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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, 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

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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

  18. 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.

  19. 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

  20. 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 ).

  1. 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).

  2. 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

  3. 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.

  4. 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.

  5. 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).

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  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. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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)).

  16. 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

  17. 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

  18. 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).

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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…

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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).

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  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. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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).

  20. 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

  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. 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.

  3. 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.

  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. 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.

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  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. 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

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  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. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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

  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. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  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. 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

  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. 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.

  10. 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

  11. 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.

  12. 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.

  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.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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].

  7. Synthesis of BODIPY derivatives substituted with various bioconjugatable linker groups: a construction kit for fluorescent labeling of receptor ligands.

    PubMed

    Heisig, Fabian; Gollos, Sabrina; Freudenthal, Sven J; El-Tayeb, Ali; Iqbal, Jamshed; Müller, Christa E

    2014-01-01

    The goal of the present study was to design small, functionalized green-emitting BODIPY dyes, which can readily be coupled to target molecules such as receptor ligands, or even be integrated into their pharmacophores. A simple two-step one-pot procedure starting from 2,4-dimethylpyrrole and ω-bromoalkylcarboxylic acid chlorides was used to obtain new ω-bromoalkyl-substituted BODIPY fluorophores (1a-1f) connected via alkyl spacers of different length to the 8-position of the fluorescent dye. The addition of radical inhibitors reduced the amount of side products. The ω-bromoalkyl-substituted BODIPYs were further converted to introduce various functional groups: iodo-substituted dyes were obtained by Finkelstein reaction in excellent yields; microwave-assisted reaction with methanolic ammonia led to fast and clean conversion to the amino-substituted dyes; a hydroxyl-substituted derivative was prepared by reaction with sodium ethylate, and thiol-substituted BODIPYs were obtained by reaction of 1a-1f with potassium thioacetate followed by alkaline cleavage of the thioesters. Water-soluble derivatives were prepared by introducing sulfonate groups into the 2- and 6-position of the BODIPY core. The synthesized BODIPY derivatives showed high fluorescent yields and appeared to be stable under basic, reducing and oxidative conditions. As a proof of concept, 2-thioadenosine was alkylated with bromoethyl-BODIPY 1b. The resulting fluorescent 2-substituted adenosine derivative 15 displayed selectivity for the A3 adenosine receptor (ARs) over the other AR subtypes, showed agonistic activity, and may thus become a useful tool for studying A3ARs, or a lead structure for further optimization. The new functionalized dyes may be widely used for fluorescent labeling allowing the investigation of biological targets and processes.

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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).

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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

  19. 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

  20. 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.

  1. 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

  2. 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

  3. 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).

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Dysprosium(III) complexes with a square-antiprism configuration featuring mononuclear single-molecule magnetic behaviours based on different β-diketonate ligands and auxiliary ligands.

    PubMed

    Zhang, Sheng; Ke, Hongshan; Shi, Quan; Zhang, Jangwei; Yang, Qi; Wei, Qing; Xie, Gang; Wang, Wenyuan; Yang, Desuo; Chen, Sanping

    2016-03-28

    Three mononuclear dysprosium(III) complexes derived from three β-diketonate ligands, 4,4,4-trifluoro-1-(4-methylphenyl)-1,3-butanedione (tfmb), 4,4,4-trifluoro-1-(4-fluorophenyl)-1,3-butanedione (tffb) and 4,4,4-trifluoro-1-(2-naphthyl)-1,3-butanedione (tfnb) as well as auxiliary ligands, 5-nitro-1,10-phenanthroline (5-NO2-Phen), DMF and 2,2'-bipyridine (bpy) have been synthesized and structurally characterized, namely [Dy(5-NO2-Phen)(tfmb)3] (1), [Dy(DMF)2(tffb)3] (2) and [Dy(bpy)2(tfnb)3]·0.5(1,4-dioxane) (3). The metal ions in 1-3 adopt an approximately square-antiprismatic (SAP) coordination environment with D4d axial symmetry. The magnetic properties of 1-3 have been investigated, displaying weak out-of-phase AC signals under a zero-DC field. With an applied DC field of 1200 Oe, the quantum tunnelling of the magnetization was suppressed in 1-3 with the pre-exponential factor τ0 = 5.3 × 10(-7) s and the effective barrier ΔE/kB = 83 K for 1 as well as the pre-exponential factor τ0 = 3.09 × 10(-7) s and the effective barrier ΔE/kB = 39 K for 3. Interestingly, for the frequency dependence of the out-of-phase (χ'') of the AC susceptibility of 2, two slow relaxation of the magnetization processes occurred under the applied magnetic field of 1200 Oe, corresponding to the fast relaxation (FR) phase and slow relaxation (SR) phase, respectively. Arrhenius analysis gave the effective energy barrier (ΔE/kB) of 55 K and the pre-exponential factor (τ0) of 8.23 × 10(-12) for the SR. It is thus very likely that the FR process in complex 2 results from QTM enhanced by dipolar interactions between the Dy ions or the presence of the applied field. The structure-property relationship of some Dy(III) based mononuclear SMMs with the SAP configuration was further discussed.

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. 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.

  13. 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

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  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. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. 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

  14. 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.

  15. 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).

  16. 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.

  17. 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

  18. 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

  19. 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 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.

  20. Chelate effects in sulfate binding by amide/urea-based ligands.

    PubMed

    Jia, Chuandong; Wang, Qi-Qiang; Begum, Rowshan Ara; Day, Victor W; Bowman-James, Kristin

    2015-07-07

    The influence of chelate and mini-chelate effects on sulfate binding was explored for six amide-, amide/amine-, urea-, and urea/amine-based ligands. Two of the urea-based hosts were selective for SO4(2-) in water-mixed DMSO-d6 systems. Results indicated that the mini-chelate effect provided by a single urea group with two NH binding sites appears to provide enhanced binding over two amide groups. Furthermore, additional urea binding sites incorporated into the host framework appeared to overcome to some extent competing hydration effects with increasing water content.

  1. Tyrosinase and catechol oxidase activity of copper(I) complexes supported by imidazole-based ligands: structure-reactivity correlations.

    PubMed

    Wendt, Franziska; Näther, Christian; Tuczek, Felix

    2016-09-01

    Four new imidazole-based ligands, 4-((1H-imidazol-4-yl)methyl)-2-phenyl-4,5-dihydrooxyzole (L OL 1), 4-((1H-imidazol-4-yl)methyl)-2-(tert-butyl)-4,5-dihydrooxyzole (L OL 2), 4-((1H-imidazol-4-yl)methyl)-2-methyl-4,5-dihydrooxyzole (L OL 3), and N-(2,2-dimethylpropylidene)-2-(1-trityl-1H-imidazol-4-yl-)ethyl amine (L imz 1), have been synthesized. The corresponding copper(I) complexes [Cu(I)(L OL 1)(CH3CN)]PF6 (CuL OL 1), [Cu(I)(L OL 2)(CH3CN)]PF6 (CuL OL 2), [Cu(I)(L OL 3)(CH3CN)]PF6 (CuL OL 3), [Cu(I)(L imz 1)(CH3CN)2]PF6 (CuL imz 1) as well as the Cu(I) complex derived from the known ligand bis(1-methylimidazol-2-yl)methane (BIMZ), [Cu(I)(BIMZ)(CH3CN)]PF6 (CuBIMZ), are screened as catalysts for the oxidation of 3,5-di-tert-butylcatechol (3,5-DTBC-H2) to 3,5-di-tert-butylquinone (3,5-DTBQ). The primary reaction product of these oxidations is 3,5-di-tert-butylsemiquinone (3,5-DTBSQ) which slowly converts to 3,5-DTBQ. Saturation kinetic studies reveal a trend of catalytic activity in the order CuL OL 3 ≈ CuL OL 1 > CuBIMZ > CuL OL 2 > CuL imz 1. Additionally, the catalytic activity of the copper(I) complexes towards the oxygenation of monophenols is investigated. As substrates 2,4-di-tert-butylphenol (2,4-DTBP-H), 3-tert-butylphenol (3-TBP-H), 4-methoxyphenol (4-MeOP-H), N-acetyl-L-tyrosine ethyl ester monohydrate (NATEE) and 8-hydroxyquinoline are employed. The oxygenation products are identified and characterized with the help of UV/Vis and NMR spectroscopy, mass spectrometry, and fluorescence measurements. Whereas the copper complexes with ligands containing combinations of imidazole and imine functions or two imidazole units (CuL imz 1 and CuBIMZ) are found to exhibit catalytic tyrosinase activity, the systems with ligands containing oxazoline just mediate a stoichiometric conversion. Correlations between the structures of the complexes and their reactivities are discussed.

  2. Assembly of new polyoxometalate–templated metal–organic frameworks based on flexible ligands

    SciTech Connect

    Li, Na; Mu, Bao; Lv, Lei; Huang, Rudan

    2015-03-15

    Four new polyoxometalate(POM)–templated metal–organic frameworks based on flexible ligands, namely, [Cu{sub 6}(bip){sub 12}(PMo{sup VI}{sub 12}O{sub 40}){sub 2}(PMo{sup V}Mo{sup VI}{sub 11}O{sub 40}O{sub 2})]·8H{sub 2}O(1), [Cu{sup I}{sub 3}Cu{sup II}{sub 3}(bip){sub 12}(PMo{sup VI}{sub 12}O{sub 40}){sub 2}(PMo{sup V}{sub 12}O{sub 34})]·8H{sub 2}O(2), [Ni{sub 6}(bip){sub 12}(PMo{sup VI}{sub 12}O{sub 40})(PMo{sup VI}{sub 11}Mo{sup V}O{sub 40}){sub 2}]Cl·6H{sub 2}O(3), [Co{sup II}{sub 3}Co{sup III}{sub 2}(H{sub 2}bib){sub 2}(Hbib){sub 2}(PW{sub 9}O{sub 34}){sub 2}(H{sub 2}O){sub 6}]·6H{sub 2}O(4) (bip=1,3-bis(imidazolyl)propane, bib=1,4-bis(imidazolyl)butane) have been obtained under hydrothermal condition and characterized by single-crystal X-ray diffraction analyses, elemental analyses, and thermogravimetric (TG) analyses. The studies of single crystal X-ray indicate that compounds 1–3 crystallize in the trigonal space group P-3, and compound 4 crystallizes in the triclinic space group P-1. Compounds 1 and 3 represent 3D frameworks, and POMs as the guest molecules are incorporated into the cages which are composed of the ligands and metals, while compounds 2 and 4 show 3D frameworks by hydrogen bonds. This compounds provide new examples of host–guest compounds based on flexible bis(imidazole) ligands. In addition, the electrochemical property and the catalytic property of compound 1 have also been investigated. - Graphical abstract: Four inorganic–organic hybrid compounds based polyoxometalates (POMs) and flexible ligands, namely, have been obtained under hydrothermal conditions and characterized by single-crystal X-ray diffraction analyses, elemental analyses, IR spectra, and thermogravimetric (TG) analyses. Compounds 1–3 are new examples of host–guest compounds based on flexible bis(imidazole) ligands and POMs as the guest molecules are incorporated into the cages which are composed of the ligands and metals. - Highlights: • Polyoxometalate

  3. mutLBSgeneDB: mutated ligand binding site gene DataBase

    PubMed Central

    Kim, Pora; Zhao, Junfei; Lu, Pinyi; Zhao, Zhongming

    2017-01-01

    Mutations at the ligand binding sites (LBSs) can influence protein structure stability, binding affinity with small molecules, and drug resistance in cancer patients. Our recent analysis revealed that ligand binding residues had a significantly higher mutation rate than other parts of the protein. Here, we built mutLBSgeneDB (mutated Ligand Binding Site gene DataBase) available at http://zhaobioinfo.org/mutLBSgeneDB. We collected and curated over 2300 genes (mutLBSgenes) having ∼12 000 somatic mutations at ∼10 000 LBSs across 16 cancer types and selected 744 drug targetable genes (targetable_mutLBSgenes) by incorporating kinases, transcription factors, pharmacological genes, and cancer driver genes. We analyzed LBS mutation information, differential gene expression network, drug response correlation with gene expression, and protein stability changes for all mutLBSgenes using integrated genetic, genomic, transcriptomic, proteomic, network and functional information. We calculated and compared the binding affinities of 20 carefully selected genes with their drugs in wild type and mutant forms. mutLBSgeneDB provides a user-friendly web interface for searching and browsing through seven categories of annotations: Gene summary, Mutated information, Protein structure related information, Differential gene expression and gene-gene network, Phenotype information, Pharmacological information, and Conservation information. mutLBSgeneDB provides a useful resource for functional genomics, protein structure, drug and disease research communities. PMID:27907895

  4. Thyroid receptor ligands. Part 8: Thyromimetics derived from N-acylated-alpha-amino acid derivatives displaying modulated pharmacological selectivity compared with KB-141.

    PubMed

    Garg, Neeraj; Li, Yi-Lin; Garcia Collazo, Ana Maria; Litten, Chris; Ryono, Denis E; Zhang, Minsheng; Caringal, Yolanda; Brigance, Robert P; Meng, Wei; Washburn, William N; Agback, Peter; Mellström, Karin; Rehnmark, Stefan; Rahimi-Ghadim, Mahmoud; Norin, Thomas; Grynfarb, Marlena; Sandberg, Johnny; Grover, Gary; Malm, Johan

    2007-08-01

    Based on the scaffold of the pharmacologically selective thyromimetic 2b, structurally a close analog to KB-141 (2a), a number of novel N-acylated-alpha-amino acid derivatives were synthesized and tested in a TR radioligand binding assay as well as in a reporter cell assay. On the basis of TRbeta(1)-isoform selectivity and affinity, as well as affinity to the reporter cell assay, 3d was selected for further studies in the cholesterol-fed rat model. In this model 3d revealed an improved therapeutic window between cholesterol and TSH lowering but decreased margins versus tachycardia compared with 2a.

  5. Design, synthesis, pharmacological evaluation and molecular dynamics of β-amino acids morphan-derivatives as novel ligands for opioid receptors.

    PubMed

    Nieto, Carlos T; Gonzalez-Nunez, Veronica; Rodríguez, Raquel E; Diez, David; Garrido, Narciso M

    2015-08-28

    Structure-Activity Relationship (SAR) is a current approach in the design of new pharmacological agents. We previously reported the synthesis of a novel analogue of morphine, a 2-azabicyclo[3.3.1]nonane, which contains a β-amino acid. This bicyclic core exhibits two distinctive chemical handles for further elaboration, which allowed us to create a library of morphan-containing compounds by in silico molecular docking on the μ opioid receptor. Lead candidates were synthesized and biological tests were performed to evaluate their ability to bind to opioid receptors. The four top compounds, three phenyl esters and an N-phenylethyl morphan derivative, were selected for Molecular Dynamics simulations to get topological and thermodynamic information. Aromatic morphan derivatives displayed an interacting domain which fits into a hydrophobic cleft and the effect of the substituents in their affinity was explained by the differences in the calculated binding free energies. Our results indicate that the 3D arrangement of the aromatic ring in the morphine derivatives is not a key issue for a specific ligand - μ receptor interaction. Thus, these morphan derivatives represent a new class of opioid receptor ligands which may be of great use in the clinical practice.

  6. Construction of Ligand Group Orbitals for Polyatomics and Transition-Metal Complexes Using an Intuitive Symmetry-Based Approach

    ERIC Educational Resources Information Center

    Johnson, Adam R.

    2013-01-01

    A molecular orbital (MO) diagram, especially its frontier orbitals, explains the bonding and reactivity for a chemical compound. It is therefore important for students to learn how to construct one. The traditional methods used to derive these diagrams rely on linear algebra techniques to combine ligand orbitals into symmetry-adapted linear…

  7. Structural, DFT and biological studies on Cr(III) complexes of semi and thiosemicarbazide ligands derived from diketo hydrazide

    NASA Astrophysics Data System (ADS)

    Yousef, T. A.; Alduaij, O. K.; Ahmed, Sara F.; Abu El-Reash, G. M.; El-Gammal, O. A.

    2016-12-01

    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 Cr(III) chloride complexes were prepared and characterized by conventional techniques. The data confirmed that the complexes have the following formulaes, [Cr(H2PAPS)Cl3], [Cr(HPAPT)Cl2(H2O)2] and [Cr(HPABT)Cl2(H2O)]. The IR spectra of complexes shows that H2PAPS behaves as neutral tridentate via both CO of hydrazide moiety and Cdbnd N(azomethine) due to enolization of CO isocyanate without deprotonation. H2PAPT suggests the coordination as mononegative bidentate via both CO of hydrazide moiety in keto and deprotonated enolic oxygen atoms. H2PABT act as mononegative tridentate via carbonyl oxygen (Cdbnd O)3, the deprotonated enolic oxygen atom (dbnd Csbnd Osbnd)1 and NH1 groups. The experimental IR data of ligands 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 higher stability of metal complexes than of ligands. Also, the kinetic and thermodynamic parameters for the different thermal degradation steps of the complexes were determined by Coats-Redfern and Horowitz-Metzger methods.

  8. Identification of opioid ligands possessing mixed micro agonist/delta antagonist activity among pyridomorphinans derived from naloxone, oxymorphone, and hydromorphone [correction of hydropmorphone].

    PubMed

    Ananthan, Subramaniam; Khare, Naveen K; Saini, Surendra K; Seitz, Lainne E; Bartlett, Jeffrey L; Davis, Peg; Dersch, Christina M; Porreca, Frank; Rothman, Richard B; Bilsky, Edward J

    2004-03-11

    A series of pyridomorphinans derived from naloxone, oxymorphone, and hydromorphone (7a-k) were synthesized and evaluated for binding affinity at the opioid delta, micro, and kappa receptors in brain membranes using radioligand binding assays and for functional activity in vitro using [(35)S]GTP-gamma-S binding assays in brain tissues and bioassays using guinea pig ileum (GPI) and mouse vas deferens (MVD) smooth muscle preparations. The pyridine ring unsubstituted pyridomorphinans possessing the oxymorphone and hydromorphone framework displayed nearly equal binding affinity at the micro and delta receptors. Their affinities at the kappa site were nearly 10-fold less than their binding affinities at the micro and delta sites. Introduction of aryl substituents at the 5'-position on the pyridine ring improved the binding affinity at the delta site while decreasing the binding affinity at the micro site. Nearly all of the ligands possessing an N-methyl group at the17-position with or without a hydroxyl group at the 14-position of the morphinan moiety displayed agonist activity at the micro receptor with varying potencies and efficacies. In the [(35)S]GTP-gamma-S binding assays, most of these pyridomorphinans were devoid of any significant agonist activity at the delta and kappa receptors but displayed moderate to potent antagonist activity at the delta receptors. In antinociceptive evaluations using the warm-water tail-withdrawal assay in mice, the pyridomorphinans produced analgesic effects with varying potencies and efficacies when administered by the intracerebroventricular route. Among the ligands studied, the hydromorphone-derived 4-chlorophenylpyridomorphinan 7h was identified as a ligand possessing a promising profile of mixed micro agonist/delta antagonist activity in vitro and in vivo. In a repeated administration paradigm in which the standard micro agonist morphine produces significant tolerance, repeated administration of the micro agonist/delta antagonist

  9. New aniline-containing amino alcohols from trans-(R,R)-2-(2-nitrophenyl)-3-phenyloxirane as useful intermediates for the synthesis of chiral ligands, bases, and benzoxazine nucleus.

    PubMed

    Solladié-Cavallo, Arlette; Lupattelli, Paolo; Bonini, Carlo; Ostuni, Valeria; Blasio, Nadia Di

    2006-12-22

    New enantiopure aniline-containing amino alcohols are directly derived from trans-(R,R)-2-(2-nitrophenyl)-3-phenyloxirane, by alternative regioselective double reductions. Subsequent selective alkylation procedures and derivatizations provide a rapid and high-yielding access to different chiral ligands, bases, and benzoxazines, without loss of optical purity.

  10. Ligand-based molecular design of 4-benzylpiperidinealkylureas and amides as CCR3 antagonists.

    PubMed

    Jain, Vaibhav; Pandey, Ashish; Gupta, Shikhar; Mohan, C Gopi

    2010-04-01

    Asthma is an inflammatory disease of the lungs. Clinical studies suggest that eotaxin and chemokine receptor-3 (CCR3) play a primary role in the recruitment of eosinophils in allergic asthma. Development of novel and potent CCR3 antagonists could provide a novel mechanism for inhibition of this recruitment process, thereby preventing asthma. With the intention of designing new ligands with enhanced inhibitor potencies against CCR3, a 3D-QSAR CoMFA study was carried out on 41 4-benzylpiperidinealkylureas and amide derivatives. The best statistics of the developed CoMFA model were r (2) = 0.960, r(2)cv, n = 32 for the training set and r(2)pred, n = 9 for the test set. The generated 3D-QSAR contribution maps shed some light on the effects of the substitution pattern related to CCR3 antagonist activity.

  11. Protonation states and conformational ensemble in ligand-based QSAR modeling.

    PubMed

    De Benedetti, Pier G

    2013-01-01

    Drug affinity and function depend on the different protonation species (present in the biological context) that generate different conformational ensembles with different structural features and, hence, different physico-chemical properties. In the present review article these strongly interdependent structural features will be considered for their crucial role in ligand-based QSAR modeling and drug design by using quantum chemical electronic/reactivity descriptors and molecular shape description. Some selected and relevant examples illustrate the role of these molecular descriptors, computed on the bioactive protonation states and conformers, as determinant factors in mechanistic/causative QSAR analysis.

  12. Synthesis, spectral, optical properties and theoretical calculations on schiff bases ligands containing o-tolidine

    NASA Astrophysics Data System (ADS)

    Arroudj, S.; Bouchouit, M.; Bouchouit, K.; Bouraiou, A.; Messaadia, L.; Kulyk, B.; Figa, V.; Bouacida, S.; Sofiani, Z.; Taboukhat, S.

    2016-06-01

    This paper explores the synthesis, structure characterization and optical properties of two new schiff bases. These compounds were obtained by condensation of o-tolidine with salicylaldehyde and cinnamaldehyde. The obtained ligands were characterized by UV, 1H and NMR. Their third-order NLO properties were measured using the third harmonic generation technique on thin films at 1064 nm. The electric dipole moment (μ), the polarizability (α) and the first hyperpolarizability (β) were calculated using the density functional B3LYP method with the lanl2dz basis set. For the results, the title compound shows nonzero β value revealing second order NLO behaviour.

  13. Fluorescence Properties and Electrochemical Behavior of Some Schiff Bases Derived from N-Aminopyrimidine.

    PubMed

    Gulcan, Mehmet; Doğru, Ümit; Öztürk, Gülsiye; Levent, Abdulkadir; Akbaş, Esvet

    2014-03-01

    A series of Schiff bases (L 1 , L 2 and L 3) were prepared by refluxing aromatic aldehydes with N-Aminopyrimidine derivatives in methanol and ethanol. The structures of synthesized compounds were characterized by FTIR, (1)H NMR, (13)C NMR and microanalysis. The electrochemical behaviors of the Schiff base ligands were also discussed. Moreover, the evaluation of absorption and emission properties of the structures were carried out in five different solvents. The products show visible absorption maxima in the range of 304-576 nm, and emission maxima from 636 to 736 nm in all solvents tested.

  14. 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

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

    2016-01-15

    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.

  15. Anticancer Activity of Stilbene-based Derivatives.

    PubMed

    De Filippis, Barbara; Ammazzalorso, Alessandra; Fantacuzzi, Marialuigia; Giampietro, Letizia; Maccallini, Cristina; Amoroso, Rosa

    2017-03-07

    Anticancer Activity of Stilbene-based Derivatives Barbara De Filippis,* Alessandra Ammazzalorso, Marialuigia Fantacuzzi, Letizia Giampietro, Cristina Maccallini, Rosa Amoroso Dipartimento di Farmacia, Università "G. d'Annunzio", via dei Vestini 31, 66100 Chieti, Italy; * E-mail: barbara.defilippis@unich.it Stilbene is a very present structural scaffold in nature and stilbene-based compounds are largely described for their biological activity such as cardioprotective, potent antioxidant, anti-inflammatory, and anticancer agents. Starting from their potent chemotherapeutic activity against a wide variety of cancers, stilbene scaffold of resveratrol has been subjected to synthetic manipulations with the aim to obtaining new resveratrol analogues with improved anticancer activity and better bioavailability. In the last decade, majority of new synthetic stilbenoids demonstrated significant anticancer activity against a large number of cancer cell lines employed, depending on the type and position of substituents on stilbene skeleton. Given the importance of this topic and the vast therapeutic potential, especially in the field of cancer research, in the last years, some reviews have been published focusing on general pharmacological activity or, more recently, on the usefulness of hybrid molecule containing stilbene scaffold. The present review article focuses on the pharmacological profile of the key compounds containing stilbene scaffold and classify them on the type of structural modifications in stilbene skeleton.

  16. Light-Controlled Release and Uptake of Zinc Ions in Solution by a Photochromic Terthiazole-Based Ligand.

    PubMed

    Guérin, Juliette; Léaustic, Anne; Berthet, Jérôme; Métivier, Rémi; Guillot, Régis; Delbaere, Stéphanie; Nakatani, Keitaro; Yu, Pei

    2017-03-22

    We have synthesized and fully characterized a photochromic zinc complex with a terphenylthiazole-based ligand with a salen-like cavity. The solution stability of the complex was found to be greatly dependent on the state of the photochromic ligand and an interesting photo-triggered release and uptake of zinc ions was found as well as monitored by its fluorescence. The contrasting stability difference of the zinc complex between its two isomeric states was rationalized by DFT calculations.

  17. An immunocytochemical-derived correlate for evaluating the bridging of heteromeric mu-delta opioid protomers by bivalent ligands.

    PubMed

    Yekkirala, Ajay S; Kalyuzhny, Alexander E; Portoghese, Philip S

    2013-07-19

    Bivalent ligands that contain two pharmacophores linked by a spacer are promising tools to investigate the pharmacology of opioid receptor heteromers. Evidence for occupation of neighboring protomers by two phamacophores of a single bivalent ligand (bridging) has relied mainly on pharmacological data. In the present study, we have employed an immunocytochemical correlate to support in vivo biological studies that are consistent with bridging. We show that a bivalent mu agonist/delta antagonist (MDAN-21) that is devoid of tolerance due to possible bridging of mu and delta protomers prevents endocytosis of the heteromeric receptors in HEK-293 cells. Conversely, a bivalent ligand (MDAN-16) with a short spacer or monovalent mu agonist give rise to robust internalization. The data suggest that the immobilization of proximal mu and delta protomers is due to bridging by MDAN-21. The finding that MDAN-21 and its shorter spacer homologue MDAN-16 possess equivalent activity in HEK-293 cells, but produce dramatically divergent internalization of mu-delta heteromer, is relevant to the role of internalization and tolerance.

  18. Zn-OH2 and Zn-OH complexes with hydroborate-derived tripod ligands: a comprehensive study.

    PubMed

    Ibrahim, Mohamed M; Olmo, Cristina Pérez; Tekeste, Teame; Seebacher, Jan; He, Guosen; Maldonado Calvo, José A; Böhmerle, Karin; Steinfeld, Gunther; Brombacher, Horst; Vahrenkamp, Heinrich

    2006-09-04

    The complete array of those hydrotris(pyrazolyl/thioimidazolyl)borate ligands that were developed and used in the author's laboratories, with N3, N2S, NS2, and S3 donor sets, was scanned for their ability to form Zn-OH2 and Zn-OH complexes. The coordination motifs found were Zn-OH2, Zn-OH, Zn-OH-Zn, and Zn-O2H3-Zn. Of these, the well-established Zn-OH motif was complemented with novel species bearing N3, NS2, and S3 tripods. The Zn-OH2 motif was observed only with pyrazolylborate ligands and only in unusual situations with coordination numbers higher than 4 for zinc. The new Zn-OH-Zn motif was realized for three different pyrazolylborates, for one NS2 tripod, and for two S3 tripods. Finally, it was verified that the Zn-O2H3-Zn motif again occurs only with pyrazolylborate ligands. The new complexes were identified by a total of 11 structure determinations.

  19. Six new inorganic–organic hybrids based on rigid triangular ligands: Syntheses, structures and properties

    SciTech Connect

    Li, Na; Huang, Rudan

    2016-01-15

    Six new inorganic–organic hybrids based on rigid triangular N-containing ligands, NaCu{sup I}{sub 2}(tib){sub 4}(H{sub 2}O){sub 4}[H{sub 2}PW{sup V}W{sup VI}{sub 11}O{sub 40}][H{sub 2}PW{sup VI}{sub 12}O{sub 40}]·6H{sub 2}O (1), Cu{sup II}{sub 3}(tib){sub 4}Cl{sub 4}[H{sub 2}PW{sup VI}{sub 12}O{sub 40}]{sub 2}·4H{sub 2}O (2), Co(tib){sub 2}[PW{sup V}{sub 3}W{sup VI}{sub 9}O{sub 38}]·5H{sub 2}O (3), Cu{sup II}{sub 3}(tib){sub 2}[P{sub 2}Mo{sup VI}{sub 5}O{sub 22}(O{sub 2})]·4H{sub 2}O (4), Mn(pytpy){sub 2}Mo{sup VI}{sub 4}O{sub 13} (5) and Co(pytpy){sub 2}Mo{sup VI}{sub 4}O{sub 13} (6) (tib=1,3,5-tris(1-imidazolyl)benzene, pytpy=4’-(4”-pyridyl)2,4’:6’,4”-terpyridine), have been hydrothermally synthesized. Single crystal X-ray diffraction studies revealed that compounds 1–4 display two-dimensional (2D) layered structures, and in compounds 1–3, the adjacent Keggin anions link with each other by W–O–W covalent interactions to form 1D inorganic chains. Compounds 5–6 are 3D “pillar-layer” frameworks based on bimetal–oxide layers pillared by the pytpy ligands. The compounds have been characterized by elemental analysis, powder X−ray diffraction, X-ray photoelectron spectroscopy and thermo gravimetric analyses. Moreover, the electrochemical and catalytic properties of compound 1 have been investigated as well. - Graphical abstract: Six new inorganic–organic hybrids based on rigid triangular N-containing ligands have been obtained under hydrothermal conditions and characterized by single-crystal X-ray diffraction analyses, elemental analyses, IR spectra, and thermogravimetric (TG) analyses. Compounds 1–4 display two-dimensional (2D) layers structure, and in compounds 1–3, the adjacent Keggin anions link with each other by W–O–W covalent interactions to form 1D inorganic Keggin anions chains. Compounds 5–6 are 3D “pillar-layer” frameworks based on bimetal–oxide layers pillared by the pytpy ligands. - Highlights: • MOFs

  20. Synthesis and luminescence properties of polymer-rare earth complexes containing salicylaldehyde-type bidentate Schiff base ligand.

    PubMed

    Zhang, Dandan; Gao, Baojiao; Li, Yanbin

    2017-01-24

    Using molecular design and polymer reactions, two types of bidentate Schiff base ligands, salicylaldehyde-aniline (SAN) and salicylaldehyde-cyclohexylamine (SCA), were synchronously synthesized and bonded onto the side chain of polysulfone (PSF), giving two bidentate Schiff base ligand-functionalized PSFs, PSF-SAN and PSF-SCA, referred to as macromolecular ligands. Following coordination reactions between the macromolecular ligands and Eu(III) and Tb(III) ions (the reaction occurred between the bonded ligands SAN or SCA and the lanthanide ion), two series of luminescent polymer-rare earth complexes, PSF-SAN-Eu(III) and PSF-SCA-Tb(III), were obtained. The two macromolecular ligands were fully characterized by Fourier transform infrared (FTIR), (1) H NMR and UV absorption spectroscopy, and the prepared complexes were also characterized by FTIR, UV absorption spectroscopy and thermo-gravity analysis. On this basis, the photoluminescence properties of these complexes and the relationships between their structure and luminescence were investigated in depth. The results show that the bonded bidentate Schiff base ligands, SAN and SCA, can effectively sensitize the fluorescence emission of Eu(III) and Tb(III) ions, respectively. PSF-SAN-Eu(III) series complexes, namely the binary complex PSF-(SAN)3 -Eu(III) and the ternary complex PSF-(SAN)3 -Eu(III)-(Phen)1 (Phen is the small-molecule ligand 1,10-phenanthroline), produce strong red luminescence, suggesting that the triplet state energy level of SAN is lower and well matched with the resonant energy level of the Eu(III) ion. By contrast, PSF-SAN-Eu(III) series complexes, namely the binary complex PSF-(SCA)3 -Tb(III) and the ternary complex PSF-(SCA)3 -Tb(III)-(Phen)1 , display strong green luminescence, suggesting that the triplet state energy level of SCA is higher and is well matched with the resonant energy level of Tb(III).

  1. Discovery of a novel IKK-β inhibitor by ligand-based virtual screening techniques

    PubMed Central

    Noha, Stefan M.; Atanasov, Atanas G.; Schuster, Daniela; Markt, Patrick; Fakhrudin, Nanang; Heiss, Elke H.; Schrammel, Olivia; Rollinger, Judith M.; Stuppner, Hermann; Dirsch, Verena M.; Wolber, Gerhard

    2011-01-01

    Various inflammatory stimuli that activate the nuclear factor kappa B (NF-κB) signaling pathway converge on a serine/threonine kinase that displays a key role in the activation of NF-κB: the I kappa B kinase β (IKK-β). Therefore, IKK-β is considered an interesting target for combating inflammation and cancer. In our study, we developed a ligand-based pharmacophore model for IKK-β inhibitors. This model was employed to virtually screen commercial databases, giving a focused hit list of candidates. Subsequently, we scored by molecular shape to rank and further prioritized virtual hits by three-dimensional shape-based alignment. One out of ten acquired and biologically tested compounds showed inhibitory activity in the low micromolar range on IKK-β enzymatic activity in vitro and on NF-κB transactivation in intact cells. Compound 8 (2-(1-adamantyl)ethyl 4-[(2,5-dihydroxyphenyl)methylamino]benzoate) represents a novel chemical class of IKK-β inhibitors and shows that the presented model is a valid approach for identification and development of new IKK-β ligands. PMID:21078555

  2. Pentanuclear lanthanide pyramids based on thiacalix[4]arene ligand exhibiting slow magnetic relaxation.

    PubMed

    Ge, Jing-Yuan; Ru, Jing; Gao, Feng; Song, You; Zhou, Xin-Hui; Zuo, Jing-Lin

    2015-09-21

    A series of pentanuclear Ln(III) clusters, [Ln5(μ4-OH)(μ3-OH)4(L1)(acac)6] (H4L1 = p-tert-butylthiacalix[4]arene; acac = acetylacetonate; Ln = Dy, Ho, Er) and [Ln5(μ5-OH)(μ3-OH)4(L1)(L2)2(acac)2(CH3OH)2] (H3L2 = 5,11,17,23-tetrakis(1,1-dimethylethyl)-25,26,27-trihydroxy-28-methoxy thiacalix[4]arene; Ln = Dy, Ho, Er), have been synthesized based on the thiacalix[4]arene ligand. All of these complexes feature a square-based pyramid with four triangular Ln3 structural motifs. One μ4-OH group bridges four Ln(III) ions in the basal plane of , while the OH group in complexes adopts the μ5-coordination mode. Our results illuminate the coordination modes of the versatile thiacalix[4]arene ligands and their application to new cluster compounds. The structural and magnetic studies confirm that the molecular symmetries and coordination geometries for lanthanide metal cores have a significant effect on some parameters as single-molecule magnets. Among them, two Dy5 pyramids exhibit distinct slow magnetic relaxation.

  3. Synthesis and pharmacological evaluation of novel 9- and 10-substituted cytisine derivatives. Nicotinic ligands of enhanced subtype selectivity.

    PubMed

    Chellappan, Sheela K; Xiao, Yingxian; Tueckmantel, Werner; Kellar, Kenneth J; Kozikowski, Alan P

    2006-05-04

    We report the synthesis and pharmacological properties of several cytisine derivatives. Among them, two 10-substituted derivatives showed much higher selectivities for the alpha4beta2 nAChR subtype in binding assays than cytisine. The 9-vinyl derivative was found to have a very similar agonist activity profile to that of cytisine.

  4. Molecular structure effect of pyridine-based surface ligand on the performance of P3HT:TiO₂ hybrid solar cell.

    PubMed

    Lin, Jhih-Fong; Tu, Guang-Yao; Ho, Chun-Chih; Chang, Chun-Yu; Yen, Wei-Che; Hsu, Sheng-Hao; Chen, Yang-Fang; Su, Wei-Fang

    2013-02-01

    Colloid TiO(2) nanorods are used for solution-processable poly(3-hexyl thiophene): TiO(2) hybrid solar cell. The nanorods were covered by insulating ligand of oleic acid (OA) after sol-gel synthesis. Three more conducting pyridine type ligands: pyridine, 2,6-lutidine (Lut) and 4-tert-butylpyridine (tBP) were investigated respectively to replace OA. The power conversion efficiency (PCE) of the solar cell was increased because the electronic mobility of pyridine-type ligand-modified TiO(2) is higher than that of TiO(2)-OA. The enhancement of PCE is in the descending order of Lut > pyridine > tBP because of the effective replacement of OA by Lut. The PCE of solar cell can be further enhanced by ligand exchange of pyridine type ligand with conjugating molecule of 2-cyano-3-(5-(7-(thiophen-2-yl)-benzothiadiazol-4-yl) thiophen-2-yl) acrylic acid (W4) on TiO(2) nanorods because W4 has aligned bandgap with P3HT and TiO(2) to facilitate charge separation and transport. The electronic mobility of two-stage ligand exchanged TiO(2) is improved furthermore except Lut, because it adheres well and difficult to be replaced by W4. The amount of W4 on TiO(2)-tBP is 3 times more than that of TiO(2)-Lut (0.20 mol % vs. 0.06 mol %). Thus, the increased extent of PCE of solar cell is in the decreasing order of tBP > pyridine > Lut. The TiO(2)-tBP-W4 device has the best performance with 1.4 and 2.6 times more than TiO(2)-pyridine-W4 and TiO(2)-Lut-W4 devices, respectively. The pKa of the pyridine derivatives plays the major role to determine the ease of ligand exchange on TiO(2) which is the key factor mandating the PCE of P3HT:TiO(2) hybrid solar cell. The results of this study provide new insights of the significance of acid-base reaction on the TiO(2) surface for TiO(2)-based solar cells. The obtained knowledge can be extended to other hybrid solar cell systems.

  5. Fluorescence-based strategies to investigate the structure and dynamics of aptamer-ligand complexes

    NASA Astrophysics Data System (ADS)

    Perez-Gonzalez, Cibran; Lafontaine, Daniel; Penedo, J.

    2016-08-01

    In addition to the helical nature of double-stranded DNA and RNA, single-stranded oligonucleotides can arrange themselves into tridimensional structures containing loops, bulges, internal hairpins and many other motifs. This ability has been used for more than two decades to generate oligonucleotide sequences, so-called aptamers, that can recognize certain metabolites with high affinity and specificity. More recently, this library of artificially-generated nucleic acid aptamers has been expanded by the discovery that naturally occurring RNA sequences control bacterial gene expression in response to cellular concentration of a given metabolite. The application of fluorescence methods has been pivotal to characterize in detail the structure and dynamics of these aptamer-ligand complexes in solution. This is mostly due to the intrinsic high sensitivity of fluorescence methods and also to significant improvements in solid-phase synthesis, post-synthetic labelling strategies and optical instrumentation that took place during the last decade. In this work, we provide an overview of the most widely employed fluorescence methods to investigate aptamer structure and function by describing the use of aptamers labelled with a single dye in fluorescence quenching and anisotropy assays. The use of 2-aminopurine as a fluorescent analog of adenine to monitor local changes in structure and fluorescence resonance energy transfer (FRET) to follow long-range conformational changes is also covered in detail. The last part of the review is dedicated to the application of fluorescence techniques based on single-molecule microscopy, a technique that has revolutionized our understanding of nucleic acid structure and dynamics. We finally describe the advantages of monitoring ligand-binding and conformational changes, one molecule at a time, to decipher the complexity of regulatory aptamers and summarize the emerging folding and ligand-binding models arising from the application of these

  6. Fluorescence-Based Strategies to Investigate the Structure and Dynamics of Aptamer-Ligand Complexes

    PubMed Central

    Perez-Gonzalez, Cibran; Lafontaine, Daniel A.; Penedo, J. Carlos

    2016-01-01

    In addition to the helical nature of double-stranded DNA and RNA, single-stranded oligonucleotides can arrange themselves into tridimensional structures containing loops, bulges, internal hairpins and many other motifs. This ability has been used for more than two decades to generate oligonucleotide sequences, so-called aptamers, that can recognize certain metabolites with high affinity and specificity. More recently, this library of artificially-generated nucleic acid aptamers has been expanded by the discovery that naturally occurring RNA sequences control bacterial gene expression in response to cellular concentration of a given metabolite. The application of fluorescence methods has been pivotal to characterize in detail the structure and dynamics of these aptamer-ligand complexes in solution. This is mostly due to the intrinsic high sensitivity of fluorescence methods and also to significant improvements in solid-phase synthesis, post-synthetic labeling strategies and optical instrumentation that took place during the last decade. In this work, we provide an overview of the most widely employed fluorescence methods to investigate aptamer structure and function by describing the use of aptamers labeled with a single dye in fluorescence quenching and anisotropy assays. The use of 2-aminopurine as a fluorescent analog of adenine to monitor local changes in structure and fluorescence resonance energy transfer (FRET) to follow long-range conformational changes is also covered in detail. The last part of the review is dedicated to the application of fluorescence techniques based on single-molecule microscopy, a technique that has revolutionized our understanding of nucleic acid structure and dynamics. We finally describe the advantages of monitoring ligand-binding and conformational changes, one molecule at a time, to decipher the complexity of regulatory aptamers and summarize the emerging folding and ligand-binding models arising from the application of these

  7. Synthesis and characterization of crystalline structures based on phenylboronate ligands bound to alkaline earth cations.

    PubMed

    Reinholdt, Marc; Croissant, Jonas; Di Carlo, Lidia; Granier, Dominique; Gaveau, Philippe; Bégu, Sylvie; Devoisselle, Jean-Marie; Mutin, P Hubert; Smith, Mark E; Bonhomme, Christian; Gervais, Christel; van der Lee, Arie; Laurencin, Danielle

    2011-08-15

    We describe the preparation of the first crystalline compounds based on arylboronate ligands PhB(OH)(3)(-) coordinated to metal cations: [Ca(PhB(OH)(3))(2)], [Sr(PhB(OH)(3))(2)]·H(2)O, and [Ba(PhB(OH)(3))(2)]. The calcium and strontium structures were solved using powder and single-crystal X-ray diffraction, respectively. In both cases, the structures are composed of chains of cations connected through phenylboronate ligands, which interact one with each other to form a 2D lamellar structure. The temperature and pH conditions necessary for the formation of phase-pure compounds were investigated: changes in temperature were found to mainly affect the morphology of the crystallites, whereas strong variations in pH were found to affect the formation of pure phases. All three compounds were characterized using a wide range of analytical techniques (TGA, IR, Raman, XRD, and high resolution (1)H, (11)B, and (13)C solid-state NMR), and the different coordination modes of phenylboronate ligands were analyzed. Two different kinds of hydroxyl groups were identified in the structures: those involved in hydrogen bonds, and those that are effectively "free" and not involved in hydrogen bonds of any significant strength. To position precisely the OH protons within the structures, an NMR-crystallography approach was used: the comparison of experimental and calculated NMR parameters (determined using the Gauge Including Projector Augmented Wave method, GIPAW) allowed the most accurate positions to be identified. In the case of the calcium compound, it was found that it is the (43)Ca NMR data that are critical to help identify the best model of the structure.

  8. Syntheses, crystal structures, and properties of four complexes based on polycarboxylate and imidazole ligands

    NASA Astrophysics Data System (ADS)

    Qiao, Rui; Chen, Shui-Sheng; Sheng, Liang-Quan; Yang, Song; Li, Wei-Dong

    2015-08-01

    Four metal-organic coordination polymers [Zn(HL)(H2O)]·4H2O (1), [Zn(HL)(L1)]·4H2O (2), [Cu(HL)(H2O)]·3H2O (3) and [Cu(HL)(L1)]·5H2O (4) were synthesized by reactions of the corresponding metal(II) salts with semirigid polycarboxylate ligand (5-((4-carboxypiperidin-1-yl)methyl)isophthalic acid hydrochloride, H3L·HCl) or auxiliary ligand (1,4-di(1H-imidazol-4-yl)benzene, L1). The structures of the compounds were characterized by elemental analysis, FT-IR spectroscopy and single-crystal X-ray diffraction. The use of auxiliary ligand L1 has great influence on the structures of two pairs of complexes 1, 2 and 3, 4. Complex 1 is a uninodal 3-connected rare 2-fold interpenetrating ZnSc net with a Point (Schlafli) symbol of (103) while 2 is a one-dimensional (1D) ladder structure. Compound 3 features a two-dimensional (2D) honeycomb network with typical 63-hcb topology, while 4 is 2D network with (4, 4) sql topology based on binuclear CuII subunits. The non-covalent bonding interactions such as hydrogen bonds, π···π stacking and C-H···π exist in complexes 1-4, which contributes to stabilize crystal structure and extend the low-dimensional entities into high-dimensional frameworks. And the photoluminescent property of 1 and 2 and gas sorption property of 4 have been investigated.

  9. Supramolecular polymers constructed by orthogonal self-assembly based on host-guest and metal-ligand interactions.

    PubMed

    Wei, Peifa; Yan, Xuzhou; Huang, Feihe

    2015-02-07

    Supramolecular polymers constructed by orthogonal self-assembly based on host-guest and metal-ligand interactions are attracting increasing attention currently because of their interesting properties and potential applications. Host-guest interactions impart these polymers with good selectivity and convenient enviro-responsiveness, and metal-ligand interactions endow them with various coordination geometries, strong yet tunable coordination binding abilities, as well as magnetic, redox, photophysical, and electrochromic properties. Therefore, supramolecular polymers constructed by orthogonal host-guest and metal-ligand interactions have wide applications in the fields of soft matter, fluorescence sensing, heterocatalysis, electronics, gas storage, etc. In this critical review, we will address the recent development of supramolecular polymeric systems involving metal-ligand interactions and host-guest molecular recognition. Specifically, we classify the related supramolecular polymers depending on the types of macrocyclic hosts, and highlight their intriguing properties originating from the elegant combination of host-guest complexation and metal centers.

  10. Two tridentate Schiff base ligands and their mononuclear cobalt (III) complexes: Synthesis, characterization, antibacterial and antifungal activities.

    PubMed

    Gungor, Elif; Celen, Selma; Azaz, Dilek; Kara, Hulya

    2012-08-01

    Two Schiff base ligands (HL1, HL2) and their Co(III) complexes, [Co(HL1)(L1)] (1) and [Co(HL2)(L2)] (2) [where HL1=2-((E)-(2-hydroxyethylimino)methyl)-4-chlorophenol and HL2=2-((E)-(2-hydroxyethylimino)methyl)-4-bromophenol] were synthesized and characterized using spectroscopic methods. The crystal structures of 1 and 2 have been re-determined by single crystal diffraction at 100K. The ligands and their Co(III) complexes were screened for antibacterial and antifungal activities by the disc diffusion, microdilution broth and single spore culture techniques. The antimicrobial activity of the Co(III) complexes and the free ligands exhibit antimicrobial properties and the Co(III) complexes show enhanced inhibitory activity compared with their parent ligand.

  11. An unbiased method to build benchmarking sets for ligand-based virtual screening and its application to GPCRs.

    PubMed

    Xia, Jie; Jin, Hongwei; Liu, Zhenming; Zhang, Liangren; Wang, Xiang Simon

    2014-05-27

    Benchmarking data sets have become common in recent years for the purpose of virtual screening, though the main focus had been placed on the structure-based virtual screening (SBVS) approaches. Due to the lack of crystal structures, there is great need for unbiased benchmarking sets to evaluate various ligand-based virtual screening (LBVS) methods for important drug targets such as G protein-coupled receptors (GPCRs). To date these ready-to-apply data sets for LBVS are fairly limited, and the direct usage of benchmarking sets designed for SBVS could bring the biases to the evaluation of LBVS. Herein, we propose an unbiased method to build benchmarking sets for LBVS and validate it on a multitude of GPCRs targets. To be more specific, our methods can (1) ensure chemical diversity of ligands, (2) maintain the physicochemical similarity between ligands and decoys, (3) make the decoys dissimilar in chemical topology to all ligands to avoid false negatives, and (4) maximize spatial random distribution of ligands and decoys. We evaluated the quality of our Unbiased Ligand Set (ULS) and Unbiased Decoy Set (UDS) using three common LBVS approaches, with Leave-One-Out (LOO) Cross-Validation (CV) and a metric of average AUC of the ROC curves. Our method has greatly reduced the "artificial enrichment" and "analogue bias" of a published GPCRs benchmarking set, i.e., GPCR Ligand Library (GLL)/GPCR Decoy Database (GDD). In addition, we addressed an important issue about the ratio of decoys per ligand and found that for a range of 30 to 100 it does not affect the quality of the benchmarking set, so we kept the original ratio of 39 from the GLL/GDD.

  12. Syntheses, crystal structures, and properties of four complexes based on polycarboxylate and imidazole ligands

    SciTech Connect

    Qiao, Rui; Chen, Shui-Sheng; Sheng, Liang-Quan; Yang, Song; Li, Wei-Dong

    2015-08-15

    Four metal–organic coordination polymers [Zn(HL)(H{sub 2}O)]·4H{sub 2}O (1), [Zn(HL)(L{sub 1})]·4H{sub 2}O (2), [Cu(HL)(H{sub 2}O)]·3H{sub 2}O (3) and [Cu(HL)(L{sub 1})]·5H{sub 2}O (4) were synthesized by reactions of the corresponding metal(II) salts with semirigid polycarboxylate ligand (5-((4-carboxypiperidin-1-yl)methyl)isophthalic acid hydrochloride, H{sub 3}L·HCl) or auxiliary ligand (1,4-di(1H-imidazol-4-yl)benzene, L{sub 1}). The structures of the compounds were characterized by elemental analysis, FT-IR spectroscopy and single-crystal X-ray diffraction. The use of auxiliary ligand L{sub 1} has great influence on the structures of two pairs of complexes 1, 2 and 3, 4. Complex 1 is a uninodal 3-connected rare 2-fold interpenetrating ZnSc net with a Point (Schlafli) symbol of (10{sup 3}) while 2 is a one-dimensional (1D) ladder structure. Compound 3 features a two-dimensional (2D) honeycomb network with typical 6{sup 3}-hcb topology, while 4 is 2D network with (4, 4) sql topology based on binuclear Cu{sup II} subunits. The non-covalent bonding interactions such as hydrogen bonds, π···π stacking and C–H···π exist in complexes 1–4, which contributes to stabilize crystal structure and extend the low-dimensional entities into high-dimensional frameworks. And the photoluminescent property of 1 and 2 and gas sorption property of 4 have been investigated. - Graphical abstract: Four new coordination polymers have been obtained and their photoluminescent and gas sorption properties have also been investigated. - Highlights: • Two pairs of Zn{sup II}/ Cu{sup II} compounds have been synthesized. • Auxiliary ligand-controlled assembly of the complexes is reported. • The luminescent properties of complexes 1–2 were investigated. • The gas sorption property of 4 has been investigated.

  13. A computational fragment-based de novo design protocol guided by ligand efficiency indices (LEI).

    PubMed

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

    2015-01-01

    We present a new protocol aimed at the structure-based design of drug-like molecules using a fragment approach. It starts from a suitably placed and well-defined "base fragment" and then uses an incremental construction algorithm and a scoring function to grow the molecule into prioritized candidates. The selection of the most promising solutions for synthesis and validation is guided by the optimization of the calculated ligand efficiency indices known as binding efficiency index (BEI) and surface efficiency index (SEI), which allow the user to navigate proficiently in chemico-biological space. A test case for the protocol is exemplified here using published data for inhibitors of protein kinase B, aka AKT, a key enzyme in several signal transduction pathways. Our procedure was able to identify the main features responsible for the binding of inhibitors and guided the selection process towards molecules that included or resembled those shown as the most active in the original studies.

  14. Synthesis, structures and fluorescent properties of metal complexes based on polyphosphine ligands

    NASA Astrophysics Data System (ADS)

    Huang, Ting-Hong; Yang, Hu; Zhu, Sheng-Lan; Zhao, Bin; Yang, Yan

    2017-01-01

    Based on polyphosphine ligands, four complexes, [Cu2(pba)2(pipzdtc)]·2DMF (1), [Cu2(pbaa) (Et-dtc)2]·2DMF (2), [Cu2(pnaa) (Et-dtc)2] (3) and [Ag2(pnaa) (Et-dtc)2] ·2CH3CN (4) (pba = N,N-bis((diphenylphosphino)methyl)benzenamine, pbaa = N,N,N‧,N'-tetrakis((di-phenylphosphino)methyl)benzene-1,4-diamine, pnaa = N,N,N‧,N'-tetrakis((diphenylphosphino)- methyl)naphthalene-1,5-diamine, Et-dtc = N-ethyldithiocarbamate and pipzdtc = piperazine- 1,4-dicarbodithiolate), have been synthesized and characterized by IR, ESI-MS and X-ray crystal structure analysis. The structural analysis shows that each Cu+/Ag+ in complexes 1-4 is four coordinate P2S2, and adopts a distorted-tetrahedral geometry, and 1D infinite chain of complexes 2 and 4 is built by Csbnd H⋯π interaction of phenyl rings from pbaa and pnaa. All these indicate that the change of polyphosphine ligands and metal ions might be the key of construction of 1D infinite chain. Moreover, the emission spectra of complexes 2-4 in DMF solvent are also observed.

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

    PubMed

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

    2013-11-01

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

  16. Novel and Potent 5-Piperazinyl Methyl-N 1-aryl Sulfonyl Indole Derivatives as 5-HT6 Receptor Ligands.

    PubMed

    Nirogi, Ramakrishna V S; Kothmirkar, Prabhakar; Kambhampati, Ramasastri; Konda, Jagadish Babu; Arepalli, Sobhanadri; Pamuleti, Narasimhareddy G; Deshpande, Amol D; Bandyala, Trinathreddy; Shinde, Anil K; Dubey, P K

    2010-10-14

    The exclusive distribution of 5-HT6 receptors in the brain regions associated with learning and memory makes it an ideal target for cognitive disorders. A novel series of 5-piperazinyl methyl-N 1-aryl sulfonyl indoles were designed and synthesized as 5-HT6R ligands. Most of the synthesized compounds are potent when tested by in vitro radioligand binding assay. The lead compound from the series does not have the CYP liabilities and is active in an animal model of cognition.

  17. Hydrogen release from ammonia borane and derivatives in the presence of a ruthenium complex incorporating cooperative PNP ligands

    NASA Astrophysics Data System (ADS)

    Swinnen, Saartje; Nguyen, Vinh Son; Nguyen, Minh Tho

    2011-09-01

    A ruthenium complex bearing cooperative PNP ligands showed unprecedented activities in homogenous catalysis of the reversible dehydrogenation of ammonia borane at both N-functionality and ethylene backbone. Quantum chemical calculations on a simple model of Ru-complex are carried out to probe the H 2 release mechanism. The energy barrier for H 2 formation from NH 3BH 3 is found to be strongly reduced with the presence of Ru-catalyst, and one additional H 2 molecule can be produced. The Ru-complex can also be used as a catalyst for H 2 release from other potential materials for chemical hydrogen storage such as hydrazine and ammonia alane.

  18. N-aryl pyrrolo-tetrathiafulvalene based ligands: synthesis and metal coordination.

    PubMed

    Balandier, Jean-Yves; Chas, Marcos; Dron, Paul I; Goeb, Sébastien; Canevet, David; Belyasmine, Ahmed; Allain, Magali; Sallé, Marc

    2010-03-05

    A straightforward general synthetic access to N-aryl-1,3-dithiolo[4,5-c]pyrrole-2-thione derivatives 6 from acetylenedicarbaldehyde monoacetal is depicted. In addition to their potentiality as precursors to dithioalkyl-pyrrole derivatives, thiones 6 are key building blocks to N-aryl monopyrrolo-tetrathiafulvalene (MPTTF) derivatives 10. X-ray structures of four of these thiones intermediates, reminiscent of the corresponding MPTTF derivatives, are provided. When the aryl group is a binding pyridyl unit, the MPTTF derivative 10a can coordinate M(II) salts (M = Pt, Pd). The first examples of metal-directed orthogonal MPTTF-based dimers 11-14, obtained through coordination of 10a to cis-blocked square planar Pt or Pd complexes are described. Studies on the parameters influencing the dimer construction are presented, as well as first recognition properties of the resulting electron-rich clip for C(60).

  19. Synthesis of Pharmacological Heterocyclic Derivatives Based Surfactants.

    PubMed

    El-Sayed, Refat; Fadda, Ahmed A

    2016-01-01

    Synthesis of chromenopyrimidine derivatives and the related fused system carried out by the reaction of chromene derivative 1 with various reagents under suitable reaction conditions. Condensation of stearoyl chloride with these heterocycles, then, propoxylated the products using propylene oxide to produce surface active agents having a twofold capacity as surface and antimicrobial dynamic specialists which may be served in the production of medications, pesticides, beautifying agents or may be utilized as an antimicrobial. Some of the surface properties and antimicrobial activity were resolved.

  20. Self-assembly of metallomacrocycles with dipyrazole ligands and anion sensing of [Pd4Fe2] macrocycle with ferrocene-based dipyrazole ligand.

    PubMed

    Yao, Liao-Yuan; Yu, Zheng-Su; Qin, Lin; Li, Yi-Zhi; Qin, Yu; Yu, Shu-Yan

    2013-03-14

    By employing dipalladium corners [(bpy)(2)Pd(2)(NO(3))(2)](NO(3))(2) or [(phen)(2)Pd(2)(NO(3))(2)](NO(3))(2) (where bpy = 2,2'-bipyridine and phen = 1,10-phenanthroline) to bridge ferrocene-based dipyrazole ligand (L(1)) and m-phenylene-based dipyrazole ligands (L(2-3)) in aqueous solution, a series of positively-charged [M(4)L(2)](4+) metallomacrocycles were obtained. Their structures were characterized by (1)H NMR, electrospray ionization mass spectrometry (ESI-MS), elemental analysis, and single crystal X-ray diffraction analysis for 1·4NO(3) ({[(bpy)Pd](4)L(1)(2)}(NO(3))(4)) and 4·4NO(3) ({[(phen)Pd](4)L(2)(2)}(NO(3))(4)). In their single crystal structures, NO(3)(-) anions are located at the dipalladium corners by C-H...O hydrogen bonds. Importantly, the anion-sensing properties of ferrocene functionalized [Pd(4)Fe(2)] hetero-metallomacrocycle 1 were investigated in acetonitrile by SWV, CV and NMR analysis, showing promise for Br(-) sensing.

  1. Web application for studying the free energy of binding and protonation states of protein-ligand complexes based on HINT

    NASA Astrophysics Data System (ADS)

    Bayden, Alexander S.; Fornabaio, Micaela; Scarsdale, J. Neel; Kellogg, Glen E.

    2009-09-01

    A public web server performing computational titration at the active site in a protein-ligand complex has been implemented. This calculation is based on the Hydropathic interaction noncovalent force field. From 3D coordinate data for the protein, ligand and bridging waters (if available), the server predicts the best combination of protonation states for each ionizable residue and/or ligand functional group as well as the Gibbs free energy of binding for the ionization-optimized protein-ligand complex. The 3D structure for the modified molecules is available as output. In addition, a graph depicting how this energy changes with acidity, i.e., as a function of added protons, can be obtained. This data may prove to be of use in preparing models for virtual screening and molecular docking. A few illustrative examples are presented. In β secretase (2va7) computational titration flipped the amide groups of Gln12 and Asn37 and protonated a ligand amine yielding an improvement of 6.37 kcal mol-1 in the protein-ligand binding score. Protonation of Glu139 in mutant HIV-1 reverse transcriptase (2opq) allows a water bridge between the protein and inhibitor that increases the protein-ligand interaction score by 0.16 kcal mol-1. In human sialidase NEU2 complexed with an isobutyl ether mimetic inhibitor (2f11) computational titration suggested that protonating Glu218, deprotonating Arg237, flipping the amide bond on Tyr334, and optimizing the positions of several other polar protons would increase the protein-ligand interaction score by 0.71 kcal mol-1.

  2. Chemically engineering ligand selectivity at the free fatty acid receptor 2 based on pharmacological variation between species orthologs

    PubMed Central

    Hudson, Brian D.; Christiansen, Elisabeth; Tikhonova, Irina G.; Grundmann, Manuel; Kostenis, Evi; Adams, David R.; Ulven, Trond; Milligan, Graeme

    2012-01-01

    When it is difficult to develop selective ligands within a family of related G-protein-coupled receptors (GPCRs), chemically engineered receptors activated solely by synthetic ligands (RASSLs) are useful alternatives for probing receptor function. In the present work, we explored whether a RASSL of the free fatty acid receptor 2 (FFA2) could be developed on the basis of pharmacological variation between species orthologs. For this, bovine FFA2 was characterized, revealing distinct ligand selectivity compared with human FFA2. Homology modeling and mutational analysis demonstrated a single mutation in human FFA2 of C4.57G resulted in a human FFA2 receptor with ligand selectivity similar to the bovine receptor. This was exploited to generate human FFA2-RASSL by the addition of a second mutation at a known orthosteric ligand interaction site, H6.55Q. The resulting FFA2-RASSL displayed a >100-fold loss of activity to endogenous ligands, while responding to the distinct ligand sorbic acid with pEC50 values for inhibition of cAMP, 5.83 ± 0.11; Ca2+ mobilization, 4.63 ± 0.05; ERK phosphorylation, 5.61 ± 0.06; and dynamic mass redistribution, 5.35 ± 0.06. This FFA2-RASSL will be useful in future studies on this receptor and demonstrates that exploitation of pharmacological variation between species orthologs is a powerful method to generate novel chemically engineered GPCRs.—Hudson, B. D., Christiansen, E., Tikhonova, I. G., Grundmann, M., Kostenis, E., Adams, D. R., Ulven, T., Milligan, G. Chemically engineering ligand selectivity at the free fatty acid receptor 2 based on pharmacological variation between species orthologs. PMID:22919070

  3. Towards metabolically stable 5-HT7 receptor ligands: a study on 1-arylpiperazine derivatives and related isosters.

    PubMed

    Lacivita, Enza; De Giorgio, Paola; Patarnello, Daniela; Niso, Mauro; Colabufo, Nicola A; Berardi, Francesco; Perrone, Roberto; Satala, Grzegorz; Duszynska, Beata; Bojarski, Andrzej J; Leopoldo, Marcello

    2013-10-01

    Serotonin 7 (5-hydroxytryptamine7 or 5-HT7) is the most recently identified serotonin receptor. It is involved in mood disorders and is studied as a target for antidepressants. Here, we report on the structural manipulation of the 5-HT7 receptor ligand 4-[2-(3-methoxyphenyl)ethyl]-1-(2-methoxyphenyl)piperazine (1a) aimed at obtaining 5-HT7 receptor ligands endowed with good in vitro metabolic stability. A set of N-[3-methoxyphenyl)ethyl-substituted] 1-arylpiperazine, 4-arylpiperidine and 1-aryl-4-aminopiperidine was synthesized and tested in radioligand binding assays at human cloned 5-HT7 and 5-HT1A receptors. In vitro metabolic stability of the target compounds was assessed after incubation with rat hepatic S9 microsomal fraction. Among the new compounds, 1-(2-biphenyl)-4-[2-(3-methoxyphenyl)ethyl]piperazine (1d) and 4-(2-biphenyl)-1-[2-(3-methoxyphenyl)ethyl]piperidine (2d) showed a good compromise between affinity at 5-HT7 receptor (K i = 7.5 nM and 13 nM, respectively) and in vitro metabolic stability (26 and 65 % recovery of parent compound, respectively) but were poorly selective over 5-HT1A receptor.

  4. A new copper(II) Schiff base complex containing asymmetrical tetradentate N2O2 Schiff base ligand: Synthesis, characterization, crystal structure and DFT study

    NASA Astrophysics Data System (ADS)

    Grivani, Gholamhossein; Baghan, Sara Husseinzadeh; Vakili, Mohammad; Khalaji, Aliakbar Dehno; Tahmasebi, Vida; Eigner, Václav; Dušek, Michal

    2015-02-01

    A new copper (II) Schiff base complex, CuL1, was prepared from the reaction of asymmetrical Schiff base ligand of L1 and Cu(OAC)2 (L1 = salicylidene imino-ethylimino-pentan-2-one). The Schiff base ligand, L1, and its copper (II) complex, CuL1, have been characterized by elemental analysis (CHN) and FT-IR and UV-vis spectroscopy. In addition, 1H NMR was employed for characterization of the ligand. Thermogrametric analysis of the CuL1 reveals its thermal stability and its decomposition pattern shows that it is finally decomposed to the copper oxide (CuO). The crystal structure of CuL1 was determined by the single crystal X-ray analysis. The CuL1 complex crystallizes in the monoclinic system, with space group P21/n and distorted square planar coordination around the metal ion. The Schiff base ligand of L1 acts as a chelating ligand and coordinates via two nitrogen and two oxygen atoms to the copper (II) ion with C1 symmetry. The structure of the CuL1 complex was also studied theoretically at different levels of DFT and basis sets. According to calculated results the Csbnd O bond length of the salicylate fragment is slightly higher than that in the acetylacetonate fragment of ligand, which could be interpreted by resonance increasing between phenyl and chelated rings in ligand in relative to the acetylacetonate fragment.

  5. A combined ligand-based and target-based drug design approach for G-protein coupled receptors: application to salvinorin A, a selective kappa opioid receptor agonist

    NASA Astrophysics Data System (ADS)

    Singh, Nidhi; Chevé, Gwénaël; Ferguson, David M.; McCurdy, Christopher R.

    2006-08-01

    Combined ligand-based and target-based drug design approaches provide a synergistic advantage over either method individually. Therefore, we set out to develop a powerful virtual screening model to identify novel molecular scaffolds as potential leads for the human KOP (hKOP) receptor employing a combined approach. Utilizing a set of recently reported derivatives of salvinorin A, a structurally unique KOP receptor agonist, a pharmacophore model was developed that consisted of two hydrogen bond acceptor and three hydrophobic features. The model was cross-validated by randomizing the data using the CatScramble technique. Further validation was carried out using a test set that performed well in classifying active and inactive molecules correctly. Simultaneously, a bovine rhodopsin based "agonist-bound" hKOP receptor model was also generated. The model provided more accurate information about the putative binding site of salvinorin A based ligands. Several protein structure-checking programs were used to validate the model. In addition, this model was in agreement with the mutation experiments carried out on KOP receptor. The predictive ability of the model was evaluated by docking a set of known KOP receptor agonists into the active site of this model. The docked scores correlated reasonably well with experimental p K i values. It is hypothesized that the integration of these two independently generated models would enable a swift and reliable identification of new lead compounds that could reduce time and cost of hit finding within the drug discovery and development process, particularly in the case of GPCRs.

  6. Co(II) and Cd(II) Complexes Derived from Heterocyclic Schiff-Bases: Synthesis, Structural Characterisation, and Biological Activity

    PubMed Central

    Ahmed, Riyadh M.; Yousif, Enaam I.; Al-Jeboori, Mohamad J.

    2013-01-01

    New monomeric cobalt and cadmium complexes with Schiff-bases, namely, N′-[(E)-(3-hydroxy-4-methoxyphenyl)methylidene]furan-2-carbohydrazide (L1) and N′-[(E)-(3-hydroxy-4-methoxyphenyl)methylidene]thiophene-2-carbohydrazide (L2) are reported. Schiff-base ligands L1 and L2 were derived from condensation of 3-hydroxy-4-methoxybenzaldehyde (iso-vanillin) with furan-2-carboxylic acid hydrazide and thiophene-2-carboxylic acid hydrazide, respectively. Complexes of the general formula [M(L)2]Cl2 (where M = Co(II) or Cd(II), L = L1 or L2) have been obtained from the reaction of the corresponding metal chloride with the ligands. The ligands and their metal complexes were characterised by spectroscopic methods (FTIR, UV-Vis, 1H, and 13C NMR spectra), elemental analysis, metal content, magnetic measurement, and conductance. These studies revealed the formation of four-coordinate complexes in which the geometry about metal ion is tetrahedral. Biological activity of the ligands and their metal complexes against gram positive bacterial strain Bacillus (G+) and gram negative bacteria Pseudomonas (G−) revealed that the metal complexes become less resistive to the microbial activities as compared to the free ligands. PMID:24027449

  7. Co(II) and Cd(II) complexes derived from heterocyclic Schiff-Bases: synthesis, structural characterisation, and biological activity.

    PubMed

    Ahmed, Riyadh M; Yousif, Enaam I; Al-Jeboori, Mohamad J

    2013-01-01

    New monomeric cobalt and cadmium complexes with Schiff-bases, namely, N'-[(E)-(3-hydroxy-4-methoxyphenyl)methylidene]furan-2-carbohydrazide (L¹) and N'-[(E)-(3-hydroxy-4-methoxyphenyl)methylidene]thiophene-2-carbohydrazide (L²) are reported. Schiff-base ligands L¹ and L² were derived from condensation of 3-hydroxy-4-methoxybenzaldehyde (iso-vanillin) with furan-2-carboxylic acid hydrazide and thiophene-2-carboxylic acid hydrazide, respectively. Complexes of the general formula [M(L)₂]Cl₂ (where M = Co(II) or Cd(II), L = L¹ or L²) have been obtained from the reaction of the corresponding metal chloride with the ligands. The ligands and their metal complexes were characterised by spectroscopic methods (FTIR, UV-Vis, ¹H, and ¹³C NMR spectra), elemental analysis, metal content, magnetic measurement, and conductance. These studies revealed the formation of four-coordinate complexes in which the geometry about metal ion is tetrahedral. Biological activity of the ligands and their metal complexes against gram positive bacterial strain Bacillus (G+) and gram negative bacteria Pseudomonas (G-) revealed that the metal complexes become less resistive to the microbial activities as compared to the free ligands.

  8. Selective ligands of estrogen receptor β discovered using pharmacophore mapping and structure-based virtual screening

    PubMed Central

    Chen, Lei; Wu, Dang; Bian, Han-ping; Kuang, Guang-lin; Jiang, Jing; Li, Wei-hua; Liu, Gui-xia; Zou, Shi-en; Huang, Jin; Tang, Yun

    2014-01-01

    Aim: To discover novel ligands of estrogen receptor (ER) β using pharmacophore mapping and structure-based screening. Methods: A computer-aided strategy combining pharmacophore mapping and structure-based screening was used to screen the Maybridge and Enamine databases. Yeast two-hybrid (Y2H) assay was used to detect the activity and selectivity of the chosen compounds. The transcriptional activities of the chosen compounds were demonstrated with luciferase reporter assays. The anti-proliferative effects of ER antagonists against MCF-7 and MDA-MB-231 breast cancer cells were examined using MTT assay, and the mechanisms of action were analyzed with flow cytometry analysis and Western blotting. Results: Through in silico screen, 95 compounds were chosen for testing in Y2H assay, which led to 20 potent ligands, including 10 agonists, 8 antagonists and 2 partial agonists with EC50 or IC50 values at μmol/L. Furthermore, 6 agonists exhibited absolute selectivity for ERβ, and 3 agonists showed higher selectivity for ERβ. The agonists 1g and 1h (10, 25, and 50 μmol/L) dose-dependently increased ER transcriptional activities, whereas the antagonists 2a and 2d (10, 25, and 50 μmol/L) caused dose-dependent inhibition on the activities. The antagonists and partial agonists at 100 μmol/L suppressed the proliferation of ERα positive MCF-7 cells and ERβ positive MDA-MB-231 cells, but were more effective against MDA-MB-231 cells. Treatment of MDA-MB-231 cells with antagonists 2a and 2d (25 and 50 μmol/L) dose-dependently increased the population of cells in the S phase. Both 2a and 2d treatment dose-dependently decreased the expression levels of cyclin A and CDK2. Meanwhile, the downregulation of cyclin E was only caused by 2d, while 2a treatment did not cause significant changes in the protein levels of cyclin E. Conclusion: The selective ligands discovered in this study are promising drug candidates to be used as molecular probes to explore the differences between ER

  9. Glycan-based high-affinity ligands for toxins and pathogen receptors.

    PubMed

    Kulkarni, Ashish A; Weiss, Alison A; Iyer, Suri S

    2010-03-01

    Glycans decorate over 95% of the mammalian cell surface in the form of glycolipids and glycoproteins. Several toxins and pathogens bind to these glycans to enter the cells. Understanding the fundamentals of the complex interplay between microbial pathogens and their glycan receptors at the molecular level could lead to the development of novel therapeutics and diagnostics. Using Shiga toxin and influenza virus as examples, we describe the complex biological interface between host glycans and these infectious agents, and recent strategies to develop glycan-based high-affinity ligands. These molecules are expected to ultimately be incorporated into diagnostics and therapeutics, and can be used as probes to study important biological processes. Additionally, by focusing on the specific glycans that microbial pathogens target, we can begin to decipher the "glycocode" and how these glycans participate in normal and aberrant cellular communication.

  10. A luminescent coordination polymer based on a π-conjugated ligand: Syntheses, structure and luminescent property

    NASA Astrophysics Data System (ADS)

    Li, Dan-Yang; Xie, Hua; Yao, Xiao-Qiang; Ma, Heng-Chang; Lei, Zi-Qiang; Liu, Jia-Cheng

    2017-04-01

    A new cadmium coordination polymer [Cd(DPFE)(adip)0.5(NO3)]n (1) has been synthesized hydrothermally from the self-assembly of the Cd2+ ion with a new π-conjugated rigid ligand DPFE and the adipic acid, where DPFE = 2,7-di(pyridin-4-yl)-9H-fluorene and H2adip = adipic acid. The structure of 1 was full characterized by elemental analysis, FT-IR spectroscopy and single crystal X-ray diffraction. Structural analysis reveals compound 1 is a dinuclear Cd(II) based two-dimensional (4,4) layer and two kinds of strong intramolecular π-π stacking interactions exist between pyridyl rings and benzene rings. In addition, the thermogravimetric analysis and solid-state luminescent properties have also been investigated.

  11. Vascular Stem/Progenitor Cell Migration Induced by Smooth Muscle Cell‐Derived Chemokine (C‐C Motif) Ligand 2 and Chemokine (C‐X‐C motif) Ligand 1 Contributes to Neointima Formation

    PubMed Central

    Yu, Baoqi; Wong, Mei Mei; Potter, Claire M. F.; Simpson, Russell M. L.; Karamariti, Eirini; Zhang, Zhongyi; Zeng, Lingfang; Warren, Derek; Hu, Yanhua

    2016-01-01

    Abstract Recent studies have shown that Sca‐1+ (stem cell antigen‐1) stem/progenitor cells within blood vessel walls may contribute to neointima formation, but the mechanism behind their recruitment has not been explored. In this work Sca‐1+ progenitor cells were cultivated from mouse vein graft tissue and found to exhibit increased migration when cocultured with smooth muscle cells (SMCs) or when treated with SMC‐derived conditioned medium. This migration was associated with elevated levels of chemokines, CCL2 (chemokine (C‐C motif) ligand 2) and CXCL1 (chemokine (C‐X‐C motif) ligand 1), and their corresponding receptors on Sca‐1+ progenitors, CCR2 (chemokine (C‐C motif) receptor 2) and CXCR2 (chemokine (C‐X‐C motif) receptor 2), which were also upregulated following SMC conditioned medium treatment. Knockdown of either receptor in Sca‐1+ progenitors significantly inhibited cell migration. The GTPases Cdc42 and Rac1 were activated by both CCL2 and CXCL1 stimulation and p38 phosphorylation was increased. However, only Rac1 inhibition significantly reduced migration and p38 phosphorylation. After Sca‐1+ progenitors labeled with green fluorescent protein (GFP) were applied to the adventitial side of wire‐injured mouse femoral arteries, a large proportion of GFP‐Sca‐1+‐cells were observed in neointimal lesions, and a marked increase in neointimal lesion formation was seen 1 week post‐operation. Interestingly, Sca‐1+ progenitor migration from the adventitia to the neointima was abrogated and neointima formation diminished in a wire injury model using CCL2−/− mice. These findings suggest vascular stem/progenitor cell migration from the adventitia to the neointima can be induced by SMC release of chemokines which act via CCR2/Rac1/p38 and CXCR2/Rac1/p38 signaling pathways. Stem Cells 2016;34:2368–2380 PMID:27300479

  12. Six new inorganic-organic hybrids based on rigid triangular ligands: Syntheses, structures and properties

    NASA Astrophysics Data System (ADS)

    Li, Na; Huang, Rudan

    2016-01-01

    Six new inorganic-organic hybrids based on rigid triangular N-containing ligands, NaCuI2(tib)4(H2O)4[H2PWVWVI11O40][H2PWVI12O40]·6H2O (1), CuII3(tib)4Cl4[H2PWVI12O40]2·4H2O (2), Co(tib)2[PWV3WVI9O38]·5H2O (3), CuII3(tib)2[P2MoVI5O22(O2)]·4H2O (4), Mn(pytpy)2MoVI4O13 (5) and Co(pytpy)2MoVI4O13 (6) (tib=1,3,5-tris(1-imidazolyl)benzene, pytpy=4'-(4"-pyridyl)2,4':6',4"-terpyridine), have been hydrothermally synthesized. Single crystal X-ray diffraction studies revealed that compounds 1-4 display two-dimensional (2D) layered structures, and in compounds 1-3, the adjacent Keggin anions link with each other by W-O-W covalent interactions to form 1D inorganic chains. Compounds 5-6 are 3D "pillar-layer" frameworks based on bimetal-oxide layers pillared by the pytpy ligands. The compounds have been characterized by elemental analysis, powder X-ray diffraction, X-ray photoelectron spectroscopy and thermo gravimetric analyses. Moreover, the electrochemical and catalytic properties of compound 1 have been investigated as well.

  13. Characterization of SynCAM surface trafficking using a SynCAM derived ligand with high homophilic binding affinity

    SciTech Connect

    Breillat, Christelle; Thoumine, Olivier; Choquet, Daniel . E-mail: Daniel.Choquet@pcs.u-bordeaux2.fr

    2007-08-03

    In order to better probe SynCAM function in neurons, we produced a fusion protein between the extracellular domain of SynCAM1 and the constant fragment of human IgG (SynCAM-Fc). Whether in soluble form or immobilized on latex microspheres, the chimera bound specifically to the surface of hippocampal neurons and recruited endogenous SynCAM molecules. SynCAM-Fc was also used in combination with Quantum Dots to follow the mobility of transfected SynCAM receptors at the neuronal surface. Both immobile and highly mobile SynCAM were found. Thus, SynCAM-Fc behaves as a high affinity ligand that can be used to study the function of SynCAM at the neuronal membrane.

  14. Specific erythrocyte binding capacity and biological activity of Plasmodium falciparum erythrocyte binding ligand 1 (EBL-1)-derived peptides

    PubMed Central

    Curtidor, Hernando; Rodríguez, Luis E.; Ocampo, Marisol; López, Ramses; García, Javier E.; Valbuena, John; Vera, Ricardo; Puentes, Álvaro; Vanegas, Magnolia; Patarroyo, Manuel E.

    2005-01-01

    Erythrocyte binding ligand 1 (EBL-1) is a member of the ebl multigene family involved in Plasmodium falciparum invasion of erythrocytes. We found that five EBL-1 high-activity binding peptides (HABPs) bound specifically to erythrocytes: 29895 (41HKKKSGELNNNKSGILRSTY60), 29903 (201LYECGK-KIKEMKWICTDNQF220), 29923 (601CNAILGSYADIGDIVRGLDV620), 29924(621WRDINTNKLSEK-FQKIFMGGY640), and 30018 (2481LEDIINLSKKKKKSINDTSFY2500). We also show that binding was saturable, not sialic acid-dependent, and that all peptides specifically bound to a 36-kDa protein on the erythrocyte membrane. The five HABPs inhibited in vitro merozoite invasion depending on the peptide concentration used, suggesting their possible role in the invasion process. PMID:15659376

  15. Silver complexes of ligands derived from adamantylamines: Water-soluble silver-donating compounds with antibacterial properties.

    PubMed

    Jimenez, Jorge; Chakraborty, Indranil; Rojas-Andrade, Mauricio; Mascharak, Pradip K

    2017-03-01

    Two new silver(I) complexes, namely [Ag(qyAm)2](CF3SO3) (1) and [Ag(qyTAm)2](CF3SO3) (2), (qyAm=2-(quinonyl)iminoadamantane, qyTAm=2-(quinonyl)iminotriazaadamantane) have been synthesized and characterized by elemental analyses, (1)H NMR, IR, electronic absorption spectroscopy, and X-ray diffraction. The coordination geometry of the silver center in both complexes is distorted tetrahedral where their respective qyAm and qyTAm ligand bind in a bidentate fashion using the imine and quinoline nitrogen atoms. Complex 2 is soluble in water and exhibits strong antimicrobial actions on both Gram-negative (E. coli, and P. aeruginosa) and Gram-positive (S. aureus) bacteria. The minimal inhibitory concentration (MIC) values for complex 2 (4, 4, and 8 μg for E. coli, P. aeruginosa, and S. aureus, respectively) are comparable to MIC values of silver nitrate and silver sulfadiazine.

  16. Structure-based virtual screening of small-molecule antagonists of platelet integrin αIIbβ3 that do not prime the receptor to bind ligand

    NASA Astrophysics Data System (ADS)

    Negri, Ana; Li, Jihong; Naini, Sarasija; Coller, Barry S.; Filizola, Marta

    2012-09-01

    Integrin αIIbβ3 has emerged as an important therapeutic target for thrombotic vascular diseases owing to its pivotal role in mediating platelet aggregation through interaction with adhesive ligands. In the search for effective anti-thrombotic agents that can be administered orally without inducing the high-affinity ligand binding state, we recently discovered via high-throughput screening of 33,264 compounds a novel, αIIbβ3-selective inhibitor (RUC-1) of adenosine-5'-diphosphate (ADP) -induced platelet aggregation that exhibits a different chemical scaffold and mode of binding with respect to classical Arg-Gly-Asp (RGD)-mimicking αIIbβ3 antagonists. Most importantly, RUC-1 and its higher-affinity derivative, RUC-2, do not induce major conformational changes in the protein β3 subunit or prime the receptor to bind ligand. To identify additional αIIbβ3-selective chemotypes that inhibit platelet aggregation through similar mechanisms, we screened in silico over 2.5 million commercially available, `lead-like' small molecules based on complementarity to the predicted binding mode of RUC-2 into the RUC-1-αIIbβ3 crystal structure. This first reported structure-based virtual screening application to the αIIbβ3 integrin led to the identification of 2 αIIbβ3-selective antagonists out of 4 tested, which compares favorably with the 0.003 % "hit rate" of our previous high-throughput chemical screening study. The newly identified compounds, like RUC-1 and RUC-2, showed specificity for αIIbβ3 compared to αVβ3 and did not prime the receptor to bind ligand. They thus may hold promise as αIIbβ3 antagonist therapeutic scaffolds.

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

    PubMed Central

    Rubina, Marina; Sherrill, William M; Barkov, Alexey Yu

    2014-01-01

    Summary A novel class of chiral phosphanyl-oxazoline (PHOX) ligands with a conformationally rigid cyclopropyl backbone was synthesized and tested in the intermolecular asymmetric Heck reaction. Mechanistic modelling and crystallographic studies were used to predict the optimal ligand structure and helped to design a very efficient and highly selective catalytic system. Employment of the optimized ligands in the asymmetric arylation of cyclic olefins allowed for achieving high enantioselectivities and significantly suppressing product isomerization. Factors affecting the selectivity and the rate of the isomerization were identified. It was shown that the nature of this isomerization is different from that demonstrated previously using chiral diphosphine ligands. PMID:25161709

  18. Production and Evaluation of Antibodies and Phage Display-Derived Peptide Ligands for Immunomagnetic Separation of Mycobacterium bovis

    PubMed Central

    Stewart, Linda D.; McNair, James; McCallan, Lyanne; Thompson, Suzan; Kulakov, Leonid A.

    2012-01-01

    This study describes the development and optimization of an immunomagnetic separation (IMS) method to isolate Mycobacterium bovis cells from lymph node tissues. Gamma-irradiated whole M. bovis AF2122/97 cells and ethanol-extracted surface antigens of such cells were used to produce M. bovis-specific polyclonal and monoclonal antibodies in rabbits and mice. They were also used to generate M. bovis-specific peptide ligands by phage display biopanning. The various antibodies and peptide ligands obtained were used to coat MyOne tosyl-activated Dynabeads (Life Technologies), singly or in combination, and evaluated for IMS. Initially, M. bovis capture from Middlebrook 7H9 broth suspensions (concentration range, 10 to 105 CFU/ml) was evaluated by IMS combined with an M. bovis-specific touchdown PCR. IMS-PCR results and, subsequently, IMS-culture results indicated that the beads with greatest immunocapture capability for M. bovis in broth were those coated simultaneously with a monoclonal antibody and a biotinylated 12-mer peptide. These dually coated beads exhibited minimal capture (mean of 0.36% recovery) of 12 other Mycobacterium spp. occasionally encountered in veterinary tuberculosis (TB) diagnostic laboratories. When the optimized IMS method was applied to various M. bovis-spiked lymph node matrices, it demonstrated excellent detection sensitivities (50% limits of detection of 3.16 and 57.7 CFU/ml of lymph node tissue homogenate for IMS-PCR and IMS-culture, respectively). The optimized IMS method therefore has the potential to improve isolation of M. bovis from lymph nodes and hence the diagnosis of bovine tuberculosis. PMID:22322353

  19. Ligand-based computer-aided pesticide design. A review of applications of the CoMFA and CoMSIA methodologies.

    PubMed

    Bordás, Barna; Komíves, Tamás; Lopata, Antal

    2003-04-01

    An overview is given of the CoMFA (comparative molecular field analysis) and CoMSIA (comparative molecular similarity indices analysis) methodologies that are established ligand-based molecular design tools widely used by medicinal and pesticide chemists. In the absence of a three-dimensional structure of the target biopolymer, CoMFA and CoMSIA often provide a practical solution to an otherwise intractable problem of proper characterization of ligand-receptor interactions. These techniques are especially important in agrochemistry, where the number of known molecular structures of pesticide targets is limited. The use of CoMFA and CoMSIA in the agrochemical field for modelling the interactions of insecticides, fungicides, herbicides and herbicide safeners with their target binding sites is illustrated by using some selected published work. The CoMFA and CoMSIA models developed have been used successfully to map the properties of unknown receptors, construct hypotheses for ligand-receptor interactions, optimize lead structures, design novel active compounds, and predict biological activities. The application of CoMFA by the present authors for deriving a binding site hypothesis for dichloroacetamide-type herbicide safeners is described in somewhat more detail.

  20. Insights into the oxygen-based ligand of the low pH component of the Cu(2+)-amyloid-β complex.

    PubMed

    Gomez-Castro, Carlos Z; Vela, Alberto; Quintanar, Liliana; Grande-Aztatzi, Rafael; Mineva, Tzonka; Goursot, Annick

    2014-08-28

    In spite of significant experimental effort dedicated to the study of Cu(2+) binding to the amyloid beta (Aβ) peptide, involved in Alzheimer's disease, the nature of the oxygen-based ligand in the low pH component of the Cu(2+)-Aβ(1-16) complex is still under debate. This study reports density-functional-theory-based calculations that explore the potential energy surface of Cu(2+) complexes including N and O ligands at the N-terminus of the Aβ peptide, with a focus on evaluating the role of Asp1 carboxylate in copper coordination. Model conformers including 3, 6, and 17 amino acids have been used to systematically study several aspects of the Cu(2+)-coordination such as the Asp1 side chain conformation, local peptide backbone geometry, electrostatic and/or hydrogen bond interactions, and number and availability of Cu(2+) ligands. Our results show that the Asp1 peptide carbonyl binds to Cu(2+) only if the coordination number is less than four. In contrast, if four ligands are available, the most stable structures include the Asp1 carboxylate in equatorial position instead of the Asp1 carbonyl group. The two lowest energy Cu(2+)-Aβ(1-17) models involve Asp1 COO(-), the N-terminus, and His6 and His14 as equatorial ligands, with either a carbonyl or a water molecule in the axial position. These models are in good agreement with experimental data reported for component I of the Cu(2+)-Aβ(1-16) complex, including EXAFS- and X-ray-derived Cu(2+)-ligand distances, Cu(2+) EPR parameters, and (14)N and (13)C superhyperfine couplings. Our results suggest that at low pH, Cu(2+)-Aβ species with Asp1 carboxylate equatorial coordination coexist with species coordinating the Asp1 carbonyl. Understanding the bonding mechanism in these species is relevant to gain a deeper insight on the molecular processes involving copper-amyloid-β complexes, such as aggregation and redox activity.

  1. Decreased overall basicity of a series of new N,N'-bis(carboxymethyl) macrocylcic ether-bis(lactone) ligands derived from EDTA and the ring size effect on the stability constants of their lanthanide complexes

    SciTech Connect

    Chang, C.A.; Chang, P.H.L.; Qin, S.Y.

    1988-03-09

    In order to examine the effects of positions of the nitrogen donor atoms and the relative coordination sites of the two carboxylate groups on lanthanide complexation in the study of the characteristics of both open-chain and macrocyclic ligands for the preparation of novel metal-ion selective reagents, a series of N, N'-bis(carboxymethyl)macrocyclic ether-bis(lactone)ligands derived from ethylenediaminetetraacetic acid have been prepared and characterized. The ligand protonation constants and the lanthanide complex formation constants have been determined and are reported here. 14 references, 2 figures, 2 tables.

  2. Structural protein-ligand interaction fingerprints (SPLIF) for structure-based virtual screening: method and benchmark study.

    PubMed

    Da, C; Kireev, D

    2014-09-22

    Accurate and affordable assessment of ligand-protein affinity for structure-based virtual screening (SB-VS) is a standing challenge. Hence, empirical postdocking filters making use of various types of structure-activity information may prove useful. Here, we introduce one such filter based upon three-dimensional structural protein-ligand interaction fingerprints (SPLIF). SPLIF permits quantitative assessment of whether a docking pose interacts with the protein target similarly to a known ligand and rescues active compounds penalized by poor initial docking scores. An extensive benchmark study on 10 diverse data sets selected from the DUD-E database has been performed in order to evaluate the absolute and relative efficiency of this method. SPLIF demonstrated an overall better performance than relevant standard methods.

  3. Antioxidant, electrochemical, thermal, antimicrobial and alkane oxidation properties of tridentate Schiff base ligands and their metal complexes

    NASA Astrophysics Data System (ADS)

    Ceyhan, Gökhan; Çelik, Cumali; Uruş, Serhan; Demirtaş, İbrahim; Elmastaş, Mahfuz; Tümer, Mehmet

    2011-10-01

    In this study, two Schiff base ligands (HL 1 and HL 2) and their Cu(II), Co(II), Ni(II), Pd(II) and Ru(III) metal complexes were synthesized and characterized by the analytical and spectroscopic methods. Alkane oxidation activities of the metal complexes were studied on cyclohexane as substrate. The ligands and their metal complexes were evaluated for their antimicrobial activity against Corynebacterium xerosis, Bacillus brevis, Bacillus megaterium, Bacillus cereus, Mycobacterium smegmatis, Staphylococcus aureus, Micrococcus luteus and Enterococcus faecalis (as Gram-positive bacteria) and Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli, Yersinia enterocolitica, Klebsiella fragilis, Saccharomyces cerevisiae, and Candida albicans (as Gram-negative bacteria). The antioxidant properties of the Schiff base ligands were evaluated in a series of in vitro tests: 1,1-diphenyl-2-picrylhydrazyl (DPPH rad ) free radical scavenging and reducing power activity of superoxide anion radical generated non-enzymatic systems. Electrochemical and thermal properties of the compounds were investigated.

  4. Fluorinated Carbohydrates as Lectin Ligands: 19F-Based Direct STD Monitoring for Detection of Anomeric Selectivity

    PubMed Central

    Ribeiro, João P.; Diercks, Tammo; Jiménez-Barbero, Jesús; André, Sabine; Gabius, Hans-Joachim; Cañada, Francisco Javier

    2015-01-01

    The characterization of the binding of reducing carbohydrates present as mixtures of anomers in solution to a sugar recepor (lectin) poses severe difficulties. In this situation, NMR spectroscopy enables the observation of signals for each anomer in the mixture by applying approaches based on ligand observation. Saturation transfer difference (STD) NMR allows fast and efficient screening of compound mixtures for reactivity to a receptor. Owing to the exceptionally favorable properties of 19F in NMR spectroscopy and the often complex 1H spectra of carbohydrates, 19F-containing sugars have the potential to be turned into versatile sensors for recognition. Extending the recently established 1H → 1H STDre19F-NMR technique, we here demonstrate its applicability to measure anomeric selectivity of binding in a model system using the plant lectin concanavalin A (ConA) and 2-deoxy-2-fluoro-d-mannose. Indeed, it is also possible to account for the mutual inhibition between the anomers on binding to the lectin by means of a kinetic model. The monitoring of 19F-NMR signal perturbation disclosed the relative activities of the anomers in solution and thus enabled the calculation of their binding affinity towards ConA. The obtained data show a preference for the α anomer that increases with temperature. This experimental approach can be extended to others systems of biomedical interest by testing human lectins with suitably tailored glycan derivatives. PMID:26580665

  5. Derivation of a Retinoid X Receptor Scaffold from Peroxisome Proliferator-Activated Receptor γ Ligand 1-Di(1H-indol-3-yl)methyl-4-trifluoromethylbenzene

    PubMed Central

    Dawson, Marcia I.; Ye, Mao; Cao, Xihua; Farhana, Lulu; Hu, Qiong-Ying; Zhao, Yong; Xu, Li Ping; Kiselyuk, Alice; Correa, Ricardo G.; Yang, Li; Hou, Tingjun; Reed, John C.; Itkin-Ansari, Pamela; Levine, Fred; Sanner, Michel F.; Fontana, Joseph A.; Zhang, Xiao-Kun

    2010-01-01

    1-Di(1H-indol-3-yl)methyl-4-trifluoromethylbenzene (DIM-Ph-4-CF3) is reported to inhibit cancer cell growth and to act as a transcriptional agonist of peroxisome proliferator-activated receptor γ (PPARγ) and nuclear receptor 4A subfamily member 1 (NR4A1). In addition, DIM-Ph-4-CF3 exerts anticancer effects independent of these receptors because PPARγ antagonists do not block its inhibition of cell growth, and the small pocket in the NR4A1 crystal structure suggests no ligand can bind. Because PPARγ and NR4A1 heterodimerize with retinoid X receptor (RXR), and several PPARγ ligands transcriptionally activate RXR, DIM-Ph-4-CF3 was investigated as an RXR ligand. DIM-Ph-4-CF3 displaces 9-cis-retinoic acid from RXRα but does not transactivate RXRα. Structure-based design using DIM-Ph-4-CF3 as a template led to the RXRα transcriptional agonist (E)-3-[5-di(1-methyl-1H-indol-3-yl)methyl-2-thienyl]acrylic acid. Its docked pose in the RXRα ligand binding domain suggests that binding is stabilized by interactions of its carboxylate group with arginine 316, its indoles with cysteines 269 and 432, and its 1-methyl groups with hydrophobic residues lining the binding pocket. As is expected of a selective activator of RXRα, but not of RARs and PPARγ, this RXRα agonist, unlike DIM-Ph-4-CF3, does not appreciably decrease cancer cell growth or induce apoptosis at pharmacologically relevant concentrations. PMID:19378296

  6. Implementing relevance feedback in ligand-based virtual screening using Bayesian inference network.

    PubMed

    Abdo, Ammar; Salim, Naomie; Ahmed, Ali

    2011-10-01

    Recently, the use of the Bayesian network as an alternative to existing tools for similarity-based virtual screening has received noticeable attention from researchers in the chemoinformatics field. The main aim of the Bayesian network model is to improve the retrieval effectiveness of similarity-based virtual screening. To this end, different models of the Bayesian network have been developed. In our previous works, the retrieval performance of the Bayesian network was observed to improve significantly when multiple reference structures or fragment weightings were used. In this article, the authors enhance the Bayesian inference network (BIN) using the relevance feedback information. In this approach, a few high-ranking structures of unknown activity were filtered from the outputs of BIN, based on a single active reference structure, to form a set of active reference structures. This set of active reference structures was used in two distinct techniques for carrying out such BIN searching: reweighting the fragments in the reference structures and group fusion techniques. Simulated virtual screening experiments with three MDL Drug Data Report data sets showed that the proposed techniques provide simple ways of enhancing the cost-effectiveness of ligand-based virtual screening searches, especially for higher diversity data sets.

  7. Optoelectronic Properties of Color-Tunable Mixed Ligand-Based Light-Emitting Zinc Complexes

    NASA Astrophysics Data System (ADS)

    Singh, Devender; Bhagwan, Shri; Saini, Raman Kumar; Tanwar, Vijeta; Nishal, Vandna

    2016-10-01

    A series of mixed ligand-based zinc complexes (Zn1-Zn5); [(8-hydroxyquinolinato)(2-(2-hydroxyphenyl)benzimidazolato)zinc(II)] (Zn1), [(5-chloro-8-hydroxyquinolinato)(2-(2-hydroxyphenyl)benzimidazolato)zinc(II)] (Zn2), [(5,7-dichloro-8-hydroxyquinolinato)(2-(2-hydroxyphenyl)benzimidazolato)zinc(II)] (Zn3), [(2-methyl-8-hydroxyquinolinato)(2-(2-hydroxyphenyl)benzimidazolato)zinc(II)] (Zn4) and [(5,7-dimethyl-8-hydroxyquinolinato)(2-(2-hydroxyphenyl)benzimidazolato)zinc(II)] (Zn5) were synthesized and characterized. The photophysical properties of zinc complexes were examined by ultraviolet-visible absorption and photoluminescence emission spectroscopy. All prepared metal complexes produced intense luminescence on excitation with a UV light source. In this study, the color-tunable characteristics of metal complexes were investigated by introducing the electron-donating and electron-withdrawing groups on the 8-hydroxyquinoline ligand. The emission spectra of metal complexes showed emission wavelength at 500 nm for [ZnHBI(q)], 509 nm for [ZnHBI(Clq)], 504 nm for [Zn(HBI)(Cl2q)], 496 nm for [ZnHBI (Meq)] and 573 nm for [ZnHBI(Me2Q)] materials. A temperature-dependent PL spectrum was used to study the emission profile of zinc complex and observed that variation in the temperature altered the position and the intensity of emission peak. The synthesized metal complex also exhibited good thermal stability (>300°C). Photophysical characteristics of color-tunable light-emitting zinc complexes suggested that these materials could be efficiently used for emissive display device applications.

  8. A new iron(III) complex of glycine derivative of amine-chloro substituted phenol ligand: Synthesis, characterization and catechol dioxygenase activity

    NASA Astrophysics Data System (ADS)

    Saberikia, Iraj; Safaei, Elham; Kowsari, Mohammad Hossein; Lee, Yong-Ill; Cotic, Patricia; Bruno, Giuseppe; Rudbari, Hadi Amiri

    2012-12-01

    A new iron(III) complex of the glycine derivative of amine-chloro substituted phenol ligand (H3LGDC) has been prepared and characterized by IR, 1H NMR, UV-Vis spectroscopic techniques, cyclic voltammetry, ESI-MS and magnetic susceptibility studies. X-ray analysis reveals that in iron complex of FeLGDC the iron(III) center has a distorted trigonal bipyramidal coordination sphere and is surrounded by an amine nitrogen, a carboxylate, a water and two phenolate oxygen atoms. The DFT calculations with the UB3LYP/6-311++G** level optimized structure of the complex are in good agreement with experimental X-ray structural data. The variable-temperature magnetic susceptibility indicates that FeLGDC is the paramagnetic high spin iron(III) complex. It has been shown that electrochemical oxidation of this complex is ligand-centered due to the oxidation of phenolate to the phenoxyl radicals. This enzyme mimic utilized molecular oxygen in carrying out the oxidative cleavage of catechols with complete conversion at room temperature.

  9. Structural and thermodiffractometric analysis of coordination polymers. Part I: tin 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. [Bim(Me2SnCl2)]n (1), [Bim(nBu2SnCl2)]n (3), [Bim(Ph2SnCl2)]n (4), [Bim(MeSnCl3)]n (5), and [Bim(PhSnCl3)]n (6) all contain 1D chains with octahedral tin atoms with trans N-Sn-N linkages (but 4, which displays a cis N-Sn-N linkage). Their thermodiffractometric analysis allowed the estimation of the linear thermal expansion coefficients and strain tensors derived there from. The potential-energy surface of the free Bim ligand (as defined by two torsional degrees of freedom about the two N-CH2 bonds), eventually controlling the length of the repeating unit (polymer elongation), has been estimated using molecular mechanics and correlated with experimental observations.

  10. Ruthenium-based olefin metathesis catalysts bearing pH-responsive ligands: External control of catalyst solubility and activity

    NASA Astrophysics Data System (ADS)

    Balof, Shawna Lynn

    2011-12-01

    Sixteen novel, Ru-based olefin metathesis catalysts bearing pH responsive ligands were synthesized. The pH-responsive groups employed with these catalysts included dimethylamino (NMe2) modified NHC ligands as well as N-donor dimethylaminopyridine (DMAP) and 3-(o-pyridyl)propylidene ligands. These pH-responsive ligands provided the means by which the solubility and/or activity profiles of the catalysts produced could be controlled via acid addition. The main goal of this dissertation was to design catalyst systems capable of performing ring opening metathesis (ROMP) and ring closing metathesis (RCM) reactions in both organic and aqueous media. In an effort to quickly gain access to new catalyst structures, a template synthesis for functionalized NHC ligand precursors was designed, in addition to other strategies, to obtain ligand precursors with ancillary NMe2 groups. Kinetic studies for the catalysts produced from these precursors showed external control of catalyst solubility was afforded via protonation of the NMe2 groups of their NHC ligands. Additionally, this protonation afforded external control of catalyst propagation rates for several catalysts. This is the first known independent external control for the propagation rates of ROMP catalysts. The incorporation of pH-responsive N-donor ligands into catalyst structures also provided the means for the external control of metathesis activity, as the protonation of these ligands resulted in an increased initiation rate based on their fast and irreversible dissociation from the metal center. The enhanced external control makes these catalysts applicable to a wide range of applications, some of which have been explored by us and/or through collaboration. Three of the catalysts designed showed remarkable metathesis activity in aqueous media. These catalysts displayed comparable RCM activity in aqueous media to a class of water-soluble catalysts reported by Grubbs et al., considered to be the most active catalyst for

  11. Molecular Bases for the Regulation of NKG2D Ligands in Cancer

    PubMed Central

    Huergo-Zapico, Leticia; Acebes-Huerta, Andrea; López-Soto, Alejandro; Villa-Álvarez, Mónica; Gonzalez-Rodriguez, Ana Pilar; Gonzalez, Segundo

    2014-01-01

    NKG2D is an activating receptor expressed by NK and T cells primarily involved in the elimination of transformed and infected cells. NKG2D ligands are self-proteins restrictedly expressed in healthy tissues, but induced in response to signaling pathways commonly associated with transformation. Proliferative, tumor suppressor, and stress signaling pathways linked to the tumorigenic process induce the expression of NKG2D ligands, initiating an immune response against the incipient tumor. Nevertheless, the activity of NKG2D ligands is counter-regulated in vivo by the immunoediting of cancer cells, resulting in the expression of multiple mechanisms of immune evasion in advanced tumors. The redundancy of NKG2D ligands, besides increasing the complexity of their regulation, may impair the generation of these immune evasion mechanisms. In this review, we attempt to integrate the mechanisms and pathways involved in the regulation of NKG2D ligand expression in cancer. PMID:24711808

  12. Self-assembly synthesis, structural features, and photophysical properties of dilanthanide complexes derived from a novel amide type ligand: energy transfer from Tb(III) to Eu(III) in a heterodinuclear derivative.

    PubMed

    Gao, Cunji; Kirillov, Alexander M; Dou, Wei; Tang, Xiaoliang; Liu, Liangliang; Yan, Xuhuan; Xie, Yujie; Zang, Peixian; Liu, Weisheng; Tang, Yu

    2014-01-21

    A novel amide type ligand benzyl-N,N-bis[(2'-furfurylaminoformyl)phenoxyl)ethyl]-amine (L) has been designed and applied for the self-assembly generation of homodinuclear lanthanide coordination compounds [Ln2(μ2-L)2(NO3)6(EtOH)2] [Ln = Eu (1), Tb (2), and Gd (3)] and a heterodinuclear derivative [EuTb(μ2-L)2(NO3)6(EtOH)2] (4). All the complexes have been characterized by the X-ray single-crystal diffraction analyses. They are isostructural, crystallize in a monoclinic space group P21/c, and form [2 + 2] rectangular macrocycle structures. Compound 4 is the first example of a [2 + 2] rectangular macrocycle heterodinuclear EuTb complex assembled from an amide type ligand. In 4, the discrete 0D dimeric [EuTb(μ2-L)2(NO3)6(EtOH)2] units are extended, via the multiple N-H···O hydrogen bonds, into a 2D supramolecular network that has been topologically classified as a uninodal 4-connected underlying net with the sql [Shubnikov tetragonal plane net] topology. The triplet state ((3)ππ*) of L studied by the Gd(III) complex 3 demonstrated that the ligand beautifully populates Tb(III) emission (Φ = 52%), whereas the corresponding Eu(III) derivative 1 shows weak luminescence efficiency (Φ = 0.7%) because the triplet state of L has a poor match with (5)D1 energy level of Eu(III). Furthermore, the photoluminescent properties of heterodinuclear complex 4 have been compared with those of the analogous homodinuclear compounds. The quantum yield and lifetime measurements prove that energy transfer from Tb(III) to Eu(III) is being achieved, namely, that the Tb(III) center is also acting to sensitize the Eu(III) and enhancing Eu(III) emission in 4.

  13. Overcoming the aggregation problem: a new type of fluorescent ligand for ConA-based glucose sensing.

    PubMed

    Cummins, Brian M; Li, Mingchien; Locke, Andrea K; Birch, David J S; Vigh, Gyula; Coté, Gerard L

    2015-01-15

    Competitive binding assays based on the lectin Concanavalin A (ConA) have displayed significant potential to serve in continuous glucose monitoring applications. However, to date, this type of fluorescent, affinity-based assay has yet to show the stable, glucose predictive capabilities that are required for such an application. This instability has been associated with the extensive crosslinking between traditionally-used fluorescent ligands (presenting multiple low-affinity moieties) and ConA (presenting multiple binding sites) in free solution. The work herein introduces the design and synthesis of a new type of fluorescent ligand that can avoid this aggregation and allow the assay to be sensitive across the physiologically relevant glucose concentration range. This fluorescent ligand (APTS-MT) presents a single high-affinity trimannose moiety that is recognized by ConA's full binding site and a fluorophore that can effectively track the ligand's equilibrium binding via fluorescent anisotropy. This is confirmed by comparing its measured fluorescent lifetime to experimentally-determined rotational correlation lifetimes of the free and bound populations. Using an assay comprised of 200 nM APTS-MT and 1 µM ConA, the fluorescence anisotropy capably tracks the concentration of monosaccharides that are known to bind to ConA's primary binding site, and the assay displays a MARD of 6.5% across physiologically relevant glucose concentrations. Ultimately, this rationally-designed fluorescent ligand can facilitate the realization of the full potential of ConA-based glucose sensing assays and provide the basis for a new set of competing ligands to be paired with ConA.

  14. Ligand-induced folding of the thiM TPP riboswitch investigated by a structure-based fluorescence spectroscopic approach

    PubMed Central

    Lang, Kathrin; Rieder, Renate; Micura, Ronald

    2007-01-01

    Riboswitches are genetic control elements within non-coding regions of mRNA. They consist of a metabolite-sensitive aptamer and an adjoining expression platform. Here, we describe ligand-induced folding of a thiamine pyrophosphate (TPP) responsive riboswitch from Escherichia coli thiM mRNA, using chemically labeled variants. Referring to a recent structure determination of the TPP/aptamer complex, each variant was synthesized with a single 2-aminopurine (AP) nucleobase replacement that was selected to monitor formation of tertiary interactions of a particular region during ligand binding in real time by fluorescence experiments. We have determined the rate constants for conformational adjustment of the individual AP sensors. From the 7-fold differentiation of these constants, it can be deduced that tertiary contacts between the two parallel helical domains (P2/J3-2/P3/L3 and P4/P5/L5) that grip the ligand's ends in two separate pockets, form significantly faster than the function-critical three-way junction with stem P1 fully developed. Based on these data, we characterize the process of ligand binding by an induced fit of the RNA and propose a folding model of the TPP riboswitch aptamer. For the full-length riboswitch domain and for shorter constructs that represent transcriptional intermediates, we have additionally evaluated ligand-induced folding via AP-modified variants and provide insights into the sequential folding pathway that involves a finely balanced equilibrium of secondary structures. PMID:17693433

  15. WONKA and OOMMPPAA: analysis of protein–ligand interaction data to direct structure-based drug design

    PubMed Central

    Deane, Charlotte M.; Wall, Ian D.; Green, Darren V. S.; Marsden, Brian D.; Bradley, Anthony R.

    2017-01-01

    In this work, two freely available web-based interactive computational tools that facilitate the analysis and interpretation of protein–ligand interaction data are described. Firstly, WONKA, which assists in uncovering interesting and unusual features (for example residue motions) within ensembles of protein–ligand structures and enables the facile sharing of observations between scientists. Secondly, OOMMPPAA, which incorporates protein–ligand activity data with protein–ligand structural data using three-dimensional matched molecular pairs. OOMMPPAA highlights nuanced structure–activity relationships (SAR) and summarizes available protein–ligand activity data in the protein context. In this paper, the background that led to the development of both tools is described. Their implementation is outlined and their utility using in-house Structural Genomics Consortium (SGC) data sets and openly available data from the PDB and ChEMBL is described. Both tools are freely available to use and download at http://wonka.sgc.ox.ac.uk/WONKA/ and http://oommppaa.sgc.ox.ac.uk/OOMMPPAA/. PMID:28291763

  16. Base-modified nucleosides: etheno derivatives

    NASA Astrophysics Data System (ADS)

    Jahnz-Wechmann, Zofia; Framski, Grzegorz; Januszczyk, Piotr; Boryski, Jerzy

    2016-04-01

    This review presents synthesis and chemistry of nucleoside analogs, possessing an additional fused, heterocyclic ring of the “etheno” type, such as 1,N6-ethenoadenosine, 1,N4-ethenocytidine, 1,N2-ethenoguanosine, and other related derivatives. Formation of ethenonucleosides, in the presence of α-halocarbonyl reagents and their mechanism, stability and degradation, reactions of substitution and transglycosylation, as well as their application in the nucleoside synthesis, have been described. Some of the discussed compounds may be applied as chemotherapeutic agents in antiviral and anticancer treatment, acting as pro-nucleosides of already known, biologically active nucleoside analogs..

  17. A knowledge-based weighting approach to ligand-based virtual screening.

    PubMed

    Stiefl, Nikolaus; Zaliani, Andrea

    2006-01-01

    On the basis of the recently introduced reduced graph concept of ErG (extending reduced graphs), a straightforward weighting approach to include additional (e.g., structural or SAR) knowledge into similarity searching procedures for virtual screening (wErG) is proposed. This simple procedure is exemplified with three data sets, for which interaction patterns available from X-ray structures of native or peptidomimetic ligands with their target protein are used to significantly improve retrieval rates of known actives from the MDL Drug Report database. The results are compared to those of other virtual screening techniques such as Daylight fingerprints, FTrees, UNITY, and various FlexX docking protocols. Here, it is shown that wErG exhibits a very good and stable performance independent of the target structure. On the basis of this (and the fact that ErG retrieves structurally more dissimilar compounds due to its potential to perform scaffold-hopping), the combination of wErG and FlexX is successfully explored. Overall, wErG is not only an easily applicable weighting procedure that efficiently identifies actives in large data sets but it is also straightforward to understand for both medicinal and computational chemists and can, therefore, be driven by several aspects of project-related knowledge (e.g., X-ray, NMR, SAR, and site-directed mutagenesis) in a very early stage of the hit identification process.

  18. Synthesis and reactivity of cationic triruthenium clusters derived from 2-methyl- and 4-methylpyrimidines: from conventional cyclometalated ligands to novel types of N-heterocyclic carbenes.

    PubMed

    Cabeza, Javier A; García-Álvarez, Pablo; Pérez-Carreño, Enrique; Pruneda, Vanessa

    2013-03-04

    The methylation of the uncoordinated nitrogen atom of the cyclometalated triruthenium cluster complexes [Ru(3)(μ-H)(μ-κ(2)N(1),C(6)-2-Mepyr)(CO)(10)] (1; 2-MepyrH = 2-methylpyrimidine) and [Ru(3)(μ-H)(μ-κ(2)N(1),C(6)-4-Mepyr)(CO)(10)] (9; 4-MepyrH = 4-methylpyrimidine) gives two similar cationic complexes, [Ru(3)(μ-H)(μ-κ(2)N(1),C(6)-2,3-Me(2)pyr)(CO)(10)](+) (2(+)) and [Ru(3)(μ-H)(μ-κ(2)N(1),C(6)-3,4-Me(2) pyr)(CO)(10)](+) (9(+)), respectively, whose heterocyclic ligands belong to a novel type of N-heterocyclic carbenes (NHCs) that have the C(carbene) atom in 6-position of a pyrimidine framework. The position of the C-methyl group in the ligands of complexes 2(+) (on C(2)) and 9(+) (on C(4)) is of key importance for the outcome of their reactions with K[N(SiMe(3))(2)], K-selectride, and cobaltocene. Although these reagents react with 2(+) to give [Ru(3)(μ-H)(μ-κ(2)N(1),C(6)-2-CH(2)-3-Mepyr)(CO)(10)] (3; deprotonation of the C(2)-Me group), [Ru(3)(μ-H)(μ(3)-κ(3)N(1),C(5),C(6)-4-H-2,3-Me(2)pyr)(CO)(9)] (4; hydride addition at C(4)), and [Ru(6)(μ-H)(2){μ(6)-κ(6) N(1),N(1'),C(5),C(5'),C(6),C(6')-4,4'-bis(2,3-Me(2)pyr)}(CO)(18)] (5; reductive dimerization at C(4)), respectively, similar reactions with 9(+) have only allowed the isolation of [Ru(3)(μ-H)(μ(3)-κ(2)N(1),C(6)-2-H-3,4-Me(2)pyr)(CO)(9)] (11; hydride addition at C(2)). Compounds 3 and 11 also contain novel six-membered ring NHC ligands. Theoretical studies have established that the deprotonation of 2(+) and 9(+) (that have ligand-based LUMOs) are charge-controlled processes and that both the composition of the LUMOs of these cationic complexes and the steric protection of their ligand ring atoms govern the regioselectivity of their nucleophilic addition and reduction reactions.

  19. Base ionization and ligand binding: how small ribozymes and riboswitches gain a foothold in a protein world.

    PubMed

    Liberman, Joseph A; Wedekind, Joseph E

    2011-06-01

    Genome sequencing has produced thousands of nonprotein coding (nc)RNA sequences including new ribozymes and riboswitches. Such RNAs are notable for their extraordinary functionality, which entails exquisite folding that culminates in biocatalytic or ligand-binding capabilities. Here we discuss advances in relating ncRNA form to function with an emphasis on base pK(a) shifting by the hairpin and hepatitis delta virus ribozymes. We then describe ligand binding by the two smallest riboswitches, which target preQ(1) and S-adenosyl-(l)-homocysteine, followed by an analysis of a second-messenger riboswitch that binds cyclic-di-GMP. Each riboswitch is then compared to a protein that binds the same ligand to contrast binding properties. The results showcase the breadth of functionality attainable from ncRNAs, as well as molecular features notable for antibacterial design.

  20. Synthesis and catalytic activity of heterogeneous rare-earth metal catalysts coordinated with multitopic Schiff-base ligands.

    PubMed

    Sun, Yilin; Wu, Guangming; Cen, Dinghai; Chen, Yaofeng; Wang, Limin

    2012-08-28

    Four multitopic Schiff-base ligand precursors were synthesized via condensation of 4,4'-diol-3,3'-diformyl-1,1'-diphenyl or 1,3,5-tris(4-hydroxy-5-formylphenyl)benzene with 2,6-diisopropylaniline or 2,6-dimethylaniline. Amine elimination reactions of Ln[N(SiMe(3))(2)](3) (Ln = La, Nd, Sm or Y) with these multitopic ligand precursors gave ten heterogeneous rare-earth metal catalysts. These heterogeneous rare-earth metal catalysts are active for intramolecular hydroalkoxylation of alkynols, and the catalytic activities are influenced by the ligand and metal ion. The recycling experiment on the most active heterogeneous catalyst showed the catalyst has a good reusability.

  1. Luminescent liquid crystalline materials based on palladium(II) imine derivatives containing the 2-phenylpyridine core.

    PubMed

    Micutz, Marin; Iliş, Monica; Staicu, Teodora; Dumitraşcu, Florea; Pasuk, Iuliana; Molard, Yann; Roisnel, Thierry; Cîrcu, Viorel

    2014-01-21

    In this work we report our studies concerning the synthesis and characterisation of a series of imine derivatives that incorporate the 2-phenylpyridine (2-ppy) core. These derivatives were used in the cyclometalating reactions of platinum(II) or palladium(II) in order to prepare several complexes with liquid crystalline properties. Depending on the starting materials used as well as the solvents employed, different metal complexes were obtained, some of them showing both liquid crystalline behaviour and luminescence properties at room temperature. It was found that, even if there are two competing coordination sites, the cyclometalation process takes place always at the 2-ppy core with (for Pt) or without (for Pd) the imine bond cleavage. We successfully showed that it is possible to prepare emissive room temperature liquid crystalline materials based on double cyclopalladated heteroleptic complexes by varying the volume fraction of the long flexible alkyl tails on the ancillary benzoylthiourea (BTU) ligands.

  2. Erbeta Ligands. Part 5: Synthesis and Structure-Activity Relationships of a Series of 4'-hydroxyphenyl-aryl-carbaldehyde Oxime Derivatives

    SciTech Connect

    Mewshaw,R.; Bowen, S.; Harris, H.; Xu, Z.; Manas, E.; Cohn, S.

    2007-01-01

    A series of 4'-hydroxyphenyl-aryl-carbaldehyde oximes (5b) was prepared and found to have high affinity (4 nM) and modest selectivity (39-fold) for estrogen receptor-{beta} (ER{beta}). Substitution of one of the core rings of the scaffold based around these novel ligands further expanded our knowledge in the quest toward achieving high affinity and selectivity for ER{beta}. An X-ray co-crystal of structure 11 revealed that the oxime moiety was mimicking the C-ring of genistein, as previously predicted by SAR and docking studies.

  3. Protein-ligand binding region prediction (PLB-SAVE) based on geometric features and CUDA acceleration

    PubMed Central

    2013-01-01

    Background Protein-ligand interactions are key processes in triggering and controlling biological functions within cells. Prediction of protein binding regions on the protein surface assists in understanding the mechanisms and principles of molecular recognition. In silico geometrical shape analysis plays a primary step in analyzing the spatial characteristics of protein binding regions and facilitates applications of bioinformatics in drug discovery and design. Here, we describe the novel software, PLB-SAVE, which uses parallel processing technology and is ideally suited to extract the geometrical construct of solid angles from surface atoms. Representative clusters and corresponding anchors were identified from all surface elements and were assigned according to the ranking of their solid angles. In addition, cavity depth indicators were obtained by proportional transformation of solid angles and cavity volumes were calculated by scanning multiple directional vectors within each selected cavity. Both depth and volume characteristics were combined with various weighting coefficients to rank predicted potential binding regions. Results Two test datasets from LigASite, each containing 388 bound and unbound structures, were used to predict binding regions using PLB-SAVE and two well-known prediction systems, SiteHound and MetaPocket2.0 (MPK2). PLB-SAVE outperformed the other programs with accuracy rates of 94.3% for unbound proteins and 95.5% for bound proteins via a tenfold cross-validation process. Additionally, because the parallel processing architecture was designed to enhance the computational efficiency, we obtained an average of 160-fold increase in computational time. Conclusions In silico binding region prediction is considered the initial stage in structure-based drug design. To improve the efficacy of biological experiments for drug development, we developed PLB-SAVE, which uses only geometrical features of proteins and achieves a good overall performance

  4. A range of spin-crossover temperature T1/2>300 K results from out-of-sphere anion exchange in a series of ferrous materials based on the 4-(4-imidazolylmethyl)-2-(2-imidazolylmethyl)imidazole (trim) ligand, [Fe(trim)2]X2 (X=F, Cl, Br, I): comparison of experimental results with those derived from density functional theory calculations.

    PubMed

    Lemercier, Gilles; Bréfuel, Nicolas; Shova, Sergiu; Wolny, Juliusz A; Dahan, Françoise; Verelst, Marc; Paulsen, Hauke; Trautwein, Alfred X; Tuchagues, Jean-Pierre

    2006-09-25

    The synthesis and characterization of [FeII(trim)2]Cl2 (2), [FeII(trim)2]Br2MeOH (3), and [FeII(trim)2]I2MeOH (4), including the X-ray crystal structure determinations of 2 (50 and 293 K) and 4 (293 K), have been performed and their properties have been examined. In agreement with the magnetic susceptibility results, the Mössbauer data show the presence of high-spin (HS) to low-spin (LS) crossover with a range of T1/2 larger than 300 K (from approximately 20 K for [FeII(trim)2]F2 (1) to approximately 380 K for 4). All complexes in this series include the same [Fe(trim)2]2+ complex cation: the ligand field comprises a constant contribution from the trim ligands and a variable one originating from the out-of-sphere anions, which is transmitted to the metal center by the connecting imidazole rings and hydrogen bonds. The impressive variation in the intrinsic characteristics of the spin-crossover (SCO) phenomenon in this series is then interpreted as an inductive effect of the anions transmitted to the nitrogen donors through the hydrogen bonds. Based on this qualitative analysis, an increased inductive effect of the out-of-sphere anion corresponds to a decreased SCO temperature T1/2, in agreement with the experimental results. Electronic structure calculations with periodic boundary conditions have been performed that show the importance of intermolecular effects in tuning the ligand field, and thus in determining the transition temperature. Starting with the geometries obtained from the X-ray studies, the [FeII(trim)2]X2 complex molecules 1-4 have been investigated both for the single molecules and the crystal lattices with the local density approximation of density functional theory. The bulk geometries of the complex cations deduced from the X-ray studies and those calculated are in fair agreement for both approaches. However, the trend observed for the transition temperatures of 1-4 disagrees with the trend for the spin-state splittings ES (difference EHS

  5. A new model for predicting time course toxicity of heavy metals based on Biotic Ligand Model (BLM).

    PubMed

    Hatano, Ayumi; Shoji, Ryo

    2010-01-01

    A new model for predicting time course toxicity of heavy metals was developed by extending the effective ratio of biotic ligand binding with toxic heavy metals to the total biotic ligand for 50% of test organisms (f(50)) derived by the Biotic Ligand Model (BLM). BLM has been well-known as a useful model for prediction of heavy metal toxicity. BLM can consider the effect of exposure conditions such as pH and Ca(2+) on heavy metal toxicity. In addition to the exposure conditions, heavy metal toxicity is strongly dependent on exposure time. In this study, BLM is extended to predict time dependency of heavy metal toxicity by connecting with the concept of primary reaction. The model developed in this study also generates the estimation of the 50% effect concentration (EC(50)) for toxicologically unknown organisms and heavy metals. Two toxicological and kinetic constants, f(50,0) and k, were derived from the initial value of f(50) (f(50,0)) and a time constant (k) independent of time. The model developed in this study enables us to acquire information on the toxicity of heavy metals such as Cu, Cd and Co easily.

  6. New mixed ligand zinc(II) complexes based on the antiepileptic drug sodium valproate and bioactive nitrogen-donor ligands. Synthesis, structure and biological properties.

    PubMed

    Darawsheh, Mohanad; Abu Ali, Hijazi; Abuhijleh, A Latif; Rappocciolo, Emilia; Akkawi, Mutaz; Jaber, Suhair; Maloul, Salam; Hussein, Yasmeen

    2014-07-23

    Starting from the precursor [Zinc Valproate complex] (1), new mixed ligand zinc(II) complexes of valproic acid and nitrogen-based ligands, formulating as, [Zn(valp)22,9-dmphen] (2), [Zn2(valp)4(quin)2] (3), [Zn(valp)2(2-ampy)2] (4), and [Zn(valp)2(2-ampic)2] (5) (valp = valproate, 2,9-dmphen = 2,9-dimethyl-1,10-phenanthroline, quin = quinoline, 2-ampy = 2-aminopyridine, 2-ampic = 2-amino-6-picoline) were synthesized and characterized using IR, (1)H NMR, (13)C{(1)H} NMR and UV-Vis spectrometry. The crystal structures of complexes 2, 3 and 4 were determined using single-crystal X-ray diffraction. The complexes were also evaluated for their anti-bacterial activity using in-vitro agar diffusion method against three Gram-positive (Micrococcus luteus, Staphylococcus aureus, and Bacillus subtilis) and three Gram-negative (Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis) species. Complex 2 showed considerable activity against all tested microorganisms and the effect of complexation on the anti-bacterial activity of the parent ligand of 2 was also investigated. The anti-bacterial activity of 2,9-dmphen against Gram-negative bacteria was enhanced upon complexation with zinc valproate. On the other hand, complexes 1 and 3 showed weak inhibition activity against the tested species and complexes 4 and 5 didn't show any activity at all. Two methods were used for testing the inhibition of ferriprotoporphyrinIX bio-mineralization: a semi-quantitative micro-assay and a previously self-developed quantitative in-vitro method. Both were used to study the efficiency of these complexes in inhibiting the formation of the Malaria pigment which considered being the target of many known anti-malarial drugs such as Chloroquine and Amodiaquine. Results showed that the efficiency of complex 2 in preventing the formation of β-Hematin was 80%. The efficiency of Amodiaquine as a standard drug was reported to give 91%.

  7. Syntheses, spectral, electrochemical and thermal studies of mononuclear manganese(III) complexes with ligands derived from 1,2-propanediamine and 2-hydroxy-3 or 5-methoxybenzaldehyde: Self-assembled monolayer formation on nanostructure zinc oxide thin film

    NASA Astrophysics Data System (ADS)

    Habibi, Mohammad Hossein; Askari, Elham; Amirnasr, Mehdi; Amiri, Ahmad; Yamane, Yuki; Suzuki, Takayoshi

    2011-08-01

    Mononuclear Mn(III) complexes have been prepared via the Mn(II) reaction of an equimolar of Schiff-bases derived from reaction of 2-hydroxy-3-methoxybenzaldehyde or 2-hydroxy-5-methoxybenzaldehyde with 1,2-diaminopropane. Axial ligands L include: pyridine (py) and H 2O. The resulting complexes have been characterized by FT-IR and UV-vis spectroscopy. The crystal structures of the complexes were determined and indicate that in the solid state the complex adopts a slightly distorted octahedral environment of the imine N and hydroxo O with the two axial ligands. The electrochemical reduction of these complexes at a glassy carbon electrode in acetonitrile solution indicates that the first reduction process corresponding to Mn III-Mn II is electrochemically quasi-reversible. Thermal stability of these complexes was determined by TG and DTG. Layers of these complexes were formed on nanostructure zinc oxide thin film and a red shift was observed when zinc oxide thin film is modified by complex.

  8. Syntheses, spectral, electrochemical and thermal studies of mononuclear manganese(III) complexes with ligands derived from 1,2-propanediamine and 2-hydroxy-3 or 5-methoxybenzaldehyde: self-assembled monolayer formation on nanostructure zinc oxide thin film.

    PubMed

    Habibi, Mohammad Hossein; Askari, Elham; Amirnasr, Mehdi; Amiri, Ahmad; Yamane, Yuki; Suzuki, Takayoshi

    2011-08-01

    Mononuclear Mn(III) complexes have been prepared via the Mn(II) reaction of an equimolar of Schiff-bases derived from reaction of 2-hydroxy-3-methoxybenzaldehyde or 2-hydroxy-5-methoxybenzaldehyde with 1,2-diaminopropane. Axial ligands L include: pyridine (py) and H(2)O. The resulting complexes have been characterized by FT-IR and UV-vis spectroscopy. The crystal structures of the complexes were determined and indicate that in the solid state the complex adopts a slightly distorted octahedral environment of the imine N and hydroxo O with the two axial ligands. The electrochemical reduction of these complexes at a glassy carbon electrode in acetonitrile solution indicates that the first reduction process corresponding to Mn(III)-Mn(II) is electrochemically quasi-reversible. Thermal stability of these complexes was determined by TG and DTG. Layers of these complexes were formed on nanostructure zinc oxide thin film and a red shift was observed when zinc oxide thin film is modified by complex.

  9. Calix[4]pyrrole Schiff base macrocycles. Novel binucleating ligands for mu-oxo iron complexes.

    PubMed

    Veauthier, Jacqueline M; Cho, Won-Seob; Lynch, Vincent M; Sessler, Jonathan L

    2004-02-23

    New bimetallic mu-oxo diferric complexes of several previously reported calix[4]pyrrole Schiff base macrocycles are described. The synthesis of a new member of this class of macrocycles is also reported; it was prepared via an acid-catalyzed condensation between 1,9-bisformyl-5,5-dipropyldipyrromethane and o-phenylenediamine. Reactions of the free base macrocycles or their bis-HCl salts with Fe(II) mesitylene, followed by air oxidation, gave the binuclear mu-oxo bis-Fe(III) compounds 6-10 in moderate yield. X-ray crystallography data reveal two different coordination environments for the Fe-O-Fe subunit in 6-10 that it is suggested can be controlled by altering the reaction conditions. Structural properties of these metalated pyrrolic macrocycles are also compared to those of mu-oxo diferric porphyrins and mu-oxo diferric texaphyrin. Complexes 6-10 exhibit two distinct types of M-N bonds that are similar in length to the bonds observed in metallotexaphyrin complexes. However, the electronics of the present systems are very different from those of texaphyrins and porphyrins in that no delocalized bonding patterns are observed within the ligands as a whole.

  10. Structure and Ligand Based Drug Design Strategies in the Development of Novel 5-LOX Inhibitors

    PubMed Central

    Aparoy, Polamarasetty; Kumar Reddy, Kakularam; Reddanna, Pallu

    2012-01-01

    Lipoxygenases (LOXs) are non-heme iron containing dioxygenases involved in the oxygenation of polyunsaturated fatty acids (PUFAs) such as arachidonic acid (AA). Depending on the position of insertion of oxygen, LOXs are classified into 5-, 8-, 9-, 12- and 15-LOX. Among these, 5-LOX is the most predominant isoform associated with the formation of 5-hydroperoxyeicosatetraenoic acid (5-HpETE), the precursor of non-peptido (LTB4) and peptido (LTC4, LTD4, and LTE4) leukotrienes. LTs are involved in inflammatory and allergic diseases like asthma, ulcerative colitis, rhinitis and also in cancer. Consequently 5-LOX has become target for the development of therapeutic molecules for treatment of various inflammatory disorders. Zileuton is one such inhibitor of 5-LOX approved for the treatment of asthma. In the recent times, computer aided drug design (CADD) strategies have been applied successfully in drug development processes. A comprehensive review on structure based drug design strategies in the development of novel 5-LOX inhibitors is presented in this article. Since the crystal structure of 5-LOX has been recently solved, efforts to develop 5-LOX inhibitors have mostly relied on ligand based rational approaches. The present review provides a comprehensive survey on these strategies in the development of 5-LOX inhibitors. PMID:22680930

  11. Engineered protein A ligands, derived from a histidine-scanning library, facilitate the affinity purification of IgG under mild acidic conditions

    PubMed Central

    2014-01-01

    Background In antibody purification processes, the acidic buffer commonly used to elute the bound antibodies during conventional affinity chromatograph, can damage the antibody. Herein we describe the development of several types of affinity ligands which enable the purification of antibodies under much milder conditions. Results Staphylococcal protein A variants were engineered by using both structure-based design and combinatorial screening methods. The frequency of amino acid residue substitutions was statistically analyzed using the sequences isolated from a histidine-scanning library screening. The positions where the frequency of occurrence of a histidine residue was more than 70% were thought to be effective histidine-mutation sites. Consequently, we identified PAB variants with a D36H mutation whose binding of IgG was highly sensitive to pH change. Conclusion The affinity column elution chromatograms demonstrated that antibodies could be eluted at a higher pH (∆pH**≧2.0) than ever reported (∆pH = 1.4) when the Staphylococcal protein A variants developed in this study were used as affinity ligands. The interactions between Staphylococcal protein A and IgG-Fab were shown to be important for the behavior of IgG bound on a SpA affinity column, and alterations in the affinity of the ligands for IgG-Fab clearly affected the conditions for eluting the bound IgG. Thus, a histidine-scanning library combined with a structure-based design was shown to be effective in engineering novel pH-sensitive proteins. PMID:25057290

  12. Successful virtual screening for a submicromolar antagonist of the neurokinin-1 receptor based on a ligand-supported homology model.

    PubMed

    Evers, Andreas; Klebe, Gerhard

    2004-10-21

    The neurokinin-1 (NK1) receptor belongs to the family of G-protein-coupled receptors (GPCRs), which represents one of the most relevant target families in small-molecule drug design. In this paper, we describe a homology modeling of the NK1 receptor based on the high-resolution X-ray structure of rhodopsin and the successful virtual screening based on this protein model. The NK1 receptor model has been generated using our new MOBILE (modeling binding sites including ligand information explicitly) approach. Starting with preliminary homology models, it generates improved models of the protein binding pocket together with bound ligands. Ligand information is used as an integral part in the homology modeling process. For the construction of the NK1 receptor, antagonist CP-96345 was used to restrain the modeling. The quality of the obtained model was validated by probing its ability to accommodate additional known NK1 antagonists from structurally diverse classes. On the basis of the generated model and on the analysis of known NK1 antagonists, a pharmacophore model was deduced, which subsequently guided the 2D and 3D database search with UNITY. As a following step, the remaining hits were docked into the modeled binding pocket of the NK1 receptor. Finally, seven compounds were selected for biochemical testing, from which one showed affinity in the submicromolar range. Our results suggest that ligand-supported homology models of GPCRs may be used as effective platforms for structure-based drug design.

  13. Synthesis, characterization and antibacterial studies of ruthenium(III) complexes derived from chitosan schiff base.

    PubMed

    Vadivel, T; Dhamodaran, M

    2016-09-01

    Chitosan can be modified chemically by condensation reaction of deacetylated chitosan with aldehyde in homogeneous phase. This condensation is carried by primary amine (NH2) with aldehyde (CHO) to form corresponding schiff base. The chitosan biopolymer schiff base derivatives are synthesized with substituted aldehydes namely 4-hydroxy-3-methoxy benzaldehyde, 2-hydroxy benzaldehyde, and 2-hydroxy-3-methoxy benzaldehyde, becomes a complexing agent or ligand. The Ruthenium(III) complexes were obtained by complexation of Ruthenium with schiff base ligands and this product exhibits as an excellent solubility and more biocompatibility. The novel series of schiff base Ruthenium(III) complexes are characterized by Elemental analysis, FT-IR spectroscopy, and Thermo-gravimetric analysis (TGA). The synthesized complexes have been subjected to antibacterial study. The antibacterial results indicated that the antibacterial activity of the complexes were more effective against Gram positive and Gram negative pathogenic bacteria. These findings are giving suitable support for developing new antibacterial agent and expand our scope for applications.

  14. Toward Quantitatively Accurate Calculation of the Redox-Associated Acid–Base and Ligand Binding Equilibria of Aquacobalamin

    SciTech Connect

    Johnston, Ryne C.; Zhou, Jing; Smith, Jeremy C.; Parks, Jerry M.

    2016-07-08

    In redox processes in complex transition metal-containing species are often intimately associated with changes in ligand protonation states and metal coordination number. Moreover, a major challenge is therefore to develop consistent computational approaches for computing pH-dependent redox and ligand dissociation properties of organometallic species. Reduction of the Co center in the vitamin B12 derivative aquacobalamin can be accompanied by ligand dissociation, protonation, or both, making these properties difficult to compute accurately. We examine this challenge here by using density functional theory and continuum solvation to compute Co ligand binding equilibrium constants (Kon/off), pKas and reduction potentials for models of aquacobalamin in aqueous solution. We consider two models for cobalamin ligand coordination: the first follows the hexa, penta, tetra coordination scheme for CoIII, CoII, and CoI species, respectively, and the second model features saturation of each vacant axial coordination site on CoII and CoI species with a single, explicit water molecule to maintain six directly interacting ligands or water molecules in each oxidation state. Comparing these two coordination schemes in combination with five dispersion-corrected density functionals, we find that the accuracy of the computed properties is largely independent of the scheme used, but including only a continuum representation of the solvent yields marginally better results than saturating the first solvation shell around Co throughout. PBE performs best, displaying balanced accuracy and superior performance overall, with RMS errors of 80 mV for seven reduction potentials, 2.0 log units for five pKas and 2.3 log units for two log Kon/off values for the aquacobalamin system. Furthermore, we find that the BP86 functional commonly used in corrinoid studies suffers from erratic behavior and inaccurate descriptions of

  15. Toward Quantitatively Accurate Calculation of the Redox-Associated Acid–Base and Ligand Binding Equilibria of Aquacobalamin

    DOE PAGES

    Johnston, Ryne C.; Zhou, Jing; Smith, Jeremy C.; ...

    2016-07-08

    In redox processes in complex transition metal-containing species are often intimately associated with changes in ligand protonation states and metal coordination number. Moreover, a major challenge is therefore to develop consistent computational approaches for computing pH-dependent redox and ligand dissociation properties of organometallic species. Reduction of the Co center in the vitamin B12 derivative aquacobalamin can be accompanied by ligand dissociation, protonation, or both, making these properties difficult to compute accurately. We examine this challenge here by using density functional theory and continuum solvation to compute Co ligand binding equilibrium constants (Kon/off), pKas and reduction potentials for models of aquacobalaminmore » in aqueous solution. We consider two models for cobalamin ligand coordination: the first follows the hexa, penta, tetra coordination scheme for CoIII, CoII, and CoI species, respectively, and the second model features saturation of each vacant axial coordination site on CoII and CoI species with a single, explicit water molecule to maintain six directly interacting ligands or water molecules in each oxidation state. Comparing these two coordination schemes in combination with five dispersion-corrected density functionals, we find that the accuracy of the computed properties is largely independent of the scheme used, but including only a continuum representation of the solvent yields marginally better results than saturating the first solvation shell around Co throughout. PBE performs best, displaying balanced accuracy and superior performance overall, with RMS errors of 80 mV for seven reduction potentials, 2.0 log units for five pKas and 2.3 log units for two log Kon/off values for the aquacobalamin system. Furthermore, we find that the BP86 functional commonly used in corrinoid studies suffers from erratic behavior and inaccurate descriptions of Co axial ligand binding, leading to substantial errors in predicted

  16. Toward Quantitatively Accurate Calculation of the Redox-Associated Acid-Base and Ligand Binding Equilibria of Aquacobalamin.

    PubMed

    Johnston, Ryne C; Zhou, Jing; Smith, Jeremy C; Parks, Jerry M

    2016-08-04

    Redox processes in complex transition metal-containing species are often intimately associated with changes in ligand protonation states and metal coordination number. A major challenge is therefore to develop consistent computational approaches for computing pH-dependent redox and ligand dissociation properties of organometallic species. Reduction of the Co center in the vitamin B12 derivative aquacobalamin can be accompanied by ligand dissociation, protonation, or both, making these properties difficult to compute accurately. We examine this challenge here by using density functional theory and continuum solvation to compute Co-ligand binding equilibrium constants (Kon/off), pKas, and reduction potentials for models of aquacobalamin in aqueous solution. We consider two models for cobalamin ligand coordination: the first follows the hexa, penta, tetra coordination scheme for Co(III), Co(II), and Co(I) species, respectively, and the second model features saturation of each vacant axial coordination site on Co(II) and Co(I) species with a single, explicit water molecule to maintain six directly interacting ligands or water molecules in each oxidation state. Comparing these two coordination schemes in combination with five dispersion-corrected density functionals, we find that the accuracy of the computed properties is largely independent of the scheme used, but including only a continuum representation of the solvent yields marginally better results than saturating the first solvation shell around Co throughout. PBE performs best, displaying balanced accuracy and superior performance overall, with RMS errors of 80 mV for seven reduction potentials, 2.0 log units for five pKas and 2.3 log units for two log Kon/off values for the aquacobalamin system. Furthermore, we find that the BP86 functional commonly used in corrinoid studies suffers from erratic behavior and inaccurate descriptions of Co-axial ligand binding, leading to substantial errors in predicted pKas and

  17. Small-molecule interferon inducers. Toward the comprehension of the molecular determinants through ligand-based approaches.

    PubMed

    Musmuca, Ira; Simeoni, Silvia; Caroli, Antonia; Ragno, Rino

    2009-07-01

    Hepatitis C is becoming an increasingly common cause of mortality especially in the HIV-coinfected group. Due to the efficacy of interferon (IFN) based therapy in the treatment of hepatitis C, various compounds possessing IFN-inducing activity have been hitherto reported. In the present study, we describe how steric, electrostatic, hydrophobic, and hydrogen-bonding interactions might influence the biological activity of a published set of IFN inducers, using a three-dimensional quantitative structure-activity relationship (3-D QSAR) approach. Analyses were conducted evaluating different series of compounds structurally related to 8-hydroxyadenines and 1H-imidazo[4,5-c]quinolines. A ligand-based alignment protocol in combination with the GRID/GOLPE approach was applied: 62 3-D QSAR models were derived using different GRID probes and several training sets. Performed 3-D QSAR investigations proved to be of good statistical value displaying r2, q2CV-LOO, and cross-validated SDEP values of 0.73, 0.61, 0.61 and 0.89, 0.64, 0.58 using the OH or the DRY probe, respectively. Additionally, the predictive performance was evaluated using an external test set of 20 compounds. Analyses of the resulting models led to the definition of a pharmacophore model that can be of interest to explain the observed affinities of known compounds as well as to design novel low molecular weight IFN inducers (IFNIs). To the best of our knowledge, this is the first 3-D QSAR application on IFN-inducing agents.

  18. Synthesis, characterization and antibacterial activity of a tridentate Schiff base derived from cephalothin and sulfadiazine, and its transition metal complexes.

    PubMed

    Anacona, J R; Noriega, Natiana; Camus, Juan

    2015-02-25

    Metal(II) coordination compounds of a cephalothin Schiff base (H2L) derived from the condensation of cephalothin antibiotic with sulfadiazine were synthesized. The Schiff base ligand, mononuclear [ML(H2O)3] (M(II)=Mn,Co,Ni,Zn) complexes and magnetically diluted dinuclear copper(II) complex [CuL(H2O)3]2 were characterized by several techniques, including elemental and thermal analysis, molar conductance and magnetic susceptibility measurements, electronic, FT-IR, EPR and (1)H NMR spectral studies. The cephalothin Schiff base ligand H2L behaves as a dianionic tridentate NOO chelating agent. The biological applications of complexes have been studied on two bacteria strains (Escherichia coli and Staphylococcus aureus) by agar diffusion disc method.

  19. Cr(III), Fe(III) and Co(III) complexes of tetradentate (ONNO) Schiff base ligands: Synthesis, characterization, properties and biological activity

    NASA Astrophysics Data System (ADS)

    Keskioğlu, Eren; Gündüzalp, Ayla Balaban; Çete, Servet; Hamurcu, Fatma; Erk, Birgül

    2008-08-01

    A series of metal complexes were synthesized from equimolar amounts of Schiff bases: 1,4-bis[3-(2-hydroxy-1-naphthaldimine)propyl]piperazine (bappnaf) and 1,8-bis[3-(2-hydroxy-1-naphthaldimine)- p-menthane (damnaf) with metal chlorides. All of synthesized compounds were characterized by elemental analyses, spectral (UV-vis, IR, 1H- 13C NMR, LC-MS) and thermal (TGA-DTA) methods, magnetic and conductance measurements. Schiff base complexes supposed in tetragonal geometry have the general formula [M(bappnaf or damnaf)]Cl· nH 2O, where M = Cr(III), Co(III) and n = 2, 3. But also Fe(III) complexes have octahedral geometry by the coordination of two water molecules and the formula is [Fe(bappnaf or damnaf)(H 2O) 2]Cl. The changes in the selected vibration bands in FT-IR indicate that Schiff bases behave as (ONNO) tetradentate ligands and coordinate to metal ions from two phenolic oxygen atoms and two azomethine nitrogen atoms. Conductance measurements suggest 1:1 electrolytic nature of the metal complexes. The synthesized compounds except bappnaf ligand have the antimicrobial activity against the bacteria: Escherichia coli (ATCC 11230), Yersinia enterocolitica (ATCC 1501), Bacillus magaterium (RSKK 5117), Bacillus subtilis (RSKK 244), Bacillus cereus (RSKK 863) and the fungi: Candida albicans (ATCC 10239). These results have been considerably interest in piperazine derivatives due to their significant applications in antimicrobial studies.

  20. Asymmetric Schiff bases derived from diaminomaleonitrile and their metal complexes

    NASA Astrophysics Data System (ADS)

    Yang, Jianjie; Shi, Rufei; Zhou, Pei; Qiu, Qiming; Li, Hui

    2016-02-01

    Asymmetric Schiff bases, due to its asymmetric structure, can be used as asymmetric catalyst, antibacterial, and mimic molecules during simulate biological processes, etc. In recent years, research on synthesis and properties of asymmetric Schiff bases have become an increase interest of chemists. This review summarizes asymmetric Schiff bases derived from diaminomaleonitrile (DAMN) and DAMN-based asymmetric Schiff bases metal complexes. Applications of DAMN-based asymmetric Schiff bases are also discussed in this review.

  1. Synthesis of metal complexes involving Schiff base ligand with methylenedioxy moiety: spectral, thermal, XRD and antimicrobial studies.

    PubMed

    Sundararajan, M L; Jeyakumar, T; Anandakumaran, J; Karpanai Selvan, B

    2014-10-15

    Metal complexes of Zn(II), Cd(II), Ni(II), Cu(II), Fe(III), Co(II), Mn(II) Hg(II), and Ag(I) have been synthesized from Schiff base ligand, prepared by the condensation of 3,4-(methylenedioxy)aniline and 5-bromo salicylaldehyde. All the compounds have been characterized by using elemental analysis, molar conductance, FT-IR, UV-Vis, (1)H NMR, (13)C NMR, mass spectra, powder XRD and thermal analysis (TG/DTA) technique. The elemental analysis suggests the stoichiometry to be 1:1 (metal:ligand). The FT-IR, (1)H NMR, (13)C NMR and UV-Vis spectral data suggest that the ligand coordinate to the metal atom by imino nitrogen and phenolic oxygen as bidentate manner. Mass spectral data further support the molecular mass of the compounds and their structure. Powder XRD indicates the crystalline state and morphology of the ligand and its metal complexes. The thermal behaviors of the complexes prove the presence of lattice as well as coordinated water molecules in the complexes. Melting point supports the thermal stability of all the compounds. The in vitro antimicrobial effects of the synthesized compounds were tested against five bacterial and three fungal species by well diffusion method. Antioxidant activities have also been performed for all the compounds. Metal complexes show more biological activity than the Schiff base.

  2. Synthesis of metal complexes involving Schiff base ligand with methylenedioxy moiety: Spectral, thermal, XRD and antimicrobial studies

    NASA Astrophysics Data System (ADS)

    Sundararajan, M. L.; Jeyakumar, T.; Anandakumaran, J.; Karpanai Selvan, B.

    2014-10-01

    Metal complexes of Zn(II), Cd(II), Ni(II), Cu(II), Fe(III), Co(II), Mn(II) Hg(II), and Ag(I) have been synthesized from Schiff base ligand, prepared by the condensation of 3,4-(methylenedioxy)aniline and 5-bromo salicylaldehyde. All the compounds have been characterized by using elemental analysis, molar conductance, FT-IR, UV-Vis, 1H NMR, 13C NMR, mass spectra, powder XRD and thermal analysis (TG/DTA) technique. The elemental analysis suggests the stoichiometry to be 1:1 (metal:ligand). The FT-IR, 1H NMR, 13C NMR and UV-Vis spectral data suggest that the ligand coordinate to the metal atom by imino nitrogen and phenolic oxygen as bidentate manner. Mass spectral data further support the molecular mass of the compounds and their structure. Powder XRD indicates the crystalline state and morphology of the ligand and its metal complexes. The thermal behaviors of the complexes prove the presence of lattice as well as coordinated water molecules in the complexes. Melting point supports the thermal stability of all the compounds. The in vitro antimicrobial effects of the synthesized compounds were tested against five bacterial and three fungal species by well diffusion method. Antioxidant activities have also been performed for all the compounds. Metal complexes show more biological activity than the Schiff base.

  3. Construction of five Zn(ii)/Cd(ii) coordination polymers derived from a new linear carboxylate/pyridyl ligand: design, synthesis, and photocatalytic properties.

    PubMed

    Liu, Lei-Lei; Yu, Cai-Xia; Du, Ji-Min; Liu, Shi-Min; Cao, Jing-Shuai; Ma, Lu-Fang

    2016-08-02

    Solvothermal reactions of Cd(OAc)2/Zn(OAc)2 with a new ligand, (pyridin-3-yl)methyl 4-(2-(4-((pyridin-3-yl)methoxy)phenyl)diazenyl)benzoate (L1), under different templates via an in situ ligand transformation reaction produced five coordination polymers, [CdL2(H2O)]n (1), [Cd1.5L3]n (2), [Cd2L4]n (3), [(ZnL2)·H2O]n (4) and {[Zn(1,3-BDC)(L1)]·MeCN·0.5H2O}n (5), where HL = 4-(2-(4-((pyridin-3-yl)methoxy)phenyl)diazenyl)benzoic acid, 1,3-H2BDC = 1,3-benzenedicarboxylic acid. Compound 1 is a three-dimensional (3D) wave-like structure constructed from 4-connected Cd(ii) nodes and L(-) linkers. Compounds 2 and 3 bear similar 2D networks built from metallocyclic [Cd4L4] units. Compound 4 features a wrinkled 2D layer based on metallocyclic [Zn4L4] units. Compound 5 has a novel 1D single-wall metal-organic nanotube (SWMONT) in which the 1,3-BDC ligands act as linkers to connect the [Zn2(L1)2] rings. The results reveal that the different templates have a significant effect on the final structures. Compounds 1-5 exhibited relatively high photocatalytic activity towards the degradation of methylene blue (MB) in aqueous solution under UV-Vis irradiation. The kinetics of the catalytic photodegradation reactions and the stabilities of photocatalysts were also investigated.

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

    SciTech Connect

    Bartsch, Richard A.

    2012-06-04

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

  5. A pose prediction approach based on ligand 3D shape similarity

    NASA Astrophysics Data System (ADS)

    Kumar, Ashutosh; Zhang, Kam Y. J.

    2016-06-01

    Molecular docking predicts the best pose of a ligand in the target protein binding site by sampling and scoring numerous conformations and orientations of the ligand. Failures in pose prediction are often due to either insufficient sampling or scoring function errors. To improve the accuracy of pose prediction by tackling the sampling problem, we have developed a method of pose prediction using shape similarity. It first places a ligand conformation of the highest 3D shape similarity with known crystal structure ligands into protein binding site and then refines the pose by repacking the side-chains and performing energy minimization with a Monte Carlo algorithm. We have assessed our method utilizing CSARdock 2012 and 2014 benchmark exercise datasets consisting of co-crystal structures from eight proteins. Our results revealed that ligand 3D shape similarity could substitute conformational and orientational sampling if at least one suitable co-crystal structure is available. Our method identified poses within 2 Å RMSD as the top-ranking pose for 85.7 % of the test cases. The median RMSD for our pose prediction method was found to be 0.81 Å and was better than methods performing extensive conformational and orientational sampling within target protein binding sites. Furthermore, our method was better than similar methods utilizing ligand 3D shape similarity for pose prediction.

  6. Identification of human viral protein-derived ligands recognized by individual MHCI-restricted T-cell receptors

    PubMed Central

    Szomolay, Barbara; Liu, Jie; Brown, Paul E; Miles, John J; Clement, Mathew; Llewellyn-Lacey, Sian; Dolton, Garry; Ekeruche-Makinde, Julia; Lissina, Anya; Schauenburg, Andrea J; Sewell, Andrew K; Burrows, Scott R; Roederer, Mario; Price, David A; Wooldridge, Linda; van den Berg, Hugo A

    2016-01-01

    Evidence indicates that autoimmunity can be triggered by virus-specific CD8+ T cells that crossreact with self-derived peptide epitopes presented on the cell surface by major histocompatibility complex class I (MHCI) molecules. Identification of the associated viral pathogens is challenging because individual T-cell receptors can potentially recognize up to a million different peptides. Here, we generate peptide length-matched combinatorial peptide library (CPL) scan data for a panel of virus-specific CD8+ T-cell clones spanning different restriction elements and a range of epitope lengths. CPL scan data drove a protein database search limited to viruses that infect humans. Peptide sequences were ranked in order of likelihood of recognition. For all anti-viral CD8+ T-cell clones examined in this study, the index peptide was either the top-ranked sequence or ranked as one of the most likely sequences to be recognized. Thus, we demonstrate that anti-viral CD8+ T-cell clones are highly focused on their index peptide sequence and that ‘CPL-driven database searching' can be used to identify the inciting virus-derived epitope for a given CD8+ T-cell clone. Moreover, to augment access to CPL-driven database searching, we have created a publicly accessible webtool. Application of these methodologies in the clinical setting may clarify the role of viral pathogens in the etiology of autoimmune diseases. PMID:26846725

  7. Preparation and biodistribution of copper-67 complexes with tetradentate Schiff-base ligands.

    PubMed

    John, E K; Bott, A J; Green, M A

    1994-04-01

    Uncharged, lipophilic, low molecular weight copper complexes labeled with generator-produced copper-62 are of interest as potential radiopharmaceutials for imaging the brain with positron emission tomography (PET). We report here the synthesis and biodistribution of a series of [67Cu]copper(II) complexes with tetradentate N2O2(2-)Schiff-base ligands. The compounds studied varied in lipophilicity from log P = 1.7 to log P = 3.6, where P is the octanol/water partition coefficient. In rat biodistribution studies the tracers were generally found to penetrate the blood-brain barrier following intravenous injection, but some far better than others. For closely related compounds brain uptake at 1 min postinjection increased with increasing lipophilicity, although log P was clearly not the sole determinant of high brain uptake. Substantial variations were also observed in the rate at which these various compounds are cleared from brain, with a few exhibiting the prolonged cerebral retention of tracer that would be desired for imaging with 62Cu and PET.

  8. MED-SuMoLig: a new ligand-based screening tool for efficient scaffold hopping.

    PubMed

    Sperandio, Olivier; Andrieu, Olivier; Miteva, Maria A; Vo, Minh-Quang; Souaille, Marc; Delfaud, François; Villoutreix, Bruno O

    2007-01-01

    The identification of small molecules with selective bioactivity, whether intended as potential therapeutics or as tools for experimental research, is central to progress in medicine and in the life sciences. To facilitate such study, we have developed a ligand-based program well-suited for effective screening of large compound collections. This package, MED-SuMoLig, combines a SMARTS-driven substructure search aiming at 3D pharmacophore profiling and computation of the local atomic density of the compared molecules. The screening utility was then investigated using 52 diverse active molecules (against CDK2, Factor Xa, HIV-1 protease, neuraminidase, ribonuclease A, and thymidine kinase) merged to a library of about 40,000 putative inactive (druglike) compounds. In all cases, the program recovered more than half of the actives in the top 3% of the screened library. We also compared the performance of MED-SuMoLig with that of ChemMine or of ROCS and found that MED-SuMoLig outperformed both methods for CDK2 and Factor Xa in terms of enrichment rates or performed equally well for the other targets.

  9. Multivalent display of quinic acid based ligands for targeting E-selectin expressing cells.

    PubMed

    Shamay, Yosi; Paulin, Denise; Ashkenasy, Gonen; David, Ayelet

    2009-10-08

    The site-specific expression of molecular markers on endothelial cells of blood vessels during inflammatory response and angiogenesis provides an opportunity to target drugs and imaging molecules to the vascular endothelium of diseased tissues. This paper describes an innovative strategy for selective delivery of polymer conjugates to E- and P-selectin expressing cells using a series of quinic acid (Qa) based non-carbohydrate analogues of the natural ligand sialyl Lewis(x) (sLe(x)) as targeting moieties. We demonstrate that such analogues antagonize the adhesion of sLe(x) expressing HL-60 cells to both E- and P-selectin. Significantly, the apparent avidity of polymer conjugates carrying multiple Qa copies has increased by 3 orders of magnitude relative to their monomeric forms. Furthermore, we found that the major mechanism of copolymer entry and delivery into E-selectin expressing cells is endocytosis. These selectin-targetable copolymers provide the foundation to support controlled delivery of anticancer drugs and imaging agents to tumor vasculature for therapeutic and diagnostic applications.

  10. Ligand effects on the structural dimensionality and antibacterial activities of silver-based coordination polymers.

    PubMed

    Lu, Xinyi; Ye, Junwei; Sun, Yuan; Bogale, Raji Feyisa; Zhao, Limei; Tian, Peng; Ning, Guiling

    2014-07-14

    Four Ag-based coordination polymers [Ag(Bim)] (1), [Ag2(NIPH)(HBim)] (2), [Ag6(4-NPTA)(Bim)4] (3) and [Ag2(3-NPTA)(bipy)0.5(H2O)] (4) (HBim = 1H-benzimidazole, bipy = 4,4'-bipyridyl, H2NIPH = 5-nitroisophthalic acid, H2NPTA = 3-/4-nitrophthalic acid) have been synthesized by hydrothermal reaction of Ag(i) salts with N-/O-donor ligands. Single-crystal X-ray diffraction indicated that these coordination polymers constructed from mononuclear or polynuclear silver building blocks exhibit three typical structure features from 1-D to 3-D frameworks. These compounds favour a slow release of Ag(+) ions leading to excellent and long-term antimicrobial activities, which is distinguished by their different topological structures, towards both Gram-negative bacteria, Escherichia coli (E. coli) and Gram-positive bacteria, Staphylococcus aureus (S. aureus). In addition, these compounds show good thermal stability and light stability under UV-vis and visible light, which are important characteristics for their further application in antibacterial agents.

  11. Potent HIV-1 protease inhibitors incorporating meso-bicyclic urethanes as P2-ligands: structure-based design, synthesis, biological evaluation and protein-ligand X-ray studies

    SciTech Connect

    Ghosh, Arun; Gemma, Sandra; Takayama, Jun; Baldridge, Abigail; Leshchenko-Yashchuk, Sofiya; Miller, Heather; Wang, Yuan-Fang; Kovalevsky, Andrey; Koh, Yashiro; Weber, Irene; Mitsuya, Hiroaki

    2008-12-05

    Recently, we designed a series of novel HIV-1 protease inhibitors incorporating a stereochemically defined bicyclic fused cyclopentyl (Cp-THF) urethane as the high affinity P2-ligand. Inhibitor 1 with this P2-ligand has shown very impressive potency against multi-drug-resistant clinical isolates. Based upon the 1-bound HIV-1 protease X-ray structure, we have now designed and synthesized a number of meso-bicyclic ligands which can conceivably interact similarly to the Cp-THF ligand. The design of meso-ligands is quite attractive as they do not contain any stereocenters. Inhibitors incorporating urethanes of bicyclic-1,3-dioxolane and bicyclic-1,4-dioxane have shown potent enzyme inhibitory and antiviral activities. Inhibitor 2 (K{sub i} = 0.11 nM; IC{sub 50} = 3.8 nM) displayed very potent antiviral activity in this series. While inhibitor 3 showed comparable enzyme inhibitory activity (K{sub i} = 0.18 nM) its antiviral activity (IC{sub 50} = 170 nM) was significantly weaker than inhibitor 2. Inhibitor 2 maintained an antiviral potency against a series of multi-drug resistant clinical isolates comparable to amprenavir. A protein-ligand X-ray structure of 3-bound HIV-1 protease revealed a number of key hydrogen bonding interactions at the S2-subsite. We have created an active model of inhibitor 2 based upon this X-ray structure.

  12. Structure-based design of ligands for protein basic domains: application to the HIV-1 Tat protein.

    PubMed

    Filikov, A V; James, T L

    1998-05-01

    A methodology has been developed for designing ligands to bind a flexible basic protein domain where the structure of the domain is essentially known. It is based on an empirical binding free energy function developed for highly charged complexes and on Monte Carlo simulations in internal coordinates with both the ligand and the receptor being flexible. HIV-1 encodes a transactivating regulatory protein called Tat. Binding of the basic domain of Tat to TAR RNA is required for efficient transcription of the viral genome. The structure of a biologically active peptide containing the Tat basic RNA-binding domain is available from NMR studies. The goal of the current project is to design a ligand which will bind to that basic domain and potentially inhibit the TAR-Tat interaction. The basic domain contains six arginine and two lysine residues. Our strategy was to design a ligand for arginine first and then a superligand for the basic domain by joining arginine ligands with a linker. Several possible arginine ligands were obtained by searching the Available Chemicals Directory with DOCK 3.5 software. Phytic acid, which can potentially bind multiple arginines, was chosen as a building block for the superligand. Calormetric binding studies of several compounds to methylguanidine and Arg-/Lys-containing peptides were performed. The data were used to develop an empirical binding free energy function for prediction of affinity of the ligands for the Tat basic domain. Modeling of the conformations of the complexes with both the superligand and the basic domain being flexible has been carried out via Biased Probability Monte Carlo (BPMC) simulations in internal coordinates (ICM 2.6 suite of programs). The simulations used parameters to ensure correct folding, i.e., consistent with the experimental NMR structure of a 25-residue Tat peptide, from a random starting conformation. Superligands for the basic domain were designed by joining together two molecules of phytic acid with

  13. Structure-based design of ligands for protein basic domains: Application to the HIV-1 Tat protein

    NASA Astrophysics Data System (ADS)

    Filikov, Anton V.; James, Thomas L.

    1998-05-01

    A methodology has been developed for designing ligands to bind a flexible basic protein domain where the structure of the domain is essentially known. It is based on an empirical binding free energy function developed for highly charged complexes and on Monte Carlo simulations in internal coordinates with both the ligand and the receptor being flexible. HIV-1 encodes a transactivating regulatory protein called Tat. Binding of the basic domain of Tat to TAR RNA is required for efficient transcription of the viral genome. The structure of a biologically active peptide containing the Tat basic RNA-binding domain is available from NMR studies. The goal of the current project is to design a ligand which will bind to that basic domain and potentially inhibit the TAR-Tat interaction. The basic domain contains six arginine and two lysine residues. Our strategy was to design a ligand for arginine first and then a superligand for the basic domain by joining arginine ligands with a linker. Several possible arginine ligands were obtained by searching the Available Chemicals Directory with DOCK 3.5 software. Phytic acid, which can potentially bind multiple arginines, was chosen as a building block for the superligand. Calorimetric binding studies of several compounds to methylguanidine and Arg-/Lys-containing peptides were performed. The data were used to develop an empirical binding free energy function for prediction of affinity of the ligands for the Tat basic domain. Modeling of the conformations of the complexes with both the superligand and the basic domain being flexible has been carried out via Biased Probability Monte Carlo (BPMC) simulations in internal coordinates (ICM 2.6 suite of programs). The simulations used parameters to ensure correct folding, i.e., consistent with the experimental NMR structure of a 25-residue Tat peptide, from a random starting conformation. Superligands for the basic domain were designed by joining together two molecules of phytic acid with

  14. Overcoming the aggregation problem: A new type of fluorescent ligand for ConA-based glucose sensing

    PubMed Central

    Cummins, Brian M.; Li, Mingchien; Locke, Andrea K.; Birch, David J.S.; Vigh, Gyula; Coté, Gerard L.

    2016-01-01

    Competitive binding assays based on the lectin Concanavalin A (ConA) have displayed significant potential to serve in continuous glucose monitoring applications. However, to date, this type of fluorescent, affinity-based assay has yet to show the stable, glucose predictive capabilities that are required for such an application. This instability has been associated with the extensive crosslinking between traditionally-used fluorescent ligands (presenting multiple low-affinity moieties) and ConA (presenting multiple binding sites) in free solution. The work herein introduces the design and synthesis of a new type of fluorescent ligand that can avoid this aggregation and allow the assay to be sensitive across the physiologically relevant glucose concentration range. This fluorescent ligand (APTS–MT) presents a single high-affinity trimannose moiety that is recognized by ConA’s full binding site and a fluorophore that can effectively track the ligand’s equilibrium binding via fluorescent anisotropy. This is confirmed by comparing its measured fluorescent lifetime to experimentally-determined rotational correlation lifetimes of the free and bound populations. Using an assay comprised of 200 nM APTS–MT and 1 μM ConA, the fluorescence anisotropy capably tracks the concentration of monosaccharides that are known to bind to ConA’s primary binding site, and the assay displays a MARD of 6.5% across physiologically relevant glucose concentrations. Ultimately, this rationally-designed fluorescent ligand can facilitate the realization of the full potential of ConA-based glucose sensing assays and provide the basis for a new set of competing ligands to be paired with ConA. PMID:25058939

  15. An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function.

    PubMed

    Huang, Sheng-You; Zou, Xiaoqin

    2006-11-30

    We have developed an iterative knowledge-based scoring function (ITScore) to describe protein-ligand interactions. Here, we assess ITScore through extensive tests on native structure identification, binding affinity prediction, and virtual database screening. Specifically, ITScore was first applied to a test set of 100 protein-ligand complexes constructed by Wang et al. (J Med Chem 2003, 46, 2287), and compared with 14 other scoring functions. The results show that ITScore yielded a high success rate of 82% on identifying native-like binding modes under the criterion of rmsd < or = 2 A for each top-ranked ligand conformation. The success rate increased to 98% if the top five conformations were considered for each ligand. In the case of binding affinity prediction, ITScore also obtained a good correlation for this test set (R = 0.65). Next, ITScore was used to predict binding affinities of a second diverse test set of 77 protein-ligand complexes prepared by Muegge and Martin (J Med Chem 1999, 42, 791), and compared with four other widely used knowledge-based scoring functions. ITScore yielded a high correlation of R2 = 0.65 (or R = 0.81) in the affinity prediction. Finally, enrichment tests were performed with ITScore against four target proteins using the compound databases constructed by Jacobsson et al. (J Med Chem 2003, 46, 5781). The results were compared with those of eight other scoring functions. ITScore yielded high enrichments in all four database screening tests. ITScore can be easily combined with the existing docking programs for the use of structure-based drug design.

  16. Pigment epithelium-derived factor (PEDF) promotes tumor cell death by inducing macrophage membrane tumor necrosis factor-related apoptosis-inducing ligand (TRAIL).

    PubMed

    Ho, Tsung-Chuan; Chen, Show-Li; Shih, Shou-Chuan; Chang, Shing-Jyh; Yang, Su-Lin; Hsieh, Jui-Wen; Cheng, Huey-Chuan; Chen, Lee-Jen; Tsao, Yeou-Ping

    2011-10-14

    Pigment epithelium-derived factor (PEDF) is an intrinsic anti-angiogenic factor and a potential anti-tumor agent. The tumoricidal mechanism of PEDF, however, has not been fully elucidated. Here we report that PEDF induces the apoptosis of TC-1 and SK-Hep-1 tumor cells when they are cocultured with bone marrow-derived macrophages (BMDMs). This macrophage-mediated tumor killing is prevented by blockage of TNF-related apoptosis-inducing ligand (TRAIL) following treatment with the soluble TRAIL receptor. PEDF also increases the amount of membrane-bound TRAIL on cultured mouse BMDMs and on macrophages surrounding subcutaneous tumors. PEDF-induced tumor killing and TRAIL induction are abrogated by peroxisome proliferator-activated receptor γ (PPARγ) antagonists or small interfering RNAs targeting PPARγ. PEDF also induces PPARγ in BMDMs. Furthermore, the activity of the TRAIL promoter in human macrophages is increased by PEDF stimulation. Chromatin immunoprecipitation and DNA pull-down assays confirmed that endogenous PPARγ binds to a functional PPAR-response element (PPRE) in the TRAIL promoter, and mutation of this PPRE abolishes the binding of the PPARγ-RXRα heterodimer. Also, PPARγ-dependent transactivation and PPARγ-RXRα binding to this PPRE are prevented by PPARγ antagonists. Our results provide a novel mechanism for the tumoricidal activity of PEDF, which involves tumor cell killing via PPARγ-mediated TRAIL induction in macrophages.

  17. Synthesis, characterization, cytotoxic and antitubercular activities of new gold(I) and gold(III) complexes containing ligands derived from carbohydrates.

    PubMed

    Chaves, Joana Darc Souza; Damasceno, Jaqueline Lopes; Paula, Marcela Cristina Ferreira; de Oliveira, Pollyanna Francielli; Azevedo, Gustavo Chevitarese; Matos, Renato Camargo; Lourenço, Maria Cristina S; Tavares, Denise Crispim; Silva, Heveline; Fontes, Ana Paula Soares; de Almeida, Mauro Vieira

    2015-10-01

    Novel gold(I) and gold(III) complexes containing derivatives of D-galactose, D-ribose and D-glucono-1,5-lactone as ligands were synthesized and characterized by IR, (1)H, and (13)C NMR, high resolution mass spectra and cyclic voltammetry. The compounds were evaluated in vitro for their cytotoxicity against three types of tumor cells: cervical carcinoma (HeLa) breast adenocarcinoma (MCF-7) and glioblastoma (MO59J) and one non-tumor cell line: human lung fibroblasts (GM07492A). Their antitubercular activity was evaluated as well expressed as the minimum inhibitory concentration (MIC90) in μg/mL. In general, the gold(I) complexes were more active than gold(III) complexes, for example, the gold(I) complex (1) was about 8.8 times and 7.6 times more cytotoxic than gold(III) complex (8) in MO59J and MCF-7 cells, respectively. Ribose and alkyl phosphine derivative complexes were more active than galactose and aryl phosphine complexes. The presence of a thiazolidine ring did not improve the cytotoxicity. The study of the cytotoxic activity revealed effective antitumor activities for the gold(I) complexes, being more active than cisplatin in all the tested tumor cell lines. Gold(I) compounds (1), (2), (3), (4) and (6) exhibited relevant antitubercular activity even when compared with first line drugs such as rifampicin.

  18. Vascular endothelial growth factor receptor-2 (VEGFR-2) inhibitors: development and validation of predictive 3-D QSAR models through extensive ligand- and structure-based approaches

    NASA Astrophysics Data System (ADS)

    Ragno, Rino; Ballante, Flavio; Pirolli, Adele; Wickersham, Richard B.; Patsilinakos, Alexandros; Hesse, Stéphanie; Perspicace, Enrico; Kirsch, Gilbert

    2015-08-01

    Vascular endothelial growth factor receptor-2, (VEGFR-2), is a key element in angiogenesis, the process by which new blood vessels are formed, and is thus an important pharmaceutical target. Here, 3-D quantitative structure-activity relationship (3-D QSAR) were used to build a quantitative screening and pharmacophore model of the VEGFR-2 receptors for design of inhibitors with improved activities. Most of available experimental data information has been used as training set to derive optimized and fully cross-validated eight mono-probe and a multi-probe quantitative models. Notable is the use of 262 molecules, aligned following both structure-based and ligand-based protocols, as external test set confirming the 3-D QSAR models' predictive capability and their usefulness in design new VEGFR-2 inhibitors. From a survey on literature, this is the first generation of a wide-ranging computational medicinal chemistry application on VEGFR2 inhibitors.

  19. Ligand exchange inducing efficient incorporation of CisPt derivatives into Ureasil-PPO hybrid and their interactions with the multifunctional hybrid network.

    PubMed

    Molina, Eduardo F; Pulcinelli, Sandra H; Santilli, Celso V; Briois, Valérie

    2012-07-12

    Efficient incorporation of (PtCl3EtOH)(-) anion derived from CisPt moiety into ureasil-PPO (poly(propylene oxide)) network was achieved from one-pot sol-gel synthesis carried out in the presence of water, HCl, and ethanol. Reactant proportion was adequately chosen to lead the sol-gel formation of siloxane nodes at the end of short PPO chains, to prevent the CisPt hydrolysis, and to induce platinum ligand exchange. The efficient dissolution of Pt species and the formation of a homogeneous liquid-like solution on the transparent and elastomeric ureasil-PPO hybrid were evidenced by differential scanning calorimetry and small-angle X-ray scattering. The CisPt ligand exchange and the formation of a Zeise-type salt Y(+)(PtCl3R)(-) were demonstrated by Raman spectroscopy and Pt L3-edge EXAFS analysis. In light of these results and in agreement with the proportion of reactants introduced in the media for synthesis and those self-produced by hydrolysis and condensation processes, we proposed for R the ethanol moiety and for Y the ammonium cation. The Raman spectroscopy studies indicated also that the ammonium cations are coordinated by the ether-type oxygen atoms of the PPO chains backbone, whereas the amine groups of the urea linkage participate in the (PtCl3EtOH)(-) anion coordination. In situ Raman monitoring of Pt species decomplexation induced by immersion of hybrid matrix in water highlighted the specific participation of Pt ligands in interaction with the urea group and of NH4(+) cations coordinated by ether-type oxygen atoms in the formation of supramolecular interactions between the PPO chains. The electrospray mass spectrometry analysis of the Pt species released in water from the ureasil-PPO hybrid evidenced that the structure of the complex, NH4 (PtCl3 EtOH), incorporated in the matrix is totally preserved after delivery. Due to both well-known antitumoral and catalytic activities of Pt species, the results reported herein are of prime importance for further

  20. Pigment epithelium-derived factor (PEDF) prevents retinal cell death via PEDF Receptor (PEDF-R): identification of a functional ligand binding site.

    PubMed

    Subramanian, Preeti; Locatelli-Hoops, Silvia; Kenealey, Jason; DesJardin, Jacqueline; Notari, Luigi; Becerra, S Patricia

    2013-08-16

    The extracellular pigment epithelium-derived factor (PEDF) displays retina survival activity by interacting with receptor proteins on cell surfaces. We have previously reported that PEDF binds and stimulates PEDF receptor (PEDF-R), a transmembrane phospholipase. However, the PEDF binding site of PEDF-R and its involvement in survival activity have not been identified. The purpose of this work is to identify a biologically relevant ligand-binding site on PEDF-R. PEDF bound the PEDF-R ectodomain L4 (Leu(159)-Met(325)) with affinity similar to the full-length PEDF-R (Met(1)-Leu(504)). Binding assays using synthetic peptides spanning L4 showed that PEDF selectively bound E5b (Ile(193)-Leu(232)) and P1 (Thr(210)-Leu(249)) peptides. Recombinant C-terminal truncated PEDF-R4 (Met(1)-Leu(232)) and internally truncated PEDF-R and PEDF-R4 (ΔHis(203)-Leu(232)) retained phospholipase activity of the full-length PEDF-R. However, PEDF-R polypeptides without the His(203)-Leu(232) region lost the PEDF affinity that stimulated their enzymatic activity. Cell surface labeling showed that PEDF-R is present in the plasma membranes of retina cells. Using siRNA to selectively knock down PEDF-R in retina cells, we demonstrated that PEDF-R is essential for PEDF-mediated cell survival and antiapoptotic activities. Furthermore, preincubation of PEDF with P1 and E5b peptides blocked the PEDF·PEDF-R-mediated retina cell survival activity, implying that peptide binding to PEDF excluded ligand-receptor interactions on the cell surface. Our findings establish that PEDF-R is required for the survival and antiapoptotic effects of PEDF on retina cells and has determinants for PEDF binding within its L4 ectodomain that are critical for enzymatic stimulation.

  1. A new approach for the development of tracers: data base screening and in silico modeling for the identification of new ligands for SSTR2.

    PubMed

    Cheng, Caixia; Pan, Leyun; Dimitrakopoulou-Strauss, Antonia; Strauss, Ludwig G

    2008-01-01

    New ligands are needed to improve diagnostics and treatment of SSTR2 expressing tumors. We implemented a procedure to identify ligands based on computer processing methods. A multistep procedure was used. Search entries were taken from National Cancer Institute database. Application of criteria defined by the Lipinski rules reduced the initial data set. Then a pharmacophore criterion including Lys and Trp residues was the next step of the hierarchical filtering, and the ligands considered were transformed from 2D to 3D. Finally, dedicated software was applied for docking ligand studies. Our results have shown that by virtual screening and trial docking, we identified novel ligands with better scores of docked poses compared with previously reported ligands. In conclusion, the use of a focused library that incorporates an initial probe, improved the possibility of a successful virtual screening as compared with random screening and is cost efficient by further combination of trial docking.

  2. Evaluation of Several Two-Step Scoring Functions Based on Linear Interaction Energy, Effective Ligand Size, and Empirical Pair Potentials for Prediction of Protein-Ligand Binding Geometry and Free Energy

    PubMed Central

    Rahaman, Obaidur; Estrada, Trilce P.; Doren, Douglas J.; Taufer, Michela; Brooks, Charles L.; Armen, Roger S.

    2011-01-01

    The performance of several two-step scoring approaches for molecular docking were assessed for their ability to predict binding geometries and free energies. Two new scoring functions designed for “step 2 discrimination” were proposed and compared to our CHARMM implementation of the linear interaction energy (LIE) approach using the Generalized-Born with Molecular Volume (GBMV) implicit solvation model. A scoring function S1 was proposed by considering only “interacting” ligand atoms as the “effective size” of the ligand, and extended to an empirical regression-based pair potential S2. The S1 and S2 scoring schemes were trained and five-fold cross validated on a diverse set of 259 protein-ligand complexes from the Ligand Protein Database (LPDB). The regression-based parameters for S1 and S2 also demonstrated reasonable transferability in the CSARdock 2010 benchmark using a new dataset (NRC HiQ) of diverse protein-ligand complexes. The ability of the scoring functions to accurately predict ligand geometry was evaluated by calculating the discriminative power (DP) of the scoring functions to identify native poses. The parameters for the LIE scoring function with the optimal discriminative power (DP) for geometry (step 1 discrimination) were found to be very similar to the best-fit parameters for binding free energy over a large number of protein-ligand complexes (step 2 discrimination). Reasonable performance of the scoring functions in enrichment of active compounds in four different protein target classes established that the parameters for S1 and S2 provided reasonable accuracy and transferability. Additional analysis was performed to definitively separate scoring function performance from molecular weight effects. This analysis included the prediction of ligand binding efficiencies for a subset of the CSARdock NRC HiQ dataset where the number of ligand heavy atoms ranged from 17 to 35. This range of ligand heavy atoms is where improved accuracy of

  3. Evaluation of several two-step scoring functions based on linear interaction energy, effective ligand size, and empirical pair potentials for prediction of protein-ligand binding geometry and free energy.

    PubMed

    Rahaman, Obaidur; Estrada, Trilce P; Doren, Douglas J; Taufer, Michela; Brooks, Charles L; Armen, Roger S

    2011-09-26

    The performances of several two-step scoring approaches for molecular docking were assessed for their ability to predict binding geometries and free energies. Two new scoring functions designed for "step 2 discrimination" were proposed and compared to our CHARMM implementation of the linear interaction energy (LIE) approach using the Generalized-Born with Molecular Volume (GBMV) implicit solvation model. A scoring function S1 was proposed by considering only "interacting" ligand atoms as the "effective size" of the ligand and extended to an empirical regression-based pair potential S2. The S1 and S2 scoring schemes were trained and 5-fold cross-validated on a diverse set of 259 protein-ligand complexes from the Ligand Protein Database (LPDB). The regression-based parameters for S1 and S2 also demonstrated reasonable transferability in the CSARdock 2010 benchmark using a new data set (NRC HiQ) of diverse protein-ligand complexes. The ability of the scoring functions to accurately predict ligand geometry was evaluated by calculating the discriminative power (DP) of the scoring functions to identify native poses. The parameters for the LIE scoring function with the optimal discriminative power (DP) for geometry (step 1 discrimination) were found to be very similar to the best-fit parameters for binding free energy over a large number of protein-ligand complexes (step 2 discrimination). Reasonable performance of the scoring functions in enrichment of active compounds in four different protein target classes established that the parameters for S1 and S2 provided reasonable accuracy and transferability. Additional analysis was performed to definitively separate scoring function performance from molecular weight effects. This analysis included the prediction of ligand binding efficiencies for a subset of the CSARdock NRC HiQ data set where the number of ligand heavy atoms ranged from 17 to 35. This range of ligand heavy atoms is where improved accuracy of predicted ligand

  4. A methacrylate-based polymeric imidazole ligand yields quantum dots with low cytotoxicity and low nonspecific binding

    PubMed Central

    Johnson, Colin M.; Pate, Kayla M.; Shen, Yi; Viswanath, Anand; Tan, Rui; Benicewicz, Brian C.; Moss, Melissa A.; Greytak, Andrew B.

    2016-01-01

    This paper assesses the biocompatibility for fluorescence imaging of colloidal nanocrystal quantum dots (QDs) coated with a recently-developed multiply-binding methacrylate-based polymeric imidazole ligand. The QD samples were purified prior to ligand exchange via a highly repeatable gel permeation chromatography (GPC) method. A multi-well plate based protocol was used to characterize nonspecific binding and toxicity of the QDs toward human endothelial cells. Nonspecific binding in 1% fetal bovine serum was negligible compared to anionically-stabilized QD controls, and no significant toxicity was detected on 24 h exposure. The nonspecific binding results were confirmed by fluorescence microscopy. This study is the first evaluation of biocompatibility in QDs initially purified by GPC and represents a scalable approach to comparison among nanocrystal-based bioimaging scaffolds. PMID:26247382

  5. Synthesis, spectroscopic characterization and X-ray structures of five-coordinate diorganotin(IV) complexes containing 5-hydroxypyrazoline derivatives as ligands

    NASA Astrophysics Data System (ADS)

    Sousa, Gerimário F. de; Garcia, Edgardo; Gatto, Claudia C.; Resck, Inês S.; Deflon, Victor M.; Ardisson, José D.

    2010-09-01

    Four new diorganotin(IV) complexes have been prepared from R 2SnCl 2 (R = Me, Ph) with the ligands 5-hydroxy-3-metyl-5-phenyl-1-( S-benzildithiocarbazate)-pyrazoline (H 2L 1) and 5-hydroxy-3-methyl-5-phenyl-1-(2-thiophenecarboxylic)-pyrazoline (H 2L 2). The complexes were characterized by elemental analysis, IR, 1H, 13C, 119Sn NMR and Mössbauer spectroscopies. The complexes [Me 2SnL 1], [Ph 2SnL 1] and [Me 2SnL 2] were also studied by single crystal X-ray diffraction and the results showed that the Sn(IV) central atom of the complexes adopts a distorted trigonal bipyramidal (TBP) geometry with the N atom of the ONX-tridentate (X = O and S) ligand and two organic groups occupying equatorial sites. The C-Sn-C angles for [Me 2Sn(L 1)] and [Ph 2Sn(L 1)] were calculated using a correlation between 119Sn Mössbauer and X-ray crystallographic data based on the point-charge model. Theoretical calculations were performed with the B3LYP density functional employing 3-21G(*) and DZVP all electron basis sets showing good agreement with experimental findings. General and Sn(IV) specific IR harmonic frequency scale factors for both basis sets were obtained from comparison with selected experimental frequencies.

  6. New potent αvβ3 integrin ligands based on azabicycloalkane (γ,α)-dipeptide mimics.

    PubMed

    Pilkington-Miksa, M; Araldi, E M V; Arosio, D; Belvisi, L; Civera, M; Manzoni, L

    2016-03-28

    We have designed a new synthetic strategy for the preparation of a new class of cyclic RGD integrin ligands in which the azabicycloalkane scaffold can be envisaged as a (γ,α) dipeptide mimic. The synthesis and in vitro biological evaluation of these RGD derivatives, as well as the computational study of their conformational properties and binding modes to αVβ3 integrin are described. Compound has shown to be a promising candidate as αVβ3 integrin antagonist able to interfere with both cell adhesion and movement on vitronectin with no evidence of cytotoxic effects.

  7. Ligand based virtual screening to find novel inhibitors against plant toxin Ricin by using the ZINC database.

    PubMed

    Mishra, Vinita; Siva Prasad, C V S

    2011-01-01

    Ricin is known as a potent toxin against animals. It consists of two chains, Ricin Toxin A (RTA) and Ricin Toxin B (RTB). The toxic effect is known to be caused by RTA. Inhibitors for RTA with less efficiency have been reported. Hence, it is of interest to identify new inhibitors. Virtual screening methods (computer aided drug designing) to find similar molecules in drug database were used for screening new inhibitors against RTA. We used the structure of RTA in complex with Pteroic acid (PDB code: 1BR6) as target molecule. Ligand based virtual screening approach was used in which the known inhibitory molecule Pteroic acid (PTA) served as a template to identify similar ligands from the ZINC database. These ligands were docked inside the binding pocket of RTA by using the MVD (Molegro Virtual Docker). This approach successfully identified six novel compounds. These docked ligands interacted with Asn78, Ala79, Val81, Gly121 and Ser176 amino acids, which are key residues of the RTA active site. Three compounds in particular, ZINC05156321 (6, 7 diphenylpteridin-4-ol), ZINC05156324 (6, 7-bis (3-fluorophenyl) pteridin-4-ol) and ZINC08555900 (6, 7-bis (4-fluorophenyl)-1H-pteridin-4-one), showed higher binding affinity in comparison to PTA, with high interaction energy, better space fitting and electrostatic interactions. These molecules should be tested for in vitro and in vivo activities in future for consideration as effective inhibitors.

  8. Preparation, spectral and biological investigation of formaldehyde-based ligand containing piperazine moiety and its various polymer metal complexes

    NASA Astrophysics Data System (ADS)

    Khan, Shamim Ahmad; Nishat, Nahid; Parveen, Shadma; Rasool, Raza

    2011-10-01

    A novel tetradentate salicylic acid-formaldehyde ligand containing piperazine moiety (SFP) was synthesized by condensation of salicylic acid, formaldehyde and piperazine in presence of base catalyst, which was subjected for the preparation of coordination polymers with metal ions like manganese(II), cobalt(II), copper(II), nickel(II) and zinc(II). All the synthesized polymeric compounds were characterized by elemental analysis, IR, 1H NMR and electronic spectral studies. The thermal stability was determined by thermogravimetric analysis and thermal data revealed that all the polymer metal complexes show good thermal stability than their parent ligand. Electronic spectral data and magnetic moment values revealed that polymer metal complexes of Mn(II), Co(II) and Ni(II) show an octahedral geometry while Cu(II) and Zn(II) show distorted octahedral and tetrahedral geometry respectively. The antimicrobial screening of the ligand and coordination polymers was done by using Agar well diffusion method against various bacteria and fungi. It was evident from the data that antibacterial and antifungal activity increased on chelation and all the polymer metal complexes show excellent antimicrobial activity than their parent ligand.

  9. Coordination versatility of p-hydroquinone-functionalized dibenzobarrelene-based PC(sp(3))P pincer ligands.

    PubMed

    De-Botton, Sophie; Romm, Ronit; Bensoussan, Guillaume; Hitrik, Maria; Musa, Sanaa; Gelman, Dmitri

    2016-10-12

    The manuscript describes the synthesis and coordination chemistry of a novel diphosphine pincer ligand based on a p-hydroquinone-functionalized dibenzobarrelene scaffold. The p-hydroquinone fragment of the ligand is oxidatively and coordinatively non-innocent and may render new reactivity to the metal center due to implied reversible redox behavior, tautomeric interconversion and metal-hydroxyl/alkoxide coordination switch of the pendant hydroxyl side-arm. Palladium, platinum and iridium complexes were prepared and characterized. Investigation of their coordination chemistry revealed that while tautomeric equilibrium exists in free ligands and in the chelate non-metalated complexes, it is essentially blocked in the corresponding C(sp(3))-pincer compounds due to stabilizing hemilabile coordination of the hydroxyl group. However, its presence in close proximity to the metal center is essential for catalyzing acceptorless dehydrogenation of alcohols by the iridium complexes via the outer-sphere hydrogen transfer mechanism. Remarkably, we found a similar activity for the analogous palladium complexes, which is not characteristic of this metal. This unprecedented reactivity of palladium stresses the fact that besides the choice of an active metal, transformation-oriented design of the ligand is crucial for catalysis.

  10. Rigorous Incorporation of Tautomers, Ionization Species, and Different Binding Modes into Ligand-Based and Receptor-Based 3D-QSAR Methods

    PubMed Central

    Natesan, Senthil; Balaz, Stefan

    2013-01-01

    Speciation of drug candidates and receptors caused by ionization, tautomerism, and/or covalent hydration complicates ligand- and receptor-based predictions of binding affinities by 3-dimensional structure-activity relationships (3D-QSAR). The speciation problem is exacerbated by tendency of tautomers to bind in multiple conformations or orientations (modes) in the same binding site. New forms of the 3D-QSAR correlation equations, capable of capturing this complexity, can be developed using the time hierarchy of all steps that lie behind the monitored biological process – binding, enzyme inhibition or receptor activity. In most cases, reversible interconversions of individual ligand and receptor species can be treated as quickly established equilibria because they are finished in a small fraction of the exposure time that is used to determine biological effects. The speciation equilibria are satisfactorily approximated by invariant fractions of individual ligand and receptor species for buffered experimental or in vivo conditions. For such situations, the observed drug-receptor association constant of a ligand is expressed as the sum of products, for each ligand and receptor species pair, of the association microconstant and the fractions of involved species. For multiple binding modes, each microconstant is expressed as the sum of microconstants of individual modes. This master equation leads to new 3D-QSAR correlation equations integrating the results of all molecular simulations or calculations, which are run for each ligand-receptor species pair separately. The multispecies, multimode 3D-QSAR approach is illustrated by a ligand-based correlation of transthyretin binding of thyroxine analogs and by a receptor-based correlation of inhibition of MK2 by benzothiophenes and pyrrolopyrimidines. PMID:23170882

  11. Neurobiological actions by three distinct subtypes of brain-derived neurotrophic factor: Multi-ligand model of growth factor signaling.

    PubMed

    Mizui, Toshiyuki; Ishikawa, Yasuyuki; Kumanogoh, Haruko; Kojima, Masami

    2016-03-01

    Brain-derived neurotrophic factor (BDNF) is one of the most active members of the neurotrophin family. BDNF not only regulates neuronal survival and differentiation, but also functions in activity-dependent plasticity processes such as long-term potentiation (LTP), long-term depression (LTD), learning, and memory. Like other growth factors, BDNF is produced by molecular and cellular mechanisms including transcription and translation, and functions as a bioactive molecule in the nervous system. Among these mechanisms, a particular post-translational mechanism, namely the conversion of precursor BDNF into mature BDNF by proteolytic cleavage, was not fully understood. In this review, we discuss the manner through which this post-translational mechanism alters the biological actions of BDNF protein. In addition to the initially elucidated findings on BDNF, the biological roles of precursor BDNF and the BDNF pro-peptide, especially synaptic plasticity, will be extensively discussed. Recent findings on the BDNF pro-peptide will provide new insights for understanding the mechanisms of action of the pro-peptides of growth factors.

  12. Fragment-Based Design of Ligands Targeting a Novel Site on the Integrase Enzyme of Human Immunodeficiency Virus;#8197;1

    SciTech Connect

    Wielens, Jerome; Headey, Stephen J.; Deadman, John J.; Rhodes, David I.; Parker, Michael W.; Chalmers, David K.; Scanlon, Martin J.

    2011-08-17

    Fragment-based screening has been used to identify a novel ligand binding site on HIV-1 integrase. Crystal structures of fragments bound at this site (shown) have been used to design elaborated second-generation compounds that bind with higher affinity and good ligand efficiency.

  13. Synthesis and receptor binding of N-substituted tropane derivatives. High-affinity ligands for the cocaine receptor

    SciTech Connect

    Milius, R.A.; Saha, J.K.; Madras, B.K.; Neumeyer, J.L. )

    1991-05-01

    The synthesis and pharmacological characterization of a series of N-substituted 3-(4-fluorophenyl)tropane derivatives is reported. The compounds displayed binding characteristics that paralleled those of cocaine, and several had substantially higher affinity at cocaine recognition sites. Conjugate addition of 4-fluorophenyl magnesium bromide to anhydroecgonine methyl ester gave 2 beta-(carbomethoxy)-3 beta-(4-fluorophenyl)tropane (4a, designated CFT, also known as WIN 35,428) after flash chromatography. N demethylation of 4a was effected by Zn/HOAc reduction of the corresponding 2,2,2-trichloroethyl carbamate to give 2 beta-carbomethoxy-3 beta-(4-fluorophenyl)nortropane (5), which was alkylated with allyl bromide to afford the N-allyl analogue, 6. The N-propyl analogue, 7, was prepared by catalytic reduction (Pd/C) of 6. The most potent analogue, 4a, was tritiated at a specific activity of 81.3 Ci/mmol. ({sup 3}H)4a bound rapidly and reversibly to caudate putamen membranes; the two-component binding curve typical of cocaine analogues was observed. Equilibrium was achieved within 2 h and was stable for at least 4 h. High- and low-affinity Kd values observed for ({sup 3}H)4a (4.7 and 60 nM, respectively) were more than 4 times lower than those for ({sup 3}H)cocaine, and the density of binding sites (Bmax = 50 pmol/g, high, and 290 pmol/g, low) for the two drugs were comparable. Nonspecific binding of ({sup 3}H)4a was 5-10% of total binding.

  14. Metal ion oxidation state assignment based on coordinating ligand hyperfine interaction.

    PubMed

    Oyala, Paul H; Stich, Troy A; Britt, R David

    2015-04-01

    In exchange-coupled mixed-valence spin systems, the magnitude and sign of the effective ligand hyperfine interaction (HFI) can be useful in determining the formal oxidation state of the coordinating metal ion, as well as provide information about the coordination geometry. This is due to the fact that the observed ligand HFI is a function of the projection factor (Clebsch-Gordon coefficient) that maps the site spin value S i of the local paramagnetic center onto the total spin of the exchange-coupled system, S T. Recently, this relationship has been successfully exploited in identifying the oxidation state of the Mn ion coordinated by the sole nitrogenous ligand to the oxygen-evolving complex in certain states of photosystem II. The origin and evolution of these efforts is described.

  15. A molecular-properties-based approach to understanding PDZ domain proteins and PDZ ligands

    PubMed Central

    Giallourakis, Cosmas; Cao, Zhifang; Green, Todd; Wachtel, Heather; Xie, Xiaohui; Lopez-Illasaca, Marco; Daly, Mark; Rioux, John; Xavier, Ramnik

    2006-01-01

    PDZ domain-containing proteins and their interaction partners are mutated in numerous human diseases and function in complexes regulating epithelial polarity, ion channels, cochlear hair cell development, vesicular sorting, and neuronal synaptic communication. Among several properties of a collection of documented PDZ domain–ligand interactions, we discovered embedded in a large-scale expression data set the existence of a significant level of co-regulation between PDZ domain-encoding genes and these ligands. From this observation, we show how integration of expression data, a comparative genomics catalog of 899 mammalian genes with conserved PDZ-binding motifs, phylogenetic analysis, and literature mining can be utilized to infer PDZ complexes. Using molecular studies we map novel interaction partners for the PDZ proteins DLG1 and CARD11. These results provide insight into the diverse roles of PDZ–ligand complexes in cellular signaling and provide a computational framework for the genome-wide evaluation of PDZ complexes. PMID:16825666

  16. Structural Protein–Ligand Interaction Fingerprints (SPLIF) for Structure-Based Virtual Screening: Method and Benchmark Study

    PubMed Central

    2015-01-01

    Accurate and affordable assessment of ligand–protein affinity for structure-based virtual screening (SB-VS) is a standing challenge. Hence, empirical postdocking filters making use of various types of structure–activity information may prove useful. Here, we introduce one such filter based upon three-dimensional structural protein–ligand interaction fingerprints (SPLIF). SPLIF permits quantitative assessment of whether a docking pose interacts with the protein target similarly to a known ligand and rescues active compounds penalized by poor initial docking scores. An extensive benchmark study on 10 diverse data sets selected from the DUD-E database has been performed in order to evaluate the absolute and relative efficiency of this method. SPLIF demonstrated an overall better performance than relevant standard methods. PMID:25116840

  17. Monomeric Ti(iv)-based complexes incorporating luminescent nitrogen ligands: synthesis, structural characterization, emission spectroscopy and cytotoxic activities.

    PubMed

    Khalil, Georges; Orvain, Christophe; Fang, Lu; Barloy, Laurent; Chaumont, Alain; Gaiddon, Christian; Henry, Marc; Kyritsakas, Nathalie; Mobian, Pierre

    2016-11-29

    This manuscript describes the synthesis of a series of neutral titanium(iv) monomeric complexes constructed around a TiO4N2 core. The two nitrogen atoms that compose the coordination sphere of the metallic center belong to 2,2'-bipyrimidine ligands homo-disubstituted in the 4 and 4' positions by methyl (2a), phenylvinyl (2b), naphthylvinyl (2c) or anthrylvinyl (2d) groups. The crystal structures of these complexes named [Ti(1)2(2a)], [Ti(1)2(2b)], [Ti(1)2(2c)] and [Ti(1)2(2d)] (where 1 is a 2,2'-biphenolato ligand substituted in the 6 and 6' positions by phenyl groups) are reported. The hydrolytic stability of the four complexes is evaluated by monitoring the evolution of the free 2a-d signals by (1)H NMR spectroscopy. For the conditions tested (6 mM, DMSO-d6/D2O: 8/1), a rather good stability with t1/2 ranging from 180 to 300 min is determined for the complexes. In the presence of an acid (DCl), the hydrolysis of [Ti(1)2(2a)] is faster than without an acid. The cytotoxic activity against gastric cancer cells of the titanium-based compounds and the free disubstituted 2,2'-bipyrimidine ligands is tested, showing IC50 ranging from 6.2 ± 1.2 μM to 274 ± 56 μM. The fluorescence studies of the ligands 2a-d, and the complexes [Ti(1)2(2a-d)] reveal an important fluorescence loss of the ligands 2c and 2d upon coordination with the Ti(1)2 fragment. Frontier orbitals obtained by DFT calculations permit us to explain this fluorescence quenching.

  18. Theoretical spectroscopic study of seven zinc(II) complex with macrocyclic Schiff-base ligand.

    PubMed

    Sayin, Koray; Kariper, Sultan Erkan; Sayin, Tuba Alagöz; Karakaş, Duran

    2014-12-10

    Seven zinc complexes, which are [ZnL(1)](2+), [ZnL(2)](2+), [ZnL(3)](2+), [ZnL(4)](2+), [ZnL(5)](2+), [ZnL(6)](2+) and [ZnL(7)](2+), are studied as theoretically. Structural parameters, vibration frequencies, electronic absorption spectra and (1)H and (13)C NMR spectra are obtained for Zn(II) complexes of macrocyclic penta and heptaaza Schiff-base ligand. Vibration spectra of Zn(II) complexes are studied by using Density Functional Theory (DFT) calculations at the B3LYP/LANL2DZ. The UV-VIS and NMR spectra of the zinc complexes are obtained by using Time Dependent-Density Functional Theory (TD-DFT) method and Giao method, respectively. The agreements are found between experimental data of [ZnL(5)](2+), [ZnL(6)](2+) and [ZnL(7)](2+) complex ions and their calculated results. The geometries of complexes are found as distorted pentagonal planar for [ZnL(1)](2+), [ZnL(2)](2+) and [ZnL(3)](2+) complex ions, distorted tetrahedral for [ZnL(4)](2+) complex ion and distorted pentagonal bipyramidal for [ZnL(5)](2+), [ZnL(6)](2+) and [ZnL(7)](2+) complex ions. Ranking of biological activity is determined by using quantum chemical parameters and this ranking is found as: [ZnL(7)](2+)>[ZnL(6)](2+)>[ZnL(5)](2+)>[ZnL(3)](2+)>[ZnL(2)](2+)>[ZnL(1)](2+).

  19. Chiral Phosphoric Acid-Catalyzed Enantioselective Reductive Amination of 2-Pyridyl Ketones: Construction of Structurally Chiral Pyridine-Based Ligands.

    PubMed

    Abudu Rexit, Abulikemu; Luo, Shiwei; Mailikezati, Maihemuti

    2016-11-18

    A chiral phosphoric acid-catalyzed one-pot enantioselective reductive amination of 2-pyridyl ketones was realized to provide chiral pyridine-based ligands in excellent yields with high enantioselectivities (up to 98% yield, 94% ee). Computational studies on the key intermediate imine and transition state of the hydride transfer process revealed that the nitrogen atom of the pyridyl ring might be an important factor to significantly promote both the reaction activity and enantioselectivity.

  20. ProPose: steered virtual screening by simultaneous protein-ligand docking and ligand-ligand alignment.

    PubMed

    Seifert, Markus H J

    2005-01-01

    The 'model-free' screening engine ProPose implements a general method for performing simultaneous protein-ligand docking, ligand-ligand alignment, pharmacophore queries-and combinations thereof-in order to incorporate a priori information into screening protocols. In this manuscript we describe a case study on herpes simplex virus thymidine kinase, an important antiviral drug target, where we evaluate different approaches for handling a specific type of a priori information, i.e., multiple target structures. We demonstrate that a simultaneous alignment on two target structures--in conjunction with logic operations on interactions and docking constraints derived from protein structure--is an effective means of (i) improving the enrichment of chemical substructures that are compatible with the a priori known ligands, (ii) ensuring the steric fit into the target protein, and (iii) handling target flexibility. The combination of ligand- and receptor-based methods steers the virtual screening by ranking molecules according to the similarity of their interaction pattern with known ligands, thereby--to some extent--outweighing the deficiencies of simple scoring functions often used in initial virtual screening.

  1. Unsymmetrical Schiff base (ON) ligand on complexation with some transition metal ions: Synthesis, spectral characterization, antibacterial, fluorescence and thermal studies

    NASA Astrophysics Data System (ADS)

    Ali, Omyma A. M.; El-Medani, Samir M.; Abu Serea, Maha R.; Sayed, Abeer S. S.

    2015-02-01

    A series of eight metal Schiff base complexes were synthesized by the thermal reaction of Cu(II), Ni(II), Fe(III), Co(II), Zn(II), Hg(II), La(III) or Sm(III) with a Schiff base "L" produced by the condensation of furfuraldehyde and 1,2-diaminobenzene. These compounds were characterized by elemental analysis, UV-Vis, FT-IR, molar conductance, mass spectrometry, thermal and fluorescence studies. The studies suggested the coordination of the ligand L to metal through azomethine imine nitrogen and furan oxygen atoms of Schiff base moiety. Thermogravimetric (TG/DTG) analyses data were studied and indicated high stability for all complexes and suggested the presence of lattice and/or coordinated water molecules in the complexes. Coats-Redfern method has been used to calculate the kinetic and thermodynamic parameters of the metal complexes. The spectral and thermal analysis reveal that all complexes have octahedral geometry except Cu(II) and Ni(II) complexes which can attain a square planner arrangements. The ligand and its complexes exhibited intraligand (π-π∗) fluorescence and can potentially serve as photoactive materials. Both the ligand and its complexes have been screened for antibacterial activities.

  2. Chiral Bidentate NHC Ligands Based on the 1,1'-Binaphthyl Scaffold: Synthesis and Application in Transition-Metal-Catalyzed Asymmetric Reactions.

    PubMed

    Xu, Qin; Gu, Peng; Jiang, Hanchun; Wei, Yin; Shi, Min

    2016-12-01

    The use of the chiral 1,1'-binaphthyl scaffold to construct chiral ligands can be traced back for a long time. However, the development of bidentate NHC ligands based on the same backbone has only appeared recently. In this account, we describe the design and synthesis of a new family of chiral NHC ligands based on the 1,1'-binaphthyl scaffold and demonstrate the applications of these chiral NHC-metal complexes in the catalyzed oxidative kinetic resolution of secondary alcohols, asymmetric carbon-carbon bond formations, hydrosilylations, and cyclizations of 1,6-enynes. The chiral NHC ligands containing the 1,1'-binaphthyl backbone can be synthesized in good yields from enantiomerically pure 1,1'-binaphthyl-2,2'-diamine. These transition metals coordinated with chiral bidentate NHC ligands exhibit high catalytic activities and good enantioselectivities for a wide range of metal-catalyzed asymmetric reactions.

  3. Fast O2 Binding at Dicopper Complexes Containing Schiff-Base Dinucleating Ligands

    PubMed Central

    Company, Anna; Gómez, Laura; Mas-Ballesté, Rubén; Korendovych, Ivan V.; Ribas, Xavi; Poater, Albert; Parella, Teodor; Fontrodona, Xavier; Benet-Buchholz, Jordi; Solà, Miquel; Que, Lawrence; Rybak-Akimova, Elena; Costas, Miquel

    2008-01-01

    A new family of dicopper(I) complexes [CuI2RL](X)2, (R = H, 1X, R = tBu, 2X and R = NO2, 3X, X = CF3SO3, ClO4, SbF6 or BArF, BArF = [B{3,5-(CF3)2-C6H3}4]−), where RL is a Schiff-base ligand containing two tridentate binding sites linked by a xylyl spacer have been prepared, characterized, and their reaction with O2 studied. The complexes were designed with the aim of reproducing structural aspects of the active site of type 3 dicopper proteins; they contain two three-coordinate copper sites and a rather flexible podand ligand backbone. The solid state structures of 1ClO4, 2CF3SO3, 2ClO4 and 3BArF·CH3CN have been established by single crystal X-ray diffraction analysis. 1ClO4 adopts a polymeric structure in solution while 2CF3SO3, 2ClO4 and 3BArF·CH3CN are monomeric. The complexes have been studied in solution by means of 1H and 19F NMR spectroscopy, which put forward the presence of dynamic processes in solution. 1-3BArF and 1-3CF3SO3 in acetone react rapidly with O2 to generate metaestable [CuIII2(μ-O)2(RL)]2+ 1-3(O2) and [CuIII2(μ-O)2(CF3SO3)(RL)]+ 1-3(O2)(CF3SO3) species, respectively that have been characterized by UV-vis spectroscopy and resonance Raman analysis. Instead, reaction of 1-3BArF with O2 in CH2Cl2 results in intermolecular O2 binding. DFT methods have been used to study the chemical identities and structural parameters of the O2 adducts, and the relative stability of the CuIII2(μ-O)2 form with respect to the CuII2(μ-η2: η2-peroxo) isomer. The reaction of 1X, X = CF3SO3 and BArF with O2 in acetone has been studied by stopped-flow exhibiting an unexpected very fast reaction rate (k = 3.82(4) × 103 M−1s−1, ΔH‡ = 4.9 ± 0.5 kJ·mol−1, ΔS‡ = −148 ± 5 J·K−1·mol−1), nearly three orders of magnitude faster than in the parent [CuI2(m-XYLMeAN)]2+. Thermal decomposition of 1-3(O2) does not result in aromatic hydroxylation. The mechanism and kinetics of O2 binding to 1X (X = CF3SO3 and BArF) is discussed and compared with those

  4. Lignin-derivatives based polymers, blends and composites: A review.

    PubMed

    Naseem, Amina; Tabasum, Shazia; Zia, Khalid Mahmood; Zuber, Mohammad; Ali, Muhammad; Noreen, Aqdas

    2016-12-01

    Lignin and lignin derivatives biopolymers have several properties, such as high thermal stability, antioxidant, biodegradability, antimicrobial actions, adhesive properties, etc., and thus they can be extensively used in wide range of areas. Although human history mostly depend on the biopolymers, however derivatives of lignin such as sulfonate, phenolic, organosolv, Kraft and sodium sulfonate lignin have good mechanical and physicochemical properties. Well-designed materials such as coatings and paints, manufacturing of plastics and resins, for rubber packaging, for fuel production etc., can be obtained by the functionalizations of chemically modified lignin. Considering multi purposes properties of the lignin and lignin derivatives and extensive industrial applications of derivatives, this review sheds a light on lignin derivatives based materials with their prospective applications. All the technical scientific issues have been addressed highlighting the recent advancement.

  5. Reactivity of tris(acetylacetonato) iron(III) with tridentate [ONO] donor Schiff base as an access to newer mixed-ligand iron(III) complexes

    NASA Astrophysics Data System (ADS)

    Bhattacharjee, Chira R.; Goswami, Pankaj; Pramanik, Harun A. R.; Paul, Pradip C.; Mondal, Paritosh

    2011-05-01

    Two new mixed-ligand iron(III) complexes, [Fe(L n)(acac)(C 2H 5OH)] incorporating coordinated ethanol from the reaction solvent were accessed from the reaction of [Fe(acac) 3] with [ONO] donor dibasic tridentate unsymmetrical Schiff base ligands derived from condensation of 2-hydroxy-1-napthaldehyde with 2-aminophenol (H 2L 1) or 2-aminobenzoic acid (H 2L 2). The thermal study (TGA-DTA) provided evidence for weakly bound ethanol which is readily substituted by neutral N-donor molecule imidazole, benzimidazole or pyridine to produce an array of newer complexes, [Fe(L n)(acac)X] ( n = 1, 2; X = Im, Bim, Py). The compounds were characterized by elemental analyses, FT-IR, UV-vis, solution electrical conductivity, FAB mass, 1H and 13C NMR spectroscopy. Room temperature magnetic susceptibility measurements ( μeff ˜ 5.8 B.M.) are consistent with spin-free octahedral iron(III) complexes. Cyclic voltammetry of ethanol complexes revealed a quasi-reversible one electron redox response (Δ Ep > 100 mV) for the Fe(III)/Fe(II) couple. Low half wave redox potential ( E1/2) values suggested easy redox susceptibility. The ground state geometries of the ethanol and imidazole complexes have been ascertained to be distorted octahedral by density functional theory using DMol3 program at BLYP/DNP level.

  6. Identification and synthesis of [1,2,4]triazolo[3,4-a]phthalazine derivatives as high-affinity ligands to the alpha 2 delta-1 subunit of voltage gated calcium channel.

    PubMed

    Lebsack, Alec D; Gunzner, Janet; Wang, Bowei; Pracitto, Richard; Schaffhauser, Hervé; Santini, Angelina; Aiyar, Jayashree; Bezverkov, Robert; Munoz, Benito; Liu, Wensheng; Venkatraman, Shankar

    2004-05-17

    We have identified and synthesized a series of [1,2,4]triazolo[3,4-a]phthalazine derivatives as high-affinity ligands to alpha 2 delta-1 subunit of voltage gated calcium channels. Structure-activity relationship studies directed toward improving the potency and physical properties of 2 lead to the discovery of 20 (IC(50)=15 nM) and (S)-22 (IC(50)=30 nM). A potent and selective radioligand, [(3)H]-(S)-22 was also synthesized to demonstrate that this ligand binds to the same site as gabapentin.

  7. Perchlorate mixed-ligand copper(II) complexes of beta-diketone and ethylene diamine derivatives: thermal, spectroscopic and biochemical studies.

    PubMed

    El-Ayaan, Usama; El-Metwally, Nashwa M; Youssef, Magdy M; El Bialy, Serry A A

    2007-12-31

    The present work carried out a study on perchlorate mixed-ligand copper(II) complexes which have been synthesized from ethylenediamine derivatives (3a-c) and beta-diketones. These complexes, namely [Cu(DA-Cl)(acac)H(2)O]ClO(4)4, [Cu(DA-Cl)(bzac)H(2)O]H(2)O.ClO(4)5, [Cu(DA-OMe)(acac)H(2)O]ClO(4)6, [Cu(DA-OMe)(bzac)H(2)O]ClO(4)7, [Cu(DA-H)(acac)H(2)O]2H(2)O.ClO(4)8 and [Cu(DA-H)(bzac)H(2)O]ClO(4)9 (where acac, acetylacetonate and bzac, benzoylacetonate) were characterized by elemental analysis, spectral (IR and UV-vis) and magnetic moment measurements. Thermal properties and decomposition kinetics of all complexes are investigated. The interpretation, mathematical analysis and evaluation of kinetic parameters (E, A, DeltaH, DeltaS and DeltaG) of all thermal decomposition stages have been evaluated using Coats-Redfern equation. The biochemical studies showed that, the diamines 3a-c have powerful effects on degradation of DNA and protein. The antibacterial screening demonstrated that, the diamine (DA-Cl), 3b has the maximum and broad activities against Gram +ve and Gram -ve bacterial strains.

  8. Perchlorate mixed-ligand copper(II) complexes of β-diketone and ethylene diamine derivatives: Thermal, spectroscopic and biochemical studies

    NASA Astrophysics Data System (ADS)

    El-Ayaan, Usama; El-Metwally, Nashwa M.; Youssef, Magdy M.; El Bialy, Serry A. A.

    2007-12-01

    The present work carried out a study on perchlorate mixed-ligand copper(II) complexes which have been synthesized from ethylenediamine derivatives ( 3a- c) and β-diketones. These complexes, namely [Cu(DA-Cl)(acac)H 2O]ClO 44, [Cu(DA-Cl)(bzac)H 2O]H 2O.ClO 45, [Cu(DA-OMe)(acac)H 2O]ClO 46, [Cu(DA-OMe)(bzac)H 2O]ClO 47, [Cu(DA-H)(acac)H 2O]2H 2O.ClO 48 and [Cu(DA-H)(bzac)H 2O]ClO 49 (where acac, acetylacetonate and bzac, benzoylacetonate) were characterized by elemental analysis, spectral (IR and UV-vis) and magnetic moment measurements. Thermal properties and decomposition kinetics of all complexes are investigated. The interpretation, mathematical analysis and evaluation of kinetic parameters ( E, A, Δ H, Δ S and Δ G) of all thermal decomposition stages have been evaluated using Coats-Redfern equation. The biochemical studies showed that, the diamines 3a- c have powerful effects on degradation of DNA and protein. The antibacterial screening demonstrated that, the diamine (DA-Cl), 3b has the maximum and broad activities against Gram +ve and Gram -ve bacterial strains.

  9. APL-1, an altered peptide ligand derived from heat-shock protein, alone or combined with methotrexate attenuates murine collagen-induced arthritis.

    PubMed

    Lorenzo, Norailys; Altruda, Fiorella; Silengo, Lorenzo; Del Carmen Dominguez, Maria

    2016-05-09

    Induction of tolerance to autoantigens in vivo is a complex process that involves several mechanisms such as the induction of regulatory T cells and changes in the cytokine and chemokine profiles. This approach represents an attractive alternative for treatment of autoimmune diseases. APL-1 is an altered peptide ligand derived from a novel CD4 + T cell epitope of human heat-shock protein of 60 kDa (HSP60), an autoantigen involved in the pathogenesis of rheumatoid arthritis (RA). We have shown previously that this peptide efficiently inhibited the course of adjuvant-induced arthritis in Lewis rats and induced regulatory T cell (Treg) in ex vivo assay with PBMC isolated from RA patients. This study was undertaken to evaluate the therapeutic effect of APL-1 and its combination with methotrexate (MTX) in collagen-induced arthritis (CIA). CIA was induced in male DBA/1 mice at 8 weeks of age by immunization with chicken collagen. APL, MTX or both were administrated beginning from arthritis onset. Therapeutic effect was evaluated by arthritis and joint pathologic scores. In addition, TNFα and IL-10 in sera were measured by ELISA. Treg induction was assessed by FACS analysis. APL-1 inhibits efficiently the course of arthritis in CIA, similar to MTX. In addition, therapy with APL-1 plus MTX reduced CIA in mice, associated with an increase in Treg. These facts reinforce the therapeutic possibilities of APL-1 as a candidate drug for treatment of RA.

  10. Part I. Naltrexone-derived conjugate addition ligands for opioid receptors. Part II. Chemical and enantioselective aspects of the metabolism of verapamil

    SciTech Connect

    Olsen, L.D.

    1987-01-01

    Selective chemoaffinity ligands to aid in identification and purification of opioid receptor subtypes were prepared from 6..cap alpha..- and 6..beta..-naltrexol, obtained stereoselectively from the ..mu..-receptor antagonist naltrexone. The targets were the 6..cap alpha..- and 6..beta..-methacrylate ethers and 6..cap alpha..- and 6..beta..-methacrylate esters prepared from reaction of 6..cap alpha..- and 6..beta..-naltrexol with methyl ..cap alpha..-(bromomethyl)acrylate or methacryloyl chloride. Of three methacrylate derivatives, the 6..cap alpha..-ether was the most potent in an opioid receptor binding assay with (/sup 3/H)-naltrexone. In the presence of sodium ion, preincubation of the 6..cap alpha..-ether resulted in recovery of about 60% of original (/sup 3/H)-naltrexone binding suggesting some irreversible effects. The methacrylate esters precipitated withdrawal in morphine dependent monkeys. The enantiomers of verapamil, a calcium channel antagonist, have different pharmacological and pharmacokinetic properties. The oxidative metabolism of verapamil was studied in rat and human liver microsomes and in man after a single oral dose.

  11. Glial cell line-derived neurotrophic factor family ligands enhance capsaicin-stimulated release of calcitonin gene-related peptide from sensory neurons.

    PubMed

    Schmutzler, B S; Roy, S; Hingtgen, C M

    2009-06-16

    The glial cell line-derived neurotrophic factor (GDNF) family ligands (GFLs) are a group of peptides that have been implicated as important factors in inflammation, since they are released in increased amounts during inflammation and induce thermal hyperalgesia upon injection. Mouse isolated sensory neurons in culture and freshly dissociated spinal cord slices were used to examine the enhancement in stimulated-release of the neuropeptide, calcitonin gene-related peptide (CGRP), as a measure of sensitization. Exposure of isolated sensory neurons in culture to GDNF, neurturin, and artemin enhanced the capsaicin-stimulated release of immunoreactive calcitonin gene-related peptide (iCGRP) two- to threefold, but did not increase potassium-stimulated release of iCGRP. A similar profile of sensitization was observed in freshly dissociated spinal cord slices. Persephin, another member of the GFL family thought to be important in development, was unable to induce an enhancement in the release of iCGRP. These results demonstrate that specific GFLs are important mediators affecting sensory neuronal sensitivity, likely through modulation of the capsaicin receptor. The sensitization of sensory neurons during inflammation, and the pain and neurogenic inflammation resulting from this sensitization, may be due in part to the effects of these selected GFLs.

  12. Aminoalkyl Derivatives of 8-Alkoxypurine-2,6-diones: Multifunctional 5-HT1A /5-HT7 Receptor Ligands and PDE Inhibitors with Antidepressant Activity.

    PubMed

    Chłoń-Rzepa, Grażyna; Zagórska, Agnieszka; Żmudzki, Paweł; Bucki, Adam; Kołaczkowski, Marcin; Partyka, Anna; Wesołowska, Anna; Kazek, Grzegorz; Głuch-Lutwin, Monika; Siwek, Agata; Starowicz, Gabriela; Pawłowski, Maciej

    2016-12-01

    In the search for potential psychotropic agents, a new series of 3,7-dimet