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https://www.readbyqxmd.com/read/28820938/multi-scale-simulation-of-receptor-drug-association-kinetics-application-to-neuramidase-inhibitors
#1
Fabian Zeller, Manuel P Luitz, Rainer Bomblies, Martin Zacharias
A detailed understanding of the drug-receptor association process is of fundamental importance for drug design. Due to the long timescales of typical binding kinetics, the atomistic simulation of the ligand traveling from bulk solution into the binding site is still computationally challenging. In this work, we apply a multi-scale approach of combined molecular dynamics (MD) and Brownian dynamics (BD) simulations to investigate association pathway ensembles for the two prominent H1N1 neuraminidase inhibitors oseltamivir and zanamivir...
August 18, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28805972/in-vitro-pharmacological-characterization-of-a-novel-unbiased-nop-receptor-selective-nonpeptide-agonist-at-403
#2
Federica Ferrari, Davide Malfacini, Blair V Journigan, Mark F Bird, Claudio Trapella, Remo Guerrini, David G Lambert, Girolamo Calo', Nurulain T Zaveri
Nociceptin/orphanin FQ (N/OFQ) regulates several biological functions via selective activation of the N/OFQ receptor (NOP), a member of the opioid receptor family. We recently identified a new high affinity and highly selective NOP agonist AT-403. In this study, we characterized the functional profile of AT-403 and compared it to other known nonpeptide NOP agonists Ro 65-6570, Ro 2q, SCH-221510, MCOPPB, AT-202 and SCH-486757, using the following assays: GTPγ[(35) S] stimulated binding, calcium mobilization assay in cells-expressing human NOP or classical opioid receptors and chimeric G proteins, bioluminescence resonance energy transfer (BRET) based assay for studying NOP receptor interaction with G protein and arrestin, and the electrically stimulated mouse vas deferens bioassay...
August 2017: Pharmacology Research & Perspectives
https://www.readbyqxmd.com/read/28794644/the-rank-rankl-opg-system-in-tumorigenesis-and-metastasis-of-cancer-stem-cell-potential-targets-for-anticancer-therapy
#3
REVIEW
Mekonnen Sisay, Getnet Mengistu, Dumessa Edessa
The molecular triad involving receptor activator of nuclear factor kβ (RANK)/RANK ligand (RANKL)/osteoprotegerin cytokine system has been well implicated in several physiological and pathological processes including bone metabolism, mammary gland development, regulation of the immune function, tumorigenesis and metastasis of cancer stem cell, thermoregulation, and vascular calcification. However, this review aimed to summarize several original and up-to-date articles focusing on the role of this signaling system in cancer cell development and metastasis as well as potential therapeutic agents targeting any of the three tumor necrotic factor super family proteins and/or their downstream signaling pathways...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28791343/breast-cancer-associated-gene-3-interacts-with-rac1-and-augments-nf-%C3%AE%C2%BAb-signaling-in-vitro-but-has-no-effect-on-rankl-induced-bone-resorption-in-vivo
#4
Chen Yao, Kuan-Ping Yu, William Philbrick, Ben-Hua Sun, Christine Simpson, Changqing Zhang, Karl Insogna
Breast cancer-associated gene 3 (BCA3) is a recently identified adaptor protein whose functions are still being defined. BCA3 has been reported to be an important regulator of nuclear factor-κB (NF-κB) signaling. It has also been reported to interact with the small GTPase, Rac1. Consistent with that observation, in the present study, BCA3 was found to interact with nuclear Rac1 in 293 cells and influence NF-κB signaling. Additional experiments revealed that depending on cell type, BCA3 augmented, attenuated or had no effect on NF-κB signaling in vitro...
August 4, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28766097/ranking-docking-poses-by-graph-matching-of-protein-ligand-interactions-lessons-learned-from-the-d3r-grand-challenge-2
#5
Priscila da Silva Figueiredo Celestino Gomes, Franck Da Silva, Guillaume Bret, Didier Rognan
A novel docking challenge has been set by the Drug Design Data Resource (D3R) in order to predict the pose and affinity ranking of a set of Farnesoid X receptor (FXR) agonists, prior to the public release of their bound X-ray structures and potencies. In a first phase, 36 agonists were docked to 26 Protein Data Bank (PDB) structures of the FXR receptor, and next rescored using the in-house developed GRIM method. GRIM aligns protein-ligand interaction patterns of docked poses to those of available PDB templates for the target protein, and rescore poses by a graph matching method...
August 1, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28763689/investigation-of-novel-pharmacological-chaperones-for-gaucher-disease
#6
Buge Yilmazer, Z Begum Yagci, Emre Bakar, Burcu Ozden, Kutlu Ulgen, Elif Ozkirimli
Beta-Glucocerebrosidase (GBA) is a lysosomal protein that is responsible for the hydrolysis of glycosylceramide into glucose and ceramide. Mutations in GBA lead to the accumulation of glycosylceramide in the lysosome causing an enlargement of the spleen and the liver and skeletal deformations. This disease is called Gaucher Disease. Enzyme replacement therapies and substrate reduction methods that are used to treat Gaucher Disease fail when the disease is neuropathic because they fail to pass the blood brain barrier...
July 20, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28760952/testing-inhomogeneous-solvation-theory-in-structure-based-ligand-discovery
#7
Trent E Balius, Marcus Fischer, Reed M Stein, Thomas B Adler, Crystal N Nguyen, Anthony Cruz, Michael K Gilson, Tom Kurtzman, Brian K Shoichet
Binding-site water is often displaced upon ligand recognition, but is commonly neglected in structure-based ligand discovery. Inhomogeneous solvation theory (IST) has become popular for treating this effect, but it has not been tested in controlled experiments at atomic resolution. To do so, we turned to a grid-based version of this method, GIST, readily implemented in molecular docking. Whereas the term only improves docking modestly in retrospective ligand enrichment, it could be added without disrupting performance...
August 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28753812/pd-l1-expression-and-cd8-t-cell-infiltrate-are-associated-with-clinical-progression-in-patients-with-node-positive-prostate-cancer
#8
Florent Petitprez, Nicola Fossati, Yann Vano, Massimo Freschi, Etienne Becht, Roberta Lucianò, Julien Calderaro, Tiffany Guédet, Laetitia Lacroix, Paola M V Rancoita, Francesco Montorsi, Wolf Herman Fridman, Catherine Sautès-Fridman, Alberto Briganti, Claudio Doglioni, Matteo Bellone
Prostate cancer (PCa) patients with lymph node invasion at radical prostatectomy are at higher risk of tumor recurrence and receive immediate androgen deprivation therapy (ADT). While approximately 30% of these patients do not experience recurrence, others experience disease recurrence despite ADT, and currently no biomarkers can accurately identify them. We analyzed tumors from 51 patients with node-positive prostate cancer using immunohistochemistry to investigate whether expression of the immune checkpoint ligand PD-L1 by tumor cells or the density of CD8(+) or CD20(+) cells are associated with clinical progression...
June 21, 2017: European Urology Focus
https://www.readbyqxmd.com/read/28747521/a-novel-18-f-labeled-kappa-opioid-receptor-antagonist-as-pet-radiotracer-synthesis-and-in-vivo-evaluation-of-18-f-ly2459989-in-non-human-primates
#9
Songye Li, Zhengxin Cai, Ming-Qiang Zheng, Daniel Holden, Mika Naganawa, Shu-Fei Lin, Jim Ropchan, David Labaree, Michael Kapinos, Teresa Lara-Jaime, Antonio Navarro, Yiyun Huang
The kappa opioid receptor (KOR) is implicated in depression, addictions, and other central nervous system (CNS) disorders and thus an important target for drug development. We have previously developed a number of (11)C-labeled PET radiotracers for KOR imaging in humans. Here we report the synthesis and evaluation of (18)F-LY2459989 as the first (18)F-labeled KOR antagonist radiotracer in non-human primates and its comparison with (11)C-LY2459989. Methods: The novel radioligand (18)F-LY2459989 was synthesized by (18)F-displacement of a nitro group or an iodonium ylide...
July 26, 2017: Journal of Nuclear Medicine: Official Publication, Society of Nuclear Medicine
https://www.readbyqxmd.com/read/28739166/characterizing-activation-mechanisms-and-binding-preferences-of-ruthenium-metallo-prodrugs-by-a-competitive-binding-assay
#10
Christian Artner, Hannah U Holtkamp, Christian G Hartinger, Samuel M Meier-Menches
The activation mechanisms and reactivity of ruthenium metallo-prodrug lead structures were investigated in detail using capillary zone electrophoresis mass spectrometry (CZE-MS) in a time-dependent manner and by exposing to a protein/oligonucleotide mixture. The competitive assays were performed with sodium trans-[RuCl4(HInd)2] where Hind=indazole (NKP-1339), [(η(6)-p-cymene)RuCl2(pta)], where pta=1,3,5-triaza-7-phosphaadamantane (RAPTA-C) and [(η(6)-biphenyl)RuCl(1,2-ethylenediamine)]PF6 (RM175). Molecular and quantitative information on binding preferences was obtained by coupling CZE to electrospray ionization MS (ESI-MS) and inductively coupled plasma MS (ICP-MS), respectively...
July 16, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/28732438/investigation-of-killer-immunoglobulin-like-receptor-kir-and-hla-genotypes-to-predict-the-occurrence-of-acute-allograft-rejection-after-kidney-transplantation
#11
Davood Jafari, Mohsen Nafar, Mir Saeed Yekaninejad, Razieh Abdolvahabi, Mahboob Lesan Pezeshki, Efat Razaghi, Ali Akbar Amirzargar
After kidney transplantation, natural killer (NK) cells play a pivotal role in triggering the immune response to the allogeneic grafts primarily by their killer-cell immunoglobulin-like receptors (KIR). This process may be one mechanism that contributes to graft rejection. In this study, we have evaluated whether acute rejection after kidney transplantation was associated with predicted NK cell alloreactivity based on KIR gene and ligand along with KIR/HLA compound genotype analysis. After kidney transplantation, natural killer (NK) cells play a pivotal role in triggering the immune response to the allogeneic grafts primarily by their killer-cell immunoglobulin-like receptors (KIR)...
June 2017: Iranian Journal of Allergy, Asthma, and Immunology
https://www.readbyqxmd.com/read/28731168/osteoclast-regulation-of-osteoblasts-via-rank%C3%A2-rankl-reverse-signal-transduction-in%C3%A2-vitro
#12
Shiqian Zhang, Xiaoyu Wang, Guojun Li, Yang Chong, Jie Zhang, Xinzhen Guo, Baoxin Li, Zhenggang Bi
The treatment of osteoporosis typically inhibits the activity of osteoclasts, which subsequently results in the suppression of bone formation and maintenance, however the underlying mechanism remains to be elucidated. The receptor activator of nuclear factor κ‑B ligand (RANKL)‑receptor activator of nuclear factor κ‑B (RANK) signaling axis is important in the osteoblast regulation of osteoclasts. RANKL surface‑bound molecules expressed on T cells stimulate a reverse signaling transduction in order to regulate the T cells, therefore the present study hypothesized that RANKL expressed on osteoblasts may transfer reverse signals to regulate osteoblasts...
July 20, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28727766/clinical-implications-of-the-novel-cytokine-il-38-expressed-in-lung-adenocarcinoma-possible-association-with-pd-l1-expression
#13
Kazuki Takada, Tatsuro Okamoto, Masaki Tominaga, Koji Teraishi, Takaki Akamine, Shinkichi Takamori, Masakazu Katsura, Gouji Toyokawa, Fumihiro Shoji, Masaki Okamoto, Yoshinao Oda, Tomoaki Hoshino, Yoshihiko Maehara
Interleukin (IL)-38, a novel member of the IL-1 cytokine family, is homologous to IL-1 receptor antagonist (IL-1Ra) and IL-36Ra, and has been reported to act as an antagonist. IL-38 expression is found in tonsil, placenta, and spleen, and recent studies suggest an association between IL-38 and autoimmune diseases. However, whether IL-38 plays a role in carcinogenesis or cancer growth is unclear. In the present study, we identified increases in IL-38 expression by immunohistochemistry in multiple types of cancer cells...
2017: PloS One
https://www.readbyqxmd.com/read/28712038/binding-mode-prediction-and-md-mmpbsa-based-free-energy-ranking-for-agonists-of-rev-erb%C3%AE-ncor
#14
Yvonne Westermaier, Sergio Ruiz-Carmona, Isabelle Theret, Françoise Perron-Sierra, Guillaume Poissonnet, Catherine Dacquet, Jean A Boutin, Pierre Ducrot, Xavier Barril
The knowledge of the free energy of binding of small molecules to a macromolecular target is crucial in drug design as is the ability to predict the functional consequences of binding. We highlight how a molecular dynamics (MD)-based approach can be used to predict the free energy of small molecules, and to provide priorities for the synthesis and the validation via in vitro tests. Here, we study the dynamics and energetics of the nuclear receptor REV-ERBα with its co-repressor NCoR and 35 novel agonists. Our in silico approach combines molecular docking, molecular dynamics (MD), solvent-accessible surface area (SASA) and molecular mechanics poisson boltzmann surface area (MMPBSA) calculations...
July 15, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28707576/new-strategies-for-the-prevention-and-treatment-of-systemic-and-local-bone-loss-from-pathophysiology-to-clinical-application
#15
A Fassio, Maurizio Rossini, Ombretta Viapiana, Luca Idolazzi, Camilla Benini, Elisabetta Vantaggiato, Davide Gatti
Bone loss is the result of a negative unbalance between bone formation ad bone resorption. In the last years, the studies on the Wnt canonical pathway have highlighted its crucial role in bone balance through its influence on the activity and maturation of the osteoblast line and in the Receptor Activator of Nuclear Factor κ B (RANK) - RANK ligand (RANKL)/Osteoprotegerin (OPG) system. These mechanisms are involved not only in the pathological processes inducing not only systemic bone loss (ie. Postmenopausal osteoporosis, glucocorticoid-induced osteoporosis, etc...
July 13, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/28705120/qsar-docking-admet-system-pharmacology-studies-on-tormentic-acid-derivatives-for-anticancer-activity
#16
Sarfaraz Alam, Feroz Khan
To explore the anticancer compounds from tormentic acid derivatives, a quantitative structure-activity relationship (QSAR) model was developed by the multiple linear regression methods. The developed QSAR model yielded a high activity-descriptors relationship accuracy of 94% referred by regression coefficient (r(2)= 0.94) and a high activity prediction accuracy of 91%. The QSAR study indicates that chemical descriptors, chiV5, T_T_Cl_7, T_2_T_4, SsCH3count, and Epsilon3 are significantly correlated with anticancer activity...
July 14, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28701332/circulating-rankl-and-rankl-opg-and-breast-cancer-risk-by-er-and-pr-subtype-results-from-the-epic-cohort
#17
Danja Sarink, Helena Schock, Theron Johnson, Kim Overvad, Marianne Holm, Anne Tjonneland, Marie-Christine Boutron-Ruault, Mathilde His, Marina Kvaskoff, Heiner Boeing, Pagona Lagiou, Eleni-Maria Papatesta, Antonia Trichopoulou, Domenico Palli, Valeria Pala, Amalia Mattiello, Rosario Tumino, Carlotta Sacerdote, H B As Bueno-de-Mesquita, Carla H van Gils, Petra H Peeters, Elisabete Weiderpass, Antonio Agudo, Maria-Jose Sanchez, Maria-Dolores Chirlaque, Eva Ardanaz, Pilar Amiano, Kay-Tee Khaw, Ruth C Travis, Laure Dossus, Marc J Gunter, Sabina Rinaldi, Melissa A Merritt, Elio Riboli, Rudolf Kaaks, Renee T Fortner
Receptor activator of nuclear factor kappa-B (RANK)-RANK ligand (RANKL) signaling promotes mammary tumor development in experimental models. Circulating concentrations of soluble RANKL (sRANKL) may influence breast cancer risk via activation of RANK signaling; this may be modulated by osteoprotegerin (OPG), the decoy receptor for RANKL. sRANKL and breast cancer risk by hormone receptor subtype has not previously been investigated. <p>A case-control study was nested in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort...
July 12, 2017: Cancer Prevention Research
https://www.readbyqxmd.com/read/28700003/the-effects-of-chitosan-oligosaccharides-on-opg-and-rankl-expression-in-a-rat-osteoarthritis-model
#18
Chun Zhang, Qi Liao, Jiang-Hua Ming, Ge-Liang Hu, Qing Chen, Shi-Qing Liu, Ya-Ming Li
Purpose: To investigate the effect of chitosan oligosaccharides (COS) against osteoarthritis (OA) and preliminarily discuss the osteoprotegerin (OPG), receptor activator of NF-κB ligand (RANKL) and RANK expression in a rat OA model. Methods: Thirty-six 6-week-old Male SD rats were randomly divided into three groups: sham-operated group(CON), OA-induction group(OA), COS intervention group(n=12/group). At 4 weeks after the operation, COS (50 ul) intervention weekily for consecutive 5 weeks...
June 2017: Acta Cirúrgica Brasileira
https://www.readbyqxmd.com/read/28692887/electron-magnetic-resonance-data-on-high-spin-mn-iii-s-2-ions-in-porphyrinic-and-salen-complexes-modeled-by-microscopic-spin-hamiltonian-approach
#19
Krzysztof Tadyszak, Czesław Rudowicz, Hitoshi Ohta, Takahiro Sakurai
The spin Hamiltonian (SH) parameters experimentally determined by EMR (EPR) may be corroborated or otherwise using various theoretical modeling approaches. To this end semiempirical modeling is carried out for high-spin (S=2) manganese (III) 3d(4) ions in complex of tetraphenylporphyrinato manganese (III) chloride (MnTPPCl). This modeling utilizes the microscopic spin Hamiltonians (MSH) approach developed for the 3d(4) and 3d(6) ions with spin S=2 at orthorhombic and tetragonal symmetry sites in crystals, which exhibit an orbital singlet ground state...
June 28, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/28689418/an-assay-based-on-samdi-mass-spectrometry-for-profiling-protein-interaction-domains
#20
Patrick T O'Kane, Milan Mrksich
This paper describes an assay that can profile the binding of a protein to ligands and can rank the affinities of a library of ligands. The method is based on the enhanced rate of an enzyme-mediated reaction that follows from colocalization of the enzyme and substrate by a protein-ligand interaction. This assay uses a self-assembled monolayer that presents a candidate peptide ligand for a receptor and a peptide substrate for an enzyme. The receptor is prepared as a fusion to the relevant enzyme so that binding of the receptor to the immobilized ligand brings the enzyme to the surface, where it can more rapidly modify its substrate...
July 21, 2017: Journal of the American Chemical Society
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