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Ligands and binding

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https://www.readbyqxmd.com/read/28323994/direct-regulation-of-histidine-ammonia-lyase-2-gene-by-thyroid-hormone-in-the-developing-adult-intestinal-stem-cells
#1
Nga Luu, Liezhen Fu, Kenta Fujimoto, Yun-Bo Shi
Most vertebrate organs utilize adult stem cells to maintain homeostasis and ensure proper repair when damaged. How such organ-specific stem cells are formed during vertebrate development is largely unexplored. We have been using the thyroid hormone (T3)-dependent amphibian metamorphosis to address this issue. Early studies in Xenopus laevis have shown that intestinal remodeling involves complete degeneration of the larval epithelium and de novo formation of adult stem cells through dedifferentiation of some larval epithelial cells...
February 1, 2017: Endocrinology
https://www.readbyqxmd.com/read/28323891/characterization-of-baff-and-april-subfamily-receptors-in-rainbow-trout-oncorhynchus-mykiss-potential-role-of-the-baff-april-axis-in-the-pathogenesis-of-proliferative-kidney-disease
#2
Aitor G Granja, Jason W Holland, Jaime Pignatelli, Christopher J Secombes, Carolina Tafalla
Proliferative kidney disease (PKD) is a parasitic infection of salmonid fish characterized by hyper-secretion of immunoglobulins in response to the presence of the myxozoan parasite, Tetracapsuloides bryosalmonae. In this context, we hypothesized that the BAFF/APRIL axis, known to play a major role in B cell differentiation and survival in mammals, could be affected by the parasite and consequently be involved in the apparent shift in normal B cell activity. To regulate B cell activity, BAFF and APRIL bind to transmembrane activator and calcium modulator and cyclophilin ligand interactor (TACI) and B cell maturation antigen (BCMA), whereas BAFF also binds to BAFF receptor (BAFF-R)...
2017: PloS One
https://www.readbyqxmd.com/read/28323850/ligand-guided-homology-modelling-of-the-gabab2-subunit-of-the-gabab-receptor
#3
Thibaud Freyd, Dawid Warszycki, Stefan Mordalski, Andrzej J Bojarski, Ingebrigt Sylte, Mari Gabrielsen
γ-aminobutyric acid (GABA) is the main inhibitory neurotransmitter in the central nervous system, and disturbances in the GABAergic system have been implicated in numerous neurological and neuropsychiatric diseases. The GABAB receptor is a heterodimeric class C G protein-coupled receptor (GPCR) consisting of GABAB1a/b and GABAB2 subunits. Two GABAB receptor ligand binding sites have been described, namely the orthosteric GABA binding site located in the extracellular GABAB1 Venus fly trap domain and the allosteric binding site found in the GABAB2 transmembrane domain...
2017: PloS One
https://www.readbyqxmd.com/read/28319797/non-enolisable-knoevenagel-condensate-appended-schiff-bases-metal-ii-complexes-spectral-characteristics-dna-binding-and-nuclease-activities
#4
Ammavasi Gubendran, Mookkandi Palsamy Kesavan, Srinivasan Ayyanaar, Liviu Mitu, Periyakaruppan Athappan, Jegathalaprathaban Rajesh
New Schiff base complexes [Cu(L(1))Cl] (1), [Ni(L(1))Cl] (2), [Zn(L(1))Cl] (3), and [Fe(L(2))H2OCl] (4) {L(1)=(4E)-3-(2-hydroxybenzylidene)-4-(2-hydroxyphenylimino)pentan-2-one, L(2)=2,2'-(1E,1'E)-(3-(2-hydroxybenzylidene)-pentane-2,4-diylidene)bis(azan-1-yl-1 idene)diphenol} have been synthesized and characterized by elemental analysis, UV-Vis, IR, FAB-mass, EPR, spectral studies and electrochemical studies, the ligands L(1) &L(2) were characterized by (1)H and (13)C NMR spectra. Complex 1 show a visible spectral d-d band near 600nm and display cyclic voltammetric quasireversible response for the Cu(II)/Cu(I) couple vs Ag/AgCl in DMSO...
March 16, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28319781/systematic-study-of-imidazoles-inhibiting-ido1-via-the-integration-of-molecular-mechanics-and-quantum-mechanics-calculations
#5
Yi Zou, Fang Wang, Yan Wang, Wenjie Guo, Yihua Zhang, Qiang Xu, Yisheng Lai
Indoleamine 2,3-dioxygenase 1 (IDO1) is regarded as an attractive target for cancer immunotherapy. To rationalize the detailed interactions between IDO1 and its inhibitors at the atomic level, an integrated computational approach by combining molecular mechanics and quantum mechanics methods was employed in this report. Specifically, the binding modes of 20 inhibitors was initially investigated using the induced fit docking (IFD) protocol, which outperformed other two docking protocols in terms of correctly predicting ligand conformations...
March 14, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28319380/evaluation-and-characterization-of-trk-kinase-inhibitors-for-the-treatment-of-pain-reliable-binding-affinity-predictions-from-theory-and-computation
#6
Shunzhou Wan, Agastya P Bhati, Sarah Skerratt, Kiyoyuki Omoto, Veerabahu Shanmugasundaram, Sharan K Bagal, Peter Vivian Coveney
Optimisation of ligand binding affinity to the target protein of interest is a primary objective in small-molecule drug discovery. Until now, the prediction of binding affinities by computational methods has not been widely applied in the drug discovery process, mainly due to its lack of accuracy and reproducibility, as well as the long turnaround times required to obtain results. Herein, we report on a collaborative study that compares tropomyosin receptor kinase A (TrkA) binding affinity predictions using two recently formulated fast computational approaches - namely ESMACS (Enhanced Sampling of Molecular dynamics with Approximation of Continuum Solvent) and TIES (Thermodynamic Integration with Enhanced Sampling) - to experimentally derived TrkA binding affinities for a set of Pfizer pan-Trk compounds...
March 20, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28319199/a-computational-analysis-of-in-vivo-vegfr-activation-by-multiple-co-expressed-ligands
#7
Lindsay E Clegg, Feilim Mac Gabhann
The splice isoforms of vascular endothelial growth A (VEGF) each have different affinities for the extracellular matrix (ECM) and the coreceptor NRP1, which leads to distinct vascular phenotypes in model systems expressing only a single VEGF isoform. ECM-immobilized VEGF can bind to and activate VEGF receptor 2 (VEGFR2) directly, with a different pattern of site-specific phosphorylation than diffusible VEGF. To date, the way in which ECM binding alters the distribution of isoforms of VEGF and of the related placental growth factor (PlGF) in the body and resulting angiogenic signaling is not well-understood...
March 20, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28318945/identification-and-structure-activity-relationships-of-quinoline-tertiary-alcohol-modulators-of-ror%C3%AE-t
#8
David A Kummer, Maxwell D Cummings, Marta Abad, Joseph Barbay, Glenda Castro, Ronald Wolin, Kevin D Kreutter, Umar Maharoof, Cynthia Milligan, Rachel Nishimura, Joan Pierce, Celine Schalk-Hihi, John Spurlino, Maud Urbanski, Hariharan Venkatesan, Aihua Wang, Craig Woods, Xiaohua Xue, James P Edwards, Anne M Fourie, Kristi Leonard
A high-throughput screen of the ligand binding domain of the nuclear receptor retinoic acid-related orphan receptor gamma t (RORγt) employing a thermal shift assay yielded a quinoline tertiary alcohol hit. Optimization of the 2-, 3- and 4-positions of the quinoline core using structure-activity relationships and structure-based drug design methods led to the discovery of a series of modulators with improved RORγt inhibitory potency and inverse agonism properties.
February 21, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28318942/cyclic-mu-opioid-receptor-ligands-containing-multiple-n-methylated-amino-acid-residues
#9
Anna Adamska-Bartłomiejczyk, Anna Janecka, Márton Richárd Szabó, Maria Camilla Cerlesi, Girolamo Calo, Alicja Kluczyk, Csaba Tömböly, Attila Borics
In this study we report the in vitro activities of four cyclic opioid peptides with various sequence length/macrocycle size and N-methylamino acid residue content. N-Methylated amino acids were incorporated and cyclization was employed to enhance conformational rigidity to various extent. The effect of such modifications on ligand structure and binding properties were studied. The pentapeptide containing one endocyclic and one exocyclic N-methylated amino acid displayed the highest affinity to the mu-opioid receptor...
March 7, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28318893/design-and-characterization-of-opioid-ligands-based-on-cycle-in-macrocycle-scaffold
#10
Anna Adamska-Bartłomiejczyk, Rossella De Marco, Luca Gentilucci, Alicja Kluczyk, Anna Janecka
The study reports on a series of novel cyclopeptides based on the structure Tyr-[d-Lys-Phe-Phe-Asp]NH2, a mixed mu and kappa opioid receptor agonist with low nanomolar affinity, in which Phe(4) residue was substituted by cyclic amino acids, such as Pro or its six-membered surrogates, piperidine-2-, 3- or 4-carboxylic acids (Pip, Nip and Inp, respectively). All derivatives exhibited high mu- and moderate delta-opioid receptor affinity, and almost no binding to the kappa-opioid receptor. Conformational analysis suggested that the cis conformation of the peptide bond Phe(3)-Xaa(4) influences receptor selectivity through the control of the position of Phe(3) side chain...
February 28, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28318299/lithocholic-acid-a-new-emergent-protector-of-intestinal-calcium-absorption-under-oxidant-conditions
#11
Ana M Marchionatti, Adriana Pérez, María A Rivoira, Valeria A Rodríguez, Nori G Tolosa de Talamoni
LCA and 1,25(OH)2D3 are vitamin D receptor ligands with different binding affinity. The secosteroid stimulates intestinal Ca(2+) absorption. Whether LCA alters this process remains unknown. The aim of our work was to determine the effect of LCA on intestinal Ca(2+) absorption in the absence or presence of NaDOC, bile acid that inhibits the cation transport. The data show that LCA by itself did not alter intestinal Ca(2+) absorption, but prevented the inhibitory effect of NaDOC. The concomitant administration of LCA avoided the reduction of intestinal alkaline phosphatase activity caused by NaDOC...
March 20, 2017: Biochemistry and Cell Biology, Biochimie et Biologie Cellulaire
https://www.readbyqxmd.com/read/28318252/molecular-dynamics-in-mixed-solvents-reveals-protein-ligand-interactions-improves-docking-and-allows-accurate-binding-free-energy-predictions
#12
Juan Pablo Arcon, Lucas A Alfredo Defelipe, Carlos Pablo Modenutti, Elias Daniel Lopez, Daniel Alvarez-Garcia, Xavier Barril, Adrian Gustavo Turjanski, Marcelo A Marti
One of the most important biological processes at the molecular level is the formation of protein-ligand complexes. Therefore, determining their structure and underlying key interactions is of paramount relevance and has direct applications in drug development. Due to its low cost relative to its experimental sibling, Molecular Dynamics (MD) simulations in the presence of different solvent probes mimicking specific type of interactions have been increasingly used to analyze protein binding sites and reveal protein-ligand interaction hot spots...
March 20, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28318079/design-and-synthesis-of-galactosylated-bifurcated-ligands-with-nanomolar-affinity-for-lectin-leca-from-pseudomonas-aeruginosa
#13
Anthony Angeli, Muchen Li, Lucie Dupin, Gerard Vergoten, Mathieu Noel, Mimouna Madaoui, Shuai Wang, Albert Meyer, Thomas Gehin, Sebastien Vidal, Jean-Jacques Vasseur, Yann Chevolot, Francois Morvan
Lectin LecA of Pseudomonas aeruginosa is established as a virulent factor. Glycoclusters targeting LecA able to compete with human glycoconjugates present on epithelial cells are promising candidates to treat P. aeruginosa infection. A family of 32 glycodendrimers of generation 0 and 1 displaying bifurcated bis-galactosides has been designed to interact with LecA. The influence of both the central multivalent core and the aglycon of these glycodendrimers on their affinity toward LecA has been evaluated using a microarray technology both qualitatively for a rapid screening of the binding properties but also quantitatively (Kd) leading to high affinity LecA ligands with Kd values in the low nanomolar range (Kd = 22 nM for the best one)...
March 20, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28317184/self-assembled-multivalent-samul-polyanion-binding-impact-of-hydrophobic-modifications-in-the-micellar-core-on-dna-and-heparin-binding-at-the-peripheral-cationic-ligands
#14
Buthaina Albanyan, Erik Laurini, Paola Posocco, Sabrina Pricl, David K Smith
This paper reports a small family of cationic surfactants designed to bind polyanions such as DNA and heparin. Each molecule has the same hydrophilic cationic ligand, and a hydrophobic aliphatic group with eighteen carbon atoms with either one, two or three alkene groups within the hydrophobic chain (C18-1, C18-2 and C18-3). Dynamic light scattering indicates that more alkenes lead to geometric distortion, giving rise to larger self-assembled multivalent (SAMul) nanostructures. Mallard Blue and Ethidium Bromide dye displacement assays demonstrate that heparin and DNA have markedly different binding preferences, with heparin binding most effectively to C18-1, and DNA to C18-3, even though the molecular structural differences of these SAMul systems are buried in the hydrophobic core...
March 20, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28317076/an-experimental-tool-to-estimate-the-probability-of-a-nucleotide-presence-in-the-crystal-structures-of-the-nucleotide-protein-complexes
#15
Maria Nemchinova, Vitaly Balobanov, Ekaterina Nikonova, Natalia Lekontseva, Alisa Mikhaylina, Svetlana Tishchenko, Alexey Nikulin
A correlation between the ligand-protein affinity and the identification of the ligand in the experimental electron density maps obtained by X-ray crystallography has been tested for a number of RNA-binding proteins. Bacterial translation regulators ProQ, TRAP, Rop, and Hfq together with their archaeal homologues SmAP have been used. The equilibrium dissociation constants for the N-methyl-anthraniloyl-labelled adenosine and guanosine monophosphates titrated by the proteins have been determined by the fluorescent anisotropy measurements...
March 20, 2017: Protein Journal
https://www.readbyqxmd.com/read/28316241/investigating-the-cellular-specificity-in-tumors-of-a-surface-converting-nanoparticle-by-multimodal-imaging
#16
Francois Fay, Line Hansen, Stefanie J C G Hectors, Brenda L Sanchez-Gaytan, Yiming Zhao, Jun Tang, Jazz Munitz, Amr Alaarg, Mounia S Braza, Anita Gianella, Stuart A Aaronson, Thomas Reiner, Jørgen Kjems, Robert Langer, Freek J M Hoeben, Henk M Janssen, Claudia Calcagno, Gustav J Strijkers, Zahi A Fayad, Carlos Perez-Medina, Willem J M Mulder
Active targeting of nanoparticles through surface functionalization is a common strategy to enhance tumor delivery specificity. However, active targeting strategies tend to work against long polyethylene glycol's shielding effectiveness and associated favorable pharmacokinetics. To overcome these limitations, we developed a matrix metalloproteinase-2 sensitive surface-converting polyethylene glycol coating. This coating prevents nanoparticle-cell interaction in the bloodstream but once exposed to matrix metalloproteinase-2, i...
March 19, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28316115/gabaa-and-gabab-receptor-dysregulation-in-superior-frontal-cortex-of-subjects-with-schizophrenia-and-bipolar-disorder
#17
S Hossein Fatemi, Timothy D Folsom, Paul D Thuras
Schizophrenia and bipolar disorder are complex psychiatric disorders that affect millions of people worldwide. Evidence from gene association and postmortem studies has identified abnormalities of the gamma-aminobutyric acid (GABA) signaling system in both disorders. Abnormal GABAergic signaling and transmission could contribute to the symptomatology of these disorders, potentially through impaired gamma oscillations which normally occur during cognitive processing. In the current study, we examined the protein expression of 14 GABAA and two GABAB receptor subunits in the superior frontal cortex of subjects with schizophrenia, bipolar disorder, and healthy controls...
March 18, 2017: Synapse
https://www.readbyqxmd.com/read/28316100/thermodynamics-of-an-aminoglycoside-modifying-enzyme-with-low-substrate-promiscuity-the-aminoglycoside-n3-acetyltransferase-via
#18
Prashasti Kumar, Engin H Serpersu
Kinetic, thermodynamic and structural properties of the aminoglycoside N3-acetyltransferase-VIa (AAC-VIa) are determined. Among the aminoglycoside N3-acetyltransferases, AAC-VIa has one of the most limited substrate profiles. Kinetic studies showed that only 5 aminoglycosides are substrates for this enzyme with a range of 4-fold difference in kcat values. Larger differences in KM (∼40 fold) resulted in ∼30-fold variation in kcat /KM . Binding of aminoglycosides to AAC-VIa was enthalpically favored and entropically disfavored with a net result of favorable Gibbs energy (ΔG<0)...
March 17, 2017: Proteins
https://www.readbyqxmd.com/read/28315995/ligand-based-virtual-screening-under-partial-shape-constraints
#19
Mathias M von Behren, Matthias Rarey
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...
March 18, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28315936/peptide-binding-motifs-of-two-common-equine-class-i-mhc-molecules-in-thoroughbred-horses
#20
Tobias Bergmann, Mikaela Lindvall, Erin Moore, Eugene Moore, John Sidney, Donald Miller, Rebecca L Tallmadge, Paisley T Myers, Stacy A Malaker, Jeffrey Shabanowitz, Nikolaus Osterrieder, Bjoern Peters, Donald F Hunt, Douglas F Antczak, Alessandro Sette
Quantitative peptide-binding motifs of MHC class I alleles provide a valuable tool to efficiently identify putative T cell epitopes. Detailed information on equine MHC class I alleles is still very limited, and to date, only a single equine MHC class I allele, Eqca-1*00101 (ELA-A3 haplotype), has been characterized. The present study extends the number of characterized ELA class I specificities in two additional haplotypes found commonly in the Thoroughbred breed. Accordingly, we here report quantitative binding motifs for the ELA-A2 allele Eqca-16*00101 and the ELA-A9 allele Eqca-1*00201...
March 18, 2017: Immunogenetics
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