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Ligands and binding

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https://www.readbyqxmd.com/read/28532109/lactoferrin-modified-graphene-oxide-iron-oxide-nanocomposite-for-glioma-targeted-drug-delivery
#1
Meng-Meng Song, Huai-Liang Xu, Jun-Xing Liang, Hui-Hui Xiang, Rui Liu, Yu-Xian Shen
Targeting delivery of drugs in a specific manner represents a potential powerful technology in gliomas. Herein, we prepared a multifunctional targeted delivery system based on graphene oxide (GO) that contains a molecular bio-targeting ligand and superparamagnetic iron oxide nanoparticles on the surface of GO for magnetic targeting. Superparamagnetic Fe3O4 nanoparticles was loaded on the surface of GO via chemical precipitation method to form GO@Fe3O4 nanocomposites. Lactoferrin (Lf), an iron-transporting serum glycoprotein that binds to receptors overexpressed at the surface of glioma cells and vascular endothelial cell of the blood brain barrier, was chosen as the targeted ligand to construct the targeted delivery system Lf@GO@Fe3O4 through EDC/NHS chemistry...
August 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28531373/identification-of-potential-inhibitors-for-hcv-ns3-genotype-4a-by-combining-protein-ligand-interaction-fingerprint-3d-pharmacophore-docking-and-dynamic-simulation
#2
Mahmoud Abd El-Monem El-Hasab, Eman Esmat El-Bastawissy, Tarek Faathy El-Moselhy
HCV NS3 protease domain has been one of the most attractive targets for developing new drugs for HCV infection and many drugs were successfully developed, but all of them were designed for targeting HCV genotype 1 infection. HCV genotype 4a dominant in Egypt has paid less attention. Here we describe our protocol of virtual screening in identification of novel potential potent inhibitors for HCV NS3 of genotype 4a using homology modelling, PLIF (protein ligand interaction fingerprint), docking, pharmacophore and dynamic simulation...
May 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28531353/comprehensive-thermodynamic-profiling-for-the-binding-of-a-g-quadruplex-selective-indoloquinoline
#3
Andrea Funke, Klaus Weisz
Binding of a positively charged indoloquinoline derivative to a G-quadruplex formed by the G-rich promoter element of the c-MYC oncogene was subjected to a rigorous isothermal calorimetric analysis. Binding of the indoloquinoline is primarily enthalpy-driven but is also promoted by a favorable entropy term. Both binding enthalpy ΔH° and binding entropy ΔS° exhibit a noticeable temperature dependence with almost complete enthalpy-entropy compensation as a result of a negative change in heat capacity ΔCp°...
May 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28530838/an-innovative-high-throughput-screening-approach-for-discovery-of-small-molecules-that-inhibit-tnf-receptors
#4
Chih Hung Lo, Nagamani Vunnam, Andrew K Lewis, Ting-Lan Chiu, Benjamin E Brummel, Tory M Schaaf, Benjamin D Grant, Prachi Bawaskar, David D Thomas, Jonathan N Sachs
Tumor necrosis factor receptor 1 (TNFR1) is a transmembrane receptor that binds tumor necrosis factor or lymphotoxin-alpha and plays a critical role in regulating the inflammatory response. Upregulation of these ligands is associated with inflammatory and autoimmune diseases. Current treatments reduce symptoms by sequestering free ligands, but this can cause adverse side effects by unintentionally inhibiting ligand binding to off-target receptors. Hence, there is a need for new small molecules that specifically target the receptors, rather than the ligands...
May 1, 2017: SLAS Discovery
https://www.readbyqxmd.com/read/28530834/a-facile-radiolabeling-of-18-f-fdpa-via-spirocyclic-iodonium-ylides-preliminary-pet-imaging-studies-in-preclinical-models-of-neuroinflammation
#5
Lu Wang, Ran Cheng, Masayuki Fujinaga, Jian Yang, Yiding Zhang, Akiko Hatori, Katsushi Kumata, Jing Yang, Neil Vasdev, Yunfei Du, Chongzhao Ran, Ming-Rong Zhang, Steven H Liang
A suitable TSPO PET ligand may visualize and quantify neuroinflammation in living brain. Herein we report a (18)F-ligand, [(18)F]2 ([(18)F]FDPA) is radiolabeled in high yield and high specific activity based on our spirocyclic iodonium ylide (SCIDY) strategy. [(18)F]2 demonstrated saturable specific binding to TSPO, substantially-elevated brain uptake and slow washout of bound PET signal in the preclinical models of brain neuroinflammation (cerebral ischemia and Alzheimer's disease).
May 22, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28530810/seleniranium-ions-undergo-%C3%AF-ligand-exchange-via-an-associative-mechanism-in-the-gas-phase
#6
Shea Fern Lim, Benjamin Leigh Harris, George N Khairallah, Evan John Bieske, Philippe Maître, Gabriel da Silva, Brian D Adamson, Michael S Scholz, Neville J A Coughlan, Richard A J O'Hair, Michael Rathjen, Daniel Stares, Jonathan M White
Collision-induced dissociation mass spectrometry of the ammonium ions 4a and 4b results in the formation of the seleniranium ion 5, the structure and purity of which was verified using gas phase infra-red spectroscopy coupled to mass spectrometry, and gas phase ion-mobility measurements. Ion-molecule reactions between the ion 5 (m/z = 261) and cyclopentene, cyclohexene, cycloheptene and cyclooctene, resulted in the formation of the seleniranium ions 7 (m/z = 225), 6 (m/z = 239), 8 (m/z = 253), and 9 (m/z = 267) respectively...
May 22, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28530802/discovery-of-n-5-fluoropyridin-2-yl-6-methyl-4-pyrimidin-5-yloxy-picolinamide-vu0424238-a-novel-negative-allosteric-modulator-of-metabotropic-glutamate-receptor-subtype-5-selected-for-clinical-evaluation
#7
Andrew S Felts, Alice L Rodriguez, Anna L Blobaum, Ryan D Morrison, Brittney S Bates, Analisa Thompson Gray, Jerri M Rook, Mohammed N Tantawy, Frank W Byers, Sichen Chang, Daryl F Venable, Vincent B Luscombe, Gilles D Tamagnan, Colleen M Niswender, J Scott Daniels, Carrie K Jones, P Jeffrey Conn, Craig W Lindsley, Kyle A Emmitte
Preclinical evidence in support of the potential utility of mGlu5 NAMs for the treatment of a variety of psychiatric and neurodegenerative disorders is extensive, and multiple such molecules have entered clinical trials. Despite some promising results from clinical studies, no small molecule mGlu5 NAM has yet to reach market. Here we present the discovery and evaluation of N-(5-fluoropyridin-2-yl)-6-methyl-4-(pyrimidin-5-yloxy)picolinamide (27, VU0424238), a compound selected for clinical evaluation. Compound 27 is more than 900-fold selective for mGlu5 versus the other mGlu receptors, and binding studies established a Ki value of 4...
May 22, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28530709/recognition-of-egf-like-domains-by-the-notch-modifying-o-fucosyltransferase-pofut1
#8
Zhijie Li, Kristina Han, John E Pak, Malathy Satkunarajah, Dongxia Zhou, James M Rini
Protein O-fucosyltransferase 1 (POFUT1) fucosylates the epidermal growth factor (EGF)-like domains found in cell-surface and secreted glycoproteins including Notch and its ligands. Although Notch fucosylation is critical for development, and POFUT1 deficiency leads to human disease, how this enzyme binds and catalyzes the fucosylation of its diverse EGF-like domain substrates has not been determined. Reported here is the X-ray crystal structure of mouse POFUT1 in complex with several EGF-like domains, including EGF12 and EGF26 of Notch...
May 22, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28530565/analysis-of-binding-properties-and-interaction-of-thiabendazole-and-its-metabolite-with-human-serum-albumin-via-multiple-spectroscopic-methods
#9
Qiaomei Sun, Jiawei He, Hongqin Yang, Shanshan Li, Ludan Zhao, Hui Li
Thiabendazole (TBZ), which is oxidized into 5-hydroxythiabendazole (5-OH-TBZ) in vivo, is a commonly used food preservative. Interactions of TBZ and 5-OH-TBZ with human serum albumin (HSA) were comprehensively studied via multiple spectroscopic methods and molecular docking. This study focussed on the mechanistic and structural information on binding of TBZ and 5-OH-TBZ to HSA to evaluate the impact of the food additive on HSA. (1)H NMR spectra of the two ligands showed the binding exists. ITC and fluorescence spectroscopy results revealed that TBZ was a stronger ligand, with a binding constant of 10(5)l/mol and formed a more stable complex with HSA than did 5-OH-TBZ via electrostatic interaction...
October 15, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28530534/biological-evaluation-of-99mtc-hynic-edda-tricine-ser-3-d4-peptide-for-tumor-targeting
#10
Ziba Kazemi, Mona Haddad Zahmatkesh, Seyed Mohammad Abedi, Seyed Jalal Hosseinimehr
BACKGROUND: D4 small peptide (Leu-Ala-Arg-Leu-Leu-Thr) was selected as an appropriate agent for specific targeting of epidermal growth factor receptor (EGFR). OBJECTIVE: The aim of study was to investigate the 99mTc-labeled D4 peptide for non small cell lung tumor targeting. METHOD: HYNIC-(Ser)3-D4 peptide was labeled with 99mTc using mixture of tricine and ethylenediamine diacetic acid (EDDA) as co-ligands. The in vitro cellular uptake of radiolabebled peptide was evaluated by blocking test on human non small lung cancer (A-549) cell line and its biodistribution was evaluated in A-549 xenografted nude mice...
May 19, 2017: Current Radiopharmaceuticals
https://www.readbyqxmd.com/read/28530188/simple-assay-for-screening-phytoestrogenic-compounds-using-the-oestrogen-receptor-immobilised-magnetite-nanoparticles
#11
Pimchanok Busayapongchai, Sineenat Siri
With increasing interests of phytoestrogens for their potential applications, a rapid and simple tool for screening these phytochemicals is still required. In this study, a simple assay to detect phytoestrogens was developed based on the competition binding between the tested samples and the fluorescently labelled oestrogen (E2) to the human ligand binding domain of oestrogen receptor (LBD-ER) that was immobilised on the magnetite nanoparticles (MNPs). The 40-kDa LBD-ER peptide was produced in an Escherichia coli system...
June 2017: IET Nanobiotechnology
https://www.readbyqxmd.com/read/28529973/high-affinity-mannotetraose-as-an-alternative-to-dextran-in-cona-based-fluorescent-affinity-glucose-assay-due-to-improved-fret-efficiency
#12
Andrea K Locke, Brian M Cummins, Gerard L Coté
Diabetes mellitus affects millions of people worldwide and requires that individuals tightly self-regulate their blood glucose levels to minimize the associated secondary complications. Continuous monitoring devices potentially offer patients a long-term means to tightly monitor their glucose levels. In recent years, fluorescent affinity sensors based on lectins (e.g., Concanavalin A (ConA)) have been implemented in such devices. Traditionally, these sensors pair the lectin with a multivalent ligand, like dextran, in order to develop a competitive binding assay that changes its fluorescent properties in response to the surrounding glucose concentrations...
May 27, 2016: ACS Sensors
https://www.readbyqxmd.com/read/28529724/recent-advances-in-the-management-of-osteoporosis
#13
REVIEW
Seiji Fukumoto, Toshio Matsumoto
There has been substantial progress in the management of patients with osteoporosis and the prevention of osteoporotic fractures. Currently available strong anti-resorptive agents are bisphosphonates and an anti-receptor activator of nuclear factor-kappa B ligand (RANKL) antibody, denosumab. Although bisphosphonates and denosumab both inhibit bone resorption and prevent vertebral and non-vertebral fractures, their mechanisms of action are different. Whereas bisphosphonates' effects on bone mineral density and fracture peak around 3 to 5 years and become plateaued, those of denosumab are maintained for up to 10 years...
2017: F1000Research
https://www.readbyqxmd.com/read/28529634/novel-linear-peptides-with-high-affinity-to-%C3%AE-v%C3%AE-3-integrin-for-precise-tumor-identification
#14
Yi Ma, Guanhua Ai, Congying Zhang, Menglu Zhao, Xue Dong, Zhihao Han, Zhaohui Wang, Min Zhang, Yuxi Liu, Weidong Gao, Siwen Li, Yueqing Gu
Development of alternative linear peptides for targeting αvβ3 integrin has attracted much attention, as the traditional peptide ligand, cyclic RGD, is limited by inferior water-solubility and complex synthesis. Using pharmacophore-based virtual screening and high-throughput molecular docking, we identified two novel linear small peptides RWr and RWrNM with high affinity and specificity to αvβ3 integrin. The competitive binding with cyclic RGD (c(RGDyK)) and cellular uptake related to the integrin expression levels verified their affinity to αvβ3 integrin...
2017: Theranostics
https://www.readbyqxmd.com/read/28529131/the-structure-of-the-guanidine-ii-riboswitch
#15
Lin Huang, Jia Wang, David M J Lilley
The guanidine-II (mini-ykkC) riboswitch is the smallest of the guanidine-responsive riboswitches, comprising two stem loops of similar sequence. We have solved high-resolution crystal structures of both stem loops for the riboswitch from Gloeobacter violaceus. The stem loops have a strong propensity to dimerize by intimate loop-loop interaction. The dimerization creates specific binding pockets for two guanidine molecules, explaining their cooperative binding. Within the binding pockets the ligands are hydrogen bonded to a guanine at O6 and N7, and to successive backbone phosphates...
May 18, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/28528876/modeling-covalent-modifier-drugs
#16
REVIEW
Ernest Awoonor-Williams, Andrew G Walsh, Christopher N Rowley
In this review, we present a summary of how computer modeling has been used in the development of covalent modifier drugs. Covalent modifier drugs bind by forming a chemical bond with their target. This covalent binding can improve the selectivity of the drug for a target with complementary reactivity and result in increased binding affinities due to the strength of the covalent bond formed. In some cases, this results in irreversible inhibition of the target, but some targeted covalent inhibitor (TCI) drugs bind covalently but reversibly...
May 18, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28528775/structural-basis-for-apelin-control-of-the-human-apelin-receptor
#17
Yingli Ma, Yang Yue, Yanbin Ma, Qing Zhang, Qingtong Zhou, Yunpeng Song, Yuqing Shen, Xun Li, Xiaochuan Ma, Chao Li, Michael A Hanson, Gye Won Han, E Allen Sickmier, Gayathri Swaminath, Suwen Zhao, Raymond C Stevens, Liaoyuan A Hu, Wenge Zhong, Mingqiang Zhang, Fei Xu
Apelin receptor (APJR) is a key regulator of human cardiovascular function and is activated by two different endogenous peptide ligands, apelin and Elabela, each with different isoforms diversified by length and amino acid sequence. Here we report the 2.6-Å resolution crystal structure of human APJR in complex with a designed 17-amino-acid apelin mimetic peptide agonist. The structure reveals that the peptide agonist adopts a lactam constrained curved two-site ligand binding mode. Combined with mutation analysis and molecular dynamics simulations with apelin-13 binding to the wild-type APJR, this structure provides a mechanistic understanding of apelin recognition and binding specificity...
May 11, 2017: Structure
https://www.readbyqxmd.com/read/28528665/gabaa-receptors-and-the-diversity-in-their-structure-and-pharmacology
#18
Han Chow Chua, Mary Chebib
GABAA receptors (GABAARs) are a class of ligand-gated ion channels with high physiological and therapeutic significance. In the brain, these pentameric receptors occur with diverse subunit composition, which confers highly complex pharmacology to this receptor class. An impressive range of clinically used therapeutics are known to bind to distinct sites found on GABAARs to modulate receptor function. Numerous experimental approaches have been used over the years to elucidate the binding sites of these drugs, but unequivocal identification is challenging due to subtype- and ligand-dependent pharmacology...
2017: Advances in Pharmacology
https://www.readbyqxmd.com/read/28528645/bacterial-haemoprotein-sensors-of-no-h-nox-and-nosp
#19
Bezalel Bacon, Lisa-Marie Nisbett, Elizabeth Boon
Low concentrations of nitric oxide (NO) modulate varied behaviours in bacteria including biofilm dispersal and quorum sensing-dependent light production. H-NOX (haem-nitric oxide/oxygen binding) is a haem-bound protein domain that has been shown to be involved in mediating these bacterial responses to NO in several organisms. However, many bacteria that respond to nanomolar concentrations of NO do not contain an annotated H-NOX domain. Nitric oxide sensing protein (NosP), a newly discovered bacterial NO-sensing haemoprotein, may fill this role...
2017: Advances in Microbial Physiology
https://www.readbyqxmd.com/read/28528355/increased-retinol-free-rbp4-contributes-to-insulin-resistance-in-gestational-diabetes-mellitus
#20
Yanmin Chen, Ping Lv, Mengkai Du, Zhaoxia Liang, Menglin Zhou, Danqing Chen
PURPOSE: Retinol-binding protein 4 (RBP4) is a circulating retinol transporter that is strongly associated with insulin resistance. The aim of this study was to evaluate the RBP4 and retinol level in rat model of gestational diabetes mellitus and the relationship between retinol-free RBP4 (apo-RBP4), retinol-bound RBP4 (holo-RBP4) and insulin resistance. METHODS: Pregnant rats were administered streptozotocin to induce diabetes. The RBP4 and retinol levels were evaluated in GDM and normal pregnant rats...
May 20, 2017: Archives of Gynecology and Obstetrics
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