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https://www.readbyqxmd.com/read/28735213/chemoselective-synthesis-and-biological-evaluation-of-arylated-2-trifluoromethyl-quinolines-as-nucleotide-pyrophosphatase-npps-inhibitors
#1
David Kuhrt, Syeda Abida Ejaz, Saira Afzal, Shafi Ullah Khan, Joanna Lecka, Jean Sévigny, Peter Ehlers, Anke Spannenberg, Jamshed Iqbal, Peter Langer
A new approach to arylated 2-trifluoromethylquinolines based on novel regioselective Suzuki-Miyaura coupling reactions has been developed. Moreover, site-selective, chemo-selective amination reactions were performed. The new 2-trifluoromethylquinoline derivatives were tested as potential NPPs inhibitors and evaluated for their potential to inhibit two families of ecto-nucleotidases, i.e. NPPs and nucleoside triphosphate diphosphohydrolases (NTPDases). Several derivatives were active on a nanomolecular concentration...
July 13, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28734976/structural-basis-of-the-substrate-specificity-and-instability-in-solution-of-a-glycosidase-from-lactobacillus-plantarum
#2
Iván Acebrón, Laura Plaza-Vinuesa, Blanca de Las Rivas, Rosario Muñoz, J Cumella, F Sánchez-Sancho, José Miguel Mancheño
Statistics from structural genomics initiatives reveal that around 50-55% of the expressed, non-membrane proteins cannot be purified and therefore structurally characterized due to solubility problems, which emphasized protein solubility as one of the most serious concerns in structural biology projects. Lactobacillus plantarum CECT 748(T) produces an aggregation-prone glycosidase (LpBgl) that we crystallized previously. However, this result could not be reproduced due to protein instability and therefore further high-resolution structural analyses of LpBgl were impeded...
July 19, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28734934/analysis-of-rna-protein-interactions-in-vertebrate-embryos-using-uv-crosslinking-approaches
#3
Vladimir Despic, Mario Dejung, Falk Butter, Karla M Neugebauer
A decade ago, we believed that at least 300 RNA binding proteins (RBPs) were encoded in our genomes based on annotations of known or predicted RNA binding domains. Deciphering the roles of those RBPs in regulated gene expression was a vast frontier awaiting exploration. Since then, the field has developed a number of key tools that navigate the landscape of cellular RNA. These rely principally on UV crosslinking to create covalent bonds between RBPs and target RNAs in vivo, revealing not only target identities but also local binding sites upon RNA-Seq...
July 19, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28734893/genetic-polymorphisms-in-cyp2a6-are-associated-with-a-risk-of-cigarette-smoking-and-predispose-to-smoking-at-younger-ages
#4
Gloria Pérez-Rubio, Luis Alberto López-Flores, Alejandra Ramírez-Venegas, Valeri Noé-Díaz, Leonor García-Gómez, Enrique Ambrocio-Ortiz, Candelaria Sánchez-Romero, Rafael De Jesús Hernández-Zenteno, Raúl Humberto Sansores, Ramcés Falfán-Valencia
Nicotine is the main component of cigarettes that causes addiction, which is considered a complex disease, and genetic factors have been proposed to be involved in the development of addiction. The CYP2A6 gene encodes the main enzyme responsible for nicotine metabolism. Depending on the study population, different genetic variants of CYP2A6 associated with cigarette smoking have been described. Therefore, we evaluated the possible association between SNPs in CYP2A6 with cigarette smoking and nicotine addiction-related variables in Mexican mestizo smokers...
July 19, 2017: Gene
https://www.readbyqxmd.com/read/28734839/recombinant-expression-of-ixolaris-a-kunitz-type-inhibitor-from-the-tick-salivary-gland-for-nmr-studies
#5
V S De Paula, F H S Silva, I M B Francischetti, R Q Monteiro, A P Valente
Ixolaris is an anticoagulant protein identified in the tick saliva of Ixodes scapularis. Ixolaris contains 2 Kunitz like domains and binds to Factor Xa or Factor X as a scaffold for inhibition of the Tissue Factor (TF)/Factor VIIa (FVIIa). In contrast to tissue factor pathway inhibitor (TFPI), however, Ixolaris does not bind to the active site cleft of FXa. Instead, complex formation is mediated by the FXa heparin-binding exosite. Due to its potent and long-lasting antithrombotic activity, Ixolaris is a promising agent for anticoagulant therapy...
July 19, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28734826/biophysical-constraints-arising-from-compositional-context-in-synthetic-gene-networks
#6
Enoch Yeung, Aaron J Dy, Kyle B Martin, Andrew H Ng, Domitilla Del Vecchio, James L Beck, James J Collins, Richard M Murray
Synthetic gene expression is highly sensitive to intragenic compositional context (promoter structure, spacing regions between promoter and coding sequences, and ribosome binding sites). However, much less is known about the effects of intergenic compositional context (spatial arrangement and orientation of entire genes on DNA) on expression levels in synthetic gene networks. We compare expression of induced genes arranged in convergent, divergent, or tandem orientations. Induction of convergent genes yielded up to 400% higher expression, greater ultrasensitivity, and dynamic range than divergent- or tandem-oriented genes...
July 18, 2017: Cell Systems
https://www.readbyqxmd.com/read/28734777/inhibitor-mechanisms-in-the-s1-binding-site-of-the-dopamine-transporter-defined-by-multi-site-molecular-tethering-of-photoactive-cocaine-analogs
#7
Danielle Krout, Akula Bala Pramod, Rejwi Acharya Dahal, Michael J Tomlinson, Babita Sharma, James D Foster, Mu-Fa Zou, Comfort Boatang, Amy Hauck Newman, John R Lever, Roxanne A Vaughan, L Keith Henry
Dopamine transporter (DAT) blockers like cocaine and many other abused and therapeutic drugs bind and stabilize an inactive form of the transporter inhibiting reuptake of extracellular dopamine (DA). The resulting increases in DA lead to the ability of these drugs to induce psychomotor alterations and addiction, but paradoxical findings in animal models indicate that not all DAT antagonists induce cocaine-like behavioral outcomes. How this occurs is not known, but one possibility is that uptake inhibitors may bind at multiple locations or in different poses to stabilize distinct conformational transporter states associated with differential neurochemical endpoints...
July 19, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/28734220/effect-analysis-of-quantum-chemical-descriptors-and-substituent-characteristics-on-henry-s-law-constants-of-polybrominated-diphenyl-ethers-at-different-temperatures
#8
Jiang Long, Qiu Youli, Li Yu
Twelve substituent descriptors, 17 quantum chemical descriptors and 1/T were selected to establish a quantitative structure-property relationship (QSPR) model of Henry's law constants for 7 polybrominated diphenyl ethers (PBDEs) at five different temperatures. Then, the lgH of 202 congeners at different temperatures were predicted. The variation rule and regulating mechanism of lgH was studied from the perspectives of both quantum chemical descriptors and substituent characteristics. The R(2) for modeling and testing sets of the final QSPR model are 0...
July 19, 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/28734208/effect-of-mutation-on-a%C3%AE-1-42-heme-complex-in-aggregation-mechanism-alzheimer-s-disease
#9
Subramaniam Boopathi, Ponmalai Kolandaivel
Amyloid β (Aβ) peptide aggregation is one of the root causes for Alzheimer's disease. Recently, experimental studies show that three active binding sites (His6, His13 and His14) of Aβ peptides were bound with heme to form Aβ-Heme complex, which leads to inhibit the aggregation process. We apply molecular dynamic simulation to investigate the aggregation pathways of Aβ-Heme peptides. The above three binding sites were mutated by Glycine residue individually and generate three complex systems such as Aβ(His6Gly)-Heme, Aβ(His13Gly)-Heme and Aβ(His14Gly)-Heme...
July 8, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28734204/molecular-dynamics-of-conformation-specific-dopamine-transporter-inhibitor-complexes
#10
Bernandie Jean, Christopher K Surratt, Jeffry D Madura
The recreational psychostimulant cocaine inhibits dopamine reuptake from the synapse, resulting in excessive stimulation of postsynaptic dopamine receptors in brain areas associated with reward and addiction. Cocaine binds to and stabilizes the outward- (extracellular-) facing conformation of the dopamine transporter (DAT) protein, while the low abuse potential DAT inhibitor benztropine prefers the inward- (cytoplasmic-) facing conformation. A correlation has been previously postulated between psychostimulant abuse potential and preference for the outward-facing DAT conformation...
July 11, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28734179/computational-analysis-for-the-determination-of-deleterious-nssnps-in-human-mthfd1-gene
#11
Mansi Desai, J B Chauhan
Single nucleotide polymorphisms (SNPs) are the most common genetic polymorphisms and play a major role in many inherited diseases. Methylenetetrahydrofolate dehydrogenase 1 (MTHFD1) is one of the enzymes involved in folate metabolism. In the present study, the functional and structural consequences of nsSNPs of human MTHFD1 gene was analyzed using various computational tools like SIFT, PolyPhen2, PANTHER, PROVEAN, SNAP2, nsSNPAnalyzer, PhD-SNP, SNPs&GO, I-Mutant, MuPro, ConSurf, InterPro, NCBI Conserved Domain Search tool, ModPred, SPARKS-X, RAMPAGE, FT Site and PyMol...
July 11, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28734069/pathogen-richness-and-abundance-predict-patterns-of-adaptive-mhc-variation-in-insular-amphibians
#12
Supen Wang, Conghui Liu, Anthony B Wilson, Na Zhao, Xianping Li, Wei Zhu, Xu Gao, Xuan Liu, Yiming Li
The identification of the factors responsible for genetic variation and differentiation at adaptive loci can provide important insights into the evolutionary process, and is crucial for the effective management of threatened species. We studied the impact of environmental viral richness and abundance on functional diversity and differentiation of the MHC class Ia locus in populations of the black-spotted pond frog (Pelophylax nigromaculatus), an IUCN-listed species, on 24 land-bridge islands of the Zhoushan Archipelago and 3 nearby mainland sites...
July 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28734030/a-computational-method-for-selecting-short-peptide-sequences-for-inorganic-material-binding
#13
Niloofar Nayebi, Sibel Cetinel, Sara Ibrahim Omar, Jack A Tuszynski, Carlo Montemagno
Discovering or designing biofunctionalized materials with improved quality highly depends on the ability to manipulate and control the peptide-inorganic interaction. Various peptides can be used as assemblers, synthesizers, and linkers in the material syntheses. In another context, specific and selective material-binding peptides can be used as recognition blocks in mining applications. In this study, we propose a new in silico method to select short 4-mer peptides with high affinity and selectivity for a given target material...
July 22, 2017: Proteins
https://www.readbyqxmd.com/read/28734024/effect-of-solvent-and-protein-dynamics-in-ligand-recognition-and-inhibition-of-aminoglycoside-adenyltransferase-2%C3%A2-ia
#14
Valjean R Bacot-Davis, Angelia V Bassenden, Tara Sprules, Albert M Berghuis
The aminoglycoside modifying enzyme (AME) ANT(2″)-Ia is a significant target for next generation antibiotic development. Structural studies of a related aminoglycoside-modifying enzyme, ANT(3″)(9), revealed this enzyme contains dynamic, disordered, and well-defined segments that modulate thermodynamically before and after antibiotic binding. Characterizing these structural dynamics is critical for in situ screening, design, and development of contemporary antibiotics that can be implemented in a clinical setting to treat potentially lethal, antibiotic resistant, human infections...
July 21, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28733707/angiotensin-ii-type-1-receptor-blockers-inhibit-kat-ii-activity-in-the-brain-its-possible-clinical-applications
#15
Izabela Zakrocka, Katarzyna M Targowska-Duda, Artur Wnorowski, Tomasz Kocki, Krzysztof Jóźwiak, Waldemar A Turski
Angiotensin II receptor blockers (ARBs) are one of the most frequently recommended antihypertensive drugs. Apart from their activity towards the circulatory system, ARBs also penetrate the blood-brain barrier and display neuroprotective effects. Kynurenic acid (KYNA) is an endogenous metabolite of tryptophan produced by kynurenine aminotransferase II (KAT II) in the brain. Antagonism towards all ionotropic glutamate (GLU) receptors is the main mechanism of KYNA action. An elevated brain level of KYNA is linked with memory impairment and psychotic symptoms...
July 21, 2017: Neurotoxicity Research
https://www.readbyqxmd.com/read/28733706/phage-display-selection-in-vitro-characterization-and-correlative-pet-imaging-of-a-novel-her3-peptide
#16
Benjamin M Larimer, Nicholas Phelan, Eric Wehrenberg-Klee, Umar Mahmood
PURPOSE: HER3 (ERBB3) is a receptor tyrosine kinase that is implicated in treatment resistance across multiple cancers, including those of the breast, lung, and prostate. Overexpression of HER3 following targeted therapy can occur rapidly and heterogeneously both within a single lesion and across sites of metastasis, making protein quantification by biopsy highly challenging. A global, non-invasive methodology such as positron emission tomography (PET) imaging can permit serial quantification of HER3, providing a useful approach to monitor HER3 expression across the entire tumor burden both prior to and following treatment...
July 21, 2017: Molecular Imaging and Biology: MIB: the Official Publication of the Academy of Molecular Imaging
https://www.readbyqxmd.com/read/28733598/role-of-hdac9-foxo1-axis-in-the-transcriptional-program-associated-with-hepatic-gluconeogenesis
#17
Jizheng Chen, Zhilei Zhang, Ning Wang, Min Guo, Xiumei Chi, Yu Pan, Jing Jiang, Junqi Niu, Sulaiman Ksimu, John Zhong Li, Xinwen Chen, Qian Wang
Histone deacetylase 9 (HDAC9) regulates hepatic gluconeogenesis by deacetylating Forkhead box O 1 (FoxO1). HDAC9 upregulation is involved in hepatitis C virus (HCV)-associated exaggerated gluconeogenesis. Herein, we found in addition to FoxO1, HDAC9 also regulates other gluconeogenic transcription factors, including peroxisomeproliferator-activated receptor-γ coactivator-1α (PGC-1α), cyclic AMP-responsive element-binding protein (CREB), and glucocorticoid receptor (GR). Unlike FoxO1, which is regulated by post-translational modification responses to HDAC9, HDAC9 regulates PGC-1α, CREB and GR by altering gene expression...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28733446/how-does-pressure-overload-cause-cardiac-hypertrophy-and-dysfunction-high-ouabain-affinity-cardiac-na-pumps-are-crucial
#18
Mordecai P Blaustein
Left ventricular hypertrophy is frequently observed in hypertensive patients, and is believed to be due to the pressure overload and cardiomyocyte stretch. Three recent reports on mice with genetically-engineered Na(+) pumps, however, demonstrate that cardiac ouabain-sensitive α2 Na(+) pumps play a key role in the pathogenesis of trans-aortic constriction (TAC)-induced hypertrophy. Hypertrophy was delayed/attenuated in mice with mutant, ouabain-resistant α2 Na(+) pumps and in mice with cardiac-selective knockout (KO) or transgenic overexpression (TG) of α2 Na(+) pumps...
July 21, 2017: American Journal of Physiology. Heart and Circulatory Physiology
https://www.readbyqxmd.com/read/28733422/differences-in-dna-binding-specificity-of-floral-homeotic-protein-complexes-predict-organ-specific-target-genes
#19
Cezary Smaczniak, Jose M Muiño, Dijun Chen, Gerco C Angenent, Kerstin Kaufmann
Floral organ identities in plants are specified by the combinatorial action of homeotic master regulatory transcription factors. How these factors achieve their regulatory specificities is however still largely unclear. Genome-wide in vivo DNA binding data show that homeotic MADS-domain proteins recognize partly distinct genomic regions, suggesting that DNA binding specificity contributes to functional differences of homeotic protein complexes. We used in vitro systematic evolution of ligands by exponential enrichment followed by high throughput DNA sequencing (SELEX-seq) on several floral MADS-domain protein homo- and heterodimers to measure their DNA-binding specificities...
July 21, 2017: Plant Cell
https://www.readbyqxmd.com/read/28733280/construction-and-optimization-of-a-heterologous-pathway-for-protocatechuate-catabolism-in-escherichia-coli-enables-bioconversion-of-model-aromatic-compounds
#20
Sonya M Clarkson, Richard J Giannone, Donna M Kridelbaugh, James G Elkins, Adam M Guss, Joshua K Michener
The production of biofuels from lignocellulose yields a substantial lignin byproduct stream that currently has few applications. Biological conversion of lignin-derived compounds into chemicals and fuels has the potential to improve the economics of lignocellulose-derived biofuels, but few microbes are able both to catabolize lignin-derived aromatic compounds and generate valuable products. While Escherichia coli has been engineered to produce a variety of fuels and chemicals, it is incapable of catabolizing most aromatic compounds...
July 21, 2017: Applied and Environmental Microbiology
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