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Molecular receptor affinity

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https://www.readbyqxmd.com/read/29330771/inhibition-of-human%C3%A2-immunodeficiency-type-1-virus-hiv-1-life-cycle-by-different-egg-white-lysozymes
#1
Mandana Behbahani, Mokhtar Nosrati, Hassan Mohabatkar
Lysozyme is a relatively small enzyme with different biological activities, which is found in tears, saliva, egg white, and human milk. In the study, the anti-HIV-1 activity of lysozymes purified from quail, Meleagris, and hen egg white has been determined. For this end, a time-of-drug-addition assay was performed to identify the target of anti-HIV-1 agents and for determination of probable anti HIV-1 mechanism of the studied lysozyme, the binding affinity of the lysozymes to the human CD4 receptor was studied by molecular docking method...
January 13, 2018: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/29329953/canine-macrophages-can-like-human-macrophages-be-in-vitro-activated-toward-the-m2a-subtype-relevant-in-allergy
#2
Ina Herrmann, Jelena Gotovina, Judit Fazekas-Singer, Michael B Fischer, Karin Hufnagl, Rodolfo Bianchini, Erika Jensen-Jarolim
The M2a subtype of macrophages plays an important role in human immunoglobulin E (IgE-mediated allergies) and other Th2 type immune reactions. In contrast, very little is known about these cells in the dog. Here we describe an in-vitro method to activate canine histiocytic DH82 cells and primary canine monocyte-derived macrophages (MDMs) toward the M2a macrophages using human cytokines. For a side-by-side comparison, we compared the canine cells to human MDMs, and the human monocytic cell line U937 activated towards M1-and M2a cells on the cellular and molecular level...
January 9, 2018: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/29329361/pyhvis3d-visualising-molecular-simulation-deduced-h-bond-networks-in-3d-application-to-t-cell-receptor-interactions
#3
Bernhard Knapp, Marta Alcala, Hao Zhang, Clare West, P Anton van der Merwe, Charlotte M Deane
Motivation: Hydrogen bonds (H-bonds) play an essential role for many molecular interactions but are also often transient, making visualizing them in a flexible system challenging. Results: We provide pyHVis3D which allows for an easy to interpret 3D visualisation of H-bonds resulting from molecular simulations. We demonstrate the power of pyHVis3D by using it to explain the changes in experimentally measured binding affinities for three T-cell receptor/peptide/MHC complexes and mutants of each of these complexes...
January 10, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29329002/integration-of-multi-scale-molecular-modeling-approaches-with-experiments-for-the-in-silico-guided-design-and-discovery-of-novel-herg-neutral-antihypertensive-oxazalone-and-imidazolone-derivatives-and-analysis-of-their-potential-restrictive-effects-on-cell
#4
Serdar Durdagi, Busecan Aksoydan, Ismail Erol, Isik Kantarcioglu, Yavuz Ergun, Gulay Bulut, Melih Acar, Timucin Avsar, George Liapakis, Vlasios Karageorgos, Ramin E Salmas, Barış Sergi, Sara Alkhatib, Gizem Turan, Berfu Nur Yigit, Kutay Cantasir, Bahar Kurt, Turker Kilic
AT1 antagonists is the most recent drug class of molecules against hypertension and they mediate their actions through blocking detrimental effects of angiotensin II (A-II) when acts on type I (AT1) A-II receptor. The effects of AT1 antagonists are not limited to cardiovascular diseases. AT1 receptor blockers may be used as potential anti-cancer agents - due to the inhibition of cell proliferation stimulated by A-II. Therefore, AT1 receptors and the A-II biosynthesis mechanisms are targets for the development of new synthetic drugs and therapeutic treatment of various cardiovascular and other diseases...
December 11, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29327929/development-of-candidates-for-pet-imaging-of-ghrelin-receptor-in-disease-design-synthesis-and-evaluation-of-fluorine-bearing-quinazolinone-derivatives
#5
Jin-Qiang Hou, Michael S Kovacs, Savita Dhanvantari, Leonard G Luyt
Molecular imaging with PET (Positron Emission Tomography) is an attractive platform for non-invasive detection and assessment of disease. The development of a PET imaging agent targeting the ghrelin receptor (growth hormone secretagogue receptor type 1a or GHS-R1a) has the potential to lead to the detection and assessment of the higher than normal expression of GHS-R1a in diseases such as prostate, breast, and ovarian cancer. To enable the development of 18F radiopharmaceuticals, we have designed and synthesized three series of quinazolinone derivatives, resulting in the identification of two compound (5i, 17) with sub-nanomolar binding affinity and one fluorine-bearing compound (10b) with picomolar binding affinity (20 pM), representing the highest binding affinity for GHS-R1a reported to date...
January 12, 2018: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29327758/a-computational-analysis-of-pro-angiogenic-therapies-for-peripheral-artery-disease
#6
Lindsay E Clegg, Feilim Mac Gabhann
Inducing therapeutic angiogenesis to effectively form hierarchical, non-leaky networks of perfused vessels in tissue engineering applications and ischemic disease remains an unmet challenge, despite extensive research and multiple clinical trials. Here, we use a previously-developed, multi-scale, computational systems pharmacology model of human peripheral artery disease to screen a diverse array of promising pro-angiogenic strategies, including gene therapy, biomaterials, and antibodies. Our previously-validated model explicitly accounts for VEGF immobilization, Neuropilin-1 binding, and weak activation of VEGF receptor 2 (VEGFR2) by the "VEGFxxxb" isoforms...
January 12, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29325769/the-structural-determinants-of-the-bitopic-binding-mode-of-a-negative-allosteric-modulator-of-the-dopamine-d2-receptor
#7
Christopher J Draper-Joyce, Mayako Michino, Ravi Kumar Verma, Carmen Klein Herenbrink, Jeremy Shonberg, Anitha Kopinathan, Peter J Scammells, Ben Capuano, David M Thal, Jonathan A Javitch, Arthur Christopoulos, Lei Shi, J Robert Lane
SB269652 is a negative allosteric modulator of the dopamine D2 receptor (D2R) yet possesses structural similarity to ligands with a competitive mode of interaction. In this study, we aimed to understand the ligand-receptor interactions that confer its allosteric action. We combined site-directed mutagenesis with molecular dynamics simulations using both SB269652 and derivatives from our previous structure activity studies. We identify residues within the conserved orthosteric binding site (OBS) and a secondary binding pocket (SBP) that determine affinity and cooperativity...
January 8, 2018: Biochemical Pharmacology
https://www.readbyqxmd.com/read/29323388/a-novel-thermal-detection-method-based-on-molecularly-imprinted-nanoparticles-as-recognition-elements
#8
Francesco Canfarotta, J Czulak, K Betlem, A Sachdeva, K Eersels, B van Grinsven, T J Cleij, M Peeters
Molecularly Imprinted Polymers (MIPs) are synthetic receptors that are able to selectively bind their target molecule and, for this reason, they are currently employed as recognition elements in sensors. In this work, MIP nanoparticles (nanoMIPs) are produced by solid-phase synthesis for a range of templates with different sizes, including a small molecule (biotin), two peptides (one derived from the epithelial growth factor receptor and vancomycin) and a protein (trypsin). NanoMIPs are then dipcoated on the surface of thermocouples that measure the temperature inside a liquid flow cell...
January 11, 2018: Nanoscale
https://www.readbyqxmd.com/read/29322524/a-comprehensive-analysis-of-neurotrophins-and-neurotrophin-tyrosine-kinase-receptors-expression-during-development-of-zebrafish
#9
Valeria Nittoli, Rosa M Sepe, Ugo Coppola, Ylenia D'Agostino, Elena De Felice, Antonio Palladino, Quirino A Vassalli, Annamaria Locascio, Filomena Ristoratore, Antonietta Spagnuolo, Salvatore D'Aniello, Paolo Sordino
Neurotrophins (NTF) are a family of secreted nerve growth factors with affinity for tyrosine kinase (Ntrk) and p75 receptors. To fully understand the variety of developmental roles played by NTFs, it is critical to know when and where genes encoding individual ligands and receptors are transcribed. Identification of ntf and ntrk transcripts in zebrafish development remains to be fully characterized for further uncovering the potential function(s) of the NTF signal transduction pathway. Here, we conducted a systematic analysis of the expression profiles of four ntf and five ntrk genes during zebrafish development using whole-mount in situ hybridization...
January 11, 2018: Journal of Comparative Neurology
https://www.readbyqxmd.com/read/29321242/adhesion-growth-regulatory-galectins-tested-in-combination-evidence-for-formation-of-hybrids-as-heterodimers
#10
Michelle C Miller, Anna-Kristen Ludwig, Kanin Wichapong, Herbert Kaltner, Jürgen Kopitz, Hans-Joachim Gabius, Kevin H Mayo
The delineation of the physiological significance of protein (lectin)-glycan recognition and the structural analysis of individual lectins have directed our attention to studying them in combination. In this report, we tested the hypothesis of hybrid formation by using binary mixtures of homodimeric galectins-1 and -7 as well as a proteolytically truncated version of chimera-type galectin-3. Initial supportive evidence is provided by affinity chromatography using resin-presented galectin-7. Intriguingly, extent of cell binding by cross-linking of surface counter-receptor increased significantly for monomeric galectin-3 form by presence of galectin-1 or -7...
January 10, 2018: Biochemical Journal
https://www.readbyqxmd.com/read/29311511/a-peptide-glycolipid-interaction-probed-by-retroinverso-peptide-analogues
#11
Kaori Sakurai
Cell surface glycolipids are implicated in the formation of lipid rafts and membrane microdomains, where they interact with protein receptors to mediate a variety of cellular processes such as cell-cell recognition, cell adhesion, and membrane signaling. Studies of glycolipid function at the local membrane structures have not been straightforward to date, because the locally clustered structures are labile and their protein binding affinities tend to be weak. While specific glycolipid-binding proteins have been employed as molecular probes for detecting lipid rafts, small peptides may be more suitable for probing glycolipids at the cell surface due to their small size as well as their ease of synthetic preparation and functionalization...
2018: Chemical & Pharmaceutical Bulletin
https://www.readbyqxmd.com/read/29309794/minimally-invasive-skin-tape-strip-rna-seq-identifies-novel-characteristics-of-type-2-high-atopic-dermatitis-disease-endotype
#12
Nathan Dyjack, Elena Goleva, Cydney Rios, Byung Eui Kim, Lianghua Bin, Patricia Taylor, Caroline Bronchick, Clifton F Hall, Brittany N Richers, Max A Seibold, Donald Y Leung
BACKGROUND: Expression profiling of skin biopsies has established molecular features of the skin in atopic dermatitis (AD). Invasiveness of biopsies has prevented their use in defining individual level AD pathobiological mechanisms (endotypes) in large research studies. OBJECTIVE: To determine if minimally invasive skin tape strip transcriptome analysis identifies gene expression dysregulation in AD and molecular disease endotypes. METHODS: We sampled non-lesional and lesional skin tape strips and biopsies from adult Caucasian subjects AD patients (18 males, 12 females; age (Mean±SE) 36...
January 5, 2018: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29309722/a-cell-permeable-stapled-peptide-inhibitor-of-the-estrogen-receptor-coactivator-interaction
#13
Thomas E Speltz, Jeanne M Danes, Joshua D Stender, Jonna Frasor, Terry W Moore
We and others have proposed that coactivator binding inhibitors, which block the interaction of estrogen receptor and steroid receptor coactivators, may represent a potential class of new breast cancer therapeutics. The development of coactivator binding inhibitors has been limited, however, because many of the current molecules which are active in in vitro and biochemical assays are not active in cell-based assays. Our goal in this work was to prepare a coactivator binding inhibitor active in cellular models of breast cancer...
January 8, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29309213/development-and-characterization-of-an-anti-rituximab-monoclonal-antibody-panel
#14
Minoru Tada, Takuo Suzuki, Akiko Ishii-Watabe
During the development of monoclonal antibodies (mAbs) and other therapeutic proteins, immunogenicity, in particular the induction of anti-drug antibodies (ADAs), is an important concern, and thus immunogenicity assessment is a requirement for their approval. Establishment of appropriate methods for detecting and characterizing ADAs is necessary for immunogenicity assessment, but the lack of commonly available reference standards makes it difficult to compare and evaluate the methods. It is also difficult to compare the data with those obtained by other methods or facilities without reference standards...
January 8, 2018: MAbs
https://www.readbyqxmd.com/read/29306979/discovering-new-pi3k%C3%AE-inhibitors-with-a-strategy-of-combining-ligand-based-and-structure-based-virtual-screening
#15
Miao Yu, Qiong Gu, Jun Xu
PI3Kα is a promising drug target for cancer chemotherapy. In this paper, we report a strategy of combing ligand-based and structure-based virtual screening to identify new PI3Kα inhibitors. First, naïve Bayesian (NB) learning models and a 3D-QSAR pharmacophore model were built based upon known PI3Kα inhibitors. Then, the SPECS library was screened by the best NB model. This resulted in virtual hits, which were validated by matching the structures against the pharmacophore models. The pharmacophore matched hits were then docked into PI3Kα crystal structures to form ligand-receptor complexes, which are further validated by the Glide-XP program to result in structural validated hits...
January 6, 2018: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/29304504/short-chain-chlorinated-paraffins-sccps-induced-thyroid-disruption-by-enhancement-of-hepatic-thyroid-hormone-influx-and-degradation-in-male-sprague-dawley-rats
#16
Yufeng Gong, Haijun Zhang, Ningbo Geng, Liguo Xing, Jingfeng Fan, Yun Luo, Xiaoyao Song, Xiaoqian Ren, Feidi Wang, Jiping Chen
Short-chain chlorinated paraffins (SCCPs) are known to disturb thyroid hormone (TH) homeostasis in rodents. However, the mechanism remains to be fully characterized. In this study, male Sprague Dawley rats received SCCPs (0, 1, 10, or 100mg/kg/day) via gavage once a day for consecutive 28days. Plasma and hepatic TH concentrations, thyrocyte structure, as well as thyroid and hepatic mRNA and protein levels of genes associated with TH homeostasis were examined. Moreover, we performed molecular docking to predict interactions between constitutive androstane receptor (CAR), a key regulator in xenobiotic-induced TH metabolism, with different SCCP molecules...
January 2, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29300367/rational-design-of-a-new-class-of-toll-like-receptor-4-tlr4-tryptamine-related-agonists-by-means-of-the-structure-and-ligand-based-virtual-screening-for-vaccine-adjuvant-discovery
#17
Jan Honegr, Rafael Dolezal, David Malinak, Marketa Benkova, Ondrej Soukup, Joyce S F D de Almeida, Tanos C C Franca, Kamil Kuca, Roman Prymula
In order to identify novel lead structures for human toll-like receptor 4 (hTLR4) modulation virtual high throughput screening by a peta-flops-scale supercomputer has been performed. Based on the in silico studies, a series of 12 compounds related to tryptamine was rationally designed to retain suitable molecular geometry for interaction with the hTLR4 binding site as well as to satisfy general principles of drug-likeness. The proposed compounds were synthesized, and tested by in vitro and ex vivo experiments, which revealed that several of them are capable to stimulate hTLR4 in vitro up to 25% activity of Monophosphoryl lipid A...
January 4, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29296957/%C3%AE-iib%C3%AE-3-binding-to-a-fibrinogen-fragment-lacking-the-%C3%AE-chain-dodecapeptide-is-activation-dependent-and-edta-inducible
#18
Hina Zafar, Yi Shang, Jihong Li, George A David, Joseph P Fernandez, Henrik Molina, Marta Filizola, Barry S Coller
Platelet integrin receptor αIIbβ3 supports platelet aggregation by binding fibrinogen. The interaction between the fibrinogen C-terminal γ-chain peptide composed of residues γ-404-411 (GAKQAGDV) and the Arg-Gly-Asp (RGD) binding pocket on αIIbβ3 is required for fibrinogen-mediated platelet aggregation, but data suggest that other ancillary binding sites on both fibrinogen and αIIbβ3 may lead to higher-affinity fibrinogen binding and clot retraction. To identify additional sites, we analyzed the ability of platelets and cells expressing normal and mutant αIIbβ3 to adhere to an immobilized fibrinogen plasmin fragment that lacks intact γ-404-411 ('D98')...
February 28, 2017: Blood Advances
https://www.readbyqxmd.com/read/29296674/dynamic-strategic-bond-analysis-yields-a-ten-step-synthesis-of-20-nor-salvinorin-a-a-potent-%C3%AE%C2%BA-or-agonist
#19
Jeremy J Roach, Yusuke Sasano, Cullen L Schmid, Saheem Zaidi, Vsevolod Katritch, Raymond C Stevens, Laura M Bohn, Ryan A Shenvi
Salvinorin A (SalA) is a plant metabolite that agonizes the human kappa-opioid receptor (κ-OR) with high affinity and high selectivity over mu- and delta-opioid receptors. Its therapeutic potential has stimulated extensive semisynthetic studies and total synthesis campaigns. However, structural modification of SalA has been complicated by its instability, and efficient total synthesis has been frustrated by its dense, complex architecture. Treatment of strategic bonds in SalA as dynamic and dependent on structural perturbation enabled the identification of an efficient retrosynthetic pathway...
December 27, 2017: ACS Central Science
https://www.readbyqxmd.com/read/29287378/evaluation-of-estrogenic-activity-of-red-clover-trifolium-pratense-l-sprouts-cultivated-under-different-conditions-by-content-of-isoflavones-calorimetric-study-and-molecular-modelling
#20
Grażyna Budryn, Ilona Gałązka-Czarnecka, Ewelina Brzozowska, Joanna Grzelczyk, Radosław Mostowski, Dorota Żyżelewicz, José P Cerón-Carrasco, Horacio Pérez-Sánchez
Isoflavones have an affinity for estrogen receptors (ERs) including beneficial affinity for ERβ. Widely used soy is a source of poorly absorbed isoflavones glycosides. Red clover contains mostly easily absorbed free aglycones. Red clover sprouts were cultivated under different conditions (white light, UVA or UVB for 12 or 24 h a day at 18 or 25 °C) to maximise the content of isoflavones, especially of high affinity for ERβ. The affinity of isoflavones to ERs was evaluated by molecular modelling and isothermal titration calorimetry (ITC)...
April 15, 2018: Food Chemistry
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