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Ligands and binding

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https://www.readbyqxmd.com/read/28732103/denosumab-current-use-in-the-treatment-of-primary-bone-tumors
#1
Olga D Savvidou, Ioanna K Bolia, George D Chloros, John Papanastasiou, Panagiotis Koutsouradis, Panayiotis J Papagelopoulos
Denosumab, a human monoclonal antibody that inhibits bone resorption by binding on the receptor activator of the nuclear factor kappa-β ligand, has recently emerged as an additional option in the treatment of musculoskeletal osteolytic tumors. This article focuses on the recent literature regarding the effectiveness of denosumab in the management of giant cell tumor, multiple myeloma, aneurysmal bone cyst, and osteosarcoma. The mechanism of action of denosumab in the management of these tumors and the associated side effects are discussed in detail...
July 1, 2017: Orthopedics
https://www.readbyqxmd.com/read/28732021/in-vitro-comparison-of-213bi-and-177lu-radiation-for-peptide-receptor-radionuclide-therapy
#2
Ho Sze Chan, Erik de Blois, Alfred Morgenstern, Frank Bruchertseifer, Marion de Jong, Wouter Breeman, Mark Konijnenberg
BACKGROUND: Absorbed doses for α-emitters are different from those for β-emitters, as the high linear energy transfer (LET) nature of α-particles results in a very dense energy deposition over a relatively short path length near the point of emission. This highly localized and therefore high energy deposition can lead to enhanced cell-killing effects at absorbed doses that are non-lethal in low-LET type of exposure. Affinities of DOTA-DPhe1-Tyr3-octreotate (DOTATATE), 115In-DOTATATE, 175Lu-DOTATATE and 209Bi-DOTATATE were determined in the K562-SST2 cell line...
2017: PloS One
https://www.readbyqxmd.com/read/28731684/the-binding-mode-of-n-hydroxyamidines-to-indoleamine-2-3-dioxygenase-1-ido1
#3
Ute Friederike Röhrig, Vincent Zoete, Olivier Michielin
Indoleamine 2,3-dioxygenase 1 (IDO1) is an important target in cancer immunotherapy. The most advanced clinical compound, epacadostat (INCB024360), binds to the heme cofactor of IDO1 through a N-hydroxyamidine function. Conflicting binding modes have recently been proposed, reporting iron binding either through the hydroxyamidine oxygen or nitrogen atoms. Here, we use quantum chemical calculations, docking, and QM/MM calculations based on available X-ray data to resolve this issue and to propose a physically meaningful binding mode...
July 21, 2017: Biochemistry
https://www.readbyqxmd.com/read/28731679/binding-of-bacteria-to-poly-n-isopropylacrylamide-modified-with-vancomycin-comparison-of-behavior-of-linear-and-highly-branched-polymers
#4
Pavintorn Teratanatorn, Richard Hoskins, Thomas Swift, C W Ian Douglas, Joanna Shepherd, Stephen Rimmer
The behavior of a linear copolymer of N-isopropyl acrylamide with pendant vancomycin functionality was compared to an analogous highly branched copolymer with vancomycin functionality at the chain ends. Highly branched poly(N-isopropylacrylamide) modified with vancomycin (HB-PNIPAM-van) was synthesized by functionalization of the HB-PNIPAM, prepared using reversible addition-fragmentation chain transfer polymerization. Linear PNIPAM with pendant vancomycin functionality (L-PNIPAM-van) was synthesized by functionalization of poly(N-isopropyl acrylamide-co-vinyl benzoic acid)...
July 21, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/28731574/rapid-buffer-and-ligand-screening-for-affinity-chromatography-by-multiplexed-surface-plasmon-resonance-imaging
#5
Karin P M Geuijen, Daniëlle E J W van Wijk-Basten, David F Egging, Richard B M Schasfoort, Michel H Eppink
Protein purifications are often based on the principle of affinity chromatography, where the protein of interest selectively binds to an immobilized ligand. The development of affinity purification requires selecting proper wash and elution conditions. In recent years, miniaturization of the purification process is applied to speed up the development (e.g. microtiterplates, robocolumns). We have studied the application of surface plasmon resonance imaging (SPRi) as a tool to simultaneously screen many buffer conditions for wash and elution steps in an affinity-based purification process...
July 21, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28731571/model-based-investigation-on-the-mass-transfer-and-adsorption-mechanisms-of-mono-pegylated-lysozyme-in-ion-exchange-chromatography
#6
Josefine Morgenstern, Gang Wang, Pascal Baumann, Jürgen Hubbuch
Recent studies highlighted the potential of PEGylated proteins to improve stabilities and pharmacokinetics of protein drugs. Ion-exchange chromatography (IEX) is among the most frequently used purification methods for PEGylated proteins. However, the underlying physical mechanisms allowing for a separation of different PEGamers (proteins with a varying number of attached PEG molecules) are not yet fully understood. In this work, mechanistic chromatography modeling was applied to gain a deeper understanding of the mass transfer and adsorption/desorption mechanisms of mono-PEGylated proteins in IEX...
July 21, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28731466/interaction-of-galectin-3-with-muc1-on-cell-surface-promotes-egfr-dimerization-and-activation-in-human-epithelial-cancer-cells
#7
Tushar Piyush, Anisha R Chacko, Paulina Sindrewicz, John Hilkens, Jonathan M Rhodes, Lu-Gang Yu
Epidermal growth factor receptor (EGFR) is an important regulator of epithelial cell growth and survival in normal and cancerous tissues and is a principal therapeutic target for cancer treatment. EGFR is associated in epithelial cells with the heavily glycosylated transmembrane mucin protein MUC1, a natural ligand of galectin-3 that is overexpressed in cancer. This study reveals that the expression of cell surface MUC1 is a critical enhancer of EGF-induced EGFR activation in human breast and colon cancer cells...
July 21, 2017: Cell Death and Differentiation
https://www.readbyqxmd.com/read/28731335/a-simple-representation-of-three-dimensional-molecular-structure
#8
Seth D Axen, Xi-Ping Huang, Elena L Cáceres, Leo Gendelev, Bryan L Roth, Michael J Keiser
Statistical and machine learning approaches predict drug-to-target relationships from 2D small-molecule topology patterns. One might expect 3D information to improve these calculations. Here we apply the logic of the Extended Connectivity FingerPrint (ECFP) to develop a rapid, alignment-invariant 3D representation of molecular conformers, the Extended Three-Dimensional FingerPrint (E3FP). By integrating E3FP with the Similarity Ensemble Approach (SEA), we achieve higher precision-recall performance relative to SEA with ECFP on ChEMBL20, and equivalent receiver operating characteristic performance...
July 21, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28731321/conjugation-dependent-interaction-of-folic-acid-with-folate-binding-protein
#9
Rachel Leah Merzel, Carolina Frey, Junjie Chen, Rachel Garn, Mallory A van Dongen, Casey A Dougherty, Ananda Kandaluru, Philip S Low, E Neil G Marsh, Mark M Banaszak Holl
Serum proteins play a critical role in the transport, uptake, and efficacy of targeted drug therapies, and here we investigate the interactions between folic acid-polymer conjugates and serum folate binding protein (FBP), the soluble form of the cellular membrane-bound folate receptor. We demonstrate that both choice of polymer and method of ligand conjugation affect the interactions between folic acid-polymer conjugates and serum FBP, resulting in changes in the folic acid-induced protein aggregation process...
July 21, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28731304/complex-formation-of-lead-ii-with-nucleotides-and-their-constituents
#10
Astrid Sigel, Bert P Operschall, Helmut Sigel
Lead is widely distributed in the environment; it is known to mankind for thousands of years and its toxicity is nowadays (again) well recognized, though on the molecular level only partly understood. One of the reasons for this shortcoming is that the coordination chemistry of the biologically important lead(II) is complicated due to the various coordination numbers it can adopt (CN = 4 to 10) as well as by the 6s2 electron lone pair which, with CN = 4, can shield one side of the Pb2+ coordination sphere. The chapter focuses on the properties of Pb2+ complexes formed with nucleotides and their constituents and derivatives...
April 10, 2017: Metal Ions in Life Sciences
https://www.readbyqxmd.com/read/28731301/lead-ii-complexes-of-amino-acids-peptides-and-other-related-ligands-of-biological-interest
#11
Etelka Farkas, Péter Buglyó
Lead(II) forms (NH2,COO-)-chelated mono- and bis-complexes with simple amino acids, while mono-complexes with pH-dependent coordination modes exist with simple dipeptides. These mostly hemidirected complexes have moderate stability. While a weak interaction of side chain imidazole and carboxylate in lead(II)-aminoacidato complexes is found, the thiolate group has an exceptionally high affinity to this metal ion. For example, tridentate (NH2,COO-,S-)-coordination of penicillamine (Pen) and cysteine (Cys) results in an extremely strong interaction with lead(II), but, owing to the sterical effect of the 6s2 pair, a second ligand is not able to coordinate in the above mentioned tridentate way...
April 10, 2017: Metal Ions in Life Sciences
https://www.readbyqxmd.com/read/28731300/solid-state-structures-of-lead-complexes-with-relevance-for-biological-systems
#12
Katsuyuki Aoki, Kazutaka Murayama, Ning-Hai Hu
Structural information on the interaction between lead ion and its targeting biological substances is important not only for enriching coordination chemistry of lead but for successfully treating lead poisoning that is a present-day problem. This chapter provides structural data, mainly metal binding sites/modes, observed in crystal structures of lead complexes with biorelevant molecules, obtained from the Cambridge Structural Database (the CSD version 5.36 updated to May 2015) and the Protein Data Bank (PDB updated to February 2016)...
April 10, 2017: Metal Ions in Life Sciences
https://www.readbyqxmd.com/read/28730718/impact-of-binding-mechanism-on-selective-inhibition-of-histone-deacetylase-isoforms
#13
Christian Meyners, Franz-Josef Meyer-Almes
Industrialized drug screening campaigns usually deliver hundreds of compounds that are active on a particular pharmaceutical target. In light of high failure rates of drug candidates due to unforeseeable off-target toxicity, the early identification of the most promising compounds with high potential for target selectivity is an urgent need to improve the quality of lead compounds and lower attrition rates in the drug development process. The reliable prediction of the selectivity of active substances for a target protein is a challenging task...
June 14, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28730511/intermediate-molecular-mass-hyaluronan-and-cd44-receptor-interactions-enhance-neutrophil-phagocytosis-and-il-8-production-via-p38-and-erk1-2-mapk-signalling-pathways
#14
Cheng-Hsun Lu, Chia-Huei Lin, Ko-Jen Li, Chieh-Yu Shen, Cheng-Han Wu, Yu-Min Kuo, Ting-Syuan Lin, Chia-Li Yu, Song-Chou Hsieh
CD44 is a common leukocyte adhesion molecule expressed on the surface of various cells. Hyaluronan (HA), the natural ligand of CD44, is a simple repeated disaccharide with variable molecular mass that is widely distributed on cell surfaces and the connective tissue matrix. The binding of small molecular mass HA (SMM-HA, MW < 80 kDa) to CD44 on immune-related cells elicits cell proliferation, differentiation, and cytokine production. However, the effects and molecular basis of intermediate molecular mass HA (IMM-HA, MW ≈ 500 kDa)-CD44 interactions on polymorphonuclear neutrophil (PMN) functions have not been elucidated...
July 20, 2017: Inflammation
https://www.readbyqxmd.com/read/28730475/characterization-of-ligand-binding-to-pseudokinases-using-a-thermal-shift-assay
#15
Isabelle S Lucet, James M Murphy
The protocol herein describes a robust and proven method for the measurement of pseudokinase-ligand interaction using a fluorescence-based thermal shift assay (TSA). Pseudokinases are kinase-like proteins that have recently emerged as crucial regulatory modules of signal transduction pathways and may well represent a novel class of drug targets. However, unlike kinases, the regulatory activity of pseudokinases is mainly conferred through protein-protein interactions. Understanding the mechanisms that underlie pseudokinase conformational changes through ligand binding and how such conformational changes can tune signaling pathways is a necessary step to unravel their biological functions...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730474/allosteric-modulation-of-src-family-kinases-with-atp-competitive-inhibitors
#16
Ames C Register, Sujata Chakraborty, Dustin J Maly
The Src family kinases (SFKs) are an important family of tyrosine kinases that are allosterically regulated by their SH2 and SH3 domains. Engagement of SFK SH2 and SH3 domains with their intramolecular ligands leads to reduced kinase activity by stabilizing an inactive ATP-binding site conformation. Disruption of these intramolecular interactions stabilizes a more active ATP-binding site conformation and restores SFK activity. Interestingly, this allosteric relationship is bidirectional in that ATP-competitive ligands that stabilize distinct active site conformations can divergently modulate the abilities of the regulatory SH2 and SH3 domains to participate in intermolecular interactions...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730470/dissecting-kinase-effector-signaling-using-the-raprtap-methodology
#17
Anne-Marie Ray, Jennifer E Klomp, Kerrie B Collins, Andrei V Karginov
Kinases are involved in a broad spectrum of cell behaviors. A single kinase can interact with different ligands each eliciting a specific cellular response. Dissecting downstream signaling pathways of kinases is a key step to understanding physiological and pathological cell process. However, directing kinase activity to specific substrates remains challenging. Here, we present a new tool to selectively activate a kinase in a specific protein complex in living cells. This technology uses a rapamycin-inducible kinase activation coupled to interaction with FKBP12-binding domain (FRB) tagged protein...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28729761/designing-of-a-penta-peptide-against-drug-resistant-e-coli
#18
Sachin Nagra, Deepak Kumar, Rajasri Bhattacharyya, Dibyajyoti Banerjee, Tapan Mukherjee
Drug resistant pathogens are vibrant global problem. Penicillin binding protein 5 (PBP5) plays important role in bacterial cell wall biosynthesis. Mutation in PBP5 is a well-known mechanism for development of drug resistant strain of bacteria. In this context we have designed a peptide that fits better at the ligand-binding site of mutant PBP5 compared to wild type PBP5. It is expected that the designed peptide will halt the growth of drug resistant pathogen harboring mutant variety of PBP5. We have recommended experimental validation of the above concept...
2017: Bioinformation
https://www.readbyqxmd.com/read/28729760/structural-insight-into-the-binding-of-c60-derivatives-with-enoyl-pyruvate-transferase-from-helicobacter-pylori
#19
Mohammad Teimouri, Muhammad Junaid, Abbas Khan, Houjin Zhang
Helicobacter pylori (H. pylori) is a human pathogen associated with acute gastritis and peptic ulcer. The MurA enzyme is an important drug target for the identification of ligands with improved efficacy and acceptable pharmaco-kinetic properties. We developed a homology model of H. Pylori MurA followed by refinement and molecular dynamics (MD) simulations. A total of 16 C60-derivatives were docked and its docking score were compared. Some of the known inhibitors were also similarly characterized and compared...
2017: Bioinformation
https://www.readbyqxmd.com/read/28729677/engineering-tumour-cell-binding-synthetic-polymers-with-sensing-dense-transporters-associated-with-aberrant-glutamine-metabolism
#20
Naoki Yamada, Yuto Honda, Hiroyasu Takemoto, Takahiro Nomoto, Makoto Matsui, Keishiro Tomoda, Masamitsu Konno, Hideshi Ishii, Masaki Mori, Nobuhiro Nishiyama
Increased glutamine uptake toward the elevated glutaminolysis is one of the hallmarks of tumour cells. This aberrant glutamine metabolism has recently attracted considerable attention as a diagnostic and therapeutic target. Herein, we developed glutamine-functionalized polymer to achieve a selective high affinity to tumour cells overexpressing glutaminolysis-related transporter ASCT2. In in vitro study, our developed polymer exhibited faster and higher cellular uptake in tumour cells than that in normal cells...
July 20, 2017: Scientific Reports
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