk between IgG and ficolin-3. We demonstrated that recombinant ficolin-3 interacts with IgG and IgM in a concentration-dependent manner. Although this association does not appear to influence ficolin-3-ligand interactions in vitro, it may have numerous consequences in vivo. Thus our purification procedure provides Ig-ficolin-3/MASP complexes that might be useful for gaining further insight into the crosstalk and biological activity of ficolin-3. PMID:27232184

  6. Synthesis, structure, magnetic properties and biological activity of supramolecular copper(II) and nickel(II) complexes with a Schiff base ligand derived from vitamin B6.

    PubMed

    Mukherjee, Tirtha; Costa Pessoa, João; Kumar, Amit; Sarkar, Asit R

    2013-02-21

    Three new complexes of Cu(II) and Ni(II), [Cu(II)(H(2)pydmedpt)](2+)·2Cl(-) (1), [Ni(II)(H(2)pydmedpt)](2+)·2Cl(-) (2) and [Ni(II)(pydmedpt)(OH)](-)·K(+) (3) of the Schiff base ligand [H(2)pydmedpt](2+)·2Cl(-) were synthesized by the in situ reaction of pyridoxal (pyd), a vitamer of vitamin B(6), N,N-bis[3-aminopropyl]methylamine (medpt) and copper(II) acetate or nickel(II) acetate, respectively. The molecular structures of 1 and 2 were determined by single crystal X-ray diffraction studies. The structure of 3 in the solid state was inferred by elemental analysis, diffuse reflectance spectrum, variable temperature magnetic moment studies and DFT calculations. The binding of the Schiff base ligand to the metal centers involves two phenolato oxygens, two imine nitrogens and one amine nitrogen. The coordination geometry around Cu in 1 is distorted square pyramidal and that around the Ni atom in 2 is intermediate between square-pyramidal and trigonal-bipyramidal. In the crystals the compounds form supramolecular one dimensional chain structures stabilized by hydrogen bonding and π-π stacking interactions. Variable temperature magnetic moment data of 2 indicate the presence of a momomeric high spin Ni(II) centre in the complex. The solid state diffuse reflectance spectrum, conductance and elemental analysis suggest that 3 is a Ni(II) complex with a tetragonally distorted octahedral field, the sixth position being occupied by the oxygen atom of a hydroxyl group. The variable temperature magnetic moment of 3 indicates the presence of a ferromagnetic dinuclear species (29.2%) along with the major monomeric species, the intra-dimer exchange term J value being 14.3 cm(-1). The competitive binding of 1 and 2 with DNA was studied in the concentration range 40 to 400 μM, the apparent binding constants being K = 2.9 × 10(3) and 6.7 × 10(3) M(-1), respectively. Human Serum Albumin (HSA) binding studies were carried out at concentrations of 800-1000 μM and 400-500

  7. Chitosan and Its Derivatives as Highly Efficient Polymer Ligands.

    PubMed

    Pestov, Alexander; Bratskaya, Svetlana

    2016-03-11

    The polyfunctional nature of chitosan enables its application as a polymer ligand not only for the recovery, separation, and concentration of metal ions, but for the fabrication of a wide spectrum of functional materials. Although unmodified chitosan itself is the unique cationic polysaccharide with very good complexing properties toward numerous metal ions, its sorption capacity and selectivity can be sufficiently increased and turned via chemical modification to meet requirements of the specific applications. In this review, which covers results of the last decade, we demonstrate how different strategies of chitosan chemical modification effect metal ions binding by O-, N-, S-, and P-containing chitosan derivatives, and which mechanisms are involved in binding of metal cation and anions by chitosan derivatives.

  8. Understanding the Molecular Determinant of Reversible Human Monoamine Oxidase B Inhibitors Containing 2H-chromen-2-One Core: Structure-Based and Ligand-Based Derived 3-D QSAR Predictive Models.

    PubMed

    Mladenovic, Milan; Patsilinakos, Alexandros; Pirolli, Adele; Sabatino, Manuela; Ragno, Rino

    2017-03-14

    Monoamine oxidase B (MAO B) catalyzes the oxidative deamination of aryalkylamines neurotransmitters with concomitant reduction of oxygen to hydrogen peroxide. Consequently, the enzyme's malfunction can induce oxidative damage to mitochondrial DNA and mediates development of Parkinson's disease. Thus, MAO B emerges as a promising target for developing pharmaceuticals potentially useful to treat this vicious neurodegenerative condition. Aiming to contribute to the development of drugs with the reversible mechanism of MAO B inhibition only, herein, an extended in silico-in vitro procedure for the selection of novel MAO B inhibitors is demonstrated, including: (1) definition of optimized and validated structure-based (SB) 3-D QSAR models derived from available co-crystallized inhibitor-MAO B complexes; (2) elaboration of structure-activity relationships (SAR) features for either irreversible or reversible MAO B inhibitors to characterize and improve coumarin-based inhibitor activity (Protein Data Bank ID: 2V61) as the most potent reversible lead compound; (3) definition of structure-based (SB) and ligand-based (LB) alignment rules assessments by which virtually any untested potential MAO B inhibitor might be evaluated; (4) predictive ability validation of the best 3-D QSAR model through SB/LB modeling of four coumarin-based external test sets (267 compounds); (5) design and SB/LB alignment of novel coumarin-based scaffolds experimentally validated through synthesis and biological evaluation in vitro. Due to the wide range of molecular diversity within the 3-D QSARs training set and derived features, the selected N probe-derived 3-D QSAR model proves to be a valuable tool for virtual screening (VS) of novel MAO B inhibitors and a platform for design, synthesis and evaluation of novel active structures. Accordingly, six highly active and selective MAO B inhibitors (picomolar to low nanomolar range of activity) were disclosed as a result of rational SB/LB 3-D QSAR design

  9. Synthesis, spectral and magnetic studies of mono- and bi-nuclear metal complexes of a new bis(tridentate NO2) Schiff base ligand derived from 4,6-diacetylresorcinol and ethanolamine.

    PubMed

    Shebl, Magdy

    2009-07-15

    A new bis(tridentate NO2) Schiff base ligand, H(4)L, was prepared by the reaction of the bifunctional carbonyl compound; 4,6-diacetylresorcinol (DAR) with ethanolamine. The ligand reacted with iron(III), cobalt(II), nickel(II), copper(II), zinc(II), cadmium(II), cerium(III) and uranyl(VI) ions, in absence and in presence of LiOH, to yield mono- and bi-nuclear complexes with different coordinating sites. The ligand and its metal complexes were characterized by elemental analyses, IR, (1)H NMR, electronic, ESR and mass spectra, conductivity and magnetic susceptibility measurements as well as thermal analyses. In absence of LiOH, mononuclear complexes (2, 3 and 5-9) as well as binuclear complexes (1 and 4) were obtained. In mononuclear complexes, the ligand acted as a neutral, mono- and di-basic/bi- and tetra-dentate ligand while in binuclear complexes (1 and 4), the ligand acted as a bis(mono- or di-basic/tridentate) ligand. On the other hand, in presence of LiOH, only binuclear complexes (10-15) were obtained in which the ligand acted as a bis(dibasic tridentate) ligand. The metal complexes exhibited different geometrical arrangements such as octahedral, tetrahedral, square planar, square pyramidal and pentagonal bipyramidal arrangements.

  10. Ligand-based virtual screening under partial shape constraints

    NASA Astrophysics Data System (ADS)

    von Behren, Mathias M.; Rarey, Matthias

    2017-04-01

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

  11. Ligand-based virtual screening under partial shape constraints

    NASA Astrophysics Data System (ADS)

    von Behren, Mathias M.; Rarey, Matthias

    2017-03-01

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

  12. Ligand-based virtual screening under partial shape constraints.

    PubMed

    von Behren, Mathias M; Rarey, Matthias

    2017-04-01

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

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

    SciTech Connect

    Klei, Herbert E.; Moriarty, Nigel W. Echols, Nathaniel; Terwilliger, Thomas C.; Baldwin, Eric T.; Pokross, Matt; Posy, Shana; Adams, Paul D.

    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

  14. Scouting new sigma receptor ligands: Synthesis, pharmacological evaluation and molecular modeling of 1,3-dioxolane-based structures and derivatives.

    PubMed

    Franchini, Silvia; Battisti, Umberto Maria; Prandi, Adolfo; Tait, Annalisa; Borsari, Chiara; Cichero, Elena; Fossa, Paola; Cilia, Antonio; Prezzavento, Orazio; Ronsisvalle, Simone; Aricò, Giuseppina; Parenti, Carmela; Brasili, Livio

    2016-04-13

    Herein we report the synthesis and biological activity of new sigma receptor (σR) ligands obtained by combining different substituted five-membered heterocyclic rings with appropriate σR pharmacophoric amines. Radioligand binding assay, performed on guinea pig brain membranes, identified 25b (1-(1,4-dioxaspiro[4.5]decan-2-ylmethyl)-4-benzylpiperazine) as the most interesting compound of the series, displaying high affinity and selectivity for σ1R (pKiσ1 = 9.13; σ1/σ2 = 47). The ability of 25b to modulate the analgesic effect of the κ agonist (-)-U-50,488H and μ agonist morphine was evaluated in vivo by radiant heat tail-flick test. It exhibited anti-opioid effects on both κ and μ receptor-mediated analgesia, suggesting an agonistic behavior at σ1R. Docking studies were performed on the theoretical σ1R homology model. The present work represents a new starting point for the design of more potent and selective σ1R ligands.

  15. Di- and octa-nuclear dysprosium clusters derived from pyridyl-triazole based ligand: {Dy2} showing single molecule magnetic behaviour.

    PubMed

    Akhtar, Muhammad Nadeem; Liao, Xiao-Fen; Chen, Yan-Cong; Liu, Jun-Liang; Tong, Ming-Liang

    2017-02-28

    Two dysprosium aggregates, formulated as [Dy2(μ-OH)2(H2bpte)2Cl2(MeOH)2]Cl2 (1), and [Dy8(μ-OH)8(bpte)8]·24H2O (2) (H2bpte = 1,2-bis(3-(pyridin-2-yl)-1H-1,2,4-triazol-5-yl)ethane), were obtained using solvothermal reactions. Upon changing the metal salt and synthetic reaction conditions, an eight-member {Dy8} (2) ring was isolated. Complex 1 is centrosymmetric in which two {Dy2} clusters are connecting to each other through the hydrogen bonding. Complex 2 forms an eight-member Dy(III) ring with an inner diameter of 4.5 Å and is the first reported {Dy8(μ-OH)8} core in lanthanide-hydroxo clusters. The H2bpte ligand displays trans,trans- and cis,cis-coordination modes in 1 and 2, respectively. Alternating current (ac) magnetic measurements of both complexes were carried out. In 1, the out-of-phase susceptibilities (χ''M) below 9 K confirm the slow relaxation of magnetization, which is a typical characteristic of single-molecule magnets (SMMs).

  16. Electronic communication across diamagnetic metal bridges: a homoleptic gallium(III) complex of a redox-active diarylamido-based ligand and its oxidized derivatives

    PubMed Central

    Liddle, Brendan J.; Wanniarachchi, Sarath; Hewage, Jeewantha S.; Lindeman, Sergey V.; Bennett, Brian; Gardinier, James R.

    2012-01-01

    Complexes with cations of the type [Ga(L)2]n+ where L = bis(4-methyl-2-(1H-pyrazol-1-yl)phenyl)amido and n = 1, 2, 3 have been prepared and structurally characterized. The electronic properties of each were probed by electrochemical and spectroscopic means and were interpreted with the aid of DFT calculations. The dication, best described as [Ga(L−)(L0)]2+, and is a Robin-Day class II mixed-valence species. As such, a broad, weak, solvent-dependent intervalence charge transfer (IVCT) band was found in the NIR spectrum in the range 6390 to 6925 cm−1, depending on solvent. Band shape analyses and the use of Hush and Marcus relations revealed a modest electronic coupling, Hab of about 200 cm−1, and a large rate constant for electron transfer, ket, on the order of 1010 s−1 between redox active ligands. The di-oxidized complex [Ga(L0)2]3+ shows a half-field ΔMs = 2 transition in its solid-state X-Band EPR spectrum at 5 K which indicates that the triplet state is thermally populated. DFT calculations (M06/Def2-SV(P)) suggest that the singlet state is 21.7 cm−1 lower in energy than the triplet state. PMID:23163736

  17. Container molecules based on imine type ligands.

    PubMed

    Schulze, A Carina; Oppel, Iris M

    2012-01-01

    This chapter will give a short overview about container molecules, their synthesis and possible applications. The main focus is on those which are based on imine type ligands. These containers can be used for example for guest exchange, gas separation, as chemical sensors or for the stabilisation of white phosphorus under water. The described cages have wide openings or tightly closed ones. For one cage the reversible opening and closing is also described.

  18. Chiral ligands derived from monoterpenes: application in the synthesis of optically pure secondary alcohols via asymmetric catalysis.

    PubMed

    El Alami, Mohammed Samir Ibn; El Amrani, Mohamed Amin; Agbossou-Niedercorn, Francine; Suisse, Isabelle; Mortreux, André

    2015-01-19

    The preparation of optically pure secondary alcohols in the presence of catalysts based on chiral ligands derived from monoterpenes, such as pinenes, limonenes and carenes, is reviewed. A wide variety of these ligands has been synthesized and used in several catalytic reactions, including hydrogen transfer, C-C bond formation via addition of organozinc compounds to aldehydes, hydrosilylation, and oxazaborolidine reduction, leading to high activities and enantioselectivities.

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

    PubMed Central

    Klei, Herbert E.; Moriarty, Nigel W.; Echols, Nathaniel; Terwilliger, Thomas C.; Baldwin, Eric T.; Pokross, Matt; Posy, Shana; Adams, Paul D.

    2014-01-01

    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 leverages prior knowledge from earlier structures to facilitate ligand placement in the current structure. PMID:24419386

  20. Technetium radiodiagnostic fatty acids derived from bisamide bisthiol ligands

    DOEpatents

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

    1988-05-24

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

  1. Bowl-shaped aromatic hydrocarbon precursors of fullerenes as η6-π-ligands in transition metal complexes: Complexes based on sumanene C21H12 derivatives

    NASA Astrophysics Data System (ADS)

    Gal'Pern, E. G.; Stankevich, I. V.

    2008-06-01

    The density functional theory in the PBE approximation was used to explore the geometry and electronic structure of sumanene C21H12 and its five derivatives C21H12R6 (R = H, F, Cl, Br, and CN). The R groups in C21H12R6 molecules are attached to carbon atoms in α positions with respect to the central six-membered ring. The possibility of the formation of C21H12R6η 6-π complexes with Cr(C6H6), Cr(CO)3, Mo(C6H6), and Mo(CO)3 was discussed. The relative stability of these complexes was evaluated. The attachment of M(C6H6) and M(CO)3 (M = Cr, Mo) to sumanene C21H12 with the formation of η6-π bonds is energetically less favorable than their attachment to sumanene derivatives C21H12R6. The complexes of sumanene derivatives with Cr(C6H6), Cr(CO)3, Mo(C6H6), and Mo(CO)3 were found to be the most promising objects for synthesis. The C60 and η6-(C6H6)M-C60 and η6-(CO)3M-C60 (M = Cr, Mo) fullerene complexes were predicted to be much less stable than the η6-(CO)3M-C60R6 and η6-(C6H6)M-C60R6 complexes (M = Cr, Mo; R = H, Hal, CN), where R groups bordered one of the fullerene C60 six-membered rings comprising the atoms to which metal atoms were coordinated.

  2. Structural insights of JAK2 inhibitors: pharmacophore modeling and ligand-based 3D-QSAR studies of pyrido-indole derivatives.

    PubMed

    Gade, Deepak Reddy; Kunala, Pavan; Raavi, Divya; Reddy, Pavan Kumar K; Prasad, Rajendra V V S

    2015-04-01

    In this study we have performed pharmacophore modeling and built a 3D QSAR model for pyrido-indole derivatives as Janus Kinase 2 inhibitors. An efficient pharmacophore has been identified from a data set of 51 molecules and the identified pharmacophore hypothesis consisted of one hydrogen bond acceptor, two hydrogen bond donors and three aromatic rings, i.e. ADDRRR. A powerful 3D-QSAR model has also been constructed by employing Partial Least Square regression analysis with a regression coefficient of 0.97 (R(2)) and Q(2) of 0.95, and Pearson-R of 0.98.

  3. Design and synthesis of novel bivalent ligands (MOR and DOR) by conjugation of enkephalin analogues with 4-anilidopiperidine derivatives.

    PubMed

    Deekonda, Srinivas; Wugalter, Lauren; Rankin, David; Largent-Milnes, Tally M; Davis, Peg; Wang, Yue; Bassirirad, Neemah M; Lai, Josephine; Kulkarni, Vinod; Vanderah, Todd W; Porreca, Frank; Hruby, Victor J

    2015-10-15

    We describe the design and synthesis of novel bivalent ligands based on the conjugation of 4-anilidopiperidine derivatives with enkephalin analogues. The design of non-peptide analogues is explored with 5-amino substituted (tetrahydronaphthalen-2yl) methyl containing 4-anilidopiperidine derivatives, while non-peptide-peptide ligands are explored by conjugating the C-terminus of enkephalin analogues (H-Xxx-DAla-Gly-Phe-OH) to the amino group of 4-anilidopiperidine small molecule derivatives with and without a linker. These novel bivalent ligands are evaluated for biological activities at μ and δ opioid receptors. They exhibit very good affinities at μ and δ opioid receptors, and potent agonist activities in MVD and GPI assays. Among these the lead bivalent ligand 17 showed excellent binding affinities (0.1 nM and 0.5 nM) at μ and δ opioid receptors respectively, and was found to have very potent agonist activities in MVD (56 ± 5.9 nM) and GPI (4.6 ± 1.9 nM) assays. In vivo the lead bivalent ligand 17 exhibited a short duration of action (<15 min) comparable to 4-anilidopiperidine derivatives, and moderate analgesic activity. The ligand 17 has limited application against acute pain but may have utility in settings where a highly reversible analgesic is required. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. Synthesis characterization and cytotoxicity studies of platinum(II) complexes with reduced amino pyridine schiff base and its derivatives as ligands.

    PubMed

    Li, Li-Jun; Yan, Qin-Qin; Liu, Guo-Jun; Yuan, Zhen; Lv, Zhen-Hua; Fu, Bin; Han, Yan-Jun; Du, Jian-Long

    2017-03-14

    A series of reduced amino pyridine Schiff base platinum(II) complexes were prepared as potential anticancer drugs, and characterized by NMR, IR spectroscopy, elemental analysis, and molar conductivity. UV and CD results showed the binding mode between these compounds and salmon sperm DNA may be intercalation. The cytotoxicity of these complexes was validated against A549, Hela, and MCF-7 cell lines by MTT assay. Some complexes exhibited better cytotoxic activity than cisplatin against Hela and MCF-7 cell lines.

  5. Syntheses, structures and characteristics of four alkaline-earth metal-organic frameworks (MOFs) based on benzene-1,2,4,5-tetracarboxylicacid and its derivative ligand

    NASA Astrophysics Data System (ADS)

    Du, Shunfu; Ji, Chunqing; Xin, Xuelian; Zhuang, Mu; Yu, Xuying; Lu, Jitao; Lu, Yukun; Sun, Daofeng

    2017-02-01

    Two new pillar-layered Ba(II)-based 3D frameworks and two new Ca(II)-based 3D supramolecular frameworks, [Ba2(dbtec)(H2O)2]n (1), [Ca2(dbtec)(H2O)8]n (2), {[Ba2(H2btec)·H2O]·0.5H2O}n (3) and [Ca(H2btec)·H2O]n (4) (H4dbtec = 3,6-dibromobenzene-1,2,4,5-tetracarboxylic acid; H4btec = benzene-1,2,4,5-tetracarboxylic acid), have been synthesized under similar reaction conditions and stoichiometry. Single crystal X-ray diffraction study reveals axial-orientation Br···π supramolecular interactions exist in the crystal structure of 1, which keeps an 3D binodal network with the (32.412.510.62.72)(32.46.56.6)2 topology. Whereas in 2, intramolecular and intermolecular H-bonding interactions with the ligated water molecules promote the formation of 3D supramolecular frameworks network. For 3, a new 3D 3-nodal network occurs in the structure and some rare coordination modes for the H4btec are observed. There is a 2D double layer with the thickness of 7.60 Å in 4. In addition, besides the high thermal stability, the FTIR spectra, PXRD patterns and the photoluminescent of these compounds are also discussed.

  6. Increasing the CO2 /N2 Selectivity with a Higher Surface Density of Pyridinic Lewis Basic Sites in Porous Carbon Derived from a Pyridyl-Ligand-Based Metal-Organic Framework.

    PubMed

    Li, Liangjun; Wang, Ying; Gu, Xin; Yang, Qipeng; Zhao, Xuebo

    2016-07-05

    The development of functional porous carbon with high CO2 /N2 selectivity is of great importance for CO2 capture. In this paper, a type of porous carbon with doped pyridinic sites (termed MOFC) was prepared from the carbonization of a pyridyl-ligand based MOF. Four MOFCs derived from different carbonizing temperatures were prepared. Structural studies revealed high contents of pyridinic-N groups and nearly the same pore-size distributions for these MOFCs. Gas-sorption studies revealed outstanding CO2 uptake at low pressures and room temperature. Owing to the high content of pyridinic-N groups, the CO2 /N2 selectivity on these MOFCs exhibits values of about 40-50, which are among the top values in carbon materials. Further correlation studies demonstrated that the CO2 /N2 selectivities show a positive linear relationship with the surface density of pyridinic-N groups, thus validating the synergistic effect of the doped pyridinic-N groups on CO2 adsorption selectivity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Predicting Monoamine Oxidase Inhibitory Activity through Ligand-Based Models

    PubMed Central

    Vilar, Santiago; Ferino, Giulio; Quezada, Elias; Santana, Lourdes; Friedman, Carol

    2013-01-01

    The evolution of bio- and cheminformatics associated with the development of specialized software and increasing computer power has produced a great interest in theoretical in silico methods applied in drug rational design. These techniques apply the concept that “similar molecules have similar biological properties” that has been exploited in Medicinal Chemistry for years to design new molecules with desirable pharmacological profiles. Ligand-based methods are not dependent on receptor structural data and take into account two and three-dimensional molecular properties to assess similarity of new compounds in regards to the set of molecules with the biological property under study. Depending on the complexity of the calculation, there are different types of ligand-based methods, such as QSAR (Quantitative Structure-Activity Relationship) with 2D and 3D descriptors, CoMFA (Comparative Molecular Field Analysis) or pharmacophoric approaches. This work provides a description of a series of ligand-based models applied in the prediction of the inhibitory activity of monoamine oxidase (MAO) enzymes. The controlled regulation of the enzymes’ function through the use of MAO inhibitors is used as a treatment in many psychiatric and neurological disorders, such as depression, anxiety, Alzheimer’s and Parkinson’s disease. For this reason, multiple scaffolds, such as substituted coumarins, indolylmethylamine or pyridazine derivatives were synthesized and assayed toward MAO-A and MAO-B inhibition. Our intention is to focus on the description of ligand-based models to provide new insights in the relationship between the MAO inhibitory activity and the molecular structure of the different inhibitors, and further study enzyme selectivity and possible mechanisms of action. PMID:23231398

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

    PubMed Central

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

    2005-01-01

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

  9. Antimicrobial metal-based thiophene derived compounds.

    PubMed

    Yasmeen, Shakeela; Sumrra, Sajjad Hussain; Akram, Muhammad Safwan; Chohan, Zahid H

    2017-12-01

    A novel series of thiophene derived Schiff bases and their transition metal- [Co(II), Cu(II), Zn(II), Ni(II)] based compounds are reported. The Schiff bases act as tridentate ligands toward metal ions via azomethine-N, deprotonated-N of ammine substituents and S-atom of thienyl moiety. The synthesized ligands along with their metal complexes were screened for their in vitro antibacterial activity against six bacterial pathogens (Escherichia coli, Shigella flexneri, Pseudomonas aeruginosa, Salmonella typhi, Staphylococcus aureus and Bacillus subtilis) and for antifungal activity against six fungal pathogens (Trichophytonlongifusus, Candida albicans, Aspergillus flavus, Microsporum canis, Fusarium solani and Candida glabrata). The results of antimicrobial studies revealed the free ligands to possess potential activity which significantly increased upon chelation.

  10. Triphos derivatives and diphosphines as ligands in the ruthenium-catalysed alcohol amination with NH3.

    PubMed

    Nakagawa, N; Derrah, E J; Schelwies, M; Rominger, F; Trapp, O; Schaub, T

    2016-04-28

    The ruthenium-triphos and diphosphine-catalysed amination of alcohols with ammonia is reported. Various types of triphos derivatives with electron-donating functional group were synthesized and used as ligands in the Ru-catalysed alcohol amination with NH3. The triphos derivatives are effective for the formation of primary amines. On the other hand, if hemilabile diphosphines as tridentate ligands are used, mixtures of secondary-along with primary amines are obtained. It was found that even simple diphosphines can be used as ligands for the selective formation of the secondary amines. The diphosphine system allows a new entry to the Ru-catalysed formation of secondary amines.

  11. The effect of wastewater effluent derived ligands on copper and zinc complexation.

    PubMed

    Constantino, C; Comber, S D W; Scrimshaw, M D

    2017-03-01

    The shift toward bioavailability-based standards for metals such as copper and zinc not only improves the ecological relevance of the standard but also introduces significant complexity into assessing compliance. This study examined differences in the copper and zinc complexation characteristics of effluents from a range of different sewage treatment works and in relation to so-called 'natural' samples. This information is essential to determine whether the inclusion of effluent-specific complexation characteristics within the regulatory framework could enhance the environmental relevance of compliance criteria. The data show that for copper, binding affinity was not greater than that measured for materials derived from the receiving water environment, with a mean log K of between 4.4 and 5.15 and mean complexation capacity ranging from 38 to 120 μg/mg dissolved organic carbon (DOC) for effluents compared with a log K of 5.6 and complexation capacity of 37 μg/mg DOC for the Suwannee River fulvic acid. For zinc, however, effluents exhibited a much higher complexation capacity, with effluent means ranging from 3 to 23 μg/mg DOC compared with the Suwannee River fulvic acid, for which the complexation capacity could not be determined. Synthetic ligands in sewage effluent, such as ethylenediaminetetraacetic acid (EDTA), are implicated as contributing to these observed differences. This suggests that the current biotic ligand models for zinc might overstate the risk of harm in effluent-impacted waters. The data also show that the copper and zinc complexation characteristics of effluent samples obtained from the same sewage treatment works were less different from one another than those of effluents from other treatment works and therefore that sewage source has an important influence on complexation characteristics. The findings from this study support the case that the contribution to complexation from effluent-derived ligands could enhance the environmental

  12. Receptor-based 3D QSAR analysis of estrogen receptor ligands - merging the accuracy of receptor-based alignments with the computational efficiency of ligand-based methods

    NASA Astrophysics Data System (ADS)

    Sippl, Wolfgang

    2000-08-01

    One of the major challenges in computational approaches to drug design is the accurate prediction of binding affinity of biomolecules. In the present study several prediction methods for a published set of estrogen receptor ligands are investigated and compared. The binding modes of 30 ligands were determined using the docking program AutoDock and were compared with available X-ray structures of estrogen receptor-ligand complexes. On the basis of the docking results an interaction energy-based model, which uses the information of the whole ligand-receptor complex, was generated. Several parameters were modified in order to analyze their influence onto the correlation between binding affinities and calculated ligand-receptor interaction energies. The highest correlation coefficient ( r 2 = 0.617, q 2 LOO = 0.570) was obtained considering protein flexibility during the interaction energy evaluation. The second prediction method uses a combination of receptor-based and 3D quantitative structure-activity relationships (3D QSAR) methods. The ligand alignment obtained from the 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, a significant and robust model was obtained ( r 2 = 0.991, q 2 LOO = 0.921). The predictive ability of the established model was further evaluated by using a test set of six additional compounds. The comparison with the generated interaction energy-based model and with a traditional CoMFA model obtained using a ligand-based alignment ( r 2 = 0.951, q 2 LOO = 0.796) indicates that the combination of receptor-based and 3D QSAR methods is able to improve the quality of the underlying model.

  13. Asymmetric catalysis based on tropos ligands.

    PubMed

    Aikawa, Kohsuke; Mikami, Koichi

    2012-11-21

    All enantiopure atropisomeric (atropos) ligands essentially require enantiomeric resolution or synthetic transformation from a chiral pool. In sharp contrast, the use of tropos (chirally flexible) ligands, which are highly modular, versatile, and easy to synthesize without enantiomeric resolution, has recently been the topic of much interest in asymmetric catalysis. Racemic catalysts bearing tropos ligands can be applied to asymmetric catalysis through enantiomeric discrimination by the addition of a chiral source, which preferentially transforms one catalyst enantiomer into a highly activated catalyst enantiomer. Additionally, racemic catalysts bearing tropos ligands can also be utilized as atropos enantiopure catalysts obtained via the control of chirality by a chiral source followed by the memory of chirality. In this feature article, our results on the asymmetric catalysis via the combination of various central metals and tropos ligands are summarized.

  14. Synthesis, characterization, X-ray crystal structures and antibacterial activities of Schiff base ligands derived from allylamine and their vanadium(IV), cobalt(III), nickel(II), copper(II), zinc(II) and palladium(II) complexes

    NASA Astrophysics Data System (ADS)

    Amiri Rudbari, Hadi; Iravani, Mohammad Reza; Moazam, Vahid; Askari, Banafshe; Khorshidifard, Mahsa; Habibi, Neda; Bruno, Giuseppe

    2016-12-01

    A new Schiff base ligand, HL2, and four new Schiff base complexes, NiL12, PdL12, NiL22 and ZnL22, have been prepared and characterized by elemental analysis (CHN), FT-IR and UV-Vis spectroscopy. 1H and 13C NMR techniques were employed for characterization of the ligand (HL2) and the diamagnetic complexes (PdL12 and ZnL22). The molecular structures of PdL12, NiL22 and ZnL22 complexes were determined by the single crystal X-ray diffraction technique. The crystallographic data reveal that in these complexes the metal centers are four-coordinated by two phenolate oxygen and two imine nitrogen atoms of two Schiff base ligands. The geometry around the metal center in the PdL12 and NiL22 complexes is square-planar and for ZnL22 it is a distorted tetrahedral.In the end, five new (HL2, NiL12, PdL12, NiL22 and ZnL22) and six reported (HL1, VOL12, CoL13, CuL12, ZnL12 and Zn2L14) Schiff base compounds were tested for their in vitro antimicrobial activity against Staphylococcus aureus and Escherichia coli as examples of Gram-positive and Gram-negative bacterial strains, respectively, by disc diffusion method.

  15. Expansion of the Ligand Knowledge Base for Chelating P,P-Donor Ligands (LKB-PP)†

    PubMed Central

    2012-01-01

    We have expanded the ligand knowledge base for bidentate P,P- and P,N-donor ligands (LKB-PP, Organometallics2008, 27, 1372–1383) by 208 ligands and introduced an additional steric descriptor (nHe8). This expanded knowledge base now captures information on 334 bidentate ligands and has been processed with principal component analysis (PCA) of the descriptors to produce a detailed map of bidentate ligand space, which better captures ligand variation and has been used for the analysis of ligand properties. PMID:24882917

  16. Copper(II) complexes of lipophilic aminoglycoside derivatives for the amino acid enantiomeric separation by ligand-exchange liquid chromatography.

    PubMed

    Zaher, Mustapha; Baussanne, Isabelle; Ravelet, Corinne; Halder, Somnath; Haroun, Mohamed; Fize, Jennifer; Décout, Jean-Luc; Peyrin, Eric

    2008-03-28

    In this paper, a new class of ligand-exchange chiral stationary phase (LE-CSP) based on the copper complexes of lipophilic aminoglycoside derivatives was reported. Different stationary phases were developed by coating reversed-phase liquid chromatography supports with three neamine derivatives carrying a lipophilic octadecyl chain at the 4', 5 and 6 positions, respectively. The enantioselective ability of these LE neamine-based CSPs was evaluated and the 4'-derivative coated column was found to be the most interesting one for the amino acid resolution. The effects of the variation of several chromatographic parameters on the enantioseparation were evaluated in order to identify the analysis optimal conditions.

  17. Ligand expansion in ligand-based virtual screening using relevance feedback

    NASA Astrophysics Data System (ADS)

    Abdo, Ammar; Saeed, Faisal; Hamza, Hentabli; Ahmed, Ali; Salim, Naomie

    2012-03-01

    Query expansion is the process of reformulating an original query to improve retrieval performance in information retrieval systems. Relevance feedback is one of the most useful query modification techniques in information retrieval systems. In this paper, we introduce query expansion into ligand-based virtual screening (LBVS) using the relevance feedback technique. In this approach, a few high-ranking molecules of unknown activity are filtered from the outputs of a Bayesian inference network based on a single ligand molecule to form a set of ligand molecules. This set of ligand molecules is used to form a new ligand molecule. Simulated virtual screening experiments with the MDL Drug Data Report and maximum unbiased validation data sets show that the use of ligand expansion provides a very simple way of improving the LBVS, especially when the active molecules being sought have a high degree of structural heterogeneity. However, the effectiveness of the ligand expansion is slightly less when structurally-homogeneous sets of actives are being sought.

  18. Spectroscopic studies and biological evaluation of some transition metal complexes of azo Schiff-base ligand derived from (1-phenyl-2,3-dimethyl-4-aminopyrazol-5-one) and 5-((4-chlorophenyl)diazenyl)-2-hydroxybenzaldehyde

    NASA Astrophysics Data System (ADS)

    Anitha, C.; Sheela, C. D.; Tharmaraj, P.; Sumathi, S.

    2012-10-01

    A series of metal(II) complexes of VO(II), Co(II), Ni(II), Cu(II) and Zn(II) have been synthesized from the azo Schiff base ligand 4-((E)-4-((E)-(4-chlorophenyl)diazenyl)-2-hydroxybenzylideneamino)-1,5-dimethyl-2-phenyl-1H-pyrazol-3(2H)-one (CDHBAP) and characterized by elemental analysis, spectral (IR, UV-Vis, 1H NMR, ESR and EI-mass), magnetic moment measurements, molar conductance, DNA, SEM, X-ray crystallography and fluorescence studies. The electronic absorption spectra and magnetic susceptibility measurements of the complexes indicate square pyramidal geometry for VO(II) and octahedral geometry for all the other complexes. The important infrared (IR) spectral bands corresponding to the active groups in the ligand and the solid complexes under investigation were studied and implies that CDHBAP is coordinated to the metal ions in a neutral tridentate manner. The redox behavior of copper(II) and vanadyl(II) complexes have been studied by cyclic voltammetry. The nuclease activity of the above metal(II) complexes shows that the complexes cleave DNA. All the synthesized complexes can serve as potential photoactive materials as indicated from their characteristic fluorescence properties. The antibacterial and antifungal activities of the synthesized ligand and its metal complexes were screened against bacterial species (Staphylococcus aureus, Salmonella typhi, Escherichia coli, Bacillus subtilis, Shigella sonnie) and fungi (Candida albicans, Aspergillus niger, Rhizoctonia bataicola). Amikacin and Ketoconozole were used as references for antibacterial and antifungal studies. The activity data show that the metal complexes have a promising biological activity comparable with the parent Schiff base ligand against bacterial and fungal species. The second harmonic generation (SHG) efficiency of the ligand was measured and the NLO (non-linear optical) properties of the ligand are expected to result in the realization of advanced optical devices in optical fiber

  19. Spectroscopic studies and biological evaluation of some transition metal complexes of azo Schiff-base ligand derived from (1-phenyl-2,3-dimethyl-4-aminopyrazol-5-one) and 5-((4-chlorophenyl)diazenyl)-2-hydroxybenzaldehyde.

    PubMed

    Anitha, C; Sheela, C D; Tharmaraj, P; Sumathi, S

    2012-10-01

    A series of metal(II) complexes of VO(II), Co(II), Ni(II), Cu(II) and Zn(II) have been synthesized from the azo Schiff base ligand 4-((E)-4-((E)-(4-chlorophenyl)diazenyl)-2-hydroxybenzylideneamino)-1,5-dimethyl-2-phenyl-1H-pyrazol-3(2H)-one (CDHBAP) and characterized by elemental analysis, spectral (IR, UV-Vis, (1)H NMR, ESR and EI-mass), magnetic moment measurements, molar conductance, DNA, SEM, X-ray crystallography and fluorescence studies. The electronic absorption spectra and magnetic susceptibility measurements of the complexes indicate square pyramidal geometry for VO(II) and octahedral geometry for all the other complexes. The important infrared (IR) spectral bands corresponding to the active groups in the ligand and the solid complexes under investigation were studied and implies that CDHBAP is coordinated to the metal ions in a neutral tridentate manner. The redox behavior of copper(II) and vanadyl(II) complexes have been studied by cyclic voltammetry. The nuclease activity of the above metal(II) complexes shows that the complexes cleave DNA. All the synthesized complexes can serve as potential photoactive materials as indicated from their characteristic fluorescence properties. The antibacterial and antifungal activities of the synthesized ligand and its metal complexes were screened against bacterial species (Staphylococcus aureus, Salmonella typhi, Escherichia coli, Bacillus subtilis, Shigella sonnie) and fungi (Candida albicans, Aspergillus niger, Rhizoctonia bataicola). Amikacin and Ketoconozole were used as references for antibacterial and antifungal studies. The activity data show that the metal complexes have a promising biological activity comparable with the parent Schiff base ligand against bacterial and fungal species. The second harmonic generation (SHG) efficiency of the ligand was measured and the NLO (non-linear optical) properties of the ligand are expected to result in the realization of advanced optical devices in optical fiber

  20. Vanadium complexes with mixed O,S anionic ligands derived from maltol: synthesis, characterization, and biological studies.

    PubMed

    Monga, Vishakha; Thompson, Katherine H; Yuen, Violet G; Sharma, Vijay; Patrick, Brian O; McNeill, John H; Orvig, Chris

    2005-04-18

    Four mixed O,S binding bidentate ligand precursors derived from maltol (3-hydroxy-2-methyl-4-pyrone) have been chelated to vanadium to yield new bis(ligand)oxovanadium(IV) and tris(ligand)vanadium(III) complexes. The four ligand precursors include two pyranthiones, 3-hydroxy-2-methyl-4-pyranthione, commonly known as thiomaltol (Htma), and 2-ethyl-3-hydroxy-4-pyranthione, commonly known as ethylthiomaltol (Hetma), as well as two pyridinethiones, 3-hydroxy-2-methyl-4(H)-pyridinethione (Hmppt) and 3-hydroxy-1,2-dimethyl-4-pyridinethione (Hdppt). Vanadium complex formation was confirmed by elemental analysis, mass spectrometry, and IR and EPR (where possible) spectroscopies. The X-ray structure of oxobis(thiomaltolato)vanadium(IV),VO(tma)(2), was also determined; both cis and trans isomers were isolated in the same asymmetric unit. In both isomers, the two thiomaltolato ligands are arranged around the base of the square pyramid with the V=O linkage perpendicular; the vanadium atom is slightly displaced from the basal plane [V(1) = 0.656(3) A, V(2) = 0.664(2) A]. All of the new complexes were screened for insulin-enhancing effectiveness in streptozotocin-induced diabetes in rats, and VO(tma)(2) was profiled metabolically for urinary vanadium and ligand clearance by GFAAS and ESIMS, respectively. The new vanadium complexes did not lower blood glucose levels acutely, possibly because of rapid dissociation and excretion.

  1. Ligand exchange between proteins. Exchange of biotin and biotin derivatives between avidin and streptavidin.

    PubMed

    Pazy, Yael; Kulik, Tikva; Bayer, Edward A; Wilchek, Meir; Livnah, Oded

    2002-08-23

    We have studied the structural elements that affect ligand exchange between the two high affinity biotin-binding proteins, egg white avidin and its bacterial analogue, streptavidin. For this purpose, we have developed a simple assay based on the antipodal behavior of the two proteins toward hydrolysis of biotinyl p-nitrophenyl ester (BNP). The assay provided the experimental basis for these studies. It was found that biotin migrates unidirectionally from streptavidin to avidin. Conversely, the biotin derivative, BNP, is transferred in the opposite direction, from avidin to streptavidin. A previous crystallographic study (Huberman, T., Eisenberg-Domovich, Y., Gitlin, G., Kulik, T., Bayer, E. A., Wilchek, M., and Livnah, O. (2001) J. Biol. Chem. 276, 32031-32039) provided insight into a plausible explanation for these results. These data revealed that the non-hydrolyzable BNP analogue, biotinyl p-nitroanilide, was almost completely sheltered in streptavidin as opposed to avidin in which the disordered conformation of a critical loop resulted in the loss of several hydrogen bonds and concomitant exposure of the analogue to the solvent. In order to determine the minimal modification of the biotin molecule required to cause the disordered loop conformation, the structures of avidin and streptavidin were determined with norbiotin, homobiotin, and a common long-chain biotin derivative, biotinyl epsilon-aminocaproic acid. Six new crystal structures of the avidin and streptavidin complexes with the latter biotin analogues and derivatives were thus elucidated. It was found that extending the biotin side chain by a single CH(2) group (i.e. homobiotin) is sufficient to result in this remarkable conformational change in the loop of avidin. These results bear significant biotechnological importance, suggesting that complexes containing biotinylated probes with streptavidin would be more stable than those with avidin. These findings should be heeded when developing new drugs

  2. Supramolecular chirality induction in bis(zinc porphyrin) by amino acid derivatives: rationalization and applications of the ligand bulkiness effect.

    PubMed

    Borovkov, V V; Yamamoto, N; Lintuluoto, J M; Tanaka, T; Inoue, Y

    2001-06-01

    The achiral syn conformer (face-to-face) of the ethane-bridged bis(zinc porphyrin) (syn-ZnD) transforms into the corresponding chiral extended anti bis-ligated species (anti-ZnD.L2) in the presence of enantiopure ligands (L: amino acid derivatives). The mechanism of the supramolecular chirality induction is based on chiral ligand binding to zinc porphyrins and subsequent formation of either right- or left-handed screw structures in anti-ZnD.L2. The screw structure formation arises from steric interactions between the bulkiest substituent at the asymmetric carbon of the ligand and the peripheral ethyl groups of the neighboring porphyrin ring directed towards the covalent bridge. The sign and amplitude of the induced circular dichroism (CD) are dependent on the steric bulk of the substituents at the chiral center. The greater difference in size between the chiral center's substituents gives the stronger induced CD signal. Rationalization of the ligand bulkiness effect on chirality induction by amino acid derivatives, application of this supramolecular system for the determination of ligand absolute configuration, and relative bulkiness of the substituents at the asymmetric carbon are discussed. Copyright 2001 Wiley-Liss, Inc.

  3. Synthesis, XAFS and X-ray structural studies of mono- and binuclear metal-chelates of N,O,O(N,O,S) tridentate Schiff base pyrazole derived ligands

    NASA Astrophysics Data System (ADS)

    Burlov, Anatolii S.; Uraev, Ali I.; Garnovskii, Dmitrii A.; Lyssenko, Konstantin A.; Vlasenko, Valery G.; Zubavichus, Yan V.; Murzin, Vadim Yu.; Korshunova, Eugenie V.; Borodkin, Gennadii S.; Levchenkov, Sergey I.; Vasilchenko, Igor S.; Minkin, Vladimir I.

    2014-05-01

    The syntheses of a series of novel N,O,O and N,O,S donor tridentate Schiff base ligands H2L1 and H2L2via the condensation of 1-phenyl-3-methyl-4-formylpyrazol-5-ol(thiol) with 2-hydroxymethylaniline and their Co(II), Ni(II), Cu(II), Fe(III), and Mn(II) complexes are reported. The compounds are characterized by the C, H, N, S, metal elemental analysis, IR spectroscopy; 1H NMR data for ligands, low-temperature magnetic measurements, X-ray absorption spectroscopy. The crystal structures for Ni(II) and Cu(II) coordination compounds with the compositions NiL21 and Cu2L21 are established by X-ray crystallography.

  4. Cd(II) and Zn(II) complexes of two new hexadentate Schiff base ligands derived from different aldehydes and ethanol amine; X-ray crystal structure, IR and NMR spectroscopy studies

    NASA Astrophysics Data System (ADS)

    Golbedaghi, Reza; Rezaeivala, Majid; Albeheshti, Leila

    2014-11-01

    Four new [Cd(H2L1)(NO3)]ClO4 (1), [Zn(H2L1)](ClO4)2 (2), [Cd(H2L2)(NO3)]ClO4 (3), and [Zn(H2L2)](ClO4)2 (4), complexes were prepared by the reaction of two new Schiff base ligands and Cd(II) and Zn(II) metal ions in equimolar ratios. The ligands H2L1 and H2L2 were synthesized by reaction of 2-[2-(2-formyl phenoxy)ethoxy]benzaldehyde and/or 2-[2-(3-formyl phenoxy)propoxy]benzaldehyde and ethanol amine and characterized by IR, 1H and 13C NMR spectroscopy. All complexes were characterized by IR, 1H and 13C NMR, COSY, and elemental analysis. Also, the complex 1 was characterized by X-ray in addition to the above methods. The X-ray crystal structure of compound 1 showed that all nitrogen and oxygen atoms of ligand (N2O4) and a molecule of nitrate with two donor oxygen atom have been coordinated to the metal ion and the Cd(II) ion is in an eight-coordinate environment that is best described as a distorted dodecahedron geometry.

  5. A new trinuclear zinc(II) complex and a heptacoordinated mononuclear cadmium(II) complex with a pyrimidine derived Schiff base ligand: Syntheses, crystal structures, photoluminescence and DFT calculations

    NASA Astrophysics Data System (ADS)

    Das, Kinsuk; Jana, Atanu; Konar, Saugata; Chatterjee, Sudipta; Mondal, Tapan Kumar; Barik, Anil Kumar; Kar, Susanta Kumar

    2013-09-01

    The new N6 donor hexadentate Schiff base 2,4-bis [2-(pyridine-2-ylmethylidene) hydrazinyl] pyrimidine (L), its trinuclear Zn(II) complex, [Zn3(L)2Cl6] (1) and mononuclear heptacoordinate Cd(II) complex [Cd(L)(H2O)2](ClO4)2 (2) have been synthesised and characterised by crystallographically and spectroscopically. Complex 1 is featured by the triangular arrangement of three zinc atoms where the neighbouring Zn atoms are linked via half portion (N3 chromophore) of the same ligand molecule. In 1, the ligand molecules behave as hexadentate ones (employing both pyrimidine nitrogen atoms as active donor centres) to create the octahedral environment around Zn(II). The central and terminal Zn(II) atom has N6 and N3Cl3 chromophores respectively. In 2 the same ligand (L) behaves as pentadentate one (ignoring one pyrimidine nitrogen in the coordination process) to produce a pentagonal bipyramidal geometry with two apical water molecules. The geometries of both complexes were optimised in the singlet state by DFT method. The TDDFT calculations have been done on the optimised geometries to understand the electronic structure and spectral transition in the complexes. Complex 1 exhibits intraligand 1(π → π*) fluorescence in aqueous methanol solvent at room temperature.

  6. Exploring the potential of protein-based pharmacophore models in ligand pose prediction and ranking

    PubMed Central

    Hu, Bingjie; Lill, Markus A.

    2013-01-01

    Protein-based pharmacophore models derived from the protein binding site atoms without the inclusion of any ligand information have become more popular in virtual screening studies. However, the accuracy of protein-based pharmacophore models for reproducing the critical protein-ligand interactions has never been explicitly assessed. In this study, we used known protein-ligand contacts from a large set of experimentally determined protein-ligand complexes to assess the quality of the protein-based pharmacophores in reproducing these critical contacts. We demonstrate how these contacts can be used to optimize the pharmacophore generation procedure to produce pharmacophore models that optimally cover the known protein-ligand interactions. Finally, we explored the potential of the optimized protein-based pharmacophore models for pose prediction and pose rankings. Our results demonstrate that there are significant variations in the success of protein-based pharmacophore models to reproduce native contacts and consequently native ligand poses dependent on the details of the pharmacophore-generation process. We show that the generation of optimized protein-based pharmacophore models is a promising approach for ligand pose prediction and pose rankings. PMID:23621564

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

    NASA Astrophysics Data System (ADS)

    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.

  8. Combined biophysical and cell-based approaches for the assessment of ligand binding to PPARγ.

    PubMed

    Zorrilla, Silvia; Pérez-Sala, Dolores

    2013-01-01

    Transcription factors of the peroxisome proliferator-activated receptor (PPAR) family are ligand-activated receptors that play key roles in lipid metabolism and inflammation. The γ isoform (PPARγ) is involved in adipocyte differentiation, insulin sensitization, and vascular pathophysiology, including inflammation and atherosclerosis, for which it is considered an important drug target. PPARγ ligands display varied structures and include fatty acids, electrophilic lipids, and certain drugs. These agonists promote conformational changes allowing interaction of PPARγ with coactivators and hence transcriptional regulation. Here we present a panoply of methods to study PPARγ interactions with ligands and activation in vitro and in cells. The first method is based on the competition of the fluorescent dye 1-anilinonaphthalene-8-sulfonic acid (ANS) with PPARγ ligands for the ligand binding pocket, allowing detection and quantification of ligand binding to PPARγ. This method is specific for PPARγ while ANS displays negligible interaction with other nuclear receptors such as PPARα and retinoid X receptor α (RXRα). The ANS competition assay has been validated through comparison of the affinities determined for well-known PPARγ ligands by this method with those reported in the literature. We also describe here gel-based competition assays that show limited performance with non-covalently bound ligands. In addition, we present a fluorescence anisotropy assay to analyze PPARγ activation by ligands in vitro through their capacity of eliciting PPARγ interaction with a fluorescently labeled peptide derived from one of its coactivators (SRC-1). Finally, we show cell-based assays to investigate PPARγ activation by interaction with its ligands. We believe that combined approaches using ANS, fluorescent coactivator peptides, and in-cell assays to monitor PPARγ binding and interactions may provide valuable strategies for the identification and characterization of PPAR

  9. Two novel bipyrazole derivative ligands: Synthesis, crystal structure, theoretical studies, and sensitive response toward Fe3+

    NASA Astrophysics Data System (ADS)

    Du, Wei; Zhu, Yingzhong; Wang, Hui; Zhao, Xuesong; Wu, Jieying; Tian, Yupeng

    2015-02-01

    Two novel bipyrazole derivative ligands L1 (4-(di(1H-pyrazol-1-yl)methyl)-N,N-diphenylaniline) and L2 (4-(di(1H-pyrazol-1-yl)methyl)-N,N-bis(4-ethoxy phenyl)aniline), were synthesized, and fully characterized. The crystal structures of the two ligands were confirmed by single-crystal X-ray diffraction analysis. The structural analysis revealed that two pyrazole units are attached to the same carbon atom connected with triphenylamine moiety. The UV-vis absorption and fluorescence spectral properties of the ligands were investigated and explained relying on theoretical calculation. Significantly, it was found that the ligands display an exclusively selective and sensitive response toward Fe3+ with aid of UV-vis absorption spectroscopic methods.

  10. Brain-Derived Neurotrophic Factor: Three Ligands, Many Actions.

    PubMed

    Hempstead, Barbara L

    2015-01-01

    Brain-derived neurotrophic factor (BDNF) is a member of a family of neurotrophins which include nerve growth factor, neurotrophin 3, and neurotrophin 4. Studies over the last three decades have identified mature BDNF as a key regulator of neuronal differentiation, structure, and function; actions mediated by the TrkB receptor. More recently identified isoforms which are translated from the bdnf gene, including the uncleaved precursor, pro-BDNF, and the cleaved prodomain, have been found to elicit opposing functions in neurons through the activation of distinct receptors. This work emphasizes the critical roles for all three isoforms of BDNF in modulating neuronal activity that impact complex human behaviors including memory, anxiety, depression, and hyperphagia.

  11. Crystal structures of complexes of vitamin D receptor ligand-binding domain with lithocholic acid derivatives

    PubMed Central

    Masuno, Hiroyuki; Ikura, Teikichi; Morizono, Daisuke; Orita, Isamu; Yamada, Sachiko; Shimizu, Masato; Ito, Nobutoshi

    2013-01-01

    The secondary bile acid lithocholic acid (LCA) and its derivatives act as selective modulators of the vitamin D receptor (VDR), although their structures fundamentally differ from that of the natural hormone 1α,25-dihydroxyvitamin D3 [1,25(OH)2D3)]. Here, we have determined the crystal structures of the ligand-binding domain of rat VDR (VDR-LBD) in ternary complexes with a synthetic partial peptide of the coactivator MED1 (mediator of RNA polymerase II transcription subunit 1) and four ligands, LCA, 3-keto LCA, LCA acetate, and LCA propionate, with the goal of elucidating their agonistic mechanism. LCA and its derivatives bind to the same ligand-binding pocket (LBP) of VDR-LBD that 1,25(OH)2D3 binds to, but in the opposite orientation; their A-ring is positioned at the top of the LBP, whereas their acyclic tail is located at the bottom of the LBP. However, most of the hydrophobic and hydrophilic interactions observed in the complex with 1,25(OH)2D3 are reproduced in the complexes with LCA and its derivatives. Additional interactions between VDR-LBD and the C-3 substituents of the A-ring are also observed in the complexes with LCA and its derivatives. These may result in the observed difference in the potency among the LCA-type ligands. PMID:23723390

  12. Binary and ternary copper(II) complexes of a new Schiff base ligand derived from 4-acetyl-5,6-diphenyl-3(2H)-pyridazinone: Synthesis, spectral, thermal, antimicrobial and antitumor studies

    NASA Astrophysics Data System (ADS)

    Shebl, Magdy; Adly, Omima M. I.; Abdelrhman, Ebtesam M.; El-Shetary, B. A.

    2017-10-01

    A new Schiff base ligand was synthesized by the reaction of 4-acetyl-5,6-diphenyl-3(2H)-pyridazinone with ethylenediamine. A series of binary copper(II) Schiff base complexes have been synthesized by using various copper(II) salts; AcO-, NO3-, ClO4-, Cl- and Br-. Ternary complexes were synthesized by using auxiliary ligands (L‧) [N,O-donor; 8-hydroxyquinoline and glycine or N,N-donor; 1,10-phenanthroline, bipyridyl and 2-aminopyridine]. The structures of the Schiff base and its complexes were characterized by elemental and thermal analyses, IR, electronic, mass, 1H NMR and ESR spectra in addition to conductivity and magnetic susceptibility measurements. The obtained complexes include neutral binuclear complexes as well as neutral and cationic mononuclear complexes according to the anion used and the experimental conditions. The ESR spin Hamiltonian parameters of some complexes were calculated and discussed. The metal complexes exhibited octahedral and square planar geometrical arrangements depending on the nature of the anion. Kinetic parameters (Ea, A, ΔH, ΔS and ΔG) of the thermal decomposition stages were evaluated using Coats-Redfern equations. The antimicrobial activity of the Schiff base and its complexes was screened against Gram-positive bacteria (Staphylococcus aureus and Bacillus subtilis), Gram-negative bacteria (Salmonella typhimurium and Escherichia coli), yeast (Candida albicans) and fungus (Aspergillus fumigatus). The antitumor activity of the Schiff base and some of its Cu(II) complexes was investigated against HepG-2 cell line.

  13. Scoring ligand similarity in structure-based virtual screening.

    PubMed

    Zavodszky, Maria I; Rohatgi, Anjali; Van Voorst, Jeffrey R; Yan, Honggao; Kuhn, Leslie A

    2009-01-01

    Scoring to identify high-affinity compounds remains a challenge in virtual screening. On one hand, protein-ligand scoring focuses on weighting favorable and unfavorable interactions between the two molecules. Ligand-based scoring, on the other hand, focuses on how well the shape and chemistry of each ligand candidate overlay on a three-dimensional reference ligand. Our hypothesis is that a hybrid approach, using ligand-based scoring to rank dockings selected by protein-ligand scoring, can ensure that high-ranking molecules mimic the shape and chemistry of a known ligand while also complementing the binding site. Results from applying this approach to screen nearly 70 000 National Cancer Institute (NCI) compounds for thrombin inhibitors tend to support the hypothesis. EON ligand-based ranking of docked molecules yielded the majority (4/5) of newly discovered, low to mid-micromolar inhibitors from a panel of 27 assayed compounds, whereas ranking docked compounds by protein-ligand scoring alone resulted in one new inhibitor. Since the results depend on the choice of scoring function, an analysis of properties was performed on the top-scoring docked compounds according to five different protein-ligand scoring functions, plus EON scoring using three different reference compounds. The results indicate that the choice of scoring function, even among scoring functions measuring the same types of interactions, can have an unexpectedly large effect on which compounds are chosen from screening. Furthermore, there was almost no overlap between the top-scoring compounds from protein-ligand versus ligand-based scoring, indicating the two approaches provide complementary information. Matchprint analysis, a new addition to the SLIDE (Screening Ligands by Induced-fit Docking, Efficiently) screening toolset, facilitated comparison of docked molecules' interactions with those of known inhibitors. The majority of interactions conserved among top-scoring compounds for a given scoring

  14. An experimental and theoretical study on the interaction of DNA and BSA with novel Ni2 +, Cu2 + and VO2 + complexes derived from vanillin bidentate Schiff base ligand

    NASA Astrophysics Data System (ADS)

    Dostani, Morteza; Kianfar, Ali Hossein; Mahmood, Wan Ahmad Kamil; Dinari, Mohammad; Farrokhpour, Hossein; Sabzalian, Mohammad R.; Abyar, Fatemeh; Azarian, Mohammad Hossein

    2017-06-01

    In this investigation, the structure of bidentate N,N-Schiff base ligand of vanillin, (E)-4-(((2-amino-5-nitrophenyl)imino)methyl)-2-methoxyphenol (HL) was determined by single crystal X-ray diffraction. The interaction of new [CuL2], [NiL2] and [VOL2] complexes with DNA and BSA was explored through UV-Vis and fluorescence spectroscopy. The electronic spectra changes displayed an isosbestic point for the complexes upon titration with DNA. The Kb values for the complexes [CuL2], [NiL2] and [VOL2] were 2.4 × 105, 1.9 × 105 and 4.2 × 104, respectively. [CuL2] complex was bound more toughly than [NiL2] and [VOL2] complexes. These complexes had a significant interaction with Bovine Serum Albumin (BSA) and the results demonstrated that the quenching mechanism was a static procedure. Also, the complexes interacted with BSA by more than one binding site (n > 1). Finally, the theoretical studies were performed using the docking method to calculate the binding constants and recognize the binding site of the DNA and BSA with the complexes. The ligand and complexes including Ni2 +, Cu2 + and VO2 + ions were colonized by fungal growth.

  15. Synthesis, X-ray crystal structure, photo luminescent property, antimicrobial activities and DFT computational study of Zn(II) coordination polymer derived from multisite N,O donor Schiff base ligand (H2L1)

    NASA Astrophysics Data System (ADS)

    Majumdar, Dhrubajyoti; Surendra Babu, M. S.; Das, Sourav; Biswas, Jayanta Kumar; Mondal, Monojit; Hazra, Suman

    2017-06-01

    A unique thiocyanato linked 1D chain of Zn(II) coordination polymer [Zn2L1(μ1,3-SCN)(η1SCN)]n (1) has been synthesized using potential multisite compartmental N,O donor Schiff base blocker ligand (L1H2) in presence of Zn(OAc)2 and KSCN. The Schiff base ligand [N, N‧-bis(3-methoxysalicylidenimino)-1,3-daminopropane] (L1H2) is 2:1 M ratio condensation product of O-vaniline and 1,3-diaminopropane in methanol medium. The characterization of Complex 1 was accomplished by means of different micro analytical techniques like elemental analyses, IR, UV-Vis, 1H NMR, emission spectroscopy and Single X-ray crystallographic study. Complex 1 crystallizes in Orthorhombic system, space group Pbca, with values a = 11.579(2), b = 18.538(3), and c = 22.160(4) Å; α = β = γ = 90.00°; V = 4756.6(14) and Z = 8. The single crystal X-ray revealed that the one dimensional chain system with the repeating unit [Zn2(μ1,3-SCN)(η1SCN)(L1)]n bridge by an end to end μ1,3 thiocyanate anion. Within each repeating unit two different types of Zn(II) ions are present. One of these is five-coordinate in a square pyramidal geometry while the other is six-coordinate in an octahedral geometry. A brief but lucid comparative approach has been demonstrated in between Schiff base (L1H2) and complex 1 with respect to their photoluminescence activities. Active luminescence behavior of complex 1 in presence of ligand (L1H2) is due to quenching of PET process which is mediated by 'chelating effect'. Complex 1 exhibits strong antimicrobial efficacy against some important Gram + ve and Gram -ve bacteria. Apart from antimicrobial potential, a combined experimental and theoretical investigation has been performed via DFT on molecular structure of complex 1 with respect to Hirshfeld surface analysis.

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

    PubMed

    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. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Bidentate coordinating behaviour of chalcone based ligands towards oxocations: VO(IV) and Mo(V)

    NASA Astrophysics Data System (ADS)

    Thaker, B. T.; Barvalia, R. S.

    2013-08-01

    We synthesized and studied the coordinating behaviour of chalcone based ligands derived from DHA and n-alkoxy benzaldehyde and their complexes of VO(IV) and MoO(V). The chalcone ligands are characterized by elemental analyses, UV-visible, IR, 1H NMR, and mass spectra. The resulting oxocation complexes are also characterized by elemental analyses, IR, 1H NMR, electronic, electron spin resonance spectra, magnetic susceptibility measurement and molar conductance studies. The IR and 1H NMR spectral data suggest that the chalcone ligands behave as a monobasic bidentate with O:O donor sequence towards metal ion. The molar conductivity data show them to be non-electrolytes. From the electronic, magnetic and ESR spectral data suggest that all the chalcone ligand complexes of VO(IV) and MoO(V) have distorted octahedral geometry.

  18. Ligand- and receptor-based docking with LiBELa

    NASA Astrophysics Data System (ADS)

    dos Santos Muniz, Heloisa; Nascimento, Alessandro S.

    2015-08-01

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

  19. Polymer light-emitting diodes based on cationic iridium(III) complexes with a 1,10-phenanthroline derivative containing a bipolar carbazole-oxadiazole unit as the auxiliary ligand

    NASA Astrophysics Data System (ADS)

    Tang, Huaijun; Wei, Liying; Meng, Guoyun; Li, Yanhu; Wang, Guanze; Yang, Furui; Wu, Hongbin; Yang, Wei; Cao, Yong

    2014-11-01

    A 1,10-phenanthroline derivative (co-phen) containing a bipolar carbazole-oxadiazole unit was synthesized and used as the auxiliary ligand in cationic iridium(III) complexes [(ppy)2Ir(co-phen)]PF6 (ppy: 2-phenylpyridine) and [(npy)2Ir(co-phen)]PF6 (npy: 2-(naphthalen-1-yl)pyridine). Two complexes have high thermal stability with the glass-transition temperatures (Tg) of 207 °C and 241 °C, and the same 5% weight-reduction temperatures (ΔT5%) of 402 °C. Both of them were used as phosphorescent dopants in solution-processed polymer light-emitting diodes (PLEDs): ITO/PEDOT: PSS/PVK: PBD: complex (mass ratios 100: 40: x, x = 1.0, 2.0, and 4.0)/CsF/Al. The maximum luminances of the PLEDs using [(ppy)2Ir(co-phen)]PF6 and [(npy)2Ir(co-phen)]PF6 were 12567 cd m-2 and 11032 cd m-2, the maximum luminance efficiencies were 17.3 cd A-1 and 20.4 cd A-1, the maximum power efficiencies were 9.8 lm W-1 and 10.3 lm W-1, and the maximum external quantum efficiencies were 9.3% and 11.4% respectively. The CIE color coordinates were around (0.37, 0.57) and (0.44, 0.54) respectively, corresponding to the yellow green region.

  20. Synthesis, biological evaluation, and three-dimensional in silico pharmacophore model for sigma(1) receptor ligands based on a series of substituted benzo[d]oxazol-2(3H)-one derivatives.

    PubMed

    Zampieri, Daniele; Mamolo, Maria Grazia; Laurini, Erik; Florio, Chiara; Zanette, Caterina; Fermeglia, Maurizio; Posocco, Paola; Paneni, Maria Silvia; Pricl, Sabrina; Vio, Luciano

    2009-09-10

    Novel benzo[d]oxazol-2(3H)-one derivatives were designed and synthesized, and their affinities against sigma receptors were evaluated. On the basis of 31 compounds, a three-dimensional pharmacophore model for the sigma(1) receptor binding site was developed using the Catalyst 4.9 software package. The best 3D pharmacophore hypothesis, consisting of one positive ionizable, one hydrogen bond acceptor, two hydrophobic aromatic, and one hydrophobic features provided a 3D-QSAR model with a correlation coefficient of 0.89. The best hypothesis was also validated by three independent methods, i.e., the Fisher randomization test included in the CatScramble functionality of Catalyst, the leave-one-out test, and activity prediction of an additional test set. The achieved results will allow researchers to use this 3D pharmacophore model for the design and synthesis of a second generation of high affinity sigma(1) ligands, as well as to discover other lead compounds for this class of receptors.

  1. Synthesis, characterization and DNA binding studies of platinum(II) complexes with benzimidazole derivative ligands.

    PubMed

    Tarı, Özden; Gümüş, Fatma; Açık, Leyla; Aydın, Betül

    2017-10-01

    The aim of this study was to synthesize and evaluate plasmid DNA interaction of new platinum(II) complexes with some 2-substituted benzimidazole derivatives as carrier ligands which may have potent anticancer activity and low toxicity. Twelve benzimidazole derivatives carrying indole, 2-/or 3-/or 4-methoxyphenyl, 4-methylphenyl, 3,4-dimethoxyphenyl, 3,4,5-trimethoxyphenyl, 4-methoxybenzyl, 3,4,5-trimethoxybenzyl, 3,4,5-trimethoxystyryl, 3,4,5-trimethoxybenzylthio or dimethylamino ethyl groups in their position 2 and twelve platinum(II) complexes with these carrier ligands were synthesized. The chemical structure of the platinum complexes have been characterized by their elemental analysis and FIR, (1)H NMR and mass spectra and their (1)H NMR and FIR spectra were interpreted by comparison with those of the ligands. The interaction of all the ligands and their complexes with plasmid DNA and their restriction endonuclease reactions by BamHI and HindIII enzymes were studied by agarose gel electrophoresis. It was determined that complex 1 [dichloro-di(2-(1H-indole-3-yl)benzimidazole)platinum(II)·2H2O] has stronger interaction than carboplatin and complex 10 [dichloro-di(2-(3,4,5-trimethoxystyryl)benzimidazole)platinum(II)·2H2O] has stronger interaction than both carboplatin and cisplatin with plasmid DNA. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Death ligands designed to kill: development and application of targeted cancer therapeutics based on proapoptotic TNF family ligands.

    PubMed

    Gerspach, Jeannette; Wajant, Harald; Pfizenmaier, Klaus

    2009-01-01

    The identification of molecular markers associated with cancer development or progression, opened a new era in the development of therapeutics. The successful introduction of a few low molecular weight chemicals and recombinant protein therapeutics with targeted actions into clinical practice have raised great expectations to broadly improve cancer therapy with respect to both overall clinical responses and tolerability. Targeting the apoptotic machinery of malignant cells is an attractive concept to combat cancer, which is currently exploited for the proapoptotic members of the TNF ligand family at various stages of preclinical and clinical development. This review summarizes recent progress in this rapidly progressing field of "biologic" therapies targeting the death receptors of TNF, CD95L, and TRAIL by means of its cognate protein ligands, receptor specific antibodies, and gene therapeutic approaches. Preclinical data on newly derived variants and fusion proteins based on these death ligands, designed to act in a tumor restricted manner, thereby preventing a systemic, potentially harmful action, will also be discussed.

  3. Pharmacophore-based discovery of ligands for drug transporters

    PubMed Central

    Chang, Cheng; Ekins, Sean; Bahadduri, Praveen; Swaan, Peter W.

    2006-01-01

    The ability to identify ligands for drug transporters is an important step in drug discovery and development. It can both improve accurate profiling of lead pharmacokinetic properties and assist in the discovery of new chemical entities targeting transporters. In silico approaches, especially pharmacophore-based database screening methods have great potential in improving the throughput of current transporter ligand identification assays, leading to a higher hit rate by focusing in vitro testing to the most promising hits. In this review, the potential of different in silico methods in transporter ligand identification studies are compared and summarized with an emphasis on pharmacophore modeling. Various implementations of pharmacophore model generation, database compilation and flexible screening algorithms are also introduced. Recent successful utilization of database searching with pharmacophores to identify novel ligands for the pharmaceutically significant transporters hPepT1, P-gp, BCRP, MRP1 and DAT are reviewed and challenges encountered with current approaches are discussed. PMID:17097188

  4. Design and Synthesis of Potent HIV-1 Protease Inhibitors Incorporating Hexahydrofuropyranol-derived High Affinity P2 ligands: Structure-activity Studies and Biological Evaluation

    PubMed Central

    Ghosh, Arun K.; Chapsal, Bruno D.; Baldridge, Abigail; Steffey, Melinda P.; Walters, D. Eric; Koh, Yasuhiro; Amano, Masayuki; Mitsuya, Hiroaki

    2011-01-01

    The design, synthesis, and evaluation of a new series of hexahydrofuropyran-derived HIV-1 protease inhibitors are described. We have designed a stereochemically defined hexahydrofuropyranol-derived urethane as the P2-ligand. The current ligand is designed based upon the X-ray structure of 1a-bound HIV-1 protease. The synthesis of (3aS,4S,7aR)-hexahydro-2H-furo[2,3-b] pyran-4-ol (−)-7 was carried out in optically active form. Incorporation of this ligand provided inhibitor 35a, which has shown excellent enzyme inhibitory activity and antiviral potency. Our structure activity studies have indicated that the stereochemistry and the position of oxygens in the ligand are important to the observed potency of the inhibitor. Inhibitor 35a has maintained excellent potency against multidrug-resistant HIV-1 variants. An active site model of 35a was created based upon the X-ray structure of 1b-bound HIV-1 protease. The model offers molecular insights regarding ligand-binding site interactions of the hexahydrofuropyranol-derived novel P2-ligand. PMID:21194227

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

    NASA Astrophysics Data System (ADS)

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

    2013-01-01

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

  6. The crucial role of polyatomic anions in molecular architecture: structural and magnetic versatility of five nickel(II) complexes derived from A N,N,O-donor Schiff base ligand.

    PubMed

    Mukherjee, Pampa; Drew, Michael G B; Gómez-García, Carlos J; Ghosh, Ashutosh

    2009-07-06

    Five new nickel(II) complexes [Ni(2)L(2)(N(3))(2)(H(2)O)(2)] (1), [Ni(2)L(2)(NO(3))(2)] (2), [Ni(2)L(2)(O(2)CPh)(CH(3)OH)(2)]ClO(4).0.5CH(3)OH (3), [Ni(3)L(2)(O(2)CPh)(4)] (4), and [Ni(2)L(2)(NO(2))(2)](n) (5) have been synthesized by using a tridentate Schiff base ligand, HL (2-[(3-Methylamino-propylimino)-methyl]-phenol), and the polyatomic monoanions N(3)(-), NO(3)(-), PhCOO(-), or NO(2)(-). The complexes have been structurally and magnetically characterized. The structural analysis reveals that in all five complexes, the Ni(II) ions possess a distorted octahedral geometry. Complexes 1 and 2 are dinuclear with di-mu-1,1-azido and di-mu(2)-phenoxo bridges, respectively. Complex 3 is also a di-mu(2)-phenoxo-bridged dinuclear Ni(II) complex but has an additional syn-syn benzoate bridge. Compound 4 possesses a linear trinuclear structure with the tridentate Schiff base ligand coordinated to the terminal nickel atoms which are linked to the central Ni(II) by phenoxo and carboxylate bridges. Complex 5 consists of a dinuclear entity, bridged by di-mu(2)-phenoxo together with a cis-(mu-nitrito-1kappaO:2kappaN) nitrite ion. The dinuclear units are linked each other by another bridging trans-(mu-nitrito-1kappaO:2kappaN) nitrite to form a Ni(II) chain that shows the presence of unprecedented alternating cis- and trans-N,O bridging mode of the nitrite anion. Variable-temperature magnetic susceptibility measurements of complex 1 indicate the presence of ferromagnetic exchange interactions within the dimer (J = 23.5(3) cm(-1)) together with antiferromagnetic interdimer interactions (J' = -0.513(3) cm(-1)), whereas compounds 2 and 3 show intradimer antiferromagnetic interactions (J = -24.27(6) and -16.48(4) cm(-1), respectively). Ferromagnetic coupling (J = 6.14(2) cm(-1)) is observed in complex 4 for the linear centro-symmetric Ni(II) trimer, whereas complex 5 shows an alternating intra-chain antiferromagnetic coupling (J(1) = -32.1(1) cm(-1) and J(2) = -3.2(1) cm(-1)).

  7. Somatostatin receptor staining in FFPE sections using a ligand derivative dye as an alternative to immunostaining

    PubMed Central

    Kudoh, Shinji; Ito, Takaaki

    2017-01-01

    The confirmation of target expression in tissues is a prerequisite for molecular-targeted therapy. However, difficulties are sometimes associated with the production of appropriate antibodies against receptors. We herein developed a ligand derivative dye for the staining of receptors. The somatostatin receptor (sstr) was selected as the target and FITC-octreotate as the detective agent. We performed a blot analysis to detect sstr in the transfer membrane. The sstr2 recombinant protein or cell lysate from a small cell lung carcinoma cell line (H69) was boiled and loaded onto SDS-PAGE, and the proteins were transferred to a membrane. Even after denaturing processes, FITC-octreotate still bound sstr on the membrane. Furthermore, FITC-octreotate depicted the expression of sstr in formalin-fixed and paraffin-embedded (FFPE) sections, a method that we named ligand derivative staining (LDS). The accuracies of immunostaining and LDS were compared at the points of the detection of sstr using FFPE sections of 30 neuroendocrine tumor specimens. The sensitivity of LDS was 81.8%, while those of immunostaining using anti-sstr2 and sstr5 antibodies were 72.7% and 63.6%, respectively. Thus, LDS appears to be superior to immunostaining. A ligand derivative may be used as a substitute for antibodies, and has the potential to support economical, simple, and accurate detection methods. PMID:28182792

  8. Somatostatin receptor staining in FFPE sections using a ligand derivative dye as an alternative to immunostaining.

    PubMed

    Hasegawa, Koki; Kudoh, Shinji; Ito, Takaaki

    2017-01-01

    The confirmation of target expression in tissues is a prerequisite for molecular-targeted therapy. However, difficulties are sometimes associated with the production of appropriate antibodies against receptors. We herein developed a ligand derivative dye for the staining of receptors. The somatostatin receptor (sstr) was selected as the target and FITC-octreotate as the detective agent. We performed a blot analysis to detect sstr in the transfer membrane. The sstr2 recombinant protein or cell lysate from a small cell lung carcinoma cell line (H69) was boiled and loaded onto SDS-PAGE, and the proteins were transferred to a membrane. Even after denaturing processes, FITC-octreotate still bound sstr on the membrane. Furthermore, FITC-octreotate depicted the expression of sstr in formalin-fixed and paraffin-embedded (FFPE) sections, a method that we named ligand derivative staining (LDS). The accuracies of immunostaining and LDS were compared at the points of the detection of sstr using FFPE sections of 30 neuroendocrine tumor specimens. The sensitivity of LDS was 81.8%, while those of immunostaining using anti-sstr2 and sstr5 antibodies were 72.7% and 63.6%, respectively. Thus, LDS appears to be superior to immunostaining. A ligand derivative may be used as a substitute for antibodies, and has the potential to support economical, simple, and accurate detection methods.

  9. Electronic Structure Determination of Pyridine N-Heterocyclic Carbene Iron Dinitrogen Complexes and Neutral Ligand Derivatives

    PubMed Central

    2015-01-01

    The electronic structures of pyridine N-heterocyclic dicarbene (iPrCNC) iron complexes have been studied by a combination of spectroscopic and computational methods. The goal of these studies was to determine if this chelate engages in radical chemistry in reduced base metal compounds. The iron dinitrogen example (iPrCNC)Fe(N2)2 and the related pyridine derivative (iPrCNC)Fe(DMAP)(N2) were studied by NMR, Mössbauer, and X-ray absorption spectroscopy and are best described as redox non-innocent compounds with the iPrCNC chelate functioning as a classical π acceptor and the iron being viewed as a hybrid between low-spin Fe(0) and Fe(II) oxidation states. This electronic description has been supported by spectroscopic data and DFT calculations. Addition of N,N-diallyl-tert-butylamine to (iPrCNC)Fe(N2)2 yielded the corresponding iron diene complex. Elucidation of the electronic structure again revealed the CNC chelate acting as a π acceptor with no evidence for ligand-centered radicals. This ground state is in contrast with the case for the analogous bis(imino)pyridine iron complexes and may account for the lack of catalytic [2π + 2π] cycloaddition reactivity. PMID:25328270

  10. Kappa-opioid receptor-selective dicarboxylic ester-derived salvinorin A ligands.

    PubMed

    Polepally, Prabhakar R; White, Kate; Vardy, Eyal; Roth, Bryan L; Ferreira, Daneel; Zjawiony, Jordan K

    2013-05-15

    Salvinorin A, the active ingredient of the hallucinogenic plant Salvia divinorum is the most potent known naturally occurring hallucinogen and is a selective κ-opioid receptor agonist. To better understand the ligand-receptor interactions, a series of dicarboxylic ester-type of salvinorin A derivatives were synthesized and evaluated for their binding affinity at κ-, δ- and μ-opioid receptors. Most of the analogues show high affinity to the κ-opioid receptor. Methyl malonyl derivative 4 shows the highest binding affinity (Ki=2nM), analogues 5, 7, and 14 exhibit significant affinity for the κ-receptor (Ki=21, 36 and 39nM).

  11. Kappa-Opioid Receptor-Selective Dicarboxylic Ester-Derived Salvinorin A Ligands

    PubMed Central

    Polepally, Prabhakar R.; White, Kate; Vardy, Eyal; Roth, Bryan L.; Ferreira, Daneel; Zjawiony, Jordan K.

    2013-01-01

    Salvinorin A, the active ingredient of the hallucinogenic plant Salvia divinorum is the most potent known naturally occurring hallucinogen and is a selective κ-opioid receptor agonist. To better understand the ligand-receptor interactions, a series of dicarboxylic ester-type of salvinorin A derivatives were synthesized and evaluated for their binding affinity at κ, δ, and μ-opioid receptors. Most of the analogues show high affinity to the κ-opioid receptor. Methyl malonyl derivative 4 shows the highest binding affinity (Ki = 2 nM), analogues 5, 7, and 14 exhibit significant affinity for the κ-receptor (Ki = 21, 36 and 39 nM). PMID:23587424

  12. Group 13 and lanthanide complexes with mixed O,S anionic ligands derived from maltol.

    PubMed

    Monga, Vishakha; Patrick, Brian O; Orvig, Chris

    2005-04-18

    Four mixed O,S binding ligand precursors derived from maltol (3-hydroxy-2-methyl-4-pyrone) have been chelated to gallium(III), indium(III), and lanthanide(III) ions to yield a series of metal complexes. The four ligand precursors include two pyranthiones, 3-hydroxy-2-methyl-4-pyranthione, commonly known as thiomaltol (Htma), and 2-ethyl-3-hydroxy-4-pyranthione, commonly known as ethylthiomaltol (Hetma), and two pyridinethiones, 3-hydroxy-2-methyl-4(H)-pyridinethione (Hmppt) and 3-hydroxy-1,2-dimethyl-4-pyridinethione (Hdppt). Dimeric forms of the pyridinethiones, Hmppt dimer and Hdppt dimer, were also isolated and characterized. Complete characterization of the monomeric organic compounds is reported including acidity constants and crystal structures of Htma, Hetma, and Hdppt dimer. Reacting the four monomeric ligand precursors with Ga(3+) and In(3+) ions yielded new tris(bidentate ligand) complexes. X-ray-quality crystals of the fac isomer of Ga(tma)(3) were also obtained. New complexes with a range of lanthanides (Ln(3+)) were also synthesized with the two pyranthiones, Htma and Hetma. The synthesis reactions yielded complexes of the type LnL(3).xH(2)O and LnL(2)(OH).xH(2)O, as indicated by elemental analysis and spectroscopic evidence such as mass spectral data and IR and NMR spectra.

  13. A Nuclear Receptor Ligand-based Probe Enables Temporal Control of C. elegans Development

    PubMed Central

    Judkins, Joshua C.; Mahanti, Parag; Hoffman, Jacob; Yim, Isaiah; Antebi, Adam; Schroeder, Frank C.

    2014-01-01

    C. elegans development and lifespan are controlled by the nuclear hormone receptor DAF-12, an important model for vertebrate vitamin D and liver-X receptors. Similar to its mammalian homologs, DAF-12 function is regulated by bile acid-like steroidal ligands, the dafachronic acids; however, tools for investigating their biosynthesis and function in vivo are lacking. We report a flexible synthesis for DAF-12 ligands and masked ligand derivatives that enable precise temporal control of DAF-12 function. For ligand masking, we introduce photocleavable amides of 5-methoxy-N-methyl-2-nitroaniline (MMNA). MMNA-masked ligands are bioavailable and after incorporation into the worm can be used to trigger expression of DAF-12 target genes and initiate development from dauer larvae to adults by brief, innocuous UV-irradiation. In-vivo release of DAF-12 ligands and other small-molecule signals using MMNA-based probes will enable functional studies with precise spatial and temporal resolution. PMID:24453122

  14. Chiral ligand-exchange chromatography of amino acids using porous graphitic carbon coated with a dinaphthyl derivative of neamine.

    PubMed

    Zaher, Mustapha; Ravelet, Corinne; Baussanne, Isabelle; Ravel, Anne; Grosset, Catherine; Décout, Jean-Luc; Peyrin, Eric

    2009-01-01

    In this paper, we describe the preparation and the evaluation of a porous graphitic carbon (PGC) column coated with a new dinaphthyl derivative of neamine for chiral ligand-exchange (LE) chromatography. It was shown that the graphitic surface/dinaphthyl anchor system efficiently (1.15 micromol/m(2)) and stably (three months of intensive use) adsorbs the neamine template onto the chromatographic support. The resulting coated PGC stationary phase showed appreciable LE-based enantioselective properties towards several native amino acids.

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

    PubMed

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

    2015-05-04

    Comprehensive studies on the coordination properties of tridentate nitrenium-based ligands are presented. N-heterocyclic nitrenium ions demonstrate general and versatile binding abilities to various transition metals, as exemplified by the synthesis and characterization of Rh(I) , Rh(III) , Mo(0) , Ru(0) , Ru(II) , Pd(II) , Pt(II) , Pt(IV) , and Ag(I) complexes based on these unusual ligands. Formation of nitrenium-metal bonds is unambiguously confirmed both in solution by selective (15) N-labeling experiments and in the solid state by X-ray crystallography. The generality of N-heterocyclic nitrenium as a ligand is also validated by a systematic DFT study of its affinity towards all second-row transition and post-transition metals (Y-Cd) in terms of the corresponding bond-dissociation energies.

  16. Competition STD NMR for the detection of high-affinity ligands and NMR-based screening.

    PubMed

    Wang, Yu-Sen; Liu, Dingjiang; Wyss, Daniel F

    2004-06-01

    The reported competition STD NMR method combines saturation transfer difference (STD) NMR with competition binding experiments to allow the detection of high-affinity ligands that undergo slow chemical exchange on the NMR time-scale. With this technique, the presence of a competing high-affinity ligand in the compound mixture can be detected by the disappearance or reduction of the STD signals of a low-affinity indicator ligand. This is demonstrated on a BACE1 (beta-site amyloid precursor protein cleaving enzyme 1) protein-inhibitor system. This method can also be used to derive an approximate value, or a lower limit, for the dissociation constant of the potential ligand based on the reduction of the signal intensity of the STD indicator, which is illustrated on an HSA (human serum albumin) model system. This leads to important applications of the competition STD NMR method for lead discovery: it can be used (i) for compound library screening against a broad range of drug targets to identify both high- and low-affinity ligands and (ii) to rank order analogs rapidly and derive structure-activity relationships, which are used to optimize these NMR hits into viable drug leads. Copyright 2004 John Wiley & Sons, Ltd.

  17. N6-benzyladenosine derivatives as novel N-donor ligands of platinum(II) dichlorido complexes.

    PubMed

    Starha, Pavel; Popa, Igor; Trávníček, Zdeněk; Vančo, Ján

    2013-06-14

    The platinum(II) complexes trans-[PtCl₂(Ln)₂]∙xSolv 1-13 (Solv = H₂O or CH3OH), involving N6-benzyladenosine-based N-donor ligands, were synthesized; L(n) stands for N6-(2-methoxybenzyl)adenosine (L₁, involved in complex 1), N6-(4-methoxy-benzyl)adenosine (L₂, 2), N6-(2-chlorobenzyl)adenosine (L₃, 3), N6-(4-chlorobenzyl)-adenosine (L₄, 4), N6-(2-hydroxybenzyl)adenosine (L₅, 5), N6-(3-hydroxybenzyl)-adenosine (L₆, 6), N6-(2-hydroxy-3-methoxybenzyl)adenosine (L₇, 7), N6-(4-fluoro-benzyl)adenosine (L₈, 8), N6-(4-methylbenzyl)adenosine (L₉, 9), 2-chloro-N6-(3-hydroxy-benzyl)adenosine (L₁₀, 10), 2-chloro-N6-(4-hydroxybenzyl)adenosine (L₁₁, 11), 2-chloro-N6-(2-hydroxy-3-methoxybenzyl)adenosine (L₁₂, 12) and 2-chloro-N6-(2-hydroxy-5-methylbenzyl)adenosine (L₁₃, 13). The compounds were characterized by elemental analysis, mass spectrometry, IR and multinuclear (¹H-, ¹³C-, ¹⁹⁵Pt- and ¹⁵N-) and two-dimensional NMR spectroscopy, which proved the N7-coordination mode of the appropriate N6-benzyladenosine derivative and trans-geometry of the title complexes. The complexes 1-13 were found to be non-toxic in vitro against two selected human cancer cell lines (HOS and MCF7; with IC₅₀ > 50.0 µM). However, they were found (by ESI-MS study) to be able to interact with the physiological levels of the sulfur-containing biogenic biomolecule L-methionine by a relatively simple 1:1 exchange mechanism (one L(n) molecule was replaced by one L-methionine molecule), thus forming a mixed-nitrogen/sulfur-ligand dichlorido-platinum(II) coordination species.

  18. Cholinesterase inhibitory activity of chlorophenoxy derivatives-Histamine H3 receptor ligands.

    PubMed

    Łażewska, Dorota; Jończyk, Jakub; Bajda, Marek; Szałaj, Natalia; Więckowska, Anna; Panek, Dawid; Moore, Caitlin; Kuder, Kamil; Malawska, Barbara; Kieć-Kononowicz, Katarzyna

    2016-08-15

    In recent years, multitarget-directed ligands have become an interesting strategy in a search for a new treatment of Alzheimer's disease. Combination of both: a histamine H3 receptor antagonist/inverse agonist and a cholinesterases inhibitor in one molecule could provide a new therapeutic opportunity. Here, we present biological evaluation of histamine H3 receptor ligands-chlorophenoxyalkylamine derivatives against cholinesterases: acetyl- and butyrylcholinesterase. The target compounds showed cholinesterase inhibitory activity in a low micromolar range. The most potent in this group was 1-(7-(4-chlorophenoxy)heptyl)homopiperidine (18) inhibiting the both enzymes (EeAChE IC50=1.93μM and EqBuChE IC50=1.64μM). Molecular modeling studies were performed to explain the binding mode of 18 with histamine H3 receptor as well as with cholinesterases.

  19. Synthesis, Characterization and Biological Evaluation of Transition Metal Complexes Derived from N, S Bidentate Ligands

    PubMed Central

    Md Yusof, Enis Nadia; Ravoof, Thahira Begum S. A.; Tiekink, Edward R. T.; Veerakumarasivam, Abhimanyu; Crouse, Karen Anne; Mohamed Tahir, Mohamed Ibrahim; Ahmad, Haslina

    2015-01-01

    Two bidentate NS ligands were synthesized by the condensation reaction of S-2-methylbenzyldithiocarbazate (S2MBDTC) with 2-methoxybenzaldehyde (2MB) and 3-methoxybenzaldehyde (3MB). The ligands were reacted separately with acetates of Cu(II), Ni(II) and Zn(II) yielding 1:2 (metal:ligand) complexes. The metal complexes formed were expected to have a general formula of [M(NS)2] where M = Cu2+, Ni2+, and Zn2+. These compounds were characterized by elemental analysis, molar conductivity, magnetic susceptibility and various spectroscopic techniques. The magnetic susceptibility measurements and spectral results supported the predicted coordination geometry in which the Schiff bases behaved as bidentate NS donor ligands coordinating via the azomethine nitrogen and thiolate sulfur. The molecular structures of the isomeric S2M2MBH (1) and S2M3MBH (2) were established by X-ray crystallography to have very similar l-shaped structures. The Schiff bases and their metal complexes were evaluated for their biological activities against estrogen receptor-positive (MCF-7) and estrogen receptor-negative (MDA-MB-231) breast cancer cell lines. Only the Cu(II) complexes showed marked cytotoxicity against the cancer cell lines. Both Schiff bases and other metal complexes were found to be inactive. In concordance with the cytotoxicity studies, the DNA binding studies indicated that Cu(II) complexes have a strong DNA binding affinity. PMID:25988384

  20. Protein-Ligand Docking Based on Beta-Shape

    NASA Astrophysics Data System (ADS)

    Kim, Chong-Min; Won, Chung-In; Kim, Jae-Kwan; Ryu, Joonghyun; Bhak, Jong; Kim, Deok-Soo

    Protein-ligand docking is to predict the location and orientation of a ligand with respect to a protein within its binding site, and has been known to be essential for the development of new drugs. The protein-ligand docking problem is usually formulated as an energy minimization problem to identify the docked conformation of the ligand. A ligand usually docks around a depressed region, called a pocket, on the surface of a protein. Presented in this paper is a docking method, called BetaDock, based on the newly developed geometric construct called the β-shape and the β-complex. To cope with the computational intractability, the global minimum of the potential energy function is searched using the genetic algorithm. The proposed algorithm first locates initial chromosomes at some locations within the pocket recognized according to the local shape of the β-shape. Then, the algorithm proceeds generations by taking advantage of powerful properties of the β-shape to achieve an extremely fast and good solution. We claim that the proposed method is much faster than other popular docking softwares including AutoDock.

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

    ERIC Educational Resources Information Center

    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…

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

    ERIC Educational Resources Information Center

    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…

  3. Novel Chalcone-Based Fluorescent Human Histamine H3 Receptor Ligands as Pharmacological Tools

    PubMed Central

    Tomasch, Miriam; Schwed, J. Stephan; Weizel, Lilia; Stark, Holger

    2012-01-01

    Novel fluorescent chalcone-based ligands at human histamine H3 receptors (hH3R) have been designed, synthesized, and characterized. Compounds described are non-imidazole analogs of ciproxifan with a tetralone motif. Tetralones as chemical precursors and related fluorescent chalcones exhibit affinities at hH3R in the same concentration range like the reference antagonist ciproxifan (hH3R pKi value of 7.2). Fluorescence characterization of our novel ligands shows emission maxima about 570 nm for yellow fluorescent chalcones and ≥600 nm for the red fluorescent derivatives. Interferences to cellular autofluorescence could be excluded. All synthesized chalcone compounds could be used to visualize hH3R proteins in stably transfected HEK-293 cells using confocal laser scanning fluorescence microscopy. These novel fluorescent ligands possess high potential to be used as pharmacological tools for hH3R visualization in different tissues. PMID:22470321

  4. Mononuclear nickel (II) and copper (II) coordination complexes supported by bispicen ligand derivatives: Experimental and computational studies

    SciTech Connect

    Singh, Nirupama; Niklas, Jens; Poluektov, Oleg; Van Heuvelen, Katherine M.; Mukherjee, Anusree

    2017-01-01

    The synthesis, characterization and density functional theory calculations of mononuclear Ni and Cu complexes supported by the N,N’-Dimethyl-N,N’-bis-(pyridine-2-ylmethyl)-1,2-diaminoethane ligand and its derivatives are reported. The complexes were characterized by X-ray crystallography as well as by UV-visible absorption spectroscopy and EPR spectroscopy. The solid state structure of these coordination complexes revealed that the geometry of the complex depended on the identity of the metal center. Solution phase characterization data are in accord with the solid phase structure, indicating minimal structural changes in solution. Optical spectroscopy revealed that all of the complexes exhibit color owing to d-d transition bands in the visible region. Magnetic parameters obtained from EPR spectroscopy with other structural data suggest that the Ni(II) complexes are in pseudo-octahedral geometry and Cu(II) complexes are in a distorted square pyramidal geometry. In order to understand in detail how ligand sterics and electronics affect complex topology detailed computational studies were performed. The series of complexes reported in this article will add significant value in the field of coordination chemistry as Ni(II) and Cu(II) complexes supported by tetradentate pyridyl based ligands are rather scarce.

  5. Metal complexes of ONO donor Schiff base ligand as a new class of bioactive compounds; Synthesis, characterization and biological evolution

    NASA Astrophysics Data System (ADS)

    Kumar Naik, K. H.; Selvaraj, S.; Naik, Nagaraja

    2014-10-01

    Present work reviews that, the synthesis of (E)-N";-((7-hydroxy-4-methyl-2-oxo-2H-chromen-8-yl)methylene)benzohydrazide [L] ligand and their metal complexes. The colored complexes were prepared of type [M2+L]X2, where M2+ = Mn, Co, Ni, Cu, Sr and Cd, L = (7-hydroxy-4-methyl-2-oxo-2H-chromen-8-yl)methylene)benzohydrazide, X = Cl-. Ligand derived from the condensation of 8-formyl-7-hydroxy-4-methylcoumarin and benzohydrazide in the molar ratio 1:1 and in the molar ratio 1:2 for metal complexes have been prepared. The chelation of the ligand to metal ions occurs through the both oxygen groups, as well as the nitrogen atoms of the azomethine group of the ligand. Reactions of the Schiff base ligand with Manganese(II), Cobalt(II), Nickel(II), Copper(II), Strontium(II), and Cadmium(II) afforded the corresponding metal complexes. The structures of the obtained ligand and their respective metal complexes were elucidated by infra-red, elemental analysis, Double beam UV-visible spectra, conductometric measurements, magnetic susceptibility measurements and also thermochemical studies. The metal complex exhibits octahedral coordination geometrical arrangement. Schiff base ligand and their metal complexes were tested against antioxidants, antidiabetic and antimicrobial activities have been studied. The Schiff base metal complexes emerges effective α-glucosidase inhibitory activity than free Schiff base ligand.

  6. Steric and electronic effects of 1,3-disubstituted cyclopentadienyl ligands on metallocene derivatives of Cerium, Titanium, Manganese, and Iron

    SciTech Connect

    Sofield, Chadwick Dean

    2000-05-01

    Sterically demanding 1,3-disubstituted cyclopentadienyl ligands were used to modify the physical properties of the corresponding metallocenes. Sterically demanding ligands provided kinetic stabilization for trivalent cerium compounds. Tris(di-t-butylcyclopentadienyl)cerium was prepared and anion competition between halides and cyclopentadienyl groups which had complicated synthesis of the tris(cyclopentadienyl)compound was qualitatively examined. Bis(di-t-butylcyclopentadienyl)cerium methyl was prepared and its rate of decomposition, by ligand redistribution, to tris(di-t-butylcyclopentadienyl)cerium was shown to be slower than the corresponding rate for less sterically demanding ligands. Asymmetrically substituted ligands provided a symmetry label for examination of chemical exchange processes. Tris[trimethylsilyl(t-butyl)cyclopentadienyl]cerium was prepared and the rate of interconversion between the C1 and C3 isomers was examined. The enthalpy difference between the two distereomers is 7.0 kJ/mol. The sterically demanding cyclopentadienyl ligands ansa-di-t-butylcyclopentadiene (Me2Si[(Me3C)2C5H3]2), ansa-bis(trimethylsilyl)cyclopentadiene (Me2Si[(Me3Si)2C5H3]2) and tetra-t-butylfulvalene and metallocene derivatives of the ligands were prepared and their structures were examined by single crystal X-ray crystallography. The effect that substituents on the cyclopentadienyl ring have on the pi-electron system of the ligand was examined through interaction between ligand and metal orbitals. A series of 1,3-disubstituted manganocenes was prepared and their electronic states were determined by solid-state magnetic susceptibility, electron paramagnetic resonance, X-ray crystallography, and variable temperature UV-vis spectroscopy. Spin-equilibria in [(Me3C)2C5H3]2Mn and [(Me3

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

    NASA Astrophysics Data System (ADS)

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

    2009-11-01

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

  8. Ligand and Structure-based Methodologies for the Prediction of the Activity of G Protein-Coupled Receptor Ligands

    PubMed Central

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

    2008-01-01

    Summary Accurate in silico models for the quantitative prediction of the activity of G protein-coupled receptor (GPCR) ligands would greatly facilitate the process of drug discovery and development. Several methodologies have been developed based on the properties of the ligands, the direct study of the receptor-ligand interactions, or a combination of both approaches. Ligand-based three-dimensional quantitative structure-activity relationships (3D-QSAR) techniques, not requiring knowledge of the receptor structure, have been historically the first to be applied to the prediction of the activity of GPCR ligands. They are generally endowed with robustness and good ranking ability; however they are highly dependent on training sets. Structure-based techniques generally do not provide the level of accuracy necessary to yield meaningful rankings when applied to GPCR homology models. However, they are essentially independent from training sets and have a sufficient level of accuracy to allow an effective discrimination between binders and nonbinders, thus qualifying as viable lead discovery tools. The combination of ligand and structure-based methodologies in the form of receptor-based 3D-QSAR and ligand and structure-based consensus models results in robust and accurate quantitative predictions. The contribution of the structure-based component to these combined approaches is expected to become more substantial and effective in the future, as more sophisticated scoring functions are developed and more detailed structural information on GPCRs is gathered. PMID:18483766

  9. Redox-derived damage-associated molecular patterns: Ligand function of lipid peroxidation adducts.

    PubMed

    Uchida, Koji

    2013-02-12

    Endogenous electrophiles, such as α,β-unsaturated aldehydes and ketones generated during lipid peroxidation, exhibit a facile reactivity with proteins, generating a variety of intra and intermolecular covalent adducts. It has been postulated that these host-derived, modified proteins with electrophiles, which constitute the products of diverse classes of oxidative reactions, represent damage-associated molecular patterns (DAMPs). The DAMPs, that occur in vivo, can be a ligand of multiple proteins, which in turn, may lead to the profound innate and adaptive immune responses and mediate homeostatic functions consequent to inflammation and cell death.

  10. Carboline- and phenothiazine-derivated heterocycles as potent SIGMA-1 protein ligands.

    PubMed

    Donnier-Maréchal, Marion; Larchanché, Paul-Emmanuel; Le Broc, Delphine; Furman, Christophe; Carato, Pascal; Melnyk, Patricia

    2015-01-07

    Sigma 1 receptors are associated with neurodegenerative and psychiatric disorders. These receptors, via their chaperoning functions that counteract endoplasmic reticulum stress and block neurodegeneration, may serve as a target for a new generation of antidepressants or neuroprotective agents. The involvement of these receptors has also been observed in neuropathic pain and cancer. Only a few ligands, such as Igmesine and Anavex 2-73, have been involved in clinical trials. Thus the development of sigma 1 ligands is of interest to a new generation of drugs. Previous work in our lab underlined the potency of benzannulated bicyclic compounds as interesting ligands. Herein the work was extended to a series of novel tricyclic compounds. Carboline- and phenothiazine-derivated compounds were designed and synthesized. In vitro competition binding assays for sigma 1 and 2 receptors showed that most of them have high affinity for sigma 1 receptor (Ki = 2.5-18 nM), and selectivity toward sigma 2 receptor, without cytotoxic effects on SY5Y cells.

  11. Lanthanide complexes derived from hexadentate macrocyclic ligand: synthesis, spectroscopic and thermal investigation.

    PubMed

    Chandra, Sulekh; Tyagi, Monika; Rani, Soni; Kumar, Sumit

    2010-02-01

    The lanthanide complexes derived from (3,5,13,15-tetramethyl 2,6,12,16,21-22-hexaazatricyclo[15.3.I(1-17)I(7-11)]cosa-1(21),2,5,7,9,11(22),12,15,17,19-decane) were synthesized. The complexes were found to have general composition [Ln(L)X(2).H(2)O]X, where Ln=La(3+), Ce(3+), Nd(3+), Sm(3+) and Eu(3+) and X=NO(3)(-) and Cl(-). The ligand was characterized by elemental analyses, IR, Mass, and (1)H NMR spectral studies. All the complexes were characterized by elemental analyses, molar conductance measurements, magnetic susceptibility measurements, IR, Mass, electronic spectral techniques and thermal studies. The ligand acts as a hexadentate and coordinates through four nitrogen atoms of azomethine groups and two nitrogen of pyridine ring. The lanthanum complexes are diamagnetic while the other Ln(III) complexes are paramagnetic. The spectral parameters i.e. nephelauxetic ratio (beta), covalency factor (b(1/2)), Sinha parameter (delta%) and covalency angular overlap parameter (eta) have been calculated from absorption spectra of Nd(III) and Sm(III) complexes. These parameters suggest the metal-ligand covalent bonding. In the present study, the complexes were found to have coordination number nine.

  12. Lanthanide complexes derived from hexadentate macrocyclic ligand: Synthesis, spectroscopic and thermal investigation

    NASA Astrophysics Data System (ADS)

    Chandra, Sulekh; Tyagi, Monika; Rani, Soni; Kumar, Sumit

    2010-02-01

    The lanthanide complexes derived from (3,5,13,15-tetramethyl 2,6,12,16,21-22-hexaazatricyclo[15.3.I 1-17I 7-11]cosa-1(21),2,5,7,9,11(22),12,15,17,19-decane) were synthesized. The complexes were found to have general composition [Ln(L)X 2·H 2O]X, where Ln = La 3+, Ce 3+, Nd 3+, Sm 3+ and Eu 3+ and X = NO 3- and Cl -. The ligand was characterized by elemental analyses, IR, Mass, and 1H NMR spectral studies. All the complexes were characterized by elemental analyses, molar conductance measurements, magnetic susceptibility measurements, IR, Mass, electronic spectral techniques and thermal studies. The ligand acts as a hexadentate and coordinates through four nitrogen atoms of azomethine groups and two nitrogen of pyridine ring. The lanthanum complexes are diamagnetic while the other Ln(III) complexes are paramagnetic. The spectral parameters i.e. nephelauxetic ratio ( β), covalency factor ( b1/2), Sinha parameter ( δ%) and covalency angular overlap parameter ( η) have been calculated from absorption spectra of Nd(III) and Sm(III) complexes. These parameters suggest the metal-ligand covalent bonding. In the present study, the complexes were found to have coordination number nine.

  13. Spectroscopic, Structural, and Computational Characterization of Three Bispidinone Derivatives, as Ligands for Enantioselective Metal Catalyzed Reactions.

    PubMed

    Castellano, Carlo; Sacchetti, Alessandro; Meneghetti, Fiorella

    2016-04-01

    Three chiral derivatives of the alkaloid sparteine (bispidines), characterized by the 3,7-diazabicyclo[3.3.1]nonane moiety, were designed as efficient ligands in a number of enantioselective reactions due to their metal coordination properties. A full evaluation of the 3D properties of the compounds was carried out, as the geometrical features of the bicyclic framework are strictly related to the efficiency of the ligands in the asymmetric catalysis. The selected molecules have different molecular complexity for investigating the effects of different chiral groups on the bicycle conformation. We report here a thorough analysis of their molecular arrangement, by NMR spectroscopy, single crystal X-ray crystallography, and computational techniques, which put in evidence their conformational preferences and the parameters needed for the design of more efficient ligands in asymmetric synthetic routes. The results confirmed the high molecular flexibility of the compounds, and indicated how to achieve a control of the chair-chair/boat-chair conformational ratio, by adjusting the relative size of the substituents on the piperidine nitrogens.

  14. Optimal ligand descriptor for pocket recognition based on the Beta-shape.

    PubMed

    Kim, Jae-Kwan; Won, Chung-In; Cha, Jehyun; Lee, Kichun; Kim, Deok-Soo

    2015-01-01

    Structure-based virtual screening is one of the most important and common computational methods for the identification of predicted hit at the beginning of drug discovery. Pocket recognition and definition is frequently a prerequisite of structure-based virtual screening, reducing the search space of the predicted protein-ligand complex. In this paper, we present an optimal ligand shape descriptor for a pocket recognition algorithm based on the beta-shape, which is a derivative structure of the Voronoi diagram of atoms. We investigate six candidates for a shape descriptor for a ligand using statistical analysis: the minimum enclosing sphere, three measures from the principal component analysis of atoms, the van der Waals volume, and the beta-shape volume. Among them, the van der Waals volume of a ligand is the optimal shape descriptor for pocket recognition and best tunes the pocket recognition algorithm based on the beta-shape for efficient virtual screening. The performance of the proposed algorithm is verified by a benchmark test.

  15. Optimal Ligand Descriptor for Pocket Recognition Based on the Beta-Shape

    PubMed Central

    Kim, Jae-Kwan; Won, Chung-In; Cha, Jehyun; Lee, Kichun; Kim, Deok-Soo

    2015-01-01

    Structure-based virtual screening is one of the most important and common computational methods for the identification of predicted hit at the beginning of drug discovery. Pocket recognition and definition is frequently a prerequisite of structure-based virtual screening, reducing the search space of the predicted protein-ligand complex. In this paper, we present an optimal ligand shape descriptor for a pocket recognition algorithm based on the beta-shape, which is a derivative structure of the Voronoi diagram of atoms. We investigate six candidates for a shape descriptor for a ligand using statistical analysis: the minimum enclosing sphere, three measures from the principal component analysis of atoms, the van der Waals volume, and the beta-shape volume. Among them, the van der Waals volume of a ligand is the optimal shape descriptor for pocket recognition and best tunes the pocket recognition algorithm based on the beta-shape for efficient virtual screening. The performance of the proposed algorithm is verified by a benchmark test. PMID:25835497

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

    PubMed

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

    2009-05-01

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

  17. Optimization of 3,5-dimethylisoxazole derivatives as potent bromodomain ligands.

    PubMed

    Hewings, David S; Fedorov, Oleg; Filippakopoulos, Panagis; Martin, Sarah; Picaud, Sarah; Tumber, Anthony; Wells, Christopher; Olcina, Monica M; Freeman, Katherine; Gill, Andrew; Ritchie, Alison J; Sheppard, David W; Russell, Angela J; Hammond, Ester M; Knapp, Stefan; Brennan, Paul E; Conway, Stuart J

    2013-04-25

    The bromodomain protein module, which binds to acetylated lysine, is emerging as an important epigenetic therapeutic target. We report the structure-guided optimization of 3,5-dimethylisoxazole derivatives to develop potent inhibitors of the BET (bromodomain and extra terminal domain) bromodomain family with good ligand efficiency. X-ray crystal structures of the most potent compounds reveal key interactions required for high affinity at BRD4(1). Cellular studies demonstrate that the phenol and acetate derivatives of the lead compounds showed strong antiproliferative effects on MV4;11 acute myeloid leukemia cells, as shown for other BET bromodomain inhibitors and genetic BRD4 knockdown, whereas the reported compounds showed no general cytotoxicity in other cancer cell lines tested.

  18. Optimization of 3,5-Dimethylisoxazole Derivatives as Potent Bromodomain Ligands

    PubMed Central

    2013-01-01

    The bromodomain protein module, which binds to acetylated lysine, is emerging as an important epigenetic therapeutic target. We report the structure-guided optimization of 3,5-dimethylisoxazole derivatives to develop potent inhibitors of the BET (bromodomain and extra terminal domain) bromodomain family with good ligand efficiency. X-ray crystal structures of the most potent compounds reveal key interactions required for high affinity at BRD4(1). Cellular studies demonstrate that the phenol and acetate derivatives of the lead compounds showed strong antiproliferative effects on MV4;11 acute myeloid leukemia cells, as shown for other BET bromodomain inhibitors and genetic BRD4 knockdown, whereas the reported compounds showed no general cytotoxicity in other cancer cell lines tested. PMID:23517011

  19. Hydroxyalkylation with cyclic sulfates: synthesis of carbazole derived CB(2) ligands with increased polarity.

    PubMed

    Lueg, Corinna; Galla, Fabian; Frehland, Bastian; Schepmann, Dirk; Daniliuc, Constantin G; Deuther-Conrad, Winnie; Brust, Peter; Wünsch, Bernhard

    2014-01-01

    In order to increase the polarity of the potent CB2 ligand 1a, the homologous hydroxyalkyl carbazoles 2a-c were prepared and pharmacologically evaluated. An important step in the synthesis is the hydroxyalkylation of carbazole with cyclic sulfates providing the 2-hydroxyethyl and 3-hydroxypropyl derivatives 5a and 5b in a one-step reaction. The final propionamides 2a-c were prepared using the recently reported coupling reagent COMU®. The X-ray crystal structure of 2c displays an almost coplanar arrangement of the 3-phenyl-1,2,4-oxadiazole biaryl system. The increased polarity of 2a is associated with an almost 100-fold reduced CB2 affinity. The 3-hydroxypropyl derivative 2b represents the best compromise between lipophilicity and CB2 affinity (Ki  = 33 nM). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Ligand peptide-grafted PEGylated liposomes using HER2 targeted peptide-lipid derivatives for targeted delivery in breast cancer cells: The effect of serine-glycine repeated peptides as a spacer.

    PubMed

    Suga, Tadaharu; Fuchigami, Yuki; Hagimori, Masayori; Kawakami, Shigeru

    2017-02-22

    Ligand peptide-grafted PEGylated liposomes have been widely studied for targeted drug delivery systems. Because ligand peptides are commonly grafted using PEG as a spacer on the surface of PEGylated liposomes, the interaction between ligand peptides and their corresponding receptors can be interrupted by steric hindrance of the PEG layer. Therefore, we aimed to develop ligand peptide-lipid derivatives to enhance the targeting efficiency of ligand peptide-grafted PEGylated liposomes, and designed a new ligand peptide-lipid derivatives having serine-glycine repeats (SG)n as a spacer based on the peptide length calculated by PyMol (v0.99). We selected KCCYSL (KCC) as the ligand peptide for binding to human epidermal growth factor receptor-2 (HER2). We synthesized new KCC-(SG)n-lipid derivatives (n=3, 5, 7) and evaluated their cellular association in breast cancer cells. KCC-(SG)n/PEGylated liposomes dramatically increased cellular association on HER2-positive breast cancer cells. The results suggest that KCC can be grafted on the surface of KCC-(SG)n/PEGylated liposomes prepared from KCC-(SG)n-lipid derivatives (n=3, 5, 7). In summary, we succeeded in developing KCC-(SG)n-lipid derivatives for the preparation of ligand peptide-grafted PEGylated liposomes.

  1. Fluorescent pirenzepine derivatives as potential bitopic ligands of the human M1 muscarinic receptor.

    PubMed

    Tahtaoui, Chouaib; Parrot, Isabelle; Klotz, Philippe; Guillier, Fabrice; Galzi, Jean-Luc; Hibert, Marcel; Ilien, Brigitte

    2004-08-12

    Following a recent description of fluorescence resonance energy transfer between enhanced green fluorescent protein (EGFP)-fused human muscarinic M1 receptors and Bodipy-labeled pirenzepine, we synthesized seven fluorescent derivatives of this antagonist in order to further characterize ligand-receptor interactions. These compounds carry Bodipy [558/568], Rhodamine Red-X [560/580], or Fluorolink Cy3 [550/570] fluorophores connected to pirenzepine through various linkers. All molecules reversibly bind with high affinity to M1 receptors (radioligand and energy transfer binding experiments) provided that the linker contains more than six atoms. The energy transfer efficiency exhibits modest variations among ligands, indicating that the distance separating EGFP from the fluorophores remains almost constant. This also supports the notion that the fluorophores may bind to the receptor protein. Kinetic analyses reveal that the dissociation of two Bodipy derivatives (10 or 12 atom long linkers) is sensitive to the presence of the allosteric modulator brucine, while that of all other molecules (15-24 atom long linkers) is not. The data favor the idea that these analogues might interact with both the acetylcholine and the brucine binding domains. Copyright 2004 American Chemical Society

  2. Multiphase enantioselective Kharasch-Sosnovsky allylic oxidation based on neoteric solvents and copper complexes of ditopic ligands.

    PubMed

    Aldea, Luis; García, José I; Mayoral, José A

    2012-07-21

    Recoverable multiphase enantioselective catalytic systems for the Kharasch-Sosnovsky oxidation of cycloalkenes with tert-butyl peroxybenzoate are described, based on the use of [BMIM][PF(6)] and a new solvent derived from glycerol as the catalyst reservoir phases, and chiral copper complexes with different ligands from the bis(oxazoline) family. The best results are obtained with the glycerol-derived solvent and a recently described azabisoxazoline-based ditopic ligand, allowing up to four uses of the catalytic phase with good results.

  3. Ferro- and anti-ferromagnetically coupled tetracopper(II) 2 x 2 homoleptic rectangular grids supported by both mu-O and mu-(N-N) bridges derived from a new pyrazole based polydentate Schiff base ligand-magneto-structural correlations and DFT calculation.

    PubMed

    Roy, Somnath; Mandal, Tarak Nath; Barik, Anil Kumar; Gupta, Samik; El Fallah, Mohamed Salah; Tercero, Javier; Butcher, Ray J; Kar, Susanta Kumar

    2009-10-21

    The pyrazole derived Schiff base polytopic ligand 5-methyl-N'-[1-(pyridin-2-yl)ethylidene]-1H-pyrazole-3-carbohydrazide (PzCAP), prepared by the reaction between 5-methylpyrazole-3-carbohydrazide and 2-acetyl pyridine, has two potentially bridging functional groups [mu-O and mu-(N-N)] and consequently can exhibit different coordination conformations. Two tetranuclear homoleptic copper(II) 2 x 2 rectangular grid-complexes [Cu(4)(PzCAP)(4)(NO(3))(2)] (NO(3))(2).8H(2)O (1) and [Cu(4)(PzCAP)(4)(ClO(4))(2)] (ClO(4))(2) (2) were formed by a strict self-assembly process employing metal and ligand under 1:1 mol proportion. Each pair of the ligand molecules in the two complexes are arranged in roughly parallel fashion but under different conformations. The ligand PzCAP contains terminal pyridine and pyrazole residues bound to a central flexible diazine subunit (N-N). The rectangular Cu(II) 2 x 2 grid complexes having [Cu(4)(mu-N-N)(2)(mu-O)(2)] core involve a mixture of two diazine (Cu-N-N-Cu approximately 160 degrees ) and two alkoxo (Cu-O-Cu approximately 138 degrees ) bridges along the length and breadth respectively. In the [Cu(4)(mu-N-N)(2)(mu-O)(2)] core in , out of the four Cu(II) centers, all are hexa-coordinated but there are two penta-coordinated and two hexa-coordinated Cu(II) centers in the same core of . Each complex having the central [Cu(4)(mu-N-N)(2)(mu-O)(2)] core, exhibits quite different magnetic interactions among the metal centers. The paramagnetic Cu(II) centers bridged through the diazine fragment are involved in anti-ferromagnetic interaction while a dominant ferromagnetic interaction prevails between the alkoxo-bridged Cu(II) centers. The [Cu(4)(mu-N-N)(2)(mu-O)(2)] cluster in shows both ferromagnetic and anti-ferromagnetic interaction (J(1) = -0.80 cm(-1) and J(2) = +3.49 cm(-1)), a very unusual characteristic in this system while the same cluster in exhibits dominant anti-ferromagnetic coupling (J(1) = -89.1 cm(-1) and J(2) = +5.5 cm(-1)) through

  4. A sandwich-type triple-decker lanthanide complex with mixed phthalocyanine and Schiff base ligands.

    PubMed

    Gao, Feng; Li, Yu-Yang; Liu, Cai-Ming; Li, Yi-Zhi; Zuo, Jing-Lin

    2013-08-21

    A new triple-decker dinuclear sandwich-type dysprosium complex based on both the phthalocyanine ligand and the tetradentate Schiff base ligand was synthesized, which is of interest for synthetic chemistry and also shows single-molecule magnetic behaviour.

  5. Chemical Sensors Based on Cyclodextrin Derivatives.

    PubMed

    Ogoshi, Tomoki; Harada, Akira

    2008-08-25

    This review focuses on chemical sensors based on cyclodextrin (CD) derivatives. This has been a field of classical interest, and is now of current interest for numerous scientists. First, typical chemical sensors using chromophore appended CDs are mentioned. Various "turn-off" and "turn-on" fluorescent chemical sensors, in which fluorescence intensity was decreased or increased by complexation with guest molecules, respectively, were synthesized. Dye modified CDs and photoactive metal ion-ligand complex appended CDs, metallocyclodextrins, were also applied for chemical sensors. Furthermore, recent novel approaches to chemical sensing systems using supramolecular structures such as CD dimers, trimers and cooperative binding systems of CDs with the other macrocycle [2]rotaxane and supramolecular polymers consisting of CD units are mentioned. New chemical sensors using hybrids of CDs with p-conjugated polymers, peptides, DNA, nanocarbons and nanoparticles are also described in this review.

  6. Chemical Sensors Based on Cyclodextrin Derivatives

    PubMed Central

    Ogoshi, Tomoki; Harada, Akira

    2008-01-01

    This review focuses on chemical sensors based on cyclodextrin (CD) derivatives. This has been a field of classical interest, and is now of current interest for numerous scientists. First, typical chemical sensors using chromophore appended CDs are mentioned. Various “turn-off” and “turn-on” fluorescent chemical sensors, in which fluorescence intensity was decreased or increased by complexation with guest molecules, respectively, were synthesized. Dye modified CDs and photoactive metal ion-ligand complex appended CDs, metallocyclodextrins, were also applied for chemical sensors. Furthermore, recent novel approaches to chemical sensing systems using supramolecular structures such as CD dimers, trimers and cooperative binding systems of CDs with the other macrocycle [2]rotaxane and supramolecular polymers consisting of CD units are mentioned. New chemical sensors using hybrids of CDs with π-conjugated polymers, peptides, DNA, nanocarbons and nanoparticles are also described in this review. PMID:27873795

  7. Synthesis, characterization and biological activity of ferrocene-based Schiff base ligands and their metal (II) complexes

    NASA Astrophysics Data System (ADS)

    Liu, Yu-Ting; Lian, Gui-Dan; Yin, Da-Wei; Su, Bao-Jun

    Metal (II) complexes derived from S-benzyl-N-(1-ferrocenyl-3-(4-methylbenzene)acrylketone) dithiocarbazate; HL1, S-benzyl-N-(1-ferrocenyl-3-(4-chlorobenzene)acrylketone)dithiocarbazate; HL2, all the compounds were characterized using various spectroscopic techniques. The molar conductance data revealed that the chelates were non-electrolytes. IR spectra showed that the Schiff bases were coordinated to the metal ions in a bidentate manner with N, S donor sites. The ligands and their metal complexes have been screened for in vitro antibacterial, antifungal properties. The result of these studies have revealed that zinc (II) complexes 6 and 13 of both the ligands and copper (II) complexes 9 of the HL2 were observed to be the most active against all bacterial strains, antifungal activity was overall enhanced after complexation of the ligands.

  8. Synthesis, characterization and biological activity of ferrocene-based Schiff base ligands and their metal (II) complexes.

    PubMed

    Liu, Yu-Ting; Lian, Gui-Dan; Yin, Da-Wei; Su, Bao-Jun

    2013-01-01

    Metal (II) complexes derived from S-benzyl-N-(1-ferrocenyl-3-(4-methylbenzene)acrylketone) dithiocarbazate; HL(1), S-benzyl-N-(1-ferrocenyl-3-(4-chlorobenzene)acrylketone)dithiocarbazate; HL(2), all the compounds were characterized using various spectroscopic techniques. The molar conductance data revealed that the chelates were non-electrolytes. IR spectra showed that the Schiff bases were coordinated to the metal ions in a bidentate manner with N, S donor sites. The ligands and their metal complexes have been screened for in vitro antibacterial, antifungal properties. The result of these studies have revealed that zinc (II) complexes 6 and 13 of both the ligands and copper (II) complexes 9 of the HL(2) were observed to be the most active against all bacterial strains, antifungal activity was overall enhanced after complexation of the ligands.

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

    NASA Astrophysics Data System (ADS)

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

    2017-09-01

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

  10. Synthesis of extended uridine phosphonates derived from an allosteric P2Y2 receptor ligand.

    PubMed

    Song, Lijun; Risseeuw, Martijn D P; Karalic, Izet; Barrett, Matthew O; Brown, Kyle A; Harden, T Kendall; Van Calenbergh, Serge

    2014-04-04

    In this study we report the synthesis of C5/C6-fused uridine phosphonates that are structurally related to earlier reported allosteric P2Y2 receptor ligands. A silyl-Hilbert-Johnson reaction of six quinazoline-2,4-(1H,3H)-dione-like base moieties with a suitable ribofuranosephosphonate afforded the desired analogues after full deprotection. In contrast to the parent 5-(4-fluoropheny)uridine phosphonate, the present extended-base uridine phosphonates essentially failed to modulate the P2Y2 receptor.

  11. An agent based model of integrin clustering: Exploring the role of ligand clustering, integrin homo-oligomerization, integrin-ligand affinity, membrane crowdedness and ligand mobility

    NASA Astrophysics Data System (ADS)

    Jamali, Yousef; Jamali, Tahereh; Mofrad, Mohammad R. K.

    2013-07-01

    Integrins are cell-surface protein heterodimers that coordinate cellular responses to mechanochemical cues from the extracellular matrix (ECM) and stimulate the assembly of small adhesion complexes, which are the initial sites of cell-ECM adhesion. Clustering of integrins is known to mediate signaling through a variety of signal transduction pathways. Yet, the molecular mechanisms of integrin clustering are poorly understood. In this paper, we develop computational models, using agent based modeling (ABM) techniques, to explore two key underlying mechanisms of integrin clustering, namely ligand organization and integrin homo-oligomerization. Our models help to shed light on the potential roles ligand clustering and integrin homo-oligomerization may play in controlling integrin clustering. A potential mechanism for the clustering of integrin is discussed and the effects of other parameters such as integrin-ligand affinity, membrane crowdedness and ligand mobility on integrin clustering are examined.

  12. Computational insights into the photophysical and electroluminescence properties of homoleptic fac-Ir(C^N)3 complexes employing different phenyl-derivative-featuring phenylimidazole-based ligands for promising phosphors in OLEDs.

    PubMed

    Li, Jieqiong; Wang, Li; Sun, Kenan; Zhang, Jinglai

    2016-02-21

    The electronic structures and photophysical properties of three homoleptic iridium(iii) complexes IrL3 with C^N ligands, including 2a (L = 1-(2,6-diisopropylphenyl)-2-phenyl-1H-imidazole), 5a (L = 1-(2,6-dimethylphenyl)-2-phenyl-1H-imidazole), and 6a (L = 1-(3,5-diisopropylbiphenyl-4-yl)-2-phenyl-1H-imidazole), are investigated by means of the density functional method. Furthermore, seven new complexes are theoretically designed, including 1a (L = 1,2-diphenyl-1H-imidazole), 3a (L = 1-(2,6-dimethoxyphenyl)-2-phenyl-1H-imidazol), 4a (L = 2-(2-phenyl-1H-imidazol-1-yl)isophthalaldehyde), 1b (L = 2-(biphenyl-3-yl)-1H-imidazole), 2b (L = 2-(2',6'-diisopropylbiphenyl-3-yl)-1H-imidazole), 3b (L = 2-(2',6'-dimethoxybiphenyl-3-yl)-1H-imidazole), and 4b (L = 3'-(1H-imidazol-2-yl)biphenyl-2,6-dicarbaldehyde), to explore the influence of different substituents and different substituted positions on the electronic structures, phosphorescence properties, and organic light-emitting diode (OLED) performance. The HOMO-LUMO energy gap is greatly decreased by introduction of the -CHO group into the phenyl ring (4a and 4b see -sketched structures for all the investigated Ir(iii) complexes). As a result, their absorption and emission spectra present red-shifting leading them to be potential red-emitting phosphors. Other complexes are all blue-emitting materials, indicating that the effect of the substituted position on the emitting color is negligible. However, the addition of the substituent on the para-position of the phenyl ring in the phenylimidazole ligand would increase the quantum yield and electroluminescence (EL) performance compared with that on the imidazole ring.

  13. FLUORINATED CANNABINOID CB2 RECEPTOR LIGANDS: SYNTHESIS AND IN VITRO BINDING CHARACTERISTICS OF 2-OXOQUINOLINE DERIVATIVES

    PubMed Central

    Turkman, Nashaat; Shavrin, Aleksander; Ivanov, Roman A.; Rabinovich, Brian; Volgin, Andrei; Gelovani, Juri G.; Alauddin, Mian M.

    2011-01-01

    Cannabinoid receptor 2 (CB2) plays an important role in human physiology and the pathophysiology of different diseases, including neuroinflammation, neurodegeneration, and cancer. Several classes of CB2 receptor ligands, including 2-oxoquinoline derivatives, have been previously reported. We report the synthesis and results of in vitro receptor binding of a focused library of new fluorinated 2-oxoquinoline CB2 ligands. Twelve compounds, 13-16 18, 19, 21-24, 27, and 28 were synthesized in good yields in multiple steps. Human U87 glioma cells expressing either hCB1 (control) or hCB2 were generated via lentiviral transduction. In vitro competitive binding assay was performed using [3H]CP-55,940 in U87hCB1 and U87hCB2 cells. Inhibition constant (Ki) values of compounds 13, 14, 15, 16, 18, 19, 21, 22, 23, 24, 27, and 28 for CB2 were >10000, 2.8, 5.0, 2.4, 22, 0.8, 1.4, >10000, 486, 58, 620, and 2400 nM, respectively, and those for CB1 were >10000 nM. Preliminary in vitro results suggest that six of these compounds may be useful for therapy of neuropathic pain, neuroinflammatory diseases and immune disorders. In addition, compound 19, with its subnanomolar Ki value, could be radiolabeled with 18F and explored for PET imaging of CB2 expression. PMID:21872477

  14. A benzoboroxole-based affinity ligand for glycoprotein purification at physiological pH.

    PubMed

    Rowe, Laura; El Khoury, Graziella; Lowe, Christopher R

    2016-05-01

    Developing ligands capable of carbohydrate recognition has become increasingly important as the essential roles of glycoproteins and glycolipids in a diverse array of cellular signaling, pathophysiology, and immune response mechanisms are elucidated. Effective ligands for the glycan portion of glycoproteins and glycolipids are needed for pre-enrichment proteomics strategies, as well as for the purification of individual glycoproteins from complex biological milieu encountered both in biochemistry research and bio-pharmaceutical development. In this work, we developed a carbohydrate specific affinity ligand for glycoprotein purification using a one-pot, multi-component synthesis reaction (Ugi synthesis) and an amine-functionalized benzoboroxole moiety immobilized on agarose beads. Benzoboroxoles are unique boronic acid derivatives that have recently been found to bind specifically to the cis-diol groups of carbohydrates at physiological pH, with superior affinity to any other Wulff-type boronic acid. The solid-phase affinity ligand developed herein specifically binds the carbohydrate moiety of the glycoprotein glucose oxidase, as well as a fluorescein isothiocyanate-dextran, as shown through deglycosylation binding studies. Additionally, the ligand is able to purify glucose oxidase from crude Escherichia coli lysate, at physiological pH, equitably to commercially available boronic acid-functionalized agarose beads that required alkaline pH conditions. Thus, this affinity ligand is a marked improvement on current, commercially available boronic acid-based glycoprotein enrichment matrices and has the potential to exhibit high individual glycoprotein specificity because of the additional functional groups available for variation on the Ugi scaffold.

  15. LBVS: an online platform for ligand-based virtual screening using publicly accessible databases.

    PubMed

    Zheng, Minghao; Liu, Zhihong; Yan, Xin; Ding, Qianzhi; Gu, Qiong; Xu, Jun

    2014-11-01

    Abundant data on compound bioactivity and publicly accessible chemical databases increase opportunities for ligand-based drug discovery. In order to make full use of the data, an online platform for ligand-based virtual screening (LBVS) using publicly accessible databases has been developed. LBVS adopts Bayesian learning approach to create virtual screening models because of its noise tolerance, speed, and efficiency in extracting knowledge from data. LBVS currently includes data derived from BindingDB and ChEMBL. Three validation approaches have been employed to evaluate the virtual screening models created from LBVS. The tenfold cross validation results of twenty different LBVS models demonstrate that LBVS achieves an average AUC value of 0.86. Our internal and external testing results indicate that LBVS is predictive for lead identifications. LBVS can be publicly accessed at http://rcdd.sysu.edu.cn/lbvs.

  16. 4-Phenyl quinoline derivatives as potential serotonin receptor ligands with antiproliferative activity.

    PubMed

    Joshi, Pranaya V; Sayed, Alim A; RaviKumar, Ameeta; Puranik, Vedavati G; Zinjarde, Smita S

    2017-08-18

    Antagonists of signaling receptors are often effective non-toxic therapeutic agents. Over the years, there have been evidences describing the role of serotonin or 5-hydroxytryptamine (5-HT) in development of cancer. Although there are reports on the antiproliferative effects of some serotonin receptor antagonists, there are very few investigations related to understanding their structure-activity relationships. In this study, we report the screening of a library of 4-phenyl quinoline derivatives for their antiproliferative activities. Preliminary docking studies indicated that these ligands had the ability to bind to two of the serotonin receptors, 5-HT1B and 5-HT2B. The results of the in silico experiments were validated by performing in vitro studies on MCF-7 breast cancer cell line. The ethylpiperazine derivatives showed maximum toxicity against this cancer cell line. The compounds inhibited Calcium ion efflux (induced by serotonin) and ERK activation. One of the most active 4-phenyl quinoline derivatives (H3a) also induced apoptosis, thereby, suggesting the use of this scaffold as a potential anticancer drug. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  17. Multiple myeloma-derived Jagged ligands increases autocrine and paracrine interleukin-6 expression in bone marrow niche

    PubMed Central

    Bulfamante, Gaetano; Falleni, Monica; Tosi, Delfina; Todoerti, Katia; Lazzari, Elisa; Crews, Leslie A.; Jamieson, Catriona H.M.; Ravaioli, Sara; Baccianti, Francesco; Garavelli, Silvia; Platonova, Natalia; Neri, Antonino; Chiaramonte, Raffaella

    2016-01-01

    Multiple myeloma cell growth relies on intrinsic aggressiveness, due to a high karyotypic instability, or on the support from bone marrow (BM) niche. We and other groups have provided evidences that Notch signaling is related to tumor cell growth, pharmacological resistance, localization/recirculation in the BM and bone disease. This study indicates that high gene expression levels of Notch signaling members (JAG1, NOTCH2, HES5 and HES6) correlate with malignant progression or high-risk disease, and Notch signaling may participate in myeloma progression by increasing the BM levels of interleukin-6 (IL-6), a major player in myeloma cell growth and survival. Indeed, in vitro results, confirmed by correlation analysis on gene expression profiles of myeloma patients and immunohistochemical studies, demonstrated that Notch signaling controls IL-6 gene expression in those myeloma cells capable of IL-6 autonomous production as well as in surrounding BM stromal cells. In both cases Notch signaling activation may be triggered by myeloma cell-derived Jagged ligands. The evidence that Notch signaling positively controls IL-6 in the myeloma-associated BM makes this pathway a key mediator of tumor-directed reprogramming of the bone niche. This work strengthens the rationale for a novel Notch-directed therapy in multiple myeloma based on the inhibition of Jagged ligands. PMID:27463014

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

    SciTech Connect

    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.

  19. Redox, thermodynamic and spectroscopic of some transition metal complexes containing heterocyclic Schiff base ligands

    NASA Astrophysics Data System (ADS)

    Abu-Hussen, Azza A. A.; Linert, Wolfgang

    2009-09-01

    Complexes of two series of Schiff base ligands, H 2L a and H 2L b derived from the reaction of 2,6-diacetyl pyridine with semicarbazide, H 2L a and thiosemicarbazide, H 2L b, with the metal ions, Co(II), Ni(II), Cu(II), VO(IV) and UO 2(VI) have been prepared. The ligands are characterized by elemental analysis, IR, UV-vis and 1H NMR. The structures of the complexes are investigated with the IR, UV-vis, X-band ESR spectra, 1H NMR and thermal gravimetric analysis as well as conductivity and magnetic moment measurements. The IR-spectra reveal the presence of variable modes of chelation for the investigated ligands. A variety of binuclear or mononuclear complexes were obtained with the two ligands in tri-, tetra or pentadentate forms. The bonding sites are the pyridine nitrogen, two azomethine nitrogen atoms and ketonic oxygen in case of H 2L a or sulphur atoms in case of H 2L b. The Coats-Redfern equation has been used to calculate the kinetic and thermodynamic parameters for the different thermal decomposition steps of some complexes. Cyclic voltammograms of Co(II) and Ni(II) show quasi-reversible peaks. The redox properties and the nature of the electro-active species of the complexes have been characterized.

  20. Redox, thermodynamic and spectroscopic of some transition metal complexes containing heterocyclic Schiff base ligands.

    PubMed

    Abu-Hussen, Azza A A; Linert, Wolfgang

    2009-09-15

    Complexes of two series of Schiff base ligands, H(2)L(a) and H(2)L(b) derived from the reaction of 2,6-diacetyl pyridine with semicarbazide, H(2)L(a) and thiosemicarbazide, H(2)L(b), with the metal ions, Co(II), Ni(II), Cu(II), VO(IV) and UO(2)(VI) have been prepared. The ligands are characterized by elemental analysis, IR, UV-vis and (1)H NMR. The structures of the complexes are investigated with the IR, UV-vis, X-band ESR spectra, (1)H NMR and thermal gravimetric analysis as well as conductivity and magnetic moment measurements. The IR-spectra reveal the presence of variable modes of chelation for the investigated ligands. A variety of binuclear or mononuclear complexes were obtained with the two ligands in tri-, tetra or pentadentate forms. The bonding sites are the pyridine nitrogen, two azomethine nitrogen atoms and ketonic oxygen in case of H(2)L(a) or sulphur atoms in case of H(2)L(b). The Coats-Redfern equation has been used to calculate the kinetic and thermodynamic parameters for the different thermal decomposition steps of some complexes. Cyclic voltammograms of Co(II) and Ni(II) show quasi-reversible peaks. The redox properties and the nature of the electro-active species of the complexes have been characterized.

  1. Modeling approaches for ligand-based 3D similarity.

    PubMed

    Tresadern, Gary; Bemporad, Daniele

    2010-10-01

    3D ligand-based similarity approaches are widely used in the early phases of drug discovery for tasks such as hit finding by virtual screening or compound design with quantitative structure-activity relationships. Here in we review widely used software for performing such tasks. Some techniques are based on relatively mature technology, shape-based similarity for instance. Typically, these methods remained in the realm of the expert user, the experienced modeler. However, advances in implementation and speed have improved usability and allow these methods to be applied to databases comprising millions of compounds. There are now many reports of such methods impacting drug-discovery projects. As such, the medicinal chemistry community has become the intended market for some of these new tools, yet they may consider the wide array and choice of approaches somewhat disconcerting. Each method has subtle differences and is better suited to certain tasks than others. In this article we review some of the widely used computational methods via application, provide straightforward background on the underlying theory and provide examples for the interested reader to pursue in more detail. In the new era of preclinical drug discovery there will be ever more pressure to move faster and more efficiently, and computational approaches based on 3D ligand similarity will play an increasing role in in this process.

  2. MOST: most-similar ligand based approach to target prediction.

    PubMed

    Huang, Tao; Mi, Hong; Lin, Cheng-Yuan; Zhao, Ling; Zhong, Linda L D; Liu, Feng-Bin; Zhang, Ge; Lu, Ai-Ping; Bian, Zhao-Xiang

    2017-03-11

    Many computational approaches have been used for target prediction, including machine learning, reverse docking, bioactivity spectra analysis, and chemical similarity searching. Recent studies have suggested that chemical similarity searching may be driven by the most-similar ligand. However, the extent of bioactivity of most-similar ligands has been oversimplified or even neglected in these studies, and this has impaired the prediction power. Here we propose the MOst-Similar ligand-based Target inference approach, namely MOST, which uses fingerprint similarity and explicit bioactivity of the most-similar ligands to predict targets of the query compound. Performance of MOST was evaluated by using combinations of different fingerprint schemes, machine learning methods, and bioactivity representations. In sevenfold cross-validation with a benchmark Ki dataset from CHEMBL release 19 containing 61,937 bioactivity data of 173 human targets, MOST achieved high average prediction accuracy (0.95 for pKi ≥ 5, and 0.87 for pKi ≥ 6). Morgan fingerprint was shown to be slightly better than FP2. Logistic Regression and Random Forest methods performed better than Naïve Bayes. In a temporal validation, the Ki dataset from CHEMBL19 were used to train models and predict the bioactivity of newly deposited ligands in CHEMBL20. MOST also performed well with high accuracy (0.90 for pKi ≥ 5, and 0.76 for pKi ≥ 6), when Logistic Regression and Morgan fingerprint were employed. Furthermore, the p values associated with explicit bioactivity were found be a robust index for removing false positive predictions. Implicit bioactivity did not offer this capability. Finally, p values generated with Logistic Regression, Morgan fingerprint and explicit activity were integrated with a false discovery rate (FDR) control procedure to reduce false positives in multiple-target prediction scenario, and the success of this strategy it was demonstrated with a case of fluanisone

  3. Synthesis and Characterization of a Triphos Ligand Derivative and the Corresponding Pd II Complexes: Triphos Ligand Derivative and Corresponding Pd II Complexes

    SciTech Connect

    Miller, Deanna L.; Boro, Brian J.; Grubel, Katarzyna; Helm, Monte L.; Appel, Aaron M.

    2015-11-16

    The synthesis of the new bis(2-(diphenylphosphino)ethyl)methylhydroxyphosphine tridentate phosphine ligand, LCH2OH/Ph, is reported. The ligand reacts with [Pd(Cl)2(PhCN)2 to form [Pd(LCH2OH/Ph)Cl]Cl. Exchange of the chloride ions for triflate (OTf–) using AgOTf yielded pure [Pd(LCH2OH/Ph)OTf]OTf. In addition to spectral characterization the free ligand, LCH2OH/Ph, and Pd(II) complex, [Pd(LCH2OH/Ph)OTf]OTf, are structurally characterized. This research was supported by the US Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Biosciences, and Geosciences. Pacific Northwest National Laboratory is a multiprogram national laboratory operated by Battelle for DOE.

  4. A new Ni12 cluster based on polyoxometalate ligands.

    PubMed

    Zhang, Hong-Mei; Li, Yang-Guang; Lu, Ying; Clérac, Rodolphe; Zhang, Zhi-Ming; Wu, Qiong; Feng, Xiao-Jia; Wang, En-Bo

    2009-12-07

    A new Ni(12) cluster based on polyoxometalate ligands [Ni(12)(OH)(9)WO(4)(W(7)O(26)(OH))(PW(9)O(34))(3)](25-) (1) has been assembled in aqueous solution containing [PW(9)O(34)](9-), WO(4)(2-), and NiCl(2) x 6 H(2)O. The Ni(12) core in 1 shows a unique three-petal flower-shaped structure composed of three Ni(4) cubane units. Magnetic investigation indicates the presence of dominantly ferromagnetic interactions within the Ni(12) core.

  5. Development of Ar-BINMOL-Derived Atropisomeric Ligands with Matched Axial and sp(3) Central Chirality for Catalytic Asymmetric Transformations.

    PubMed

    Xu, Zheng; Xu, Li-Wen

    2015-10-01

    Recently, academic chemists have renewed their interest in the development of 1,1'-binaphthalene-2,2'-diol (BINOL)-derived chiral ligands. Six years ago, a working hypothesis, that the chirality matching of hybrid chirality on a ligand could probably lead to high levels of stereoselective induction, prompted us to use the axial chirality of BINOL derivatives to generate new stereogenic centers within the same molecule with high stereoselectivity, obtaining as a result sterically favorable ligands for applications in asymmetric catalysis. This Personal Account describes our laboratory's efforts toward the development of a novel class of BINOL-derived atropisomers bearing both axial and sp(3) central chirality, the so-called Ar-BINMOLs, for asymmetric synthesis. Furthermore, on the basis of the successful application of Ar-BINMOLs and their derivatives in asymmetric catalysis, the search for highly efficient and enantioselective processes also compelled us to give special attention to the BINOL-derived multifunctional ligands with multiple stereogenic centers for use in catalytic asymmetric reactions.

  6. Metal-Ligand Interactions and Salt Bridges as Sacrificial Bonds in Mussel Byssus-Derived Materials.

    PubMed

    Byette, Frédéric; Laventure, Audrey; Marcotte, Isabelle; Pellerin, Christian

    2016-10-10

    The byssus that anchors mussels to solid surfaces is a protein-based material combining strength and toughness as well as a self-healing ability. These exceptional mechanical properties are explained in part by the presence of metal ions forming sacrificial bonds with amino acids. In this study, we show that the properties of hydrogel films prepared from a byssus protein hydrolyzate (BPH) can also be improved following the biomimetic formation of sacrificial bonds. Strengthening and toughening of the materials are both observed when treating films with multivalent ions (Ca(2+) or Fe(3+)) or at the BPH isoelectric point (pI) as a result of the formation of metal-ligand bonds and salt bridges, respectively. These treatments also provide a self-healing behavior to the films during recovery time following a deformation. While pI and Ca(2+) treatments have a similar but limited pH-dependent effect, the modulus, strength, and toughness of the films increase largely with Fe(3+) concentration and reach much higher values. The affinity of Fe(3+) with multiple amino acid ligands, as shown by vibrational spectroscopy, and the more covalent nature of this interaction can explain these observations. Thus, a judicious choice of treatments on polyampholyte protein-based materials enables control of their mechanical performance and self-healing behavior through the strategic exploitation of reversible sacrificial bonds.

  7. Ligand Biological Activity Predictions Using Fingerprint-Based Artificial Neural Networks (FANN-QSAR)

    PubMed Central

    Myint, Kyaw Z.; Xie, Xiang-Qun

    2015-01-01

    This chapter focuses on the fingerprint-based artificial neural networks QSAR (FANN-QSAR) approach to predict biological activities of structurally diverse compounds. Three types of fingerprints, namely ECFP6, FP2, and MACCS, were used as inputs to train the FANN-QSAR models. The results were benchmarked against known 2D and 3D QSAR methods, and the derived models were used to predict cannabinoid (CB) ligand binding activities as a case study. In addition, the FANN-QSAR model was used as a virtual screening tool to search a large NCI compound database for lead cannabinoid compounds. We discovered several compounds with good CB2 binding affinities ranging from 6.70 nM to 3.75 μM. The studies proved that the FANN-QSAR method is a useful approach to predict bioactivities or properties of ligands and to find novel lead compounds for drug discovery research. PMID:25502380

  8. New ligands of the tubulin colchicine site based on X-ray structures.

    PubMed

    Álvarez, Raquel; Medarde, Manuel; Peláez, Rafael

    2014-01-01

    Colchicine site ligands have proved to be potent inhibitors of tubulin polymerization, which leads them not only to display cytotoxic effects but also vascular disrupting effects on tumour neovasculature. In recent years, many compounds have been designed, synthesized and evaluated in order to improve the potency, stability and physicochemical properties of these agents with the aim of developing an agent that could reach the clinical assay level. Here we analyze the eleven X-ray structures of tubulin in complex with ligands at the colchicine site by dividing it into four different zones of interaction, we review the new compounds that have appeared in the literature since 2008 and that were designed based on any of these X-ray structures and, finally, we describe our latest results in the design of new potent antimitotic indole derivatives that have confirmed the flexibility of one of the zones described for the colchicine site.

  9. Emissive bis-salicylaldiminato Schiff base ligands and their zinc(II) complexes: Synthesis, photophysical properties, mesomorphism and DFT studies

    NASA Astrophysics Data System (ADS)

    Paul, Manoj Kr.; Dilipkumar Singh, Y.; Bedamani Singh, N.; Sarkar, Utpal

    2015-02-01

    Bis-salicylaldiminato Schiff base ligands and their Zn(II) complexes derived from 2,3-Diaminomaleonitrile (DAMN) were synthesized. Their molecular structures, photophysical properties and mesogenic behaviors were investigated. The ligands and their Zn(II) complexes were characterized by using elemental analysis, FT-IR, 1H NMR and molar conductivity measurements. Photophysical properties of ligands and their Zn(II) complexes were investigated in different polar solvents by using UV-visible and fluorescence spectroscopic studies. Ligands emit green light whereas complexes emit orange light upon irradiation with UV-visible light. The liquid crystalline phases of ligands and their Zn(II) complexes were characterized by polarizing optical microscopy and differential scanning calorimetry. The ligand having longer 4-n-octadecyloxy chain (n = 18) displays columnar phase whereas the lower homologues (n = 16, 12) did not show mesophase. The Zn(II) complexes having 4-n-octadecyloxy end chain display smectic B like phase whereas other lower homologues are non mesogenic in nature. The thermal stability of the compounds were studied by using thermo gravimetric analysis. The density functional theory was carried out to obtain the stable molecular conformation, dipole moment, molecular orbitals and polarizability of the ligands and their Zn(II) complexes.

  10. A new class of transition metal pincer ligand: tantalum complexes that feature a [CCC] X3-donor array derived from a terphenyl ligand.

    PubMed

    Sattler, Aaron; Parkin, Gerard

    2012-02-01

    A new class of [CCC] X(3)-donor pincer ligand for transition metals has been constructed via cyclometalation of a 2,6-di-p-tolylphenyl ([Ar(Tol(2))]) derivative. Specifically, addition of PMe(3) to [Ar(Tol(2))]TaMe(3)Cl induces elimination of methane and formation of the pincer complex, [κ(3)-Ar(Tol'(2))]Ta(PMe(3))(2)MeCl (Tol' = C(6)H(3)Me), which may also be obtained by treatment of Ta(PMe(3))(2)Me(3)Cl(2) with [Ar(Tol(2))]Li. Solutions of [κ(3)-Ar(Tol'(2))]Ta(PMe(3))(2)MeCl undergo ligand redistribution with the formation of [κ(3)-Ar(Tol'(2))]Ta(PMe(3))(2)Me(2)and [κ(3)-Ar(Tol'(2))]Ta(PMe(3))(2)Cl(2), which may also be synthesized by the reactions of [κ(3)-Ar(Tol'(2))]Ta(PMe(3))(2)MeCl with MeMgBr and ZnCl(2), respectively. Reduction of [κ(3)-Ar(Tol'(2))]Ta(PMe(3))(2)Cl(2) with KC(8) in benzene gives the benzene complex [κ(3)-Ar(Tol'(2))]Ta(PMe(3))(2)(η(6)-C(6)H(6)) that is better described as a 1,4-cyclohexadienediyl derivative. Deuterium labeling employing Ta(PMe(3))(2)(CD(3))(3)Cl(2) demonstrates that the pincer ligand is created by a pair of Ar-H/Ta-Me sigma-bond metathesis transformations, rather than by a mechanism that involves α-H abstraction by a tantalum methyl ligand. © 2012 American Chemical Society

  11. Identification of Ligand Templates using Local Structure Alignment for Structure-based Drug Design

    PubMed Central

    Lee, Hui Sun; Im, Wonpil

    2012-01-01

    With a rapid increase in the number of high-resolution protein-ligand structures, the known protein-ligand structures can be used to gain insight into ligand-binding modes in a target protein. Based on the fact that the structurally similar binding sites share information about their ligands, we have developed a local structure alignment tool, G-LoSA (Graph-based Local Structure Alignment). In G-LoSA, the known protein-ligand binding-site structure library is searched to detect binding-site structures with similar geometry and physicochemical properties to a query binding-site structure regardless of sequence continuity and protein fold. Then, the ligands in the identified complexes are used as templates (i.e., template ligands) to predict/design a ligand for the target protein. The performance of G-LoSA is validated against 76 benchmark targets from the Astex diverse set. Using the currently available protein-ligand structure library, G-LoSA is able to identify a single template ligand (from a non-homologous protein complex) that is highly similar to the target ligand in more than half of the benchmark targets. In addition, our benchmark analyses show that an assembly of structural fragments from multiple template ligands with partial similarity to the target ligand can be used to design novel ligand structures specific to the target protein. This study clearly indicates that a template-based ligand modeling has potential for de novo ligand design and can be a complementary approach to the receptor structure based methods. PMID:22978550

  12. Selective extraction of histidine derivatives by metal affinity with a copper(II)-chelating ligand complex in an aqueous two-phase system.

    PubMed

    Oshima, Tatsuya; Oshima, Chinatsu; Baba, Yoshinari

    2015-05-15

    Affinity extraction based on the interaction between a target molecule and a specific affinity ligand offers a novel separation system for biomolecules in an aqueous two-phase system, however, most of affinity ligands are expensive. In the present study, metal affinity extraction of histidine (His) derivatives using a complex between Cu(II) and a commercially available chelating ligand was studied in a poly(ethylene glycol) (PEG)/Li2SO4 ATPS. Alizarin complexone (3-[N,N-bis(carboxymethyl)amino methyl]-1,2-dihydroxy anthraquinone, AC) was selected as the chelating ligand because of the good extractability of Cu(II) into the upper PEG-rich phase. On the basis of coordinate bonding with Cu(II), the extraction of His in the presence of the Cu(II)-AC complex under neutral condition was 73%, which was much higher than that under Cu(II) free condition (13%). Among a series of divalent transition metal ions (Cu(II), Ni(II), Co(II), and Zn(II)), Cu(II) was the most effective for the extraction of His. Derivatives of His were selectively extracted in the presence of many other amino acids because of the specificity of the interaction between Cu(II) and imidazole group of His. Extracted His was quantitatively stripped from the Cu(II)-AC complex using competitive complexation with agents such as iminodiacetic acid and imidazole. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. Six [Tp*WS3Cu2]-based clusters derived from [Et4N][Tp*WS3], Cu(I) salts and phosphine ligands: syntheses, structures and enhanced third-order NLO properties.

    PubMed

    Zhou, Li-Kuan; Liu, Quan; Zhao, Xin; Hu, Fei-Long; Liu, Shu-Chen; Ren, Zhi-Gang; Sun, Zhen-Rong; Lang, Jian-Ping

    2014-03-28

    Treatment of [Et4N][Tp*WS3] (Tp* = hydridotris(3,5-dimethylpyrazol-1-yl)borate) (1) with CuX (X = Br, SCN) and PPh3 or 1,1-bis(diphenylphosphino)methane (dppm) produced two neutral trinuclear clusters [Tp*W(μ3-S)(μ-S)2Cu2Br(PPh3)] (2) and [Tp*W(μ3-S)(μ-S)2Cu2(SCN)(dppm)]2·MeCN·Et2O (3·MeCN·Et2O). Reactions of 1 with [Cu(MeCN)4]PF6, NH4PF6 and 1,3-bis(diphenylphosphino)propane (dppp), N,N-bi(diphenylphosphanylmethyl)-2-aminopyridine (bdppmapy), N,N,N',N'-tetra(diphenylphosphanylmethyl)ethylenediamine (dppeda), or 1,4-N,N,N',N'-tetra(diphenylphosphanylmethyl)benzenediamine (dpppda) afforded four clusters containing butterfly-shaped [Tp*WS3Cu2] cores, [Tp*W(μ3-S)(μ-S)2Cu2(dpppds)](PF6)·1.25MeCN (dpppds = 1,3-bis(diphenylphosphino)propane disulfide) (4·1.25MeCN), [Tp*W(μ3-S)(μ-S)2Cu2(bdppmapy)](PF6)·3MeCN (5·3MeCN) and {[Tp*W(μ3-S)(μ-S)2Cu2]2(L)]}(PF6)2·Sol (6·Et2O: L = dppeda, Sol = Et2O; 7·1.25MeCN: L = dpppda, Sol = 1.25MeCN). Compounds 2-7 were characterized by elemental analysis, IR, UV-Vis, (1)H and (31)P{(1)H} NMR spectra, electrospray ion mass spectra (ESI-MS) and single-crystal X-ray diffraction. Compound 2 or 3 has a butterfly-shaped [Tp*WS3Cu2] core in which one [Tp*WS3] unit binds two Cu(I) centers via one μ3-S and two μ-S atoms. In the cationic structure of 4 or 5, one in situ-formed dpppds or bdppmapy combines with the [Tp*WS3Cu2] core via each of its two S atoms or two P atoms coordinated at each Cu(I) center. In the bicationic structure of 6 or 7, two [Tp*WS3Cu2] cores are linked by one dppeda or dpppda bridge to form a bicyclic structure. The isolation of 2-7 with unstable [Tp*WS3Cu2] cores may be ascribed to the coordination of P- or S-donor ligands at Cu(i) centers of these cores. The third-order nonlinear optical (NLO) properties of 2-7 in DMF were also investigated by using the femtosecond degenerate four-wave mixing (DFWM) technique at 800 nm.

  14. Identification of ligand templates using local structure alignment for structure-based drug design.

    PubMed

    Lee, Hui Sun; Im, Wonpil

    2012-10-22

    With a rapid increase in the number of high-resolution protein-ligand structures, the known protein-ligand structures can be used to gain insight into ligand-binding modes in a target protein. On the basis of the fact that the structurally similar binding sites share information about their ligands, we have developed a local structure alignment tool, G-LoSA (graph-based local structure alignment). The known protein-ligand binding-site structure library is searched by G-LoSA to detect binding-site structures with similar geometry and physicochemical properties to a query binding-site structure regardless of sequence continuity and protein fold. Then, the ligands in the identified complexes are used as templates (i.e., template ligands) to predict/design a ligand for the target protein. The performance of G-LoSA is validated against 76 benchmark targets from the Astex diverse set. Using the currently available protein-ligand structure library, G-LoSA is able to identify a single template ligand (from a nonhomologous protein complex) that is highly similar to the target ligand in more than half of the benchmark targets. In addition, our benchmark analyses show that an assembly of structural fragments from multiple template ligands with partial similarity to the target ligand can be used to design novel ligand structures specific to the target protein. This study clearly indicates that a template-based ligand modeling has potential for de novo ligand design and can be a complementary approach to the receptor structure based methods.

  15. Stamping vital cells - a force-based ligand receptor assay.

    PubMed

    Wienken, Uta; Gaub, Hermann E

    2013-12-17

    Gaining information about receptor profiles on cells, and subsequently finding the most efficient ligands for these signaling receptors, remain challenging tasks in stem cell and cancer research as well as drug development. We introduce a live-cell method with great potential in both screening for surface receptors and analysing binding forces of different ligands. The technique is based on the molecular force assay, a parallel-format, high-throughput experiment on a single-molecule level. On human red blood cells, we demonstrate the detection of the interaction of N-acetyl-α-D-galactosaminyl residues with the lectin helix pomatia agglutinine and of the CD47 receptor with its antibody. The measurements are performed under nearly physiological conditions and still provide a highly specific binding signal. Moreover, with a detailed comparative force analysis on two cell types with different morphology, we show that our method even allows the determination of a DNA force equivalent for the interaction of the CD47 receptor and its antibody. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  16. A 1,8-naphthalenediol-based unsymmetrical dinucleating ligand.

    PubMed

    Glaser, Thorsten; Liratzis, Ioannis; Fröhlich, Roland

    2005-09-07

    A facile synthesis of 2-formyl-1,8-naphthalenediol is reported. Its potential as a general precursor for the preparation of unsymmetrical multidentate chelating ligand systems based on 1,8-naphthalenediol is demonstrated by the synthesis of the dinucleating ligand L(4-)(H(4)L=N,N'-bis(2-(1,8-naphthalenediol)methylidene)propylenediamine). Reaction of H(4) L with copper acetate results in the formation of the unsymmetrical dinuclear Cu(II) complex [LCu(2)](3), which has been structurally characterized by single-crystal X-ray diffraction. One Cu(II) ion is coordinated by a N(2)O(2) compartment of L(4-) and the other Cu(II) ion is coordinated by an O(4) compartment of L(4-) while they are bridged by two aryloxide functions of L(4-). A dimerization of two molecules of 3 to a tetranuclear entity 3(2) occurs through formation of weak apical Cu--O interactions. Analysis of the temperature dependent magnetic susceptibility measurements (2--290 K) established a strong intradimer exchange coupling J(12)=-371 cm(-1). This strong superexchange interaction fits nicely in a magneto-structural correlation which has been established for dinuclear bis(phenoxide)-bridged Cu(II) complexes demonstrating the electronic equivalence of the aryloxides of a phenol and 1,8-naphthalenediol.

  17. NMR-Based screening with competition water-ligand observed via gradient spectroscopy experiments: detection of high-affinity ligands.

    PubMed

    Dalvit, Claudio; Fasolini, Marina; Flocco, Maria; Knapp, Stefan; Pevarello, Paolo; Veronesi, Marina

    2002-06-06

    Water-ligand observed via gradient spectroscopy (WaterLOGSY) represents a powerful method for primary NMR screening in the identification of compounds interacting with macromolecules, including proteins and DNA or RNA fragments. The method is useful for the detection of compounds binding to a receptor with binding affinity in the micromolar range. The Achille's heel of the method, as with all the techniques that detect the ligand resonances, is its inability to identify strong ligands with slow dissociation rates. We show here that the use of a reference compound with a known K(D) in the micromolar range together with properly designed competition binding experiments (c-WaterLOGSY) permits the detection of strong binders. A derived mathematical expression is used for the selection of the appropriate setup NMR experimental conditions and for an approximate determination of the binding constant. The experiment requires low ligand concentration, therefore allowing its application in the identification of potential strong inhibitors that are only marginally soluble. The technique is particularly suitable for rapid screening of chemical mixtures and plant or fungi extracts.

  18. Half-sandwich complexes of rhodium containing cysteine-derived ligands.

    PubMed

    Carmona, María; Rodríguez, Ricardo; Lahoz, Fernando J; García-Orduña, Pilar; Osante, Iñaki; Cativiela, Carlos; López, José A; Carmona, Daniel

    2016-09-28

    The modified cysteine ligand, S-benzyl-α-methyl-l-cysteine (HL2), was prepared from l-cysteine hydrochloride methyl ester. The reaction of commercial S-benzyl-l-cysteine (HL1) or HL2 with the dimer, [{(η(5)-C5Me5)RhCl}2(μ-Cl)2], gives rise to the cationic complexes, [(η(5)-C5Me5)RhCl(HL)]Cl (HL = HL1 (1), HL2 (2)), in which the cysteine ligand exhibits a κ(2)N,S coordination mode. In a basic medium, HL1 or HL2 reacts with [{(η(5)-C5Me5)RhCl}2(μ-Cl)2] to afford mixtures of two epimers at the metal centre of the neutral complexes, [(η(5)-C5Me5)RhCl(κ(2)N,O-L)] (HL = HL1 (3), HL2 (4)), in which amino carboxylate adopts a κ(2)N,O mode of coordination along with variable amounts of the cationic compounds, [(η(5)-C5Me5)Rh(κ(3)N,O,S-L)]Cl (HL = HL1 (6Cl), HL2 (7Cl)), which contain κ(3)N,O,S coordinated cysteine-derived ligands. However, in a basic medium, the N-Boc substituted cysteine S-benzyl-N-Boc-l-cysteine (HL3) only yields the κ(2)O,S coordinated derivative, [(η(5)-C5Me5)RhCl(κ(2)O,S-L3)] (5), as a mixture of two diastereomers depending on the configuration of the metal centre. The bidentate chelate complexes 3-5 react with AgSbF6 to give the hexafluoroantimonates [(η(5)-C5Me5)Rh(κ(3)N,O,S-L)][SbF6] (HL = HL1 (6Sb), HL2 (7Sb), HL3 (8Sb)) with tridentate coordination. Compound 8Sb reacts with NaHCO3 to give the neutral complex [(η(5)-C5Me5)Rh(κ(3)N,O,S-L3-H)] (9), which can also be prepared by reacting the dimer [{(η(5)-C5Me5)RhCl}2(μ-Cl)2] with HL3 in the presence of two equivalents of NaHCO3. The new compounds contain up to four stereogenic centres, namely, Rh, S, N, and C. The absolute configuration of the complexes has been established by spectroscopic and diffractometric investigations, including the crystal structure determination of [(η(5)-C5Me5)RhCl(κ(2)O,S-L3)] (5), [(η(5)-C5Me5)Rh(κ(3)N,O,S-L1)][SbF6] (6Sb), [(η(5)-C5Me5)Rh(κ(3)N,O,S-L2)][SbF6] (7Sb) and [(η(5)-C5Me5)Rh(κ(3)N,O,S-L3-H)] (9). Variable temperature (1)H NMR

  19. Training based on ligand efficiency improves prediction of bioactivities of ligands and drug target proteins in a machine learning approach.

    PubMed

    Sugaya, Nobuyoshi

    2013-10-28

    Machine learning methods based on ligand-protein interaction data in bioactivity databases are one of the current strategies for efficiently finding novel lead compounds as the first step in the drug discovery process. Although previous machine learning studies have succeeded in predicting novel ligand-protein interactions with high performance, all of the previous studies to date have been heavily dependent on the simple use of raw bioactivity data of ligand potencies measured by IC50, EC50, K(i), and K(d) deposited in databases. ChEMBL provides us with a unique opportunity to investigate whether a machine-learning-based classifier created by reflecting ligand efficiency other than the IC50, EC50, K(i), and Kd values can also offer high predictive performance. Here we report that classifiers created from training data based on ligand efficiency show higher performance than those from data based on IC50 or K(i) values. Utilizing GPCRSARfari and KinaseSARfari databases in ChEMBL, we created IC50- or K(i)-based training data and binding efficiency index (BEI) based training data then constructed classifiers using support vector machines (SVMs). The SVM classifiers from the BEI-based training data showed slightly higher area under curve (AUC), accuracy, sensitivity, and specificity in the cross-validation tests. Application of the classifiers to the validation data demonstrated that the AUCs and specificities of the BEI-based classifiers dramatically increased in comparison with the IC50- or K(i)-based classifiers. The improvement of the predictive power by the BEI-based classifiers can be attributed to (i) the more separated distributions of positives and negatives, (ii) the higher diversity of negatives in the BEI-based training data in a feature space of SVMs, and (iii) a more balanced number of positives and negatives in the BEI-based training data. These results strongly suggest that training data based on ligand efficiency as well as data based on classical IC50

  20. A new strategy towards tridentate N-heterocyclic carbene ligands derived from benzimidazolium and mixed-azolium salt

    NASA Astrophysics Data System (ADS)

    Fatima, Tabinda; Haque, Rosenani A.; Razali, Mohd. R.

    2017-08-01

    The tridentate N-heterocyclic carbenes (NHC) ligands derived from tris azolium salts by a new synthetic approach are described. The tris azolium salts have been obtained by reacting the initially synthesized precursor 3-(2-bromoethyl)-1-methylbenzimidazolium bromide (I) with benzimidazole/imidazole resulting in the tris azolium salts namely, 1 and 2. The ligand potential of the salts 1 and 2 was investigated by the formation of NHC-Ag(I) complexes 3 and 4, using Ag2O. The most downfield resonances in 13C NMR around 180-190 ppm indicates the successful coordination of carbene with Ag(I).

  1. Purified human platelet-derived growth factor receptor has ligand-stimulated tyrosine kinase activity.

    PubMed Central

    Bishayee, S; Ross, A H; Womer, R; Scher, C D

    1986-01-01

    The platelet-derived growth factor receptor (PDGF-R), a 180-kDa single-chain polypeptide, was purified from membranes of the human osteogenic sarcoma cell line MG-63. Purification was achieved by treatment of membranes with PDGF and ATP, followed by solubilization with nonionic detergent and successive chromatography on solid-phase anti-phosphotyrosine monoclonal antibody and DEAE-cellulose. The PDGF-R, which was estimated to be 50-80% pure by NaDodSO4/polyacrylamide gel electrophoresis of 32P-labeled preparations, was free of contaminating epidermal growth factor receptor and had no detectable phosphatase activity. It specifically bound 125I-labeled PDGF, a reaction quantified by binding of the ligand-PDGF-R complex to the anti-phosphotyrosine antibody. The purified receptor displayed PDGF-stimulatable tyrosine kinase activity, assayed by autophosphorylation of PDGF-R at tyrosine residues and by phosphorylation of angiotensin II. The Km for ATP in the autophosphorylation reaction was 7.5 microM. Addition of PDGF did not change the Km but increased the Vmax 1.7-fold. Images PMID:3018745

  2. Cyclic ferrocenylnaphthalene diimide derivative as a new class of G-quadruplex DNA binding ligand.

    PubMed

    Islam, Md Monirul; Sato, Shinobu; Shinozaki, Shingo; Takenaka, Shigeori

    2017-01-15

    To identify an effective ligand that binds to a G-quadruplex structure but not a double-stranded DNA (dsDNA), a set of biophysical and biochemical experiments were carried out using newly synthesized cyclic ferrocenylnaphthalene diimide (cFNDI, 1) or the non-cyclic derivative (2) with various structures of G-quadruplex DNAs and dsDNA. Compound 1 bound strongly to G-quadruplexes DNAs (10(6)M(-1) order) with diminished binding to dsDNA (10(4)M(-1) order) in 100mM AcOH-AcOK buffer (pH 5.5) containing 100mM KCl. Interestingly, 1 showed an approximately 50-fold higher selectivity to mixed hybrid-type telomeric G-quadruplex DNA (K=3.4×10(6)M(-1) and a 2:1 stoichiometry) than dsDNA (K=7.5×10(4)M(-1)) did. Furthermore, 1 showed higher thermal stability to G-quadruplex DNAs than it did to dsDNA with a preference for c-kit and c-myc G-quadruplex DNAs over telomeric and thrombin binding aptamers. Additionally, 1 exhibited telomerase inhibitory activity with a half-maximal inhibitory concentration (IC50) of 0.4μM. Compound 2 showed a preference for G-quadruplex; however, the binding affinity magnitude and preference were improved in 1 because the former had a cyclic structure.

  3. Porphyrin derivatives inhibit the interaction between receptor activator of NF-κB and its ligand.

    PubMed

    Chypre, Melanie; Madel, Maria-Bernadette; Chaloin, Olivier; Blin-Wakkach, Chlaudine; Morice, Christophe; Mueller, Christopher G

    2017-09-08

    Receptor Activator of NF-κB (RANK), a member of the TNF-receptor superfamily, plays an important role in bone resorption and stimulates immune and epithelial cell activation. Denosumab, a human monoclonal antibody blocking RANK ligand (RANKL), is approved for the treatment of osteoporosis and bone metastasis. However, a small molecule inhibiting RANK-RANKL interaction would be beneficial to reduce costs and to facilitate treatments with orally available therapeutic agents. Here, we report the discovery of the first non-peptidic inhibitors of RANK-RANKL interactions. By screening a chemical library using a competitive ELISA assay, the porphyrin verteporfin was identified as a hit. Derivatives were screened and the chlorin-macrocycle-containing pheophorbide A and purpurin 18 were found to bind recombinant RANKL, to inhibit RANK-RANKL interaction in the ELISA assay, to suppress the RANKL-dependent activation of model cells and the differentiation of RANK-expressing precursors into osteoclasts. This discovery of a family of small molecules inhibiting RANK-activation presents a first basis for further development of non-peptidic therapeutic agents targeting the interaction between RANK and RANKL. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. A 3-fold-symmetric ligand based on 2-hydroxypyridine: regulation of ligand binding by hydrogen bonding.

    PubMed

    Moore, Cameron M; Quist, David A; Kampf, Jeff W; Szymczak, Nathaniel K

    2014-04-07

    A tripodal ligand based on 2-hydroxypyridine is presented. Cu-Cl adducts of H3thpa with Cu(I) and Cu(II) provide complexes featuring highly directed, intramolecular hydrogen-bonding interactions. An upper limit for the hydrogen-bonding free energy to Cu(I)-Cl was estimated at ∼18 kcal/mol.

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

    NASA Astrophysics Data System (ADS)

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

    2008-06-01

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

  6. Synthesis and structural characterization of Pd(II) complexes derived from perimidine ligand and their in vitro antimicrobial studies

    NASA Astrophysics Data System (ADS)

    Azam, Mohammad; Warad, Ismail; Al-Resayes, Saud I.; Alzaqri, Nabil; Khan, Mohammad Rizwan; Pallepogu, Raghavaiah; Dwivedi, Sourabh; Musarrat, Javed; Shakir, Mohammad

    2013-09-01

    A novel series of Pd(II) complexes derived from 2-thiophenecarboxaldehyde and 1,8-diaminonaphthalene has been synthesized and characterized by various physico-chemical and spectroscopic techniques viz., elemental analyses, IR, UV-vis, 1H and 13C NMR spectroscopy, and ESI-mass spectrometry. The structure of ligand, 2-(2-thienyl)-2,3-dihydro-1H-perimidine has been ascertained on the basis of single crystal X-ray diffraction. All Pd(II) complexes together with the corresponding ligand have been evaluated for their ability to suppress the in vitro growth of microbes, Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, Citrobacter sp., Bacillus subtilis and Stenotrophomonas acidaminiphila and results show that Pd(II) complexes have more significant antimicrobial activity than their corresponding ligand. Fluorescence spectroscopic measurements clearly support that both of the Pd(II) complexes show significant DNA binding with calf thymus DNA.

  7. Pharmacological Role of Anions (Sulphate, Nitrate, Oxalate and Acetate) on the Antibacterial Activity of Cobalt(II), Copper(II) and Nickel(II) Complexes With Nicotinoylhydrazine-Derived ONO, NNO and SNO Ligands

    PubMed Central

    Rauf, Abdur

    1996-01-01

    Mixed ligands biologically active complexes of cobalt(II), copper(II) and nickel(II) with nicotinoylhydrazine-derived ONO, NNO and SNO donor schiff-base ligands having the same metal ion but different anions such as sulphate, nitrate, oxalate and acetate have been synthesised and characterised on the basis of their physical, analytical and spectral data. In order to evaluate the role of anions on their bioability, these ligands and their synthesised metal complexes with various anions have been screened against bacterial species such as Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus and the title studies have proved a definative role of anions in increasing the biological activity PMID:18472896

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

    PubMed

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

    2017-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

  11. Structure-based design of a superagonist ligand for the vitamin D nuclear receptor.

    PubMed

    Hourai, Shinji; Rodrigues, Luis Cezar; Antony, Pierre; Reina-San-Martin, Bernardo; Ciesielski, Fabrice; Magnier, Benjamin Claude; Schoonjans, Kristina; Mouriño, Antonio; Rochel, Natacha; Moras, Dino

    2008-04-01

    Vitamin D nuclear receptor (VDR), a ligand-dependent transcriptional regulator, is an important target for multiple clinical applications, such as osteoporosis and cancer. Since exacerbated increase of calcium serum level is currently associated with VDR ligands action, superagonists with low calcium serum levels have been developed. Based on the crystal structures of human VDR (hVDR) bound to 1alpha,25-dihydroxyvitamin D(3) and superagonists-notably, KH1060-we designed a superagonist ligand. In order to optimize the aliphatic side chain conformation with a subsequent entropy benefit, we incorporated an oxolane ring and generated two stereo diasteromers, AMCR277A and AMCR277B. Only AMCR277A exhibits superagonist activity in vitro, but is as calcemic in vivo as the natural ligand. The crystal structures of the complexes between the ligand binding domain of hVDR and these ligands provide a rational approach to the design of more potent superagonist ligands for potential clinical application.

  12. DNA-Based Nanostructures: Changes of Mechanical Properties of DNA upon Ligand Binding

    NASA Astrophysics Data System (ADS)

    Nechipurenko, Yury; Grokhovsky, Sergey; Gursky, Georgy; Nechipurenko, Dmitry; Polozov, Robert

    The formation of DNA-based nanostructures involves the binding of different kinds of ligands to DNA as well as the interaction of DNA molecules with each other. Complex formation between ligand and DNA can alter physicochemical properties of the DNA molecule. In the present work, the accessibility of DNA-ligand complexes to cleavage by DNase I are considered, and the exact algorithms for analysis of diagrams of DNase I footprinting for ligand-DNA complexes are obtained. Changes of mechanical properties of the DNA upon ligand binding are also demonstrated by the cleavage patterns generated upon ultrasound irradiation of cis-platin-DNA complexes. Propagation of the mechanical perturbations along DNA in the presence of bound ligands is considered in terms of a string model with a heterogeneity corresponding to the position of a bound ligand on DNA. This model can reproduce qualitatively the cleavage patterns obtained upon ultrasound irradiation of cis-platin-DNA complexes.

  13. Structural and thermodiffractometric analysis of coordination polymers. Part II: zinc and cadmium derivatives of the Bim ligand [Bim = bis(1-imidazolyl)methane].

    PubMed

    Masciocchi, Norberto; Pettinari, Claudio; Alberti, Enrica; Pettinari, Riccardo; Nicola, Corrado Di; Albisetti, Alessandro Figini; Sironi, Angelo

    2007-12-10

    New polynuclear coordination species containing the ditopic bis(1-imidazolyl)methane (Bim) ligand have been prepared as microcrystalline powders and structurally characterized by ab initio X-ray powder diffraction methods. [Zn(CH3COO)2(Bim)]n contains 1D chains with tetrahedral metal atoms bridged by Bim ligands; [CdBr2(Bim)]n shows a dense packing with hexacoordinated Cd(II) ions and mu-Br and mu-Bim bridges; at variance, the isomorphous [ZnCl2(Bim)]n and [ZnBr2(Bim)]n species contain cyclic dimers based on tetrahedral Zn(II) ions. Thermodiffractometric analysis allowed estimation of the linear thermal expansion coefficients and strain tensors derived there from. Bim-rich phases, with 2:1 ligand-to-metal ratio, were also isolated: ZnBr2(Bim)2(H2O)3 and [Cd(CH3COO)2(Bim)2]n containing cis and trans MN4O2 chromophores, respectively, show 1D polymers built upon M2Bim2 cycles, hinged on the metal ions. In all species the conformation of the Bim ligands is Cs (or nearly so), while in the few sparse reports of similar coordination polymers the alternative C2 one was preferentially observed.

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

    SciTech Connect

    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 [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.

  15. Thermodynamic Characterization of Hydration Sites from Integral Equation-Derived Free Energy Densities: Application to Protein Binding Sites and Ligand Series.

    PubMed

    Güssregen, Stefan; Matter, Hans; Hessler, Gerhard; Lionta, Evanthia; Heil, Jochen; Kast, Stefan M

    2017-07-24

    Water molecules play an essential role for mediating interactions between ligands and protein binding sites. Displacement of specific water molecules can favorably modulate the free energy of binding of protein-ligand complexes. Here, the nature of water interactions in protein binding sites is investigated by 3D RISM (three-dimensional reference interaction site model) integral equation theory to understand and exploit local thermodynamic features of water molecules by ranking their possible displacement in structure-based design. Unlike molecular dynamics-based approaches, 3D RISM theory allows for fast and noise-free calculations using the same detailed level of solute-solvent interaction description. Here we correlate molecular water entities instead of mere site density maxima with local contributions to the solvation free energy using novel algorithms. Distinct water molecules and hydration sites are investigated in multiple protein-ligand X-ray structures, namely streptavidin, factor Xa, and factor VIIa, based on 3D RISM-derived free energy density fields. Our approach allows the semiquantitative assessment of whether a given structural water molecule can potentially be targeted for replacement in structure-based design. Finally, PLS-based regression models from free energy density fields used within a 3D-QSAR approach (CARMa - comparative analysis of 3D RISM Maps) are shown to be able to extract relevant information for the interpretation of structure-activity relationship (SAR) trends, as demonstrated for a series of serine protease inhibitors.

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

    PubMed

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

    2012-09-03

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

  17. On the use of nonfluorescent dye labeled ligands in FRET-based receptor binding studies.

    PubMed

    Tahtaoui, Chouaib; Guillier, Fabrice; Klotz, Philippe; Galzi, Jean-Luc; Hibert, Marcel; Ilien, Brigitte

    2005-12-01

    The efficiency of fluorescence resonance energy transfer (FRET) is dependent upon donor-acceptor proximity and spectral overlap, whether the acceptor partner is fluorescent or not. We report here on the design, synthesis, and characterization of two novel pirenzepine derivatives that were coupled to patent blue VF and pinacyanol dyes. These nonfluorescent compounds, when added to cells stably expressing enhanced green fluorescent protein (EGFP)-fused muscarinic M1 receptors, promote EGFP fluorescence extinction in a time-, concentration-, and atropine-dependent manner. They display nanomolar affinity for the muscarinic receptor, determined using either FRET or classical radioligand binding conditions. We provide evidence that these compounds behave as potent acceptors of energy from excited EGFP with quenching efficiencies comparable to those of analogous fluorescent bodipy or rhodamine red pirenzepine derivatives. The advantages they offer over fluorescent ligands are illustrated and discussed in terms of reliability, sensitivity, and wider applicability of FRET-based receptor binding assays.

  18. Herbo-mineral based Schiff base ligand and its metal complexes: Synthesis, characterization, catalytic potential and biological applications.

    PubMed

    Kareem, Abdul; Laxmi; Arshad, Mohammad; Nami, Shahab A A; Nishat, Nahid

    2016-07-01

    Schiff base ligand, (L), derived from condensation reaction of 1,7-bis-(4-hydroxy-3-methoxyphenyl)-1,6-heptadiene-3,5-dione, (curcumin), with pyridine-3-carboxamide, (nicotinamide), and its complexes of Co(II), Ni(II) and Cu(II) ions, containing 1,10-phenanthroline as auxiliary ligand were synthesized and characterized by various physico-chemical techniques. From the micro analytical data, the stoichiometry of the complexes 1:1 (metal: ligand) was ascertained. The Co(II) and Cu(II) forms octahedral complexes, while the geometric structure around Ni(II) atom can be described as square planar. The catalytic potential of the metal complexes have been evaluated by recording the rate of decomposition of hydrogen peroxide. The results reveal that the percent decomposition of H2O2increases with time and the highest value (50.50%) was recorded for Co(II) complex. The ligand and its complexes were also screened for their in vitro antibacterial activity against Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Streptococcus pyogenes and Pseudomonas aeruginosa. The relative order of antibacterial activity against S. Pyogenes, S. aureus and E. coli is Cu(II)>Ni(II)>Co(II)>(L); while with P. aeruginosa, K. pneumoniae the order of activity is Cu(II)>Co(II)>Ni(II)>(L). The anthelmintic screening was performed using Pheretima posthuma. The order of anthelmintic activity of ligand and its complexes is [(Phen)CuLCl2]>[(Phen)CoLCl2]>[(Phen)NiL]Cl2>(L).

  19. Identification of Novel HIV 1- Protease Inhibitors: Application of Ligand and Structure Based Pharmacophore Mapping and Virtual Screening

    PubMed Central

    Yadav, Divya; Paliwal, Sarvesh; Yadav, Rakesh; Pal, Mahima; Pandey, Anubhuti

    2012-01-01

    A combined ligand and structure-based drug design approach provides a synergistic advantage over either methods performed individually. Present work bestows a good assembly of ligand and structure-based pharmacophore generation concept. Ligand-oriented study was accomplished by employing the HypoGen module of Catalyst in which we have translated the experimental findings into 3-D pharmacophore models by identifying key features (four point pharmacophore) necessary for interaction of the inhibitors with the active site of HIV-1 protease enzyme using a training set of 33 compounds belonging to the cyclic cyanoguanidines and cyclic urea derivatives. The most predictive pharmacophore model (hypothesis 1), consisting of four features, namely, two hydrogen bond acceptors and two hydrophobic, showed a correlation (r) of 0.90 and a root mean square of 0.71 and cost difference of 56.59 bits between null cost and fixed cost. The model was validated using CatScramble technique, internal and external test set prediction. In the second phase of our study, a structure-based five feature pharmacophore hypothesis was generated which signifies the importance of hydrogen bond donor, hydrogen bond acceptors and hydrophobic interaction between the HIV-1 protease enzyme and its inhibitors. This work has taken a significant step towards the full integration of ligand and structure-based drug design methodologies as pharmacophoric features retrieved from structure-based strategy complemented the features from ligand-based study hence proving the accuracy of the developed models. The ligand-based pharmacophore model was used in virtual screening of Maybridge and NCI compound database resulting in the identification of four structurally diverse druggable compounds with nM activities. PMID:23145032

  20. Integrating structure-based and ligand-based approaches for computational drug design.

    PubMed

    Wilson, Gregory L; Lill, Markus A

    2011-04-01

    Methods utilized in computer-aided drug design can be classified into two major categories: structure based and ligand based, using information on the structure of the protein or on the biological and physicochemical properties of bound ligands, respectively. In recent years there has been a trend towards integrating these two methods in order to enhance the reliability and efficiency of computer-aided drug-design approaches by combining information from both the ligand and the protein. This trend resulted in a variety of methods that include: pseudoreceptor methods, pharmacophore methods, fingerprint methods and approaches integrating docking with similarity-based methods. In this article, we will describe the concepts behind each method and selected applications.

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

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

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

  2. Preparation, spectroscopic characterization and antimicrobial activities of mixed metal (Sb and Bi) bridged derivatives with mixed sulfur donor ligands

    NASA Astrophysics Data System (ADS)

    Joshi, Sapana; Chauhan, H. P. S.; Carpenter, Nitin

    2017-01-01

    This article explores the syntheses of six mixed metal derivatives of antimony(III) and bismuth(III) by the reaction of ethane-1,2-dithiol and metal bis derivatives of dithiocarbamates and/or dithiophosphates ligands in 1:1:1 M stoichiometry. These derivatives have been characterized by physicochemical [elemental analysis (C, H, N, S, Sb and Bi), molecular weight and melting point determinations], spectral [UV-Visible, FTIR, NMR (1H, 13C and 31P)], powder X-ray diffraction studies. These derivatives have nano-ranged crystallite size (8.18-18.04 nm) with monoclinic crystal system. All the synthesized derivatives have two metal centers (Sb and Bi) which elevate the zone of inhibition against four bacterial and two fungal species as compared to single metal species (metal precursors) as well as standard drugs.

  3. Information theory-based scoring function for the structure-based prediction of protein-ligand binding affinity.

    PubMed

    Kulharia, Mahesh; Goody, Roger S; Jackson, Richard M

    2008-10-01

    The development and validation of a new knowledge based scoring function (SIScoreJE) to predict binding energy between proteins and ligands is presented. SIScoreJE efficiently predicts the binding energy between a small molecule and its protein receptor. Protein-ligand atomic contact information was derived from a Non-Redundant Data set (NRD) of over 3000 X-ray crystal structures of protein-ligand complexes. This information was classified for individual "atom contact pairs" (ACP) which is used to calculate the atomic contact preferences. In addition to the two schemes generated in this study we have assessed a number of other common atom-type classification schemes. The preferences were calculated using an information theoretic relationship of joint entropy. Among 18 different atom-type classification schemes "ScoreJE Atom Type set2" (SATs2) was found to be the most suitable for our approach. To test the sensitivity of the method to the inclusion of solvent, Single-body Solvation Potentials (SSP) were also derived from the atomic contacts between the protein atom types and water molecules modeled using AQUARIUS2. Validation was carried out using an evaluation data set of 100 protein-ligand complexes with known binding energies to test the ability of the scoring functions to reproduce known binding affinities. In summary, it was found that a combined SSP/ScoreJE (SIScoreJE) performed significantly better than ScoreJE alone, and SIScoreJE and ScoreJE performed better than GOLD::GoldScore, GOLD::ChemScore, and XScore.

  4. NMR-based analysis of protein-ligand interactions.

    PubMed

    Cala, Olivier; Guillière, Florence; Krimm, Isabelle

    2014-02-01

    Physiological processes are mainly controlled by intermolecular recognition mechanisms involving protein-protein and protein-ligand (low molecular weight molecules) interactions. One of the most important tools for probing these interactions is high-field solution nuclear magnetic resonance (NMR) through protein-observed and ligand-observed experiments, where the protein receptor or the organic compounds are selectively detected. NMR binding experiments rely on comparison of NMR parameters of the free and bound states of the molecules. Ligand-observed methods are not limited by the protein molecular size and therefore have great applicability for analysing protein-ligand interactions. The use of these NMR techniques has considerably expanded in recent years, both in chemical biology and in drug discovery. We review here three major ligand-observed NMR methods that depend on the nuclear Overhauser effect-transferred nuclear Overhauser effect spectroscopy, saturation transfer difference spectroscopy and water-ligand interactions observed via gradient spectroscopy experiments-with the aim of reporting recent developments and applications for the characterization of protein-ligand complexes, including affinity measurements and structural determination.

  5. Three novel indium MOFs derived from dicarboxylate ligands: Syntheses, structures and photoluminescent properties

    SciTech Connect

    Wang Liping; Song Tianyou; Li Chao; Xia Jing; Wang Shengyan; Wang Li; Xu Jianing

    2012-06-15

    The self-assembly of InCl{sub 3} with 1,4-phenylenediacetic acid (1,4-H{sub 2}pda), 1,3-benzendicarboxylic acid (1,3-H{sub 2}bdc) and 1,4-cyclohexanedicarboxylic acid (1,4- H{sub 2}chdc) generates three new In(III) MOFs, (Me{sub 2}NH{sub 2})[In(cis-1,4-pda){sub 2}] (1), HIn(1,3-bdc){sub 2}{center_dot}2DMF (2) and In(OH)(trans-1,4-chdc) (3) (Me{sub 2}NH=dimethylamine, DMF=N, N'-dimethylformamide). Compound 1 displays a novel 1D no-planar double chain. Although a mixture of cis- and trans-1,4-H{sub 2}pda was used, the product of compound 1 is a single phase with only cis-pda{sup 2-} ligands. Compound 2 possesses a 2D square lattice with sql topology. Interestingly, in compound 2, the 4-connected building unit containing InO{sub 6} octahedron is firstly occurred in In-MOFs. Compound 3 is built up from the infinite metal-oxide chains cross-linked by trans-1,4-chdc{sup 2-} to form 3D framework with rhombus-shaped channels. Furthermore, compounds 1-3 present intense solid-state fluorescent emissions at room temperature. - Graphical abstract: Three new In-MOFs based on different dicaboxylate acids display 1D chain, 2D layer and 3D open-framework, respectively and show strong luminescence emissions at room temperature. Highlights: Black-Right-Pointing-Pointer Three new indium metal-organic frameworks have been solvothermal synthesized. Black-Right-Pointing-Pointer The structural variation is attributed to the diverse coordination modes of ligands. Black-Right-Pointing-Pointer Compounds 1-3 exhibit 1D double chain, 2D layer and 3D open-framework, respectively. Black-Right-Pointing-Pointer These compounds exhibit strong solid-state luminescence emission at room temperature.

  6. LigandRNA: computational predictor of RNA-ligand interactions.

    PubMed

    Philips, Anna; Milanowska, Kaja; Lach, Grzegorz; Bujnicki, Janusz M

    2013-12-01

    RNA molecules have recently become attractive as potential drug targets due to the increased awareness of their importance in key biological processes. The increase of the number of experimentally determined RNA 3D structures enabled structure-based searches for small molecules that can specifically bind to defined sites in RNA molecules, thereby blocking or otherwise modulating their function. However, as of yet, computational methods for structure-based docking of small molecule ligands to RNA molecules are not as well established as analogous methods for protein-ligand docking. This motivated us to create LigandRNA, a scoring function for the prediction of RNA-small molecule interactions. Our method employs a grid-based algorithm and a knowledge-based potential derived from ligand-binding sites in the experimentally solved RNA-ligand complexes. As an input, LigandRNA takes an RNA receptor file and a file with ligand poses. As an output, it returns a ranking of the poses according to their score. The predictive power of LigandRNA favorably compares to five other publicly available methods. We found that the combination of LigandRNA and Dock6 into a "meta-predictor" leads to further improvement in the identification of near-native ligand poses. The LigandRNA program is available free of charge as a web server at http://ligandrna.genesilico.pl.

  7. Kavalactones and the endocannabinoid system: the plant-derived yangonin is a novel CB₁ receptor ligand.

    PubMed

    Ligresti, Alessia; Villano, Rosaria; Allarà, Marco; Ujváry, István; Di Marzo, Vincenzo

    2012-08-01

    To investigate the possible interactions between kavalactone-based molecules and proteins of the endocannabinoid system and provide novel and synthetically accessible structural scaffolds for the design of cannabinoid receptor ligands sharing pharmacological properties with kavapyrones, a preliminary SAR analysis was performed on five commercially available natural kavalactones and nine kavalactone-analogues properly synthesized. These compounds were investigated for assessing their cannabinoid receptor binding affinity and capability of inhibiting the activity of the two major metabolic enzymes of the endocannabinoid system, fatty acid amide hydrolase (FAAH) and monoacylglycerol lipase (MAGL). Among the molecules tested, only yangonin exhibited affinity for the human recombinant CB₁ receptor with a K(i)=0.72 μM and selectivity vs. the CB₂ receptor (K(i)>10 μM). None of the compounds exhibited strong inhibitory effects on the two enzymes analyzed. The CB₁ receptor affinity of yangonin suggests that the endocannabinoid system might contribute to the complex human psychopharmacology of the traditional kava drink and the anxiolytic preparations obtained from the kava plant. Copyright © 2012 Elsevier Ltd. All rights reserved.

  8. Cell-based assays for screening androgen receptor ligands

    PubMed Central

    Campana, Carmela; Pezzi, Vincenzo; Rainey, William E

    2015-01-01

    The androgen receptor (AR, NR3C4), mediates the majority of androgen effects on target cells. The AR is activated following ligand binding that result in activation of target gene transcription. Several cell based model systems have been developed that allow sensitive detection and monitoring of steroids or other compounds with AR bioactivity. Most cell based AR reporter models use transgenic gene constructs that include an androgen response element (ARE) that controls reporter gene expression. The DNA cis-regulatory elements that respond to AR share sequence similarity with cis-regulatory elements for glucocorticoid (GR, NR3C1), mineralocorticoid (MR, NR3C2) and progesterone (PGR, NR3C3) receptors, which has compromised AR selectivity for some models. In recent years, the sensitivity and selectivity of AR bioassays have been significantly improved through careful selection of cell models, utilization of improved reporter genes and the use of yeast two hybrid AR systems. This review summarizes and compares the currently available androgen-responsive cell model systems. PMID:26036905

  9. Polyethylene glycol-based homologated ligands for nicotinic acetylcholine receptors☆

    PubMed Central

    Scates, Bradley A.; Lashbrook, Bethany L.; Chastain, Benjamin C.; Tominaga, Kaoru; Elliott, Brandon T.; Theising, Nicholas J.; Baker, Thomas A.; Fitch, Richard W.

    2010-01-01

    A homologous series of polyethylene glycol (PEG) monomethyl ethers were conjugated with three ligand series for nicotinic acetylcholine receptors. Conjugates of acetylaminocholine, the cyclic analog 1-acetyl-4,4-dimethylpiperazinium, and pyridyl ether A-84543 were prepared. Each series was found to retain significant affinity at nicotinic receptors in rat cerebral cortex with tethers of up to six PEG units. Such compounds are hydrophilic ligands which may serve as models for fluorescent/affinity probes and multivalent ligands for nAChR. PMID:19006672

  10. Paired Ig-Like Type 2 Receptor-Derived Agonist Ligands Ameliorate Inflammatory Reactions by Downregulating β1 Integrin Activity

    PubMed Central

    Lee, Kyoung-Jin; Lim, Dongyoung; Yoo, Yeon Ho; Park, Eun-Ji; Lee, Sun-Hee; Yadav, Birendra Kumar; Lee, Yong-Ki; Park, Jeong Hyun; Kim, Daejoong; Park, Kyeong Han; Hahn, Jang-Hee

    2016-01-01

    The paired immunoglobulin-like type 2 receptor (PILR) family consists of two functionally opposite members, inhibitory PILRα and activating PILRβ receptors. PILRs are widely expressed in various immune cells and interact with their ligands, especially CD99 expressed on activated T cells, to participate in immune responses. Here we investigated whether PILR-derived agonists inhibit β1 integrin activity as ligands for CD99. PILR-derived peptides as well as PILR-Fc fusion proteins prevented cell adhesion to fibronectin through the regulation of β1 integrin activity. Especially, PILRpep3, a representative 3-mer peptide covering the conserved motifs of the PILR extracellular domain, prevented the clustering and activation of β1 integrin by dephosphorylating FAK and vinculin, which are major components of focal adhesion. In addition, PILRpep3 inhibited transendothelial migration of monocytes as well as endothelial cell tube formation. Furthermore, upon intraperitoneal injection of PILRpep3 into mice with collagen-induced arthritis, the inflammatory response of rheumatoid arthritis was strongly suppressed. Taken together, these results suggest that PILR-derived agonist ligands may prevent the inflammatory reactions of rheumatoid arthritis by activating CD99. PMID:27306643

  11. Amide Coupling Reaction for the Synthesis of Bispyridine-based Ligands and Their Complexation to Platinum as Dinuclear Anticancer Agents

    PubMed Central

    Apps, Michael G.; Johnson, Ben W.; Sutcliffe, Oliver B.; Brown, Sarah D.; Wheate, Nial J.

    2014-01-01

    Amide coupling reactions can be used to synthesize bispyridine-based ligands for use as bridging linkers in multinuclear platinum anticancer drugs. Isonicotinic acid, or its derivatives, are coupled to variable length diaminoalkane chains under an inert atmosphere in anhydrous DMF or DMSO with the use of a weak base, triethylamine, and a coupling agent, 1-propylphosphonic anhydride. The products precipitate from solution upon formation or can be precipitated by the addition of water. If desired, the ligands can be further purified by recrystallization from hot water. Dinuclear platinum complex synthesis using the bispyridine ligands is done in hot water using transplatin. The most informative of the chemical characterization techniques to determine the structure and gross purity of both the bispyridine ligands and the final platinum complexes is 1H NMR with particular analysis of the aromatic region of the spectra (7-9 ppm). The platinum complexes have potential application as anticancer agents and the synthesis method can be modified to produce trinuclear and other multinuclear complexes with different hydrogen bonding functionality in the bridging ligand. PMID:24893964

  12. Ligand efficiency based approach for efficient virtual screening of compound libraries.

    PubMed

    Ke, Yi-Yu; Coumar, Mohane Selvaraj; Shiao, Hui-Yi; Wang, Wen-Chieh; Chen, Chieh-Wen; Song, Jen-Shin; Chen, Chun-Hwa; Lin, Wen-Hsing; Wu, Szu-Huei; Hsu, John T A; Chang, Chung-Ming; Hsieh, Hsing-Pang

    2014-08-18

    Here we report for the first time the use of fit quality (FQ), a ligand efficiency (LE) based measure for virtual screening (VS) of compound libraries. The LE based VS protocol was used to screen an in-house database of 125,000 compounds to identify aurora kinase A inhibitors. First, 20 known aurora kinase inhibitors were docked to aurora kinase A crystal structure (PDB ID: 2W1C); and the conformations of docked ligand were used to create a pharmacophore (PH) model. The PH model was used to screen the database compounds, and rank (PH rank) them based on the predicted IC50 values. Next, LE_Scale, a weight-dependant LE function, was derived from 294 known aurora kinase inhibitors. Using the fit quality (FQ = LE/LE_Scale) score derived from the LE_Scale function, the database compounds were reranked (PH_FQ rank) and the top 151 (0.12% of database) compounds were assessed for aurora kinase A inhibition biochemically. This VS protocol led to the identification of 7 novel hits, with compound 5 showing aurora kinase A IC50 = 1.29 μM. Furthermore, testing of 5 against a panel of 31 kinase reveals that it is selective toward aurora kinase A & B, with <50% inhibition for other kinases at 10 μM concentrations and is a suitable candidate for further development. Incorporation of FQ score in the VS protocol not only helped identify a novel aurora kinase inhibitor, 5, but also increased the hit rate of the VS protocol by improving the enrichment factor (EF) for FQ based screening (EF = 828), compared to PH based screening (EF = 237) alone. The LE based VS protocol disclosed here could be applied to other targets for hit identification in an efficient manner.

  13. Production of canine soluble CD40 ligand to induce maturation of monocyte derived dendritic cells for cancer immunotherapy.

    PubMed

    Wijewardana, Viskam; Sugiura, Kikuya; Yahata, Mana; Akazawa, Takashi; Wijesekera, Daluthgamage Patsy H; Imamoto, Shigeki; Hatoya, Shingo; Inoue, Norimitsu; Inaba, Toshio

    2013-11-15

    CD40 ligand (CD40L) expressed by activated T cells is shown to induce maturation of immature dendritic cells (DCs) and this maturation is a vital part in DC based tumor immunotherapy. We constructed an expression vector by cloning the extracellular domain of canine CD40L fused to the signal sequence of canine IL-12p40. When PBMCs were incubated with canine granulocyte-macrophage (GM) -CSF and IL-4, expression of CD86 was significantly elevated, but the majority of cells displayed the morphology of immature DCs. Following addition of the expressed canine soluble CD40L (csCD40L) to the DC-inducing culture, the cell morphology shifted to that of mature DCs, and expression of CD80, CD86, MHC class II and CD1a was significantly enhanced. This morphological change and enhancement of expression was observed even when the csCD40L was present only in the second half period of the culture. Furthermore, the csCD40L caused a significant increase in IL-12 production from DCs. These results show that the csCD40L significantly promotes the maturation and activation of canine monocyte derived DCs. Copyright © 2013 Elsevier B.V. All rights reserved.

  14. Docking study, synthesis, and in vitro evaluation of fluoro-MADAM derivatives as SERT ligands for PET imaging.

    PubMed

    Mavel, Sylvie; Vercouillie, Johnny; Garreau, Lucette; Raguza, Tiziana; Ravna, Aina Westrheim; Chalon, Sylvie; Guilloteau, Denis; Emond, Patrick

    2008-10-01

    In order to predict affinity of new diphenylsulfides for the serotonin transporter (SERT), a molecular modeling model was used to compare potential binding affinity of new compounds with known potent ligands. The aim of this study is to identify a suitable PET radioligand for imaging the SERT, new derivatives, and their precursors for a C-11 or F-18 radiolabeling, were synthesized. Two fluorinated derivatives displayed good in vitro affinity for the SERT (K(i)=14.3+/-1 and 10.1+/-2.7 nM) and good selectivity toward the other monoamine transporters as predicted by the docking study.

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

    PubMed Central

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

    2016-01-01

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

  16. Synthesis, characterization, biological activity and equilibrium studies of metal(II) ion complexes with tridentate hydrazone ligand derived from hydralazine

    NASA Astrophysics Data System (ADS)

    El-Sherif, Ahmed A.; Shoukry, Mohamed M.; Abd-Elgawad, Mohamed M. A.

    2012-12-01

    In the present study, a new hydrazone ligand (2-((2-phthalazin-1-yl)hydrazono)methyl)phenol) prepared by condensation of hydralazine (1-Hydralazinophthalazine) with salicylaldehyde (SAH). The synthesized SAH-hydrazone and its metal complexes have been characterized by elemental analyses, IR, 1H NMR, solid reflectance, magnetic moment, molar conductance, mass spectra, UV-vis and thermal analysis (TGA). The analytical data of the complexes show the formation of 1:1 [M:L] ratio, where M represents Ni(II), Co(II) and Cu(II) ions, while L represents the deprotonated hydrazone ligand. IR spectra show that SAH is coordinated to the metal ions in a tridentate manner through phthalazine-N, azomethine-N and phenolic-oxygen groups. The ligand and their metal chelates have been screened for their antimicrobial activities using the disc diffusion method against the selected bacteria and fungi. Proton-ligand association constants of (SAH) and the stepwise stability constants of its metal complexes are determined potentiometrically in 0.1 M NaNO3 at different temperatures and the corresponding thermodynamic parameters were derived and discussed. The order of -ΔG° and -ΔH° were found to obey Mn2+ < Co2+ < Ni2+ < Cu2+, in accordance with the Irving-Williams order. The complexes were stabilized by enthalpy changes and the results suggest that the complexation is an enthalpy-driven process. The concentration distribution diagrams of the complexes are evaluated.

  17. Monomeric and dimeric nickel complexes derived from a pincer ligand featuring a secondary amine donor moiety.

    PubMed

    Spasyuk, Denis M; Zargarian, Davit

    2010-07-05

    Reaction of NiBr(2)(CH(3)CN)(x) with the unsymmetrical pincer ligand m-(i-Pr(2)PO)(CH(2)NHBn)C(6)H(4) (Bn = CH(2)Ph) gives the complex (R,S)-kappa(P),kappa(C),kappa(N)-{2-(i-Pr(2)PO),6-(CH(2)NHBn)-C(6)H(3)}Ni(II)Br, 1, featuring an asymmetric secondary amine donor moiety. Deprotonation of the latter with methyl lithium gave a dark brown compound that could not be characterized directly, but fully characterized derivatives prepared from this compound indicate that it is the LiBr adduct of the 14-electron amido species [kappa(P),kappa(C),kappa(N)-{2-(i-Pr(2)PO),6-(CH(2)NBn)-C(6)H(3)}Ni], 2. Thus, 2.LiBr reacts with water to regenerate 1, while reaction with excess benzyl or allyl bromide gave the POCN-type pincer complexes 3 and 4, respectively, featuring tertiary amine donor moieties. On the other hand, heating 2.LiBr at 60 degrees C led to loss of LiBr and dimerization to generate the orange crystalline compound [mu(N);kappa(P),kappa(C),kappa(N)-{2-(i-Pr(2)PO),6-(CH(2)NBn)-C(6)H(3)}Ni](2), 5. Solid state structural studies show that 1, 3, and 4 are monomeric, square planar complexes involving one Ni-N interaction, whereas complex 5 is a C(2)-symmetric dimer involving four Ni-N interactions and a Ni(2)N(2) core featuring a short Ni-Ni distance (2.51 A). Preliminary reactivity tests have shown that 5 is stable toward weak nucleophiles such as acetonitrile but reacts with strong nucleophiles such as CO or 2,6-Me(2)(C(6)H(3))NC. Reactions with protic reagents showed that phthalimide appears to break the dimer to generate a monomeric species, whereas alcohols appear to leave the dimer intact, giving rise instead to adducts through N...H...O interactions. These ROH adducts of 5 were found to be active precatalysts for the alchoholysis of acrylonitrile with up to 2000 catalytic turnover numbers.

  18. Ligand-supported homology modelling of protein binding-sites using knowledge-based potentials.

    PubMed

    Evers, Andreas; Gohlke, Holger; Klebe, Gerhard

    2003-11-21

    A new approach, MOBILE, is presented that models protein binding-sites including bound ligand molecules as restraints. Initially generated, homology models of the target protein are refined iteratively by including information about bioactive ligands as spatial restraints and optimising the mutual interactions between the ligands and the binding-sites. Thus optimised models can be used for structure-based drug design and virtual screening. In a first step, ligands are docked into an averaged ensemble of crude homology models of the target protein. In the next step, improved homology models are generated, considering explicitly the previously placed ligands by defining restraints between protein and ligand atoms. These restraints are expressed in terms of knowledge-based distance-dependent pair potentials, which were compiled from crystallographically determined protein-ligand complexes. Subsequently, the most favourable models are selected by ranking the interactions between the ligands and the generated pockets using these potentials. Final models are obtained by selecting the best-ranked side-chain conformers from various models, followed by an energy optimisation of the entire complex using a common force-field. Application of the knowledge-based pair potentials proved efficient to restrain the homology modelling process and to score and optimise the modelled protein-ligand complexes. For a test set of 46 protein-ligand complexes, taken from the Protein Data Bank (PDB), the success rate of producing near-native binding-site geometries (rmsd<2.0A) with MODELLER is 70% when the ligand restrains the homology modelling process in its native orientation. Scoring these complexes with the knowledge-based potentials, in 66% of the cases a pose with rmsd <2.0A is found on rank 1. Finally, MOBILE has been applied to two case studies modelling factor Xa based on trypsin and aldose reductase based on aldehyde reductase.

  19. Supramolecular structure and spectral studies on mixed-ligand complexes derived from β-diketone with azodye rhodanine derivatives.

    PubMed

    El-Sonbati, A Z; Diab, M A; Belal, A A M; Morgan, Sh M

    2012-12-01

    A novel method to synthesize some mononuclear ternary palladium(II) complexes of the general formula [Pd(L(n))L] (where LH=diketone=acetylacetone, HL(n)=azorhodanine) has been synthesize. The structure of the new mononuclear ternary palladium(II) complexes was characterized using elemental analysis, spectral (electronic, infrared and (1)H &(13)C NMR) studies, magnetic susceptibility measurements and thermal studies. The IR showed that the ligands (HL(n) & LH) act as monobasic bidentate through the azodye nitrogen, oxygen keto moiety and two enolato oxygen atoms. The molar conductivities show that all the complexes are non-electrolytes. Bidentate chelating nature of β-diketone and azorhodanine anions in the complexes was characterized by (electronic, infrared and (1)H &(13)C NMR) spectra. Square planar geometry around palladium has been assigned in all complexes. Various ligand and nephelouxetic parameter have been calculated for the complexes. The thermal decomposition for complexes was studied.

  20. Supramolecular structure and spectral studies on mixed-ligand complexes derived from β-diketone with azodye rhodanine derivatives

    NASA Astrophysics Data System (ADS)

    El-Sonbati, A. Z.; Diab, M. A.; Belal, A. A. M.; Morgan, Sh. M.

    2012-12-01

    A novel method to synthesize some mononuclear ternary palladium(II) complexes of the general formula [Pd(Ln)L] (where LH = diketone = acetylacetone, HLn = azorhodanine) has been synthesize. The structure of the new mononuclear ternary palladium(II) complexes was characterized using elemental analysis, spectral (electronic, infrared and 1H &13C NMR) studies, magnetic susceptibility measurements and thermal studies. The IR showed that the ligands (HLn & LH) act as monobasic bidentate through the azodye nitrogen, oxygen keto moiety and two enolato oxygen atoms. The molar conductivities show that all the complexes are non-electrolytes. Bidentate chelating nature of β-diketone and azorhodanine anions in the complexes was characterized by (electronic, infrared and 1H &13C NMR) spectra. Square planar geometry around palladium has been assigned in all complexes. Various ligand and nephelouxetic parameter have been calculated for the complexes. The thermal decomposition for complexes was studied.

  1. Fluorescence‐ and bioluminescence‐based approaches to study GPCR ligand binding

    PubMed Central

    Stoddart, Leigh A; White, Carl W; Nguyen, Kim; Hill, Stephen J

    2015-01-01

    Ligand binding is a vital component of any pharmacologist's toolbox and allows the detailed investigation of how a molecule binds to its receptor. These studies enable the experimental determination of binding affinity of labelled and unlabelled compounds through kinetic, saturation (Kd) and competition (Ki) binding assays. Traditionally, these studies have used molecules labelled with radioisotopes; however, more recently, fluorescent ligands have been developed for this purpose. This review will briefly cover receptor ligand binding theory and then discuss the use of fluorescent ligands with some of the different technologies currently employed to examine ligand binding. Fluorescent ligands can be used for direct measurement of receptor‐associated fluorescence using confocal microscopy and flow cytometry as well as in assays such as fluorescence polarization, where ligand binding is monitored by changes in the free rotation when a fluorescent ligand is bound to a receptor. Additionally, fluorescent ligands can act as donors or acceptors for fluorescence resonance energy transfer (FRET) with the development of assays based on FRET and time‐resolved FRET (TR‐FRET). Finally, we have recently developed a novel bioluminescence resonance energy transfer (BRET) ligand binding assay utilizing a small (19 kDa), super‐bright luciferase subunit (NanoLuc) from a deep sea shrimp. In combination with fluorescent ligands, measurement of RET now provides an array of methodologies to study ligand binding. While each method has its own advantages and drawbacks, binding studies using fluorescent ligands are now a viable alternative to the use of radioligands. Linked Articles This article is part of a themed section on Molecular Pharmacology of G Protein‐Coupled Receptors. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v173.20/issuetoc PMID:26317175

  2. Fluorescence- and bioluminescence-based approaches to study GPCR ligand binding.

    PubMed

    Stoddart, Leigh A; White, Carl W; Nguyen, Kim; Hill, Stephen J; Pfleger, Kevin D G

    2016-10-01

    Ligand binding is a vital component of any pharmacologist's toolbox and allows the detailed investigation of how a molecule binds to its receptor. These studies enable the experimental determination of binding affinity of labelled and unlabelled compounds through kinetic, saturation (Kd ) and competition (Ki ) binding assays. Traditionally, these studies have used molecules labelled with radioisotopes; however, more recently, fluorescent ligands have been developed for this purpose. This review will briefly cover receptor ligand binding theory and then discuss the use of fluorescent ligands with some of the different technologies currently employed to examine ligand binding. Fluorescent ligands can be used for direct measurement of receptor-associated fluorescence using confocal microscopy and flow cytometry as well as in assays such as fluorescence polarization, where ligand binding is monitored by changes in the free rotation when a fluorescent ligand is bound to a receptor. Additionally, fluorescent ligands can act as donors or acceptors for fluorescence resonance energy transfer (FRET) with the development of assays based on FRET and time-resolved FRET (TR-FRET). Finally, we have recently developed a novel bioluminescence resonance energy transfer (BRET) ligand binding assay utilizing a small (19 kDa), super-bright luciferase subunit (NanoLuc) from a deep sea shrimp. In combination with fluorescent ligands, measurement of RET now provides an array of methodologies to study ligand binding. While each method has its own advantages and drawbacks, binding studies using fluorescent ligands are now a viable alternative to the use of radioligands. Linked Articles This article is part of a themed section on Molecular Pharmacology of G Protein-Coupled Receptors. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v173.20/issuetoc. © 2015 The Authors. British Journal of Pharmacology published by John Wiley & Sons Ltd on

  3. A reverse combination of structure-based and ligand-based strategies for virtual screening

    NASA Astrophysics Data System (ADS)

    Cortés-Cabrera, Álvaro; Gago, Federico; Morreale, Antonio

    2012-03-01

    A new approach is presented that combines structure- and ligand-based virtual screening in a reverse way. Opposite to the majority of the methods, a docking protocol is first employed to prioritize small ligands ("fragments") that are subsequently used as queries to search for similar larger ligands in a database. For a given chemical library, a three-step strategy is followed consisting of (1) contraction into a representative, non-redundant, set of fragments, (2) selection of the three best-scoring fragments docking into a given macromolecular target site, and (3) expansion of the fragments' structures back into ligands by using them as queries to search the library by means of fingerprint descriptions and similarity criteria. We tested the performance of this approach on a collection of fragments and ligands found in the ZINC database and the directory of useful decoys, and compared the results with those obtained using a standard docking protocol. The new method provided better overall results and was several times faster. We also studied the chemical diversity that both methods cover using an in-house compound library and concluded that the novel approach performs similarly but at a much smaller computational cost.

  4. A reverse combination of structure-based and ligand-based strategies for virtual screening.

    PubMed

    Cortés-Cabrera, Alvaro; Gago, Federico; Morreale, Antonio

    2012-03-01

    A new approach is presented that combines structure- and ligand-based virtual screening in a reverse way. Opposite to the majority of the methods, a docking protocol is first employed to prioritize small ligands ("fragments") that are subsequently used as queries to search for similar larger ligands in a database. For a given chemical library, a three-step strategy is followed consisting of (1) contraction into a representative, non-redundant, set of fragments, (2) selection of the three best-scoring fragments docking into a given macromolecular target site, and (3) expansion of the fragments' structures back into ligands by using them as queries to search the library by means of fingerprint descriptions and similarity criteria. We tested the performance of this approach on a collection of fragments and ligands found in the ZINC database and the directory of useful decoys, and compared the results with those obtained using a standard docking protocol. The new method provided better overall results and was several times faster. We also studied the chemical diversity that both methods cover using an in-house compound library and concluded that the novel approach performs similarly but at a much smaller computational cost.

  5. Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR

    NASA Astrophysics Data System (ADS)

    Filikov, Anton V.; Mohan, Venkatraman; Vickers, Timothy A.; Griffey, Richard H.; Cook, P. Dan; Abagyan, Ruben A.; James, Thomas L.

    2000-08-01

    Binding of the Tat protein to TAR RNA is necessary for viral replication of HIV-1. We screened the Available Chemicals Directory (ACD) to identify ligands to bind to a TAR RNA structure using a four-step docking procedure: rigid docking first, followed by three steps of flexible docking using a pseudobrownian Monte Carlo minimization in torsion angle space with progressively more detailed conformational sampling on a progressively smaller list of top-ranking compounds. To validate the procedure, we successfully docked ligands for five RNA complexes of known structure. For ranking ligands according to binding avidity, an empirical binding free energy function was developed which accounts, in particular, for solvation, isomerization free energy, and changes in conformational entropy. System-specific parameters for the function were derived on a training set of RNA/ligand complexes with known structure and affinity. To validate the free energy function, we screened the entire ACD for ligands for an RNA aptamer which binds l-arginine tightly. The native ligand ranked 17 out of ca. 153,000 compounds screened, i.e., the procedure is able to filter out >99.98% of the database and still retain the native ligand. Screening of the ACD for TAR ligands yielded a high rank for all known TAR ligands contained in the ACD and suggested several other potential TAR ligands. Eight of the highest ranking compounds not previously known to be ligands were assayed for inhibition of the Tat-TAR interaction, and two exhibited a CD50 of ca. 1 μM.

  6. Site-specific metal and ligand substitutions in a microporous Mn(2+)-based metal-organic framework.

    PubMed

    Huxley, Michael; Coghlan, Campbell J; Burgun, Alexandre; Tarzia, Andrew; Sumida, Kenji; Sumby, Christopher J; Doonan, Christian J

    2016-03-14

    The precise tuning of the structural and chemical features of microporous metal-organic frameworks (MOFs) is a crucial endeavour for developing materials with properties that are suitable for specific applications. In recent times, techniques for preparing frameworks consisting of mixed-metal or ligand compositions have emerged. However, controlled spatial organisation of the components within these structures at the molecular scale is a difficult challenge, particularly when species possessing similar geometries or chemical properties are used. Here, we describe the synthesis of mixed-metal and ligand variants possessing the Mn3L3 (Mn-MOF-1; H2L = bis(4-(4'-carboxyphenyl)-3,5-dimethylpyrazolyl)methane) structure type. In the case of mixed-ligand synthesis using a mixture of L and its trifluoromethyl-functionalised derivative (H2L' = bis(4-(4'-carboxyphenyl)-3,5-di(trifluoromethyl)pyrazolyl)methane), a mixed-ligand product in which the L' species predominanantly occupies the pillar sites lining the pores is obtained. Meanwhile, post-synthetic metal exchange of the parent Mn3L3 compound using Fe(2+) or Fe(3+) ions results in a degree of cation exchange at the trinuclear carboxylate-based clusters and metalation at the pillar bispyrazolate sites. The results demonstrate the versatility of the Mn3L3 structure type toward both metal and ligand substitutions, and the potential utility of site-specific functionalisations in achieving even greater precision in the tuning of MOFs.

  7. Triptycene-Based Chiral and meso-N-Heterocyclic Carbene Ligands and Metal Complexes.

    PubMed

    Savka, Roman; Bergmann, Marvin; Kanai, Yuki; Foro, Sabine; Plenio, Herbert

    2016-07-04

    Based on 1-amino-4-hydroxy-triptycene, new saturated and unsaturated triptycene-NHC (N-heterocyclic carbene) ligands were synthesized from glyoxal-derived diimines. The respective carbenes were converted into metal complexes [(NHC)MX] (M=Cu, Ag, Au; X=Cl, Br) and [(NHC)MCl(cod)] (M=Rh, Ir; cod=1,5-cyclooctadiene) in good yields. The new azolium salts and metal complexes suffer from limited solubility in common organic solvents. Consequently, the introduction of solubilizing groups (such as 2-ethylhexyl or 1-hexyl by O-alkylation) is essential to render the complexes soluble. The triptycene unit infers special steric properties onto the metal complexes that enable the steric shielding of selected areas close to the metal center. Next, chiral and meso-triptycene based N-heterocyclic carbene ligands were prepared. The key step in the synthesis of the chiral ligand is the Buchwald-Hartwig amination of 1-bromo-4-butoxy-triptycene with (1S,2S)-1,2-diphenyl-1,2-diaminoethane, followed by cyclization to the azolinium salt with HC(OEt)3 . The analogous reaction with meso-1,2-diphenyl-1,2-diaminoethane provides the respective meso-azolinium salt. Both the chiral and meso-azolinium salts were converted into metal complexes including [(NHC)AuCl], [(NHC)RhCl(cod)], [(NHC)IrCl(cod)], and [(NHC)PdCl(allyl)]. An in situ prepared chiral copper complex was tested in the enantioselective borylation of α,β-unsaturated esters and found to give an excellent enantiomeric ratio (er close to 90:10). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Half-sandwich complexes of iridium and ruthenium containing cysteine-derived ligands.

    PubMed

    Carmona, María; Rodríguez, Ricardo; Lahoz, Fernando J; García-Orduña, Pilar; Cativiela, Carlos; López, José A; Carmona, Daniel

    2017-01-17

    The dimers [{(η(n)-ring)MCl}2(μ-Cl)2] ((η(n)-ring)M = (η(5)-C5Me5)Ir, (η(6)-p-MeC6H4iPr)Ru) react with the modified cysteines S-benzyl-l-cysteine (HL1) or S-benzyl-α-methyl-l-cysteine (HL2) affording cationic complexes of the formula [(η(n)-ring)MCl(κ(2)N,S-HL)]Cl (1, 2) in good yield. Addition of NaHCO3 to complexes 1 and 2 gave equilibrium mixtures of neutral [(η(n)-ring)MCl(κ(2)N,O-L)] (3, 4) and cationic [(η(n)-ring)M(κ(3)N,O,S-L)]Cl (6Cl, 7Cl) complexes. Similar mixtures were obtained in one-pot reaction by successive addition of the modified cysteine and NaHCO3 to the above formulated dimers. Addition of the N-Boc substituted cysteine derivative S-benzyl-N-Boc-l-cysteine (HL3) and NaHCO3 to the dimers [{(η(n)-ring)MCl}2(μ-Cl)2] affords the neutral compounds [(η(n)-ring)MCl(κ(2)O,S-L3)] ((η(n)-ring)M = (η(5)-C5Me5)Ir (5a), (η(6)-p-MeC6H4iPr)Ru (5b)). Complexes of the formula [(η(n)-ring)MCl(κ(3)N,O,S-L)][SbF6] (6Sb-8Sb), in which the cysteine derivative acts as a tridentate chelate ligand, can be prepared by adding one equivalent of AgSbF6 to the solutions of compounds 5 or to the mixtures of complexes 3/6Cl and 4/7Cl. The amide proton of compounds 8aSb and 8bSb can be removed by addition of NaHCO3 affording the neutral complexes [(η(n)-ring)M(κ(3)N,O,S-L3-H)] ((η(n)-ring)M = (η(5)-C5Me5)Ir (9a), (η(6)-p-MeC6H4iPr)Ru (9b)). Complexes 9a and 9b can also be prepared by reacting the dimers [{(η(n)-ring)MCl}2(μ-Cl)2] with HL3 and two equivalents of NaHCO3. The absolute configuration of the complexes has been established by spectroscopic and diffractometric means including the crystal structure determination of (RIr,RC,RS)-[(η(5)-C5Me5)Ir(κ(3)N,O,S-L1)][SbF6] (6aSb). The thermodynamic parameters associated with the epimerization at sulphur that the iridium compound [(η(5)-C5Me5)Ir(κ(3)N,O,S-L3-H)] (9a) undergoes have been determined through variable temperature (1)H NMR studies.

  9. Relative Axial Ligand Orientation in Bis(imidazole)iron(II) Porphyrinates: Are “Picket Fence” Derivatives Different?

    PubMed Central

    Li, Jianfeng; Nair, Smitha M.; Noll, Bruce C.; Schulz, Charles E.; Scheidt, W. Robert

    2008-01-01

    The synthesis of three new bis(imidazole)-ligated iron(II) picket fence porphyrin derivatives, [Fe(TpivPP)(1-RIm)2] 1-RIm = 1-methyl-, 1-ethyl-, or 1-vinylimidazole) are reported. X-ray structure determinations reveal that the steric requirements of the four α,α,α,α-o-pivalamidophenyl groups lead to very restricted rotation of the imidazole ligand on the picket side of the porphyrin plane; the crowding leads to an imidazole plane orientation eclipsing an iron–porphyrin nitrogen bond. An unusual feature for these diamagnetic iron(II) species is that all three derivatives have the two axial ligands with a relative perpendicular orientation; the dihedral angles between the two imidazole planes are 77.2°, 62.4°, and 78.5°. All three derivatives have nearly planar porphyrin cores. Mössbauer spectroscopic characterization shows that all three derivatives have quadrupole splitting constants around 1.00 mm/s at 100K. PMID:18351735

  10. Rational Design and Synthesis of [5]Helicene-Derived Phosphine Ligands and Their Application in Pd-Catalyzed Asymmetric Reactions

    NASA Astrophysics Data System (ADS)

    Yamamoto, Kosuke; Shimizu, Takashi; Igawa, Kazunobu; Tomooka, Katsuhiko; Hirai, Go; Suemune, Hiroshi; Usui, Kazuteru

    2016-11-01

    A series of novel optically active [5]helicene-derived phosphine ligands (L1, with a 7,8-dihydro[5]helicene core structure- and L2, with a fully aromatic [5]helicene core structure) were synthesized. Despite their structural similarities, L1 and L2 exhibit particularly different characteristics in their use as chiral ligands. L1 was highly effective in the asymmetric allylation of indoles with 1,3-diphenylallyl acetate (up to 99% ee), and in the etherification of alcohols (up to 96% ee). In contrast, L2 was highly effective in the stereocontrol of helical chirality in Suzuki–Miyaura coupling (SMC) reaction (up to 99% ee). Density functional theory analysis was employed to propose a model that accounts for the origin of the enantioselectivity in these reactions.

  11. SERS Activity of Silver Nanoparticles Functionalized with A Desferrioxamine B Derived Ligand for FE(III) Binding and Sensing

    NASA Astrophysics Data System (ADS)

    Galinetto, P.; Taglietti, A.; Pasotti, L.; Pallavicini, P.; Dacarro, G.; Giulotto, E.; Grandi, M. S.

    2016-01-01

    We report the SERS activity of colloidal silver nanoparticles functionalized with a ligand, derived from the siderophore desferrioxamine B (desferal, DFO), an iron chelator widely used in biological and medical applications. The ligand was equipped with a sulfur-containing moiety to ensure optimal binding with silver surfaces. By means of Raman and SERS effects we monitored the route of material preparation from the modified DFO-S molecule to the colloidal aggregates. The results indicate that the functionalization of the chelating agent does not affect its binding ability towards Fe(III). The resulting functionalized silver nanoparticles are a promising SERS tag for operation in biological environments. The Fe-O stretching signature, arising when DFO-S grafted to silver nanoparticles binds Fe(III), could provide a tool for cation sensing in solution.

  12. Carbohydrate-derived 1,3-diphosphite ligands as chiral nanoparticle stabilizers: promising catalytic systems for asymmetric hydrogenation.

    PubMed

    Gual, Aitor; Godard, Cyril; Philippot, Karine; Chaudret, Bruno; Denicourt-Nowicki, Audrey; Roucoux, Alain; Castillón, Sergio; Claver, Carmen

    2009-01-01

    Metallic Ru, Rh, and Ir nanoparticles were prepared by the decomposition of organometallic precursors under H(2) pressure in the presence of 1,3-diphosphite ligands, derived from carbohydrates, as stabilizing agents. Structural modifications to the diphosphite backbone were found to influence the nanoparticles' size, dispersion, and catalytic activity. In the hydrogenation of o- and m-methylanisole, the Rh nanoparticles showed higher catalytic activity than the corresponding Ru nanoparticles. The Ir nanoparticles presented the lowest catalytic activity of the series. In all cases, the hydrogenation of o-methylanisole gave total selectivity for the cis-product, however, the ee of the product was always less than 6 %. A maximum of 81 % cis-selectivity was obtained for the hydrogenation of m-methylanisole, however, no asymmetric induction was observed. These results show that the catalytic activity is affected by a combination of influences from the substrate, the diphosphite ligands, and the metallic nanoparticles.

  13. Rational Design and Synthesis of [5]Helicene-Derived Phosphine Ligands and Their Application in Pd-Catalyzed Asymmetric Reactions

    PubMed Central

    Yamamoto, Kosuke; Shimizu, Takashi; Igawa, Kazunobu; Tomooka, Katsuhiko; Hirai, Go; Suemune, Hiroshi; Usui, Kazuteru

    2016-01-01

    A series of novel optically active [5]helicene-derived phosphine ligands (L1, with a 7,8-dihydro[5]helicene core structure- and L2, with a fully aromatic [5]helicene core structure) were synthesized. Despite their structural similarities, L1 and L2 exhibit particularly different characteristics in their use as chiral ligands. L1 was highly effective in the asymmetric allylation of indoles with 1,3-diphenylallyl acetate (up to 99% ee), and in the etherification of alcohols (up to 96% ee). In contrast, L2 was highly effective in the stereocontrol of helical chirality in Suzuki–Miyaura coupling (SMC) reaction (up to 99% ee). Density functional theory analysis was employed to propose a model that accounts for the origin of the enantioselectivity in these reactions. PMID:27824074

  14. Catalysts by the meter: rapid screening approach of N-heterocyclic carbene ligand based catalysts.

    PubMed

    Lang, Carolin; Gärtner, Ute; Trapp, Oliver

    2011-01-07

    Here, we demonstrate a versatile screening platform for NHC ligand based catalysts by coating fused-silica micro capillaries with a bonded 1,3-bismesityl-2-imidazolidinylidene ligand. Such micro capillaries can be efficiently converted into (pre)-catalysts from various organometallic precursors by solid-phase chemistry techniques and can be quantitatively screened using on-column reaction chromatography.

  15. Preparation of a functional fluorescent human Fas ligand extracellular domain derivative using a three-dimensional structure guided site-specific fluorochrome conjugation.

    PubMed

    Muraki, Michiro

    2016-01-01

    Human Fas ligand extracellular domain has been investigated as an important target protein in the field of medical biotechnology. In a recent study, the author developed an effective method to produce biologically active human Fas ligand extracellular domain derivatives using site-specific chemical modifications. A human Fas ligand extracellular domain derivative containing a reactive cysteine residue within its N-terminal tag sequence, which locates not proximal to the binding interface between the ligand and the receptor in terms of the three-dimensional structure, was modified by Fluorescein-5-Maleimide without impairing the specific binding activity toward human Fas receptor extracellular domain. The purified protein sample free of low molecular-weight contaminants showed a characteristic fluorescence spectrum derived from the attached Fluorescein moieties, and formed a stable binding complex with human Fas receptor extracellular domain-human IgG1 Fc domain fusion protein in solution. The conjugation number of the fluorochrome was estimated to be 2.5 per a single human Fas ligand extracellular domain trimer from the ratio of the absorbance value at 280 nm to that at 495 nm. A functional fluorescent human Fas ligand extracellular domain derivative was prepared via a site-specific conjugation of fluorochrome, which was guided by the three-dimensional structure information on the ligand-receptor complex. Fluorescent derivatives created by this method may contribute to the development of an improved diagnosis system for the diseases related to Fas receptor.

  16. Sensing of the concentration and enantiomeric excess of chiral compounds with tropos ligand derived metal complexes.

    PubMed

    Zhang, Peng; Wolf, Christian

    2013-08-11

    Palladium(II) complexes carrying chromophoric tropos ligands show a characteristic UV change and strong Cotton effects upon coordination of amino alcohols or diamines. The distinct (chir)optical responses can be used for instantaneous in situ determination of the concentration and ee of diamines and amino alcohols at low concentrations.

  17. Spectroscopic characterization of Lanthanoid derived from a hexadentate macrocyclic ligand: study on antifungal capacity of complexes.

    PubMed

    Chandra, Sulekh; Agrawal, Swati

    2014-04-24

    Complexes of Ce(III), Nd(III), Sm(III) and Eu(III) were synthesized with NO-donor macrocyclic ligand, i.e. 3,5,13,15,21,22-hexaaza-2,6,12,16-tetramethyl-4,14-dithia-tricyclo[15.3.1.1(7-11)]docosane-1(21),2,5,7,9,11(22),12,15,17,19-decaene. The ligand was obtained by the condensation of 2,6-diacetylpyridine with thiourea and characterized by elemental analysis, mass, IR and (1)H NMR spectral studies. All the complexes were characterized by elemental analyses, molar conductance measurements, magnetic susceptibility measurements, IR, mass, electronic spectral techniques and thermal studies. The ligand acts as a hexadentate and coordinated through four nitrogen atoms of azomethine groups and two nitrogen atoms of pyridine ring. The value of spectral parameters i.e. nephelauxetic effect (b), covalency factor (b(1/2)), Sinha parameter (δ%) and covalency angular overlap parameter (η) account for the covalent nature of the complexes. The macrocyclic ligand and its Lanthanoid were tested in vitro against two plant pathogenic fungi in order to assess their antifungal capacity.

  18. Two new metal-organic frameworks based on tetrazole-heterocyclic ligands accompanied by in situ ligand formation.

    PubMed

    Li, Qin; Yu, Mei-Hui; Xu, Jian; Li, Ai-Lin; Hu, Tong-Liang; Bu, Xian-He

    2017-03-07

    Based on the same in situ formed ligand, two new MOFs, namely {[Zn2(HL)2]·0.5DMF·H2O}n (1) and {[Cd2(HL)2]·1.5H2O}n (2) (H3L = 5-[(2H-tetrazol-5-yl)amino]isophthalic acid), have been solvothermally synthesized and structurally characterized by elemental analysis, IR, PXRD, and single-crystal X-ray diffraction. During the self-assembly process, the original ligand H2ATBDC (5-(5-amino-1H-tetrazol-1-yl)-1,3-benzenedicarboxylic acid) undergoes the Dimroth rearrangement to form a new ligand H3L, consequently contributing to the construction of the two new MOFs. Structural analysis reveals that both 1 and 2 possess a three-directional intersecting channel system and pts topology. The major structural difference between them is the metal coordination, which displays four- and six-coordinated modes in 1 and 2, respectively, and results in diverse channels and different stabilities. Moreover, the adsorption properties of 1a (i.e., the desolvated 1) have been studied, and the results show that 1a possesses moderate capability of gas sorption for N2, CO2, and CH4 gases, along with high selectivity ratios of 102 and 20 for CO2/N2 (15 : 85) and CO2/CH4 (50 : 50) at 273 K, respectively.

  19. Modulating structural dimensionality of cadmium(II) coordination polymers by means of pyrazole, tetrazole and pyrimidine derivative ligands

    NASA Astrophysics Data System (ADS)

    Seco, Jose Manuel; Calahorro, Antonio; Cepeda, Javier; Rodríguez-Diéguez, Antonio

    2015-06-01

    Six new compounds with functionalized pyrazole, tetrazole, and pyrimidine ligands, namely [Cd(μ-4-Hampz)(μ-Cl)2]n(1), [Cd(μ3-pzdc)(μ-H2O)(H2O)]n(2), [Cd(μ-5-amtz)2(eda)]n(3), {[Cd9(μ4-5-amtz)8(μ-Cl)10(H2O)2]ṡxH2O}n(4), {[Cd2(μ-dm2-pmc)2Cl2(H2O)2]ṡH2O}n(5), and [Cd2(μ-Br2-pmc)(μ-Cl)3(H2O)2]n(6) (where 4-Hampz = 4-aminopyrazole, pzdc = 3,5-pyrazoledicarboxylate, 5-amtz = 5-aminotetrazolate, eda = ethylenediamine, dm2-pmc = 4,6-dimethoxy-2-pyrimidinecarboxylate, Br2-pmc = 5-bromopyrimidine-2-carboxylate) have been synthesized under hydrothermal conditions and structurally characterized by single crystal X-ray diffraction. Compounds 1 and 2 share the structural feature of being constructed from dinuclear building units that are further connected through the pyrazole based ligands, rendering a compact and a potentially open 3D frameworks, respectively. On the other hand, 5-amtz ligand exhibits two different coordination modes in compounds 3 and 4 as a result of the presence or absence of an additional blocking ligand. In this way, the μ-κ4N,N‧,N″,N‴ mode in 4 affords robust clusters that are joined in a topologically novel 3D open architecture containing two types of channels, whereas a simple bidentate bridging mode is limited for 5-amtz in 3 due to the presence of the chelating eda ligand. 1D and 3D structures are obtained with pyrimidine ligands in compounds 5 and 6 according to the steric hindrance of the substituents.

  20. Antibacterial activity of Pd(II) complexes with salicylaldehyde-amino acids Schiff bases ligands.

    PubMed

    Rîmbu, Cristina; Danac, Ramona; Pui, Aurel

    2014-01-01

    Palladium(II) complexes with Schiff bases ligands derived from salicylaldehyde and amino acids (Ala, Gly, Met, Ser, Val) have been synthesized and characterized by Fourier transform (FT)-IR, UV-Vis and (1)H-NMR spectroscopy. The electrospray mass spectrometry (ES-MS) spectrometry confirms the formation of palladium(II) complexes in 1/2 (M/L) molar ratio. All the Pd(II) complexes 1, [Pd(SalAla)2]Cl2; 2, [Pd(SalGly)2]Cl2; 3, [Pd(SalMet)2]Cl2; 4, [Pd(SalSer)2]Cl2; 5, [Pd(SalVal)2]Cl2; have shown antibacterial activity against Gram-positive bacteria Staphylococcus aureus and Gram-negative bacteria Escherichia coli.

  1. Biferrocene-Based Diphosphine Ligands: Synthesis and Application of Walphos Analogues in Asymmetric Hydrogenations

    PubMed Central

    2013-01-01

    A total of four biferrocene-based Walphos-type ligands have been synthesized, structurally characterized, and tested in the rhodium-, ruthenium- and iridium-catalyzed hydrogenation of alkenes and ketones. Negishi coupling conditions allowed the biferrocene backbone of these diphosphine ligands to be built up diastereoselectively from the two nonidentical and nonracemic ferrocene fragments (R)-1-(N,N-dimethylamino)ethylferrocene and (SFc)-2-bromoiodoferrocene. The molecular structures of (SFc)-2-bromoiodoferrocene, the coupling product, two ligands, and the two complexes ([PdCl2(L)] and [RuCl(p-cymene)(L)]PF6) were determined by X-ray diffraction. The structural features of complexes and the catalysis results obtained with the newly synthesized biferrocene-based ligands were compared with those of the corresponding Walphos ligands. PMID:23457421

  2. Synthesis, crystal structure, fluorescence and electrochemical studies of a new tridentate Schiff base ligand and its nickel(II) and palladium(II) complexes

    NASA Astrophysics Data System (ADS)

    Shafaatian, Bita; Soleymanpour, Ahmad; Kholghi Oskouei, Nasim; Notash, Behrouz; Rezvani, Seyyed Ahmad

    2014-07-01

    A new unsymmetrical tridentate Schiff base ligand was derived from the 1:1 M condensation of ortho-vanillin with 2-mercaptoethylamine. Nickel and palladium complexes were obtained by the reaction of the tridentate Schiff base ligand with nickel(II) acetate tetrahydrate and palladium(II) acetate in 2:1 M ratio. In nickel and palladium complexes the ligand was coordinated to metals via the imine N and enolic O atoms. The S groups of Schiff bases were not coordinated to the metals and S-S coupling was occured. The complexes have been found to possess 1:2 Metal:Ligand stoichiometry and the molar conductance data revealed that the metal complexes were non-electrolytes. The complexes exhibited octahedral coordination geometry. The emission spectra of the ligand and its complexes were studied in methanol. Electrochemical properties of the ligand and its metal complexes were investigated in the CH3CN solvent at the 100 mV s-1 scan rate. The ligand and metal complexes showed both reversible and quasi-reversible processes at this scan rate. The Schiff base and its complexes have been characterized by IR, 1H NMR, UV/Vis, elemental analyses and conductometry. The crystal structure of nickel complex has been determined by single crystal X-ray diffraction.

  3. Synthesis, crystal structure, fluorescence and electrochemical studies of a new tridentate Schiff base ligand and its nickel(II) and palladium(II) complexes.

    PubMed

    Shafaatian, Bita; Soleymanpour, Ahmad; Kholghi Oskouei, Nasim; Notash, Behrouz; Rezvani, Seyyed Ahmad

    2014-07-15

    A new unsymmetrical tridentate Schiff base ligand was derived from the 1:1M condensation of ortho-vanillin with 2-mercaptoethylamine. Nickel and palladium complexes were obtained by the reaction of the tridentate Schiff base ligand with nickel(II) acetate tetrahydrate and palladium(II) acetate in 2:1M ratio. In nickel and palladium complexes the ligand was coordinated to metals via the imine N and enolic O atoms. The S groups of Schiff bases were not coordinated to the metals and S-S coupling was occured. The complexes have been found to possess 1:2 Metal:Ligand stoichiometry and the molar conductance data revealed that the metal complexes were non-electrolytes. The complexes exhibited octahedral coordination geometry. The emission spectra of the ligand and its complexes were studied in methanol. Electrochemical properties of the ligand and its metal complexes were investigated in the CH3CN solvent at the 100 mV s(-1) scan rate. The ligand and metal complexes showed both reversible and quasi-reversible processes at this scan rate. The Schiff base and its complexes have been characterized by IR, (1)H NMR, UV/Vis, elemental analyses and conductometry. The crystal structure of nickel complex has been determined by single crystal X-ray diffraction.

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  5. Syntheses, characterizations and structures of NO donor Schiff base ligands and nickel(II) and copper(II) complexes

    NASA Astrophysics Data System (ADS)

    Şenol, Cemal; Hayvali, Zeliha; Dal, Hakan; Hökelek, Tuncer

    2011-06-01

    New Schiff base derivatives ( L 1 and L 2) were prepared by the condensation of 2-hydroxy-3-methoxybenzaldehyde ( o-vanillin) and 3-hydroxy-4-methoxybenzaldehyde ( iso-vanillin) with 5-methylfurfurylamine. Two new complexes [Ni(L 1) 2] and [Cu(L 1) 2] have been synthesized with bidentate NO donor Schiff base ligand ( L 1). The Ni(II) and Cu(II) atoms in each complex are four coordinated in a square planar geometry. Schiff bases ( L 1 and L 2) and complexes [Ni(L 1) 2] and [Cu(L 1) 2] were characterized by elemental analyses, FT-IR, UV-vis, mass and 1H, 13C NMR spectroscopies. The crystal structures of the ligand ( L 2) and complexes [Ni(L 1) 2] and [Cu(L 1) 2] have also been determined by using X-ray crystallographic technique.

  6. Design synthesis and structure–activity relationship of 5-substituted (tetrahydronaphthalen-2yl)methyl with N-phenyl-N-(piperidin-2-yl) propionamide derivatives as opioid ligands

    PubMed Central

    Deekonda, Srinivas; Rankin, David; Davis, Peg; Lai, Josephine; Vanderah, Todd. W.; Porecca, Frank; Hruby, Victor J.

    2016-01-01

    Here, we report the design, synthesis and structure activity relationship of novel small molecule opioid ligands based on 5-amino substituted (tetrahydronaphthalen-2-yl)methyl moiety with N-phenyl-N-(piperidin-2-yl)propionamide derivatives. We synthesized various molecules including amino, amide and hydroxy substitution on the 5th position of the (tetrahydronaphthalen-2-yl)methyl moiety. In our further designs we replaced the (tetrahydronaphthalen-2-yl)methyl moiety with benzyl and phenethyl moiety. These N-phenyl-N-(piperidin-2-yl)propionamide analogues showed moderate to good binding affinities (850–4 nM) and were selective towards the μ opioid receptor over the δ opioid receptors. From the structure activity relationship studies, we found that a hydroxyl substitution at the 5th position of (tetrahydronapthalen-2yl)methyl group, ligands 19 and 20, showed excellent binding affinities 4 and 5 nM, respectively, and 1000 fold selectivity towards the μ opioid relative to the delta opioid receptor. The ligand 19 showed potent agonist activities 75 ± 21 nM, and 190 ± 42 nM in the GPI and MVD assays. Surprisingly the fluoro analogue 20 showed good agonist activities in MVD assays 170 ± 42 nM, in contrast to its binding affinity results. PMID:26712115

  7. Structure-Based Virtual Screening for Dopamine D2 Receptor Ligands as Potential Antipsychotics.

    PubMed

    Kaczor, Agnieszka A; Silva, Andrea G; Loza, María I; Kolb, Peter; Castro, Marián; Poso, Antti

    2016-04-05

    Structure-based virtual screening using a D2 receptor homology model was performed to identify dopamine D2 receptor ligands as potential antipsychotics. From screening a library of 6.5 million compounds, 21 were selected and were subjected to experimental validation. From these 21 compounds tested, ten D2 ligands were identified (47.6% success rate, among them D2 receptor antagonists, as expected) that have additional affinity for other receptors tested, in particular 5-HT2A receptors. The affinity (Ki values) of the compounds ranged from 58 nm to about 24 μM. Similarity and fragment analysis indicated a significant degree of structural novelty among the identified compounds. We found one D2 receptor antagonist that did not have a protonatable nitrogen atom, which is a key structural element of the classical D2 pharmacophore model necessary for interaction with the conserved Asp(3.32) residue. This compound exhibited greater than 20-fold binding selectivity for the D2 receptor over the D3 receptor. We provide additional evidence that the amide hydrogen atom of this compound forms a hydrogen bond with Asp(3.32), as determined by tests of its derivatives that cannot maintain this interaction. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. A bead-based proximity assay for BRD4 ligand discovery

    PubMed Central

    Roberts, Justin M.; Bradner, James E.

    2016-01-01

    Bromodomain-containing proteins have emerged as desirable targets for anti-neoplastic and anti-inflammatory drug discovery. Toward the development of selective inhibitors of the BET family of bromodomains, we optimized bead-based assays to detect interactions between bromodomains and poly-acetylated histone peptides. Donor and acceptor beads bound to target and ligand are brought into proximity by this protein-protein interaction. After laser illumination, singlet oxygen evolved from donor beads travels to the spatially close acceptor beads, resulting in chemiluminesence. This AlphaScreen assay has proven amendable to high-throughput screening, secondary validation, and specificity profiling during lead discovery and optimization. Here we report our protocol for assay development to measure inhibition of ligand binding to bromodomain containing protein 4 (BRD4). We discuss the discovery of an appropriate probe, optimization of bead, probe, and protein concentrations, and the derivation of protein-probe inhibition curves. Finally, we explore the implementation of this technology for high-throughput screening of potential BRD4 inhibitors. PMID:26629616

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

    NASA Astrophysics Data System (ADS)

    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

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

    PubMed

    Sugaya, Nobuyoshi

    2014-10-27

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

  11. Synthesis of new microbial pesticide metal complexes derived from coumarin-imine ligand

    NASA Astrophysics Data System (ADS)

    Elhusseiny, Amel F.; Aazam, Elham S.; Al-Amri, Huda M.

    2014-07-01

    A series of metal complexes of zinc(II), cadmium(II), copper(II), nickel(II) and palladium(II) have been synthesized from coumarin-imine ligand, 8-[(1E)-1-(2-aminophenyliminio)ethyl]-2-oxo-2H-chromen-7-olate, [HL]. The structures of the complexes were proposed in the light of their spectroscopic, molar conductance, magnetic and thermal studies. The ligand coordinated in a tridentate manner through the azomethine nitrogen, the phenolic oxygen and the amine nitrogen and all complexes were non-electrolytes with different geometrical arrangements around the central metal ion. Photoluminescence data unambiguously showed remarkable fluorescence enhancement to Zn2+ over other cations. The antimicrobial screening tests revealed that copper(II) complex exhibited the highest potency and its minimum inhibitory concentration on the enzymatic activities of the tested microbial species was determined. No toxin productivity was detected for all tested toxigenic species upon the exposure of copper complex.

  12. Hypercoordinate silicon complexes based on hydrazide ligands. A remarkably flexible molecular system.

    PubMed

    Kost, Daniel; Kalikhman, Inna

    2009-02-17

    Though only one row apart on the periodic table, silicon greatly differs from carbon in its ability to readily form five- and six-coordinate complexes, termed "hypercoordinate silicon compounds". The assorted chemistry of these compounds is varied in both structures and reactivity and has generated a flurry of innovative research endeavors in recent years. This Account summarizes the latest work done on a specific class of hypercoordinate silicon compounds, specifically those with two hydrazide-derived chelate rings. This family is especially interesting due to the ability to form multiple penta- and hexacoordinate complexes, the chemical reactivity of pentacoordinate complexes, and the observation of intermolecular ligand crossovers in hexacoordinate complexes. Pentacoordinate complexes in this family exhibit marked structural flexibility, as demonstrated by the construction of a complete hypothetical Berry-pseudorotation reaction coordinate generated from individual crystallographic molecular structures. Although hexacoordinate complexes generally crystallize as octahedra, with a decrease in the ligand donor strength the complexes can crystallize as bicapped tetrahedra. Hexacoordinate complexes bearing a halogen ligand undergo a solvent-driven equilibrium ionic dissociation, which is controlled by solvent, temperature, counterion, and chelate structure and has been directly demonstrated by conductivity measurements and temperature-dependent (29)Si NMR. Hexacoordinate silicon complexes can also undergo reversible neutral nonionic dissociation of the N-Si dative bond. Ionic pentacoordinate siliconium salts react readily via methyl halide elimination, initiated by their own counterion acting as a base. Pentacoordinate complexes can also undergo intramolecular aldol condensations of imines, which may find potential as a template for organic synthesis. In addition, these complexes are capable of performing an uncatalyzed intramolecular hydrosilylation of imine double

  13. Physics-based scoring of protein-ligand interactions: explicit polarizability, quantum mechanics and free energies.

    PubMed

    Bryce, Richard A

    2011-04-01

    The ability to accurately predict the interaction of a ligand with its receptor is a key limitation in computer-aided drug design approaches such as virtual screening and de novo design. In this article, we examine current strategies for a physics-based approach to scoring of protein-ligand affinity, as well as outlining recent developments in force fields and quantum chemical techniques. We also consider advances in the development and application of simulation-based free energy methods to study protein-ligand interactions. Fuelled by recent advances in computational algorithms and hardware, there is the opportunity for increased integration of physics-based scoring approaches at earlier stages in computationally guided drug discovery. Specifically, we envisage increased use of implicit solvent models and simulation-based scoring methods as tools for computing the affinities of large virtual ligand libraries. Approaches based on end point simulations and reference potentials allow the application of more advanced potential energy functions to prediction of protein-ligand binding affinities. Comprehensive evaluation of polarizable force fields and quantum mechanical (QM)/molecular mechanical and QM methods in scoring of protein-ligand interactions is required, particularly in their ability to address challenging targets such as metalloproteins and other proteins that make highly polar interactions. Finally, we anticipate increasingly quantitative free energy perturbation and thermodynamic integration methods that are practical for optimization of hits obtained from screened ligand libraries.

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

    SciTech Connect

    Li, Jin-Feng; Sun, Yin-Yin; Li, Miao-Miao; Li, Jian-Li; Yin, Bing; Bai, Hongcun

    2015-06-15

    The superhalogen properties of polynuclear structures without halogen ligand are theoretically explored here for several [M{sub 2}(CN){sub 5}]{sup −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 [Ca{sub 2}(CN){sub 5}]{sup −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.

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

    NASA Astrophysics Data System (ADS)

    Li, Jin-Feng; Sun, Yin-Yin; Bai, Hongcun; Li, Miao-Miao; Li, Jian-Li; Yin, Bing

    2015-06-01

    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.

  16. Ligand Docking and Virtual Screening in Structure-based Drug Discovery

    NASA Astrophysics Data System (ADS)

    Cavasotto, Claudio N.

    2006-08-01

    As the number of high-resolution three-dimensional protein and nucleic acid structures continues to grow, ligand-docking—based virtual screening of chemical libraries to a receptor are playing a critical role in the drug discovery process by identifying new `drug-candidates'. The capability to correctly predict ligand-protein interaction is fundamental to any accurate docking algorithm and the necessary starting point for any reliable virtual screening protocol. Furthermore, explicit consideration of receptor flexibility in computational ligand docking is emerging in many cases as crucial for an accurate prediction of the orientation and interactions of ligands within the binding pocket. The combination of ligand docking with a fast scoring algorithm that can account for the thermodynamics of binding, and discriminate between potential active/inactive compounds, can greatly reduced the number of compounds to be tested experimentally, while predicting a detailed structure of hits bound to the receptor useful enough to help the synthetic elaboration of leads.

  17. A proline-based aminophenol ligand: synthesis, iron complexation, magnetic, electronic and redox investigation.

    PubMed

    Sheykhi, Hamid; Safaei, Elham

    2014-01-24

    A new proline-based aminophenol ligand was synthesized by a convenient procedure. The ligand was characterized by (1)H NMR, (13)C NMR and IR spectroscopies, elemental analysis and optical activity measurements. Mononuclear iron(III) complex (FeL(Pro)) of this ligand was synthesized and characterized by IR, UV-vis, ESI-MS, magnetic susceptibility studies and cyclic voltammetry techniques. The equilibrium formation constant of FeL(Pro) and the pure UV-vis spectral profile of the complex was determined by multivariate hard modeling method. The molecular structure of FeL(Pro) determined by ESI-MS consist of two aminophenolate ligands. The variation of magnetic susceptibility with temperature indicates paramagnetic iron(III) in the monomeric complex. FeL(Pro) complex undergo metal-centered reduction, and ligand-centered oxidation. Copyright © 2013 Elsevier B.V. All rights reserved.

  18. Structural insights into the coordination and extraction of Pb(II) by disulfonamide ligands derived from o-phenylenediamine.

    PubMed

    Alvarado, Robert J; Rosenberg, Jay M; Andreu, Aileen; Bryan, Jeffrey C; Chen, Wei-Zhong; Ren, Tong; Kavallieratos, Konstantinos

    2005-10-31

    The o-phenylenediamine-derived disulfonamide ligands 1 and 2 complex and efficiently extract Pb(II) from water into 1,2-dichloroethane via ion-exchange, in combination with 2,2'-bipyridine (97.5% and 95.0%, respectively, for 1:1 ligand-to-Pb ratios). The corresponding Pb(II)-sulfonamido binary complexes of ligands 1 and 2 (3 and 4, respectively), and ternary complexes with 2,2'-bipyridine (5 and 6, respectively), were isolated and characterized. (1)H NMR spectra of the organic phases after extraction show the formation of ternary Pb-sulfonamido-bipy complexes. X-ray characterization of 3, 4, and the ternary complex 5 consistently demonstrates four primary coordination sites and a stereochemically active lone pair on Pb. The X-ray structure of 3 shows a pseudo trigonal bipyramidal configuration on Pb, with the lone pair occupying one of the equatorial sites, and the formation of an unusual "hemidirected" coordination polymer via axial S=O-Pb coordination. The same axial S=O-Pb coordination pattern with two DMSO molecules is observed in the structure of 4.[2(CH(3))(2)SO)], thus rationalizing the high solubility of the binary complexes in strongly coordinating solvents. In contrast, the X-ray structure of the ternary complex 5 reveals a distorted four-coordinate configuration with only weak S=O-Pb coordination leading to dimer formation, thus explaining its higher solubility in weakly coordinating solvents. FT-IR spectroscopy confirms the X-ray data, since the ligand nu(S)(=)(O) stretching frequencies shift to lower values in the binary Pb(II)-sulfonamido complexes and are again altered upon formation of the ternary Pb(II)-sulfonamido-bipy complexes, as would be expected for 2,2'-bipy complexation and hindered S=O-Pb coordination.

  19. The CXC Chemokine Receptor 4 Ligands Ubiquitin and Stromal Cell-derived Factor-1α Function through Distinct Receptor Interactions*

    PubMed Central

    Saini, Vikas; Staren, Daniel M.; Ziarek, Joshua J.; Nashaat, Zayd N.; Campbell, Edward M.; Volkman, Brian F.; Marchese, Adriano; Majetschak, Matthias

    2011-01-01

    Recently, we identified extracellular ubiquitin as an endogenous CXC chemokine receptor (CXCR) 4 agonist. However, the receptor selectivity and molecular basis of the CXCR4 agonist activity of ubiquitin are unknown, and functional consequences of CXCR4 activation with ubiquitin are poorly defined. Here, we provide evidence that ubiquitin and the cognate CXCR4 ligand stromal cell-derived factor (SDF)-1α do not share CXCR7 as a receptor. We further demonstrate that ubiquitin does not utilize the typical two-site binding mechanism of chemokine-receptor interactions, in which the receptor N terminus is important for ligand binding. CXCR4 activation with ubiquitin and SDF-1α lead to similar Gαi-responses and to a comparable magnitude of phosphorylation of ERK-1/2, p90 ribosomal S6 kinase-l and Akt, although phosphorylations occur more transiently after activation with ubiquitin. Despite the similarity of signal transduction events after activation of CXCR4 with both ligands, ubiquitin possesses weaker chemotactic activity than SDF-lα in cell migration assays and does not interfere with productive entry of HIV-1 into P4.R5 multinuclear activation of galactosidase indicator cells. Unlike SDF-1α, ubiquitin lacks interactions with an N-terminal CXCR4 peptide in NMR spectroscopy experiments. Binding and signaling studies in the presence of antibodies against the N terminus and extracellular loops 2/3 of CXCR4 confirm that the ubiquitin CXCR4 interaction is independent of the N-terminal receptor domain, whereas blockade of extracellular loops 2/3 prevents receptor binding and activation. Our findings define ubiquitin as a CXCR4 agonist, which does not interfere with productive cellular entry of HIV-1, and provide new mechanistic insights into interactions between CXCR4 and its natural ligands. PMID:21757744

  20. Chemically Induced Degradation of Sirtuin 2 (Sirt2) by a Proteolysis Targeting Chimera (PROTAC) Based on Sirtuin Rearranging Ligands (SirReals).

    PubMed

    Schiedel, Matthias; Herp, Daniel; Hammelmann, Sören; Swyter, Sören; Lehotzky, Attila; Robaa, Dina; Oláh, Judit; Ovádi, Judit; Sippl, Wolfgang; Jung, Manfred

    2017-04-17

    Here we report the development of a proteolysis targeting chimera (PROTAC) based on the combination of the unique features of the sirtuin rearranging ligands (SirReals) as highly potent and isotype-selective Sirt2 inhibitors with thalidomide, a bona fide cereblon ligand. For the first time, we report the formation of a PROTAC by Cu(I)-catalyzed cycloaddition of a thalidomide-derived azide to an alkynylated inhibitor. This thalidomide-derived azide as well as the highly versatile linking strategy can be readily adapted to alkynylated ligands of other targets. In HeLa cells, our SirReal-based PROTAC induced isotype-selective Sirt2 degradation that results in the hyperacetylation of the microtubule network coupled with enhanced process elongation. Thus, our SirReal-based PROTAC is the first example of a probe that is able to chemically induce the degradation of an epigenetic eraser protein.

  1. Reviewing Ligand-Based Rational Drug Design: The Search for an ATP Synthase Inhibitor

    PubMed Central

    Lee, Chia-Hsien; Huang, Hsuan-Cheng; Juan, Hsueh-Fen

    2011-01-01

    Following major advances in the field of medicinal chemistry, novel drugs can now be designed systematically, instead of relying on old trial and error approaches. Current drug design strategies can be classified as being either ligand- or structure-based depending on the design process. In this paper, by describing the search for an ATP synthase inhibitor, we review two frequently used approaches in ligand-based drug design: The pharmacophore model and the quantitative structure-activity relationship (QSAR) method. Moreover, since ATP synthase ligands are potentially useful drugs in cancer therapy, pharmacophore models were constructed to pave the way for novel inhibitor designs. PMID:21954360

  2. Macrophage-derived Hedgehog Ligands Promotes Fibrogenic and Angiogenic Responses in Human Schistosomiasis mansoni

    PubMed Central

    Pereira, Thiago A.; Xie, Guanhua; Choi, Steve S.; Syn, Wing-Kin; Voieta, Izabela; Lu, Jiuyi; Chan, Isaac S.; Swiderska, Marzena; Amaral, Kirsten B.; Antunes, Carlos Maurício; Secor, William E.; Witek, Rafal P.; Lambertucci, José Roberto; Pereira, Fausto L.; Diehl, Anna Mae

    2012-01-01

    Background Schistosomiasis mansoni is a major cause of portal fibrosis and portal hypertension. The Hedgehog pathway regulates fibrogenic repair in some types of liver injury. Aims Determine if Hedgehog-pathway activation occurs during fibrosis progression in schistosomiasis and to determine if macrophage-related mechanisms are involved. Methods Immunohistochemistry was used to characterize the cells that generate and respond to Hedgehog ligands in 28 liver biopsies from patients with different grades of schistosomiasis fibrosis staged by ultrasound. Cultured macrophages (RAW264.7 and primary rat Kupffer cells) and primary rat liver sinusoidal endothelial cells (LSEC) were treated with schistosome egg antigen (SEA) and evaluated by qRT-PCR. Inhibition of the Hedgehog-pathway was used to investigate its role in alternative activation of macrophages (M2) and vascular tube formation. Results Patients with schistosomiasis expressed more ligands (Shh and Ihh) and target genes (Patched and Gli2) than healthy individuals. Activated LSEC and myofibroblasts were Hedgehog-responsive (Gli2(+)) and accumulated in parallel with fibrosis stage (p<0.05). Double IHC for Ihh/CD68 showed that Ihh(+) cells were macrophages. In vitro studies demonstrated that SEA stimulated macrophages to express Ihh and Shh mRNA (p<0.05). Conditioned media from such macrophages induced luciferase production by Shh-LightII cells (p<0.001) and Hedgehog inhibitors blocked this effect (p<0.001). SEA-treated macrophages also up-regulated their own expression of M2 markers, and Hh-pathway inhibitors abrogated this response (p<0.01). Inhibition of the Hedgehog pathway in LSEC blocked SEA-induced migration and tube formation. Conclusion SEA stimulates liver macrophages to produce Hh-ligands, which promote alternative activation of macrophages, fibrogenesis, and vascular remodeling in schistosomiasis. PMID:23121638

  3. Macrophage-derived Hedgehog ligands promotes fibrogenic and angiogenic responses in human schistosomiasis mansoni.

    PubMed

    Pereira, Thiago A; Xie, Guanhua; Choi, Steve S; Syn, Wing-Kin; Voieta, Izabela; Lu, Jiuyi; Chan, Isaac S; Swiderska, Marzena; Amaral, Kirsten B; Antunes, Carlos M; Secor, William E; Witek, Rafal P; Lambertucci, José R; Pereira, Fausto L; Diehl, Anna Mae

    2013-01-01

    Schistosomiasis mansoni is a major cause of portal fibrosis and portal hypertension. The Hedgehog pathway regulates fibrogenic repair in some types of liver injury. Determine if Hedgehog pathway activation occurs during fibrosis progression in schistosomiasis and to determine if macrophage-related mechanisms are involved. Immunohistochemistry was used to characterize the cells that generate and respond to Hedgehog ligands in 28 liver biopsies from patients with different grades of schistosomiasis fibrosis staged by ultrasound. Cultured macrophages (RAW264.7 and primary rat Kupffer cells) and primary rat liver sinusoidal endothelial cells (LSEC) were treated with schistosome egg antigen (SEA) and evaluated using qRT-PCR. Inhibition of the Hedgehog pathway was used to investigate its role in alternative activation of macrophages (M2) and vascular tube formation. Patients with schistosomiasis expressed more ligands (Shh and Ihh) and target genes (Patched and Gli2) than healthy individuals. Activated LSEC and myofibroblasts were Hedgehog responsive [Gli2(+)] and accumulated in parallel with fibrosis stage (P < 0.05). Double IHC for Ihh/CD68 showed that Ihh(+) cells were macrophages. In vitro studies demonstrated that SEA-stimulated macrophages to express Ihh and Shh mRNA (P < 0.05). Conditioned media from such macrophages induced luciferase production by Shh-LightII cells (P < 0.001) and Hedgehog inhibitors blocked this effect (P < 0.001). SEA-treated macrophages also up-regulated their own expression of M2 markers, and Hh pathway inhibitors abrogated this response (P < 0.01). Inhibition of the Hedgehog pathway in LSEC blocked SEA-induced migration and tube formation. SEA stimulates liver macrophages to produce Hh ligands, which promote alternative activation of macrophages, fibrogenesis and vascular remodelling in schistosomiasis. © 2012 John Wiley & Sons A/S.

  4. Mononuclear mercury(II) complexes containing bipyridine derivatives and thiocyanate ligands: Synthesis, characterization, crystal structure determination, and luminescent properties

    NASA Astrophysics Data System (ADS)

    Amani, Vahid; Alizadeh, Robabeh; Alavije, Hanieh Soleimani; Heydari, Samira Fadaei; Abafat, Marzieh

    2017-08-01

    A series of mercury(II) complexes, [Hg(Nsbnd N)(SCN)2] (Nsbnd N is 4,4‧-dimethyl-2,2‧-bipyridine in 1, 5,5‧-dimethyl-2,2‧-bipyridine in 2, 6,6‧-dimethyl-2,2‧-bipyridine in 3 and 6-methyl-2,2‧-bipyridine in 4), were prepared from the reactions of Hg(SCN)2 with mentioned ligands in methanol. Suitable crystals of these complexes were obtained for X-ray diffraction measurement by methanol diffusion into a DMSO solution. The four complexes were thoroughly characterized by spectral methods (IR, UV-Vis, 13C{1H}NMR, 1H NMR and luminescence), elemental analysis (CHNS) and single crystal X-ray diffraction. The X-ray structural analysis indicated that in the structures of these complexes, the mercury(II) cation is four-coordinated in a distorted tetrahedral configuration by two S atoms from two thiocyanate anions and two N atoms from one chelating 2,2‧-bipyridine derivative ligand. Also, in these complexes intermolecular interactions, for example Csbnd H⋯N hydrogen bonds (in 1-4), Csbnd H⋯S hydrogen bonds (in 1, 2 and 4), π … π interactions (in 2-4), Hg⋯N interactions (in 2) and S⋯S interactions (in 4), are effective in the stabilization of the crystal structures and the formation of the 3D supramolecular complexes. Furthermore, the luminescence spectra of the title complexes show that the intensity of their emission bands are stronger than the emission bands for the free bipyridine derivative ligands.

  5. Substituted phenylhydrazono derivatives of curcumin as new ligands, a theoretical study

    NASA Astrophysics Data System (ADS)

    Arrue, Lily; Zarate, Ximena; Schott-Verdugo, Stephan; Schott, Eduardo

    2015-03-01

    A family of phenylhydrazono curcumin ligands was studied to see the influence of the substituents over the composition of the molecular orbitals, electronic transitions and reactivity by means of DFT and TDDFT calculations. The substituents varied between electron-donor groups (EDG) to electron-withdrawing groups (EWG). The geometrical parameters remain almost unchanged when the character of the substituent was changed. On the other hand the HOMO, LUMO and HOMO-LUMO gap (HLG) energies changed dramatically. TDDFT calculations were performed in order to propose the main absorption bands of this family of compounds. All the obtained showed a good correlation with a Hammett correlation.

  6. New synthesis of a high molecular weight ligand derived from dota; thermodynamic stability of the MRI contrast agent formed with gadolinium.

    PubMed

    Pierrard, Jean-Claude; Rimbault, Jean; Aplincourt, Michel; Le Greneur, Soizic; Port, Marc

    2008-01-01

    The new total synthesis in four steps of the compound P1041 is reported. This compound is a high molecular mass ligand (MW 6.32 kDa) derived from dota in which the four substituents are hydroxylated and contain amidic groups. The attribution of the nine protonation constants of P1041 is based on the comparison with the behaviour of the precursor ligands dota and tced, a tetracarboxylated derivative of dota. From these results, the studies of the systems P1041/Na(+) and P1041/Gd(3+) lead to the determination of the stability constants corresponding to the three species Na(P1041)H(h) (h = 0, 2 or 4) and to the five complexes Gd(P1041)H(h) (h = 0, 2, 3, 4 or 5). The complexing ability of P1041 towards Gd(3+) is compared with those of dota and tced. At physiological pH = 7.4, the very stable species Gd(P1041)H(4) (-) (currently named P792 in the literature) of this rapid clearance blood pool agent is predominant. (c) 2008 John Wiley & Sons, Ltd.

  7. Incorporating Virtual Reactions into a Logic-based Ligand-based Virtual Screening Method to Discover New Leads.

    PubMed

    Reynolds, Christopher R; Muggleton, Stephen H; Sternberg, Michael J E

    2015-09-01

    The use of virtual screening has become increasingly central to the drug development pipeline, with ligand-based virtual screening used to screen databases of compounds to predict their bioactivity against a target. These databases can only represent a small fraction of chemical space, and this paper describes a method of exploring synthetic space by applying virtual reactions to promising compounds within a database, and generating focussed libraries of predicted derivatives. A ligand-based virtual screening tool Investigational Novel Drug Discovery by Example (INDDEx) is used as the basis for a system of virtual reactions. The use of virtual reactions is estimated to open up a potential space of 1.21×10(12) potential molecules. A de novo design algorithm known as Partial Logical-Rule Reactant Selection (PLoRRS) is introduced and incorporated into the INDDEx methodology. PLoRRS uses logical rules from the INDDEx model to select reactants for the de novo generation of potentially active products. The PLoRRS method is found to increase significantly the likelihood of retrieving molecules similar to known actives with a p-value of 0.016. Case studies demonstrate that the virtual reactions produce molecules highly similar to known actives, including known blockbuster drugs.

  8. Cancer cell–derived microparticles bearing P-selectin glycoprotein ligand 1 accelerate thrombus formation in vivo

    PubMed Central

    Thomas, Grace M.; Panicot-Dubois, Laurence; Lacroix, Romaric; Dignat-George, Françoise; Lombardo, Dominique

    2009-01-01

    Recent publications have demonstrated the presence of tissue factor (TF)–bearing microparticles (MPs) in the blood of patients suffering from cancer. However, whether these MPs are involved in thrombosis remains unknown. We show that pancreatic and lung cancer cells produce MPs that express active TF and P-selectin glycoprotein ligand 1 (PSGL-1). Cancer cell–derived MPs aggregate platelets via a TF-dependent pathway. In vivo, cancer cell–derived MPs, but not their parent cells, infused into a living mouse accumulate at the site of injury and reduce tail bleeding time and the time to occlusion of venules and arterioles. This thrombotic state is also observed in mice developing tumors. In such mice, the amount of circulating platelet-, endothelial cell–, and cancer cell–derived MPs is increased. Endogenous cancer cell–derived MPs shed from the growing tumor are able to accumulate at the site of injury. Infusion of a blocking P-selectin antibody abolishes the thrombotic state observed after injection of MPs or in mice developing a tumor. Collectively, our results indicate that cancer cell–derived MPs bearing PSGL-1 and TF play a key role in thrombus formation in vivo. Targeting these MPs could be of clinical interest in the prevention of thrombosis and to limit formation of metastasis in cancer patients. PMID:19667060

  9. Development of purely structure-based pharmacophores for the topoisomerase I-DNA-ligand binding pocket

    NASA Astrophysics Data System (ADS)

    Drwal, Malgorzata N.; Agama, Keli; Pommier, Yves; Griffith, Renate

    2013-12-01

    Purely structure-based pharmacophores (SBPs) are an alternative method to ligand-based approaches and have the advantage of describing the entire interaction capability of a binding pocket. Here, we present the development of SBPs for topoisomerase I, an anticancer target with an unusual ligand binding pocket consisting of protein and DNA atoms. Different approaches to cluster and select pharmacophore features are investigated, including hierarchical clustering and energy calculations. In addition, the performance of SBPs is evaluated retrospectively and compared to the performance of ligand- and complex-based pharmacophores. SBPs emerge as a valid method in virtual screening and a complementary approach to ligand-focussed methods. The study further reveals that the choice of pharmacophore feature clustering and selection methods has a large impact on the virtual screening hit lists. A prospective application of the SBPs in virtual screening reveals that they can be used successfully to identify novel topoisomerase inhibitors.

  10. Synthesis and characterization of cerium and yttrium alkoxide complexes supported by ferrocene-based chelating ligands.

    PubMed

    Broderick, Erin M; Thuy-Boun, Peter S; Guo, Neng; Vogel, Carola S; Sutter, Jörg; Miller, Jeffrey T; Meyer, Karsten; Diaconescu, Paula L

    2011-04-04

    Two series of Schiff base metal complexes were investigated, where each series was supported by an ancillary ligand incorporating a ferrocene backbone and different N=X functionalities. One ligand is based on an imine, while the other is based on an iminophosphorane group. Cerium(IV), cerium(III), and yttrium(III) alkoxide complexes supported by the two ligands were synthesized. All metal complexes were characterized by cyclic voltammetry. Additionally, NMR, Mössbauer, X-ray absorption near-edge structure (XANES), and absorption spectroscopies were used. The experimental data indicate that iron remains in the +2 oxidation state and that cerium(IV) does not engage in a redox behavior with the ancillary ligand.

  11. Ligand-decorated click polypeptide derived nanoparticles for targeted drug delivery applications.

    PubMed

    Quadir, Mohiuddin A; Morton, Stephen W; Mensah, Lawrence B; Shopsowitz, Kevin; Dobbelaar, Jeroen; Effenberger, Nicole; Hammond, Paula T

    2017-03-02

    A ligand decorated, synthetic polypeptide block copolymer platform with environment-responsive capabilities was designed. We evaluated the potential of this system to function as a polymersome for targeted-delivery of a systemic chemotherapy to tumors. Our system employed click chemistry to provide a pH-responsive polypeptide block that drives nanoparticle assembly, and a ligand (folic acid) conjugated PEG block that targets folate-receptor over-expressing cancer cells. These nanocarriers were found to encapsulate a high loading of conventional chemotherapeutics (e.g. doxorubicin at physiological pH) and release the active therapeutic at lysosomal pH upon cellular uptake. The presence of folic acid on the nanoparticle surface facilitated their active accumulation in folate-receptor-overexpressing cancer cells (KB), compared to untargeted carriers. Folate-targeted nanoparticles loaded with doxorubicin also showed enhanced tumor accumulation in folate-receptor positive KB xenografts, resulting in the suppression of tumor growth in an in vivo hind flank xenograft mouse model.

  12. Uranyl Carboxyphosphonates Derived from Hydrothermal in Situ Ligand Reaction: Syntheses, Structures, and Computational Investigations.

    PubMed

    Wu, Dai; Bai, Xiaojing; Tian, Hong-Rui; Yang, Weiting; Li, Zewen; Huang, Qing; Du, Shiyu; Sun, Zhong-Ming

    2015-09-08

    Two uranyl carboxyphosphonates (H2dipy)[(UO2)3(H2O)2(H2DPTP)2]·2H2O (DPTP-U1) and (H2bbi)[(UO2)4(H2O)2(HDPTP)2] (DPTP-U2) [H6DPTP = 2,5-diphosphonoterephthalic acid, dipy = 4,4'-bipyridine, bbi = 1,1'-(1,4-butanediyl)bis(imidazole)] were synthesized under hydrothermal conditions. The carboxyphosphonate ligand was formed through the in situ oxidation of (2,5-dimethyl-1,4-phenylene)diphosphonic acid mediated by UO2(2+). Single-crystal X-ray diffraction analyses reveal that DPTP-U1 possesses uranyl carboxyphosphonate layers that are separated by protonated dipy cations. Whereas DPTP-U2 is in a three-dimensional framework structure with channels filled by protonated bbi cations. The computational investigations give an insight into the nature of bonding interactions between uranium(VI) and carboxyphosphonate ligand. The spectroscopic properties were also studied.

  13. Nickel Complexes of a Binucleating Ligand Derived from an SCS Pincer

    SciTech Connect

    Peterson, Sonja M.; Helm, Monte L.; Appel, Aaron M.

    2015-01-01

    A binucleating ligand has been prepared that contains an SCS pincer and three oxygen donor ligands in a partial crown ether loop. To enable metalation with Ni0, a bromoarene precursor was used and resulted in the formation of a nickel-bromide complex in the SCS pincer. Reaction of the nickel complex with a lithium salt yielded a heterobimetallic complex with bromide bridging the two metal centers. The solid-state structures were determined for this heterobimetallic complex and the nickel-bromide precursor, and the two complexes were characterized electrochemically to determine the influence of coordinating the second metal. This research was supported by the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. MLH was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle.

  14. A python-based docking program utilizing a receptor bound ligand shape: PythDock.

    PubMed

    Chung, Jae Yoon; Cho, Seung Joo; Hah, Jung-Mi

    2011-09-01

    PythDock is a heuristic docking program that uses Python programming language with a simple scoring function and a population based search engine. The scoring function considers electrostatic and dispersion/repulsion terms. The search engine utilizes a particle swarm optimization algorithm. A grid potential map is generated using the shape information of a bound ligand within the active site. Therefore, the searching area is more relevant to the ligand binding. To evaluate the docking performance of PythDock, two well-known docking programs (AutoDock and DOCK) were also used with the same data. The accuracy of docked results were measured by the difference of the ligand structure between x-ray structure, and docked pose, i.e., average root mean squared deviation values of the bound ligand were compared for fourteen protein-ligand complexes. Since the number of ligands' rotational flexibility is an important factor affecting the accuracy of a docking, the data set was chosen to have various degrees of flexibility. Although PythDock has a scoring function simpler than those of other programs (AutoDock and DOCK), our results showed that PythDock predicted more accurate poses than both AutoDock4.2 and DOCK6.2. This indicates that PythDock could be a useful tool to study ligand-receptor interactions and could also be beneficial in structure based drug design.

  15. PoLi: A Virtual Screening Pipeline Based On Template Pocket And Ligand Similarity

    PubMed Central

    Roy, Ambrish; Srinivasan, Bharath; Skolnick, Jeffrey

    2015-01-01

    Often in pharmaceutical research, the goal is to identify small molecules that can interact with and appropriately modify the biological behavior of a new protein target. Unfortunately, most proteins lack both known structures and small molecule binders, prerequisites of many virtual screening, VS, approaches. For such proteins, ligand homology modeling, LHM, that copies ligands from homologous and perhaps evolutionarily distant template proteins, has been shown to be a powerful VS approach to identify possible binding ligands. However, if we want to target a specific pocket for which there is no homologous holo template protein structure, then LHM will not work. To address this issue, in a new pocket based approach, PoLi, we generalize LHM by exploiting the fact that the number of distinct small molecule ligand binding pockets in proteins is small. PoLi identifies similar ligand binding pockets in a holo-template protein library, selectively copies relevant parts of template ligands and uses them for VS. In practice, PoLi is a hybrid structure and ligand based VS algorithm that integrates 2D fingerprint-based and 3D shape-based similarity metrics for improved virtual screening performance. On standard DUD and DUD-E benchmark databases, using modeled receptor structures, PoLi achieves an average enrichment factor of 13.4 and 9.6 respectively, in the top 1% of the screened library. In contrast, traditional docking based VS using AutoDock Vina and homology-based VS using FINDSITEfilt have an average enrichment of 1.6 (3.0) and 9.0 (7.9) on the DUD (DUD-E) sets respectively. Experimental validation of PoLi predictions on dihydrofolate reductase, DHFR, using differential scanning fluorimetry, DSF, identifies multiple ligands with diverse molecular scaffolds, thus demonstrating the advantage of PoLi over current state-of-the-art VS methods. PMID:26225536

  16. First examples of hybrids based on polyoxometalates, metal halide clusters and organic ligands

    SciTech Connect

    Wang Lamei; Fan Yong; Wang Yan; Xiao Lina; Hu Yangyang; Peng Yu; Wang Tiegang; Gao Zhongmin; Zheng Dafang; Cui Xiaobing; Xu Jiqing

    2012-07-15

    Two new organic-inorganic compounds based on polyoxometalates, metal halide clusters and organic ligands: [BW{sub 12}O{sub 40}]{sub 2}[Cu{sub 2}(Phen){sub 4}Cl](H{sub 2}4, 4 Prime -bpy){sub 4}{center_dot}H{sub 3}O{center_dot}5H{sub 2}O (1) and [HPW{sub 12}O{sub 40}][Cd{sub 2}(Phen){sub 4}Cl{sub 2}](4, 4 Prime -bpy) (2) (Phen=1, 10-phenanthroline, bpy=bipyridine), have been prepared and characterized by IR, UV-vis, XPS, XRD and single crystal X-ray diffraction analyses. Crystal structure analyses reveal that compound 1 is constructed from [BW{sub 12}O{sub 40}]{sup 5-}, metal halide clusters [Cu{sub 2}(Phen){sub 4}Cl]{sup +}and 4, 4 Prime -bpy ligands, while compound 2 is constructed from [PW{sub 12}O{sub 40}]{sup 3-}, metal halide cluster [Cd{sub 2}(Phen){sub 4}Cl{sub 2}]{sup 2+} and 4, 4 Prime -bpy ligands. Compound 1 and compound 2 are not common hybrids based on polyoxometalates and metal halide clusters, they also contain dissociated organic ligands, therefore, compound 1 and 2 are the first examples of hybrids based on polyoxometalates, metal halide clusters and organic ligands. - Graphical Abstract: Two new compounds have been synthesized and characterized. Structure analyses revealed that the two compounds are the first examples of hybrids based on polyoxometalates, metal halide clusters and organic ligands. Highlights: Black-Right-Pointing-Pointer First examples of hybrids based on polyoxometalates, metal halide clusters and organic ligands. Black-Right-Pointing-Pointer Two different kinds of metal halide clusters. Black-Right-Pointing-Pointer Supramolecular structures based on polyoxometalates, metal halide clusters and organic ligands. Black-Right-Pointing-Pointer Hybridization of three different of building blocks.

  17. Self-assembly of metallosupramolecular rhombi from chiral concave 9,9'-spirobifluorene-derived bis(pyridine) ligands.

    PubMed

    Hovorka, Rainer; Hytteballe, Sophie; Piehler, Torsten; Meyer-Eppler, Georg; Topić, Filip; Rissanen, Kari; Engeser, Marianne; Lützen, Arne

    2014-01-01

    Two new 9,9'-spirobifluorene-based bis(4-pyridines) were synthesised in enantiopure and one also in racemic form. These ligands act as concave templates and form metallosupramolecular [(dppp)2M2L2] rhombi with cis-protected [(dppp)Pd](2+) and [(dppp)Pt](2+) ions. The self-assembly process of the racemic ligand preferably occurs in a narcissistic self-recognising manner. Hence, a mixture of all three possible stereoisomers [(dppp)2M2{(R)-L}2](OTf)4, [(dppp)2M2{(S)-L}2](OTf)4, and [(dppp)2M2{(R)-L}{(S)-L}](OTf)4 was obtained in an approximate 1.5:1.5:1 ratio which corresponds to an amplification of the homochiral assemblies by a factor of approximately three as evidenced by NMR spectroscopy and mass spectrometry. The racemic homochiral assemblies could also be characterised by single crystal X-ray diffraction.

  18. Self-assembly of metallosupramolecular rhombi from chiral concave 9,9’-spirobifluorene-derived bis(pyridine) ligands

    PubMed Central

    Hovorka, Rainer; Hytteballe, Sophie; Piehler, Torsten; Meyer-Eppler, Georg; Topić, Filip; Rissanen, Kari; Engeser, Marianne

    2014-01-01

    Summary Two new 9,9’-spirobifluorene-based bis(4-pyridines) were synthesised in enantiopure and one also in racemic form. These ligands act as concave templates and form metallosupramolecular [(dppp)2M2L2] rhombi with cis-protected [(dppp)Pd]2+ and [(dppp)Pt]2+ ions. The self-assembly process of the racemic ligand preferably occurs in a narcissistic self-recognising manner. Hence, a mixture of all three possible stereoisomers [(dppp)2M2{(R)-L}2](OTf)4, [(dppp)2M2{(S)-L}2](OTf)4, and [(dppp)2M2{(R)-L}{(S)-L}](OTf)4 was obtained in an approximate 1.5:1.5:1 ratio which corresponds to an amplification of the homochiral assemblies by a factor of approximately three as evidenced by NMR spectroscopy and mass spectrometry. The racemic homochiral assemblies could also be characterised by single crystal X-ray diffraction. PMID:24605163

  19. Structure-based design of estrogen receptor-beta selective ligands.

    PubMed

    Manas, Eric S; Unwalla, Rayomand J; Xu, Zhang B; Malamas, Michael S; Miller, Chris P; Harris, Heather A; Hsiao, Chulai; Akopian, Tatos; Hum, Wah-Tung; Malakian, Karl; Wolfrom, Scott; Bapat, Ashok; Bhat, Ramesh A; Stahl, Mark L; Somers, William S; Alvarez, Juan C

    2004-11-24

    We present the structure-based optimization of a series of estrogen receptor-beta (ERbeta) selective ligands. X-ray cocrystal structures of these ligands complexed to both ERalpha and ERbeta are described. We also discuss how molecular modeling was used to take advantage of subtle differences between the two binding cavities in order to optimize selectivity for ERbeta over ERalpha. Quantum chemical calculations are utilized to gain insight into the mechanism of selectivity enhancement. Despite only two relatively conservative residue substitutions in the ligand binding pocket, the most selective compounds have greater than 100-fold selectivity for ERbeta relative to ERalpha when measured using a competitive radioligand binding assay.

  20. Tripodal phenylamine-based ligands and their CoII complexes.

    PubMed

    Jones, Matthew B; MacBeth, Cora E

    2007-10-01

    The syntheses of two phenylamine-based ligand systems, N(o-PhNH(2))(3) and N(o-PhNHC(O)(i)Pr)(3), are reported. These ligands readily coordinate to Co(II) to form monomeric complexes. X-ray diffraction studies establish that the [N(o-PhNC(O)(i)Pr)(3)](3-) ligand stabilizes the Co(II) ion in a trigonal-monopyramidal coordination environment. The axial coordination site in this complex is accessible and, upon cyanide coordination, generates an electrochemically active species.

  1. Index-Based Searching of Interaction Patterns in Large Collections of Protein-Ligand Interfaces.

    PubMed

    Inhester, Therese; Bietz, Stefan; Hilbig, Matthias; Schmidt, Robert; Rarey, Matthias

    2017-02-27

    Comparison of three-dimensional interaction patterns in large collections of protein-ligand interfaces is a key element for understanding protein-ligand interactions and supports various steps in the structure-based drug design process. Different methods exist that provide query systems to search for geometrical patterns in protein-ligand complexes. However, these tools do not meet all of the requirements, which are high query variability, an adjustable search set, and high retrieval speed. Here we present a new tool named PELIKAN that is able to search for a variety of geometrical queries in large protein structure collections in a reasonably short time. The data are stored in an SQLite database that can easily be constructed from any set of protein-ligand complexes. We present different test queries demonstrating the performance of the PELIKAN approach. Furthermore, two application scenarios show the usefulness of PELIKAN in structure-based design endeavors.

  2. In-silico Screening using Flexible Ligand Binding Pockets: A Molecular Dynamics-based Approach

    NASA Astrophysics Data System (ADS)

    Sivanesan, Dakshanamurthy; Rajnarayanan, Rajendram V.; Doherty, Jason; Pattabiraman, Nagarajan

    2005-04-01

    In-silico screening of flexible ligands against flexible ligand binding pockets (LBP) is an emerging approach in structure-based drug discovery. Here, we describe a molecular dynamics (MD) based docking approach to investigate the influence on the high-throughput in-silico screening of small molecules against flexible ligand binding pockets. In our approach, an ensemble of 51 energetically favorable structures of the LBP of human estrogen receptor α (hERα) were collected from 3 ns MD simulations. In-silico screening of 3500 endocrine disrupting compounds against these flexible ligand binding pockets resulted in thousands of ER-ligand complexes of which 582 compounds were unique. Detailed analysis of MD generated structures showed that only 17 of the LBP residues significantly contribute to the overall binding pocket flexibility. Using the flexible LBP conformations generated, we have identified 32 compounds that bind better to the flexible ligand-binding pockets compared to the crystal structure. These compounds, though chemically divergent, are structurally similar to the natural hormone. Our MD-based approach in conjunction with grid-based distributed computing could be applied routinely for in-silico screening of large databases against any given target.

  3. CD133-positive dermal papilla-derived Wnt ligands regulate postnatal hair growth.

    PubMed

    Zhou, Linli; Yang, Kun; Carpenter, April; Lang, Richard A; Andl, Thomas; Zhang, Yuhang

    2016-10-01

    Active Wnt/β-catenin signaling in the dermal papilla (DP) is required for postnatal hair cycling. In addition, maintenance of the hair-inducing ability of DP cells in vitro requires external addition of Wnt molecules. However, whether DP cells are a critical source of Wnt ligands and induce both autocrine and paracrine signaling cascades to promote adult hair follicle growth and regeneration remains elusive. To address this question, we generated an animal model that allows inducible ablation of Wntless (Wls), a transmembrane Wnt exporter protein, in CD133-positive (CD133+) DP cells. CD133+ cells have been shown to be a specific subpopulation of cells in the DP, which possesses the hair-inducing capability. Here, we show that ablation of Wls expression in CD133+ DP cells results in a shortened period of postnatal hair growth. Mutant hair follicles were unable to enter full anagen (hair growth stage) and progressed toward a rapid regression. Notably, reduced size of the DP and decreased expression of anagen DP marker, versican, were observed in hair follicles when CD133+ DP cells lost Wls expression. Further analysis showed that Wls-deficient CD133+ DP cells led to reduced proliferation and differentiation in matrix keratinocytes and melanocytes that are needed for the generation of the hair follicle structure and a pigmented hair shaft. These findings clearly demonstrate that Wnt ligands produced by CD133+ DP cells play an important role in postnatal hair growth by maintaining the inductivity of DP cells and mediating the signaling cross-talk between the mesenchyme and the epithelial compartment. © 2016 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

  4. Impaired ergosterol biosynthesis mediated fungicidal activity of Co(II) complex with ligand derived from cinnamaldehyde.

    PubMed

    Shreaz, Sheikh; Shiekh, Rayees A; Raja, Vaseem; Wani, Waseem A; Behbehani, Jawad M

    2016-03-05

    In this study, we have used aldehyde function of cinnamaldehyde to synthesize N, N'-Bis (cinnamaldehyde) ethylenediimine [C20H20N2] and Co(II) complex of the type [Co(C40H40N4)Cl2]. The structures of the synthesized compounds were determined on the basis of physiochemical analysis and spectroscopic data ((1)H NMR, FTIR, UV-visible and mass spectra) along with molar conductivity measurements. Anticandidal activity of cinnamaldehyde its ligand [L] and Co(II) complex was investigated by determining MIC80, time-kill kinetics, disc diffusion assay and ergosterol extraction and estimation assay. Ligand [L] and Co(II) complex are found to be 4.55 and 21.0 folds more efficient than cinnamaldehyde in a liquid medium. MIC80 of Co(II) complex correlated well with ergosterol inhibition suggesting ergosterol biosynthesis to be the primary site of action. In comparison to fluconazole, the test compounds showed limited toxicity against H9c2 rat cardiac myoblasts. In confocal microscopy propidium iodide (PI) penetrates the yeast cells when treated with MIC of metal complex, indicating a disruption of cell membrane that results in imbibition of dye. TEM analysis of metal complex treated cells exhibited notable alterations or damage to the cell membrane and the cell wall. The structural disorganization within the cell cytoplasm was noted. It was concluded that fungicidal activity of Co(II) complex originated from loss of membrane integrity and a decrease in ergosterol content is only one consequence of this.

  5. CD133-positive dermal papilla-derived Wnt ligands regulate postnatal hair growth

    PubMed Central

    Zhou, Linli; Yang, Kun; Carpenter, April; Lang, Richard A.; Andl, Thomas; Zhang, Yuhang

    2016-01-01

    Active Wnt/β-catenin signaling in the dermal papilla (DP) is required for postnatal hair cycling. In addition, maintenance of the hair-inducing ability of DP cells in vitro requires external addition of Wnt molecules. However, whether DP cells are a critical source of Wnt ligands and induce both autocrine and paracrine signaling cascades to promote adult hair follicle growth and regeneration remains elusive. To address this question, we generated an animal model that allows inducible ablation of Wntless (Wls), a transmembrane Wnt exporter protein, in CD133-positive (CD133+) DP cells. CD133+ cells have been shown to be a specific subpopulation of cells in the DP, which possesses the hair-inducing capability. Here, we show that ablation of Wls expression in CD133+ DP cells results in a shortened period of postnatal hair growth. Mutant hair follicles were unable to enter full anagen (hair growth stage) and progressed toward a rapid regression. Notably, reduced size of the DP and decreased expression of anagen DP marker, versican, were observed in hair follicles when CD133+ DP cells lost Wls expression. Further analysis showed that Wls-deficient CD133+ DP cells led to reduced proliferation and differentiation in matrix keratinocytes and melanocytes that are needed for the generation of the hair follicle structure and a pigmented hair shaft. These findings clearly demonstrate that Wnt ligands produced by CD133+ DP cells play an important role in postnatal hair growth by maintaining the inductivity of DP cells and mediating the signaling cross-talk between the mesenchyme and the epithelial compartment. PMID:27462123

  6. Octadentate picolinic acid-based bispidine ligand for radiometal ions.

    PubMed

    Comba, Peter; Jermilova, Una; Orvig, Chris; Patrick, Brian O; Ramogida, Caterina F; Rück, Katharina; Schneider, Christina; Starke, Miriam

    2017-08-16

    The synthesis of the octadentate bispidine ligand H2bispa2 bearing two picolinic acid pendant arms and its coordination chemistry with metal ions with radionuclides relevant for nuclear medicine, i.e. indium(III) (111In), lutetium(III) (177Lu) and lanthanum(III) (as surrogate for 225Ac), are reported. The non-radioactive metal complexes of the N6O2-type bispa ligand were characterized by 1H and 13C nuclear magnetic resonance spectroscopy, elemental analysis, mass spectrometry and single crystal X-ray analysis. Experimental structural data, a computational analysis, complex stabilities determined by potentiometric titration and "radiostabilities", determined by competition studies in the presence of human serum reveal complex stabilities of H2bispa2 comparable to those of the macrocyclic "gold standard" DOTA. After an incubation time of 1 day for example, 86 and 87 % of [177Lu(bispa2)]+ and [177Lu(DOTA)]-, respectively, remain intact. Importantly, unlike DOTA, H2bispa2 is radiolabeled quantitatively with 111InIII and 225AcIII under ambient conditions, which is an essential aspect, when working with heat-sensitive antibodies as targeting vectors. In the case of 111InIII, room temperature radiolabeling of H2bispa2 yields molar activities as high as 70 MBq/nmol within 10 minutes. These are promising results for radiopharmaceutical applications of H2bispa2. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Synthesis, spectral, thermal and biological studies of mixed ligand complexes with newly prepared Schiff base and 1,10-phenanthroline ligands

    NASA Astrophysics Data System (ADS)

    Abd El-Halim, Hanan F.; Mohamed, Gehad G.; Khalil, Eman A. M.

    2017-10-01

    A series of mixed ligand complexes were prepared from the Schiff base (L1) as a primary ligand, prepared by condensation of oxamide and furan-2-carbaldehyde, and 1,10-phenanthroline (1,10-phen) as a secondary ligand. The Schiff base ligand and its mixed ligand chelates were characterized based on elemental analysis, IR, 1H NMR, thermal analysis, UV-Visible, mass, molar conductance, magnetic moment. X-ray diffraction, solid reflectance and ESR also have been studied. The mixed ligand complexes were found to have the formulae of [M(L1) (1,10-phen)]Clm.nH2O (M = Cr(III) and Fe(III) (m = 3) (n = 0); M = Mn(II), Cu(II) and Cd(II) (m = 2) (n = 0); and M = Co(II) (m = 2) (n = 1), Ni(II) (m = 2) (n = 2) and Zn(II) (m = 2) (n = 3)) and that the geometrical structure of the complexes were octahedral. The parameters of thermodynamic using Coats-Redfern and Horowitz-Metzger equations were calculated. The synthesized Schiff base ligand, 1,10-phenanthroline ligand and Their mixed ligand complexes were also investigated for their antibacterial and antifungal activity against bacterial species (Gram-Ve bacteria: Pseudomonas aeruginosa and Escherichia coli) and (Gram + Ve bacteria: Bacillus subtilis and Streptococcus pneumonia) and fungi (Aspergillus fumigates and Candida albicans). The anticancer activity of the new compounds had been tested against breast (MFC7) and colon (HCT-116) cell lines. The results showed high activity for the synthesized compounds.

  8. Synthesis, crystal structures and luminescent properties of zinc(II) metal–organic frameworks constructed from terpyridyl derivative ligand

    SciTech Connect

    Yang, Xiao-Le; Shangguan, Yi-Qing; Hu, Huai-Ming Xu, Bing; Wang, Bao-Cheng; Xie, Juan; Yuan, Fei; Yang, Meng-Lin; Dong, Fa-Xin; Xue, Gang-Lin

    2014-08-15

    Five zinc(II) metal–organic frameworks, [Zn{sub 3}(344-pytpy){sub 2}Cl{sub 6}]{sub n}·n(H{sub 2}O) (1), [Zn(344-pytpy)(ox)]{sub n} (2), [Zn{sub 2}(344-pytpy)(bdc){sub 2}]{sub n}·1.5n(H{sub 2}O) (3), [Zn{sub 2}(344-pytpy){sub 2} (sfdb){sub 2}]{sub n}·1.5n(H{sub 2}O) (4) and [Zn{sub 3}(344-pytpy){sub 2}(btc){sub 2}]{sub n}·2n(H{sub 2}O) (5), (344-pytpy=4′-(3-pyridyl)-4,2′:6′,4″-terpyridine, H{sub 2}ox=oxalic acid, H{sub 2}bdc=1,4-benzenedi-carboxylic acid, H{sub 2}sfdb=4,4′-sulfonyldibenzoic acid and H{sub 3}btc=1,3,5-benzene-tricarboxylic acid) have been prepared by hydrothermal reactions. Compound 1 is a 1D chain structure, in which 344-pytpy ligand links three Zn{sup II} centers through three of terminal N-donors. Compound 2 is a 4-connected 3D framework with the dia topological net and the Schläfli symbol of 6{sup 6}. Compound 3 displays a unusual 3-fold interpenetrating 3D coordination network which exhibits a new intriguing (3,3,4)-connected topological net with the Schläfli symbol of (4.8{sup 2})(4.8{sup 5})(8{sup 3}). Compound 4 features a two-fold interpenetrating 4-connected 2D framework with the sql topological net and the Schläfli symbol of (4{sup 4}.6{sup 2}). Compound 5 is a new self-interpenetrating (3,3,4,4)-connected topological net with the Schläfli symbol of (6.8{sup 2}){sub 2}(6{sup 2}.8{sup 2}.10.12)(6{sup 2}.8{sup 3}.10){sub 2}(6{sup 2}.8){sub 2}. The luminescence properties of 1–5 have been investigated by emission spectra and they possess great thermal stabilities which can be stable up to around 400 °C. - Graphical abstract: Five new Zn(II) metal–organic frameworks based on dicarboxylate and terpyridyl derivative ligands have been synthesized by hydrothermal reactions, giving networks from 1D to 3D structures. The thermal stability and luminescent property have been investigated. - Highlights: • Five zinc(II) metal–organic frameworks have been prepared under hydrothermal conditions. • Their crystal and

  9. Derivational Morphology and Base Morpheme Frequency

    ERIC Educational Resources Information Center

    Ford, M. A.; Davis, M. H.; Marslen-Wilson, W. D.

    2010-01-01

    Morpheme frequency effects for derived words (e.g. an influence of the frequency of the base "dark" on responses to "darkness") have been interpreted as evidence of morphemic representation. However, it has been suggested that most derived words would not show these effects if family size (a type frequency count claimed to reflect semantic…

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

    PubMed

    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.

  11. Discovery of 5-substituted tetrahydronaphthalen-2yl-methyl with N-phenyl-N-(piperidin-4-yl)propionamide derivatives as potent opioid receptor ligands.

    PubMed

    Deekonda, Srinivas; Wugalter, Lauren; Kulkarni, Vinod; Rankin, David; Largent-Milnes, Tally M; Davis, Peg; Bassirirad, Neemah M; Lai, Josephine; Vanderah, Todd W; Porreca, Frank; Hruby, Victor J

    2015-09-15

    A new series of novel opioid ligands have been designed and synthesized based on the 4-anilidopiperidine scaffold containing a 5-substituted tetrahydronaphthalen-2yl)methyl group with different N-phenyl-N-(piperidin-4-yl)propionamide derivatives to study the biological effects of these substituents on μ and δ opioid receptor interactions. Recently our group reported novel 4-anilidopiperidine analogues, in which several aromatic ring-contained amino acids were conjugated with N-phenyl-N-(piperidin-4-yl)propionamide and examined their biological activities at the μ and δ opioid receptors. In continuation of our efforts in these novel 4-anilidopiperidine analogues, we took a peptidomimetic approach in the present design, in which we substituted aromatic amino acids with tetrahydronaphthalen-2yl methyl moiety with amino, amide and hydroxyl substitutions at the 5th position. In in vitro assays these ligands, showed very good binding affinity and highly selective toward the μ opioid receptor. Among these, the lead ligand 20 showed excellent binding affinity (2 nM) and 5000 fold selectivity toward the μ opioid receptor, as well as functional selectivity in GPI assays (55.20 ± 4.30 nM) and weak or no agonist activities in MVD assays. Based on the in vitro bioassay results the lead compound 20 was chosen for in vivo assessment for efficacy in naïve rats after intrathecal administration. Compound 20 was not significantly effective in alleviating acute pain. This discrepancy between high in vitro binding affinity, moderate in vitro activity, and low in vivo activity may reflect differences in pharmacodynamics (i.e., engaging signaling pathways) or pharmacokinetics (i.e., metabolic stability). In sum, our data suggest that further optimization of this compound 20 is required to enhance in vivo activity.

  12. Cyclometalated ruthenium(II) complexes featuring tridentate click-derived ligands for dye-sensitized solar cell applications.

    PubMed

    Schulze, Benjamin; Brown, Douglas G; Robson, Kiyoshi C D; Friebe, Christian; Jäger, Michael; Birckner, Eckhard; Berlinguette, Curtis P; Schubert, Ulrich S

    2013-10-11

    A series of heteroleptic bis(tridentate) Ru(II) complexes featuring N^C^N-cyclometalating ligands is presented. The 1,2,3-triazole-containing tridentate ligands are readily functionalized with hydrophobic side chains by means of click chemistry and the corresponding cyclometalated Ru(II) complexes are easily synthesized. The performance of these thiocyanate-free complexes in a dye-sensitized solar cell was tested and a power conversion efficiency (PCE) of up to 4.0 % (Jsc =8.1 mA cm(-2) , Voc =0.66 V, FF=0.70) was achieved, while the black dye ((NBu4 )3 [Ru(Htctpy)(NCS)3 ]; Htctpy=2,2':6',2''-terpyridine-4'-carboxylic acid-4,4''-dicarboxylate) showed 5.2 % (Jsc =10.7 mA cm(-2) , Voc =0.69 V, FF=0.69) under comparable conditions. When co-adsorbed with chenodeoxycholic acid, the PCE of the best cyclometalated dye could be improved to 4.5 % (Jsc =9.4 mA cm(-2) , Voc =0.65 V, FF=0.70). The PCEs correlate well with the light-harvesting capabilities of the dyes, while a comparable incident photon-to-current efficiency was achieved with the cyclometalated dye and the black dye. Regeneration appeared to be efficient in the parent dye, despite the high energy of the highest occupied molecular orbital. The device performance was investigated in more detail by electrochemical impedance spectroscopy. Ultimately, a promising Ru(II) sensitizer platform is presented that features a highly functionalizable "click"-derived cyclometalating ligand. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Metal based synthetic routes to heavy alkaline earth aryloxo complexes involving ligands of moderate steric bulk.

    PubMed

    Deacon, Glen B; Junk, Peter C; Moxey, Graeme J; Guino-o, Marites; Ruhlandt-Senge, Karin

    2009-07-07

    Treatment of an alkaline earth metal (Ca, Sr, Ba) with 2,4,6-trimethylphenol (HOmes) at elevated temperatures in the presence of mercury under solvent-free conditions, followed by extraction of the reaction mixture with 1,2-dimethoxyethane (dme), afforded dinuclear alkaline earth aryloxo complexes [Ae2(Omes)4(dme)4] (Ae = Ca 1, Sr 3, Ba 6). Extraction of the Ca metal and HOmes reaction mixture with thf afforded [Ca3(Omes)6(thf)] 2. In contrast, redox transmetallation ligand exchange reactions between an alkaline earth metal, diphenylmercury and HOmes in dme yielded solely 1 for Ca metal, a mixture of 3 and the methoxide bridged cage [Sr5(Omes)5(OMe)5(dme)4] x 2dme 4 for Sr metal, and solely [Ba5(Omes)5(OMe)5(dme)4] x dme 7 for Ba metal. The methoxide ligands originate from the C-O activation of the dme solvent. Treatment of liquid ammonia activated Sr or Ba metal with HOmes in thf afforded the linear species [Ae3(Omes)6(thf)6] (Ae = Sr 5, Ba 8), and 8 was also obtained from barium metal and HOmes in refluxing thf. The structures of 1 and 3, determined by X-ray crystallography, consist of two six coordinate Ae metal atoms, to each of which is bound a terminal aryloxide ligand, two bridging aryloxide ligands, and chelating and unidentate dme ligands. The structures of 4 and 7 contain five Ae metal atoms arranged on the vertices of a distorted square based pyramid. The Ae atoms are linked by four mu3-OMe ligands and a mu4-OMe ligand. Four bridging aryloxide ligands and four chelating dme ligands complete the coordination spheres of the four seven coordinate Ae atoms at the base of the pyramid, and a terminal aryloxide ligand is bound to the five coordinate apical Ae atom. The structures of 5 and 8 consist of a trinuclear linear array of Ae metal atoms, and contain solely bridging aryloxide ligands. Three thf ligands are bound to each terminal Ae atom, giving all Ae atoms a coordination number of six.

  14. Syntheses, crystal structures, anticancer activities of three reduce Schiff base ligand based transition metal complexes

    NASA Astrophysics Data System (ADS)

    Chang, Hui-Qin; Jia, Lei; Xu, Jun; Zhu, Tao-Feng; Xu, Zhou-Qing; Chen, Ru-Hua; Ma, Tie-Liang; Wang, Yuan; Wu, Wei-Na

    2016-02-01

    Three nickel(II) complexes, [Ni2(L1)2(tren)2(H2O)](ClO4)3 (1), [NiL2(tren)2](ClO4)·2.5H2O (2), [NiL2(tren)2]I·1.5H2O·CH3OH (3) based on amino acid reduced Schiff ligands are synthesized and characterized by physico-chemical and spectroscopic methods. The results show that in all complexes, the amino acid ligand is deprotonated and acts as an anionic ligand. In the dinuclear complex 1, each Ni(II) atom has a distorted octahedron geometry while with different coordination environment. However, the complexes 2 and 3 are mononuclear, almost with the same coordination environment. Furthermore, in vitro experiments are carried out, including MTT assay, Annexin V/PI flow cytometry and western blotting, to assess whether the complexes have antitumor effect. And the results show that all the three complexes have moderate anticancer activity towards human hepatic cancer (HepG2), human cervical cancer (HeLa) and human prostate (PC3) cell lines, in a concentration dependent way. The complex 1 exhibit higher cytotoxicity than the other two complexes and can induce human hepatic cancer cell (HepG2) to cell apoptosis by activating caspase 3.

  15. Graphlet signature-based scoring method to estimate protein-ligand binding affinity.

    PubMed

    Singh, Omkar; Sawariya, Kunal; Aparoy, Polamarasetty

    2014-12-01

    Over the years, various computational methodologies have been developed to understand and quantify receptor-ligand interactions. Protein-ligand interactions can also be explained in the form of a network and its properties. The ligand binding at the protein-active site is stabilized by formation of new interactions like hydrogen bond, hydrophobic and ionic. These non-covalent interactions when considered as links cause non-isomorphic sub-graphs in the residue interaction network. This study aims to investigate the relationship between these induced sub-graphs and ligand activity. Graphlet signature-based analysis of networks has been applied in various biological problems; the focus of this work is to analyse protein-ligand interactions in terms of neighbourhood connectivity and to develop a method in which the information from residue interaction networks, i.e. graphlet signatures, can be applied to quantify ligand affinity. A scoring method was developed, which depicts the variability in signatures adopted by different amino acids during inhibitor binding, and was termed as GSUS (graphlet signature uniqueness score). The score is specific for every individual inhibitor. Two well-known drug targets, COX-2 and CA-II and their inhibitors, were considered to assess the method. Residue interaction networks of COX-2 and CA-II with their respective inhibitors were used. Only hydrogen bond network was considered to calculate GSUS and quantify protein-ligand interaction in terms of graphlet signatures. The correlation of the GSUS with pIC50 was consistent in both proteins and better in comparison to the Autodock results. The GSUS scoring method was better in activity prediction of molecules with similar structure and diverse activity and vice versa. This study can be a major platform in developing approaches that can be used alone or together with existing methods to predict ligand affinity from protein-ligand complexes.

  16. Graphlet signature-based scoring method to estimate protein–ligand binding affinity

    PubMed Central

    Singh, Omkar; Sawariya, Kunal; Aparoy, Polamarasetty

    2014-01-01

    Over the years, various computational methodologies have been developed to understand and quantify receptor–ligand interactions. Protein–ligand interactions can also be explained in the form of a network and its properties. The ligand binding at the protein-active site is stabilized by formation of new interactions like hydrogen bond, hydrophobic and ionic. These non-covalent interactions when considered as links cause non-isomorphic sub-graphs in the residue interaction network. This study aims to investigate the relationship between these induced sub-graphs and ligand activity. Graphlet signature-based analysis of networks has been applied in various biological problems; the focus of this work is to analyse protein–ligand interactions in terms of neighbourhood connectivity and to develop a method in which the information from residue interaction networks, i.e. graphlet signatures, can be applied to quantify ligand affinity. A scoring method was developed, which depicts the variability in signatures adopted by different amino acids during inhibitor binding, and was termed as GSUS (graphlet signature uniqueness score). The score is specific for every individual inhibitor. Two well-known drug targets, COX-2 and CA-II and their inhibitors, were considered to assess the method. Residue interaction networks of COX-2 and CA-II with their respective inhibitors were used. Only hydrogen bond network was considered to calculate GSUS and quantify protein–ligand interaction in terms of graphlet signatures. The correlation of the GSUS with pIC50 was consistent in both proteins and better in comparison to the Autodock results. The GSUS scoring method was better in activity prediction of molecules with similar structure and diverse activity and vice versa. This study can be a major platform in developing approaches that can be used alone or together with existing methods to predict ligand affinity from protein–ligand complexes. PMID:26064572

  17. Ruthenium(II) Complexes Containing Lutidine-Derived Pincer CNC Ligands: Synthesis, Structure, and Catalytic Hydrogenation of C-N bonds.

    PubMed

    Hernández-Juárez, Martín; López-Serrano, Joaquín; Lara, Patricia; Morales-Cerón, Judith P; Vaquero, Mónica; Álvarez, Eleuterio; Salazar, Verónica; Suárez, Andrés

    2015-05-11

    A series of Ru complexes containing lutidine-derived pincer CNC ligands have been prepared by transmetalation with the corresponding silver-carbene derivatives. Characterization of these derivatives shows both mer and fac coordination of the CNC ligands depending on the wingtips of the N-heterocyclic carbene fragments. In the presence of tBuOK, the Ru-CNC complexes are active in the hydrogenation of a series of imines. In addition, these complexes catalyze the reversible hydrogenation of phenantridine. Detailed NMR spectroscopic studies have shown the capability of the CNC ligand to be deprotonated and get involved in ligand-assisted activation of dihydrogen. More interestingly, upon deprotonation, the Ru-CNC complex 5 e(BF4 ) is able to add aldimines to the metal-ligand framework to yield an amido complex. Finally, investigation of the mechanism of the hydrogenation of imines has been carried out by means of DFT calculations. The calculated mechanism involves outer-sphere stepwise hydrogen transfer to the C-N bond assisted either by the pincer ligand or a second coordinated H2 molecule. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Best of both worlds: on the complementarity of ligand-based and structure-based virtual screening.

    PubMed

    Broccatelli, Fabio; Brown, Nathan

    2014-06-23

    Virtual screening with docking is an integral component of drug design, particularly during hit finding phases. While successful prospective studies of virtual screening exist, it remains a significant challenge to identify best practices a priori due to the many factors that influence the final outcome, including targets, data sets, software, metrics, and expert knowledge of the users. This study investigates the extent to which ligand-based methods can be applied to improve structure-based methods. The use of ligand-based methods to modulate the number of hits identified using the protein-ligand complex and also the diversity of these hits from the crystallographic ligand is discussed. In this study, 40 CDK2 ligand complexes were used together with two external data sets containing both actives and inactives from GlaxoSmithKline (GSK) and actives and decoys from the Directory of Useful Decoys (DUD). Results show how ligand-based modeling can be used to select a more appropriate protein conformation for docking, as well as to assess the reliability of the docking experiment. The time gained by reducing the pool of virtual screening candidates via ligand-based similarity can be invested in more accurate docking procedures, as well as in downstream labor-intensive approaches (e.g., visual inspection) maximizing the use of the chemical and biological information available. This provides a framework for molecular modeling scientists that are involved in initiating virtual screening campaigns with practical advice to make best use of the information available to them.

  19. CoMSIA and Docking Study of Rhenium Based Estrogen Receptor Ligand Analogs

    PubMed Central

    Wolohan, Peter; Reichert, David E.

    2007-01-01

    OPLS all atom force field parameters were developed in order to model a diverse set of novel rhenium based estrogen receptor ligands whose relative binding affinities (RBA) to the estrogen receptor alpha isoform (ERα) with respect to 17β-Estradiol were available. The binding properties of these novel rhenium based organometallic complexes were studied with a combination of Comparative Molecular Similarity Indices Analysis (CoMSIA) and docking. A total of 29 estrogen receptor ligands consisting of 11 rhenium complexes and 18 organic ligands were docked inside the ligand-binding domain (LBD) of ERα utilizing the program Gold. The top ranked pose was used to construct CoMSIA models from a training set of 22 of the estrogen receptor ligands which were selected at random. In addition scoring functions from the docking runs and the polar volume (PV) were also studied to investigate their ability to predict RBA ERα. A partial least-squares analysis consisting of the CoMSIA steric, electrostatic and hydrophobic indices together with the polar volume proved sufficiently predictive having a correlation coefficient, r2, of 0.94 and a cross-validated correlation coefficient, q2, utilizing the leave one out method of 0.68. Analysis of the scoring functions from Gold showed particularly poor correlation to RBA ERα which did not improve when the rhenium complexes were extracted to leave the organic ligands. The combined CoMSIA and polar volume model ranked correctly the ligands in order of increasing RBA ERα, illustrating the utility of this method as a prescreening tool in the development of novel rhenium based estrogen receptor ligands. PMID:17280694

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

    DOEpatents

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

    2017-02-14

    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.

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

    DOEpatents

    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. MR1 presentation of vitamin B-based metabolite ligands.

    PubMed

    McWilliam, Hamish E G; Birkinshaw, Richard W; Villadangos, Jose A; McCluskey, James; Rossjohn, Jamie

    2015-06-01

    The major histocompatibility complex class I-related molecule MR1 can bind a novel class of antigens, namely a family of related small organic vitamin B metabolites. When bound to MR1 these metabolites are presented to a population of innate-like T cells, mucosal-associated invariant T (MAIT) cells that express a semi-invariant T cell receptor (TCR). Several non-activating and activating MR1-restricted ligands have been described, which are the degradation products of, or intermediates of, vitamin B9 (folic acid) or vitamin B2 (riboflavin), respectively. The MAIT-activating intermediates of the riboflavin synthesis pathway are unique to a wide range of microbes, and accordingly represent a molecular signature of microbial infection. Recently insights into the binding of these vitamin B metabolites to MR1, and subsequent recognition by the MAIT TCR, have been gleaned, illustrating a novel antigen presentation system. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Multimetallic complexes based on a diphosphine-dithiocarbamate "Janus" ligand.

    PubMed

    Sherwood, Rebecca; Gonzàlez de Rivera, Ferran; Wan, Jane Hui; Zhang, Qi; White, Andrew J P; Rossell, Oriol; Hogarth, Graeme; Wilton-Ely, James D E T

    2015-05-04

    The HCl salt of the aminodiphosphine ligand HN(CH2CH2PPh2)2 reacts with [M(CO)4(pip)2] (M = Mo, W; pip = piperidine) to yield [M{κ(2)-HN(CH2CH2PPh2)2}(CO)4]. The molybdenum analogue readily loses a carbonyl ligand to form [Mo{κ(3)-HN(CH2CH2PPh2)2}(CO)3], which was structurally characterized. The same ligand backbone is used to form the new bifunctional ligand, KS2CN(CH2CH2PPh2)2, which reacts with nickel and cobalt precursors to yield [Ni{S2CN(CH2CH2PPh2)2}2] and [Co{S2CN(CH2CH2PPh2)2}3]. Addition of [AuCl(tht)] (tht = tetrahydrothiophene) to [Ni{S2CN(CH2CH2PPh2)2}2] leads to formation of the pentametallic complex, [Ni{S2CN(CH2CH2PPh2AuCl)2}2]. In contrast, addition of [PdCl2(py)2] (py = pyridine) to [Ni{S2CN(CH2CH2PPh2)2}2] does not lead to a trimetallic complex but instead yields the transmetalated cyclic compound [Pd{S2CN(CH2CH2PPh2)2}]2, which was structurally characterized. The same product is obtained directly from [PdCl2(py)2] and KS2CN(CH2CH2PPh2)2. In contrast, the same reaction with [PtCl2(NCPh)2] yields the oligomer, [Pt{S2CN(CH2CH2PPh2)2}]n. Reaction of KS2CN(CH2CH2PPh2)2 with cis-[RuCl2(dppm)2] provides [Ru{S2CN(CH2CH2PPh2)2}(dppm)2](+), which reacts with [AuCl(tht)] to yield [Ru{S2CN(CH2CH2PPh2AuCl)2}(dppm)2](+). Addition of [M(CO)4(pip)2] (M = Mo, W) to the same precursor leads to formation of the bimetallic compounds [(dppm)2Ru{S2CN(CH2CH2PPh2)2}M(CO)4](+), while treatment with [ReCl(CO)5] yields [(dppm)2Ru{S2CN(CH2CH2PPh2)2}ReCl(CO)3](+). Reaction of KS2CN(CH2CH2PPh2)2 with [Os(CH═CHC6H4Me-4)Cl(CO)(BTD)(PPh3)2] (BTD = 2,1,3-benzothiadiazole) provides [Os(CH═CHC6H4Me-4){S2CN(CH2CH2PPh2)2}(CO)(PPh3)2], but reaction with the analogous ruthenium precursor fails to yield a clean product.

  4. Synthesis, Characterization, and Cytotoxicity of the First Oxaliplatin Pt(IV) Derivative Having a TSPO Ligand in the Axial Position

    PubMed Central

    Savino, Salvatore; Denora, Nunzio; Iacobazzi, Rosa Maria; Porcelli, Letizia; Azzariti, Amalia; Natile, Giovanni; Margiotta, Nicola

    2016-01-01

    The first Pt(IV) derivative of oxaliplatin carrying a ligand for TSPO (the 18-kDa mitochondrial translocator protein) has been developed. The expression of the translocator protein in the brain and liver of healthy humans is usually low, oppositely to steroid-synthesizing and rapidly proliferating tissues, where TSPO is much more abundant. The novel Pt(IV) complex, cis,trans,cis-[Pt(ethanedioato)Cl{2-(2-(4-(6,8-dichloro-3-(2-(dipropylamino)-2-oxoethyl)imidazo[1,2-a]pyridin-2-yl)phenoxy)acetate)-ethanolato}(1R,2R-DACH)] (DACH = diaminocyclohexane), has been fully characterized by spectroscopic and spectrometric techniques and tested in vitro against human MCF7 breast carcinoma, U87 glioblastoma, and LoVo colon adenocarcinoma cell lines. In addition, affinity for TSPO (IC50 = 18.64 nM), cellular uptake (ca. 2 times greater than that of oxaliplatin in LoVo cancer cells, after 24 h treatment), and perturbation of cell cycle progression were investigated. Although the new compound was less active than oxaliplatin and did not exploit a synergistic proapoptotic effect due to the presence of the TSPO ligand, it appears to be promising in a receptor-mediated drug targeting context towards TSPO-overexpressing tumors, in particular colorectal cancer (IC50 = 2.31 μM after 72 h treatment). PMID:27347942

  5. 6β-N-Heterocyclic Substituted Naltrexamine Derivative BNAP: A Peripherally Selective Mixed MOR/KOR Ligand

    PubMed Central

    Williams, Dwight A.; Zheng, Yi; David, Bethany G.; Yuan, Yunyun; Zaidi, Saheem A.; Stevens, David L.; Scoggins, Krista L.; Selley, Dana E.; Dewey, William L.; Akbarali, Hamid I.; Zhang, Yan

    2016-01-01

    The 6β-N-heterocyclic naltrexamine derivative, NAP, has been demonstrated to be a peripherally selective mu opioid receptor modulator. To further improve peripheral selectivity of this highly potent ligand, its pyridal ring was quaterinized with benzyl bromide to produce BNAP. In radioligand binding assay, the Ki of BNAP for MOR was 0.76 ± 0.09 nM and was >900 fold more selective for MOR than DOR. The Ki for KOR was 3.46 ± 0.05 nM. In [35S]GTPγS ligand stimulated assay, BNAP showed low agonist efficacy with 14.6% of the maximum response of DAMGO with an EC50 of 4.84 ± 0.6 nM. However, unlike its parent compound NAP, BNAP displayed partial agonist activity at KOR with % maximum response at 45.9 ± 1.7% of U50,488H. BNAP did not reverse morphine-induced antinociception when administered subcutaneously but did antagonize when administered intracerebroventricularly. BNAP antagonized morphine-induced contractions of the circular muscle in mice colon. BNAP inhibition of field-stimulated contractions in longitudinal muscle strips for the guinea-pig ileum were also blocked by nor-BNI, a kappa opioid receptor antagonist. BNAP induced inhibition of acetic acid induced abdominal stretching in chronic morphine treated mice. These findings suggest that BNAP is a dual MOR antagonist/KOR agonist and may have functional use in irritable bowel patients. PMID:27269866

  6. 6β-N-Heterocyclic Substituted Naltrexamine Derivative BNAP: A Peripherally Selective Mixed MOR/KOR Ligand.

    PubMed

    Williams, Dwight A; Zheng, Yi; David, Bethany G; Yuan, Yunyun; Zaidi, Saheem A; Stevens, David L; Scoggins, Krista L; Selley, Dana E; Dewey, William L; Akbarali, Hamid I; Zhang, Yan

    2016-08-17

    The 6β-N-heterocyclic naltrexamine derivative, NAP, has been demonstrated to be a peripherally selective mu opioid receptor modulator. To further improve peripheral selectivity of this highly potent ligand, its pyridal ring was quaterinized with benzyl bromide to produce BNAP. In radioligand binding assay, the Ki of BNAP for MOR was 0.76 ± 0.09 nM and was >900-fold more selective for MOR than DOR. The Ki for KOR was 3.46 ± 0.05 nM. In [(35)S]GTPγS ligand stimulated assay, BNAP showed low agonist efficacy with 14.6% of the maximum response of DAMGO with an EC50 of 4.84 ± 0.6 nM. However, unlike its parent compound NAP, BNAP displayed partial agonist activity at KOR with % maximum response at 45.9 ± 1.7% of U50,488H. BNAP did not reverse morphine-induced antinociception when administered subcutaneously but did antagonize when administered intracerebroventricularly. BNAP antagonized morphine-induced contractions of the circular muscle in mice colon. BNAP inhibition of field-stimulated contractions in longitudinal muscle strips for the guinea-pig ileum were also blocked by nor-BNI, a kappa opioid receptor antagonist. BNAP induced inhibition of acetic acid induced abdominal stretching in chronic morphine treated mice. These findings suggest that BNAP is a dual MOR antagonist/KOR agonist and may have functional use in irritable bowel patients.

  7. A Fluid Membrane-Based Soluble Ligand Display System for Live CellAssays

    SciTech Connect

    Nam, Jwa-Min; Nair, Pradeep N.; Neve, Richard M.; Gray, Joe W.; Groves, Jay T.

    2005-10-14

    Cell communication modulates numerous biological processes including proliferation, apoptosis, motility, invasion and differentiation. Correspondingly, there has been significant interest in the development of surface display strategies for the presentation of signaling molecules to living cells. This effort has primarily focused on naturally surface-bound ligands, such as extracellular matrix components and cell membranes. Soluble ligands (e.g. growth factors and cytokines) play an important role in intercellular communications, and their display in a surface-bound format would be of great utility in the design of array-based live cell assays. Recently, several cell microarray systems that display cDNA, RNAi, or small molecules in a surface array format were proven to be useful in accelerating high-throughput functional genetic studies and screening therapeutic agents. These surface display methods provide a flexible platform for the systematic, combinatorial investigation of genes and small molecules affecting cellular processes and phenotypes of interest. In an analogous sense, it would be an important advance if one could display soluble signaling ligands in a surface assay format that allows for systematic, patterned presentation of soluble ligands to live cells. Such a technique would make it possible to examine cellular phenotypes of interest in a parallel format with soluble signaling ligands as one of the display parameters. Herein we report a ligand-modified fluid supported lipid bilayer (SLB) assay system that can be used to functionally display soluble ligands to cells in situ (Figure 1A). By displaying soluble ligands on a SLB surface, both solution behavior (the ability to become locally enriched by reaction-diffusion processes) and solid behavior (the ability to control the spatial location of the ligands in an open system) could be combined. The method reported herein benefits from the naturally fluid state of the supported membrane, which allows

  8. Structure-based discovery of selective serotonin 5-HT(1B) receptor ligands.

    PubMed

    Rodríguez, David; Brea, José; Loza, María Isabel; Carlsson, Jens

    2014-08-05

    The development of safe and effective drugs relies on the discovery of selective ligands. Serotonin (5-hydroxytryptamine [5-HT]) G protein-coupled receptors are therapeutic targets for CNS disorders but are also associated with adverse drug effects. The determination of crystal structures for the 5-HT1B and 5-HT2B receptors provided an opportunity to identify subtype selective ligands using structure-based methods. From docking screens of 1.3 million compounds, 22 molecules were predicted to be selective for the 5-HT1B receptor over the 5-HT2B subtype, a requirement for safe serotonergic drugs. Nine compounds were experimentally verified as 5-HT1B-selective ligands, with up to 300-fold higher affinities for this subtype. Three of the ligands were agonists of the G protein pathway. Analysis of state-of-the-art homology models of the two 5-HT receptors revealed that the crystal structures were critical for predicting selective ligands. Our results demonstrate that structure-based screening can guide the discovery of ligands with specific selectivity profiles.

  9. Structure and properties of silver sulfate complexes derived from dipyridyl methylthio ligands with secondary donor site

    NASA Astrophysics Data System (ADS)

    Chen, Wen-Hua; Yan, Hao-Jie; Chen, Hui; Liu, Rui-Heng; Li, Ai-Min; Wang, Guo; Wan, Chong-Qing

    2017-06-01

    Dipyridyl sulphide ligands 4-(pyridin-4-ylmethylthio)pyridine (abbreviated as L1) and 3-(pyridin-4-ylmethylthio)pyridine (abbreviated as L2) have been designed and used as μ-N,N-bridging linkages to construct coordination polymers with free -S-CH2- groups as secondary donor sites. By use solvent control method, coordination polymers {[Ag3SO4(L1)3](Cl)·4.5H2O}∞(1), {[Ag2SO4(L1)2]·6H2O·2CH3OH}∞(2), {[Ag2SO4(L2)2]·H2O}∞(3) and {[Ag4(SO4)2(L2)4]·5H2O}∞(4) with different architectures were obtained. Complexes 1, 3 and 4 feature 1D channel with different sizes and structures. Complex 1 exhibits guest exchange by THF and 1,4-dioxane, and Hg2+ sorption ability from solution due to its relative larger channel and available bonding sites of -S- exposed to the channel region. All complexes have been characterized through single-crystal and powder X-ray diffraction (PXRD), FT-IR spectra, X-ray photoelectron spectroscopy (XPS), elemental and thermogravimetric analyses. The guest exchange and Hg2+ sorption were monitored and identified, and the structure-property relationship of coordination polymers 1-4 are discussed.

  10. Synthesis, structure and spectroscopic study of Rh III polypyridine complexes with phenylcyanamide derivative ligands

    NASA Astrophysics Data System (ADS)

    Hadadzadeh, Hassan; Rezvani, Ali R.; Belanger-Gariepy, Francine

    2005-04-01

    Several new Rh III complexes, [Rh(tpy)(bpy)L](PF 6) 2 (tpy=2,2':6',2″-terpyridine, bpy=2,2'-bipyridine, and L=monoanions of phenylcyanamide(pcyd)), 4-methylphenylcyanamide (4-MePcyd), 2,4-dimethylphenylcyanamide (2,4-Me 2pcyd), 4-methoxyphenylcyanamide (4-MeOPcyd), 2-chlorophenylcyanamide (2-Clpcyd) and 2,5-dichlorophenylcyanamide (2,5-Cl 2pcyd) have been synthesized and characterized by elemental analysis, IR, 1H NMR and electronic absorption spectroscopies. ORTEP drawing of [Rh(tpy)(bpy)(2,5-Cl 2pcyd)](PF 6) 2·1/2CH 3CN shows three pyridyl rings of the tpy ligand that are nearly coplanar, as are the two rings of bpy. The anionic cyanamide group is coordinated end-on by the nitrile nitrogen to the Rh III. The Rh III-NCN bond is bent, having an angle of 125.4°. This bent bond is largely determined by the σ-bonding interaction of a cyanamide non-bonding electron pair in a sp 2 hybrid orbital.

  11. Heteroaromatic and aniline derivatives of piperidines as potent ligands for vesicular acetylcholine transporter

    PubMed Central

    Li, Junfeng; Zhang, Xiang; Zhang, Zhanbin; Padakanti, Prashanth K.; Jin, Hongjun; Cui, Jinquan; Li, Aixiao; Zeng, Dexing; Rath, Nigam P.; Flores, Hubert; Perlmutter, Joel S.; Parsons, Stanley M.; Tu, Zhude

    2013-01-01

    To identify suitable lipophilic compounds having high potency and selectivity for vesicular acetylcholine transporter (VAChT), a heteroaromatic ring or a phenyl group was introduced into the carbonyl-containing scaffold for VAChT ligands. Twenty new compounds with ALog D values between 0.53-3.2 were synthesized, and their in vitro binding affinities were assayed. Six of them (19a, 19e, 19g, 19k and 24a-b) displayed high affinity for VAChT (Ki = 0.93 – 18 nM for racemates) and moderate to high selectivity for VAChT over σ1 and σ2 receptors (Ki = 44 – 4400-fold). These compounds have a methyl or a fluoro substitution that provides the position for incorporating PET radioisotopes C-11 or F-18. Compound (-)-[11C]24b (Ki = 0.78 for VAChT, 900-fold over σ receptors) was successfully synthesized and evaluated in vivo in rats and nonhuman primates. The data revealed that (-)-[11C]24b has highest binding in striatum and has favorable pharmacokinetics in the brain. PMID:23802889

  12. Generalized Molecular Descriptors Derived From Event-Based Discrete Derivative.

    PubMed

    Martínez-Santiago, Oscar; Cabrera, Reisel Millán; Marrero-Ponce, Yovani; Barigye, Stephen J; Le-Thi-Thu, Huong; Torres, F Javier; Zambrano, Cesar H; Yaber-Goenaga, Ivan; Cruz-Monteagudo, Maykel; López, Yoan Martínez; Giménez, Facundo Pérez; Torrens, Francisco

    2016-01-01

    In the present study, a generalized approach for molecular structure characterization is introduced, based on the relation frequency matrix (F) representation of the molecular graph and the subsequent calculation of the corresponding discrete derivative (finite difference) over a pair of elements (atoms). In earlier publications (22- 24), an unique event, named connected subgraphs, (based on the Kier-Hall's subgraphs) was systematically employed for the computation of the matrix F. The present report is a generalization of this notion, in which eleven additional events are introduced, classified in three categories, namely, topological (terminal paths, vertex path incidence, quantum subgraphs, walks of length k, Sach's subgraphs), fingerprints (MACCs, E-state and substructure fingerprints) and atomic contributions (Ghose and Crippen atom-types for hydrophobicity and refractivity) for F generation. The events are intended to capture diverse information by the generation or search of different kinds of substructures from the graph representation of a molecule. The discrete derivative over duplex atom relations are calculated for each event, and the resulting derivatives, local vertex invariants (LOVIs) are finally obtained. These LOVIs are subsequently employed as the basis for the calculation of global and local indices over groups of atoms (heteroatoms, halogens, methyl carbons, etc.), by using norms, means, statistics and classical algorithms as aggregator (fusion) operators. These indices were implemented in our house software DIVATI (Derivative Type Indices, a new module of TOMOCOMDCARDD system). DIVATI provides a friendly and cross-platform graphical user interface, developed in the Java programming language and is freely available at: http: //www.tomocomd.com. Factor analysis shows that the presented events are rather orthogonal and collect diverse information about the chemical structure. Finally, QSPR models were built to describe the logP and logK of 34

  13. Effects of active immunisation with myelin basic protein and myelin-derived altered peptide ligand on pain hypersensitivity and neuroinflammation.

    PubMed

    Perera, Chamini J; Lees, Justin G; Duffy, Samuel S; Makker, Preet G S; Fivelman, Brett; Apostolopoulos, Vasso; Moalem-Taylor, Gila

    2015-09-15

    Neuropathic pain is a debilitating condition in multiple sclerosis and experimental autoimmune encephalomyelitis (EAE). Specific myelin basic protein (MBP) peptides are encephalitogenic, and myelin-derived altered peptide ligands (APLs) are capable of preventing and ameliorating EAE. We investigated the effects of active immunisation with a weakly encephalitogenic epitope of MBP (MBP87-99) and its mutant APL (Cyclo-87-99[A(91),A(96)]MBP87-99) on pain hypersensitivity and neuroinflammation in Lewis rats. MBP-treated rats exhibited significant mechanical and thermal pain hypersensitivity associated with infiltration of T cells, MHC class II expression and microglia activation in the spinal cord, without developing clinical signs of paralysis. Co-immunisation with APL significantly decreased pain hypersensitivity and neuroinflammation emphasising the important role of neuroimmune crosstalk in neuropathic pain. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. Synthesis, characterization and cytotoxicity of a new palladium(II) complex with a coumarine-derived ligand.

    PubMed

    Ilić, Dragoslav R; Jevtić, Verica V; Radić, Gordana P; Arsikin, Katarina; Ristić, Biljana; Harhaji-Trajković, Ljubica; Vuković, Nenad; Sukdolak, Slobodan; Klisurić, Olivera; Trajković, Vladimir; Trifunović, Srećko R

    2014-03-03

    The new coumarine derivative, 3-(1-(2-hydroxyethylamino)ethylidene)chroman-2,4--dione, and corresponding palladium(II) complex have been synthesized and characterized by microanalysis, infrared, (1)H and (13)C NMR spectroscopy. The proposed structure of the complex was confirmed on the basis of the X-ray structural study. The palladium(II) complex decreased viability of L929 mouse fibrosarcoma, U251 human glioma and B16 mouse melanoma cell lines in a dose dependent manner, while its ligand exhibited no significant cytotoxicity. The cytotoxic effect of the complex was comparable to that of cisplatin, and mediated by apoptosis associated with oxidative stress, mitochondrial depolarization and caspase activation. Therefore, our results indicate that newly synthesized palladium(II) complex might be a potential candidate for anticancer therapy.

  15. Cyclopentadienyl-ruthenium(II) and iron(II) organometallic compounds with carbohydrate derivative ligands as good colorectal anticancer agents.

    PubMed

    Florindo, Pedro R; Pereira, Diane M; Borralho, Pedro M; Rodrigues, Cecília M P; Piedade, M F M; Fernandes, Ana C

    2015-05-28

    New ruthenium(II) and iron(II) organometallic compounds of general formula [(η(5)-C5H5)M(PP)Lc][PF6], bearing carbohydrate derivative ligands (Lc), were prepared and fully characterized and the crystal structures of five of those compounds were determined by X-ray diffraction studies. Cell viability of colon cancer HCT116 cell line was determined for a total of 23 organometallic compounds and SAR's data analysis within this library showed an interesting dependency of the cytotoxic activity on the carbohydrate moiety, linker, phosphane coligands, and metal center. More importantly, two compounds, 14Ru and 18Ru, matched oxaliplatin IC50 (0.45 μM), the standard metallodrug used in CC chemotherapeutics, and our leading compound 14Ru was shown to be significantly more cytotoxic than oxaliplatin to HCT116 cells, triggering higher levels of caspase-3 and -7 activity and apoptosis in a dose-dependent manner.

  16. Synthesis and structural features of U VI and V IV chelate complexes with (hhmmbH)Cl·H 2O [hhmmb = {3-hydroxyl-5-(hydroxymethyl)-2-methylpyridine-4-yl-methylene}benzohydrazide], a new Schiff base ligand derived from vitamin B6

    NASA Astrophysics Data System (ADS)

    Back, Davi Fernando; Ballin, Marco Aurélio; de Oliveira, Gelson Manzoni

    2009-10-01

    The Schiff base ligand {3-hydroxyl-5-(hydroxymethyl)-2-methylpyridine-4-yl-methylene}benzohydrazide hydrochloride monohydrated {(hhmmbH)Cl·H 2O} ( 1) was prepared by reaction of pyridoxine hydrochloride with benzoic acid hydrazide. The reaction of 1 with [VO(acac) 2] and triethylamine yields the neutral vanadium IV complex [VO 2(hhmmb)]·Py ( 2), with a distorted quadratic pyramidal configuration. The Schiff base 1 reacts also with UO 2(NO 3) 2·6H 2O and triethylamine under deprotonation giving the uranium VI cationic complexes [UO 2(hhmmb)(H 2O)Cl] + ( 3) and [UO 2(hhmmb)(CH 3OH)Cl] + ( 4), both showing the classical pentagonal bipyrimidal geometry of UO22+ complexes. The structural features of all compounds are discussed.

  17. Discovery of pyrrolidine-based β-secretase inhibitors: lead advancement through conformational design for maintenance of ligand binding efficiency.

    PubMed

    Stachel, Shawn J; Steele, Thomas G; Petrocchi, Alessia; Haugabook, Sharie J; McGaughey, Georgia; Katharine Holloway, M; Allison, Timothy; Munshi, Sanjeev; Zuck, Paul; Colussi, Dennis; Tugasheva, Katherine; Wolfe, Abigail; Graham, Samuel L; Vacca, Joseph P

    2012-01-01

    We have developed a novel series of pyrrolidine derived BACE-1 inhibitors. The potency of the weak initial lead structure was enhanced using library-based SAR methods. The series was then further advanced by rational design while maintaining a minimal ligand binding efficiency threshold. Ultimately, the co-crystal structure was obtained revealing that these inhibitors interacted with the enzyme in a unique fashion. In all, the potency of the series was enhanced by 4 orders of magnitude from the HTS lead with concomitant increases in physical properties needed for series advancement. The progression of these developments in a systematic fashion is described.

  18. Diphosphite ligands derived from carbohydrates as stabilizers for ruthenium nanoparticles: promising catalytic systems in arene hydrogenation.

    PubMed

    Gual, Aitor; Axet, M Rosa; Philippot, Karine; Chaudret, Bruno; Denicourt-Nowicki, Audrey; Roucoux, Alain; Castillon, Sergio; Claver, Carmen

    2008-06-28

    Ruthenium nanoparticles (RuNPs) were prepared through the hydrogenation of [Ru(COD)(COT)] (COD = 1,5-cyclooctadiene, COT = 1,3,5-cyclooctatriene) in the presence of diphosphites derived from carbohydrates as stabilizing agents, and interestingly, structural modifications of the diphosphite backbone were found to influence nanoparticle size and dispersity, as well as their catalytic activity in arene hydrogenation.

  19. Chemokine Ligand 5 (CCL5) Derived from Endothelial Colony-Forming Cells (ECFCs) Mediates Recruitment of Smooth Muscle Progenitor Cells (SPCs) toward Critical Vascular Locations in Moyamoya Disease

    PubMed Central

    Phi, Ji Hoon; Suzuki, Naoko; Moon, Youn Joo; Park, Ae Kyung; Wang, Kyu-Chang; Lee, Ji Yeoun; Choi, Seung-Ah; Chong, Sangjoon; Shirane, Reizo; Kim, Seung-Ki

    2017-01-01

    The etiology and pathogenesis of moyamoya disease (MMD) are still obscure. Previous studies indicated that angiogenic chemokines may play an important role in the pathogenesis of the disease. Recently, it was discovered that peripheral blood-derived endothelial colony-forming cells (ECFCs) and smooth muscle progenitor cells (SPCs) have defective functions in MMD patients. Therefore, the interaction of ECFCs and SPCs, the precursors of two crucial cellular components of vascular walls, with some paracrine molecules is an intriguing subject. In this study, co-culture of ECFCs and SPCs from MMD patients and healthy normal subjects revealed that MMD ECFCs, not SPCs, are responsible for the defective functions of both ECFCs and SPCs. Enhanced migration of SPCs toward MMD ECFCs supported the role for some chemokines secreted by MMD ECFCs. Expression arrays of MMD and normal ECFCs suggested that several candidate cytokines differentially produced by MMD ECFCs. We selected chemokine (C-X-C motif) ligand 6 (CXCR6), interleukin-8 (IL8), chemokine (C-C motif) ligand 2 (CCL2), and CCL5 for study, based on the relatively higher expression of these ligands in MMD ECFCs and their cognate receptors in MMD SPCs. Migration assays showed that only CCL5 significantly augmented the migration activities of SPCs toward ECFCs. Treatment with siRNA for the CCL5 receptor (CCR5) abrogated the effect, confirming that CCL5 is responsible for the interaction of MMD ECFCs and SPCs. These data indicate that ECFCs, not SPCs, are the major players in MMD pathogenesis and that the chemokine CCL5 mediates the interactions. It can be hypothesized that in MMD patients, defective ECFCs direct aberrant SPC recruitment to critical vascular locations through the action of CCL5. PMID:28072843

  20. Development of the knowledge-based and empirical combined scoring algorithm (KECSA) to score protein-ligand interactions.

    PubMed

    Zheng, Zheng; Merz, Kenneth M

    2013-05-24

    We describe a novel knowledge-based protein-ligand scoring function that employs a new definition for the reference state, allowing us to relate a statistical potential to a Lennard-Jones (LJ) potential. In this way, the LJ potential parameters were generated from protein-ligand complex structural data contained in the Protein Databank (PDB). Forty-nine (49) types of atomic pairwise interactions were derived using this method, which we call the knowledge-based and empirical combined scoring algorithm (KECSA). Two validation benchmarks were introduced to test the performance of KECSA. The first validation benchmark included two test sets that address the training set and enthalpy/entropy of KECSA. The second validation benchmark suite included two large-scale and five small-scale test sets, to compare the reproducibility of KECSA, with respect to two empirical score functions previously developed in our laboratory (LISA and LISA+), as well as to other well-known scoring methods. Validation results illustrate that KECSA shows improved performance in all test sets when compared with other scoring methods, especially in its ability to minimize the root mean square error (RMSE). LISA and LISA+ displayed similar performance using the correlation coefficient and Kendall τ as the metric of quality for some of the small test sets. Further pathways for improvement are discussed for which would allow KECSA to be more sensitive to subtle changes in ligand structure.

  1. Development of the Knowledge-based & Empirical Combined Scoring Algorithm (KECSA) to Score Protein-Ligand Interactions

    PubMed Central

    Zheng, Zheng

    2013-01-01

    We describe a novel knowledge-based protein-ligand scoring function that employs a new definition for the reference state, allowing us to relate a statistical potential to a Lennard-Jones (LJ) potential. In this way, the LJ potential parameters were generated from protein-ligand complex structural data contained in the PDB. Forty-nine types of atomic pairwise interactions were derived using this method, which we call the knowledge-based and empirical combined scoring algorithm (KECSA). Two validation benchmarks were introduced to test the performance of KECSA. The first validation benchmark included two test sets that address the training-set and enthalpy/entropy of KECSA The second validation benchmark suite included two large-scale and five small-scale test sets to compare the reproducibility of KECSA with respect to two empirical score functions previously developed in our laboratory (LISA and LISA+), as well as to other well-known scoring methods. Validation results illustrate that KECSA shows improved performance in all test sets when compared with other scoring methods especially in its ability to minimize the RMSE. LISA and LISA+ displayed similar performance using the correlation coefficient and Kendall τ as the metric of quality for some of the small test sets. Further pathways for improvement are discussed which would KECSA more sensitive to subtle changes in ligand structure. PMID:23560465

  2. Modern spectroscopic technique in the characterization of biosensitive macrocyclic Schiff base ligand and its complexes: Inhibitory activity against plantpathogenic fungi

    NASA Astrophysics Data System (ADS)

    Tyagi, Monika; Chandra, Sulekh; Akhtar, Jameel; Chand, Dinesh

    2014-01-01

    Complexes of the type [M(L)Cl2], where M = Co(II), Ni(II) and Cu(II) have been synthesized with a macrocyclic Schiff base ligand (1,4,5,7,10,11,12,15-octaaza,5,11,16,18-tetraphenyl, 3,4,12,13-tetramethyl cyclo-octadecane) derived from Schiff base (obtained by the condensation of 4-aminoantipyrine and dibenzoyl methane) and ethylenediamine. The ligand was characterized on the basis of elemental analysis, IR, 1H NMR, EI Mass and molecular modeling studies while the complexes were characterized by elemental analysis, molar conductance measurements, magnetic susceptibility measurements, IR, electronic and EPR spectral studies. All the complexes are non-electrolyte in nature. The covalency factor (β) and coefficient factor (α) suggest the covalent nature of the complexes. The ligand and its metal complexes have shown antifungal activity with their LD50 values determined by probit analysis against two economically important fungal plant pathogens i.e. Macrophomina phaseolina and Fusarium solani.

  3. Visually interpretable models of kinase selectivity related features derived from field-based proteochemometrics.

    PubMed

    Subramanian, Vigneshwari; Prusis, Peteris; Pietilä, Lars-Olof; Xhaard, Henri; Wohlfahrt, Gerd

    2013-11-25

    Achieving selectivity for small organic molecules toward biological targets is a main focus of drug discovery but has been proven difficult, for example, for kinases because of the high similarity of their ATP binding pockets. To support the design of more selective inhibitors with fewer side effects or with altered target profiles for improved efficacy, we developed a method combining ligand- and receptor-based information. Conventional QSAR models enable one to study the interactions of multiple ligands toward a single protein target, but in order to understand the interactions between multiple ligands and multiple proteins, we have used proteochemometrics, a multivariate statistics method that aims to combine and correlate both ligand and protein descriptions with affinity to receptors. The superimposed binding sites of 50 unique kinases were described by molecular interaction fields derived from knowledge-based potentials and Schrödinger's WaterMap software. Eighty ligands were described by Mold(2), Open Babel, and Volsurf descriptors. Partial least-squares regression including cross-terms, which describe the selectivity, was used for model building. This combination of methods allows interpretation and easy visualization of the models within the context of ligand binding pockets, which can be translated readily into the design of novel inhibitors.

  4. A current perspective on applications of macrocyclic‐peptide‐based high‐affinity ligands

    PubMed Central

    Leenheer, Daniël; ten Dijke, Peter

    2016-01-01

    Abstract Monoclonal antibodies can bind with high affinity and high selectivity to their targets. As a tool in therapeutics or diagnostics, however, their large size (∼150 kDa) reduces penetration into tissue and prevents passive cellular uptake. To overcome these and other problems, minimized protein scaffolds have been chosen or engineered, with care taken to not compromise binding affinity or specificity. An alternate approach is to begin with a minimal non‐antibody scaffold and select functional ligands from a de novo library. We will discuss the structure, production, applications, strengths, and weaknesses of several classes of antibody‐derived ligands, that is, antibodies, intrabodies, and nanobodies, and nonantibody‐derived ligands, that is, monobodies, affibodies, and macrocyclic peptides. In particular, this review is focussed on macrocyclic peptides produced by the Random non‐standard Peptides Integrated Discovery (RaPID) system that are small in size (typically ∼2 kDa), but are able to perform tasks typically handled by larger proteinaceous ligands. PMID:27352774

  5. Bifunctional cyclam-based ligands with phosphorus acid pendant moieties for radiocopper separation: thermodynamic and kinetic studies.

    PubMed

    Paúrová, Monika; Havlíčková, Jana; Pospíšilová, Aneta; Vetrík, Miroslav; Císařová, Ivana; Stephan, Holger; Pietzsch, Hans-Jürgen; Hrubý, Martin; Hermann, Petr; Kotek, Jan

    2015-03-16

    Two macrocyclic ligands based on cyclam with trans-disposed N-methyl and N-(4-aminobenzyl) substituents as well as two methylphosphinic (H2L1) or methylphosphonic (H4L2) acid pendant arms were synthesised and investigated in solution. The ligands form stable complexes with transition metal ions. Both ligands show high thermodynamic selectivity for divalent copper over nickel(II) and zinc(II)-K(CuL) is larger than K(Ni/ZnL) by about seven orders of magnitude. Complexation is significantly faster for the phosphonate ligand H4L2, probably due to the stronger coordination ability of the more basic phosphonate groups, which efficiently bind the metal ion in an "out-of-cage" complex and thus accelerate its "in-cage" binding. The rate of Cu(II) complexation by the phosphinate ligand H2L1 is comparable to that of cyclam itself and its derivatives with non-coordinating substituents. Acid-assisted decomplexation of the copper(II) complexes is relatively fast (τ1/2 = 44 and 42 s in 1 M aq. HClO4 at 25 °C for H2L1 and H4L2, respectively). This combination of properties is convenient for selective copper removal/purification. Thus, the title ligands were employed in the preparation of ion-selective resins for radiocopper(II) separation. Glycidyl methacrylate copolymer beads were modified with the ligands through a diazotisation reaction. The separation ability of the modified polymers was tested with cold copper(II) and non-carrier-added (64)Cu in the presence of a large excess of both nickel(II) and zinc(II). The experiments exhibited high overall separation efficiency leading to 60-70% recovery of radiocopper with high selectivity over the other metal ions, which were originally present in 900-fold molar excess. The results showed that chelating resins with properly tuned selectivity of their complexing moieties can be employed for radiocopper separation.

  6. The expression of the beta cell-derived autoimmune ligand for the killer receptor nkp46 is attenuated in type 2 diabetes.

    PubMed

    Gur, Chamutal; Enk, Jonatan; Weitman, Efraim; Bachar, Etty; Suissa, Yaron; Cohen, Guy; Schyr, Rachel Ben-Haroush; Sabanay, Helena; Horwitz, Elad; Glaser, Benjamin; Dor, Yuval; Pribluda, Ariel; Hanna, Jacob H; Leibowitz, Gill; Mandelboim, Ofer

    2013-01-01

    NK cells rapidly kill tumor cells, virus infected cells and even self cells. This is mediated via killer receptors, among which NKp46 (NCR1 in mice) is prominent. We have recently demonstrated that in type 1 diabetes (T1D) NK cells accumulate in the diseased pancreas and that they manifest a hyporesponsive phenotype. In addition, we found that NKp46 recognizes an unknown ligand expressed by beta cells derived from humans and mice and that blocking of NKp46 activity prevented diabetes development. Here we investigated the properties of the unknown NKp46 ligand. We show that the NKp46 ligand is mainly located in insulin granules and that it is constitutively secreted. Following glucose stimulation the NKp46 ligand translocates to the cell membrane and its secretion decreases. We further demonstrate by using several modalities that the unknown NKp46 ligand is not insulin. Finally, we studied the expression of the NKp46 ligand in type 2 diabetes (T2D) using 3 different in vivo models and 2 species; mice and gerbils. We demonstrate that the expression of the NKp46 ligand is decreased in all models of T2D studied, suggesting that NKp46 is not involved in T2D.

  7. Affinity ligands for glycoprotein purification based on the multi-component Ugi reaction.

    PubMed

    Chen, Chen; Khoury, Graziella El; Lowe, Christopher R

    2014-10-15

    One challenge facing the purification of therapeutic glycoproteins by affinity chromatography is creating ligands specific for the glycan moiety. Affinity chromatography of glycoproteins is currently conducted with immobilized lectins or boronates, although biomimetic ligands could present a more desirable option. This work describes the rational design and combinatorial synthesis of carbohydrate-binding ligands based on the solid phase multi-component Ugi reaction. An aldehyde-functionalized Sepharose™ solid support constitutes one component (aldehyde) in the four-component reaction, while the other three components (a primary/secondary amine, a carboxylic acid and an isocyanide) are varied in a combinatorial fashion to generate a tri-substituted Ugi scaffold which provides a degree of rigidity and is functionally suitable for interacting with the glycan moiety of glycoproteins. An Ugi library containing 48 ligands was initially screened against glucose oxidase (GOx) as the model glycoprotein to identify a candidate ligand, A13C24I8, which showed affinity to GOx through its carbohydrate moiety. Immobilized ligand A13C24I8 demonstrated a static binding capacity of 16.7mg GOx/ml resin and an apparent dissociation constant (Kd) of 1.45×10(-6)M at pH 7.4. The adsorbent can also bind 8.1mg AGP/ml resin and displays an apparent affinity constant Kd=1.44×10(-5)M. The ligand has a sugar specificity in the following sequence: sorbitol>fructose>mannitol>ribose>arabinose>xylose>galactose>mannose>glucose>fructose; however, it did not display any specificity for sialic acid or methyl α-D-glycosides. A control ligand, generated by substitution of C24 (3-carboxyphenylboronic acid) with C7 (4-hydroxyphenyl acetic acid), failed to show affinity to the carbohydrate moiety, supporting the importance of the role that boronic acid group plays in sugar binding. GOx spiked E. coli samples were loaded onto immobilized ligand A13C24I8, 3-aminophenylboronic acid (APBA) and

  8. Derivation of GFDM Based on OFDM Principles

    SciTech Connect

    Hussein Moradi; Behrouz Farhang-Boroujeny

    2015-06-01

    This paper starts with discussing the principle based on which the celebrated orthogonal frequency division multiplexing (OFDM) signals are constructed. It then extends the same principle to construct the newly introduced generalized frequency division multiplexing (GFDM) signals. This novel derivation sheds light on some interesting properties of GFDM. In particular, our derivation seamlessly leads to an implementation of GFDM transmitter which has significantly lower complexity than what has been reported so far. Our derivation also facilitates a trivial understanding of how GFDM (similar to OFDM) can be applied in MIMO channels.

  9. Multiple automatic base selection: protein-ligand docking based on incremental construction without manual intervention.

    PubMed

    Rarey, M; Kramer, B; Lengauer, T

    1997-07-01

    A possible way of tackling the molecular docking problem arising in computer-aided drug design is the use of the incremental construction method. This method consists of three steps: the selection of a part of a molecule, a so-called base fragment, the placement of the base fragment into the active site of a protein, and the subsequent reconstruction of the complete drug molecule. Assuming that a part of a drug molecule is known, which is specific enough to be a good base fragment, the method is proven to be successful for a large set of docking examples. In addition, it leads to the fastest algorithms for flexible docking published so far. In most real-world applications of docking, large sets of ligands have to be tested for affinity to a given protein. Thus, manual selection of a base fragment is not practical. On the other hand, the selection of a base fragment is critical in that only few selections lead to a low-energy structure. We overcome this limitation by selecting a representative set of base fragments instead of a single one. In this paper, we present a set of rules and algorithms to automate this selection. In addition, we extend the incremental construction method to deal with multiple fragmentations of the drug molecule. Our results show that with multiple automated base selection, the quality of the docking predictions is almost as good as with one manually preselected base fragment. In addition, the set of solutions is more diverse and alternative binding modes with low scores are found. Although the run time of the overall algorithm increases, the method remains fast enough to search through large ligand data sets.

  10. Effects of inductive bias on computational evaluations of ligand-based modeling and on drug discovery

    NASA Astrophysics Data System (ADS)

    Cleves, Ann E.; Jain, Ajay N.

    2008-03-01

    Inductive bias is the set of assumptions that a person or procedure makes in making a prediction based on data. Different methods for ligand-based predictive modeling have different inductive biases, with a particularly sharp contrast between 2D and 3D similarity methods. A unique aspect of ligand design is that the data that exist to test methodology have been largely man-made, and that this process of design involves prediction. By analyzing the molecular similarities of known drugs, we show that the inductive bias of the historic drug discovery process has a very strong 2D bias. In studying the performance of ligand-based modeling methods, it is critical to account for this issue in dataset preparation, use of computational controls, and in the interpretation of results. We propose specific strategies to explicitly address the problems posed by inductive bias considerations.

  11. Chemokine CCR3 ligands-binding peptides derived from a random phage-epitope library.

    PubMed

    Houimel, Mehdi; Mazzucchelli, Luca

    2013-01-01

    peritoneal eosinophilia. The development of peptides inhibiting the interactions between hCCR3 and its chemokine ligands will facilitate the development of small peptides antagonists with the hope of ameliorating chronic inflammatory diseases in humans.

  12. Methanethiosulfonate derivatives as ligands of the STAT3-SH2 domain.

    PubMed

    Gabriele, Elena; Ricci, Chiara; Meneghetti, Fiorella; Ferri, Nicola; Asai, Akira; Sparatore, Anna

    2017-12-01

    With the aim to discover new STAT3 direct inhibitors, potentially useful as anticancer agents, a set of methanethiosulfonate drug hybrids were synthesized. The in vitro tests showed that all the thiosulfonic compounds were able to strongly and selectively bind STAT3-SH2 domain, whereas the parent drugs were completely devoid of this ability. In addition, some of them showed a moderate antiproliferative activity on HCT-116 cancer cell line. These results suggest that methanethiosulfonate moiety can be considered a useful scaffold in the preparation of new direct STAT3 inhibitors. Interestingly, an unusual kind of organo-sulfur derivative, endowed with valuable antiproliferative activity, was occasionally isolated. [Formula: see text].

  13. A novel ligand-mapping method based on molecular liquid theory.

    PubMed

    Imai, Takashi

    2011-01-01

    The recent development of a novel ligand-mapping method is reviewed. The method is based on a statistical-mechanical molecular theory of solvation, known as the three-dimensional reference interaction site model (3D-RISM). In the 3D-RISM-based ligand mapping (3D-RISM-LM) method, using the all-atom model for a target protein immersed in a ligand-water mixture solvent, the 3D-spatial distributions of the ligand atomic sites around the protein are first obtained, and then the most probable binding modes of the ligand molecule are constructed from the distributions. Unlike conventional docking simulations, 3D-RISM-LM can incorporate the effect of water from the atomic to thermodynamic level into the binding affinity through statistical mechanics. It has been demonstrated that 3D-RISM-LM can sensitively detect even weak binding modes of small molecules over the entire surface of protein. Therefore, this approach is expected to be particularly useful in fragment-based drug design.

  14. First examples of hybrids based on polyoxometalates, metal halide clusters and organic ligands

    NASA Astrophysics Data System (ADS)

    Wang, La-Mei; Fan, Yong; Wang, Yan; Xiao, Li-Na; Hu, Yang-Yang; Peng, Yu; Wang, Tie-Gang; Gao, Zhong-Min; Zheng, Da-Fang; Cui, Xiao-Bing; Xu, Ji-Qing

    2012-07-01

    Two new organic-inorganic compounds based on polyoxometalates, metal halide clusters and organic ligands: [BW12O40]2[Cu2(Phen)4Cl](H24, 4'-bpy)4·H3O·5H2O (1) and [HPW12O40][Cd2(Phen)4Cl2](4, 4'-bpy) (2) (Phen=1, 10-phenanthroline, bpy=bipyridine), have been prepared and characterized by IR, UV-vis, XPS, XRD and single crystal X-ray diffraction analyses. Crystal structure analyses reveal that compound 1 is constructed from [BW12O40]5-, metal halide clusters [Cu2(Phen)4Cl]+and 4, 4'-bpy ligands, while compound 2 is constructed from [PW12O40]3-, metal halide cluster [Cd2(Phen)4Cl2]2+ and 4, 4'-bpy ligands. Compound 1 and compound 2 are not common hybrids based on polyoxometalates and metal halide clusters, they also contain dissociated organic ligands, therefore, compound 1 and 2 are the first examples of hybrids based on polyoxometalates, metal halide clusters and organic ligands.

  15. Identification of mangiferin as a potential Glucokinase activator by structure-based virtual ligand screening

    PubMed Central

    Min, Qiuxia; Cai, Xinpei; Sun, Weiguang; gao, Fei; Li, Zhimei; Zhang, Qian; Wan, Luo-Sheng; Li, Hua; Chen, Jiachun

    2017-01-01

    The natural product mangiferin (compound 7) has been identified as a potential glucokinase activator by structure-based virtual ligand screening. It was proved by enzyme activation experiment and cell-based assays in vitro, with potency in micromolar range. Meanwhile, this compound showed good antihyperglycemic activity in db/db mice without obvious side effects such as excessive hypoglycaemia. PMID:28317897

  16. Development of a protein-ligand-binding site prediction method based on interaction energy and sequence conservation.

    PubMed

    Tsujikawa, Hiroto; Sato, Kenta; Wei, Cao; Saad, Gul; Sumikoshi, Kazuya; Nakamura, Shugo; Terada, Tohru; Shimizu, Kentaro

    2016-09-01

    We present a new method for predicting protein-ligand-binding sites based on protein three-dimensional structure and amino acid conservation. This method involves calculation of the van der Waals interaction energy between a protein and many probes placed on the protein surface and subsequent clustering of the probes with low interaction energies to identify the most energetically favorable locus. In addition, it uses amino acid conservation among homologous proteins. Ligand-binding sites were predicted by combining the interaction energy and the amino acid conservation score. The performance of our prediction method was evaluated using a non-redundant dataset of 348 ligand-bound and ligand-unbound protein structure pairs, constructed by filtering entries in a ligand-binding site structure database, LigASite. Ligand-bound structure prediction (bound prediction) indicated that 74.0 % of predicted ligand-binding sites overlapped with real ligand-binding sites by over 25 % of their volume. Ligand-unbound structure prediction (unbound prediction) indicated that 73.9 % of predicted ligand-binding residues overlapped with real ligand-binding residues. The amino acid conservation score improved the average prediction accuracy by 17.0 and 17.6 points for the bound and unbound predictions, respectively. These results demonstrate the effectiveness of the combined use of the interaction energy and amino acid conservation in the ligand-binding site prediction.

  17. Virtual Lead Identification of Farnesyltransferase Inhibitors Based on Ligand and Structure-Based Pharmacophore Techniques

    PubMed Central

    Al-Balas, Qosay A.; Amawi, Haneen A.; Hassan, Mohammad A.; Qandil, Amjad M.; Almaaytah, Ammar M.; Mhaidat, Nizar M.

    2013-01-01

    Farnesyltransferase enzyme (FTase) is considered an essential enzyme in the Ras signaling pathway associated with cancer. Thus, designing inhibitors for this enzyme might lead to the discovery of compounds with effective anticancer activity. In an attempt to obtain effective FTase inhibitors, pharmacophore hypotheses were generated using structure-based and ligand-based approaches built in Discovery Studio v3.1. Knowing the presence of the zinc feature is essential for inhibitor’s binding to the active site of FTase enzyme; further customization was applied to include this feature in the generated pharmacophore hypotheses. These pharmacophore hypotheses were thoroughly validated using various procedures such as ROC analysis and ligand pharmacophore mapping. The validated pharmacophore hypotheses were used to screen 3D databases to identify possible hits. Those which were both high ranked and showed sufficient ability to bind the zinc feature in active site, were further refined by applying drug-like criteria such as Lipiniski’s “rule of five” and ADMET filters. Finally, the two candidate compounds (ZINC39323901 and ZINC01034774) were allowed to dock using CDOCKER and GOLD in the active site of FTase enzyme to optimize hit selection. PMID:24276257

  18. Setting up a large set of protein-ligand PDB complexes for the development and validation of knowledge-based docking algorithms

    PubMed Central

    Diago, Luis A; Morell, Persy; Aguilera, Longendri; Moreno, Ernesto

    2007-01-01

    Background The number of algorithms available to predict ligand-protein interactions is large and ever-increasing. The number of test cases used to validate these methods is usually small and problem dependent. Recently, several databases have been released for further understanding of protein-ligand interactions, having the Protein Data Bank as backend support. Nevertheless, it appears to be difficult to test docking methods on a large variety of complexes. In this paper we report the development of a new database of protein-ligand complexes tailored for testing of docking algorithms. Methods Using a new definition of molecular contact, small ligands contained in the 2005 PDB edition were identified and processed. The database was enriched in molecular properties. In particular, an automated typing of ligand atoms was performed. A filtering procedure was applied to select a non-redundant dataset of complexes. Data mining was performed to obtain information on the frequencies of different types of atomic contacts. Docking simulations were run with the program DOCK. Results We compiled a large database of small ligand-protein complexes, enriched with different calculated properties, that currently contains more than 6000 non-redundant structures. As an example to demonstrate the value of the new database, we derived a new set of chemical matching rules to be used in the context of the program DOCK, based on contact frequencies between ligand atoms and points representing the protein surface, and proved their enhanced efficiency with respect to the default set of rules included in that program. Conclusion The new database constitutes a valuable resource for the development of knowledge-based docking algorithms and for testing docking programs on large sets of protein-ligand complexes. The new chemical matching rules proposed in this work significantly increase the success rate in DOCKing simulations. The database developed in this work is available at . PMID:17718923

  19. Design, engineering, and production of human recombinant t cell receptor ligands derived from human leukocyte antigen DR2.

    PubMed

    Chang, J W; Mechling, D E; Bächinger, H P; Burrows, G G

    2001-06-29

    Major histocompatibility complex (MHC) class II molecules are membrane-anchored heterodimers on the surface of antigen-presenting cells that bind the T cell receptor, initiating a cascade of interactions that results in antigen-specific activation of clonal populations of T cells. Susceptibility to multiple sclerosis is associated with certain MHC class II haplotypes, including human leukocyte antigen (HLA) DR2. Two DRB chains, DRB5*0101 and DRB1*1501, are co-expressed in the HLA-DR2 haplotype, resulting in the formation of two functional cell surface heterodimers, HLA-DR2a (DRA*0101, DRB5*0101) and HLA-DR2b (DRA*0101, DRB1*1501). Both isotypes can present an immunodominant peptide of myelin basic protein (MBP-(84-102)) to MBP-specific T cells from multiple sclerosis patients. We have previously demonstrated that the peptide binding/T cell recognition domains of rat MHC class II (alpha1 and beta1 domains) could be expressed as a single exon for structural and functional characterization; Burrows, G. G., Chang, J. W., Bächinger, H.-P., Bourdette, D. N., Wegmann, K. W., Offner, H., and Vandenbark A. A. (1999) Protein Eng. 12, 771-778; Burrows, G. G., Adlard, K. L., Bebo, B. F., Jr., Chang, J. W., Tenditnyy, K., Vandenbark, A. A., and Offner, H. (2000) J. Immunol. 164, 6366-6371). Single-chain human recombinant T cell receptor ligands (RTLs) of approximately 200 amino acid residues derived from HLA-DR2b were designed using the same principles and have been produced in Escherichia coli with and without amino-terminal extensions containing antigenic peptides. Structural characterization using circular dichroism predicted that these molecules retained the antiparallel beta-sheet platform and antiparallel alpha-helices observed in the native HLA-DR2 heterodimer. The proteins exhibited a cooperative two-state thermal unfolding transition, and DR2-derived RTLs with a covalently linked MBP peptide (MBP-(85-99)) showed increased stability to thermal unfolding relative to the

  20. Exploring weak ligand-protein interactions by long-lived NMR states: improved contrast in fragment-based drug screening.

    PubMed

    Buratto, Roberto; Mammoli, Daniele; Chiarparin, Elisabetta; Williams, Glyn; Bodenhausen, Geoffrey

    2014-10-13

    Ligands that have an affinity for protein targets can be screened very effectively by exploiting favorable properties of long-lived states (LLS) in NMR spectroscopy. In this work, we describe the use of LLS for competitive binding experiments to measure accurate dissociation constants of fragments that bind weakly to the ATP binding site of the N-terminal ATPase domain of heat shock protein 90 (Hsp90), a therapeutic target for cancer treatment. The LLS approach allows one to characterize ligands with an exceptionally wide range of affinities, since it can be used for ligand concentrations [L] that are several orders of magnitude smaller than the dissociation constants K(D). This property makes the LLS method particularly attractive for the initial steps of fragment-based drug screening, where small molecular fragments that bind weakly to a target protein must be identified, which is a difficult task for many other biophysical methods. © 2014 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the Creative Commons Attribution Non-Commercial NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

  1. Bivalent Approach for Homodimeric Estradiol Based Ligand: Synthesis and Evaluation for Targeted Theranosis of ER(+) Breast Carcinomas.

    PubMed

    Chauhan, Kanchan; Arun, Ashutosh; Singh, Saurabh; Manohar, Murli; Chuttani, Krishna; Konwar, Rituraj; Dwivedi, Anila; Soni, Ravi; Singh, Ajai Kumar; Mishra, Anil K; Datta, Anupama

    2016-04-20

    The synthesis of estradiol based bivalent ligand [(EST)2DT] is reported and its potential for targeted imaging and therapy of ER(+) tumors has been evaluated. For the purpose, ethinylestradiol was functionalized with an azidoethylamine moiety via click chemistry. The resultant derivative was reacted in a bivalent mode with DTPA-dianhydride to form the multicoordinate chelating agent, (EST)2DT which displayed capability to bind (99m)Tc. The radiolabeled complex, (99m)Tc-(EST)2DT was obtained in >99% radiochemical purity and 20-48 GBq/μmol of specific activity. RBA assay revealed ∼15% binding with estrogen receptor. Evaluation of ligand on ER(+)-cell line (MCF-7) suggested enhanced and ER-mediated uptake. In vivo assays displayed early tracer accumulation in MCF-7 xenografts with tumor to muscle ratio ∼6 in 2 h and negligible uptakes in nontargeted organs. MTT assay performed on ER(+) and ER(-) cell lines displayed selective inhibition of ER(+) cancer cell growth with IC50 = 14.3 μM which was comparable to tamoxifen. The anticancer activity of the ligand is possibly due to the increase in ERβ and suppression of ERα protein levels in gene transcription. The studies reveal the potential of (EST)2DT as diagnostic imaging agent with the additional benefits in therapy.

  2. Zn(II), Ni(II), Cu(II) and Pb(II) complexes of tridentate asymmetrical Schiff base ligands: Synthesis, characterization, properties and biological activity

    NASA Astrophysics Data System (ADS)

    Şahin, Mustafa; Koçak, Nuriye; Erdenay, Damla; Arslan, Uğur

    2013-02-01

    New asymmetrical tridentate Schiff base ligands were synthesized using 1,2-phenylenediamine, 4-methyl-1,2-phenylenediamine, 2-hydroxy-1-napthaldehyde, 9-anthracenecarboxaldehyde. Schiff base ligands and their metal complexes were synthesised and characterized by using FT-IR, 1H NMR, 13C NMR, UV-Vis, XRD, ESR, elemental analysis and fluorescence studies. The antimicrobial activity of the ligands and their metal complexes were studied against Staphylococcus aureus ATCC 29213, S. aureus ATCC 25923, Streptococcus mutans RSHM 676, Enterococcus faecalis ATCC 29212, Escherichia coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853. The determination of the antibacterial activity was done using the broth microdilution methods. In general, it has been determined that the studied compounds have MIC values similar to Gram-positive and Gram-negative bacteria. It has been found that Ni, Pb, Zn derivatives of HL1A and ZnL2A has lower MIC values than ampicillin for P. aeruginosa ATCC 27853 strain.

  3. Zn(II), Ni(II), Cu(II) and Pb(II) complexes of tridentate asymmetrical Schiff base ligands: synthesis, characterization, properties and biological activity.

    PubMed

    Şahin, Mustafa; Koçak, Nuriye; Erdenay, Damla; Arslan, Uğur

    2013-02-15

    New asymmetrical tridentate Schiff base ligands were synthesized using 1,2-phenylenediamine, 4-methyl-1,2-phenylenediamine, 2-hydroxy-1-napthaldehyde, 9-anthracenecarboxaldehyde. Schiff base ligands and their metal complexes were synthesised and characterized by using FT-IR, (1)H NMR, (13)C NMR, UV-Vis, XRD, ESR, elemental analysis and fluorescence studies. The antimicrobial activity of the ligands and their metal complexes were studied against Staphylococcus aureus ATCC 29213, S. aureus ATCC 25923, Streptococcus mutans RSHM 676, Enterococcus faecalis ATCC 29212, Escherichia coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853. The determination of the antibacterial activity was done using the broth microdilution methods. In general, it has been determined that the studied compounds have MIC values similar to Gram-positive and Gram-negative bacteria. It has been found that Ni, Pb, Zn derivatives of HL1A and ZnL(2)A has lower MIC values than ampicillin for P. aeruginosa ATCC 27853 strain.

  4. Effect of doping of calcium fluoride nanoparticles on the photoluminescence properties of europium complexes with benzoic acid derivatives as secondary ligands and 2-aminopyridine as primary ligand

    NASA Astrophysics Data System (ADS)

    Sharma, Garima; Narula, Anudeep Kumar

    2015-08-01

    The present article reports the synthesis of three Eu(III) complexes [Eu(BA)3(2-ap)] (1), [Eu(HBA)3(2-ap)] (2) and [Eu(ABA)3(2-ap)] (3) (BA = benzoic acid, HBA = 2-hydroxy benzoic acid, ABA = 2-amino benzoic acid and 2-ap = 2-aminopyridine) carried out in ethanol solution. The complexes were further doped with CaF2 nanoparticles and a change in the photoluminescence properties was observed. The compositions and structural investigation of the complexes were determined by elemental analysis and Fourier transform infrared spectroscopy (FTIR) which suggest the coordination of ligands with the central Eu(III) ion. The optical properties of the complexes were studied by Ultraviolet Visible absorption spectroscopy (UV-Vis) and photoluminescence studies (PL). The relative PL intensity was enhanced in the Eu(III) complexes doped with CaF2 nanoparticles as compared to the pure Eu(III) complexes, however the increase in intensity varied in the order of ligands ABA > HBA > BA. The photoluminescence lifetime decay curves also revealed the longer lifetime (τ) and higher quantum efficiency (η) for europium complexes with ABA ligands suggesting the efficient energy transfer and better sensitizing ability of the ligand to europium ion. The morphology of the synthesized compounds were studied by Scanning Electron Microscopy (SEM) revealing spherical morphology with agglomeration of the nanoparticles.

  5. 8-(2-Furyl)adenine derivatives as A₂A adenosine receptor ligands.

    PubMed

    Dal Ben, Diego; Buccioni, Michela; Lambertucci, Catia; Thomas, Ajiroghene; Klotz, Karl-Norbert; Federico, Stephanie; Cacciari, Barbara; Spalluto, Giampiero; Volpini, Rosaria

    2013-01-01

    Selective adenosine receptor modulators are potential tools for numerous therapeutic applications, including cardiovascular, inflammatory, and neurodegenerative diseases. In this work, the synthesis and biological evaluation at the four human adenosine receptor subtypes of a series of 9-substituted 8-(2-furyl)adenine derivatives are reported. Results show that 8-(2-furyl)-9-methyladenine is endowed with high affinity at the A₂A subtype. Further modification of this compound with introduction of arylacetyl or arylcarbamoyl groups in N(6)-position takes to different effects on the A₂A affinity and in particular on the selectivity versus the other three adenosine receptor subtypes. A molecular modelling analysis at three different A₂A receptor crystal structures provides an interpretation of the obtained biological results. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  6. Structural dynamics of myoglobin: ligand migration among protein cavities studied by Fourier transform infrared/temperature derivative spectroscopy.

    PubMed

    Lamb, Don C; Nienhaus, Karin; Arcovito, Alessandro; Draghi, Federica; Miele, Adriana E; Brunori, Maurizio; Nienhaus, G Ulrich

    2002-04-05

    Fourier transform infrared (FTIR) spectroscopy in the CO stretch bands combined with temperature derivative spectroscopy (TDS) was used to characterize intermediate states obtained by photolysis of two sperm whale mutant myoglobins, YQR (L29(B10)Y, H64(E7)Q, T67(E10)R) and YQRF (with an additional I107(G8)F replacement). Both mutants assume two different bound-state conformations, A(0) and A(3), which can be distinguished by their different CO bands near 1965 and 1933 cm(-1). They most likely originate from different conformations of the Gln-64 side chain. Within each A substate, a number of photoproduct states have been characterized on the basis of the temperature dependence of recombination in TDS experiments. Different locations and orientations of the ligand within the protein can be distinguished by the infrared spectra of the photolyzed CO. Recombination from the primary docking site, B, near the heme dominates below 50 K. Above 60 K, ligand rebinding occurs predominantly from a secondary docking site, C', in which the CO is trapped in the Xe4 cavity on the distal side, as shown by crystallography of photolyzed YQR and L29W myoglobin CO. Another kinetic state (C") has been identified from which rebinding occurs around 130 K. Moreover, a population appearing above the solvent glass transition at approximately 180 K (D state) is assigned to rebinding from the Xe1 cavity, as suggested by the photoproduct structure of the L29W sperm whale myoglobin mutant. For both the YQR and YQRF mutants, rebinding from the B sites near the heme differs for the two A substates, supporting the view that the return of the ligand from the C', C", and D states is not governed by the recombination barrier at the heme iron but rather by migration to the active site. Comparison of YQR and YQRF shows that access to the Xe4 site (C') is severely restricted by introduction of the bulky Phe side chain at position 107.

  7. Identification of novel RHPS4-derivative ligands with improved toxicological profiles and telomere-targeting activities.

    PubMed

    Rizzo, Angela; Iachettini, Sara; Zizza, Pasquale; Cingolani, Chiara; Porru, Manuela; Artuso, Simona; Stevens, Malcolm; Hummersone, Marc; Biroccio, Annamaria; Salvati, Erica; Leonetti, Carlo

    2014-10-06

    The pentacyclic acridinium salt RHPS4 (3,11-difluoro-6,8,13-trimethyl-8H-quino [4,3,2-kl] acridinium methosulfate, compound 1) is one of the most interesting DNA G-quadruplex binding molecules due to its high efficacy in tumor cell growth inhibition both in in vitro models and in vivo against human tumor xenografts in combination with conventional chemotherapeutics. Despite compound 1 having desirable chemical and pharmaceutical properties, its potential as a therapeutic agent is compromised by off-target effects on cardiovascular physiology. In this paper we report a new series of structurally-related compounds which were developed in an attempt to minimize its off-target profile, but maintaining the same favorable chemical and pharmacological features of the lead compound. By performing a comparative analysis it was possible to identify which derivatives had the following properties: (i) to show a reduced capacity in respect to compound 1 to inhibit the hERG tail current tested in a patch clamp assay and/or to interact with the human recombinant β2 receptor; (ii) to maintain both a good G4-binding affinity and cancer cell selectivity; and (iii) to trigger DNA damage with specific telomere uncapping. These studies allowed us to identify a novel G4-stabilizing molecule, compound 8, being characterized by reduced off-target effects and potent telomere on-target properties compared to the prototypic compound 1. Moreover, compound 8 shares with compound 1 the same molecular mode of action and an anti-tumour activity specifically restricted to replicating cells, as evident with its particularly efficient activity in combination therapy with a topoisomerase I inhibitor. In conclusion, we have identified a new pentacyclic derivative 8 having suitable properties to be the focus of further investigations as a clinical candidate for cancer therapy.

  8. Genetically Encoded Fragment-Based Discovery of Glycopeptide Ligands for Carbohydrate-Binding Proteins

    DOE PAGES

    Ng, Simon; Lin, Edith; Kitov, Pavel I.; ...

    2015-04-10

    Here we describe an approach to accelerate the search for competitive inhibitors for carbohydrate-recognition domains (CRDs). Genetically encoded fragment-based-discovery (GE-FBD) uses selection of phagedisplayed glycopeptides to dock a glycan fragment at the CRD and guide selection of Synergistic peptide motifs adjacent to the CRD. Starting from concanavalin A (ConA), a mannose (Man)-binding protein, as a bait, we narrowed a library of 108 glycopeptides to 86 leads that share a consensus motif, Man-WYD. Validation of synthetic leads yielded Man-WYDLF that exhibited 40 50-fold enhancement in affinity over methyl α-D-mannopyranoside (MeMan). Lectin array Suggested specificity: Man-WYD derivative bound only to 3 outmore » of 17 proteins-ConA, LcH, and PSA-that bind to Man. An X-ray structure of ConA.:Man-WYD proved that the trimannoside core and Man-WYD exhibit identical CRD docking; but their extra-CRD binding modes are significantly. different. Still, they have comparable affinity and selectivity for various Man-binding proteins. The intriguing observation provides new insight into functional mimicry :of carbohydrates by peptide ligands. GE-FBD may provide an alternative to rapidly search for competitive inhibitors for lectins.« less

  9. Genetically Encoded Fragment-Based Discovery of Glycopeptide Ligands for Carbohydrate-Binding Proteins

    SciTech Connect

    Ng, Simon; Lin, Edith; Kitov, Pavel I.; Tjhung, Katrina F.; Gerlits, Oksana O.; Deng, Lu; Kasper, Brian; Sood, Amika; Paschal, Beth M.; Zhang, Ping; Ling, Chang-Chun; Klassen, John S.; Noren, Christopher J.; Mahal, Lara K.; Woods, Robert J.; Coates, Leighton; Derda, Ratmir

    2015-04-10

    Here we describe an approach to accelerate the search for competitive inhibitors for carbohydrate-recognition domains (CRDs). Genetically encoded fragment-based-discovery (GE-FBD) uses selection of phagedisplayed glycopeptides to dock a glycan fragment at the CRD and guide selection of Synergistic peptide motifs adjacent to the CRD. Starting from concanavalin A (ConA), a mannose (Man)-binding protein, as a bait, we narrowed a library of 108 glycopeptides to 86 leads that share a consensus motif, Man-WYD. Validation of synthetic leads yielded Man-WYDLF that exhibited 40 50-fold enhancement in affinity over methyl α-D-mannopyranoside (MeMan). Lectin array Suggested specificity: Man-WYD derivative bound only to 3 out of 17 proteins-ConA, LcH, and PSA-that bind to Man. An X-ray structure of ConA.:Man-WYD proved that the trimannoside core and Man-WYD exhibit identical CRD docking; but their extra-CRD binding modes are significantly. different. Still, they have comparable affinity and selectivity for various Man-binding proteins. The intriguing observation provides new insight into functional mimicry :of carbohydrates by peptide ligands. GE-FBD may provide an alternative to rapidly search for competitive inhibitors for lectins.

  10. Fast force field-based optimization of protein-ligand complexes with graphics processor.

    PubMed

    Heinzerling, Lennart; Klein, Robert; Rarey, Matthias

    2012-12-15

    Usually based on molecular mechanics force fields, the post-optimization of ligand poses is typically the most time-consuming step in protein-ligand docking procedures. In return, it bears the potential to overcome the limitations of discretized conformation models. Because of the parallel nature of the problem, recent graphics processing units (GPUs) can be applied to address this dilemma. We present a novel algorithmic approach for parallelizing and thus massively speeding up protein-ligand complex optimizations with GPUs. The method, customized to pose-optimization, performs at least 100 times faster than widely used CPU-based optimization tools. An improvement in Root-Mean-Square Distance (RMSD) compared to the original docking pose of up to 42% can be achieved. Copyright © 2012 Wiley Periodicals, Inc.

  11. Generating "fragment-based virtual library" using pocket similarity search of ligand-receptor complexes.

    PubMed

    Khashan, Raed S

    2015-01-01

    As the number of available ligand-receptor complexes is increasing, researchers are becoming more dedicated to mine these complexes to aid in the drug design and development process. We present free software which is developed as a tool for performing similarity search across ligand-receptor complexes for identifying binding pockets which are similar to that of a target receptor. The search is based on 3D-geometric and chemical similarity of the atoms forming the binding pocket. For each match identified, the ligand's fragment(s) corresponding to that binding pocket are extracted, thus forming a virtual library of fragments (FragVLib) that is useful for structure-based drug design. The program provides a very useful tool to explore available databases.

  12. Development of a quantitative fluorescence-based ligand-binding assay

    PubMed Central

    Breen, Conor J.; Raverdeau, Mathilde; Voorheis, H. Paul

    2016-01-01

    A major goal of biology is to develop a quantitative ligand-binding assay that does not involve the use of radioactivity. Existing fluorescence-based assays have a serious drawback due to fluorescence quenching that accompanies the binding of fluorescently-labeled ligands to their receptors. This limitation of existing fluorescence-based assays prevents the number of cellular receptors under investigation from being accurately measured. We have developed a method where FITC-labeled proteins bound to a cell surface are proteolyzed extensively to eliminate fluorescence quenching and then the fluorescence of the resulting sample is compared to that of a known concentration of the proteolyzed FITC-protein employed. This step enables the number of cellular receptors to be measured quantitatively. We expect that this method will provide researchers with a viable alternative to the use of radioactivity in ligand binding assays. PMID:27161290

  13. PyPLIF: Python-based Protein-Ligand Interaction Fingerprinting.

    PubMed

    Radifar, Muhammad; Yuniarti, Nunung; Istyastono, Enade Perdana

    2013-01-01

    Structure-based virtual screening (SBVS) methods often rely on docking score. The docking score is an over-simplification of the actual ligand-target binding. Its capability to model and predict the actual binding reality is limited. Recently, interaction fingerprinting (IFP) has come and offered us an alternative way to model reality. IFP provides us an alternate way to examine protein-ligand interactions. The docking score indicates the approximate affinity and IFP shows the interaction specificity. IFP is a method to convert three dimensional (3D) protein-ligand interactions into one dimensional (1D) bitstrings. The bitstrings are subsequently employed to compare the protein-ligand interaction predicted by the docking tool against the reference ligand. These comparisons produce scores that can be used to enhance the quality of SBVS campaigns. However, some IFP tools are either proprietary or using a proprietary library, which limits the access to the tools and the development of customized IFP algorithm. Therefore, we have developed PyPLIF, a Python-based open source tool to analyze IFP. In this article, we describe PyPLIF and its application to enhance the quality of SBVS in order to identify antagonists for estrogen α receptor (ERα). PyPLIF is freely available at http://code.google.com/p/pyplif.

  14. The Development of Quantitative Structure-Binding Affinity Relationship (QSBR) Models Based on Novel Geometrical Chemical Descriptors of the Protein-Ligand Interfaces

    PubMed Central

    Zhang, Shuxing; Golbraikh, Alexander; Tropsha, Alexander

    2009-01-01

    Novel geometrical chemical descriptors have been derived based on the computational geometry of protein-ligand interfaces and Pauling atomic electronegativities (EN). Delaunay tessellation has been applied to a diverse set of 517 X-ray characterized protein-ligand complexes yielding a unique collection of interfacial nearest neighbor atomic quadruplets for each complex. Each quadruplet composition was characterized by a single descriptor calculated as the sum of the EN values for the four participating atom types. We termed these simple descriptors generated from atomic EN values and derived with the Delaunay Tessellation the ENTess descriptors and used them in the variable selection k-Nearest Neighbor quantitative structure-binding affinity relationship (QSBR) studies of 264 diverse protein-ligand complexes with known binding constants. 24 complexes with chemically dissimilar ligands were set aside as an independent validation set, and the remaining dataset of 240 complexes was divided into multiple training and test sets. The best models were characterized by the leave-one-out cross-validated correlation coefficient q2 as high as 0.66 for the training set and the correlation coefficient R2 as high as 0.83 for the test set. High predictive power of these models was confirmed independently by applying them to the validation set of 24 complexes yielding R2 as high as 0.85. We conclude that QSBR models built with the ENTess descriptors can be instrumental for predicting the binding affinity of receptor-ligand complexes. PMID:16640331

  15. An Analysis of Central Residues Between Ligand-Bound and Ligand-Free Protein Structures Based on Network Approach.

    PubMed

    Amala, Arumugam; Emerson, Isacc Arnold

    2017-08-01

    Depiction of protein structures as networks of interacting residues has enabled us to understand the structure and function of the protein. Previous investigations on closeness centrality have identified protein functional sites from three- dimensional structures. It is well recognized that ligand binding to a receptor protein induces a wide range of structural changes. An interesting question is how central residues function during conformational changes triggered during ligand binding? The aim of this study is to comprehend at what extent central residues change during ligand binding to receptor proteins. To determine this, we examined 37 pairs of protein structures consisting of ligand-bound and ligand-free forms. These protein structures were modelled as an undirected network and significant central residues were obtained using residue centrality measures. In addition to these, the basic network parameters were also analysed. On analysing the residue centrality measures, we observed that 60% of central residues were common in both the ligand-bound and ligand-free states. The geometry of the central residues revealed that they were situated closer to the protein center of the mass. Finally, we demonstrated the effectiveness of central residues in amino acids substitutions and in the evolution itself. The closeness centrality was also analyzed among different protein domain sizes and the values gradually declined from single-domains to multi-domain proteins suggesting that the network has potential for hierarchical organization. Betweenness centrality measure was also used to determine the central residues and 31% of these residues were common between the holo/apo states. Findings reveal that central residues play a significant role in determining the functional properties of proteins. These results have implications in predicting binding/active site residues, specifically in the context of drug designing, if additional information concerning ligand binding is

  16. Deriving Framework Usages Based on Behavioral Models

    NASA Astrophysics Data System (ADS)

    Zenmyo, Teruyoshi; Kobayashi, Takashi; Saeki, Motoshi

    One of the critical issue in framework-based software development is a huge introduction cost caused by technical gap between developers and users of frameworks. This paper proposes a technique for deriving framework usages to implement a given requirements specification. By using the derived usages, the users can use the frameworks without understanding the framework in detail. Requirements specifications which describe definite behavioral requirements cannot be related to frameworks in as-is since the frameworks do not have definite control structure so that the users can customize them to suit given requirements specifications. To cope with this issue, a new technique based on satisfiability problems (SAT) is employed to derive the control structures of the framework model. In the proposed technique, requirements specifications and frameworks are modeled based on Labeled Transition Systems (LTSs) with branch conditions represented by predicates. Truth assignments of the branch conditions in the framework models are not given initially for representing the customizable control structure. The derivation of truth assignments of the branch conditions is regarded as the SAT by assuming relations between termination states of the requirements specification model and ones of the framework model. This derivation technique is incorporated into a technique we have proposed previously for relating actions of requirements specifications to ones of frameworks. Furthermore, this paper discuss a case study of typical use cases in e-commerce systems.

  17. Evaluation of the genotoxic potential of three phenyltetrahydropyridinyl butylazole-derived sigma-receptor ligand drug candidates.

    PubMed

    Guzmán, Antonio; García, Concepción; Marín, Ana-Paz; Proudlock, Raymond J; Fernández de Henestrosa, Antonio R; Ruiz, Maria Teresa; Tortajada, Araceli; Lloyd, Mel; Marcos, Ricard

    2008-05-31

    Three structurally related phenyltetrahydropyridinyl butylazole (PTHPB)-derived drug candidates with sigma receptor-binding properties were evaluated for genotoxic potential in the ICH standard battery of genetic toxicology assays. These comprised an Ames test, a mouse-lymphoma assay, and a mouse bone-marrow micronucleus test. The maximum test concentrations in the in vitro assays were determined by the solubility and/or the cytotoxicity of the compounds. In the mouse micronucleus assay, the compounds were administered orally at three levels up to the maximum tolerated dose (MTD). Negative results were obtained for all three drug candidates in the Ames test and in the mouse-lymphoma assay, both in the absence or presence of metabolic activation. In the mouse micronucleus test, there was no effect on the frequency of micronucleated polychromatic erythrocytes (MNPCE) in bone marrow after oral administration of any of the three test compounds, at any dose level or sampling time (24 and 48h). Administration of all three compounds at the MTD induced a clear decrease in mouse body-temperature of 3.1-4.8 degrees C below normal; the temperature returned to normal within 8h of dose administration. The produced mild hypothermia and absence of micronucleus induction was in contrast to the induction of MNPCE secondary to marked hypothermia reported for a structurally similar PTHPB-derived sigma-receptor ligand, the antipsychotic compound E-5842. The results obtained in the current series of studies suggest that exposure to the three tested PTHPB-derived drug candidates would not pose a genotoxic risk under clinical conditions.

  18. Synthesis and evaluation of tetrahydroindazole derivatives as sigma-2 receptor ligands.

    PubMed

    Wu, Zong-Wen; Song, Shu-Yong; Li, Li; Lu, He-Lin; Lieberman, Brian; Huang, Yun-Sheng; Mach, Robert H

    2015-04-01

    A series of tetrahydroindazole derivatives were synthesized and evaluated for their affinities for both sigma-1 and sigma-2 receptors. These compounds are hybrid structures of a tetrahydroindazole substituted benzamide and a 6,7-dimethoxy-1,2,3,4-tetrahydroisoquinoline moiety or a 9-azabicyclo[3.3.1]nonan-3-yl-amine moiety. These newly synthesized hybrid analogs showed various affinities for sigma-2 receptor without any significant affinities for sigma-1 receptor. In particular, compounds 12, 15b, 15c, and 15d, demonstrated moderate affinity and excellent selectivity for sigma-2 receptor. It is interesting to note that 3-5 carbon units between the tetrahydroindazole substituted benzamide and the 6,7-dimethoxy-1,2,3,4-tetrahydroisoquinoline moiety are appropriate for sigma-2 receptor binding. No substitution on the 9-aza nitrogen is proper for sigma-2 affinity in the 2-(9-azabicyclo[3.3.1]nonan-3-yl-amino)-4-(3,6,6-trimethyl-4-oxo-4,5,6,7-tetrahydro-1H-indazol-1-yl)benzamide analogs.

  19. Exploring conformational search protocols for ligand-based virtual screening and 3-D QSAR modeling

    NASA Astrophysics Data System (ADS)

    Cappel, Daniel; Dixon, Steven L.; Sherman, Woody; Duan, Jianxin

    2015-02-01

    3-D ligand conformations are required for most ligand-based drug design methods, such as pharmacophore modeling, shape-based screening, and 3-D QSAR model building. Many studies of conformational search methods have focused on the reproduction of crystal structures (i.e. bioactive conformations); however, for ligand-based modeling the key question is how to generate a ligand alignment that produces the best results for a given query molecule. In this work, we study different conformation generation modes of ConfGen and the impact on virtual screening (Shape Screening and e-Pharmacophore) and QSAR predictions (atom-based and field-based). In addition, we develop a new search method, called common scaffold alignment, that automatically detects the maximum common scaffold between each screening molecule and the query to ensure identical coordinates of the common core, thereby minimizing the noise introduced by analogous parts of the molecules. In general, we find that virtual screening results are relatively insensitive to the conformational search protocol; hence, a conformational search method that generates fewer conformations could be considered "better" because it is more computationally efficient for screening. However, for 3-D QSAR modeling we find that more thorough conformational sampling tends to produce better QSAR predictions. In addition, significant improvements in QSAR predictions are obtained with the common scaffold alignment protocol developed in this work, which focuses conformational sampling on parts of the molecules that are not part of the common scaffold.

  20. Enhanced association for C70 over C60 with a metal complex with corannulene derivate ligands.

    PubMed

    Álvarez, Celedonio M; García-Escudero, Luis A; García-Rodríguez, Raúl; Martín-Álvarez, Jose M; Miguel, Daniel; Rayón, Víctor M

    2014-11-14

    The geometry imposed by the coordination sphere around the metal, together with the choice of the "arms" can be advantageously used to build corannulene-based molecular tweezers, which show great affinities for C60 and C70, as revealed by NMR titration experiments, mass spectroscopy, DFT calculations and the single crystal X-ray structural analysis of the compound C60 ⊂1.

  1. Asymmetric Hydrogenation of Quinoline Derivatives Catalyzed by Cationic Transition Metal Complexes of Chiral Diamine Ligands: Scope, Mechanism and Catalyst Recycling.

    PubMed

    Luo, Yi-Er; He, Yan-Mei; Fan, Qing-Hua

    2016-12-01

    This personal account is focused on the asymmetric hydrogenation of quinolines and their analogues recently developed by using phosphorus-free chiral cationic ruthenium(II)/η(6) -arene-N-monosulfonylated diamine complexes. In our initial study, the chiral Ru-diamine complexes were found to be highly effective catalysts for the asymmetric hydrogenation of difficult quinoline substrates in room temperature ionic liquids (RTILs) with unprecedentedly excellent enantioselectivity. Our further systematic study revealed that a wide range of quinoline derivatives could be efficiently hydrogenated in alcoholic solvents, or under solvent-free and concentrated conditions with good to excellent stereoselectivity. Complexes of iridium analogues could also efficiently catalyze the asymmetric hydrogenation of quinolines in undegassed solvent. Asymmetric tandem reduction of various 2-(aroylmethyl)quinolines was achieved in high yield with excellent enantioselectivity and good diastereoselectivity. More challenging substrates, alkyl- and aryl-substituted 1,5- and 1,8-naphthyridine derivatives were successfully hydrogenated with these chiral ruthenium catalysts to give 1,2,3,4-tetrahydronaphthyridines with good to excellent enantioselectivity. Unlike the asymmetric hydrogenation of ketones, quinoline is reduced via a stepwise H(+) /H(-) transfer process outside the coordination sphere rather than a concerted mechanism. The enantioselectivity originates from the CH/π attraction between the η(6) -arene ligand in the Ru-complex and the fused phenyl ring of dihydroquinoline via a 10-membered ring transition state with the participation of TfO(-) anion. In addition, the Ru-catalyzed asymmetric hydrogenation of quinolines could be carried out in some environmentally benign reaction media, such as undegassed water, RTILs and oligo(ethylene glycol)s (OEGs). In the latter two cases, unique chemoselectivity and/or reactivity were observed. Catalyst recycling could also be realized by using

  2. An ELISA Based Binding and Competition Method to Rapidly Determine Ligand-receptor Interactions.

    PubMed

    Syedbasha, Mohameedyaseen; Linnik, Janina; Santer, Deanna; O'Shea, Daire; Barakat, Khaled; Joyce, Michael; Khanna, Nina; Tyrrell, D Lorne; Houghton, Michael; Egli, Adrian

    2016-03-14

    A comprehensive understanding of signaling pathways requires detailed knowledge regarding ligand-receptor interaction. This article describes two fast and reliable point-by-point protocols of enzyme-linked immunosorbent assays (ELISAs) for the investigation of ligand-receptor interactions: the direct ligand-receptor interaction assay (LRA) and the competition LRA. As a case study, the ELISA based analysis of the interaction between different lambda interferons (IFNLs) and the alpha subunit of their receptor (IL28RA) is presented: the direct LRA is used for the determination of dissociation constants (KD values) between receptor and IFN ligands, and the competition LRA for the determination of the inhibitory capacity of an oligopeptide, which was designed to compete with the IFNLs at their receptor binding site. Analytical steps to estimate KD and half maximal inhibitory concentration (IC50) values are described. Finally, the discussion highlights advantages and disadvantages of the presented method and how the results enable a better molecular understanding of ligand-receptor interactions.

  3. Highly active chromium-based selective ethylene tri-/tetramerization catalysts supported by PNPO phosphazane ligands.

    PubMed

    Zhou, Yusheng; Wu, Hongfei; Xu, Sheng; Zhang, Xuejun; Shi, Min; Zhang, Jun

    2015-05-28

    Novel Cr(iii) catalysts supported by PNPO phosphazane ligands of the type Ph2PN(R)P(Ph)OAr have been prepared, all of which, upon activation with MMAO-3A, are highly active in ethylene tri-/tetramerization with considerable selectivity. The effect of ligand substitution on the catalytic performance has been examined. The Cr precatalyst supported by the PNPO phosphazane ligand with an N-cyclohexyl achieved high activity of 316.7 kg (g Cr h(-1))(-1) and a high total selectivity of 85.1% towards valuable 1-hexene (45.7%) and 1-octene (39.4%) using chlorobenzene as the solvent at 35 bar and 40 °C. In methylcyclohexane, the precatalyst supported by [Ph2PN((i)Pr)P(Ph)OPh] exhibited a higher 1-octene selectivity (54.0%) with a considerable activity of 73.3 kg (g Cr h(-1))(-1) at 35 bar and 40 °C. With the fine-tuned ligand backbone, such a PNPO phosphazane-based catalyst system provides a mode for precise understanding of the impact of ligand variations on catalytic performance.

  4. A DNA-Based T Cell Receptor Reveals a Role for Receptor Clustering in Ligand Discrimination.

    PubMed

    Taylor, Marcus J; Husain, Kabir; Gartner, Zev J; Mayor, Satyajit; Vale, Ronald D

    2017-03-23

    A T cell mounts an immune response by measuring the binding strength of its T cell receptor (TCR) for peptide-loaded MHCs (pMHC) on an antigen-presenting cell. How T cells convert the lifetime of the extracellular TCR-pMHC interaction into an intracellular signal remains unknown. Here, we developed a synthetic signaling system in which the extracellular domains of the TCR and pMHC were replaced with short hybridizing strands of DNA. Remarkably, T cells can discriminate between DNA ligands differing by a single base pair. Single-molecule imaging reveals that signaling is initiated when single ligand-bound receptors are converted into clusters, a time-dependent process requiring ligands with longer bound times. A computation model reveals that receptor clustering serves a kinetic proofreading function, enabling ligands with longer bound times to have disproportionally greater signaling outputs. These results suggest that spatial reorganization of receptors plays an important role in ligand discrimination in T cell signaling. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. A computational approach to predicting ligand selectivity for the size-based separation of trivalent lanthanides

    DOE PAGES

    Ivanov, Alexander S.; Bryantsev, Vyacheslav S.

    2016-06-20

    An accurate description of solvation effects for trivalent lanthanide ions is a main stumbling block to the qualitative prediction of selectivity trends along the lanthanide series. In this work, we propose a simple model to describe the differential effect of solvation in the competitive binding of a ligand by lanthanide ions by including weakly co-ordinated counterions in the complexes of more than a +1 charge. The success of the approach to quantitatively reproduce selectivities obtained from aqueous phase complexation studies demonstrates its potential for the design and screening of new ligands for efficient size-based separation.

  6. A computational approach to predicting ligand selectivity for the size-based separation of trivalent lanthanides

    SciTech Connect

    Ivanov, Alexander S.; Bryantsev, Vyacheslav S.

    2016-06-20

    An accurate description of solvation effects for trivalent lanthanide ions is a main stumbling block to the qualitative prediction of selectivity trends along the lanthanide series. In this work, we propose a simple model to describe the differential effect of solvation in the competitive binding of a ligand by lanthanide ions by including weakly co-ordinated counterions in the complexes of more than a +1 charge. The success of the approach to quantitatively reproduce selectivities obtained from aqueous phase complexation studies demonstrates its potential for the design and screening of new ligands for efficient size-based separation.

  7. Novel multiple opioid ligands based on 4-aminobenzazepinone (Aba), azepinoindole (Aia) and tetrahydroisoquinoline (Tic) scaffolds

    PubMed Central

    Ballet, Steven; Marczak, Ewa D.; Feytens, Debby; Salvadori, Severo; Sasaki, Yusuke; Abell, Andrew D.; Lazarus, Lawrence H.; Balboni, Gianfranco; Tourwé, Dirk

    2010-01-01

    The dimerization and trimerization of the Dmt-Tic, Dmt-Aia and Dmt-Aba pharmacophores provided multiple ligands which were evaluated in vitro for opioid receptor binding and functional activity. Whereas the Tic- and Aba multimers proved to be dual and balanced δ/μ antagonists, as determined by the functional [S35]GTPγS binding assay, the dimerization of potent Aia-based ‘parent’ ligands unexpectedly resulted in substantial less efficient receptor binding and non-active dimeric compounds. PMID:20137938

  8. Calix[6]azacryptand Ligand with a Sterically Protected Tren-Based Coordination Site for Metal Ions.

    PubMed

    Zahim, Sara; Wickramasinghe, Lasantha A; Evano, Gwilherm; Jabin, Ivan; Schrock, Richard R; Müller, Peter

    2016-04-01

    A new calix[6]azacryptand ligand has been prepared in six steps starting from 1,3,5-trismethoxycalix[6]arene. An X-ray study shows that this ligand has a sterically protected tren-based binding site at the bottom of a polyaromatic bowl and ether sites around its rim. It binds Zn(2+) to give a complex in which zinc is in a trigonal bipyramidal geometry with a water bound in one apical position and two additional hydrogen-bonded waters that fill the calixarene cavity.

  9. Fragment-Based Design of Selective Nanomolar Ligands of the CREBBP Bromodomain.

    PubMed

    Unzue, Andrea; Xu, Min; Dong, Jing; Wiedmer, Lars; Spiliotopoulos, Dimitrios; Caflisch, Amedeo; Nevado, Cristina

    2016-02-25

    Novel ligands of the CREBBP bromodomain were identified by fragment-based docking. The in silico discovered hits have been optimized by chemical synthesis into selective nanomolar compounds, thereby preserving the ligand efficiency. The selectivity for the CREBBP bromodomain over other human bromodomain subfamilies has achieved by a benzoate moiety which was predicted by docking to be involved in favorable electrostatic interactions with the Arg1173 side chain, a prediction that could be verified a posteriori by the high-resolution crystal structure of the CREBBP bromodomain in complex with ligand 6 and also by MD simulations (see Xu, M.; Unzue, A.; Dong, J.; Spiliotopoulos, D.; Nevado, C.; Caflisch, A. Discovery of CREBBP bromodomain inhibitors by high-throughput docking and hit optimization guided by molecular dynamics. J. Med. Chem. 2015, DOI: 10.1021/acs.jmedchem.5b00171).

  10. Fragment-based Analysis of Ligand Dockings Improves Classification of Actives

    PubMed Central

    Forli, Stefano; Goodsell, David; O’Donnell, T. J.; Olson, Arthur

    2016-01-01

    We describe ADChemCast, a method for using results from virtual screening to create a richer representation of a target binding site, which may be used to improve ranking of compounds and characterize the determinants of ligand-receptor specificity. ADChemCast clusters docked conformations of ligands based on shared pairwise receptor-ligand interactions within chemically similar structural fragments, building a set of attributes characteristic of binders and non-binders. Machine learning is then used to build rules from the most informational attributes for use in reranking of compounds. In this report, we use ADChemCast to improve the ranking of compounds in 11 diverse proteins from the Database of Useful Decoys-Enhanced (DUD-E), and demonstrate the utility of the method for characterizing relevant binding attributes in HIV reverse transcriptase. PMID:27384036

  11. Iminosugar-based ceramide mimicry for the design of new CERT START domain ligands.

    PubMed

    Santos, Cécile; Stauffert, Fabien; Ballereau, Stéphanie; Dehoux, Cécile; Rodriguez, Frédéric; Bodlenner, Anne; Compain, Philippe; Génisson, Yves

    2017-03-15

    The enigmatical dichotomy between the two CERT/GPBP protein isoforms, their vast panel of biological implications and the scarcity of known antagonist series call for new ligand chemotypes identification. We report the design of iminosugar-based ceramide mimics for the development of new START domain ligands potentially targeting either protein isoforms. Strategic choice of (i) an iminoxylitol core structure and (ii) the positioning of two dodecyl residues led to an extent of protein binding comparable to that of the natural cargo lipid ceramide or the archetypical inhibitor HPA-12. Molecular docking study evidenced a possible mode of protein binding fully coherent with the one observed in crystalline co-structures of known ligands. The present study thus paves the way for cellular CERT inhibition studies en route to the development of pharmacological tools aiming at deciphering the respective function and therapeutic potential of the two CERT/GPBP protein isoforms.

  12. Design of α7 nicotinic acetylcholine receptor ligands in quinuclidine, tropane and quinazoline series. Chemistry, molecular modeling, radiochemistry, in vitro and in rats evaluations of a [(18)F] quinuclidine derivative.

    PubMed

    Pin, Frédéric; Vercouillie, Johnny; Ouach, Aziz; Mavel, Sylvie; Gulhan, Zuhal; Chicheri, Gabrielle; Jarry, Christian; Massip, Stephane; Deloye, Jean-Bernard; Guilloteau, Denis; Suzenet, Franck; Chalon, Sylvie; Routier, Sylvain

    2014-07-23

    In this report, we describe the synthesis of a novel library of α7 nAChR ligands based on the modulation of the quinuclidine, quinazoline and tropane moieties. Spirane derivatives were newly synthesized under stereo specific 1,3 dipolar cylcoadditions. Only amide derivatives bonded efficiently to the receptor with Ki measured between 14 and 133 nM. The best fluorinated candidate was selected and radiolabeled. The potent [(18)F]4 PET tracer was evaluated in rats and its brain accumulation quantified. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  13. New Cu(II) coordination polymer by chiral tridentate Schiff base ligand

    NASA Astrophysics Data System (ADS)

    Messai, Amel; Bilge, Duygu; Bilge, Metin; Parlak, Cemal

    2017-06-01

    The present research reports the synthesis, X-ray, magnetic and electronic properties for novel coordination polymer based upon copper (II) with chiral tridentate Schiff base ligand synthesized at condensation of acetylacetone and L-leucine amino acid. The investigation was also conducted by quantum mechanical calculations. The large energy gap indicates a high kinetic stability. Magnetic measurement gives predominant antiferromagnetic interactions within the chain. Results reveals further insight into copper(II) chiral tridentate Schiff base complexes.

  14. Synthesis, spectroscopic, thermal and antimicrobial studies of neodymium(III) and samarium(III) complexes derived from tetradentate ligands containing N and S donor atoms

    NASA Astrophysics Data System (ADS)

    Ain, Qurratul; Pandey, S. K.; Pandey, O. P.; Sengupta, S. K.

    2015-04-01

    Trivalent lanthanide complexes of the type [Ln(L)Cl(H2O)2] (where Ln = Nd(III) or Sm(III) and LH2 = Schiff bases derived by the condensation of 3-(phenyl/substitutedphenyl)-4-amino-5-mercapto-1,2,4-triazole with diacetyl/benzil) have been synthesized by the reactions of anhydrous lanthanide(III) chloride with Schiff bases in methanol. The structures of the complexes have been proposed on the basis of elemental analysis, electrical conductance, magnetic moment, spectroscopic measurements (IR, 1H, 13C NMR and UV-vis spectra) and X-ray diffraction studies. The spectral data reveal that the Schiff base ligands behave as dibasic tetradentate chelating agents having coordination sites at two thiol sulfur atoms and two azomethine nitrogen atoms. The presence of coordinated water in metal complexes was confirmed by thermal and IR data of the complexes. All the Schiff bases and their metal complexes have also been screened for their antibacterial activity against Bacillus subtilis, Staphylococcus aureus and antifungal activities against Aspergillus niger, Curvularia pallescens and Colletotrichum capsici.

  15. Synthesis, spectroscopic, thermal and antimicrobial studies of neodymium(III) and samarium(III) complexes derived from tetradentate ligands containing N and S donor atoms.

    PubMed

    Ain, Qurratul; Pandey, S K; Pandey, O P; Sengupta, S K

    2015-04-05

    Trivalent lanthanide complexes of the type [Ln(L)Cl(H2O)2] (where Ln=Nd(III) or Sm(III) and LH2=Schiff bases derived by the condensation of 3-(phenyl/substitutedphenyl)-4-amino-5-mercapto-1,2,4-triazole with diacetyl/benzil) have been synthesized by the reactions of anhydrous lanthanide(III) chloride with Schiff bases in methanol. The structures of the complexes have been proposed on the basis of elemental analysis, electrical conductance, magnetic moment, spectroscopic measurements (IR, 1H, 13C NMR and UV-vis spectra) and X-ray diffraction studies. The spectral data reveal that the Schiff base ligands behave as dibasic tetradentate chelating agents having coordination sites at two thiol sulfur atoms and two azomethine nitrogen atoms. The presence of coordinated water in metal complexes was confirmed by thermal and IR data of the complexes. All the Schiff bases and their metal complexes have also been screened for their antibacterial activity against Bacillus subtilis, Staphylococcus aureus and antifungal activities against Aspergillus niger, Curvularia pallescens and Colletotrichum capsici.

  16. Synthesis, characterization and biological studies of sulfonamide Schiff's bases and some of their metal derivatives.

    PubMed

    Chohan, Zahid H; Shad, Hazoor A; Supuran, Claudiu T

    2012-02-01

    A new series of Schiff base ligands derived from sulfonamide and their metal(II) complexes [cobalt(II), copper(II), nickel(II) and zinc(II)] have been synthesized and characterized. The nature of bonding and structure of all the synthesized compounds has been explored by physical, analytical and spectral data of the ligands and their metal(II) complexes. The authors suggest that all the prepared complexes possess an octahedral geometry. The ligands and metal(II) complexes have been screened for their in vitro antibacterial activity against bacterial strains, Escherichia coli, Shigella flexneri, Pseudomonas aeruginosa, Salmonella typhi and for antifungal activity against fungal strains, Trichophyton longifusus, Candida albicans, Aspergillus flavus, Microsporum canis, Fusarium solani and Candida glabrata. These assays enabled the identification of the metal complexes as an effective antimicrobial agent with low cytotoxicity.

  17. On-the-Fly Integration of Data from a Spin-Diffusion-Based NMR Experiment into Protein-Ligand Docking.

    PubMed

    Onila, Ionut; ten Brink, Tim; Fredriksson, Kai; Codutti, Luca; Mazur, Adam; Griesinger, Christian; Carlomagno, Teresa; Exner, Thomas E

    2015-09-28

    INPHARMA (interligand nuclear Overhauser enhancement for pharmacophore mapping) determines the relative orientation of two competitive ligands in the protein binding pocket. It is based on the observation of interligand transferred NOEs mediated by spin diffusion through protons of the protein and is, therefore, sensitive to the specific interactions of each of the two ligands with the protein. We show how this information can be directly included into a protein-ligand docking program to guide the prediction of the complex structures. Agreement between the experimental and back-calculated spectra based on the full relaxation matrix approach is translated into a score contribution that is combined with the scoring function ChemPLP of our docking tool PLANTS. This combined score is then used to predict the poses of five weakly bound cAMP-dependent protein kinase (PKA) ligands. After optimizing the setup, which finally also included trNOE data and optimized protonation states, very good success rates were obtained for all combinations of three ligands. For one additional ligand, no conclusive results could be obtained due to the ambiguous electron density of the ligand in the X-ray structure, which does not disprove alternative ligand poses. The failures of the remaining ligand are caused by suboptimal locations of specific protein side chains. Therefore, side-chain flexibility should be included in an improved INPHARMA-PLANTS version. This will reduce the strong dependence on the used protein input structure leading to improved scores overall, not only for this last ligand.

  18. Diversity of coordination modes in the polymers based on 3,3',4,4'-biphenylcarboxylate ligand

    SciTech Connect

    Du Xiaodi; Xiao Hongping; Zhou Xinhui; Wu Tao; You Xiaozeng

    2010-06-15

    Four new compounds [Ni{sub 2}(4,4'-bpy)(3,4-bptc)(H{sub 2}O){sub 4}]{sub n} (1), [Ni(4,4'-bpy)(3,4-H{sub 2}bptc)(H{sub 2}O){sub 3}]{sub n} (2), [Mn{sub 2}(2,2'-bpy){sub 4}(3,4-H{sub 2}bptc){sub 2}] (3) and {l_brace}[Mn(1,10-phen){sub 2}(3,4-H{sub 2}bptc)].4H{sub 2}O{r_brace}{sub n} (4) (3,4-H{sub 4}bptc=3,3',4,4'-biphenyltetracarboxylic acid, 4,4'-bpy=4,4'-bipyridine, 2,2'-bpy=2,2'-bipyridine, 1, 10-phen=1, 10-phenanthroline), have been prepared and structurally characterized. In all compounds, the derivative ligands of 3,4-H{sub 4}bptc (3,4-bptc{sup 4-} and 3,4-H{sub 2}bptc{sup 2-}) exhibit different coordination modes and lead to the formation of various architectures. Compounds 1 and 2 display the three-dimensional (3D) framework: 1 shows a 3,4-connected topological network with (8{sup 3})(8{sup 5}.10) topology symbol based on the coordination bonds while in 2, the hydrogen-bonding interactions are observed to connect the 1D linear chain generating a final 3D framework. 3 exhibits the 2D layer constructed from the hydrogen-bonding interactions between the dinuclear manganese units. Complex 4 shows the double layers motif through connecting the 1D zigzag chains with hydrogen-bonded rings. The thermal stability of 1-4 and magnetic property of 1 were also reported. - Graphical abstract: Four coordination compounds exhibiting four coordination modes of the 3,3',4,4'-biphenylcarboxylate ligand, with three of new in this system, are obtained showing diversified architectures.

  19. Endothelial cell-derived CD95 ligand serves as a chemokine in induction of neutrophil slow rolling and adhesion

    PubMed Central

    Gao, Liang; Gülcüler, Gülce Sila; Golbach, Lieke; Block, Helena; Zarbock, Alexander; Martin-Villalba, Ana

    2016-01-01

    Integrin activation is crucial for the regulation of leukocyte rolling, adhesion and trans-vessel migration during inflammation and occurs by engagement of myeloid cells through factors presented by inflamed vessels. However, endothelial-dependent mechanisms of myeloid cell recruitment are not fully understood. Here we show using an autoperfused flow chamber assay of whole blood neutrophils and intravital microscopy of the inflamed cremaster muscle that CD95 mediates leukocyte slow rolling, adhesion and transmigration upon binding of CD95-ligand (CD95L) that is presented by endothelial cells. In myeloid cells, CD95 triggers activation of Syk-Btk/PLCγ2/Rap1 signaling that ultimately leads to integrin activation. Excitingly, CD95-deficient myeloid cells exhibit impaired bacterial clearance in an animal model of sepsis induced by cecal ligation and puncture (CLP). Our data identify the cellular and molecular mechanisms underlying the chemoattractant effect of endothelial cell-derived CD95L in induction of neutrophil recruitment and support the use of therapeutic inhibition of CD95’s activity in inflammatory diseases. DOI: http://dx.doi.org/10.7554/eLife.18542.001 PMID:27763263

  20. Hydroxylated derivatives of dimethoxy-1,4-benzoquinone as redox switchable earth-alkaline metal ligands and radical scavengers

    PubMed Central

    Gulaboski, Rubin; Bogeski, Ivan; Mirčeski, Valentin; Saul, Stephanie; Pasieka, Bastian; Haeri, Haleh H.; Stefova, Marina; Stanoeva, Jasmina Petreska; Mitrev, Saša; Hoth, Markus; Kappl, Reinhard

    2013-01-01

    Benzoquinones (BQ) have important functions in many biological processes. In alkaline environments, BQs can be hydroxylated at quinoid ring proton positions. Very little is known about the chemical reaction leading to these structural transformations as well as about the properties of the obtained hydroxyl benzoquinones. We analyzed the behavior of the naturally occurring 2,6-dimethoxy-1,4-benzoquinone under alkaline conditions and show that upon substitution of methoxy-groups, poly-hydroxyl-derivatives (OHBQ) are formed. The emerging compounds with one or several hydroxyl-substituents on single or fused quinone-rings exist in oxidized or reduced states and are very stable under physiological conditions. In comparison with the parent BQs, OHBQs are stronger radical scavengers and redox switchable earth-alkaline metal ligands. Considering that hydroxylated quinones appear as biosynthetic intermediates or as products of enzymatic reactions, and that BQs present in food or administered as drugs can be hydroxylated by enzymatic pathways, highlights their potential importance in biological systems. PMID:23689559

  1. Ligand Independent and Subtype-Selective Actions of Thyroid Hormone Receptors in Human Adipose Derived Stem Cells

    PubMed Central

    Cvoro, Aleksandra; Bajic, Aleksandar; Zhang, Aijun; Simon, Marisa; Golic, Igor; Sieglaff, Douglas H.; Maletic-Savatic, Mirjana; Korac, Aleksandra; Webb, Paul

    2016-01-01

    Thyroid hormone (TH) receptors (TRs α and β) are homologous ligand-dependent transcription factors (TFs). While the TRs display distinct actions in development, metabolic regulation and other processes, comparisons of TRα and TRβ dependent gene regulation mostly reveal similar mechanisms of action and few TR subtype specific genes. Here, we show that TRα predominates in multipotent human adipose derived stem cells (hADSC) whereas TRβ is expressed at lower levels and is upregulated during hADSC differentiation. The TRs display several unusual properties in parental hADSC. First, TRs display predominantly cytoplasmic intracellular distribution and major TRα variants TRα1 and TRα2 colocalize with mitochondria. Second, knockdown experiments reveal that endogenous TRs influence hADSC cell morphology and expression of hundreds of genes in the absence of hormone, but do not respond to exogenous TH. Third, TRα and TRβ affect hADSC in completely distinct ways; TRα regulates cell cycle associated processes while TRβ may repress aspects of differentiation. TRα splice variant specific knockdown reveals that TRα1 and TRα2 both contribute to TRα-dependent gene expression in a gene specific manner. We propose that TRs work in a non-canonical and hormone independent manner in hADSC and that prominent subtype-specific activities emerge in the context of these unusual actions. PMID:27732649

  2. Hydroxylated derivatives of dimethoxy-1,4-benzoquinone as redox switchable earth-alkaline metal ligands and radical scavengers

    NASA Astrophysics Data System (ADS)

    Gulaboski, Rubin; Bogeski, Ivan; Mirčeski, Valentin; Saul, Stephanie; Pasieka, Bastian; Haeri, Haleh H.; Stefova, Marina; Stanoeva, Jasmina Petreska; Mitrev, Saša; Hoth, Markus; Kappl, Reinhard

    2013-05-01

    Benzoquinones (BQ) have important functions in many biological processes. In alkaline environments, BQs can be hydroxylated at quinoid ring proton positions. Very little is known about the chemical reaction leading to these structural transformations as well as about the properties of the obtained hydroxyl benzoquinones. We analyzed the behavior of the naturally occurring 2,6-dimethoxy-1,4-benzoquinone under alkaline conditions and show that upon substitution of methoxy-groups, poly-hydroxyl-derivatives (OHBQ) are formed. The emerging compounds with one or several hydroxyl-substituents on single or fused quinone-rings exist in oxidized or reduced states and are very stable under physiological conditions. In comparison with the parent BQs, OHBQs are stronger radical scavengers and redox switchable earth-alkaline metal ligands. Considering that hydroxylated quinones appear as biosynthetic intermediates or as products of enzymatic reactions, and that BQs present in food or administered as drugs can be hydroxylated by enzymatic pathways, highlights their potential importance in biological systems.

  3. Bio-inspired nitrile hydration by peptidic ligands based on L-cysteine, L-methionine or L-penicillamine and pyridine-2,6-dicarboxylic acid.

    PubMed

    Byrne, Cillian; Houlihan, Kate M; Devi, Prarthana; Jensen, Paul; Rutledge, Peter J

    2014-12-12

    Nitrile hydratase (NHase, EC 4.2.1.84) is a metalloenzyme which catalyses the conversion of nitriles to amides. The high efficiency and broad substrate range of NHase have led to the successful application of this enzyme as a biocatalyst in the industrial syntheses of acrylamide and nicotinamide and in the bioremediation of nitrile waste. Crystal structures of both cobalt(III)- and iron(III)-dependent NHases reveal an unusual metal binding motif made up from six sequential amino acids and comprising two amide nitrogens from the peptide backbone and three cysteine-derived sulfur ligands, each at a different oxidation state (thiolate, sulfenate and sulfinate). Based on the active site geometry revealed by these crystal structures, we have designed a series of small-molecule ligands which integrate essential features of the NHase metal binding motif into a readily accessible peptide environment. We report the synthesis of ligands based on a pyridine-2,6-dicarboxylic acid scaffold and L-cysteine, L-S-methylcysteine, L-methionine or L-penicillamine. These ligands have been combined with cobalt(III) and iron(III) and tested as catalysts for biomimetic nitrile hydration. The highest levels of activity are observed with the L-penicillamine ligand which, in combination with cobalt(III), converts acetonitrile to acetamide at 1.25 turnovers and benzonitrile to benzamide at 1.20 turnovers.

  4. A Fluorescence Displacement Assay for Antidepressant Drug Discovery Based on Ligand-Conjugated Quantum Dots

    SciTech Connect

    Chang, Jerry; Tomlinson, Ian; Warnement, Michael; Iwamoto, Hideki

    2011-01-01

    The serotonin (5-hydroxytryptamine, 5-HT) transporter (SERT) protein plays a central role in terminating 5-HT neurotransmission and is the most important therapeutic target for the treatment of major depression and anxiety disorders. We report an innovative, versatile, and target-selective quantum dot (QD) labeling approach for SERT in single Xenopus oocytes that can be adopted as a drug-screening platform. Our labeling approach employs a custom-made, QD-tagged indoleamine derivative ligand, IDT318, that is structurally similar to 5-HT and accesses the primary binding site with enhanced human SERT selectivity. Incubating QD-labeled oocytes with paroxetine (Paxil), a high-affinity SERT-specific inhibitor, showed a concentration- and time-dependent decrease in QD fluorescence, demonstrating the utility of our approach for the identification of SERT modulators. Furthermore, with the development of ligands aimed at other pharmacologically relevant targets, our approach may potentially form the basis for a multitarget drug discovery platform.

  5. Ligand and Target Discovery by Fragment-Based Screening in Human Cells.

    PubMed

    Parker, Christopher G; Galmozzi, Andrea; Wang, Yujia; Correia, Bruno E; Sasaki, Kenji; Joslyn, Christopher M; Kim, Arthur S; Cavallaro, Cullen L; Lawrence, R Michael; Johnson, Stephen R; Narvaiza, Iñigo; Saez, Enrique; Cravatt, Benjamin F

    2017-01-26

    Advances in the synthesis and screening of small-molecule libraries have accelerated the discovery of chemical probes for studying biological processes. Still, only a small fraction of the human proteome has chemical ligands. Here, we describe a platform that marries fragment-based ligand discovery with quantitative chemical proteomics to map thousands of reversible small molecule-protein interactions directly in human cells, many of which can be site-specifically determined. We show that fragment hits can be advanced to furnish selective ligands that affect the activity of proteins heretofore lacking chemical probes. We further combine fragment-based chemical proteomics with phenotypic screening to identify small molecules that promote adipocyte differentiation by engaging the poorly characterized membrane protein PGRMC2. Fragment-based screening in human cells thus provides an extensive proteome-wide map of protein ligandability and facilitates the coordinated discovery of bioactive small molecules and their molecular targets. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. Ligand-Based Peptide Design and Combinatorial Peptide Libraries to Target G Protein-Coupled Receptors

    PubMed Central

    Gruber, Christian W.; Muttenthaler, Markus; Freissmuth, Michael

    2016-01-01

    G protein-coupled receptors (GPCRs) are considered to represent the most promising drug targets; it has been repeatedly said that a large fraction of the currently marketed drugs elicit their actions by binding to GPCRs (with cited numbers varying from 30–50%). Closer scrutiny, however, shows that only a modest fraction of (~60) GPCRs are, in fact, exploited as drug targets, only ~20 of which are peptide-binding receptors. The vast majority of receptors in the humane genome have not yet been explored as sites of action for drugs. Given the drugability of this receptor class, it appears that opportunities for drug discovery abound. In addition, GPCRs provide for binding sites other than the ligand binding sites (referred to as the “orthosteric site”). These additional sites include (i) binding sites for ligands (referred to as “allosteric ligands”) that modulate the affinity and efficacy of orthosteric ligands, (ii) the interaction surface that recruits G proteins and arrestins, (iii) the interaction sites of additional proteins (GIPs, GPCR interacting proteins that regulate G protein signaling or give rise to G protein-independent signals). These sites can also be targeted by peptides. Combinatorial and natural peptide libraries are therefore likely to play a major role in identifying new GPCR ligands at each of these sites. In particular the diverse natural peptide libraries such as the venom peptides from marine cone-snails and plant cyclotides have been established as a rich source of drug leads. High-throughput screening and combinatorial chemistry approaches allow for progressing from these starting points to potential drug candidates. This will be illustrated by focusing on the ligand-based drug design of oxytocin (OT) and vasopressin (AVP) receptor ligands using natural peptide leads as starting points. PMID:20687879

  7. Mononuclear and polynuclear copper(II) complexes derived from pyridylalkylaminomethylphenol polypodal ligands.

    PubMed

    Manzur, Jorge; Mora, Hector; Vega, Andrés; Venegas-Yazigi, Diego; Novak, Miguel A; Sabino, José Ricardo; Paredes-García, Verónica; Spodine, Evgenia

    2009-09-21

    Four mononuclear complexes [Cu(HL(1))Cl]PF(6).CH(3)OH (1), [Cu(HSL(1))Cl]PF(6).0.75H(2)O (2), [Cu(HL(2))Cl]PF(6).CH (3)OH (3), [Cu(HSL(2))Cl]PF(6).1.5CH(3)OH (4), and two polynuclear complexes [Cu (2)(SL(2))(2)](PF(6))(2).2CH(3)OH (5) and {Cu[Cu(SL(2))(Cl)](2)}(PF(6))(2) (6) (HL(1): 2-[(bis(2-pyridylmethyl)-amino)methyl]-4-methylphenol; HSL(1): 2-[(bis(2-pyridylmethyl)amino) methyl]-4-methyl-6-(methyl-thio)phenol; HL(2): 2-[(2-pyridylmethyl)(2'-pyridylethyl)-aminomethyl)]-4-methylphenol; HSL(2): 2-[(2-pyridylmethyl)(2'-pyridylethyl)amino-methyl]-4-methyl-6-(methylthio)phenol were obtained and characterized. The crystal structures of the mononuclear complexes 1-4 show the copper centers in a square-base pyramidal environment with the phenolic oxygen coordinated at the axial position. Dinuclear complex 5 has two copper centers with different geometry and bridged by phenoxo oxygens; one of the copper atoms is square pyramidal while the other can be described with a highly distorted octahedral geometry with a long Cu-S distance (2.867 A). Density functional theory calculations were used to obtain the reported structure of 6, since single crystals suitable for X-ray diffraction were not isolated. Magnetic studies done for 5 and 6 show an antiferromagnetic behavior for 5 (J = -134 cm(-1)) and a ferromagnetic behavior for 6 (J = +11.9 cm(-1)). Redox potentials for the mononuclear complexes were measured by cyclic voltammetry; the values show the effect of the chelating ring size (-213 mV and -142 mV for Cu-HL(1) and Cu-HL(2), respectively) and the presence of the thiomethyl substituent (-213 mV and -184 mV for Cu-HL(1) and Cu-HSL(1), respectively).

  8. Mass spectrometry-based monitoring of millisecond protein–ligand binding dynamics using an automated microfluidic platform

    SciTech Connect

    Cong, Yongzheng; Katipamula, Shanta; Trader, Cameron D.; Orton, Daniel J.; Geng, Tao; Baker, Erin S.; Kelly, Ryan T.

    2016-01-01

    Characterizing protein-ligand binding dynamics is crucial for understanding protein function and developing new therapeutic agents. We have developed a novel microfluidic platform that features rapid mixing of protein and ligand solutions, variable incubation times, and on-chip electrospray ionization to perform label-free, solution-based monitoring of protein-ligand binding dynamics. This platform offers many advantages including automated processing, rapid mixing, and low sample consumption.

  9. Statistical Estimation of the Protein-Ligand Binding Free Energy Based On Direct Protein-Ligand Interaction Obtained by Molecular Dynamics Simulation

    PubMed Central

    Fukunishi, Yoshifumi; Nakamura, Haruki

    2012-01-01

    We have developed a method for estimating protein-ligand binding free energy (ΔG) based on the direct protein-ligand interaction obtained by a molecular dynamics simulation. Using this method, we estimated the ΔG value statistically by the average values of the van der Waals and electrostatic interactions between each amino acid of the target protein and the ligand molecule. In addition, we introduced fluctuations in the accessible surface area (ASA) and dihedral angles of the protein-ligand complex system as the entropy terms of the ΔG estimation. The present method included the fluctuation term of structural change of the protein and the effective dielectric constant. We applied this method to 34 protein-ligand complex structures. As a result, the correlation coefficient between the experimental and calculated ΔG values was 0.81, and the average error of ΔG was 1.2 kcal/mol with the use of the fixed parameters. These results were obtained from a 2 nsec molecular dynamics simulation. PMID:24281257

  10. Recent Advances in Ligand-Based Drug Design: Relevance and Utility of the Conformationally Sampled Pharmacophore Approach

    PubMed Central

    Acharya, Chayan; Coop, Andrew; Polli, James E.; MacKerell, Alexander D.

    2010-01-01

    In the absence of three-dimensional (3D) structures of potential drug targets, ligand-based drug design is one of the popular approaches for drug discovery and lead optimization. 3D structure-activity relationships (3D QSAR) and pharmacophore modeling are the most important and widely used tools in ligand-based drug design that can provide crucial insights into the nature of the interactions between drug target and ligand molecule and provide predictive models suitable for lead compound optimization. This review article will briefly discuss the features and potential application of recent advances in ligand-based drug design, with emphasis on a detailed description of a novel 3D QSAR method based on the conformationally sample pharmacophore (CSP) approach (denoted CSP-SAR). In addition, data from a published study is used to compare the CSP-SAR approach to the Catalyst method, emphasizing the utility of the CSP approach for ligand-based model development. PMID:20807187

  11. Identifying ligands at orphan GPCRs: current status using structure-based approaches.

    PubMed

    Ngo, Tony; Kufareva, Irina; Coleman, James Lj; Graham, Robert M; Abagyan, Ruben; Smith, Nicola J

    2016-10-01

    GPCRs are the most successful pharmaceutical targets in history. Nevertheless, the pharmacology of many GPCRs remains inaccessible as their endogenous or exogenous modulators have not been discovered. Tools that explore the physiological functions and pharmacological potential of these 'orphan' GPCRs, whether they are endogenous and/or surrogate ligands, are therefore of paramount importance. Rates of receptor deorphanization determined by traditional reverse pharmacology methods have slowed, indicating a need for the development of more sophisticated and efficient ligand screening approaches. Here, we discuss the use of structure-based ligand discovery approaches to identify small molecule modulators for exploring the function of orphan GPCRs. These studies have been buoyed by the growing number of GPCR crystal structures solved in the past decade, providing a broad range of template structures for homology modelling of orphans. This review discusses the methods used to establish the appropriate signalling assays to test orphan receptor activity and provides current examples of structure-based methods used to identify ligands of orphan GPCRs. Linked Articles This article is part of a themed section on Molecular Pharmacology of G Protein-Coupled Receptors. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v173.20/issuetoc.

  12. Microfluidic-based G-quadruplex ligand displacement assay for alkaloid anticancer drug screening.

    PubMed

    Shen, Haihui; Zhang, Bo; Xu, Huiyan; Sun, Yue; Wu, Qiwang; Shen, Hong; Liu, Yingchun

    2017-02-05

    Some natural heterocyclic alkaloids containing planar group show potential to complex with specific promoter region of protooncogene for stabilizing the G-quadruplex (G4) structure which nowadays promises to be a target in anticancer drug design. However, in view of the polymorphic characteristics and structural complexity of heterocyclic alkaloids, it is desirable to develop high-throughput and low-consumption approach for anticancer drug screening. In this paper, an intensive study on alkaloid ligand/G4 DNA interaction has been conducted, demonstrating that the end-stacking interaction is the favorable binding mode between the oncogene-related Pu22 G4 DNA and the heterocyclic alkaloid ligand. Based on structural feasibility and energy minimization, a ligand displacement assay for screening alkaloid ligand in stabilizing the oncogene target G4 has been developed, which also helps to facilitate the assessment of drug specificity. Coupled with microfluidic-based DNAzyme-catalytic chemiluminescence detection, the approach showed the advantages of high sensitivity, high throughput with low sample and reagent consumptions.

  13. Structural bases for heme binding and diatomic ligand recognition in truncated hemoglobins.

    PubMed

    Milani, Mario; Pesce, Alessandra; Nardini, Marco; Ouellet, Hugues; Ouellet, Yannick; Dewilde, Sylvia; Bocedi, Alessio; Ascenzi, Paolo; Guertin, Michel; Moens, Luc; Friedman, Joel M; Wittenberg, Jonathan B; Bolognesi, Martino

    2005-01-01

    Truncated hemoglobins (trHbs) are low-molecular-weight oxygen-binding heme-proteins distributed in eubacteria, cyanobacteria, unicellular eukaryotes, and in higher plants, constituting a distinct group within the hemoglobin (Hb) superfamily. TrHbs display amino acid sequences 20-40 residues shorter than classical (non)vertebrate Hbs and myoglobins, to which they are scarcely related by sequence similarity. The trHb tertiary structure is based on a 2-on-2 alpha-helical sandwich, which represents a striking editing of the highly conserved 3-on-3 alpha-helical globin fold, achieved through deletion/truncation of alpha-helices and specific residue substitutions. Despite their 'minimal' polypeptide chain span, trHbs display an inner tunnel/cavity system held to support ligand diffusion to/from the heme distal pocket, accumulation of heme ligands within the protein matrix, and/or multiligand reactions. Moreover, trHbs bind and effectively stabilize the heme and recognize diatomic ligands (i.e., O2, CO, NO, and cyanide), albeit with varying thermodynamic and kinetic parameters. Here, structural bases for heme binding and diatomic ligand recognition by trHbs are reviewed.

  14. Modeling the retention mechanism for high-performance liquid chromatography with a chiral ligand mobile phase and enantioseparation of mandelic acid derivatives.

    PubMed

    Tong, Shengqiang; Shen, Mangmang; Zhang, Hu; Cheng, Dongping; Yan, Jizhong

    2015-06-01

    The chromatographic retention mechanism describing relationship between retention factor and concentration of Cu(2+) (l-phenylalanine)2 using chiral ligand mobile phase was investigated and eight mandelic acid derivatives were enantioseparated by chiral ligand exchange chromatography. The relationship between retention factor and concentration of the Cu(2+) (l-phenylalanine)2 complex was proven to be in conformity with chromatographic retention mechanism in which chiral discrimination occurred both in mobile and stationary phase. Different copper(II) salts, chiral ligands, organic modifier, pH of aqueous phase, and conventional temperature on retention behavior were optimized. Eight racemates were successfully enantioseparated on a common reversed-phase column with an optimized mobile phase composed of 6 mmol/L of l-phenylalanine or N,N-dimethyl-l-phenylalanine and 3 mmol/Lof copper(II) acetate or copper(II) sulfate aqueous solution and methanol. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Mass spectrometry-based ligand binding assays on adenosine A1 and A2A receptors.

    PubMed

    Massink, A; Holzheimer, M; Hölscher, A; Louvel, J; Guo, D; Spijksma, G; Hankemeier, T; IJzerman, A P

    2015-12-01

    Conventional methods to measure ligand-receptor binding parameters typically require radiolabeled ligands as probes. Despite the robustness of radioligand binding assays, they carry inherent disadvantages in terms of safety precautions, expensive synthesis, special lab requirements, and waste disposal. Mass spectrometry (MS) is a method that can selectively detect ligands without the need of a label. The sensitivity of MS equipment increases progressively, and currently, it is possible to detect low ligand quantities that are usually found in ligand binding assays. We developed a label-free MS ligand binding (MS binding) assay on the adenosine A(1) and A(2A) receptors (A(1)AR and A(2A)AR), which are well-characterized members of the class A G protein-coupled receptor (GPCR) family. Radioligand binding assays for both receptors are well established, and ample data is available to compare and evaluate the performance of an MS binding assay. 1,3-Dipropyl-8-cyclopentyl-xanthine (DPCPX) and 4-(2-((7-amino-2-(furan-2-yl)-[1,2,4]triazolo[1,5-a]-[1,3,5]triazin-5-yl)amino)ethyl)phenol (ZM-241,385) are high-affinity ligands selective for the A(1)AR and A(2A)AR, respectively. To proof the feasibility of MS binding on the A(1)AR and A(2A)AR, we first developed an MS detection method for unlabeled DPCPX and ZM-241,385. To serve as internal standards, both compounds were also deuterium-labeled. Subsequently, we investigated whether the two unlabeled compounds could substitute for their radiolabeled counterparts as marker ligands in binding experiments, including saturation, displacement, dissociation, and competition association assays. Furthermore, we investigated the accuracy of these assays if the use of internal standards was excluded. The results demonstrate the feasibility of the MS binding assay, even in the absence of a deuterium-labeled internal standard, and provide great promise for the further development of label-free assays based on MS for other GPCRs.

  16. Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase

    SciTech Connect

    Landon, Melissa R.; Lieberman, Raquel L.; Hoang, Quyen Q.; Ju, Shulin; Caaveiro, Jose M.M.; Orwig, Susan D.; Kozakov, Dima; Brenke, Ryan; Chuang, Gwo-Yu; Beglov, Dmitry; Vajda, Sandor; Petsko, Gregory A.; Ringe, Dagmar

    2010-08-04

    The identification of hot spots, i.e., binding regions that contribute substantially to the free energy of ligand binding, is a critical step for structure-based drug design. Here we present the application of two fragment-based methods to the detection of hot spots for DJ-1 and glucocerebrosidase (GCase), targets for the development of therapeutics for Parkinson's and Gaucher's diseases, respectively. While the structures of these two proteins are known, binding information is lacking. In this study we employ the experimental multiple solvent crystal structures (MSCS) method and computational fragment mapping (FTMap) to identify regions suitable for the development of pharmacological chaperones for DJ-1 and GCase. Comparison of data derived via MSCS and FTMap also shows that FTMap, a computational method for the identification of fragment binding hot spots, is an accurate and robust alternative to the performance of expensive and difficult crystallographic experiments.

  17. Ligand-Independent Activation of Platelet-Derived Growth Factor Receptor β during Human Immunodeficiency Virus-Transactivator of Transcription and Cocaine-Mediated Smooth Muscle Hyperplasia.

    PubMed

    Dalvi, Pranjali N; Gupta, Vijayalaxmi G; Griffin, Brooke R; O'Brien-Ladner, Amy; Dhillon, Navneet K

    2015-09-01

    Our previous study supports an additive effect of cocaine to human immunodeficiency virus infection in the development of pulmonary arteriopathy through enhancement of proliferation of pulmonary smooth muscle cells (SMCs), while also suggesting involvement of platelet-derived growth factor receptor (PDGFR) activation in the absence of further increase in PDGF-BB ligand. Redox-related signaling pathways have been shown to regulate tyrosine kinase receptors independent of ligand binding, so we hypothesized that simultaneous treatment of SMCs with transactivator of transcription (Tat) and cocaine may be able to indirectly activate PDGFR through modulation of reactive oxygen species (ROS) without the need for PDGF binding. We found that blocking the binding of ligand using suramin or monoclonal IMC-3G3 antibody significantly reduced ligand-induced autophosphorylation of Y1009 without affecting ligand-independent transphosphorylation of Y934 residue on PDGFRβ in human pulmonary arterial SMCs treated with both cocaine and Tat. Combined treatment of human pulmonary arterial SMCs with cocaine and Tat resulted in augmented production of superoxide radicals and hydrogen peroxide when compared with either treatment alone. Inhibition of this ROS generation prevented cocaine- and Tat-mediated Src activation and transphosphorylation of PDGFRβ at Y934 without any changes in phosphorylation of Y1009, in addition to attenuation of smooth muscle hyperplasia. Furthermore, pretreatment with an Src inhibitor, PP2, also suppressed cocaine- and Tat-mediated enhanced Y934 phosphorylation and smooth muscle proliferation. Finally, we report total abrogation of cocaine- and Tat-mediated synergistic increase in cell proliferation on inhibition of both ligand-dependent and ROS/Src-mediated ligand-independent phosphorylation of PDGFRβ.

  18. Nonlinear scoring functions for similarity-based ligand docking and binding affinity prediction.

    PubMed

    Brylinski, Michal

    2013-11-25

    A common strategy for virtual screening considers a systematic docking of a large library of organic compounds into the target sites in protein receptors with promising leads selected based on favorable intermolecular interactions. Despite a continuous progress in the modeling of protein-ligand interactions for pharmaceutical design, important challenges still remain, thus the development of novel techniques is required. In this communication, we describe eSimDock, a new approach to ligand docking and binding affinity prediction. eSimDock employs nonlinear machine learning-based scoring functions to improve the accuracy of ligand ranking and similarity-based binding pose prediction, and to increase the tolerance to structural imperfections in the target structures. In large-scale benchmarking using the Astex/CCDC data set, we show that 53.9% (67.9%) of the predicted ligand poses have RMSD of <2 Å (<3 Å). Moreover, using binding sites predicted by recently developed eFindSite, eSimDock models ligand binding poses with an RMSD of 4 Å for 50.0-39.7% of the complexes at the protein homology level limited to 80-40%. Simulations against non-native receptor structures, whose mean backbone rearrangements vary from 0.5 to 5.0 Å Cα-RMSD, show that the ratio of docking accuracy and the estimated upper bound is at a constant level of ∼0.65. Pearson correlation coefficient between experimental and predicted by eSimDock Ki values for a large data set of the crystal structures of protein-ligand complexes from BindingDB is 0.58, which decreases only to 0.46 when target structures distorted to 3.0 Å Cα-RMSD are used. Finally, two case studies demonstrate that eSimDock can be customized to specific applications as well. These encouraging results show that the performance of eSimDock is largely unaffected by the deformations of ligand binding regions, thus it represents a practical strategy for across-proteome virtual screening using protein models. eSimDock is freely

  19. Structural diversity and photocatalytic properties of Cd(II) coordination polymers constructed by a flexible V-shaped bipyridyl benzene ligand and dicarboxylate derivatives.

    PubMed

    Liu, Lei-Lei; Yu, Cai-Xia; Ma, Feng-Ji; Li, Ya-Ru; Han, Jing-Jing; Lin, Lu; Ma, Lu-Fang

    2015-01-28

    Hydrothermal reactions of Cd(OAc)2·2H2O with a flexible V-shaped bipyridyl benzene ligand and five benzenedicarboxylic acid derivatives gave rise to five new coordination polymers i.e., [Cd(1,4-BDC)(bpmb)(H2O)]n (1), {[Cd(1,3-BDC)(bpmb)]·0.125H2O}n (2), [Cd2(5-Me-1,3-BDC)2(bpmb)2]n (3), [Cd(5-NO2-1,3-BDC)(bpmb)(H2O)]n (4) and [Cd(5-OH-1,3-BDC)(bpmb)(H2O)]n (5) (bpmb = 1,3-bis(pyridine-3-ylmethoxy)benzene, 1,4-H2BDC = 1,4-benzenedicarboxylic acid, 1,3-H2BDC = 1,3-benzenedicarboxylic acid, 5-Me-1,3-H2BDC = 5-methyl-1,3-benzenedicarboxylic acid, 5-NO2-1,3-H2BDC = 5-nitro-1,3-benzenedicarboxylic acid, 5-OH-1,3-H2BDC = 5-hydroxy-1,3-benzenedicarboxylic acid). Their structures have been determined by single-crystal X-ray diffraction analyses, elemental analyses, IR spectra, powder X-ray diffraction (PXRD) and thermogravimetric analyses (TGA). Compound 1 is a two-fold interpenetrating network showing the coexistence of polyrotaxane and polycatenane characters. Compounds 2 and 3 exhibit similar 2D (3,5)-connected (4(2)·6(7)·8)(4(2)·6) nets in which the bpmb ligands work as lockers in interlocking 1D [Cd(1,3-BDC/5-Me-1,3-BDC)]n chains. Compound 4 shows a 2D 4-connected (6(6)) sandwich-like structure with differently oriented [Cd(5-NO2-1,3-BDC)]n chains. Compound 5 is a 3D supramolecular pcu net based on a 1D ladder-shaped chain. These results suggest that the substituted positions of carboxylate groups and changes in substituted R groups in the 5-position of BDC ligands have significant effect on the final structures. These compounds exhibited relatively good photocatalytic activity towards the degradation of methylene blue (MB) in aqueous solution under UV irradiation. Moreover, solid-state photoluminescence properties of 1-5 were also investigated.

  20. A nonplanar porphyrin-based receptor molecule for chiral amine ligands

    SciTech Connect

    MUZZI,CINZIA M.; MEDFORTH,CRAIG J.; SMITH,KEVIN M.; JIA,SONG-LING; SHELNUTT,JOHN A.

    2000-03-06

    A novel porphyrin-based receptor molecule for chiral amine ligands is described in which nonplanarity of the porphyrin macrocycle is used to orient the ligand and to enhance porphyrin-ligand interactions. The porphyrin macrocycle provides a versatile platform upon which to build elaborate superstructures, and this feature coupled with a rich and well-developed synthetic chemistry has led to the synthesis of many elegant models of heme protein active sites and numerous porphyrin-based receptor molecules. One design feature which is not usually considered in the design of porphyrin-based receptor molecules is nonplanarity of the porphyrin ring, although there are a few systems such as the pyridine sensitive Venus Flytrap and the chirality-memory molecule which illustrate that nonplanar porphyrin-based receptors can display unique and interesting behavior. Given the novel properties of these receptors and the continuing interest in the effects of nonplanarity on the properties of porphyrins the authors decided to investigate in more detail the potential applications of nonplanarity in the design of porphyrin-based receptors. Herein, they describe the design, synthesis, and characterization of a new kind of nonplanar porphyrin-based receptor molecule for chiral amines.

  1. Diversity of natural self-derived ligands presented by different HLA class I molecules in transporter antigen processing-deficient cells.

    PubMed

    Lorente, Elena; Infantes, Susana; Barnea, Eilon; Beer, Ilan; Barriga, Alejandro; García-Medel, Noel; Lasala, Fátima; Jiménez, Mercedes; Admon, Arie; López, Daniel

    2013-01-01

    The transporter associated with antigen processing (TAP) translocates the cytosol-derived proteolytic peptides to the endoplasmic reticulum lumen where they complex with nascent human leukocyte antigen (HLA) class I molecules. Non-functional TAP complexes and viral or tumoral blocking of these transporters leads to reduced HLA class I surface expression and a drastic change in the available peptide repertoire. Using mass spectrometry to analyze complex human leukocyte antigen HLA-bound peptide pools isolated from large numbers of TAP-deficient cells, we identified 334 TAP-independent ligands naturally presented by four different HLA-A, -B, and -C class I molecules with very different TAP dependency from the same cell line. The repertoire of TAP-independent peptides examined favored increased peptide lengths and a lack of strict binding motifs for all four HLA class I molecules studied. The TAP-independent peptidome arose from 182 parental proteins, the majority of which yielded one HLA ligand. In contrast, TAP-independent antigen processing of very few cellular proteins generated multiple HLA ligands. Comparison between TAP-independent peptidome and proteome of several subcellular locations suggests that the secretory vesicle-like organelles could be a relevant source of parental proteins for TAP-independent HLA ligands. Finally, a predominant endoproteolytic peptidase specificity for Arg/Lys or Leu/Phe residues in the P(1) position of the scissile bond was found for the TAP-independent ligands. These data draw a new and intricate picture of TAP-independent pathways.

  2. Development and application of hybrid structure based method for efficient screening of ligands binding to G-protein coupled receptors

    NASA Astrophysics Data System (ADS)

    Kortagere, Sandhya; Welsh, William J.

    2006-12-01

    G-protein coupled receptors (GPCRs) comprise a large superfamily of proteins that are targets for nearly 50% of drugs in clinical use today. In the past, the use of structure-based drug design strategies to develop better drug candidates has been severely hampered due to the absence of the receptor's three-dimensional structure. However, with recent advances in molecular modeling techniques and better computing power, atomic level details of these receptors can be derived from computationally derived molecular models. Using information from these models coupled with experimental evidence, it has become feasible to build receptor pharmacophores. In this study, we demonstrate the use of the Hybrid Structure Based (HSB) method that can be used effectively to screen and identify prospective ligands that bind to GPCRs. Essentially; this multi-step method combines ligand-based methods for building enriched libraries of small molecules and structure-based methods for screening molecules against the GPCR target. The HSB method was validated to identify retinal and its analogues from a random dataset of ˜300,000 molecules. The results from this study showed that the 9 top-ranking molecules are indeed analogues of retinal. The method was also tested to identify analogues of dopamine binding to the dopamine D2 receptor. Six of the ten top-ranking molecules are known analogues of dopamine including a prodrug, while the other thirty-four molecules are currently being tested for their activity against all dopamine receptors. The results from both these test cases have proved that the HSB method provides a realistic solution to bridge the gap between the ever-increasing demand for new drugs to treat psychiatric disorders and the lack of efficient screening methods for GPCRs.

  3. A High Performance Cloud-Based Protein-Ligand Docking Prediction Algorithm

    PubMed Central

    Chen, Jui-Le; Yang, Chu-Sing

    2013-01-01

    The potential of predicting druggability for a particular disease by integrating biological and computer science technologies has witnessed success in recent years. Although the computer science technologies can be used to reduce the costs of the pharmaceutical research, the computation time of the structure-based protein-ligand docking prediction is still unsatisfied until now. Hence, in this paper, a novel docking prediction algorithm, named fast cloud-based protein-ligand docking prediction algorithm (FCPLDPA), is presented to accelerate the docking prediction algorithm. The proposed algorithm works by leveraging two high-performance operators: (1) the novel migration (information exchange) operator is designed specially for cloud-based environments to reduce the computation time; (2) the efficient operator is aimed at filtering out the worst search directions. Our simulation results illustrate that the proposed method outperforms the other docking algorithms compared in this paper in terms of both the computation time and the quality of the end result. PMID:23762864

  4. Ligand-Based Virtual Screening in a Search for Novel Anti-HIV-1 Chemotypes.

    PubMed

    Kurczyk, Agata; Warszycki, Dawid; Musiol, Robert; Kafel, Rafał; Bojarski, Andrzej J; Polanski, Jaroslaw

    2015-10-26

    In a search for new anti-HIV-1 chemotypes, we developed a multistep ligand-based virtual screening (VS) protocol combining machine learning (ML) methods with the privileged structures (PS) concept. In its learning step, the VS protocol was based on HIV integrase (IN) inhibitors fetched from the ChEMBL database. The performances of various ML methods and PS weighting scheme were evaluated and applied as VS filtering criteria. Finally, a database of 1.5 million commercially available compounds was virtually screened using a multistep ligand-based cascade, and 13 selected unique structures were tested by measuring the inhibition of HIV replication in infected cells. This approach resulted in the discovery of two novel chemotypes with moderate antiretroviral activity, that, together with their topological diversity, make them good candidates as lead structures for future optimization.

  5. Synthesis and evaluation of 7-substituted-5,6-dihydrobenzo[c]acridine derivatives as new c-KIT promoter G-quadruplex binding ligands.

    PubMed

    Guo, Qian-Liang; Su, Hua-Fei; Wang, Ning; Liao, Sheng-Rong; Lu, Yu-Ting; Ou, Tian-Miao; Tan, Jia-Heng; Li, Ding; Huang, Zhi-Shu

    2017-04-21

    It has been shown that treatment of cancer cells with c-KIT G-quadruplex binding ligands can reduce their c-KIT expression levels thus inhibiting cell proliferation and inducing cell apoptosis. Herein, a series of new 7-substituted-5,6-dihydrobenzo[c]acridine derivatives were designed and synthesized. Subsequent biophysical evaluation demonstrated that the derivatives could effectively bind to and stabilize c-KIT G-quadruplex with good selectivity against duplex DNA. It was found that 12-N-methylated derivatives with a positive charge introduced at 12-position of 5,6-dihydrobenzo[c]acridine ring had similar binding affinity but lower stabilizing ability to c-KIT G-quadruplex DNA, compared with those of nonmethylated derivatives. Further molecular modeling studies showed possible binding modes of G-quadruplex with the ligands. RT-PCR assay and Western blot showed that compound 2b suppressed transcription and translation of c-KIT gene in K562 cells, which was consistent with the property of an effective G-quadruplex binding ligand targeting c-KIT oncogene promoter. Further biological evaluation showed that compound 2b could induce apoptosis through activation of the caspase-3 cascade pathway.

  6. Structure-Based Ligand Discovery Targeting Orthosteric and Allosteric Pockets of Dopamine Receptors

    PubMed Central

    Lane, J. Robert; Chubukov, Pavel; Liu, Wei; Canals, Meritxell; Cherezov, Vadim; Abagyan, Ruben; Stevens, Raymond C.

    2013-01-01

    Small molecules targeting allosteric pockets of G protein–coupled receptors (GPCRs) have a great therapeutic potential for the treatment of neurologic and other chronic disorders. Here we performed virtual screening for orthosteric and putative allosteric ligands of the human dopamine D3 receptor (D3R) using two optimized crystal-structure–based models: the receptor with an empty binding pocket (D3RAPO), and the receptor complex with dopamine (D3RDopa). Subsequent biochemical and functional characterization revealed 14 novel ligands with a binding affinity of better than 10 μM in the D3RAPO candidate list (56% hit rate), and 8 novel ligands in the D3RDopa list (32% hit rate). Most ligands in the D3RAPO model span both orthosteric and extended pockets and behave as antagonists at D3R, with compound 7 showing the highest potency of dopamine inhibition (IC50 = 7 nM). In contrast, compounds identified by the D3RDopa model are predicted to occupy an allosteric site at the extracellular extension of the pocket, and they all lack the anchoring amino group. Compounds targeting the allosteric site display a variety of functional activity profiles, where behavior of at least two compounds (23 and 26) is consistent with noncompetitive allosteric modulation of dopamine signaling in the extracellular signal-regulated kinase 1 and 2 phosphorylation and β-arrestin recruitment assays. The high affinity and ligand efficiency of the chemically diverse hits identified in this study suggest utility of structure-based screening targeting allosteric sites of GPCRs. PMID:24021214

  7. Octapeptide-based affinity chromatography of human immunoglobulin G: comparisons of three different ligands.

    PubMed

    Zhao, Wei-Wei; Liu, Fu-Feng; Shi, Qing-Hong; Sun, Yan

    2014-09-12

    In an earlier work, we have developed a biomimetic design strategy based on the human IgG (hIgG)-Protein A interactions and identified an affinity ligand for hIgG, FYWHCLDE, which ranked top one in a pool of 14 potential candidates. Herein, two more octapeptides, FYCHWALE and FYCHTIDE, were identified, and the binding and purification of hIgG on the affinity columns packed with the three octapeptide-modified Sepharose gels were extensively studied and compared to find more effective octapeptide-based affinity ligands. It was found that all the three ligands bound hIgG and Fc fragment but barely bound Fab fragment, and the binding to hIgG and Fc was mainly by electrostatic interactions. The optimum binding pH values for the three ligands were different from each other, but kept in the range of 5.0-6.0. Ligand binding competition revealed that the binding sites on hIgG for the three octapeptides were similar to those for Protein A. Adsorption isotherms revealed that hIgG binding capacity was in the range of 64-104mg/mL drained gel in the order of FYWHCLDE>FYCHWALE>FYCHTIDE. Then, purifications of hIgG and human monoclonal antibody from human serum and cell culture supernatant, respectively, were achieved with the three affinity columns at high purities and recovery yields. Finally, the molecular basis for the binding affinity of the peptides for the Fc fragment of hIgG was elucidated by molecular dynamics simulations. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. PharmaGist: a webserver for ligand-based pharmacophore detection

    PubMed Central

    Schneidman-Duhovny, Dina; Dror, Oranit; Inbar, Yuval; Nussinov, Ruth; Wolfson, Haim J.

    2008-01-01

    Predicting molecular interactions is a major goal in rational drug design. Pharmacophore, which is the spatial arrangement of features that is essential for a molecule to interact with a specific target receptor, is an important model for achieving this goal. We present a freely available web server, named PharmaGist, for pharmacophore detection. The employed method is ligand based. Namely, it does not require the structure of the target receptor. Instead, the input is a set of structures of drug-like molecules that are known to bind to the receptor. The output consists of candidate pharmacophores that are computed by multiple flexible alignment of the input ligands. The method handles the flexibility of the input ligands explicitly and in deterministic manner within the alignment process. PharmaGist is also highly efficient, where a typical run with up to 32 drug-like molecules takes seconds to a few minutes on a stardard PC. Another important characteristic is the capability of detecting pharmacophores shared by different subsets of input molecules. This capability is a key advantage when the ligands belong to different binding modes or when the input contains outliers. The webserver has a user-friendly interface available at http://bioinfo3d.cs.tau.ac.il/PharmaGist. PMID:18424800

  9. A comprehensive ligand based mapping of the σ₂ receptor binding pocket.

    PubMed

    Rhoades, Derek J; Kinder, David H; Mahfouz, Tarek M

    2014-01-01

    The sigma (σ) receptor system consists of at least two major receptor subtypes: σ₁ and σ₂. Several potential therapeutic applications would benefit from structural knowledge of the σ₂ receptor but gaining this knowledge has been hampered by the difficulties associated with its isolation and, thus, characterization. Here, a ligand based approach has been adopted using the program PHASE® and a group of 41 potent and structurally diverse σ₂ ligands to develop several pharmacophore models for different families of σ₂ ligands. These pharmacophores were analyzed to identify the different binding modes to the receptor and were combined together to construct a comprehensive pharmacophore that was used to develop a structural model for the σ₂ binding pocket. A total of six binding modes were identified and could be classified as neutral or charged modes. The results presented here also indicate the significance of hydrophobic interactions to σ₂ binding and the requirement of hydrogen bonding interactions to increase the affinity for this receptor subtype. This work adds breadth to our knowledge of this receptor's binding site, and should contribute significantly to the development of novel selective σ₂ ligands.

  10. Syntheses, characterization, biological activities and photophysical properties of lanthanides complexes with a tetradentate Schiff base ligand

    NASA Astrophysics Data System (ADS)

    Taha, Ziyad A.; Ajlouni, Abdulaziz M.; Al Momani, Waleed; Al-Ghzawi, Abeer A.

    2011-10-01

    A tetradentate Schiff base ligand L (N,N'-bis(1-naphthaldimine)-o-phenylenediamine) was prepared from the condensation of 2-hydroxy-1-naphthaldehyde with o-phenylenediamine in a molar ratio of 2:1. New eight lanthanide metal complexes [Ln L(NO 3) 2(H 2O) x](NO 3) {Ln(III) = Nd, Dy, Sm, Pr, Gd, Tb, La and Er, x = 0 for Nd, Sm, 1 for La, Gd, Pr, Nd, Dy, and 2 for Tb} were prepared. The characterization and nature of bonding of these complexes were elucidated by elemental analysis, spectral analysis ( 1H NMR, FT-IR, UV-vis), molar conductivity measurements, luminescence spectra and thermogravimetric studies. Analytical and spectral data revealed that the ligand L coordinates to the central Ln(III) ions by its two imine nitrogen atoms and two phenolic oxygen atoms with 1:1 stoichiometry. Under the excitation with 329 nm at room temperature, Tb and Dy complexes exhibited characteristic luminescence of the central metal ions attributed to efficient energy transfer from the ligand to the metal center. Most of Ln(III) complexes found to exhibit antibacterial activities against a number of pathogenic bacteria. We found that the antioxident activity of Ln(III) complexes on DPPH rad is concentration dependent and higher than that of the free ligand L.

  11. Virtual ligand screening against Escherichia coli dihydrofolate reductase: improving docking enrichment using physics-based methods.

    PubMed

    Bernacki, Katarzyna; Kalyanaraman, Chakrapani; Jacobson, Matthew P

    2005-10-01

    Motivated by their participation in the McMaster Data-Mining and Docking Competition, the authors developed 2 new computational technologies and applied them to docking against Escherichia coli dihydrofolate reductase: a receptor preparation procedure that incorporates rotamer optimization of side chains and a physics-based rescoring procedure for estimating relative binding affinities of the protein-ligand complexes. Both methods use the same energy function, consisting of the all-atom OPLS-AA force field and a generalized Born solvent model, which treats the protein receptor and small-molecule ligands in a consistent manner. Thus, the energy function is similar to that used in more sophisticated approaches, such as free-energy perturbation and the molecular mechanics Poisson-Boltzmann/surface area, but sampling during the rescoring procedure is limited to simple energy minimization of the ligand. The use of a highly efficient minimization algorithm permitted the authors to apply this rescoring procedure to hundreds of thousands of protein-ligand complexes during the competition, using a modest Linux cluster. To test these methods, they used the 12 competitive inhibitors identified in the training set, plus methotrexate, as positive controls in enrichment studies with both the training and test sets, each containing 50,000 compounds. The key conclusion is that combining the receptor preparation and rescoring methods makes it possible to identify most of the positive controls within the top few tenths of a percent of the rank-ordered training and test set libraries.

  12. Network of nuclear receptor ligands in multiple sclerosis: Common pathways and interactions of sex-steroids, corticosteroids and vitamin D3-derived molecules.

    PubMed

    Rolf, Linda; Damoiseaux, Jan; Hupperts, Raymond; Huitinga, Inge; Smolders, Joost

    2016-09-01

    Sex-steroids, corticosteroids and vitamin D3-derived molecules have all been subject to experimental studies and clinical trials in a plethora of autoimmune diseases. These molecules are all derived from cholesterol metabolites and are ligands for nuclear receptors. Ligation of these receptors results in direct regulation of multiple gene transcription involved in general homeostatic and adaptation networks, including the immune system. Indeed, the distinct ligands affect the function of both myeloid and lymphoid cells, eventually resulting in a less pro-inflammatory immune response which is considered beneficial in autoimmune diseases. Next to the immune system, also the central nervous system is prone to regulation by these nuclear receptor ligands. Understanding of the intricate interactions between sex-steroids, corticosteroids and vitamin D3 metabolites, on the one hand, and the immune and central nervous system, on the other hand, may reveal novel approaches to utilize these nuclear receptor ligands to full extent as putative treatments in multiple sclerosis, the prototypic immune-driven disease of the central nervous system. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Receptor- and ligand-based study of fullerene analogues: comprehensive computational approach including quantum-chemical, QSAR and molecular docking simulations.

    PubMed

    Ahmed, Lucky; Rasulev, Bakhtiyor; Turabekova, Malakhat; Leszczynska, Danuta; Leszczynski, Jerzy

    2013-09-21

    Fullerene and its derivatives have potential antiviral activity due to their specific binding interactions with biological molecules. In this study fullerene derivatives were investigated by the synergic combination of three approaches: quantum-mechanical calculations, protein-ligand docking and quantitative structure-activity relationship methods. The protein-ligand docking studies and improved structure-activity models have been able both to predict binding affinities for the set of fullerene-C60 derivatives and to help in finding mechanisms of fullerene derivative interactions with human immunodeficiency virus type 1 aspartic protease, HIV-1 PR. Protein-ligand docking revealed several important molecular fragments that are responsible for the interaction with HIV-1 PR. In addition, a density functional theory method has been utilized to identify the optimal geometries and predict physico-chemical parameters of the studied compounds. The 5-variable GA-MLRA based model showed the best predictive ability (r(2)training = 0.882 and r(2)test = 0.738), with high internal and external correlation coefficients.

  14. PL-PatchSurfer: A Novel Molecular Local Surface-Based Method for Exploring Protein-Ligand Interactions

    PubMed Central

    Hu, Bingjie; Zhu, Xiaolei; Monroe, Lyman; Bures, Mark G.; Kihara, Daisuke

    2014-01-01

    Structure-based computational methods have been widely used in exploring protein-ligand interactions, including predicting the binding ligands of a given protein based on their structural complementarity. Compared to other protein and ligand representations, the advantages of a surface representation include reduced sensitivity to subtle changes in the pocket and ligand conformation and fast search speed. Here we developed a novel method named PL-PatchSurfer (Protein-Ligand PatchSurfer). PL-PatchSurfer represents the protein binding pocket and the ligand molecular surface as a combination of segmented surface patches. Each patch is characterized by its geometrical shape and the electrostatic potential, which are represented using the 3D Zernike descriptor (3DZD). We first tested PL-PatchSurfer on binding ligand prediction and found it outperformed the pocket-similarity based ligand prediction program. We then optimized the search algorithm of PL-PatchSurfer using the PDBbind dataset. Finally, we explored the utility of applying PL-PatchSurfer to a larger and more diverse dataset and showed that PL-PatchSurfer was able to provide a high early enrichment for most of the targets. To the best of our knowledge, PL-PatchSurfer is the first surface patch-based method that treats ligand complementarity at protein binding sites. We believe that using a surface patch approach to better understand protein-ligand interactions has the potential to significantly enhance the design of new ligands for a wide array of drug-targets. PMID:25167137

  15. Symbolic derivation of potential based constitutive equations

    NASA Astrophysics Data System (ADS)

    Arnold, S. M.; Tan, H. Q.

    1990-05-01

    Structural alloys used in high temperature applications exhibit complex thermomechanical behavior that is inherently time dependent and hereditary, as the current behavior depends not only on current conditions but on the thermomechanical history. Derivation of mathematical expressions (constitutive equations) which describe this high temperature material behavior can be quite time consuming, involved, and error-prone, thus intelligent application of symbolic systems to facilitate this tedious processes can be of significant benefit. Here a computerized package, running under MACSYMA, capable of efficiently deriving potential based constitutive models, in analytical form (involving tensors, partial differentiation, invariants, and the like) is presented. Special purpose utility algorithms are designed and implemented to perform partial differentiation (chain rule), tensor manipulation, case distinction and simplification. Four constitutive theories reported in the literature are utilized to verify implementation accuracy. It is expected that this symbolic package can and will provide a significant incentive to the development of new constitutive theories.

  16. Chemokines and other GPCR ligands synergize in receptor-mediated migration of monocyte-derived immature and mature dendritic cells.

    PubMed

    Gouwy, Mieke; Struyf, Sofie; Leutenez, Lien; Pörtner, Noëmie; Sozzani, Silvano; Van Damme, Jo

    2014-03-01

    Dendritic cells (DCs) are potent antigen presenting cells, described as the initiators of adaptive immune responses. Immature monocyte-derived DCs (MDDC) showed decreased CD14 expression, increased cell surface markers DC-SIGN and CD1a and enhanced levels of receptors for the chemokines CCL3 (CCR1/CCR5) and CXCL8 (CXCR1/CXCR2) compared with human CD14⁺ monocytes. After further MDDC maturation by LPS, the markers CD80 and CD83 and the chemokine receptors CXCR4 and CCR7 were upregulated, whereas CCR1, CCR2 and CCR5 expression was reduced. CCL3 dose-dependently synergized with CXCL8 or CXCL12 in chemotaxis of immature MDDC. CXCL12 augmented the CCL3-induced ERK1/2 and Akt phosphorylation in immature MDDC, although the synergy between CCL3 and CXCL12 in chemotaxis of immature MDDC was dependent on the Akt signaling pathway but not on ERK1/2 phosphorylation. CCL2 also synergized with CXCL12 in immature MDDC migration. Moreover, two CXC chemokines not sharing receptors (CXCL12 and CXCL8) cooperated in immature MDDC chemotaxis, whereas two CC chemokines (CCL3 and CCL7) sharing CCR1 did not. Further, the non-chemokine G protein-coupled receptor ligands chemerin and fMLP synergized with respectively CCL7 and CCL3 in immature MDDC signaling and migration. Finally, CXCL12 and CCL3 did not cooperate, but CXCL12 synergized with CCL21 in mature MDDC chemotaxis. Thus, chemokine synergy in immature and mature MDDC migration is dose-dependently regulated by chemokines via alterations in their chemokine receptor expression pattern according to their role in immune responses.

  17. Derivative based sensitivity analysis of gamma index

    PubMed Central

    Sarkar, Biplab; Pradhan, Anirudh; Ganesh, T.

    2015-01-01

    Originally developed as a tool for patient-specific quality assurance in advanced treatment delivery methods to compare between measured and calculated dose distributions, the gamma index (γ) concept was later extended to compare between any two dose distributions. It takes into effect both the dose difference (DD) and distance-to-agreement (DTA) measurements in the comparison. Its strength lies in its capability to give a quantitative value for the analysis, unlike other methods. For every point on the reference curve, if there is at least one point in the evaluated curve that satisfies the pass criteria (e.g., δDD = 1%, δDTA = 1 mm), the point is included in the quantitative score as “pass.” Gamma analysis does not account for the gradient of the evaluated curve - it looks at only the minimum gamma value, and if it is <1, then the point passes, no matter what the gradient of evaluated curve is. In this work, an attempt has been made to present a derivative-based method for the identification of dose gradient. A mathematically derived reference profile (RP) representing the penumbral region of 6 MV 10 cm × 10 cm field was generated from an error function. A general test profile (GTP) was created from this RP by introducing 1 mm distance error and 1% dose error at each point. This was considered as the first of the two evaluated curves. By its nature, this curve is a smooth curve and would satisfy the pass criteria for all points in it. The second evaluated profile was generated as a sawtooth test profile (STTP) which again would satisfy the pass criteria for every point on the RP. However, being a sawtooth curve, it is not a smooth one and would be obviously poor when compared with the smooth profile. Considering the smooth GTP as an acceptable profile when it passed the gamma pass criteria (1% DD and 1 mm DTA) against the RP, the first and second order derivatives of the DDs (δD’, δD”) between these two curves were derived and used as the boundary

  18. Phosphite-Thiother Ligands Derived from Carbohydrates allow the Enantioswitchable Hydrogenation of Cyclic β-Enamides by using either Rh or Ir Catalysts.

    PubMed

    Margalef, Jèssica; Pàmies, Oscar; Diéguez, Montserrat

    2017-01-18

    Phosphite-thioether ligands with a simple modular architecture, derived from inexpensive l-(+)-tartaric acid and d-mannitol, have been for the first time successfully applied (ee values up to 99 %) in the synthesis of 2-aminotetralines and 3-aminochromanes by metal-catalyzed asymmetric hydrogenation of cyclic β-enamides. The ligands have the advantages of the robustness of the thioether/phosphite moieties and the extra control provided by the flexibility of the chiral pocket through the presence of a biaryl phosphite group and a modular carbohydrate-derived backbone. Moreover, they are solid and stable to air and they are therefore easy to handle, manipulate, and store. Usefully, both enantiomers of the hydrogenated products were obtained by simply switching from Rh to Ir. Low hydrogen pressure and environmentally friendly propylene carbonate can be used, with no loss of selectivity.

  19. Construction of Protein-Based Biosensors Using Ligand-Directed Chemistry for Detecting Analyte Binding.

    PubMed

    Yamaura, Kei; Kiyonaka, Shigeki; Hamachi, Itaru

    2017-01-01

    Protein-based fluorescent biosensors are powerful tools for quantitative detection of biomolecules or drugs with high sensitivity under physiological conditions. However, conventional methods for construction of biosensors require structural data with high resolution or amino acid sequence information in most cases, which hampers applicability of this method to structurally complicated receptor proteins. To sidestep such limitations, we recently developed a new method that employs ligand-directed chemistry coupled with a bimolecular fluorescence quenching and recovery system, which enabled the conversion of various kinds of membrane-bound receptors to "turn-on" type fluorescent sensors. Here, we describe a protocol for construction of "turn-on" type fluorescent biosensors based on the GABAA receptor which permits quantitative analysis of the ligand affinity.

  20. Novel FXa Inhibitor Identification through Integration of Ligand- and Structure-Based Approaches.

    PubMed

    Lagos, Carlos F; Segovia, Gerardine F; Nuñez-Navarro, Nicolás; Faúndez, Mario A; Zacconi, Flavia C

    2017-09-22

    Factor Xa (FXa), a vitamin K-dependent serine protease plays a pivotal role in the coagulation cascade, one of the most interesting targets for the development of new anticoagulants. In the present work, we performed a virtual screening campaign based on ligand-based shape and electrostatic similarity search and protein-ligand docking to discover novel FXa-targeted scaffolds for further development of inhibitors. From an initial set of 260,000 compounds from the NCI Open database, 30 potential FXa inhibitors were identified and selected for in vitro biological evaluation. Compound 5 (NSC635393, 4-(3-methyl-4H-1,4-benzothiazin-2-yl)-2,4-dioxo-N-phenylbutanamide) displayed an IC50 value of 2.02 nM against human FXa. The identified compound may serve as starting point for the development of novel FXa inhibitors.

  1. ProPose: a docking engine based on a fully configurable protein-ligand interaction model.

    PubMed

    Seifert, Markus H J; Schmitt, Frank; Herz, Thomas; Kramer, Bernd

    2004-12-01

    Virtual high-throughput screening of molecular databases and in particular high-throughput protein-ligand docking are both common methodologies that identify and enrich hits in the early stages of the drug design process. Current protein-ligand docking algorithms often implement a program-specific model for protein-ligand interaction geometries. However, in order to create a platform for arbitrary queries in molecular databases, a new program is desirable that allows more manual control of the modeling of molecular interactions. For that reason, ProPose, an advanced incremental construction docking engine, is presented here that implements a fast and fully configurable molecular interaction and scoring model. This program uses user-defined, discrete, pharmacophore-like representations of molecular interactions that are transformed on-the-fly into a continuous potential energy surface, allowing for the incorporation of target specific interaction mechanisms into docking protocols in a straightforward manner. A torsion angle library, based on semi-empirical quantum chemistry calculations, is used to provide minimum energy torsion angles for the incremental construction algorithm. Docking results of a diverse set of protein-ligand complexes from the Protein Data Bank demonstrate the feasibility of this new approach. As a result, the seamless integration of pharmacophore-like interaction types into the docking and scoring scheme implemented in ProPose opens new opportunities for efficient, receptor-specific screening protocols. [figure: see text]. ProPose--a fully configurable protein-ligand docking program--transforms pharmacophores into a smooth potential energy surface.

  2. Development of peptoid-based ligands for the removal of cadmium from biological media

    DOE PAGES

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

    2015-05-14

    Cadmium poisoning poses a serious health concern due to cadmium's increasing industrial use, yet there is currently no recommended treatment. The selective coordination of cadmium in a biological environment—i.e. in the presence of serum ions, small molecules, and proteins—is a difficult task. To address this challenge, a combinatorial library of peptoid-based ligands has been evaluated to identify structures that selectively bind to cadmium in human serum with minimal chelation of essential metal ions. Eighteen unique ligands were identified in this screening procedure, and the binding affinity of each was measured using metal titrations monitored by UV-vis spectroscopy. To evaluate themore » significance of each chelating moiety, sequence rearrangements and substitutions were examined. Analysis of a metal–ligand complex by NMR spectroscopy highlighted the importance of particular residues. Depletion experiments were performed in serum mimetics and human serum with exogenously added cadmium. These depletion experiments were used to compare and demonstrate the ability of these peptoids to remove cadmium from blood-like mixtures. In one of these depletion experiments, the peptoid sequence was able to deplete the cadmium to a level comparable to the reported acute toxicity limit. Evaluation of the metal selectivity in buffered solution and in human serum was performed to verify minimal off-target binding. These studies highlight a screening platform for the identification of metal–ligands that are capable of binding in a complex environment. They additionally demonstrate the potential utility of biologically-compatible ligands for the treatment of heavy metal poisoning.« less

  3. Development of peptoid-based ligands for the removal of cadmium from biological media

    SciTech Connect

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

    2015-05-14

    Cadmium poisoning poses a serious health concern due to cadmium's increasing industrial use, yet there is currently no recommended treatment. The selective coordination of cadmium in a biological environment—i.e. in the presence of serum ions, small molecules, and proteins—is a difficult task. To address this challenge, a combinatorial library of peptoid-based ligands has been evaluated to identify structures that selectively bind to cadmium in human serum with minimal chelation of essential metal ions. Eighteen unique ligands were identified in this screening procedure, and the binding affinity of each was measured using metal titrations monitored by UV-vis spectroscopy. To evaluate the significance of each chelating moiety, sequence rearrangements and substitutions were examined. Analysis of a metal–ligand complex by NMR spectroscopy highlighted the importance of particular residues. Depletion experiments were performed in serum mimetics and human serum with exogenously added cadmium. These depletion experiments were used to compare and demonstrate the ability of these peptoids to remove cadmium from blood-like mixtures. In one of these depletion experiments, the peptoid sequence was able to deplete the cadmium to a level comparable to the reported acute toxicity limit. Evaluation of the metal selectivity in buffered solution and in human serum was performed to verify minimal off-target binding. These studies highlight a screening platform for the identification of metal–ligands that are capable of binding in a complex environment. They additionally demonstrate the potential utility of biologically-compatible ligands for the treatment of heavy metal poisoning.

  4. Development of Peptoid-Based Ligands for the Removal of Cadmium from Biological Media

    PubMed Central

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

    2015-01-01

    Cadmium poisoning poses a serious health concern due to cadmium’s increasing industrial use, yet there is currently no recommended treatment. The selective coordination of cadmium in a biological environment—i.e. in the presence of serum ions, small molecules, and proteins—is a difficult task. To address this challenge, a combinatorial library of peptoid-based ligands has been evaluated to identify structures that selectively bind to cadmium in human serum with minimal chelation of essential metal ions. Eighteen unique ligands were identified in this screening procedure, and the binding affinity of each was measured using metal titrations monitored by UV-vis spectroscopy. To evaluate the significance of each chelating moiety, sequence rearrangements and substitutions were examined. Analysis of a metal-ligand complex by NMR spectroscopy highlighted the importance of particular residues. Depletion experiments were performed in serum mimetics and human serum with exogenously added cadmium. These depletion experiments were used to compare and demonstrate the ability of these peptoids to remove cadmium from blood-like mixtures. In one of these depletion experiments, the peptoid sequence was able to deplete the cadmium to a level comparable to the reported acute toxicity limit. Evaluation of the metal selectivity in buffered solution and in human serum was performed to verify minimal off-target binding. These studies highlight a screening platform for of the identification of metal-ligands that are capable of binding in a complex environment. They additionally demonstrate the potential utility of biologically-compatible ligands for the treatment of heavy metal poisoning. PMID:26918113

  5. Comparison of ligand- and structure-based virtual screening on the DUD data set.

    PubMed

    von Korff, Modest; Freyss, Joel; Sander, Thomas

    2009-02-01

    Several in-house developed descriptors and our in-house docking tool ActDock were compared with virtual screening on the data set of useful decoys (DUD). The results were compared with the chemical fingerprint descriptor from ChemAxon and with the docking results of the original DUD publication. The DUD is the first published data set providing active molecules, decoys, and references for crystal structures of ligand-target complexes. The DUD was designed for the purpose of evaluating docking programs. It contains 2950 active compounds against a total of 40 target proteins. Furthermore, for every ligand the data set contains 36 structurally dissimilar decoy compounds with similar physicochemical properties. We extracted the ligands from the target proteins to extend the applicability of the data set to include ligand based virtual screening. From the 40 target proteins, 37 contained ligands that we used as query molecules for virtual screening evaluation. With this data set a large comparison was done between four different chemical fingerprints, a topological pharmacophore descriptor, the Flexophore descriptor, and ActDock. The Actelion docking tool relies on a MM2 forcefield and a pharmacophore point interaction statistic for scoring; the details are described in this publication. In terms of enrichment rates the chemical fingerprint descriptors performed better than the Flexophore and the docking tool. After removing molecules chemically similar to the query molecules the Flexophore descriptor outperformed the chemical descriptors and the topological pharmacophore descriptors. With the similarity matrix calculations used in this study it was shown that the Flexophore is well suited to find new chemical entities via "scaffold hopping". The Flexophore descriptor can be explored with a Java applet at http://www.cheminformatics.ch in the submenu Tools-->Flexophore. Its usage is free of charge and does not require registration.

  6. Enantioselective Addition of Diethylzinc to Aldehydes Catalyzed by Chiral O,N,O-tridentate Phenol Ligands Derived From Camphor.

    PubMed

    Lee, Dong-Sheng; Chang, Shu-Ming; Ho, Chun-Ying; Lu, Ta-Jung

    2016-01-01

    Chiral O,N,O-tridentate phenol ligands bearing a camphor backbone were found to be effective chiral catalysts for the enantioselective addition of diethylzinc to aromatic aldehydes, resulting in high enantioselectivities (80-95% ee) at room temperature.

  7. Identification of Programmed Death Ligand 1-derived Peptides Capable of Inducing Cancer-reactive Cytotoxic T Lymphocytes From HLA-A24+ Patients With Renal Cell Carcinoma.

    PubMed

    Minami, Takafumi; Minami, Tomoko; Shimizu, Nobutaka; Yamamoto, Yutaka; De Velasco, Marco; Nozawa, Masahiro; Yoshimura, Kazuhiro; Harashima, Nanae; Harada, Mamoru; Uemura, Hirotsugu

    2015-09-01

    Molecular therapy targeting tumor angiogenesis has been the standard treatment for metastatic renal cell carcinoma (mRCC). However, despite their significant antitumor effects, most of patients with mRCC have not been cured. Under such circumstances, anticancer immunotherapy has been considered a promising treatment modality for mRCC, and cancer-reactive cytotoxic T lymphocytes (CTLs) are the most powerful effectors among several immune cells. However, anticancer CTLs can be inhibited by several immune inhibitory mechanisms, including the interaction between programmed death 1 (PD-1) and its ligand PD-L1, on T cells and cancer cells, respectively. Alternatively, this also means that PD-L1 could be a promising target for anticancer immunotherapy. Therefore, we searched for PD-L1-derived peptides that are applicable for anticancer vaccine for HLA-A24(+) RCC patients. Among 5 peptides derived from PD-L1, which were prepared based on the binding motif to the HLA-A24(+) allele, both PD-L1(11-19) and PD-L1(41-50) peptides induced peptide-specific CTLs from peripheral blood mononuclear cells of HLA-A24(+) RCC patients. Such PD-L1 peptide-stimulated CD8 T cells showed cytotoxicity against HLA-A24(+) and PD-L1-expressing RCC cells. Although IFN-γ treatment increased PD-L1 expression on PD-L1(low) RCC cells, their sensitivity to cytotoxicity of PD-L1 peptide-stimulated CD8(+) T cells varied between patients. Altogether, these results indicate that both PD-L1(11-19) and PD-L1(41-50) peptides could be candidates for peptide-based anticancer vaccines for HLA-A24(+) mRCC patients.

  8. Discovery of nonsteroidal glucocorticoid receptor ligands based on 6-indole-1,2,3,4-tetrahydroquinolines.

    PubMed

    Roach, Steven L; Higuchi, Robert I; Adams, Mark E; Liu, Yan; Karanewsky, Donald S; Marschke, Keith B; Mais, Dale E; Miner, Jeffrey N; Zhi, Lin

    2008-06-15

    A series of nonsteroidal glucocorticoid receptor (GR) ligands based on a 6-indole-1,2,3,4-tetrahydroquinoline scaffold are reported. Structure-activity relationship (SAR) of the pendent indole group identified compound 20 exhibiting good GR binding affinity (K(i)=1.5nM) and 100- to 1000-fold selectivity over MR, PR, and AR while showing activity in an E-selectin repression assay.

  9. When Weaker Can Be Tougher: The Role of Oxidation State (I) in P- vs N-Ligand-Derived Ni-Catalyzed Trifluoromethylthiolation of Aryl Halides

    PubMed Central

    2017-01-01

    The direct introduction of the valuable SCF3 moiety into organic molecules has received considerable attention. While it can be achieved successfully for aryl chlorides under catalysis with Ni0(cod)2 and dppf, this report investigates the Ni-catalyzed functionalization of the seemingly more reactive aryl halides ArI and ArBr. Counterintuitively, the observed conversion triggered by dppf/Ni0 is ArCl > ArBr > ArI, at odds with bond strength preferences. By a combined computational and experimental approach, the origin of this was identified to be due to the formation of (dppf)NiI, which favors β-F elimination as a competing pathway over the productive cross-coupling, ultimately generating the inactive complex (dppf)Ni(SCF2) as a catalysis dead end. The complexes (dppf)NiI–Br and (dppf)NiI–I were isolated and resolved by X-ray crystallography. Their formation was found to be consistent with a ligand-exchange-induced comproportionation mechanism. In stark contrast to these phosphine-derived Ni complexes, the corresponding nitrogen-ligand-derived species were found to be likely competent catalysts in oxidation state I. Our computational studies of N-ligand derived NiI complexes fully support productive NiI/NiIII catalysis, as the competing β-F elimination is disfavored. Moreover, N-derived NiI complexes are predicted to be more reactive than their Ni0 counterparts in catalysis. These data showcase fundamentally different roles of NiI in carbon–heteroatom bond formation depending on the ligand sphere. PMID:28286695

  10. Novel Treatment of Melanoma: Combined Parasite-Derived Peptide GK-1 and Anti-Programmed Death Ligand 1 Therapy.

    PubMed

    Vera-Aguilera, Jesus; Perez-Torres, Armando; Beltran, Diego; Villanueva-Ramos, Cynthia; Wachtel, Mitchell; Moreno-Aguilera, Eduardo; Vera-Aguilera, Carlos; Ventolini, Gary; Martínez-Zaguilán, Raul; Sennoune, Souad R

    2017-03-01

    Recent successes in the development of new therapies for metastatic melanoma, such as mitogen-activated protein kinase pathway inhibitors, anticytotoxic T lymphocyte-associated antigen-4, and programmed cell death protein 1/programmed cell death ligand 1 (PD-L1) pathway-blocking antibodies, as well as combination strategies, all yielded promising results, changing the continually evolving landscape of therapeutic options for patients with melanoma. One promising new treatment modality is based on the use of immunomodulatory monoclonal antibodies that enhance the function of components of the antitumor immune response such as T cells or block immunologic checkpoints that restrain effective antitumor immunity. Program death-1 receptor and its ligand, PD-L1, is a major mechanism by which a tumor suppresses T cell-mediated antitumor immune responses. Studies in mice have shown that GK-1, an 18 amino acid peptide from Taenia crassiceps cisticerci, has the potential to be used as a primary or adjuvant component for the treatment of cancers by stimulating proinflammatory cytokines. The authors hypothesized that treatment with GK-1 in combination with anti-PD-L1 will increase survival in mice bearing melanoma tumors. C57BL/6 mice were injected with B16-F10-luc2 cells and separated into four groups: control, GK-1, anti-PD-L1, and GK-1/anti-PD-L1. The tumor sizes were measured and monitored using calipers and bioluminescence. The GK-1 peptide in combination with anti-PD-L1 showed significantly longer survival (34 days) compared with the other groups (23-27 days). This means an increase; survival increased 47.82% in the mice treated with GK-1+anti-PD-L1, 21.7% in mice treated with GK-1 alone, and 6.08% in those mice treated with anti-PD-L1 only. Blood samples were collected at days 0, 14, and at euthanization or end of the experiment and monitored for cytokines using mouse-specific V-PLEX Proinflammatory Panel. A decrease in TNF-α, IL-4, IL-5, IL-6, and IL-10 serum levels

  11. Ligand redox activity and mixed valency in first-row transition-metal complexes containing tetrachlorocatecholate and radical tetrachlorosemiquinonate ligands.

    PubMed

    Pierpont, Cortlandt G

    2011-10-17

    Ligand noninnocence occurs for complexes composed of redox-active ligands and metals, with frontier orbitals of similar energy. Usually methods of analysis can be used to define the charge distribution, and cases where the metal oxidation state and ligand charge are unclear are unusual. Ligands derived from o-benzoquinones can bond with metals as radical semiquinonates (SQ(•-)) or as catecholates (Cat(2-)). Spectroscopic, magnetic, and structural properties can be used to assess the metal and ligand charges. With the redox activity at both the metal and ligands, reversible multicomponent redox series can be observed using electrochemical methods. Steps in the series may occur at either the ligand or metal, and ligand substituent effects can be used to tune the range of ligand-based redox steps. Complexes that appear as intermediates in a ligand-based redox series may contain both SQ and Cat ligands "bridged" by the metal as mixed-valence complexes. Properties reflect the strength of metal-mediated interligand electronic coupling in the same way that ligand-bridged bimetallics conform to the Robin and Day classification scheme. In this review, we will focus specifically on complexes of first-row transition-metal ions coordinated with three ligands derived from tetrachloro-1,2-benzoquinone (Cl(4)BQ). The redox activity of this ligand overlaps with the potentials of common metal oxidation states, providing examples of metal- and ligand-based redox activity, in some cases, within a single redox series. The strength of the interligand electronic coupling is important in defining the separation between ligand-based couples of a redox series. The complex of ferric iron will be described as an example where coupling is weak, and the steps associated with the Fe(III)(Cl(4)SQ)(3)/[Fe(III)(Cl(4)Cat)(3)](3-) redox series are observed over a narrow range in electrochemical potential.

  12. Green and facile synthesis of water-soluble ZnS quantum dots nanohybrids using chitosan derivative ligands

    NASA Astrophysics Data System (ADS)

    Ramanery, Fábio P.; Mansur, Alexandra A. P.; Borsagli, Fernanda G. L. M.; Mansur, Herman S.

    2014-07-01

    Semiconductor quantum dots (QDs) are fluorescent nanocrystals with great potential for use in biomedical and environmental applications. However, eliminating the potential cytotoxicity of the QDs comprised of a core containing heavy metals and using a green chemical process are still challenges faced by the research community. Thus, the aim of this work was to develop a novel green and facile route for synthesizing biocompatible water-soluble QDs using chemically modified chitosan as a capping ligand in aqueous media, with their chemical and optical properties tuned by the nanoparticle size. The synthesis of ZnS QDs capped by carboxymethylchitosan (CMC) was performed using a single-step aqueous colloidal process at room temperature. The nanohybrids were extensively characterized by several imaging and spectroscopic techniques, and the results demonstrated that ultra-small ZnS nanocrystals were produced with average nanoparticles ranging from 3.2 to 4.2 nm. In addition, the luminescent properties of ZnS QDs were influenced by the pH during the synthesis due to the size distribution of the nanoparticles produced. Hence, new "heavy metal free" nanohybrids were successfully developed based on ZnS QDs directly surface-functionalized by biopolymer exhibiting fluorescent activity that may be potentially used in a large number of eco-friendly and biomedical applications.

  13. Challenges, applications, and recent advances of protein-ligand docking in structure-based drug design.

    PubMed

    Grinter, Sam Z; Zou, Xiaoqin

    2014-07-11

    The docking methods used in structure-based virtual database screening offer the ability to quickly and cheaply estimate the affinity and binding mode of a ligand for the protein receptor of interest, such as a drug target. These methods can be used to enrich a database of compounds, so that more compounds that are subsequently experimentally tested are found to be pharmaceutically interesting. In addition, like all virtual screening methods used for drug design, structure-based virtual screening can focus on curated libraries of synthesizable compounds, helping to reduce the expense of subsequent experimental verification. In this review, we introduce the protein-ligand docking methods used for structure-based drug design and other biological applications. We discuss the fundamental challenges facing these methods and some of the current methodological topics of interest. We also discuss the main approaches for applying protein-ligand docking methods. We end with a discussion of the challenging aspects of evaluating or benchmarking the accuracy of docking methods for their improvement, and discuss future directions.

  14. Designing multivalent proteins based on natural killer cell receptors and their ligands as immunotherapy for cancer.

    PubMed

    Smits, Nicole C; Coupet, Tiffany A; Godbersen, Claire; Sentman, Charles L

    2016-09-01

    Natural killer (NK) cells are an important component of the innate immune system that play a key role in host immunity against cancer. NK cell recognition and activation is based on cell surface receptors recognizing specific ligands that are expressed on many types of tumor cells. Some of these receptors are capable of activating NK cell function while other receptors inhibit NK cell function. Therapeutic approaches to treat cancer have been developed based on preventing NK cell inhibition or using NK cell receptors and their ligands to activate NK cells or T cells to destroy tumor cells. This article describes the various strategies for targeting NK cell receptors and NK cell receptor ligands using multivalent proteins to activate immunity against cancer. NK cell receptors work in synergy to activate NK cell effector responses. Effective anti-cancer strategies will need to not only kill tumor cells but must also lead to the destruction of the tumor microenvironment. Immunotherapy based on NK cells and their receptors has the capacity to accomplish this through triggering lymphocyte cytotoxicity and cytokine production.

  15. mRAISE: an alternative algorithmic approach to ligand-based virtual screening.

    PubMed

    von Behren, Mathias M; Bietz, Stefan; Nittinger, Eva; Rarey, Matthias

    2016-08-01

    Ligand-based virtual screening is a well established method to find new lead molecules in todays drug discovery process. In order to be applicable in day to day practice, such methods have to face multiple challenges. The most important part is the reliability of the results, which can be shown and compared in retrospective studies. Furthermore, in the case of 3D methods, they need to provide biologically relevant molecular alignments of the ligands, that can be further investigated by a medicinal chemist. Last but not least, they have to be able to screen large databases in reasonable time. Many algorithms for ligand-based virtual screening have been proposed in the past, most of them based on pairwise comparisons. Here, a new method is introduced called mRAISE. Based on structural alignments, it uses a descriptor-based bitmap search engine (RAISE) to achieve efficiency. Alignments created on the fly by the search engine get evaluated with an independent shape-based scoring function also used for ranking of compounds. The correct ranking as well as the alignment quality of the method are evaluated and compared to other state of the art methods. On the commonly used Directory of Useful Decoys dataset mRAISE achieves an average area under the ROC curve of 0.76, an average enrichment factor at 1 % of 20.2 and an average hit rate at 1 % of 55.5. With these results, mRAISE is always among the top performing methods with available data for comparison. To access the quality of the alignments calculated by ligand-based virtual screening methods, we introduce a new dataset containing 180 prealigned ligands for 11 diverse targets. Within the top ten ranked conformations, the alignment closest to X-ray structure calculated with mRAISE has a root-mean-square deviation of less than 2.0 Å for 80.8 % of alignment pairs and achieves a median of less than 2.0 Å for eight of the 11 cases. The dataset used to rate the quality of the calculated alignments is freely available

  16. mRAISE: an alternative algorithmic approach to ligand-based virtual screening

    NASA Astrophysics Data System (ADS)

    von Behren, Mathias M.; Bietz, Stefan; Nittinger, Eva; Rarey, Matthias

    2016-08-01

    Ligand-based virtual screening is a well established method to find new lead molecules in todays drug discovery process. In order to be applicable in day to day practice, such methods have to face multiple challenges. The most important part is the reliability of the results, which can be shown and compared in retrospective studies. Furthermore, in the case of 3D methods, they need to provide biologically relevant molecular alignments of the ligands, that can be further investigated by a medicinal chemist. Last but not least, they have to be able to screen large databases in reasonable time. Many algorithms for ligand-based virtual screening have been proposed in the past, most of them based on pairwise comparisons. Here, a new method is introduced called mRAISE. Based on structural alignments, it uses a descriptor-based bitmap search engine (RAISE) to achieve efficiency. Alignments created on the fly by the search engine get evaluated with an independent shape-based scoring function also used for ranking of compounds. The correct ranking as well as the alignment quality of the method are evaluated and compared to other state of the art methods. On the commonly used Directory of Useful Decoys dataset mRAISE achieves an average area under the ROC curve of 0.76, an average enrichment factor at 1 % of 20.2 and an average hit rate at 1 % of 55.5. With these results, mRAISE is always among the top performing methods with available data for comparison. To access the quality of the alignments calculated by ligand-based virtual screening methods, we introduce a new dataset containing 180 prealigned ligands for 11 diverse targets. Within the top ten ranked conformations, the alignment closest to X-ray structure calculated with mRAISE has a root-mean-square deviation of less than 2.0 Å for 80.8 % of alignment pairs and achieves a median of less than 2.0 Å for eight of the 11 cases. The dataset used to rate the quality of the calculated alignments is freely available at

  17. Growth of II-VI thin-films from single-source precursors based on sterically encumbered sitel ligands

    SciTech Connect

    Arnold, J.; Seligson, A.L.; Walker, J.M.; Bourret, E.D.; Bonasia, P.J.

    1992-04-01

    We have developed a new route to MOCVD of II-VI compounds based on the use of novel single-source precursors in which the II-VI elements are combined at the molecular level in a single covalent compound. We have prepared and fully characterized a number of new derivatives of zinc, cadmium and mercury incorporating large, sterically demanding tellurolate ligands of general formula: M(sitel){sub 2} where sitel = -TeSi(SiMe{sub 3}){sub 3}. The crystalline compounds are relatively volatile and are easily manipulated under nitrogen. Several of these compounds have been tested for their suitability as precursors in the MOCVD process. Clean pyrolysis reactions and deposition of thin films were achieved. The stoichiometry of the pyrolysis reaction has been determined by analysis of the reaction by-products.

  18. Growth of II-VI thin-films from single-source precursors based on sterically encumbered sitel ligands

    SciTech Connect

    Arnold, J.; Seligson, A.L.; Walker, J.M.; Bourret, E.D.; Bonasia, P.J.

    1992-04-01

    We have developed a new route to MOCVD of II-VI compounds based on the use of novel single-source precursors in which the II-VI elements are combined at the molecular level in a single covalent compound. We have prepared and fully characterized a number of new derivatives of zinc, cadmium and mercury incorporating large, sterically demanding tellurolate ligands of general formula: M(sitel){sub 2} where sitel = -TeSi(SiMe{sub 3}){sub 3}. The crystalline compounds are relatively volatile and are easily manipulated under nitrogen. Several of these compounds have been tested for their suitability as precursors in the MOCVD process. Clean pyrolysis reactions and deposition of thin films were achieved. The stoichiometry of the pyrolysis reaction has been determined by analysis of the reaction by-products.

  19. Combinatorial peptide library-based identification of peptide ligands for tumor-reactive cytolytic T lymphocytes of unknown specificity.

    PubMed

    Rubio-Godoy, Verena; Ayyoub, Maha; Dutoit, Valerie; Servis, Catherine; Schink, Amy; Rimoldi, Donata; Romero, Pedro; Cerottini, Jean-Charles; Simon, Richard; Zhao, Yindong; Houghten, Richard A; Pinilla, Clemencia; Valmori, Danila

    2002-08-01

    A novel approach for the identification of tumor antigen-derived sequences recognized by CD8(+) cytolytic T lymphocytes (CTL) consists in using synthetic combinatorial peptide libraries. Here we have screened a library composed of 3.1 x 10(11) nonapeptides arranged in a positional scanning format, in a cytotoxicity assay, to search the antigen recognized by melanoma-reactive CTL of unknown specificity. The results of this analysis enabled the identification of several optimal peptide ligands, as most of the individual nonapeptides deduced from the primary screening were efficiently recognized by the CTL. The results of the library screening were also analyzed with a mathematical approach based on a model of independent and additive contribution of individual amino acids to antigen recognition. This biometrical data analysis enabled the retrieval, in public databases, of the native antigenic peptide SSX-2(41-49), whose sequence is highly homologous to the ones deduced from the library screening, among the ones with the highest stimulatory score. These results underline the high predictive value of positional scanning synthetic combinatorial peptide library analysis and encourage its use for the identification of CTL ligands.

  20. Coordination polymers assembled from semirigid fluorene-based ligand: A couple of enantiomers

    SciTech Connect

    Li, Liang; Wang, Zihao; Chen, Qiang; Zhou, Xinhui; Yang, Tao; Zhao, Qiang; Huang, Wei

    2015-11-15

    A couple of Mg(II)-based coordination polymer enantiomers [MgL(DMF)(H{sub 2}O){sub 3}]{sub n} (R-MgL and S-MgL), and a Zn(II)-based coordination polymer [ZnL(DMF)]{sub n} (ZnL) have been synthesized by the solvothermal reactions between the achiral ligand 4,4′-(9,9-dimethyl-9H-fluorene-2,7-diyl)dibenzoic acid (H{sub 2}L) and the corresponding metal salts. The MgL was obtained as the racemic conglomerate from the one pot reaction. The single crystal X-ray structural analyses reveal that MgL crystallize in the chiral space group P2{sub 1} and possesses the right- or left-handed homochiral 1D Mg–O–C helical chain. The ZnL crystallize in the non-centrosymmetrical space group Aba2 and possesses the 2D network comprised of 1D Zn–O–C meso-helical chains and ligands. The MgL and ZnL complexes exhibit strong coordination-perturbed ligand-centered blue emissions when excited at 320 nm. Their second-order nonlinear optical effects and thermal properties have also been studied. - Highlights: • A couple of Mg(II)-based enantiomers were obtained as the racemic conglomerate. • The ligand is 4,4′-(9,9-dimethyl-9H-fluorene-2,7-diyl)dibenzoic acid. • MgL features the right- or left-handed homochiral 1D Mg–O–C helical chain. • ZnL features the 1D Zn–O–C meso-helical chain. • Both MgL and ZnL display the intense solid-state blue emissions.

  1. A very simple, highly stereoselective and modular synthesis of ferrocene-based P-chiral phosphine ligands.

    PubMed

    Chen, Weiping; Mbafor, William; Roberts, Stanley M; Whittall, John

    2006-03-29

    A very simple, highly stereoselective and modular synthesis of ferrocene-based P-chiral phosphine ligands has been developed. On the basis of this new methodology, several new families of ferrocene-based phosphine ligands have been prepared coupling chirality at phosphorus with other, more standard stereogenic features. The introduction of P-chirality into ferrocene-based phosphine ligands enhances the enantioselective discrimination produced by the corresponding Rh catalyst when a matching among the planar chirality, carbon chirality, and the chirality of phosphorus is achieved.

  2. Arctigenin suppresses receptor activator of nuclear factor κB ligand (RANKL)-mediated osteoclast differentiation in bone marrow-derived macrophages.

    PubMed

    Kim, A-Ram; Kim, Hyuk Soon; Lee, Jeong Min; Choi, Jung Ho; Kim, Se Na; Kim, Do Kyun; Kim, Ji Hyung; Mun, Se Hwan; Kim, Jie Wan; Jeon, Hyun Soo; Kim, Young Mi; Choi, Wahn Soo

    2012-05-05

    Osteoclasts, multinucleated bone-resorbing cells, are closely associated with bone diseases such as rheumatoid arthritis and osteoporosis. Osteoclasts are derived from hematopoietic precursor cells, and their differentiation is mediated by two cytokines, including macrophage colony stimulating factor and receptor activator of nuclear factor κB ligand (RANKL). Previous studies have shown that arctigenin exhibits an anti-inflammatory effect. However, the effect of arctigenin on osteoclast differentiation is yet to be elucidated. In this study, we found that arctigenin inhibited RANKL-mediated osteoclast differentiation in bone marrow macrophages in a dose-dependent manner and suppressed RANKL-mediated bone resorption. Additionally, the expression of typical marker proteins, such as NFATc1, c-Fos, TRAF6, c-Src, and cathepsin K, were significantly inhibited. Arctigenin inhibited the phosphorylation of Erk1/2, but not p38 and JNK, in a dose-dependent manner. Arctigenin also dramatically suppressed immunoreceptor tyrosine-based activation motif-mediated costimulatory signaling molecules, including Syk and PLCγ2, and Gab2. Notably, arctigenin inhibited the activation of Syk through RANKL stimulation. Furthermore, arctigenin prevented osteoclast differentiation in the calvarial bone of mice following stimulation with lipopolysaccharide. Our results show that arctigenin inhibits osteoclast differentiation in vitro and in vivo. Therefore, arctigenin may be useful for treating rheumatoid arthritis and osteoporosis. Copyright © 2012 Elsevier B.V. All rights reserved.

  3. Ligand mapping on protein surfaces by the 3D-RISM theory: toward computational fragment-based drug design.

    PubMed

    Imai, Takashi; Oda, Koji; Kovalenko, Andriy; Hirata, Fumio; Kidera, Akinori

    2009-09-02

    In line with the recent development of fragment-based drug design, a new computational method for mapping of small ligand molecules on protein surfaces is proposed. The method uses three-dimensional (3D) spatial distribution functions of the atomic sites of the ligand calculated using the molecular theory of solvation, known as the 3D reference interaction site model (3D-RISM) theory, to identify the most probable binding modes of ligand molecules. The 3D-RISM-based method is applied to the binding of several small organic molecules to thermolysin, in order to show its efficiency and accuracy in detecting binding sites. The results demonstrate that our method can reproduce the major binding modes found by X-ray crystallographic studies with sufficient precision. Moreover, the method can successfully identify some binding modes associated with a known inhibitor, which could not be detected by X-ray analysis. The dependence of ligand-binding modes on the ligand concentration, which essentially cannot be treated with other existing computational methods, is also investigated. The results indicate that some binding modes are readily affected by the ligand concentration, whereas others are not significantly altered. In the former case, it is the subtle balance in the binding affinity between the ligand and water that determines the dominant ligand-binding mode.

  4. Ab initio study of phosphorescent emitters based on rare-earth complexes with organic ligands for organic electroluminescent devices.

    PubMed

    Freidzon, Alexandra Ya; Scherbinin, Andrei V; Bagaturyants, Alexander A; Alfimov, Michael V

    2011-05-12

    An ab initio approach is developed for calculation of low-lying excited states in Ln(3+) complexes with organic ligands. The energies of the ground and excited states are calculated using the XMCQDPT2/CASSCF approximation; the 4f electrons of the Ln(3+) ion are included in the core, and the effects of the core electrons are described by scalar quasirelativistic 4f-in-core pseudopotentials. The geometries of the complexes in the ground and triplet excited states are fully optimized at the CASSCF level, and the resulting excited states have been found to be localized on one of the ligands. The efficiency of ligand-to-lanthanide energy transfer is assessed based on the relative energies of the triplet excited states localized on the organic ligands with respect to the receiving and emitting levels of the Ln(3+) ion. It is shown that ligand relaxation in the excited state should be properly taken into account in order to adequately describe energy transfer in the complexes. It is demonstrated that the efficiency of antenna ligands for lanthanide complexes used as phosphorescent emitters in organic light-emitting devices can be reasonably predicted using the procedure suggested in this work. Hence, the best antenna ligands can be selected in silico based on theoretical calculations of ligand-localized excited energy levels.

  5. Neutral and anionic tetrazole-based ligands in designing novel ruthenium dyes for dye-sensitized solar cells

    NASA Astrophysics Data System (ADS)

    Wu, Guohua; Kaneko, Ryuji; Zhang, Yaohong; Shinozaki, Yoshinao; Sugawa, Kosuke; Islam, Ashraful; Han, Liyuan; Bedja, Idriss; Gupta, Ravindra Kumar; Shen, Qing; Otsuki, Joe

    2016-03-01

    Two novel thiocyanate-free Ru(II) complexes have been synthesized, characterized and evaluated as dyes for dye-sensitized solar cells. Both complexes have two tridentate ligands: one is the tricarboxyterpyridine as an anchoring ligand and the other is one of the two bis(tetrazolyl)pyridine derivatives. One of the bis(tetrazolyl)pyridine ligand coordinates to the Ru(II) ion as a doubly deprotonated tetrazolate anion with a formal charge of -2 to form a neutral complex, which is coded as BTP dye, while the other bis(methyltetrazolyl)pyridine ligand coordinates to the Ru(II) ion as a neutral ligand forming a divalent cationic complex, coded as BMTP dye. Unexpectedly, the oxidation potentials for these two compounds are similar, implying similar electron-donating effects of the anionic tetrazolate ligand and the neutral methyltetrazole ligand to the Ru(II) ion. Despite similar HOMO/LUMO levels, BTP dye performs much better, recording 6.10% efficiency, than BMTP dye for DSSCs. Electrochemical impedance spectroscopy as well as nanosecond transient absorption spectroscopy indicates that the differences in the electron injection and electron recombination processes, which may be the consequences of the difference in the localization of LUMO as suggested by DFT calculations, are the main causes for the differences in performance.

  6. Metal-based biologically active azoles and β-lactams derived from sulfa drugs.

    PubMed

    Ebrahimi, Hossein Pasha; Hadi, Jabbar S; Almayah, Abdulelah A; Bolandnazar, Zeinab; Swadi, Ali G; Ebrahimi, Amirpasha

    2016-03-01

    Metal complexes of Schiff bases derived from sulfamethoxazole (SMZ) and sulfathiazole (STZ), converted to their β-lactam derivatives have been synthesized and experimentally characterized by elemental analysis, spectral (IR, (1)H NMR, (13)C NMR, and EI-mass), molar conductance measurements and thermal analysis techniques. The structural and electronic properties of the studied molecules were investigated theoretically by performing density functional theory (DFT) to access reliable results to the experimental values. The spectral and thermal analysis reveals that the Schiff bases act as bidentate ligands via the coordination of azomethine nitrogen to metal ions as well as the proton displacement from the phenolic group through the metal ions; therefore, Cu complexes can attain the square planner arrangement and Zn complexes have a distorted tetrahedral structure. The thermogravimetric (TG/DTG) analyses confirm high stability for all complexes followed by thermal decomposition in different steps. In addition, the antibacterial activities of synthesized compounds have been screened in vitro against various pathogenic bacterial species. Inspection of the results revealed that all newly synthesized complexes individually exhibit varying degrees of inhibitory effects on the growth of the tested bacterial species, therefore, they may be considered as drug candidates for bacterial pathogens. The free Schiff base ligands (1-2) exhibited a broad spectrum antibacterial activity against Gram negative Escherichia coli, Pseudomonas aeruginosa, and Proteus spp., and Gram positive Staphylococcus aureus bacterial strains. The results also indicated that the β-lactam derivatives (3-4) have high antibacterial activities on Gram positive bacteria as well as the metal complexes (5-8), particularly Zn complexes, have a significant activity against all Gram negative bacterial strains. It has been shown that the metal complexes have significantly higher activity than corresponding

  7. High-nuclearity ruthenium carbonyl cluster complexes derived from 2-amino-6-methylpyridine: synthesis of nonanuclear derivatives containing mu4- and mu5-oxo ligands.

    PubMed

    Cabeza, Javier A; del Río, Ignacio; García-Alvarez, Pablo; Miguel, Daniel

    2006-07-24

    Nonanuclear cluster complexes [Ru9(mu3-H)2(mu-H)(mu5-O)(mu4-ampy)(mu3-Hampy)(CO)21] (4) (H2ampy = 2-amino-6-methylpyridine), [Ru9(mu5-O)2(mu4-ampy)(mu3-Hampy)2(mu-CO)(CO)20] (5), [Ru9(mu5-O)2(mu4-ampy)(mu3-Hampy)2(mu-CO)2(CO)19] (6), and [Ru9(mu4-O)(mu5-O)(mu4-ampy)(mu3-Hampy)(mu-Hampy)(mu-CO)(CO)19] (7), together with the known hexanuclear [Ru6(mu3-H)2(mu5-ampy)(mu-CO)2(CO)14] (2) and the novel pentanuclear [Ru5(mu4-ampy)(2)(mu-CO)(CO)12] (3) complexes, are products of the thermolysis of [Ru3(mu-H)(mu3-Hampy)(CO)9] (1) in decane at 150 degrees C. Two different and very unusual quadruply bridging coordination modes have been observed for the ampy ligand. Compounds 4-7 also feature one (4) or two (5-7) bridging oxo ligands. With the exception of one of the oxo ligands of 7, which is in a distorted tetrahedral environment, the remaining oxo ligands of 4-7 are surrounded by five metal atoms. In carbonyl metal clusters, quadruply bridging oxo ligands are very unusual, whereas quintuply bridging oxo ligands are unprecedented. By using 18O-labeled water, we have unambiguously established that these oxo ligands arise from water.

  8. Structure-based DNA-targeting strategies with small molecule ligands for drug discovery.

    PubMed

    Sheng, Jia; Gan, Jianhua; Huang, Zhen

    2013-09-01

    Nucleic acids are the molecular targets of many clinical anticancer drugs. However, compared with proteins, nucleic acids have traditionally attracted much less attention as drug targets in structure-based drug design, partially because limited structural information of nucleic acids complexed with potential drugs is available. Over the past several years, enormous progresses in nucleic acid crystallization, heavy-atom derivatization, phasing, and structural biology have been made. Many complicated nucleic acid structures have been determined, providing new insights into the molecular functions and interactions of nucleic acids, especially DNAs complexed with small molecule ligands. Thus, opportunities have been created to further discover nucleic acid-targeting drugs for disease treatments. This review focuses on the structure studies of DNAs complexed with small molecule ligands for discovering lead compounds, drug candidates, and/or therapeutics. © 2013 Wiley Periodicals, Inc.

  9. Structure-Based DNA-Targeting Strategies with Small Molecule Ligands for Drug Discovery

    PubMed Central

    Sheng, Jia; Gan, Jianhua; Huang, Zhen

    2014-01-01

    Nucleic acids are the molecular targets of many clinical anticancer drugs. However, compared with proteins, nucleic acids have traditionally attracted much less attention as drug targets in structure-based drug design, partially because limited structural information of nucleic acids complexed with potential drugs is available. Over the past several years, enormous progresses in nucleic acid crystallization, heavy-atom derivatization, phasing, and structural biology have been made. Many complicated nucleic acid structures have been determined, providing new insights into the molecular functions and interactions of nucleic acids, especially DNAs complexed with small molecule ligands. Thus, opportunities have been created to further discover nucleic acid-targeting drugs for disease treatments. This review focuses on the structure studies of DNAs complexed with small molecule ligands for discovering lead compounds, drug candidates, and/or therapeutics. PMID:23633219

  10. Prediction of the Iron-Based Polynuclear Magnetic Superhalogens with Pseudohalogen CN as Ligands.

    PubMed

    Ding, Li-Ping; Shao, Peng; Lu, Cheng; Zhang, Fang-Hui; Liu, Yun; Mu, Qiang

    2017-07-17

    To explore stable polynuclear magnetic superhalogens, we perform an unbiased structure search for polynuclear iron-based systems based on pseudohalogen ligand CN using the CALYPSO method in conjunction with density functional theory. The superhalogen properties, magnetic properties, and thermodynamic stabilities of neutral and anionic Fe2(CN)5 and Fe3(CN)7 clusters are investigated. The results show that both of the clusters have superhalogen properties due to their electron affinities (EAs) and that vertical detachment energies (VDEs) are significantly larger than those of the chlorine element and their ligand CN. The distribution of the extra electron analysis indicates that the extra electron is aggregated mainly into pseudohalogen ligand CN units in Fe2(CN)5(¯) and Fe3(CN)7(¯) cluster. These features contribute significantly to their high EA and VDE. Besides superhalogen properties, these two anionic clusters carry a large magnetic moment just like the Fe2F5(¯) cluster. Additionally, the thermodynamic stabilities are also discussed by calculating the energy required to fragment the cluster into various smaller stable clusters. It is found that Fe(CN)2 is the most favorable fragmentation product for anionic Fe2(CN)5(¯) and Fe3(CN)7(¯) clusters, and both of the anions are less stable against ejection of Fe atoms than Fe(CN)n-x.

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

    PubMed

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

    2017-08-18

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

  12. Zinc (II) complex with a cationic Schiff base ligand: Synthesis, characterization, and biological studies

    NASA Astrophysics Data System (ADS)

    Lee, Sze Koon; Tan, Kong Wai; Ng, Seik Weng; Ooi, Kah Kooi; Ang, Kok Pian; Abdah, Md Akim

    2014-03-01

    A cationic Schiff base ligand, TSB (L) and its Zn (II) complex (1) were synthesized and characterized by using CHN, 1H-NMR, FT-IR, UV, LC-MS, and X-ray methods. Their ability to inhibit topoisomerase I, DNA cleavage activities, and cytotoxicity were studied. X-ray diffraction study shows that the mononuclear complex 1 is four coordinated with distorted tetrahedral geometry. The singly deprotonated Schiff base ligand L acts as a bidentate ON-donor ligand. Complexation of L increases the inhibitory strength on topoisomerase I activity. Complex 1 could fully inhibit topoisomerase I activity at 250 μM, while L did not show any inhibitory effect on topoisomerase I activity. In addition, L and complex 1 could cleave pBR322 DNA in a concentration and time dependent profile. Surprisingly, L has better DNA cleavage activity than complex 1. The cleavage of DNA by complex 1 is altered in the presence of hydrogen peroxide. Furthermore, L and complex 1 are mildly cytotoxic towards human ovarian cancer A2780 and hepatocellular carcinoma HepG2.

  13. Diverse CdII coordination complexes derived from bromide isophthalic acid binding with auxiliary N-donor ligands

    NASA Astrophysics Data System (ADS)

    Tang, Meng; Dong, Bao-Xia; Wu, Yi-Chen; Yang, Fang; Liu, Wen-Long; Teng, Yun-Lei

    2016-12-01

    The coordination characteristics of 4-bromoisophthalic acid (4-Br-H2ip) have been investigated in a series of CdII-based frameworks. Hydrothermal reactions of CdII salts and 4-Br-H2ip together with flexible or semiflexible N-donor auxiliary ligands resulted in the formation of four three-dimensional coordination complexes with diverse structures: {Cd(bix)0.5(bix)0.5(4-Br-ip)]·H2O}n (1), [Cd(bbi)0.5(bbi)0.5(4-Br-ip)]n (2), {[Cd(btx)0.5(4-Br-ip)(H2O)]·0.5CH3OH·H2O}n (3) and {[Cd(bbt)0.5(4-Br-ip)(H2O)]·3·5H2O}n (4). These compounds were characterized by elemental analyses, IR spectra, single-crystal and powder X-ray diffraction. They displayed diverse structures depending on the configuration of the 4-connected metal node, the coordination mode of the 4-Br-H2ip, the coordination ability and conformationally flexibility of the N-donor auxiliary. Compound 1 exhibits 3-fold interpenetrated 66 topology and compound 2 has a 412 topology. Compounds 3-4 have similar 3D pillar-layered structures based on 3,4-connected binodal net with the Schläfli symbol of (4·38). The thermal stabilities and photoluminescence properties of them were discussed in detail.

  14. Auxiliary Ligand-Dependent Assembly of Several Ni/Ni-Cd Compounds with N 2 O 2 Donor Tetradentate Symmetrical Schiff Base Ligand

    SciTech Connect

    Ge, Ying-Ying; Li, Guo-Bi; Fang, Hua-Cai; Zhan, Xu-Lin; Gu, Zhi-Gang; Chen, Jin-Hao; Sun, Feng; Cai, Yue-Peng; Thallapally, Praveen K.

    2010-11-03

    Several low-dimensional Ni/Ni-Cd complexes containing N2O2 donor tetradentate symmetrical Schiff base ligand bis(acetylacetone)ethylene-diamine (sy-H2L2), namely, [Ni(sy-L2)]2∙HLa∙ClO4 (2), (HLa)2∙(ClO4)∙(NO3) (3), [Ni(sy-L2)X]2](4,4’-bipy) (where La = 5,7-dimethyl-3,6-dihydro-2H-1,4-diazepine, X = ClO4 (4), X=NO3 (5), [Ni(sy-L2)Cd(SCN)2]n (6) and [Ni(sy-L2)∙Cd(N3)2]n (7) have been synthesized from [Ni(sy-L2)]2∙H2O (1). Complex 2, is three component discrete assembly generated from (HLa)+ moiety bridged with [Ni(sy-L2)] unit and ClO4- anion. A solution containing complex 2 and Cd(NO3)2 results in a mixture of 1 and 3. Further re-crystallization of 1 and 3 with various auxiliary ligands, provides coordination complexes 4 – 7 stabilized by weak hydrogen bonds in which 6 and 7 represent the first 1D heteronuclear complexes based on symmetric acacen-base Schiff base ligand.

  15. Coordination polymers of Ag(I) based on iminocarbene ligands involving metal-carbon and metal-heteroatom interactions

    NASA Astrophysics Data System (ADS)

    Netalkar, Sandeep P.; Netalkar, Priya P.; Revankar, Vidyanand K.

    2016-03-01

    The reaction of Ag2O with three novel imino-NHC ligands derived from 2-chloroacetophenone with pendant N-donor functional group incorporated by reaction with methoxyamine and 1-methyl/ethyl/n-butyl-substituted imidazoles afforded one-dimensional coordination polymers with [(-NHCarbene)Ag(NHCarbene-)PF6]n formulation involving both carbon-metal and heteroatom-metal interactions, the carbon and heteroatom involved in coordination to silver being from different molecule of the ligand. The complexes as well as the ligands were characterized by spectroscopic methods as well as the solid state structures determined in case of 2a, 3a and complex 5. The iminocarbene ligands serve as non-chelating building block for supramolecular silver assemblies.

  16. Synthesis and catalytic activity of group 5 metal amides with chiral biaryldiamine-based ligands.

    PubMed

    Zhang, Furen; Song, Haibin; Zi, Guofu

    2011-02-21

    A new series of group 5 metal amides have been prepared from the reaction between V(NMe(2))(4) or M(NMe(2))(5) (M = Nb, Ta) and chiral ligands, (R)-2,2'-bis(mesitoylamino)-1,1'-binaphthyl (1H(2)), (R)-5,5',6,6',7,7',8,8'-octahydro-2,2'-bis(mesitoylamino)-1,1'-binaphthyl (2H(2)), (R)-6,6'-dimethyl-2,2'-bis(mesitoylamino)-1,1'-biphenyl (3H(2)), (R)-2,2'-bis(mesitylenesulfonylamino)-6,6'-dimethyl-1,1'-biphenyl (4H(2)), (R)-2,2'-bis(diphenylthiophosphoramino)-1,1'-binaphthyl (5H(2)), (R)-2,2'-bis[(3-tert-butyl-2-hydroxybenzylidene)amino]-6,6'-dimethyl-1,1'-biphenyl (6H(2)), (R)-2,2'-bis[(3,5-di-tert-butyl-2-hydroxybenzylidene)amino]-6,6'-dimethyl-1,1'-biphenyl (7H(2)), (R)-2,2'-bis[(3-tert-butyl-2-hydroxybenzylidene)amino]-1,1'-binaphthyl (8H(2)), (S)-2-(mesitoylamino)-2'-(dimethylamino)-1,1'-binaphthyl (9H), and (R)-2-(mesitoylamino)-2'-(dimethylamino)-6,6'-dimethyl-1,1'-biphenyl (10H), which are derived from (R) or (S)-2,2'-diamino-1,1'-binaphthyl, and (R)-2,2'-diamino-6,6'-dimethyl-1,1'-biphenyl, respectively. Treatment of V(NMe(2))(4) or M(NMe(2))(5) (M = Nb, Ta) with 1 equiv of C(2)-symmetric amidate ligands 1H(2), 2H(2), 3H(2), 4H(2), and 5H(2), or Schiff base ligands 6H(2), 7H(2) and 8H(2) at room temperature gives, after recrystallization from a benzene, toluene or n-hexane solution, the vanadium amides (1)V(NMe(2))(2) (11), (2)V(NMe(2))(2) (14), (3)V(NMe(2))(2) (17), (5)V(NMe(2))(2) (22), (6)V(NMe(2))(2) (23) and (7)V(NMe(2))(2) (24), and niobium amides (1)Nb(NMe(2))(3) (12), (2)Nb(NMe(2))(3) (15), (3)Nb(NMe(2))(3) (18), (4)Nb(NMe(2))(3) (20) and [2-(3-Me(3)C-2-O-C(6)H(3)CHN)-2'-(N)-C(20)H(12)][2-(Me(2)N)(2)CH-6-CMe(3)-C(6)H(3)O]NbNMe(2)·C(7)H(8) (25·C(7)H(8)), and tantalum amides (1)Ta(NMe(2))(3) (13), (2)Ta(NMe(2))(3) (16), (3)Ta(NMe(2))(3) (19) and (4)Ta(NMe(2))(3) (21) respectively, in good yields. Reaction of V(NMe(2))(4) or M(NMe(2))(5) (M = Nb, Ta) with 2 equiv of C(1)-symmetric amidate ligands 9H or 10H at room temperature gives, after

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

    PubMed

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

    2013-10-01

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

  18. Structural, DFT and biological studies on Co(II) complexes of semi and thiosemicarbazide ligands derived from diketo hydrazide

    NASA Astrophysics Data System (ADS)

    Yousef, T. A.; El-Gammal, O. A.; Ahmed, Sara F.; Abu El-Reash, G. M.

    2014-11-01

    Three ligands have been prepared by addition ethanolic suspension of 2-hydrazino-2-oxo-N-phenyl-acetamide to phenyl isocyanate (H2PAPS), phenyl isothiocyanate (H2PAPT) and benzoyl isothiocyanate (H2PABT). The Co(II) chloride complexes were prepared and characterized by conventional techniques. The isolated complexes were assigned the formulaes, [Co(HPAPS)Cl(H2O)2]H2O, [Co(HPAPT)Cl]H2O and [Co(H2PABT)Cl2], respectively. The IR spectra of complexes shows that H2PAPS behaves as a mononegative tridentate via CO of hydrazide moiety and enolized CO of hydrazide moiety and CN (azomethine) group due to enolization of CO isocyanate moiety. H2PAPT behaves as mononegative tridentate via one CO of hydrazide moiety and thiol CS and NH groups and finally H2PABT behaves as neutral tetradentate via one CO of hydrazide moiety, CO of benzoyl moiety, Cdbnd S due to enolization of the second CO of hydrazide moiety and new CN (azomethine) groups. The vibrational frequencies of the IR spectra of ligands which were determined experimentally are compared with those obtained theoretically from DFT calculations. Also, the bond lengths, bond angles, HOMO, LUMO and dipole moments have been calculated. The calculated HOMO-LUMO energy gap reveals that charge transfer occurs within the ligand molecules. The calculated values of binding energies indicates the stability of metal complexes is higher that of ligand. Also, the kinetic and thermodynamic parameters for the different thermal degradation steps of the complexes were determined by Coats-Redfern and Horowitz-Metzger methods. The antibacterial activities were also tested against Bacillus subtilis and Escherichia coli bacteria. The free ligands showed a higher antibacterial effect than their Co(II) complexes except [Co(HPAPS)Cl(H2O)2]H2O which shows higher activity than corresponding ligand. The antitumor activities of the Ligands and their Co(II) complexes have been evaluated against liver (HePG2) and breast (MCF-7) cancer cells. All ligands

  19. Edge-bridging and face-capping coordination of alkenyl ligands in triruthenium carbonyl cluster complexes derived from hydrazines: synthetic, structural, theoretical, and kinetic studies.

    PubMed

    Cabeza, Javier A; del Río, Ignacio; Fernández-Colinas, José M; García-Granda, Santiago; Martínez-Méndez, Lorena; Pérez-Carreño, Enrique

    2004-12-03

    The reactions of the triruthenium cluster complex [Ru3(mu-H)(mu3-eta2-HNNMe2)(CO)9] (1; H2NNMe2=1,1-dimethylhydrazine) with alkynes (PhC triple bond CPh, HC triple bond CH, MeO2CC triple bond CCO2Me, PhC triple bond CH, MeO2CC triple bond CH, HOMe2CC triple bond CH, 2-pyC triple bond CH) give trinuclear complexes containing edge-bridging and/or face-capping alkenyl ligands. Whereas the edge-bridged products are closed triangular species (three Ru-Ru bonds), the face-capped products are open derivatives (two Ru-Ru bonds). For terminal alkynes, products containing gem (RCCH2) and/or trans (RHCCH) alkenyl ligands have been identified in both edge-bridging and face-capping positions, except for the complex [Ru3(mu3-eta2-HNNMe2)(mu3-eta3-HCCH-2-py)(mu-CO)(CO)7], which has the two alkenyl H atoms in a cis arrangement. Under comparable reaction conditions (1:1 molar ratio, THF at reflux, time required for the consumption of complex 1), some reactions give a single product, but most give mixtures of isomers (not all the possible ones), which were separated. To determine the effect of the hydrazido ligand, the reactions of [Ru3(mu-H)(mu3-eta2-MeNNHMe)(CO)9] (2; HMeNNHMe=1,2-dimethylhydrazine) with PhC triple bond CPh, PhC triple bond CH, and HC triple bond CH were also studied. For edge-bridged alkenyl complexes, the Ru--Ru edge that is spanned by the alkenyl ligand depends on the position of the methyl groups on the hydrazido ligand. For face-capped alkenyl complexes, the relative orientation of the hydrazido and alkenyl ligands also depends on the position of the methyl groups on the hydrazido ligand. A kinetic analysis of the reaction of 1 with PhC[triple chemical bond]CPh revealed that the reaction follows an associative mechanism, which implies that incorporation of the alkyne in the cluster is rate-limiting and precedes the release of a CO ligand. X-ray diffraction, IR and NMR spectroscopy, and calculations of minimum-energy structures by DFT methods were used to

  20. Derivatives of the pyrazolo[1,5-a]pyrimidine acetamide DPA-713 as translocator protein (TSPO) ligands and pro-apoptotic agents in human glioblastoma.

    PubMed

    Werry, Eryn L; King, Victoria A; Barron, Melissa L; Banister, Samuel D; Sokias, Renee; Kassiou, Michael

    2017-01-01

    The 18kDa translocator protein (TSPO) is a target for novel glioblastoma therapies due to its upregulation in this cancer and relatively low levels of expression in the healthy cortex. The pyrazolo[1,5-a]pyrimidine acetamides, exemplified by DPA-713 and DPA-714, are a class of high affinity TSPO ligands with selectivity over the central benzodiazepine receptor. In this study we have explored the potential anti-glioblastoma activity of a library of DPA-713 and DPA-714 analogues, and investigated the effect of amending the alkyl ether chain on TSPO affinity and functional potential. All ligands demonstrated nanomolar affinity for TSPO, but showed diverse functional activity, for example DPA-713 and DPA-714 did not affect the proliferation or viability of human T98G glioblastoma cells, while the hexyl ether and benzyl ether derivatives decreased proliferation of T98G cells without affecting proliferation in human fetal glial SVGp12 cells. These ligands also induced apoptosis and dissipated T98G mitochondrial membrane potential. This suggests that the nature of the alkyl ether chain of pyrazolo[1,5-a]pyrimidine acetamides has little influence on TSPO affinity but is important for functional activity of this class of TSPO ligands. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Oxidation of phenyl and hydride ligands of bis(pentamethylcyclopentadienyl)hafnium derivatives by nitrous oxide via selective oxygen atom transfer reactions: insights from quantum chemistry calculations.

    PubMed

    Xie, Hujun; Liu, Chengcheng; Yuan, Ying; Zhou, Tao; Fan, Ting; Lei, Qunfang; Fang, Wenjun

    2016-01-21

    The mechanisms for the oxidation of phenyl and hydride ligands of bis(pentamethylcyclopentadienyl)hafnium derivatives (Cp* = η(5)-C5Me5) by nitrous oxide via selective oxygen atom transfer reactions have been systematically studied by means of density functional theory (DFT) calculations. On the basis of the calculations, we investigated the original mechanism proposed by Hillhouse and co-workers for the activation of N2O. The calculations showed that the complex with an initial O-coordination of N2O to the coordinatively unsaturated Hf center is not a local minimum. Then we proposed a new reaction mechanism to investigate how N2O is activated and why N2O selectively oxidize phenyl and hydride ligands of . Frontier molecular orbital theory analysis indicates that N2O is activated by nucleophilic attack by the phenyl or hydride ligand. Present calculations provide new insights into the activation of N2O involving the direct oxygen atom transfer from nitrous oxide to metal-ligand bonds instead of the generally observed oxygen abstraction reaction to generate metal-oxo species.

  2. Palladium(II) and platinum(II) derivatives of benzothiazoline ligands: Synthesis, characterization, antimicrobial and antispermatogenic activity

    NASA Astrophysics Data System (ADS)

    Sharma, Krishna; Singh, R. V.; Fahmi, Nighat

    2011-01-01

    A series of Pd(II) and Pt(II) complexes with two N ∩S donor ligands, 5-chloro-3-(indolin-2-one)benzothiazoline and 6-nitro-3-(indolin-2-one)benzothiazoline, have been synthesized by the reaction of metal chlorides (PdCl 2 and PtCl 2) with ligands in 1:2 molar ratios. All the synthesized compounds were characterized by elemental analyses, melting point determinations and a combination of electronic, IR, 1H NMR and 13C NMR spectroscopic techniques for structure elucidation. In order to evaluate the effect of metal ions upon chelation, both the ligands and their complexes have been screened for their antimicrobial activity against the various pathogenic bacterial and fungal strains. The metal complexes have shown to be more antimicrobial against the microbial species as compared to free ligands. One of the ligands, 5-chloro-3-(indolin-2-one)benzothiazoline and its corresponding palladium and platinum complexes have been tested for their antifertility activity in male albino rats. The marked reduction in sperm motility and density resulted in infertility by 62-90%. Significant alterations were found in biochemical parameters of reproductive organs in treated animals as compared to control group. It is concluded that all these effects may finally impair the fertility of male rats.

  3. 1,2,4-triazole-derived carbene complexes of gold: characterization, solid-state aggregation and ligand disproportionation.

    PubMed

    Guo, Shuai; Bernhammer, Jan Christopher; Huynh, Han Vinh

    2015-09-14

    Ligand redistribution reactions are well documented for silver(I) N-heterocyclic carbene (NHC) complexes of the type [AgX(NHC)] (X = halido ligand), but only two reports have been described in the literature for gold analogues of the general formula [AuX(NHC)]. In both cases, the NHCs in question were exceptionally strong donors. To probe the dependence of ligand redistribution processes on NHC donor strength, a model study was conducted using a weakly donating 1,2,4-triazolin-5-ylidene (tazy) ligand and different halido coligands. For [AuX(tazy)] (X = Cl, Br, OAc, tazy = 4-benzyl-1-methyl-1,2,4-triazolin-5-ylidene), no ligand redistribution was found, while a reversible disproportionation between [AuI(tazy)] in solution and [Au(tazy)2][AuI2] in the solid state was observed and studied by means of X-ray crystallography, NMR and UV-Vis spectroscopy, as well as DFT calculations.

  4. Bis(methylpyridine)-EDTA derivative as a potential ligand for PET imaging: synthesis, complexation, and biological evaluation.

    PubMed

    Singh, Pooja; Aggarwal, Swati; Tiwari, Anjani K; Kumar, Vikas; Pratap, Ramendra; Chuttani, Krishna; Mishra, Anil K

    2014-12-01

    A novel transitional metal ligand derivatized from EDTA-conjugated 2-amino-4-methyl pyridine, an acyclic vehicle (EDTA-Mepy2 ) was designed, synthesized, and characterized for PET imaging with ⁶⁸Ga. The drug likeliness and appropriate lipophilicity were first analyzed by molecular docking studies which shows interactive property of ligand with serum albumin protein (HSA: PDB 1E78), at Lys199, Arg257, and His242 residues, which make it more appropriate in transportation as a specific ligand for PET imaging. As a confirmation, binding constant of the ligand with human serum albumin was calculated at λex = 350 nm which was found to be 4.9 × 10³ m⁻¹. The pharmacokinetics of (68) Ga-EDTA-Mepy2 was analyzed by blood kinetics (t(1/2) slow: 3 h 56 min and t(1/2) fast: 32 min) and biodistribution (maximum % ID/g was found in kidney at 1 h). Further the capability of this ligand was analyzed as optical marker also, by recording λex = 380 nm, RFU = 8000; 710 nm, RFU = 1000 units at fixed λem = 280 nm. Additionally, in physiological conditions where its stability was calculated, suggests 15-20 times selectivity over the endogenously present metal ions (KG aL /KZ nL = 14.3, KG aL /KC uL = 18.1).

  5. Boronyl ligand as a member of the isoelectronic series BO(-) → CO → NO(+): viable cobalt carbonyl boronyl derivatives?

    PubMed

    Gong, Xiaoli; Li, Qian-Shu; Xie, Yaoming; King, R Bruce; Schaefer, Henry F

    2010-12-06

    Recently the first boronyl (oxoboryl) complex [(c-C(6)H(11))(3)P](2)Pt(BO)Br was synthesized. The boronyl ligand in this complex is a member of the isoelectronic series BO(-) → CO → NO(+). The cobalt carbonyl boronyls Co(BO)(CO)(4) and Co(2)(BO)(2)(CO)(7), with cobalt in the formal d(8) +1 oxidation state, are thus isoelectronic with the familiar homoleptic iron carbonyls Fe(CO)(5) and Fe(2)(CO)(9). Density functional theory predicts Co(BO)(CO)(4) to have a trigonal bipyramidal structure with the BO group in an axial position. The tricarbonyl Co(BO)(CO)(3) is predicted to have a distorted square planar structure, similar to those of other 16-electron complexes of d(8) transition metals. Higher energy Co(BO)(CO)(n) (n = 3, 2) structures may be derived by removal of one (for n = 3) or two (for n = 2) CO groups from a trigonal bipyramidal Co(BO)(CO)(4) structure. Structures with a CO group bridging 17-electron Co(CO)(4) and Co(BO)(2)(CO)(3) units and no Co-Co bond are found for Co(2)(BO)(2)(CO)(8). However, Co(2)(BO)(2)(CO)(8) is not viable because of the predicted exothermic loss of CO to give Co(2)(BO)(2)(CO)(7). The lowest lying Co(2)(BO)(2)(CO)(7) structure is a triply bridged (2BO + CO) structure closely related to the experimental Fe(2)(CO)(9) structure. However, other relatively low energy Co(2)(BO)(2)(CO)(7) structures are found, either with a single CO bridge, similar to the experimental Os(2)(CO)(8)(μ-CO) structure; or with 17-electron Co(CO)(4) and Co(BO)(2)(CO)(3) units joined by a single Co-Co bond with or without semibridging carbonyl groups. Both triplet and singlet Co(2)(BO)(2)(CO)(6) structures are found. The lowest lying triplet Co(2)(BO)(2)(CO)(6) structures have a Co(CO)(3)(BO)(2) unit coordinated to a Co(CO)(3) unit through the oxygen atoms of the boronyl groups with a non-bonding ∼4.3 Å Co···Co distance. The lowest lying singlet Co(2)(BO)(2)(CO)(6) structures have either two three-electron donor bridging η(2)-μ-BO groups and no Co

  6. A non-radioactive in situ hybridization method based on mercurated nucleic acid probes and sulfhydryl-hapten ligands.

    PubMed Central

    Hopman, A H; Wiegant, J; Tesser, G I; Van Duijn, P

    1986-01-01

    Mercurated nucleic acid probes can be used for non-radioactive in situ hybridization. The principle of the method is based on the reaction of the mercurated pyrimidine residues of the in situ hybridized probe with the sulfhydryl group of a ligand which contains a hapten. Next, the hapten is immunocytochemically detected. Previous experiments showed that stable coupling of the sulfhydryl ligands could only be obtained when positively charged amino groups are present in the ligand. On basis of this finding, ligands were synthesized containing a sulfhydryl group, two lysyl residues and hapten groups such as trinitrophenyl, fluorescyl and biotinyl. The ligands, free or bound to mercurated nucleic acids, were immunochemically characterized in ELISAs. The method was shown to be specific and sensitive in the detection of target DNA in situ on microscopic preparations and in dot-blot hybridization reactions on nitrocellulose. Images PMID:3748817

  7. Mini-ISES identifies promising carbafructopyranose-based salens for asymmetric catalysis: Tuning ligand shape via the anomeric effect

    PubMed Central

    Karukurichi, Kannan R.; Fei, Xiang; Swyka, Robert A.; Broussy, Sylvain; Shen, Weijun; Dey, Sangeeta; Roy, Sandip K.; Berkowitz, David B.

    2015-01-01

    This study introduces new methods of screening for and tuning chiral space and in so doing identifies a promising set of chiral ligands for asymmetric synthesis. The carbafructopyranosyl-1,2-diamine(s) and salens constructed therefrom are particularly compelling. It is shown that by removing the native anomeric effect in this ligand family, one can tune chiral ligand shape and improve chiral bias. This concept is demonstrated by a combination of (i) x-ray crystallographic structure determination, (ii) assessment of catalytic performance, and (iii) consideration of the anomeric effect and its underlying dipolar basis. The title ligands were identified by a new mini version of the in situ enzymatic screening (ISES) procedure through which catalyst-ligand combinations are screened in parallel, and information on relative rate and enantioselectivity is obtained in real time, without the need to quench reactions or draw aliquots. Mini-ISES brings the technique into the nanomole regime (200 to 350 nmol catalyst/20 μl organic volume) commensurate with emerging trends in reaction development/process chemistry. The best-performing β-d-carbafructopyranosyl-1,2-diamine–derived salen ligand discovered here outperforms the best known organometallic and enzymatic catalysts for the hydrolytic kinetic resolution of 3-phenylpropylene oxide, one of several substrates examined for which the ligand is “matched.” This ligand scaffold defines a new swath of chiral space, and anomeric effect tunability defines a new concept in shaping that chiral space. Both this ligand set and the anomeric shape-tuning concept are expected to find broad application, given the value of chiral 1,2-diamines and salens constructed from these in asymmetric catalysis. PMID:26501130

  8. PDZ Affinity Chromatography: A general method for affinity purification of proteins based on PDZ domains and their ligands

    PubMed Central

    Walkup, Ward G.; Kennedy, Mary B.

    2014-01-01

    PDZ (PSD-95, DiscsLarge, ZO1) domains function in nature as protein binding domains within scaffold and membrane-associated proteins. They comprise ~ 90 residues and make specific, high affinity interactions with complementary C-terminal peptide sequences, with other PDZ domains, and with phospholipids. We hypothesized that the specific, strong interactions of PDZ domains with their ligands would make them well suited for use in affinity chromatography. Here we describe a novel affinity chromatography method applicable for the purification of proteins that contain PDZ domain-binding ligands, either naturally or introduced by genetic engineering. We created a series of affinity resins comprised of PDZ domains from the scaffold protein PSD-95, or from neuronal nitric oxide synthase (nNOS), coupled to solid supports. We used them to purify heterologously expressed neuronal proteins or protein domains containing endogenous PDZ domain ligands, eluting the proteins with free PDZ domain peptide ligands. We show that Proteins of Interest (POIs) lacking endogenous PDZ domain ligands can be engineered as fusion products containing C-terminal PDZ domain ligand peptides or internal, N- or C-terminal PDZ domains and then can be purified by the same method. Using this method, we recovered recombinant GFP fused to a PDZ-domain ligand in active form as verified by fluorescence yield. Similarly, chloramphenicol acetyltransferase (CAT) and β-Galactosidase (LacZ) fused to a C-terminal PDZ domain ligand or an N-terminal PDZ domain were purified in active form as assessed by enzymatic assay. In general, PDZ domains and ligands derived from PSD-95 were superior to those from nNOS for this method. PDZ Domain Affinity Chromatography promises to be a versatile and effective method for purification of a wide variety of natural and recombinant proteins. PMID:24607360

  9. PDZ affinity chromatography: a general method for affinity purification of proteins based on PDZ domains and their ligands.

    PubMed

    Walkup, Ward G; Kennedy, Mary B

    2014-06-01

    PDZ (PSD-95, DiscsLarge, ZO1) domains function in nature as protein binding domains within scaffold and membrane-associated proteins. They comprise ∼90 residues and make specific, high affinity interactions with complementary C-terminal peptide sequences, with other PDZ domains, and with phospholipids. We hypothesized that the specific, strong interactions of PDZ domains with their ligands would make them well suited for use in affinity chromatography. Here we describe a novel affinity chromatography method applicable for the purification of proteins that contain PDZ domain-binding ligands, either naturally or introduced by genetic engineering. We created a series of affinity resins comprised of PDZ domains from the scaffold protein PSD-95, or from neuronal nitric oxide synthase (nNOS), coupled to solid supports. We used them to purify heterologously expressed neuronal proteins or protein domains containing endogenous PDZ domain