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Hydrogen bond surrogate

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https://www.readbyqxmd.com/read/27909346/copper-i-dioxygen-adducts-and-copper-enzyme-mechanisms
#1
Jeffrey J Liu, Daniel E Diaz, David A Quist, Kenneth D Karlin
Primary copper(I)-dioxygen (O2) adducts, cupric-superoxide complexes, have been proposed intermediates in copper-containing dioxygen-activating monooxygenase and oxidase enzymes. Here, mechanisms of C-H activation by reactive copper-(di)oxygen intermediates are discussed, with an emphasis on cupric-superoxide species. Over the past 25 years, many synthetically derived cupric-superoxide model complexes have been reported. Due to the thermal instability of these intermediates, early studies focused on increasing their stability and obtaining physical characterization...
October 2016: Israel Journal of Chemistry
https://www.readbyqxmd.com/read/27862441/heteroacene-synthesis-through-c-s-cross-coupling-5-endo-dig-cyclization
#2
Peter Oechsle, Ulrich Flörke, Hans Egold, Jan Paradies
Highly efficient, one-step synthesis of sulfur-containing heteroacenes was achieved through palladium-catalyzed C-S cross-coupling of bis-alkynes with thioacetate as hydrogen sulfide surrogate. Heteroacenes consisting of three, five, and seven fused aromatic rings were obtained in a single catalytic step by four-, six-, and eightfold C-S bond formation.
November 11, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27762555/synthesis-of-gly-%C3%AE-z-cf-ch-phe-a-fluoroalkene-dipeptide-isostere-and-its-incorporation-into-a-leu-enkephalin-peptidomimetic
#3
Jean-Francois Nadon, Kristina Rochon, Sébastien Grastilleur, Guillaume Langlois, Thi Thanh Hà Dao, Véronique Blais, Brigitte Guérin, Louis Gendron, Yves L Dory
A new Leu-enkephalin peptidomimetic designed to explore the hydrogen bond acceptor ability of the third peptide bond has been prepared and studied. This new analog is produced by replacing the third amide of Leu-enkephalin with a fluoroalkene. An efficient and innovative synthesis of the corresponding dipeptide surrogate Fmoc-Gly-Ψ[(Z)CF=CH]-Phe-OH is described. The key step involves the alkylation of a tin dienolate from the less hindered face of its chiral sulfonamide auxiliary derived from camphor. Once its synthesis was complete, its incorporation into the peptidomimetic sequence was achieved on a solid support with chlorotrityl resin and following the Fmoc strategy...
October 20, 2016: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/27311877/hydrogenation-and-transfer-hydrogenation-promoted-by-tethered-ru-s-complexes-from-cooperative-dihydrogen-activation-to-hydride-abstraction-proton-release-from-dihydrogen-surrogates
#4
Alice Lefranc, Zheng-Wang Qu, Stefan Grimme, Martin Oestreich
Hydrogenation and transfer hydrogenation of imines with cyclohexa-1,4-dienes, as well as with a representative Hantzsch ester dihydrogen surrogate, are reported. Both processes are catalyzed by tethered Ru-S complexes but differ in the activation mode of the dihydrogen source: cooperative activation of the H-H bond at the Ru-S bond leads to the corresponding Ru-H complex and protonation of the sulfur atom, whereas the same cationic Ru-S catalyst abstracts a hydride from a donor-substituted cyclohexa-1,4-diene to form the neutral Ru-H complex and a low-energy Wheland intermediate...
July 11, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27302426/effect-of-monoglycerides-and-fatty-acids-on-a-ceramide-bilayer
#5
Anna Akinshina, Chinmay Das, Massimo G Noro
Monoglycerides and unsaturated fatty acids, naturally present in trace amounts in the stratum corneum (top layer of skin) lipid matrix, are commonly used in pharmaceutical, cosmetic and health care formulations. However, a detailed molecular understanding of how the oil additives get incorporated into the skin lipids from topical application and, once incorporated, how they affect the properties and integrity of the lipid matrix remains unexplored. Using ceramide 2 bilayers as skin lipid surrogates, we use a series of molecular dynamics simulations with six different natural oil ingredients at multiple concentrations to investigate the effect of the oils on the properties and stability of the bilayers...
July 14, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27188873/triazole-resistance-mediated-by-mutations-of-a-conserved-active-site-tyrosine-in-fungal-lanosterol-14%C3%AE-demethylase
#6
Alia A Sagatova, Mikhail V Keniya, Rajni K Wilson, Manya Sabherwal, Joel D A Tyndall, Brian C Monk
Emergence of fungal strains showing resistance to triazole drugs can make treatment of fungal disease problematic. Triazole resistance can arise due to single mutations in the drug target lanosterol 14α-demethylase (Erg11p/CYP51). We have determined how commonly occurring single site mutations in pathogenic fungi affect triazole binding using Saccharomyces cerevisiae Erg11p (ScErg11p) as a target surrogate. The mutations Y140F/H were introduced into full-length hexahistidine-tagged ScErg11p. Phenotypes and high-resolution X-ray crystal structures were determined for the mutant enzymes complexed with short-tailed (fluconazole and voriconazole) or long-tailed (itraconazole and posaconazole) triazoles and wild type enzyme complexed with voriconazole...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27155814/insights-into-rpob-clinical-mutants-in-mediating-rifampicin-resistance-in-mycobacterium-tuberculosis
#7
Ameeruddin Nusrath Unissa, Sameer Hassan, Venkatesan Indira Kumari, Ravi Revathy, Luke Elizabeth Hanna
Rifampicin (RIF) an essential first-line anti-tuberculosis (TB) drug, resistance to RIF is a potential threat to TB control program and widely considered as surrogate marker for detection of multi-drug resistant-TB (MDR-TB), molecular understanding of which is the utmost need of the hour. Mutations at RIF resistance-determining region (RRDR) of 81-bp in the rpoB gene coding for β subunit or RpoB protein is the major cause of RIF resistance in Mycobacterium tuberculosis (MTB). Mutation at positions 526 and 531 are generally associated with high-level RIF resistance and at codons 516, 521 and 533 with low-level resistance...
June 2016: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/27059179/emergence-of-function-in-p450-proteins-a-combined-quantum-mechanical-molecular-mechanical-and-molecular-dynamics-study-of-the-reactive-species-in-the-h2o2-dependent-cytochrome-p450sp%C3%AE-and-its-regio-and-enantioselective-hydroxylation-of-fatty-acids
#8
Rajeev Ramanan, Kshatresh Dutta Dubey, Binju Wang, Debasish Mandal, Sason Shaik
This work uses combined quantum mechanical/molecular mechanical and molecular dynamics simulations to investigate the mechanism and selectivity of H2O2-dependent hydroxylation of fatty acids by the P450SPα class of enzymes. H2O2 is found to serve as the surrogate oxidant for generating the principal oxidant, Compound I (Cpd I), in a mechanism that involves homolytic O-O bond cleavage followed by H-abstraction from the Fe-OH moiety. Our results rule out a substrate-assisted heterolytic cleavage of H2O2 en route to Cpd I...
June 1, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27046675/an-optimal-hydrogen-bond-surrogate-for-%C3%AE-helices
#9
Stephen T Joy, Paramjit S Arora
Substitution of a main chain i → i + 4 hydrogen bond with a covalent bond can nucleate and stabilize the α-helical conformation in peptides. Herein we describe the potential of different alkene isosteres to mimic intramolecular hydrogen bonds and stabilize α-helices in diverse peptide sequences.
April 28, 2016: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/27018227/adme-properties-evaluation-in-drug-discovery-prediction-of-caco-2-cell-permeability-using-a-combination-of-nsga-ii-and-boosting
#10
Ning-Ning Wang, Jie Dong, Yin-Hua Deng, Min-Feng Zhu, Ming Wen, Zhi-Jiang Yao, Ai-Ping Lu, Jian-Bing Wang, Dong-Sheng Cao
The Caco-2 cell monolayer model is a popular surrogate in predicting the in vitro human intestinal permeability of a drug due to its morphological and functional similarity with human enterocytes. A quantitative structure-property relationship (QSPR) study was carried out to predict Caco-2 cell permeability of a large data set consisting of 1272 compounds. Four different methods including multivariate linear regression (MLR), partial least-squares (PLS), support vector machine (SVM) regression and Boosting were employed to build prediction models with 30 molecular descriptors selected by nondominated sorting genetic algorithm-II (NSGA-II)...
April 25, 2016: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/26866502/overcoming-strain-induced-rearrangement-reactions-a-mild-dehydrative-aromatization-protocol-for-synthesis-of-highly-distorted-p-phenylenes
#11
Nirmal K Mitra, Rolande Meudom, Hector H Corzo, John D Gorden, Bradley L Merner
A series of p-terphenyl-based macrocycles, containing highly distorted p-phenylene units, have been synthesized. Biaryl bonds of the nonplanar p-terphenyl nuclei were constructed in the absence of Pd-catalyzed or Ni-mediated cross-coupling reactions, using 1,4-diketones as surrogates to strained arene units. A streamlined synthetic protocol for the synthesis of 1,4-diketo macrocycles has been developed, using only 2.5 mol % of the Hoveyda-Grubbs second-generation catalyst in both metathesis and transfer hydrogenation reactions...
March 9, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/26457527/structure-of-the-complex-of-carboxypeptidase-b-and-n-sulfamoyl-l-arginine
#12
Valery Akparov, Nikolay Sokolenko, Vladimir Timofeev, Inna Kuranova
Porcine pancreatic carboxypeptidase B (EC 3.4.23.6) was complexed with a stable transition-state analogue, N-sulfamoyl-L-arginine, in which an S atom imitates the sp(3)-hybridized carbon in the scissile-bond surrogate. Crystals were grown in a form belonging to the same space group, P41212, as the uncomplexed enzyme. X-ray data were collected to a resolution of 1.25 Å. The molecule was refined and the positions of non-H atoms of the inhibitor and water molecules were defined using difference Fourier maps...
October 2015: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/26391081/formal-sih4-chemistry-using-stable-and-easy-to-handle-surrogates
#13
Antoine Simonneau, Martin Oestreich
Monosilane (SiH4) is far less well behaved than its carbon analogue methane (CH4). It is a colourless gas that is industrially relevant as a source of elemental silicon, but its pyrophoric and explosive nature makes its handling and use challenging. Consequently, synthetic applications of SiH4 in academic laboratories are extremely rare and methodologies based on SiH4 are underdeveloped. Safe and controlled alternatives to the substituent redistribution approaches of hydrosilanes are desirable and cyclohexa-2,5-dien-1-ylsilanes where the cyclohexa-1,4-diene units serve as placeholders for the hydrogen atoms have been identified as potent surrogates of SiH4...
October 2015: Nature Chemistry
https://www.readbyqxmd.com/read/26352022/a-reduced-2fe2s-cluster-probe-of-sulfur-hydrogen-versus-sulfur-gold-interactions
#14
Danielle J Crouthers, Shengda Ding, Jason A Denny, Ryan D Bethel, Chung-Hung Hsieh, Michael B Hall, Marcetta Y Darensbourg
The Ph3 PAu(+) cation, renowned as an isolobal analogue of H(+) , was found to serve as a proton surrogate and form a stable Au2 Fe2 complex, [(μ-SAuPPh3 )2 {Fe(CO)3 }2 ], analogous to the highly reactive dihydrosulfide [(μ-SH)2 {Fe(CO)3 }2 ]. Solid-state X-ray diffraction analysis found the two SAuPPh3 and SH bridges in anti configurations. VT NMR studies, supported by DFT computations, confirmed substantial barriers of approximately 25 kcal mol(-1) to intramolecular interconversion between the three stereoisomers of [(μ-SH)2 {Fe(CO)3 }2 ]...
September 14, 2015: Angewandte Chemie
https://www.readbyqxmd.com/read/26085307/a-surrogate-measure-of-cortical-bone-matrix-density-by-long-t2-suppressed-mri
#15
Alan C Seifert, Cheng Li, Suzanne L Wehrli, Felix W Wehrli
Magnetic resonance has the potential to image and quantify two pools of water within bone: free water within the Haversian pore system (transverse relaxation time, T2 > 1 ms), and water hydrogen-bonded to matrix collagen (T2 ∼ 300 to 400 μs). Although total bone water concentration quantified by MRI has been shown to scale with porosity, greater insight into bone matrix density and porosity may be gained by relaxation-based separation of bound and pore water fractions. The objective of this study was to evaluate a recently developed surrogate measurement for matrix density, single adiabatic inversion recovery (SIR) zero echo-time (ZTE) MRI, in human bone...
December 2015: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
https://www.readbyqxmd.com/read/26002730/monooxygenase-peroxidase-and-peroxygenase-properties-and-reaction-mechanisms-of-cytochrome-p450-enzymes
#16
REVIEW
Eugene G Hrycay, Stelvio M Bandiera
This review examines the monooxygenase, peroxidase and peroxygenase properties and reaction mechanisms of cytochrome P450 (CYP) enzymes in bacterial, archaeal and mammalian systems. CYP enzymes catalyze monooxygenation reactions by inserting one oxygen atom from O2 into an enormous number and variety of substrates. The catalytic versatility of CYP stems from its ability to functionalize unactivated carbon-hydrogen (C-H) bonds of substrates through monooxygenation. The oxidative prowess of CYP in catalyzing monooxygenation reactions is attributed primarily to a porphyrin π radical ferryl intermediate known as Compound I (CpdI) (Por•+FeIV=O), or its ferryl radical resonance form (FeIV-O•)...
2015: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/25591543/peptide-therapeutics-targeting-the-undruggable-space
#17
REVIEW
Natia Tsomaia
Rapid advancements in genomics have brought a better understanding of molecular mechanisms for various pathologies and identified a number of highly attractive target classes. Some of these targets include intracellular protein-protein interactions (PPIs), which control many essential biological pathways. Their surfaces are part of a diverse and unexplored biological space, where traditional small molecule scaffolds are not always successful. While large biologics can effectively modulate PPIs in the extracellular region, their limitation in crossing the cellular membrane leaves intracellular protein targets outside of their reach...
April 13, 2015: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/25579571/insight-into-the-binding-mode-between-n-methyl-pyrimidones-and-prototype-foamy-virus-integrase-dna-complex-by-qm-polarized-ligand-docking-and-molecular-dynamics-simulations
#18
Karnati Konda Reddy, Sanjeev Kumar Singh
Human immunodeficiency virus type 1 (HIV-1) integrase (IN) is an essential enzyme in the viral replication cycle as it catalyzes the insertion of the reverse transcribed viral DNA into host chromosome. The structure of prototype foamy virus (PFV) IN has structural and functional homology with HIV-1 IN (no full-length structure available). In this study, we have used PFV IN-DNA complex as a surrogate model for HIV-1 IN-DNA complex to investigate the binding modes of N-methyl pyrimidones (NMPs) by QM-polarized ligand docking (QPLD), binding free energy calculations and molecular dynamics simulations...
2015: Current Topics in Medicinal Chemistry
https://www.readbyqxmd.com/read/25524168/the-structural-basis-for-specificity-in-lipoxygenase-catalysis
#19
REVIEW
Marcia E Newcomer, Alan R Brash
Many intriguing facets of lipoxygenase (LOX) catalysis are open to a detailed structural analysis. Polyunsaturated fatty acids with two to six double bonds are oxygenated precisely on a particular carbon, typically forming a single chiral fatty acid hydroperoxide product. Molecular oxygen is not bound or liganded during catalysis, yet it is directed precisely to one position and one stereo configuration on the reacting fatty acid. The transformations proceed upon exposure of substrate to enzyme in the presence of O2 (RH + O2 → ROOH), so it has proved challenging to capture the precise mode of substrate binding in the LOX active site...
March 2015: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/25424654/imidacloprid-and-thiacloprid-neonicotinoids-bind-more-favourably-to-cockroach-than-to-honeybee-%C3%AE-6-nicotinic-acetylcholine-receptor-insights-from-computational-studies
#20
Balaji Selvam, Jérôme Graton, Adèle D Laurent, Zakaria Alamiddine, Monique Mathé-Allainmat, Jacques Lebreton, Olivier Coqueret, Christophe Olivier, Steeve H Thany, Jean-Yves Le Questel
The binding interactions of two neonicotinoids, imidacloprid (IMI) and thiacloprid (THI) with the extracellular domains of cockroach and honeybee α6 nicotinic acetylcholine receptor (nAChR) subunits in an homomeric receptor have been studied through docking and molecular dynamics (MD) simulations. The binding mode predicted for the two neonicotinoids is validated through the good agreement observed between the theoretical results with the crystal structures of the corresponding complexes with Ac-AChBP, the recognized structural surrogate for insects nAChR extracellular ligand binding domain...
February 2015: Journal of Molecular Graphics & Modelling
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