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https://www.readbyqxmd.com/read/27914062/computational-design-of-ligand-binding-proteins
#1
Christine E Tinberg, Sagar D Khare
The ability to design novel small-molecule binding sites in proteins is a stringent test of our understanding of the principles of molecular recognition, and would have many practical applications, in synthetic biology and medicine. Here, we describe a computational method in the context of the macromolecular modeling suite Rosetta to designing proteins with sites featuring predetermined interactions to ligands of choice. The required inputs for the method are a model of the small molecule and the desired interactions (e...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27897273/a-novel-therapeutic-peptide-as-a-partial-agonist-of-rankl-in-ischemic-stroke
#2
Hitomi Kurinami, Munehisa Shimamura, Hironori Nakagami, Hideo Shimizu, Hiroshi Koriyama, Tomohiro Kawano, Kouji Wakayama, Hideki Mochizuki, Hiromi Rakugi, Ryuichi Morishita
The enhanced receptor activator of nuclear factor-κB (NFκB) ligand (RANKL) and its receptor (RANK) signal have been reported to attenuate ischemic brain injury through inhibition of Toll-like receptor (TLR) 4-mediated inflammation. However, augmentation of the RANKL/RANK signal also accelerates osteoporosis, which is a potential problem in clinical use of RANKL. Therefore, we developed novel peptides, microglial healing peptides (MHPs), which were based on the DE and/or EF loop of RANKL. Among them, MHP1 was the most effective inhibitor of TLR4-induced inflammations in microglia/macrophages...
November 29, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27897222/nadph-oxidase-gp91-phox-contributes-to-rankl-induced-osteoclast-differentiation-by-upregulating-nfatc1
#3
In Soon Kang, Chaekyun Kim
Bone-marrow derived monocyte-macrophages (BMMs) differentiate into osteoclasts by M-CSF along subsequent RANKL stimulation possibly in collaboration with many other unknown cytokines released by pre- or mature osteoblasts. The differentiation process requires receptor activator of nuclear factor kappa-B ligand (RANKL)/RANK signaling and reactive oxygen species (ROS) such as superoxide anion (O2(•-)). Gp91(phox), a plasma membrane subunit of NADPH oxidase (Nox), is constitutively expressed in BMMs and plays a major role in superoxide anion production...
November 29, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27895755/inhibitory-effects-of-chinese-nutritional-herbs-in-isogenic-breast-carcinoma-cells-with-modulated-estrogen-receptor-function
#4
Nitin Telang, Guo Li, Meena Katdare, Daniel Sepkovic, Leon Bradlow, George Wong
In estrogen receptor (ER)+ MCF-7 cells, ER represents a ligand-activated transcription factor, and 17β-estradiol (E2) represents its physiological ligand. Maintenance of the human breast carcinoma-derived MCF-7 cells with 0.7% serum selected a proliferative sub-population of E2-responsive cells with transiently non-functional ER due to limited availability of E2. Culture of MCF-7 cells in the presence of either 0.7% serum, <1 nM E2 or 0.7% serum + 20 nM E2 selected isogenic cells with either non-functional ER (ER-NF) or functional ER (ER-F) phenotype...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27894399/effect-of-iguratimod-and-methotrexate-on-rankl-and-opg-expression-in-serum-and-il-1%C3%AE-induced-fibroblast-like-synoviocytes-from-patients-with-rheumatoid-arthritis
#5
X T Wang, P Li, T S Xu, R Ding, X Zhang, L Q Bi
The receptor activator of nuclear factor κB ligand (RANKL)/receptor activator of nuclear factor κB (RANK)/osteoprotegerin (OPG) system plays a key role in rheumatoid arthritis (RA)-associated bone erosion. The upregulation of the RANKL/OPG ratio promotes bone erosion. The objective of this study is to explore the effects of iguratimod, a small-molecule disease-modifying antirheumatic drug (DMARD), alone or in combination with methotrexate (MTX), on RANKL and OPG expression in RA. We performed an enzyme-linked immunosorbent assay (ELISA) to investigate the modulatory effects of iguratimod, MTX, or their combination on serum RANKL and OPG levels of patients with RA before and after treatment for 12 and 24 weeks...
October 31, 2016: Cellular and Molecular Biology
https://www.readbyqxmd.com/read/27893411/plasma-osteoprotegerin-and-breast-cancer-risk-in-brca1-and-brca2-mutation-carriers
#6
Lovisa Odén, Mohammad Akbari, Tasnim Zaman, Christian F Singer, Ping Sun, Steven A Narod, Leonardo Salmena, Joanne Kotsopoulos
Emerging evidence suggests a role of receptor activator of nuclear factor κB (RANK)/RANK ligand (RANKL) signaling in breast cancer development. Lower osteoprotegerin (OPG) levels, the endogenous decoy receptor for RANKL which competes with RANK for binding of RANKL, has been reported among BRCA mutation carriers. Whether low OPG levels contribute to the high breast cancer risk in this population is unknown. OPG concentrations were measured in plasma of 206 cancer-free BRCA mutation carriers using an enzyme-linked immunosorbent assay...
November 22, 2016: Oncotarget
https://www.readbyqxmd.com/read/27882124/-5r-5-hydroxytriptolide-lldt-8-prevents-collagen-induced-arthritis-through-opg-rank-rankl-signaling-in-a-rat-model-of-rheumatoid-arthritis
#7
Ji-Zhou Zeng, Li-Feng Ma, Hai Meng, Hao-Miao Yu, Ya-Kui Zhang, Ai Guo
(5R)-5-hydroxytriptolide (LLDT-8) extracts from Tripterygium have anti-inflammatory, antineoplastic and immunity adjustment functions. The present study used a collagen-induced arthritis (CIA) model to evaluate whether LLDT-8 prevents collagen-induced arthritis, and investigated the signaling underlying this. Male Sprague-Dawley rats were induced to generate CIA, mimicking rheumatoid arthritis (RA). The presence of arthritis was determined using RA progression scores. The inflammatory cytokines interleukin (IL)-1β, IL-6 and nuclear factor-κB were detected using enzyme-linked immunosorbent assay kits...
November 2016: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/27881737/rankl-rank-from-bone-loss-to-the-prevention-of-breast-cancer
#8
REVIEW
Verena Sigl, Laundette P Jones, Josef M Penninger
RANK and RANKL, a receptor ligand pair belonging to the tumour necrosis factor family, are the critical regulators of osteoclast development and bone metabolism. Besides their essential function in bone, RANK and RANKL have also been identified as the key factors for the formation of a lactating mammary gland in pregnancy. Mechanistically, RANK and RANKL link the sex hormone progesterone with stem cell expansion and proliferation of mammary epithelial cells. Based on their normal physiology, RANKL/RANK control the onset of hormone-induced breast cancer through the expansion of mammary progenitor cells...
November 2016: Open Biology
https://www.readbyqxmd.com/read/27881707/a-cd80-biased-ctla4-ig-fusion-protein-with-superior-in-vivo-efficacy-by-simultaneous-engineering-of-affinity-selectivity-stability-and-fcrn-binding
#9
Julie Douthwaite, Jacques Moisan, Cyril Privezentzev, Blagoje Soskic, Shereen Sabbah, Suzanne Cohen, Andie Collinson, Elizabeth England, Catherine Huntington, Ben Kemp, Li Zhuang, Suzanne Hudak, D Gareth Rees, Debbie Goldberg, Chris Barton, Linda Chang, Inna Vainshtein, Meina Liang, Laurie Iciek, Philip Ambery, Mark Peakman, Tristan J Vaughan, Tim I M Tree, David M Sansom, Michael A Bowen, Ralph R Minter, Lutz Jermutus
Affinity- and stability-engineered variants of CTLA4-Ig fusion molecules with enhanced pharmacokinetic profiles could yield improved therapies with the potential of higher efficacy and greater convenience to patients. In this study, to our knowledge, we have, for the first time, used in vitro evolution to simultaneously optimize CTLA4 affinity and stability. We selected for improved binding to both ligands, CD80 and CD86, and screened as dimeric Fc fusions directly in functional assays to identify variants with stronger suppression of in vitro T cell activation...
November 23, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/27881164/administration-of-anti-receptor-activator-of-nuclear-factor-kappa-b-ligand-rankl-antibody-for-the-treatment-of-osteoporosis-was-associated-with-amelioration-of-hepatitis-in-a-female-patient-with-growth-hormone-deficiency-a-case-report
#10
Ayumu Takeno, Masahiro Yamamoto, Masakazu Notsu, Toshitsugu Sugimoto
BACKGROUND: Growth hormone deficiency (GHD) is associated with non-alcoholic fatty liver disease (NAFLD). A recent animal study showed that hepatocyte-specific receptor activator of nuclear factor-kappa B (RANK) knockout mice had significantly lower liver fat content compared with control mice concomitant with a decrease in production of inflammatory cytokines such as tumor necrosis factor-α (TNF-α) from hepatocytes and kupffer cells. The role of anti-RANK ligand (RANKL) antibody for osteoporosis on hepatitis in patients with aGHD is still unknown...
November 24, 2016: BMC Endocrine Disorders
https://www.readbyqxmd.com/read/27871200/denosumab-targeting-the-rankl-pathway-to-treat-rheumatoid-arthritis
#11
Yahui Grace Chiu, Christopher T Ritchlin
Rheumatoid arthritis (RA) is a chronic inflammatory disorder characterized by focal pathologic bone resorption due to excessive activity of osteoclasts (OC). Receptor activator of nuclear factor kappa B ligand (RANKL) is essential for the proliferation, differentiation, and survival of OC. Denosumab (DMab) is a humanized monoclonal antibody that binds to RANKL with high affinity and blocks its subsequent association with its receptor RANK on the surface of OC precursors. Area covered: The authors review the molecular and cellular mechanisms underlying therapeutic applications of DMab, provide recent highlights on pharmacology, efficacy and safety of DMab, and discuss the potential of DMab as a novel therapeutic option for the treatment of rheumatoid arthritis...
November 30, 2016: Expert Opinion on Biological Therapy
https://www.readbyqxmd.com/read/27870243/empirical-scoring-functions-for-affinity-prediction-of-protein-ligand-complexes
#12
Lukas P Pason, Christoph A Sotriffer
The ability to rapidly assess the quality of a protein-ligand complex in terms of its affinity is of fundamental importance for various methods of computer-aided drug design. While simple filtering or matching critieria may be sufficient in fast docking methods or at early stages of virtual screening, estimates of the actual free energy of binding are needed whenever refined docking solutions, ligand rankings or support for the optimization of hit compounds are required. If rigorous free energy calculations based on molecular simulations are impractical, such affinity estimates are provided by scoring functions...
December 2016: Molecular Informatics
https://www.readbyqxmd.com/read/27859454/rapid-analysis-of-interaction-between-six-drugs-and-%C3%AE-2-adrenergic-receptor-by-injection-amount-dependent-method
#13
Kaizhu Zeng, Jing Wang, Zhenyu Sun, Qian Li, Sha Liao, Xinfeng Zhao, Xiaohui Zheng
Drug-protein interaction analysis has become a considerable topic in life science which includes clarifying protein functions, explaining drug action mechanisms and uncovering novel drug candidates. This work was to determine the association constants (KA ) of six drugs to β2 -adrenergic receptor by injection amount dependent method using stationary phase containing the immobilized receptor. The association constants (KA ) were calculated to be (25.85 ± 0.035) × 10(4)  M(-1) for clorprenaline, (42...
November 15, 2016: Biomedical Chromatography: BMC
https://www.readbyqxmd.com/read/27856238/evaluation-of-known-and-novel-inhibitors-of-orai1-mediated-store-operated-ca-2-entry-in-mda-mb-231-breast-cancer-cells-using-a-fluorescence-imaging-plate-reader-assay
#14
Iman Azimi, Jack U Flanagan, Ralph J Stevenson, Marco Inserra, Irina Vetter, Gregory R Monteith, William A Denny
The Orai1 Ca(2+) permeable ion channel is an important component of store operated Ca(2+) entry (SOCE) in cells. It's over-expression in basal molecular subtype breast cancers has been linked with poor prognosis, making it a potential target for drug development. We pharmacologically characterised a number of reported inhibitors of SOCE in MDA-MB-231 breast cancer cells using a convenient Fluorescence Imaging Plate Reader (FLIPR) assay, and show that the rank order of their potencies in this assay is the same as those reported in a wide range of published assays...
November 7, 2016: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/27849171/the-nuclear-receptor-ahr-controls-bone-homeostasis-by-regulating-osteoclast-differentiation-via-the-rank-c-fos-signaling-axis
#15
Takashi Izawa, Rieko Arakaki, Hiroki Mori, Takaaki Tsunematsu, Yasusei Kudo, Eiji Tanaka, Naozumi Ishimaru
The aryl hydrocarbon receptor (AhR) pathway plays a key role in receptor activator of NF-κB ligand (RANKL)-mediated osteoclastogenesis. However, the mechanism underlying the regulation of AhR expression in osteoclasts and the signaling pathway through which AhR controls osteoclastogenesis remain unclear. We found that the expression of AhR in bone marrow-derived osteoclasts was upregulated by RANKL at an earlier stage than was the expression of signature osteoclast genes such as those encoding cathepsin K and NFAT, cytoplasmic, calcineurin-dependent 1...
December 15, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/27822475/rank-expression-and-osteoclastogenesis-in-human-monocytes-in-peripheral-blood-from-rheumatoid-arthritis-patients
#16
Yuki Nanke, Tsuyoshi Kobashigawa, Toru Yago, Manabu Kawamoto, Hisashi Yamanaka, Shigeru Kotake
Rheumatoid arthritis (RA) appears as inflammation of synovial tissue and joint destruction. Receptor activator of NF-κB (RANK) is a member of the TNF receptor superfamily and a receptor for the RANK ligand (RANKL). In this study, we examined the expression of RANK(high) and CCR6 on CD14(+) monocytes from patients with RA and healthy volunteers. Peripheral blood samples were obtained from both the RA patients and the healthy volunteers. Osteoclastogenesis from monocytes was induced by RANKL and M-CSF in vitro...
2016: BioMed Research International
https://www.readbyqxmd.com/read/27814427/cation-%C3%AF-interactions-in-crebbp-bromodomain-inhibition-an-electrostatic-model-for-small-molecule-binding-affinity-and-selectivity
#17
Wilian A Cortopassi, Kiran Kumar, Robert S Paton
CREBBP bromodomains, epigenetic "reader" proteins that recognize acetylated histone lysine residues, are a current target for cancer therapy. We show that experimental CREBBP binding affinities of small-molecules with aromatic or heteroaromatic functional groups are strongly influenced by a cation-π interaction with a positively charged arginine residue. For a series of fifteen 5-isoxazolylbenzimidazole derivatives, the strength of this non-covalent interaction is directly related to improvements in binding to CREBBP...
November 4, 2016: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/27809843/risks-and-benefits-of-combining-denosumab-and-surgery-in-giant-cell-tumor-of-bone-a-case-series
#18
Daniel A Müller, Giovanni Beltrami, Guido Scoccianti, Domenico A Campanacci, Alessandro Franchi, Rodolfo Capanna
BACKGROUND: The RANK ligand inhibitor denosumab is being investigated for treatment of giant cell tumor of bone, but the available data in the literature remains sparse and controversial. This study analyzes the results of combining denosumab with surgical treatment and highlights possible changes for the oncologic surgeon in daily practice. METHODS: A total of 91 patients were treated surgically for giant cell tumor of bone between 2010 and 2014 in an institution, whereas 25 patients of the total additionally received denosumab and were part of this study...
November 4, 2016: World Journal of Surgical Oncology
https://www.readbyqxmd.com/read/27802892/osteoporosis-management-in-patients-with-breast-cancer-emas-position-statement
#19
REVIEW
Florence A Trémollieres, Iuliana Ceausu, Herman Depypere, Irene Lambrinoudaki, Alfred Mueck, Faustino R Pérez-López, Yvonne T van der Schouw, Levent M Senturk, Tommaso Simoncini, John C Stevenson, Petra Stute, Margaret Rees
Aromatase inhibitors (AIs) are the first-line recommended standard of care for postmenopausal estrogen receptor-positive breast cancer. Because they cause a profound suppression of estrogen levels, concerns regarding their potential to increase the risk of fracture were rapidly raised. There is currently a general consensus that a careful baseline evaluation is needed of the risk of fracture in postmenopausal women about to start treatment with AIs but also in all premenopausal women with early disease. Bisphosphonates have been shown in several phase III trials to prevent the bone loss induced by cancer treatment, although no fracture data are available...
January 2017: Maturitas
https://www.readbyqxmd.com/read/27802576/performance-of-mdockpp-in-capri-rounds-28-29-and-31-35-including-the-prediction-of-water-mediated-interactions
#20
Xianjin Xu, Liming Qiu, Chengfei Yan, Zhiwei Ma, Sam Z Grinter, Xiaoqin Zou
Protein-protein interactions are either through direct contacts between two binding partners or mediated by structural waters. Both direct contacts and water-mediated interactions are crucial to the formation of a protein-protein complex. During the recent CAPRI rounds, a novel parallel searching strategy for predicting water-mediated interactions is introduced into our protein-protein docking method, MDockPP. Briefly, a FFT-based docking algorithm is employed in generating putative binding modes, and an iteratively derived statistical potential-based scoring function, ITScorePP, in conjunction with biological information is used to assess and rank the binding modes...
November 1, 2016: Proteins
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