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Ligands and binding

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https://www.readbyqxmd.com/read/28433433/design-selection-and-development-of-cyclic-peptide-ligands-for-human-erythropoietin
#1
William S Kish, Hiroyuki Sachi, Amith D Naik, Matthew K Roach, Benjamin G Bobay, Robert K Blackburn, Stefano Menegatti, Ruben G Carbonell
This work presents the selection and characterization of erythropoietin (EPO)-binding cyclic peptide ligands. The sequences were selected by screening a focused library of cyclic depsipeptides cyclo[(Nα-Ac)Dap(A)-X1-X6-AE], whose structure and amino acid compositions were tailored to mimic the EPO receptor. The sequences identified through library screening were synthesized on chromatographic resin and characterized via binding-and-elution studies against EPO to select a pool of candidate ligands. Sequences with higher hydrophobicity consistently showed stronger binding to EPO, with the exception of FSLLSH, which was noted for its lower hydrophobicity and high EPO binding...
April 12, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28432980/discovery-of-potential-inhibitor-against-human-acetylcholinesterase-a-molecular-docking-and-molecular-dynamics-investigation
#2
Surya Pratap Singh, Dwijendra Gupta
Alzheimer's disease (AD) is a progressive neurodegenerative disease of central nervous system among elderly people. Human acetylcholinesterase (hAChE), an important enzyme in neuronal signaling, is responsible for the degradation of acetylcholine which in turn prevents the post synaptic signal transmissions. hAChE has been an attractive target of drug discovery for the search of therapeutics against AD. In the recent past hAChE has become hot target for the investigation of new potential therapeutics. We performed virtual screening of entire database against hAChE...
April 12, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28432959/molecular-dynamics-simulation-studies-of-novel-%C3%AE-lactamase-inhibitor
#3
Farhan Ul Haq, Asma Abro, Saad Raza, Klaus R Liedl, Syed Sikander Azam
New Delhi Metallo-β-Lactamase-1 (NDM-1) has drawn great attention due to its diverse antibiotic resistant activity. It can hydrolyze almost all clinically available β-lactam antibiotics. To inhibit the activity of NDM-1 a new strategy is proposed using computational methods. Molecular dynamics (MD) simulations are used to analyze the molecular interactions between selected inhibitor candidates and NDM-1 structure. The enzyme-ligand complex is subject to binding free energy calculations using MM(PB/GB)SA methods...
April 4, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28432819/identification-of-bioactive-compounds-in-shaoyao-gancao-decoction-using-%C3%AE-2-adrenoceptor-affinity-chromatography
#4
Zehua Li, Haiyang Gao, Jiangying Li, Yajun Zhang
Shaoyao-Gancao decoction, a Chinese herbal formula, is composed of Paeoniae Radix alba and Glycyrrhiza Radix et rhizoma. It has been widely used to treat muscle spasms and asthma. However, little is known about the bioactive components of Shaoyao-Gancao decoction. In the present study, the bioactive compounds in water-extract of Shaoyao-Gancao decoction were separated by the immobilized β2 -adrenoceptor affinity column and identified using quadrupole time-of-flight mass spectrometry. The affinity constants of the separated compounds that bound to β2 -adrenoceptor were determined by frontal analysis...
April 22, 2017: Journal of Separation Science
https://www.readbyqxmd.com/read/28432789/probing-protein-flexibility-reveals-a-mechanism-for-selective-promiscuity
#5
Nicolas A Pabon, Carlos J Camacho
Many eukaryotic regulatory proteins adopt distinct bound and unbound conformations, and use this structural flexibility to bind specifically to multiple partners. However, we lack an understanding of how an interface can select some ligands, but not others. Here, we present a molecular dynamics approach to identify and quantitatively evaluate the interactions responsible for this selective promiscuity. We apply this approach to the anti-cancer target PD-1 and its ligands PD-L1 and PD-L2. We discover that while unbound PD-1 exhibits a hard-to-drug hydrophilic interface, conserved specific triggers encoded in the cognate ligands activate a promiscuous binding pathway that reveals a flexible hydrophobic binding cavity...
April 22, 2017: ELife
https://www.readbyqxmd.com/read/28432785/phosphorylation-of-irhom2-at-the-plasma-membrane-controls-mammalian-tace-dependent-inflammatory-and-growth-factor-signalling
#6
Adam Graham Grieve, Hongmei Xu, Ulrike Künzel, Paul Bambrough, Boris Sieber, Matthew Freeman
Proteolytic cleavage and release from the cell surface of membrane-tethered ligands is an important mechanism of regulating intercellular signalling. TACE is a major shedding protease, responsible for the liberation of the inflammatory cytokine TNFα and ligands of the epidermal growth factor receptor. iRhoms, catalytically inactive members of the rhomboid-like superfamily, have been shown to control the ER-to-Golgi transport and maturation of TACE. Here, we reveal that iRhom2 remains associated with TACE throughout the secretory pathway, and is stabilised at the cell surface by this interaction...
April 22, 2017: ELife
https://www.readbyqxmd.com/read/28432702/tunable-porous-coordination-polymers-for-the-capture-recovery-and-storage-of-inhalation-anesthetics
#7
Brendan Francis Abrahams, David Dharma, Paul Stephen Donnelly, Timothy Adam Hudson, Cameron J Kepert, Richard Robson, Peter D Southon, Keith Forrest White
The uptake of inhalation anesthetics by three topologically identical frameworks is described. The 3D network materials, which possess square channels of different dimensions, are formed from the relatively simple combination of Zn(II) centres and dianionic ligands that contain a phenolate and a carboxylate group at opposite ends. All three framework materials are able to adsorb N2O, Xe and isoflurane. Whilst the framework with the widest channels is able to adsorb large quantities of the various guests from the gas phase, the frameworks with the narrower channels have superior binding enthalpies and exhibit higher levels of retention...
April 22, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28432633/synthesis-spectral-properties-and-dft-calculations-of-new-ruthenium-ii-polypyridyl-complexes-dna-binding-affinity-and-in-vitro-cytotoxicity-activity
#8
Rajender Reddy Mallepally, Nagamani Chintakuntla, Venkat Reddy Putta, Nagasuryaprasad K, Ravi Kumar Vuradi, Madhuri P, Satyanarayana Singh S, Ramesh Kumar Chitumalla, Joonkyung Jang, Nagababu Penumaka, Satyanarayana Sirasani
In this paper a novel ligand debip (2-(4-N,N-diethylbenzenamine)1H-imidazo[4,5-f] [1, 10]phenanthroline) and its Ru(II) polypyridyl complexes [Ru(L)2(debip)](2+), (L = phen (1), bpy (2) and dmb (3)) have been synthesized and characterized by spectroscopic techniques. The DNA binding studies for all these complexes were examined by absorption, emission, quenching studies, viscosity measurements and cyclic voltammetry. The light switching properties of complexes 1-3 have been evaluated. Molecular docking, Density Functional Theory (DFT) and time dependent DFT calculations were performed...
April 22, 2017: Journal of Fluorescence
https://www.readbyqxmd.com/read/28432535/exploring-the-carbamazepine-interaction-with-human-pregnane-x-receptor-and-effect-on-abcc2-using-in-vitro-and-in-silico-approach
#9
Gurpreet K Grewal, Khuraijam D Singh, Neha Kanojia, Chitra Rawat, Samiksha Kukal, Ajay Jajodia, Anshika Singhal, Richa Misra, Selvaraman Nagamani, Karthikeyan Muthusamy, Ritushree Kukreti
PURPOSE: Over expression of ATP-binding cassette transporters is considered one of the major reasons for non-responsiveness to antiepileptic drugs. Carbamazepine (CBZ), one of first line antiepileptic drug is known to influence ABCC2 expression but its exact molecular mechanism is unknown. METHODS: We investigated the effect of CBZ on expression of ABCC2 and pregnane X receptor (PXR) in HepG2 cell line and compared with hyperforin (agonist of PXR) and ketoconazole (antagonist of PXR) through realtime PCR and western blot assay...
April 21, 2017: Pharmaceutical Research
https://www.readbyqxmd.com/read/28432329/affinity-biosensors-using-recombinant-native-membrane-proteins-displayed-on-exosomes-application-to-botulinum-neurotoxin-b-receptor
#10
Richard Desplantes, Christian Lévêque, Benjamin Muller, Manuela Lotierzo, Géraldine Ferracci, Michel Popoff, Michael Seagar, Robert Mamoun, Oussama El Far
The development of simple molecular assays with membrane protein receptors in a native conformation still represents a challenging task. Exosomes are extracellular vesicles which, due to their stability and small size, are suited for analysis in various assay formats. Here, we describe a novel approach to sort recombinant fully native and functional membrane proteins to exosomes using a targeting peptide. Specific binding of high affinity ligands to the potassium channel Kv1.2, the G-protein coupled receptor CXCR4, and the botulinum neurotoxin type B (BoNT/B) receptor, indicated their correct assembly and outside out orientation in exosomes...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28432017/dual-functional-nanoparticles-for-precise-drug-delivery-to-alzheimer-s-disease-lesions-targeting-mechanisms-pharmacodynamics-and-safety
#11
Xiaoyao Zheng, Chi Zhang, Qian Guo, Xu Wan, Xiayan Shao, Qingfeng Liu, Qizhi Zhang
Alzheimer's disease (AD) is the most common form of dementia and is characterized by the cerebral accumulation of extracellular amyloid plaques. In a previous study, this histopathological hallmark was used as a target on a dual-functional nanoparticle (TQNP) to deliver biotechnological drugs, such as the H102 peptide, a β-sheet breaker, to AD lesions precisely. This delivery system could reduce the amyloid-β (Aβ) burden in the brains of AD model mice, as well as ameliorated the memory impairment of the mice...
April 18, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28431630/kynurenic-acid-and-its-analogue-can-alter-the-opioid-receptor-g-protein-signaling-after-acute-treatment-via-nmda-receptor-in-rat-cortex-and-striatum
#12
Reza Samavati, Ferenc Zádor, Edina Szűcs, Bernadett Tuka, Diána Martos, Gábor Veres, Róbert Gáspár, István M Mándity, Ferenc Fülöp, László Vécsei, Sándor Benyhe, Anna Borsodi
Previously, we have shown that the N-methyl d-aspartate (NMDA)-receptor antagonist kynurenic acid (KYNA) and its analogue KYNA1 do not bind directly to mu, kappa and delta opioid receptors in vitro. On the other hand, chronic administration of KYNA and KYNA1 resulted in region (cortex vs striatum) and opioid receptor-type specific alterations in G-protein activation of mouse brain homogenates. Here we describe for the first time the acute effect of KYNA and KYNA1 on opioid receptor function with the possible involvement of the NMDA receptor...
May 15, 2017: Journal of the Neurological Sciences
https://www.readbyqxmd.com/read/28431169/spa-ln-a-scoring-function-of-ligand-nucleic-acid-interactions-via-optimizing-both-specificity-and-affinity
#13
Zhiqiang Yan, Jin Wang
Nucleic acids have been widely recognized as potential targets in drug discovery and aptamer selection. Quantifying the interactions between small molecules and nucleic acids is critical to discover lead compounds and design novel aptamers. Scoring function is normally employed to quantify the interactions in structure-based virtual screening. However, the predictive power of nucleic acid-ligand scoring functions is still a challenge compared to other types of biomolecular recognition. With the rapid growth of experimentally determined nucleic acid-ligand complex structures, in this work, we develop a knowledge-based scoring function of nucleic acid-ligand interactions, namely SPA-LN...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28430437/discovery-of-an-hcv-ns5b-replicase-palm-site-allosteric-inhibitor-bms-929075-advanced-to-phase-1-clinical-studies
#14
Kap-Sun Yeung, Brett R Beno, Kyle Parcella, John A Bender, Katherine A Grant-Young, Andrew Nickel, Prashantha Gunaga, Prakash Anjanappa, Rajesh Onkardas Bora, Kumaravel Selvakumar, Karen Rigat, Ying-Kai Wang, Mengping Liu, Julie A Lemm, Kathy Mosure, Steven Sheriff, Changhong Wan, Mark Witmer, Kevin Kish, Umesh M Hanumegowda, Xiaoliang Zhuo, Yue-Zhong Shu, Dawn Parker, Roy Haskell, Alicia Ng, Qi Gao, Elizabeth Colston, Joseph Raybon, Dennis M Grasela, Kenneth S Santone, Min Gao, Nicholas A Meanwell, Michael W Sinz, Matthew G Soars, Jay O Knipe, Susan B Roberts, John F Kadow
The hepatitis C virus NS5B replicase is a prime target for the development of direct-acting antiviral drugs for the treatment of chronic HCV infection. Inspired by the overlay of bound structures of three structurally distinct NS5B palm site allosteric inhibitors, the high throughput screening hit anthranilic acid 4, the known benzofuran analog 5 and the benzothiadiazine derivative 6, an optimization process utilizing the simple benzofuran template 7 as a starting point for a fragment growing approach was pursued...
April 21, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28430432/absolute-binding-free-energies-between-t4-lysozyme-and-141-small-molecules-calculations-based-on-multiple-rigid-receptor-configurations
#15
Bing Xie, Trung Hai Nguyen, David D L Minh
We demonstrate the feasibility of estimating protein-ligand binding free energies using multiple rigid receptor configurations. Based on T4 lysozyme snapshots extracted from six alchemical binding free energy calculations with a flexible receptor, binding free energies were estimated for a total of 141 ligands. For 24 ligands, the calculations reproduced flexible-receptor estimates with a correlation coefficient of 0.90 and a root mean square error of 1.59 kcal/mol. The accuracy of calculations based on Poisson-Boltzmann/Surface Area implicit solvent was comparable to previously reported free energy calculations...
April 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28430408/amplifying-riboswitch-signal-output-using-cellular-wiring
#16
Michael S Goodson, Annastacia C Bennett, Brenton R Jennewine, Emily Briskin, Svetlana V Harbaugh, Nancy Kelley-Loughnane
If fieldable riboswitch-based biological sensors are to fulfil their potential, it is necessary to increase their signal output. Here we report a novel modular amplification system using a riboswitch to initiate signaling between a sensing strain and a reporter strain of E. coli. A quorum sensing signaling molecule biologically wires the sensing and reporter strains together. The amplification circuit increased the amount of fluorescence generated on ligand binding compared to when the riboswitch controlled fluorescence expression directly...
April 21, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28430390/chronic-toxicity-of-binary-metal-mixtures-of-cadmium-and-zinc-to-daphnia-magna
#17
Edgar Pérez, Tham C Hoang
The present study characterized the chronic effect of binary-metal mixtures of cadmium (Cd) and zinc (Zn) on Daphnia magna. The titration design was chosen to characterize the 21-d chronic effects of the binary-metal mixtures on survival, growth, reproduction, and metal accumulation in D. magna. Using this design, increasing concentrations of Zn (10, 20, 40, 80, 120, 160 and 200µg/L) were titrated against a constant concentration of 1.5µg/L Cd. The results demonstrated that Cd was highly toxic to D. magna...
April 21, 2017: Environmental Toxicology and Chemistry
https://www.readbyqxmd.com/read/28430282/a-ratiometric-sensor-for-dna-based-on-a-dual-emission-ru-dppz-light-switch-complex
#18
Michael G Walker, Vadde Ramu, Anthony J H M Meijer, Amitava Das, Jim A Thomas
Herein we describe the DNA binding properties of two new water-soluble ruthenium complexes; experimental and computational data reveal that both complexes display dual emission from MLCT and LLCT excited states. The interaction of the new complexes with DNA was also investigated. Although one of the complexes only binds DNA though groove binding, the second complex has separate ligands capable of groove binding and intercalation. Nevertheless, it was found that both complexes interact with duplex DNA with high affinity...
April 21, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28430151/na-k-pump-and-beyond-na-k-atpase-as-a-modulator-of-apoptosis-and-autophagy
#19
REVIEW
Cassiano Felippe Gonçalves-de-Albuquerque, Adriana Ribeiro Silva, Camila Ignácio da Silva, Hugo Caire Castro-Faria-Neto, Patrícia Burth
Lung cancer is a leading cause of global cancer deaths. Na/K-ATPase has been studied as a target for cancer treatment. Cardiotonic steroids (CS) trigger intracellular signalling upon binding to Na/K-ATPase. Normal lung and tumour cells frequently express different pump isoforms. Thus, Na/K-ATPase is a powerful target for lung cancer treatment. Drugs targeting Na/K-ATPase may induce apoptosis and autophagy in transformed cells. We argue that Na/K-ATPase has a role as a potential target in chemotherapy in lung cancer treatment...
April 21, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28429758/intracellular-lipid-binding-protein-family-diversity-from-oyster-crassostrea-gigas-genomic-and-structural-features-of-invertebrate-lipid-transporters
#20
Guilherme de Toledo-Silva, Guilherme Razzera, Flavia Lucena Zacchi, Nestor Cubas Wendt, Jacó Joaquim Mattos, Afonso Celso Dias Bainy
Intracellular lipid binding proteins (iLBPs) play a role in the transport and cellular uptake of fatty acids and gene expression regulation. The aim of this work was to characterize the iLBP gene family of the Pacific oyster Crassostrea gigas, one of the most cultivated marine bivalves in the world, using bioinformatics and molecular biology approaches. A total of 26 different iLBPs transcripts were identified in the Pacific oyster genome, including alternative splicing and gene duplication events. The oyster iLBP gene family seems to be more expanded than in other invertebrates...
April 21, 2017: Scientific Reports
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