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https://www.readbyqxmd.com/read/28535663/up-regulation-of-rank-expression-via-erk1-2-by-insulin-contributes-to-the-enhancement-of-osteoclast-differentiation
#1
Ju Hee Oh, Na Kyung Lee
Despite the importance of the receptor activator of nuclear factor (NF)-kappaB ligand (RANKL)-RANK signaling mechanisms on osteoclast differentiation, little has been studied on how RANK expression is regulated or what regulates its expression during osteoclastogenesis. We show here that insulin signaling increases RANK expression, thus enhancing osteoclast differentiation by RANKL. Insulin stimulation induced RANK gene expression in time- and dose-dependent manners and insulin receptor shRNA completely abolished RANK expression induced by insulin in bone marrow-derived monocyte/ macrophage cells (BMMs)...
May 22, 2017: Molecules and Cells
https://www.readbyqxmd.com/read/28534194/assessing-protein-ligand-binding-modes-with-computational-tools-the-case-of-pde4b
#2
Gülşah Çifci, Viktorya Aviyente, E Demet Akten, Gerald Monard
In a first step in the discovery of novel potent inhibitor structures for the PDE4B family with limited side effects, we present a protocol to rank newly designed molecules through the estimation of their IC[Formula: see text] values. Our protocol is based on reproducing the linear relationship between the logarithm of experimental IC[Formula: see text] values [[Formula: see text](IC[Formula: see text])] and their calculated binding free energies ([Formula: see text]). From 13 known PDE4B inhibitors, we show here that (1) binding free energies obtained after a docking process by AutoDock are not accurate enough to reproduce this linear relationship; (2) MM-GB/SA post-processing of molecular dynamics (MD) trajectories of the top ranked AutoDock pose improves the linear relationship; (3) by taking into account all representative structures obtained by AutoDock and by averaging MM-GB/SA computations on a series of 40 independent MD trajectories, a linear relationship between [Formula: see text](IC[Formula: see text]) and the lowest [Formula: see text] is achieved with [Formula: see text]...
May 22, 2017: Journal of Computer-aided Molecular Design
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
#3
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/28529724/recent-advances-in-the-management-of-osteoporosis
#4
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/28528876/modeling-covalent-modifier-drugs
#5
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/28525946/ghrelin-attenuates-vascular-calcification-in-diabetic-patients-with-amputation
#6
Suining Xu, Fei Ye, Lihua Li, Jinchuan Yan, Zhengyang Bao, Zhen Sun, Liangjie Xu, Jie Zhu, Zhongqun Wang
Vascular calcification is established to be a critical factor in diabetes mellitus, which causes cardiovascular and amputation complication of diabetic patients. OPG/RANKL/RANK axis serves as a regulatory role in vascular calcification. Ghrelin, an endogenous ligand of growth hormone secretagogue receptor (GHSR), has been reported to exhibit potent cardiovascular protective effects. However, the role of ghrelin in the regulation of diabetic vascular calcification is still elusive. Here, we reported the role of ghrelin and its relationship with OPG/RANKL/RANK system in patients with diabetic foot amputation...
May 15, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28510083/software-for-molecular-docking-a-review
#7
REVIEW
Nataraj S Pagadala, Khajamohiddin Syed, Jack Tuszynski
Molecular docking methodology explores the behavior of small molecules in the binding site of a target protein. As more protein structures are determined experimentally using X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy, molecular docking is increasingly used as a tool in drug discovery. Docking against homology-modeled targets also becomes possible for proteins whose structures are not known. With the docking strategies, the druggability of the compounds and their specificity against a particular target can be calculated for further lead optimization processes...
April 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28508120/effects-of-arm-truncation-on-the-appearance-of-the-halo-artifact-in-68-ga-psma-11-hbed-cc-pet-mri
#8
Ali Afshar-Oromieh, Maya Wolf, Uwe Haberkorn, Marc Kachelrieß, Regula Gnirs, Klaus Kopka, Heinz-Peter Schlemmer, Martin T Freitag
PURPOSE: PSMA ligand imaging with hybrid PET/MRI scanners could be an integral part of the clinical routine in the future. However, the first study about this novel method revealed a severe photopenic artifact ("halo artifact") around the urinary bladder causing significantly reduced tumor visibility. The aim of this evaluation was to analyze the role of arm truncation on the appearance of the halo artifact in (68)Ga-PSMA-11 PET/MRI hypothesizing that this influences the appearance. METHODS: Twenty-seven consecutive patients were subjected to (68)Ga-PSMA-11 PET/CT (1 h p...
May 15, 2017: European Journal of Nuclear Medicine and Molecular Imaging
https://www.readbyqxmd.com/read/28506283/prolactin-blocks-the-expression-of-receptor-activator-of-nuclear-factor-%C3%AE%C2%BAb-ligand-and-reduces-osteoclastogenesis-and-bone-loss-in-murine-inflammatory-arthritis
#9
Maria G Ledesma-Colunga, Norma Adán, Georgina Ortiz, Mariana Solís-Gutiérrez, Fernando López-Barrera, Gonzalo Martínez de la Escalera, Carmen Clapp
BACKGROUND: Prolactin (PRL) reduces joint inflammation, pannus formation, and bone destruction in rats with polyarticular adjuvant-induced arthritis (AIA). Here, we investigate the mechanism of PRL protection against bone loss in AIA and in monoarticular AIA (MAIA). METHODS: Joint inflammation, trabecular bone loss, and osteoclastogenesis were evaluated in rats with AIA treated with PRL (via osmotic minipumps) and in mice with MAIA that were null (Prlr-/-) or not (Prlr+/+) for the PRL receptor...
May 15, 2017: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/28500914/limitations-of-experiments-performed-in-artificially-made-oecd-standard-soils-for-predicting-cadmium-lead-and-zinc-toxicity-towards-organisms-living-in-natural-soils
#10
Mateusz Sydow, Łukasz Chrzanowski, Nina Cedergreen, Mikołaj Owsianiak
Development of comparative toxicity potentials of cationic metals in soils for applications in hazard ranking and toxic impact assessment is currently jeopardized by the availability of experimental effect data. To compensate for this deficiency, data retrieved from experiments carried out in standardized artificial soils, like OECD soils, could potentially be tapped as a source of effect data. It is, however, unknown whether such data are applicable to natural soils where the variability in pore water concentrations of dissolved base cations is large, and where mass transfer limitations of metal uptake can occur...
May 9, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28500617/post-chemotherapy-pd-l1-expression-correlates-with-clinical-outcomes-in-japanese-bladder-cancer-patients-treated-with-total-cystectomy
#11
Daisuke Noro, Shingo Hatakeyama, Takahiro Yoneyama, Yasuhiro Hashimoto, Takuya Koie, Toshiaki Kawaguchi, Chikara Ohyama
Programmed cell death ligand-1 (PD-L1) is a key target molecule of immunotherapy that is frequently overexpressed in bladder cancer. In the present study, we examined whether PD-L1 expression is associated with clinical outcomes in bladder cancer patients. We enrolled 102 bladder cancer patients treated with cystectomy at the Aomori Prefectural Hospital between April 2004 and May 2014. We conducted an immunohistochemical examination of PD-L1 expression using the SP142 assay. PD-L1 expression was scored at three diagnostic levels (0/1/2)...
June 2017: Medical Oncology
https://www.readbyqxmd.com/read/28488893/vdr-rankl-and-opg-polymorphisms-as-possible-predisposing-cofactors-of-postmenopausal-osteoporosis-explorative-study-in-italian-population
#12
Elisabetta Mamolini, Carlo Cervellati, Pantaleo Greco, Alberto Carrieri, Leo Massari, Ilaria Crivellari, Chiara Scapoli, Gloria Bonaccorsi
Postmenopausal osteoporosis (PO) has a strong genetic component. Presently, the published evidence on the association between the main single-nucleotide polymorphisms (SNPs) of the receptor activator of nuclear factor-kb ligand (RANKL), osteoprotegerin (OPG) and vitamin D receptor (VDR) and bone mass density (BMD) are scarce, mostly considering Italian population. This study sought to determine whether OPG (rs2073618), RANKL (rs9525641) and the VDR (rs2228570) SNPs were associated with BMD in a sample of 139 North-Italian postmenopausal women...
May 10, 2017: Gynecological Endocrinology
https://www.readbyqxmd.com/read/28487384/non-invasive-interrogation-of-dll3-expression-in-metastatic-small-cell-lung-cancer
#13
Sai Kiran Sharma, Jacob Pourat, Dalya Abdel-Atti, Sean D Carlin, Alessandra Piersigilli, Alexander J Bankovich, Eric E Gardner, Omar Hamdy, Kumiko Isse, Sheila Bheddah, Joseph Sandoval, Kristen M Cunanan, Eric B Johansen, Viola Allaj, Vikram Sisodiya, David Liu, Brian M Zeglis, Charles M Rudin, Scott J Dylla, J T Poirier, Jason S Lewis
The Notch ligand DLL3 has emerged as a novel therapeutic target expressed in small cell lung cancer (SCLC) and high-grade neuroendocrine carcinomas. Rovalpituzumab teserine (Rova-T™; SC16LD6.5) is a first-in-class DLL3-targeted antibody-drug conjugate with encouraging initial safety and efficacy profiles in SCLC in the clinic. Here we demonstrate that tumor expression of DLL3, though orders of magnitude lower in surface protein expression than typical oncology targets of immunoPET, can serve as an imaging biomarker for SCLC...
May 9, 2017: Cancer Research
https://www.readbyqxmd.com/read/28486703/ammos2-a-web-server-for-protein-ligand-water-complexes-refinement-via-molecular-mechanics
#14
Céline M Labbé, Tania Pencheva, Dessislava Jereva, Dimitri Desvillechabrol, Jérôme Becot, Bruno O Villoutreix, Ilza Pajeva, Maria A Miteva
AMMOS2 is an interactive web server for efficient computational refinement of protein-small organic molecule complexes. The AMMOS2 protocol employs atomic-level energy minimization of a large number of experimental or modeled protein-ligand complexes. The web server is based on the previously developed standalone software AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening). AMMOS utilizes the physics-based force field AMMP sp4 and performs optimization of protein-ligand interactions at five levels of flexibility of the protein receptor...
May 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28482837/selective-gene-expression-analysis-of-the-neuroepithelial-body-microenvironment-in-postnatal-lungs-with-special-interest-for-potential-stem-cell-characteristics
#15
Line Verckist, Robrecht Lembrechts, Sofie Thys, Isabel Pintelon, Jean-Pierre Timmermans, Inge Brouns, Dirk Adriaensen
BACKGROUND: The pulmonary neuroepithelial body (NEB) microenvironment (ME) consists of innervated cell clusters that occur sparsely distributed in the airway epithelium, an organization that has so far hampered reliable selective gene expression analysis. Although the NEB ME has been suggested to be important for airway epithelial repair after ablation, little is known about their potential stem cell characteristics in healthy postnatal lungs. Here we report on a large-scale selective gene expression analysis of the NEB ME...
May 8, 2017: Respiratory Research
https://www.readbyqxmd.com/read/28475928/development-and-characterization-of-mitochondrial-membrane-affinity-chromatography-columns-derived-from-skeletal-muscle-and-platelets-for-the-study-of-mitochondrial-transmembrane-proteins
#16
Nagendra Surendra Singh, Kaia-Liisa Habicht, Ruin Moaddel, Ruth Shimmo
Mitochondrial membrane fragments from human platelets and monkey skeletal muscles were successfully immobilized onto immobilized artificial membrane chromatographic support for the first time, resulting in mitochondrial membrane affinity chromatography (MMAC) columns. These columns were validated by characterization of translocator protein (TSPO), where multiple concentrations of dipyridamole were run and the binding affinities (Kd) determined. Further, the relative ranking data of TSPO ligands was consistent with previously reported rankings for both, the platelet (MMAC-Platelet) and the skeletal muscle (MMAC-Muscle) column (dipyridamole>PK11195>protoporphyrin IX>rotenone)...
April 13, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28474138/effects-of-iguratimod-on-the-levels-of-circulating-regulators-of-bone-remodeling-and-bone-remodeling-markers-in-patients-with-rheumatoid-arthritis
#17
Xuetong Wang, Cuili Ma, Ping Li, Feng Zhao, Liqi Bi
This study aims to investigate the effect of iguratimod, a novel disease-modifying antirheumatic drug, alone or combined with methotrexate (MTX), on the serum levels of regulators of bone remodeling (receptor activator of nuclear factor-κB ligand (RANKL), osteoprotegerin (OPG), and Dickkopf-1 (DKK-1)) and bone remodeling markers (C-telopeptide of type I collagen (CTX-I) and procollagen type I N-terminal propeptide (PINP)) in patients with rheumatoid arthritis (RA). Patients with RA were treated with iguratimod, MTX, or their combination for 12 months...
May 4, 2017: Clinical Rheumatology
https://www.readbyqxmd.com/read/28473963/rank-ligand-and-osteoprotegerin-as-biomarkers-in-the-differentiation-between-periprosthetic-joint-infection-and-aseptic-prosthesis-loosening
#18
Max J Friedrich, Matthias D Wimmer, Jan Schmolders, Andreas C Strauss, Milena M Ploeger, Hendrik Kohlhof, Dieter C Wirtz, Sascha Gravius, Thomas M Randau
AIM: To assess serum levels of RANK-ligand (RANKL) and osteoprotegerin (OPG) as biomarkers for periprosthetic joint infection (PJI) and compare their accuracy with standard tests. METHODS: One hundred and twenty patients presenting with a painful total knee or hip arthroplasty with indication for surgical revision were included in this prospective clinical trial. Based on standard diagnostics (joint aspirate, microbiological, and histological samples) and Musculoskeletal Infection Society consensus classification, patients were categorized into PJI, aseptic loosening, and control groups...
April 18, 2017: World Journal of Orthopedics
https://www.readbyqxmd.com/read/28472422/pharmmapper-2017-update-a-web-server-for-potential-drug-target-identification-with-a-comprehensive-target-pharmacophore-database
#19
Xia Wang, Yihang Shen, Shiwei Wang, Shiliang Li, Weilin Zhang, Xiaofeng Liu, Luhua Lai, Jianfeng Pei, Honglin Li
The PharmMapper online tool is a web server for potential drug target identification by reversed pharmacophore matching the query compound against an in-house pharmacophore model database. The original version of PharmMapper includes more than 7000 target pharmacophores derived from complex crystal structures with corresponding protein target annotations. In this article, we present a new version of the PharmMapper web server, of which the backend pharmacophore database is six times larger than the earlier one, with a total of 23 236 proteins covering 16 159 druggable pharmacophore models and 51 431 ligandable pharmacophore models...
May 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28471171/characterizing-the-chemical-space-of-erk2-kinase-inhibitors-using-descriptors-computed-from-molecular-dynamics-trajectories
#20
Jeremy Ash, Denis Fourches
Quantitative Structure-Activity Relationship (QSAR) models typically rely on 2D and 3D molecular descriptors to characterize chemicals and forecast their experimental activities. Previously, we showed that even the most reliable 2D QSAR models and structure-based 3D molecular docking techniques were not capable of accurately ranking a set of known inhibitors for the ERK2 kinase, a key player in various types of cancer. Herein, we calculated and analyzed a series of chemical descriptors computed from the molecular dynamics (MD) trajectories of ERK2-ligand complexes...
May 4, 2017: Journal of Chemical Information and Modeling
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