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Ligands and binding

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https://www.readbyqxmd.com/read/29793215/in-silico-insight-into-voltage-gated-sodium-channel-1-7-inhibition-for-anti-pain-drug-discovery
#1
Mingxing Wang, Wei Li, Ying Wang, Yongbo Song, Jian Wang, Maosheng Cheng
Studies on human genetics have implicated the voltage-gated sodium channel Nav1.7 as an appealing target for the treatment of pain. In this study, we put forward a ligand-based pharmacophore for the first time, which was generated by a set of multiple chemical scaffolds including sulfonamide and non-sulfonamide derivatives and consisted of four chemical features: an aromatic ring, a hydrophobic group and two hydrogen acceptors. The active cavity was divided into three regions according to the properties of the amino acids surrounded and was used for the docking of 16 known active inhibitors...
May 18, 2018: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29793020/epha2-stimulates-vcam-1-expression-through-calcium-dependent-nfat1-activity
#2
Steven Daniel Funk, Alexandra C Finney, Arif Yurdagul, Christopher B Pattillo, A Wayne Orr
Endothelial cell activation by proinflammatory stimuli drives leukocyte recruitment through enhanced expression of counter-receptors such as vascular cell adhesion molecule-1 (VCAM-1). We previously demonstrated that activation of the receptor tyrosine kinase EphA2 with its ligand ephrin-A1 induces VCAM-1 expression. Here, we sought to characterize the proinflammatory signaling pathways involved. Analysis of over-represented transcription factors in ephrin-A1-induced genes identified multiple potential transcriptional regulators, including the Rel family members nuclear factor-κB (NF-κB/p65) and nuclear factor of activated T-cells (NFAT)...
May 21, 2018: Cellular Signalling
https://www.readbyqxmd.com/read/29792807/micelles-protect-intact-metallo-supramolecular-block-copolymer-complexes-from-solution-to-gas-phase-during-electrospray-ionization
#3
Kai Hung Huang, Tsung-Han Tu, Shi-Cheng Wang, Yi-Tsu Chan, Cheng-Chih Hsu
Supramolecular diblock copolymers using metal-ligand coordination can be synthesized under ambient conditions by delicate design of the end groups of the homopolymer chains. However, mass spectrometric analysis of such metallo-supramolecular copolymers is challenging. One of the reasons is the nonpolarity of the polymer chains, making it hard to disperse the complexes in electrospray ionization (ESI)-friendly environments. The other difficulty is the noncovalent nature of such copolymers, which is easily disrupted during the ionization...
May 24, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29792714/docking-screens-for-dual-inhibitors-of-disparate-drug-targets-for-parkinson-s-disease
#4
Mariama Jaiteh, Alexey Zeifman, Marcus Saarinen, Per Svenningsson, José M Brea, Maria Isabel Loza, Jens Carlsson
Modulation of multiple biological targets with a single drug can lead to synergistic therapeutic effects and has been demonstrated to be essential for efficient treatment of CNS disorders. However, rational design of compounds that interact with several targets is very challenging. Here, we demonstrate that structure-based virtual screening can guide the discovery of multi-target ligands of unrelated proteins relevant for Parkinson's disease. A library with 5.4 million molecules was docked to crystal structures of the A2A adenosine receptor (A2AAR) and monoamine oxidase B (MAO-B)...
May 24, 2018: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29792710/measuring-the-adhesion-forces-for-the-multivalent-binding-of-vancomycin-conjugated-dendrimer-to-bacterial-cell-wall-peptide
#5
Elizabeth Peterson, Christine Joseph, Hannah Peterson, Rachael Bouwman, Shengzhuang Tang, Jayme Cannon, Kumar Sinniah, Seok Ki Choi
Multivalent ligand-receptor interaction provides the fundamental basis for the hypothetical notion that high binding avidity relates to the strong force of adhesion. Despite its increasing importance in the design of targeted nanoconjugates, an understanding of the physical forces underlying the multivalent interaction remains a subject of urgent investigation. In this study, we designed three vancomycin (Van)-conjugated dendrimers G5(Van)n (n = mean valency = 0, 1, 4) for bacterial targeting with generation 5 (G5) poly(amidoamine) dendrimer as a multivalent scaffold, and evaluated both their binding avidity and physical force of adhesion to a bacterial model surface by employing surface plasmon resonance (SPR) spectroscopy and atomic force microscopy (AFM)...
May 24, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29792695/bond-dissociation-energies-of-metallo-supramolecular-building-blocks-insight-from-fragmentation-of-selectively-self-assembled-heterometallic-metallo-supramolecular-aggregates
#6
Yvonne Lorenz, Albert Gutiérrez, Montserrat Ferrer, Marianne Engeser
A series of selectively self-assembled metallo-supramolecular square-like macrocycles with unsymmetric ditopic linkers and two different types of metal corners, i.e., {Pd(η3 -2-Me-C3 H4 )} and {M(dppp)} with dppp = 1,3-bis(diphenylphosphino)propane and M = Pd2+ or Pt2+ , have been studied in the gas phase using collision-induced dissociation. The aggregates show distinct fragmentation patterns determined by ligand length, i.e, aggregate size, and type of metal corner. Information on relative binding strength can be deduced...
May 24, 2018: Inorganic Chemistry
https://www.readbyqxmd.com/read/29792330/vancomycin-determination-by-disrupting-electron-transfer-in-a-fluorescence-turn-on-squaraine-anthraquinone-triad
#7
Shue Mei Ng, Xiangyang Wu, M Faisal Khyasudeen, Pawel Jacek Nowakowski, Howe-Siang Tan, Bengang Xing, Edwin K L Yeow
A highly sensitive and selective probe for Vancomycin (Van) in aqueous and serum samples is developed in this study. The probe is based on a triad consisting of a near-infrared squaraine dye (Seta-640) conjugated to two anthraquinone molecules via Lys-D-Ala-D-Ala peptides. In the absence of Van, the close proximity and efficient electron-transfer from the excited Seto-640 dye to anthraquinone result in significant fluorescence quenching of the dye ("off"-state). When Van is added, the antibiotic molecules bind with high affinity to the -D-Ala-D-Ala ligands in a 2:1 stoichiometry (Van:triad); resulting in fluorescence recovery that is as high as 30-times ("on"-state)...
May 24, 2018: ACS Sensors
https://www.readbyqxmd.com/read/29792317/in-situ-reduction-from-uranyl-ion-into-a-tetravalent-uranium-trimer-and-hexamer-featuring-ion-exchange-properties-and-the-alexandrite-effect
#8
Jian Lin, Zenghui Yue, Mark A Silver, Meiying Qie, Xiaomei Wang, Wei Liu, Xiao Lin, Hong-Liang Bao, Lin-Juan Zhang, Shuao Wang, Jian-Qiang Wang
By utilizing zinc amalgam as an in situ reductant and pH regulator, mild hydrothermal reaction between UO2 (CH3 COO)2 ·2H2 O, H2 SO4 , and Cs2 CO3 or between UO2 (CH3 COO)2 ·2H2 O, C2 H4 (SO3 H)2 , and K2 CO3 yielded a novel cesium UIV sulfate trimer Cs4 [U3 O(SO4 )7 ]·2.2H2 O (1) and a new potassium UIV disulfonic hexamer K[U6 O4 (OH)5 (H2 O)5 ][C2 H4 (SO3 )2 ]6 ·6H2 O (2), respectively. Compound 1 features a lamellar structure with a honeycomb lattice, and it represents an unprecedented trimeric UIV cluster composed of purely inorganic moieties...
May 24, 2018: Inorganic Chemistry
https://www.readbyqxmd.com/read/29792150/synthesis-and-biological-evaluation-of-novel-2-3-disubstituted-benzofuran-analogues-of-gaba-as-neurotropic-agents
#9
Arturo Coaviche-Yoval, Hector Luna, Ricardo Tovar-Miranda, Marvin Antonio Soriano-Ursua, Jose G Trujillo-Ferrara
BACKGROUND: Benzofurans are heterocyclic compounds with neurotropic activity. Some have been developed for the treatment of acute and degenerative neuronal injuries. OBJECTIVE: To evaluate the in silico binding of some promising benzofurans on the GABA receptors, and the in vivo neurotropic activity of benzofuran analogues (BZF 6-10) of gamma-aminobutyric acid (GABA) on a seizure model. METHODS: The ligands with the best physicochemical attributes were docked on two GABA receptors (the alpha-1 subunit of GABAA-R and GBR1 subunit of GABAB-R)...
May 23, 2018: Medicinal Chemistry
https://www.readbyqxmd.com/read/29792147/crystal-structure-of-mistletoe-lectin-i-ml-i-from-viscum-album-in-complex-with-4-n-furfurylcytosine-at-2-85-%C3%A3-resolution
#10
Malik Shoaib Ahmad, Saima Rasheed, Sven Falke, Binish Khaliq, Markus Perbandt, M Iqbal Choudhary, Wojciech T Markiewicz, Jan Barciszewski, Christian Betzel
BACKGROUND: Viscum album (the European mistletoe) is a semi-parasitic plant, which is of high medical interest. It is widely found in Europe, Asia and North America. It contains at least three distinct lectins (i.e. ML-I, II, and III), varying in molecular mass and specificity. Among them ML-I is in focus of medical research for various activities, including anti-cancer activities. To understand the molecular basis for such medical applications a few studies have already addressed the structural and functional analysis of ML-I in complex with ligands...
May 23, 2018: Medicinal Chemistry
https://www.readbyqxmd.com/read/29791869/ghrelin-and-the-heart
#11
Takeshi Tokudome, Kentaro Otani, Mikiya Miyazato, Kenji Kangawa
Ghrelin, a growth hormone-releasing peptide that was first discovered in the stomach of rats in 1999, is an endogenous ligand of growth hormone secretagogue receptor. Ghrelin exerts its potent growth hormone-releasing and orexigenic activities by binding to specific receptors in the brain. Subsequent studies showed that ghrelin participates in the regulation of diverse processes, including energy balance, body weight maintenance, and glucose and fat metabolism, and demonstrated that ghrelin is beneficial for treatment of cardiac diseases...
May 20, 2018: Peptides
https://www.readbyqxmd.com/read/29791798/non-natural-linker-configuration-in-2-6-dipeptidyl-anthraquinones-enhances-the-inhibition-of-tar-rna-binding-annealing-activities-by-hiv-1-nc-and-tat-proteins
#12
Alice Sosic, Irene Saccone, Caterina Carraro, Thomas Kenderdine, Elia Gamba, Giuseppe Caliendo, Angela Corvino, Ferdinando Fiorino, Paola DiVaio, Elisa Magli, Elisa Perissutti, Vincenzo Santagada, Beatrice Severino, Valentina Spada, Daniele Fabris, Francesco Frecentese, Barbara Gatto
The HIV-1 nucleocapsid (NC) protein represents an excellent molecular target for the development of antiretrovirals by virtue of its well-characterized chaperone activities, which play pivotal roles in essential steps of the viral life cycle. Our ongoing search for candidates able to impair NC binding/annealing activities led to the identification of peptidyl-anthraquinones as a promising class of nucleic acid ligands. Seeking to elucidate the inhibition determinants and increase the potency of this class of compounds, we have now explored the effects of chirality in the linker connecting the planar nucleus to the basic side chains...
May 23, 2018: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/29791793/assays-for-nucleotide-competitive-reversible-and-irreversible-inhibitors-of-ras-gtpases
#13
Sadasivam Jeganathan, Matthias Philipp Müller, Ali Imtiaz, Roger S Goody
Although the Ras protein has been seen as a potential target for cancer therapy for the past 30 years, there was a tendency to consider it undruggable until recently. This has changed with the demonstration that small molecules with specifcity for (disease related mutants of) Ras can indeed be found, and some of these molecules form covalent adducts. A subgroup of these molecules can be characterized as competing with binding of the natural ligands GTP and GDP. Because of the distinct properties of Ras and related GTPases, in particular the very high nucleotide affinities and associated very low dissociation rates, assays for characterizing such molecules are not trivial...
May 23, 2018: Biochemistry
https://www.readbyqxmd.com/read/29791485/alterations-in-the-brain-interactome-of-the-intrinsically-disordered-n-terminal-domain-of-the-cellular-prion-protein-prpc-in-alzheimer-s-disease
#14
Sarah Ulbrich, Petra Janning, Ralf Seidel, Jakob Matschke, Anika Gonsberg, Sebastian Jung, Markus Glatzel, Martin Engelhard, Konstanze F Winklhofer, Jörg Tatzelt
The cellular prion protein (PrPC) is implicated in neuroprotective signaling and neurotoxic pathways in both prion diseases and Alzheimer's disease (AD). Specifically, the intrinsically disordered N-terminal domain (N-PrP) has been shown to interact with neurotoxic ligands, such as Aβ and Scrapie prion protein (PrPSc), and to be crucial for the neuroprotective activity of PrPC. To gain further insight into cellular pathways tied to PrP, we analyzed the brain interactome of N-PrP. As a novel approach employing recombinantly expressed PrP and intein-mediated protein ligation, we used N-PrP covalently coupled to beads as a bait for affinity purification...
2018: PloS One
https://www.readbyqxmd.com/read/29790539/uranium-iii-complexes-supported-by-hydrobis-mercaptoimidazolyl-borates-synthesis-and-oxidation-chemistry
#15
Leonor Maria, Isabel C Santos, Isabel Santos
The reaction of [UI3(thf)4] with the sodium or lithium salts of hydrobis(2-mercapto-1-methylimidazolyl)borate ligands ([H(R)B(timMe)2]-) in a 1 : 2 ratio, in tetrahydrofuran, gave the U(iii) complexes [UI{κ3-H,S,S'-H(R)B(timMe)2}2(thf)2] (R = H (1), Ph (2)) in good yields. Crystals of [UI{κ3-H,S,S'-H(Ph)B(timMe)2}2(thf)2] (2) were obtained by recrystallization from a tetrahydrofuran/acetonitrile solution, and the ion-separated uranium complex [U{κ3-H,S,S'-H(Ph)B(timMe)2}2(CH3CN)3][I] (3-I) was obtained by dissolution of 2 in acetonitrile followed by recrystallization...
May 23, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/29790503/a-voltammetric-method-for-fe-iii-in-blood-serum-using-a-screen-printed-electrode-modified-with-a-schiff-base-ionophore
#16
Susheel K Mittal, Sonia Rana, Navneet Kaur, Craig E Banks
Herein, a potent electrochemical ionophore (SMS-2) based on a Schiff base has been used for the modification of a screen-printed electrode (SPE). The modified disposable electrode can selectively detect ferric ions in an aqueous medium. Redox behavior of the proposed strip was characterized using cyclic voltammetry (CV) and differential pulse voltammetry (DPV). Incorporation of the ligand in the ink of the SPE enhanced the analytical performance of the electrode, and its surface modification was confirmed by SEM and EDX analysis...
May 23, 2018: Analyst
https://www.readbyqxmd.com/read/29790048/analysis-of-mercury-adsorption-at-the-gibbsite-water-interface-using-the-cd-music-model
#17
Chang Min Park
Mercury (Hg), one of the most toxic substances in nature, has long been released during the anthropogenic activity. A correct description of the adsorptive behavior of mercury is important to gain a better insight into its fate and transport in natural mineral surfaces, which will be a prerequisite for the development of surface complexation model for the adsorption processes. In the present study, simulation experiments on macroscopic Hg(II) sorption by gibbsite (α-Al(OH)3 ), a representative aluminum (hydr)oxide mineral, were performed using the charge distribution and multi-site complexation (CD-MUSIC) approach with 1-pK triple plane model (TPM)...
May 22, 2018: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/29789967/amorphous-titania-modified-with-boric-acid-for-selective-capture-of-glycoproteins
#18
Shanxia Jin, Liping Liu, Ping Zhou
Amorphous titania was modified with boric acid, and the resulting material was characterized by scanning electron microscopy, Fourier transform infrared spectroscopy, X-ray powder diffraction and X-ray photoelectron spectrometry. The new material, in contrast to conventional boronate affinity materials containing boronic acid ligands, bears boric acid groups. It is shown to exhibit high specificity for glycoproteins, and this was applied to design a method for solid phase extraction of glycoproteins as shown for ribonuclease B, horse radish peroxidase and ovalbumin...
May 22, 2018: Mikrochimica Acta
https://www.readbyqxmd.com/read/29789845/photoswitchable-transition-metal-complexes-with-azobenzene-functionalized-imine-based-ligands-structural-and-kinetic-analysis
#19
G Markiewicz, A Walczak, F Perlitius, M Piasecka, J M Harrowfield, A R Stefankiewicz
We report on the characterization of two imine type ligands containing photoresponsive azobenzene units as side groups and their transition metal ions complexes. The ligands, both free and in their complexes undergo trans- > cis photoisomerization after irradiation with UV light, but binding of metal ions reduces both the photoisomerisation reaction rates and cis isomer concentrations in the photostationary states. The greatest diminution in the photoisomerisation rate was observed for the complex containing Cd(ii), the heaviest among the various transition metal ions tested in this study...
May 23, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/29789818/the-effect-of-hydration-on-the-electronic-structure-and-stability-of-the-superalkali-cation-li-3
#20
Jia-Huan Hou, Di Wu, Jia-Yuan Liu, Si-Yi Li, Dan Yu, Ying Li
The interaction of the superalkali cation Li3+ with water molecules, as well as the structures and stability of the resulting water complexes are theoretically studied at the MP2/6-311++G(d,p) level. A great number of geometrical configurations were obtained for the Li3+(H2O)n (n = 1-5) complexes and Li3+ is found to have a maximum coordination number of four. Natural population analysis shows that the charge distribution of Li3+ becomes seriously uneven upon interaction with five water molecules, so it loses ring conjugation and splits in the lowest-energy isomer of Li3+(H2O)5...
May 23, 2018: Physical Chemistry Chemical Physics: PCCP
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