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Ligands and binding

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https://www.readbyqxmd.com/read/28647836/from-medicinal-plant-extracts-to-defined-chemical-compounds-targeting-the-histamine-h4-receptor-curcuma-longa-in-the-treatment-of-inflammation
#1
Annika Frank, Saleh Abu-Lafi, Azmi Adawi, Johannes S Schwed, Holger Stark, Anwar Rayan
OBJECTIVES: The aim was to evaluate the activity of seven medicinal, anti-inflammatory plants at the hH4R with focus on defined chemical compounds from Curcuma longa. MATERIALS: Activities were analyzed with membrane preparations from Sf9 cells, transiently expressing the hH4R, Gαi2 and Gβ1γ2 subunits. METHODS: From the methanolic extract of C. longa curcumin (1), demethoxycurcumin (2) and bis(4-hydroxy-cinnamoyl)methane (3) were isolated, purified with HPLC (elution-time 10...
June 24, 2017: Inflammation Research: Official Journal of the European Histamine Research Society ... [et Al.]
https://www.readbyqxmd.com/read/28647360/structure-of-an-unconventional-sh3-domain-from-the-postsynaptic-density-protein-shank3-at-ultrahigh-resolution
#2
Srinivas Kumar Ponna, Matti Myllykoski, Tobias M Boeckers, Petri Kursula
The Shank family comprises three large multi-domain proteins playing central roles as protein scaffolds in the neuronal postsynaptic density. The Shank proteins are closely linked to neuropsychiatric diseases, such as autism spectrum disorders. One characteristic domain in the Shank family is the SH3 domain, assumed to play a role in protein-protein interactions; however, no specific ligand binding to any Shank SH3 domain has been described. We solved the crystal structure of the SH3 domain from Shank3 at sub-atomic resolution...
June 21, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28646754/free-energy-analysis-of-cell-spreading
#3
Eóin McEvoy, Vikram S Deshpande, Patrick McGarry
In this study we present a steady-state adaptation of the thermodynamically motivated stress fiber (SF) model of Vigliotti et al. (2015). We implement this steady-state formulation in a non-local finite element setting where we also consider global conservation of the total number of cytoskeletal proteins within the cell, global conservation of the number of binding integrins on the cell membrane, and adhesion limiting ligand density on the substrate surface. We present a number of simulations of cell spreading in which we consider a limited subset of the possible deformed spread-states assumed by the cell in order to examine the hypothesis that free energy minimization drives the process of cell spreading...
June 7, 2017: Journal of the Mechanical Behavior of Biomedical Materials
https://www.readbyqxmd.com/read/28646631/synthesis-of-novel-and-functionally-selective-non-competitive-muscarinic-antagonists-as-chemical-probes
#4
John F Boulos, Jan Jakubik, John M Boulos, Jelena Momirov, Alena Randakova
Muscarinic receptors are known to play important biological roles and are drug targets for several human diseases. In a pilot study, novel muscarinic antagonists were synthesized and used as chemical probes to obtain additional information of the muscarinic pharmacophore. The design of these ligands made use of current orthosteric and allosteric models of drug-receptor interactions together with chemical motifs known to achieve muscarinic receptor selectivity. This approach has led to the discovery of several non-competitive muscarinic ligands that strongly bind at a secondary receptor site...
June 24, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28646209/upregulation-of-circulating-microrna-134-in-adult-onset-still-s-disease-and-its-use-as-potential-biomarker
#5
Tsai-Ling Liao, Yi-Ming Chen, Chia-Wei Hsieh, Hsin-Hua Chen, Hsiu-Chin Lee, Wei-Ting Hung, Kuo-Tung Tang, Der-Yuan Chen
Adult-onset Still's disease (AOSD) is a multi-systemic inflammatory disorder of unknown etiology. To date, no single diagnostic test is available for AOSD. Herein, we investigated the pathogenic role of microRNAs in AOSD. MicroRNA profiles in plasma from AOSD patients and healthy controls were analyzed by microarray analysis, followed by quantitative reverse transcription PCR validation. The biological functions of microRNAs were evaluated using in vitro cell-based assay. Among the differentially expressed microRNAs, microRNA-134 (miR-134) expression was positively correlated with AOSD activity scores and significantly decreased after effective treatment...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28646159/yvck-a-protein-required-for-cell-wall-integrity-and-optimal-carbon-source-utilization-binds-uridine-diphosphate-sugars
#6
Elodie Foulquier, Anne Galinier
In Bacillus subtilis, Listeria monocytogenes and in two Mycobacteria, it was previously shown that yvcK is a gene required for normal cell shape, for optimal carbon source utilization and for virulence of pathogenic bacteria. Here we report that the B. subtilis protein YvcK binds to Uridine diphosphate-sugars like Uridine diphosphate-Glucose (UDP-Glc) and Uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc) in vitro. Using the crystal structure of Bacillus halodurans YvcK, we identified residues involved in this interaction...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28645930/genomic-and-non-genomic-effects-of-androgens-in-the-cardiovascular-system-clinical-implications
#7
REVIEW
Angela K Lucas Herald, Rheure Alves-Lopes, Augusto C Montezano, S Faisal Ahmed, Rhian M Touyz
The principle steroidal androgens are testosterone and its metabolite 5α-dihydrotestosterone (DHT), which is converted from testosterone by the enzyme 5α-reductase. Through the classic pathway with androgens crossing the plasma membrane and binding to the androgen receptor (AR) or via mechanisms independent of the ligand-dependent transactivation function of nuclear receptors, testosterone induces genomic and non-genomic effects respectively. AR is widely distributed in several tissues, including vascular endothelial and smooth muscle cells...
July 1, 2017: Clinical Science (1979-)
https://www.readbyqxmd.com/read/28645833/binding-kinetics-and-pathways-of-ligands-to-gpcrs
#8
REVIEW
Andrea Strasser, Hans-Joachim Wittmann, Roland Seifert
Previously, drugs were developed focusing on target affinity and selectivity. However, it is becoming evident that the drug-target residence time, related to the off-rate, is an important parameter for successful drug development. The residence time influences both the on-rate and overall effectiveness of drugs. Furthermore, ligand binding is now appreciated to be a multistep process because metastable and/or intermediate binding sites in the extracellular region have been identified. In this review, we summarize experimental ligand-binding data for G-protein-coupled receptors (GPCRs), and their binding pathways, analyzed by molecular dynamics (MD)...
June 20, 2017: Trends in Pharmacological Sciences
https://www.readbyqxmd.com/read/28645756/an-aptamer-based-pcr-method-coupled-with-magnetic-immunoseparation-for-sensitive-detection-of-salmonella-typhimurium-in-ground-turkey
#9
Lijun Wang, Ronghui Wang, Hong Wang, Michael Slavik, Hua Wei, Yanbin Li
Aptamers are single-stranded oligonucleotide ligands that can bind to targets with high affinity and specificity. They have been widely studied in the field of diagnostics as alternatives to antibodies due to their favorable features such as easy labeling, temperature tolerance, lower cost and recognition of a wide variety of targets. In this study, an aptamer-based PCR method coupled with magnetic immunoseparation was developed to detect S. Typhimurium from ground turkey. Firstly, biotinylated polyclonal anti-S...
June 20, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28644959/generation-and-characterization-of-aptamers-targeting-factor-xia
#10
R S Woodruff, I Ivanov, I M Verhamme, M-F Sun, D Gailani, B A Sullenger
BACKGROUND: The plasma protease factor XIa (FXIa) has become a target of interest for therapeutics designed to prevent or treat thrombotic disorders. METHODS: We used a solution-based, directed evolution approach called systematic evolution of ligands by exponential enrichment (SELEX) to isolate RNA aptamers that target the FXIa catalytic domain. RESULTS: Two aptamers, designated 11.16 and 12.7, were identified that bound to previously identified anion binding and serpin bindings sites on the FXIa catalytic domain...
June 9, 2017: Thrombosis Research
https://www.readbyqxmd.com/read/28644630/expanding-the-therapeutic-potential-of-the-iron-chelator-deferasirox-in-the-development-of-aqueous-stable-ti-iv-anticancer-complexes
#11
Sergio A Loza-Rosas, Alexandra M Vázquez-Salgado, Kennett I Rivero, Lenny J Negrón, Yamixa Delgado, Josué A Benjamín-Rivera, Angel L Vázquez-Maldonado, Timothy B Parks, Charlene Munet-Colón, Arthur D Tinoco
The recent X-ray structure of titanium(IV)-bound human serum transferrin (STf) exhibiting citrate as a synergistic anion reveals a difference in Ti(IV) coordination versus iron(III), the metal endogenously delivered by the protein to cells. This finding enriches our bioinspired drug design strategy for Ti(IV)-based anticancer therapeutics, which applies a family of Fe(III) chelators termed chemical transferrin mimetic (cTfm) ligands to inhibit Fe bioavailability in cancer cells. Deferasirox, a drug used for iron overload disease, is a cTfm ligand that models STf coordination to Fe(III), favoring Fe(III) binding versus Ti(IV)...
June 23, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28644609/galnac-tyrosine-is-a-ligand-of-plant-lectins-antibodies-and-human-and-murine-macrophage-galactose-type-lectins
#12
Ruslan Gibadullin, David Wayne Farnsworth, Joseph J Barchi, Jeffrey C Gildersleeve
In 2011, a new type of protein O-glycosylation was discovered in which N-acetylgalactosamine is attached to the side chain of tyrosine (GalNAc-Tyr). While present on dozens of proteins, the biological roles of GalNAc-Tyr are unknown. To gain insight into this new type of modification, we synthesized a group of GalNAc-Tyr glycopeptides, constructed microarrays, and evaluated potential recognition of GalNAc-Tyr by a series of glycan-binding proteins. Through a series of >150 microarray experiments, we assessed binding properties of a variety of plant lectins, monoclonal antibodies, and endogenous lectins...
June 23, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28644418/new-mt%C3%A2-melatonin-receptor-selective-ligands-agonists-and-partial-agonists
#13
Jean A Boutin, Anne Bonnaud, Chantal Brasseur, Olivier Bruno, Nolwenn Lepretre, Peter Oosting, Sophie Coumailleau, Philippe Delagrange, Olivier Nosjean, Céline Legros
The search for melatonin receptor agonists and antagonists specific towards one of the receptor subtypes will extend our understanding of the role of this system in relaying circadian information to the body. A series of compounds derived from a hit compound discovered in a screening process led to powerful agonists specific for one of the isoform of the melatonin receptor namely, MT₂. The compounds are based on a poorly explored skeleton in the molecular pharmacology of melatonin. By changing the steric hindrance of one substituent (i...
June 23, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28643352/cesium-s-off-the-map-valence-orbital
#14
Maarten Goesten, Martin Rahm, Matthias Bickelhaupt, Emiel Hensen
The Td-symmetric [CsO4]+ ion, featuring Cs in an oxidation state of 9, is computed to be a minimum. Cs uses outer core 5s and 5p orbitals to bind the oxygens. The valence Cs 6s orbital lies too high to be involved in bonding, and contributes to Rydberg levels only. From a Molecular Orbital perspective, the bonding scheme reminds of XeO4: an octet of electrons to bind electronegative ligands, and no low-lying acceptor orbitals on the central atom. In this sense, Cs+ resembles hypervalent Xe.
June 22, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28643343/alpha-beta-hydrolases-a-unique-structural-motif-coordinates-catalytic-acid-residue-in-40-protein-fold-families
#15
Polytimi S Dimitriou, Alexander Denesyuk, Seiji Takahashi, Satoshi Yamashita, Mark S Johnson, Toru Nakayama, Konstantin Denessiouk
The alpha/beta-hydrolases (ABH) are a family of acid-base-nucleophile catalytic triad enzymes with a common fold, but using a wide variety of substrates, having different pH optima, catalyzing unique catalytic reactions and often showing improved chemical and thermo stability. The ABH enzymes are prime targets for protein engineering. Here, we have classified active sites from 51 representative members of 40 structural ABH fold families into eight distinct conserved geometries. We demonstrate the occurrence of a common structural motif, the catalytic acid zone, at the catalytic triad acid turn...
June 23, 2017: Proteins
https://www.readbyqxmd.com/read/28643276/a-rapid-two-step-iduronate-2-sulfatatse-enzymatic-activity-assay-for-mpsii-pharmacokinetic-assessment
#16
Mitra Azadeh, Luying Pan, Yongchang Qiu, Ruben Boado
Clinical studies involving enzyme replacement therapies (ERTs) have increasingly utilized enzymatic activity assays to monitor efficacy and biofunction of the drug; as a result, these assays have become an important part of pharmacokinetic (PK) and pharmacodynamic assessments in ERT trials. This paper presents a two-step enzymatic activity assay for iduronate-2-sulfatase (I2S) (EC 3.1.6.13) which we have optimized to fit in 1 day and to complete in less than 6 h. The rapid assay presented here is a significant improvement over the original two-step method with run time of 24 h which spanned 2 days...
June 23, 2017: JIMD Reports
https://www.readbyqxmd.com/read/28643244/durvalumab-first-global-approval
#17
Yahiya Y Syed
Intravenous durvalumab (Imfinzi™; AstraZeneca) is a fully human monoclonal antibody that blocks programmed cell death ligand-1 binding to its receptors (PD-1 and CD80), resulting in enhanced T-cell responses against cancer cells. The US FDA has granted durvalumab accelerated approval for the treatment of patients with locally advanced or metastatic urothelial carcinoma who have disease progression during or following platinum-containing chemotherapy, or within 12 months of neoadjuvant or adjuvant platinum-containing chemotherapy...
June 22, 2017: Drugs
https://www.readbyqxmd.com/read/28643202/specific-igm-and-regulation-of-antibody-responses
#18
Anna Sörman, Birgitta Heyman
Specific IgM, administered together with the antigen it recognizes, enhances primary antibody responses, formation of germinal centers, and priming for secondary antibody responses. The response to all epitopes on the antigen to which IgM binds is usually enhanced. IgM preferentially enhances responses to large antigens such as erythrocytes, malaria parasites, and keyhole limpet hemocyanine. In order for an effect to be seen, antigens must be administered in suboptimal concentrations and in close temporal relationship to the IgM...
June 23, 2017: Current Topics in Microbiology and Immunology
https://www.readbyqxmd.com/read/28643161/nonlinear-biotic-ligand-model-for-assessing-alleviation-effects-of-ca-mg-and-k-on-cd-toxicity-to-soybean-roots
#19
Bo-Ching Chen, Pin-Jie Wang, Pei-Chi Ho, Kai-Wei Juang
Developing a nonlinear biotic ligand model (BLM) that considers the geometrical constraints for binding of different cations on biotic ligands will provide more reliable details about the hypothetical mechanism governing the alleviation of cadmium (Cd) toxicity by coexistent cations. Soybean seedlings under Cd stress produced by various activities of coexistent cations such as calcium (Ca(2+)), magnesium (Mg(2+)), and potassium (K(+)) were hydroponically assayed for Cd toxicity to soybean roots. The Cd(2+) activity resulting in 50% reduction of root elongation (RE), EA 50, was used for assessing the Cd toxicity to the soybean seedling...
June 22, 2017: Ecotoxicology
https://www.readbyqxmd.com/read/28642635/virtual-screening-following-rational-drug-design-based-approach-for-introducing-new-anti-amyloid-beta-aggregation-agent
#20
Garshasb Rigi, Mohammad Vala Ashdar Nakhaei, Hoda Eidipour, Arshia Najimi, Fahimeh Tajik, Niloufar Taher, Kamran Yarahmadi
Amyloid β (Aβ) sheets aggregations is the main reason of Alzheimer disease. The interacting areas between monomers are residue number 38 to 42. Inhibition of interaction between Aβ molecules prevents plaque formation. In the present study, we have performed a high-throughput virtual screening among ZINC database and top 1000 hits were checked again regarding binding affinity by AutoDock software. Top 4 successive second step screening hits was considered for drug design purpose against aggregation site of Aβ molecules...
2017: Bioinformation
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