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Hydroxymethylation

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https://www.readbyqxmd.com/read/28723648/cytosine-5-hydroxymethylation-regulates-vhl-gene-expression-in-renal-clear-cell-carcinoma
#1
En-Guang Ma, Yu-Feng Bai, Wei Cao, Yan Cao, Yong-Gang Huang, Huan-Chen Cheng, Rui-Hua An
Cytosine5-hyxymethylation (5hmC)which is a new epigenetic modification form plays important roles in the development and progression of tumors. In the present study, we observed that levels of 5hmC in the promoter region of Von Hippel-Lindau (VHL) were lower in 97 samples of renal clear cell carcinoma tissue than in matched adjacent benign tissues. Moreover, when the cancer tissue samples were divided based on pathological staging, VHL expression and the level of 5hmC in the VHL promoter were both lower in pathological grade III tumors than in grades I or II...
July 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28720326/piperidine-and-octahydropyrano-3-4-c-pyridine-scaffolds-for-drug-like-molecular-libraries-of-the-european-lead-factory
#2
Bharat D Narhe, Arjen C Breman, Jalindar Padwal, Dirk A L Vandenput, Joeri M Scheidt, Jorg C J Benningshof, Gijsbert A van der Marel, Herman S Overkleeft, Mario van der Stelt, Dmitri V Filippov
We report short and efficient scalable syntheses of enantiomerically pure (3R,4S)-3-(hydroxymethyl4-(hydroxyethyl))-piperidine and 1-hydroxymethyl-octahydro-1H-pyrano[3,4-c]pyridine scaffolds. The alkaloid core was readily synthesized from naturally occurring quinine and can serve as a valued starting point for drug-discovery. Cleavage of a terminal 1,2-diol and acid catalysed epoxide opening cyclization are the key steps involved. A number of members of a projected small-molecular library is synthesized for each scaffold...
July 10, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28715892/ethanol-solvation-in-water-studied-on-a-molecular-scale-by-photoelectron-spectroscopy
#3
Ricardo R T Marinho, Marie-Madeleine Walz, Victor Ekholm, Gunnar Öhrwall, Olle Bjorneholm, Arnaldo Naves de Brito
Due to the amphiphilic properties of alcohols, hydrophobic hydration is important in alcohol-water system. In the present paper we employ X-ray photoelectron spectroscopy (XPS) to investigate the bulk and surface molecular structure of ethanol-water mixtures from 0.2 to 95 mol%. The observed XPS binding energy splitting between the methyl C1s and hydroxymethyl C1s groups, (BES_[CH3‑CH2OH]), as a function of the ethanol molar percentage can be divided into different regions: one below 35 mol% with higher values (about 1...
July 17, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28714318/gc-ms-analysis-of-the-bioactive-phytoconstituents-of-various-organic-crude-extracts-from-the-seed-kernels-of-manilkara-bidentata-balata-collected-in-trinidad-w-i
#4
Yomica L Powder-George, Faisal K Mohammed
The present study reports the first phytochemical investigation of the seed kernels of Manilkara bidentata (Balata) harvested in Trinidad, W.I. Gas chromatography-mass spectrometry (GC-MS) analysis of the n-hexane, chloroform, ethyl acetate, ethanol and methanol extracts showed a total of 39 components. 2,6,10,14,18-pentamethyl-2,6,10,14,18-eicosapentaene (74.93%), 9-octadecenoic acid, (Z)- 2,3-dihydroxypropyl ester (79.98%), (Z)-ethyl oleate (92.75%), Z,E-2-methyl-3,13-octadecadien-1-ol (80.51%) and 5-(hydroxymethyl)-2-furancarboxyaldehyde (50...
July 16, 2017: Natural Product Research
https://www.readbyqxmd.com/read/28707898/synthesis-thermodynamic-properties-and-crystal-structure-of-rna-oligonucleotides-containing-5-hydroxymethylcytosine
#5
Christian Riml, Alexandra Lusser, Eric Ennifar, Ronald Micura
5-Hydroxymethylcytosine (hm(5)C) is an RNA modification that has attracted significant interest because of the finding that RNA hydroxymethylation can favor mRNA translation. For insight into the mechanistic details of hm(5)C function to be obtained, the availability of RNAs containing this modification at defined positions that can be used for in vitro studies is highly desirable. In this work, we present an eight-step route to 5-hydroxymethylcytidine (hm(5)rC) phosphoramidite for solid-phase synthesis of modified RNA oligonucleotides...
July 14, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28707620/a-quechers-based-sample-preparation-method-for-the-analysis-of-5-nitroimidazoles-in-bovine-milk-by-hplc-dad
#6
Tomasz Tuzimski, Tomasz Rejczak
In this study, a simple, cost-effective, and sensitive HPLC diode-array detection method was developed for thesimultaneous determination of six different 5-nitroimidazoles [metronidazole, 2-hydroxymethyl-1-methyl-5-nitro-(1)H-imidazole, dimetridazole (DMZ), ronidazole, ornidazole, and ipronidazole] in bovine milk samples. A QuEChERS-based sample preparation procedure was optimized by evaluating different cleanup sorbents, including zirconium-based sorbents (Z-Sep and Z-Sep+), C18, and primary–secondary amine (PSA), as well as EMR-Lipid cleanup solution...
July 13, 2017: Journal of AOAC International
https://www.readbyqxmd.com/read/28707599/designing-of-selective-%C3%AE-secretase-inhibitory-benzenesulfonamides-through-comparative-in-vitro-and-in-silico-analysis
#7
Neeraj Masand, Satya P Gupta, Ratan Lal Khosa
BACKGROUND: In Alzheimer's disease (AD), the gene mutations have been identified in the amyloid precursor protein (APP), the presenilin-1 (PS1) and -2 (PS2) genes. APP is a transmembrane protein which gets cleaved by α- and β-secretase enzymes and releases Aβ peptides which forms senile plaques in brain tissue. It contributes for local inflammatory response, subsequent oxidative stress, biochemical changes and neuronal death. Targeting the development of Aβ aggregates in the senile plaques is an important strategy in the treatment of AD...
July 13, 2017: Current Drug Discovery Technologies
https://www.readbyqxmd.com/read/28690383/molecular-docking-based-screening-of-listeriolysin-o-for-improved-inhibitors
#8
Sara Ghafari, Matin Komeilian, Mohaddese Sadat Hashemi, Sareh Oushani, Garshasb Rigi, Behnam Rashidieh, Kamran Yarahmadi, Fatemeh Khoddam
Listeriolysine-O (LLO) is a 50KDa protein responsible for Listeria monocytogenes pathogenicity. The structure of LLO (PDB ID: 4CDB) with domains D1 to D4 is known. Therefore, it is of interest to identify conserved regions among LLO variants for destabilizing oligomerization (50 mer complex) of its monomers using appropriate inhibitors. Therefore, it is of interest to identify suitable inhibitors for inhibiting LLO. Previous reports suggest the use of flavanoids like compounds for inhibiting LLO. Our interest is to identify improved compounds to destabilize LLO oligomerization...
2017: Bioinformation
https://www.readbyqxmd.com/read/28690379/competitive-rational-inhibitor-design-to-4-maleylaceto-acetate-isomerase
#9
Narges Zolfaghari
Tyrosinemia type I is the result of genetic disorder in fomaryl acetoacetase gene that leads to 4-fumaryl acetoacetate accumulation. The current treatment for tyrosinemia type I is nitisinone that inhibits 4-hydroxyphenyl pyruvic dioxygenase in competitive manner. In the present study, we have designed two theoretical chemicals, which could inhibit the direct enzyme responsible for fumarylacetoacetate formation. Subset 2_p.0.5 from Zinc database was screened by PyRx software using a Lamarckian genetic algorithm as the scoring function for docking...
2017: Bioinformation
https://www.readbyqxmd.com/read/28681987/single-run-capillary-electrophoresis-method-for-the-fast-simultaneous-determination-of-amoxicillin-clavulanate-and-potassium
#10
Mariana C Marra, Rafael R Cunha, Rodrigo A A Muñoz, Alex D Batista, Eduardo M Richter
We report a new fast method for the simultaneous determination of amoxicillin, clavulanate and potassium by capillary electrophoresis with capacitively coupled contactless conductivity detection. Samples containing potassium as the cation and both amoxicillin and clavulanate as anions were determined simultaneously in a single run (in less than 45 s) using 10 mmol L(-1) of both 2-amino-2-hydroxymethyl-propane-1,3-diol and 3-[{2-hydroxy-1,1-bis(hydroxymethyl)ethyl}amino]-1-propanesulfonic acid (pH 8.4) as the background electrolyte...
July 6, 2017: Journal of Separation Science
https://www.readbyqxmd.com/read/28681598/nucleophile-mediated-ring-expansion-of-5-acyl-substituted-4-mesyloxymethyl-1-2-3-4-tetrahydropyrimidin-2-ones-in-the-synthesis-of-7-membered-analogues-of-biginelli-compounds-and-related-heterocycles
#11
Anastasia A Fesenko, Mikhail S Grigoriev, Anatoly D Shutalev
A general six-step approach to alkyl 2-oxo-2,3,6,7-tetrahydro-1H-1,3-diazepine-5-carboxylates and 5-acyl-2,3,6,7-tetrahydro-1H-1,3-diazepin-2-ones based on the nucleophile-mediated ring expansion reaction of 5-functionalized 4-mesyloxymethyl-1,2,3,4-tetrahydropyrimidin-2-ones has been developed. Synthesis of the latter involved nucleophilic substitution of tosyl group in readily available N-[(2-benzoyloxy-1-tosyl)ethyl]urea with sodium enolates of β-oxoesters or 1,3-diketones, followed by dehydration or heterocyclization-dehydration of resulting products, removal of benzoyl protection, and conversion of hydroxymethyl group into mesyloxymethyl group...
July 18, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28678232/kinetic-differences-in-the-intercalation-of-linear-and-cyclic-penta-ethylene-oxide-s-into-graphite-oxide-leading-to-separation-by-topology
#12
Fabienne Barroso-Bujans, Angel Alegria
In the present study, the structural differences between linear and cyclic oligo(ethylene oxide)s are demonstrated to cause large kinetic differences in the intercalation of both topologies into the interlayer space of graphite oxide (GO). This study is performed with room-temperature liquid oligomers: penta(ethylene glycol), penta(ethylene glycol) dimethyl ether, 15-crown-5 and 2-hydroxymethyl-15-crown-5. Cyclic compounds exhibit 100 to 1000 times slower intercalation rates than the linear oligomers and exhibit induction periods of several hours prior to intercalation...
July 5, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28674342/hydroxymethylation-of-rutin-induced-by-radiolysis-as-novel-%C3%AE-glucosidase-inhibitors
#13
Gyeong Han Jeong, Tae Hoon Kim
Rutin, a major flavonoid glycoside found in many higher plants, was exposed at 25 kGy of γ-ray and produced three new hydroxymethylated products 2-4 in the C-ring by γ-irradiation. Structures of the new compounds, including absolute configurations, were elucidated based on spectroscopic interpretation (NMR, UV, [α]D, MS, and circular dichroism (CD)). The new unusual rutin derivatives 2 and 3 exhibited significantly enhanced inhibitory effects against α-glucosidase with IC50 values of 23.1±1.2 and 11...
2017: Chemical & Pharmaceutical Bulletin
https://www.readbyqxmd.com/read/28661123/mononuclear-lanthanide-complexes-energy-barrier-enhancement-by-ligand-substitution-in-field-induced-dy-iii-sims
#14
Sourav Biswas, Kochan S Bejoymohandas, Sourav Das, Pankaj Kalita, Mundalapudi L P Reddy, Itziar Oyarzabal, Enrique Colacio, Vadapalli Chandrasekhar
The sequential reaction of 2-((6-(hydroxymethyl)pyridin-2-yl)-methyleneamino)phenol (LH2), LnCl3·6H2O, and 1,1,1-trifluoroacetylacetone (Htfa) in the presence of Et3N afforded [Ln(LH) (tfa)2] [Ln = Dy(3+) (1), Ln = Tb(3+) (2), and Ln = Gd(3+) (3)], while under the same reaction conditions, but in the absence of the coligand, another series of mononuclear complexes, namely, [Ln(LH)2]·Cl·2MeOH] [Ln = Dy(3+) (4) and Tb(3+) (5)] are obtained. Single-crystal X-ray diffraction analysis revealed that the former set contains a mono-deprotonated [LH](-) and two tfa ligands, while the latter set comprises of two mono-deprotonated [LH](-) ligands that are nearly perpendicular to each other at an angle of 86...
July 17, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28649282/asymmetric-dna-methylation-of-cpg-dyads-is-a-feature-of-secondary-dmrs-associated-with-the-dlk1-gtl2-imprinting-cluster-in-mouse
#15
Megan Guntrum, Ekaterina Vlasova, Tamara L Davis
BACKGROUND: Differential DNA methylation plays a critical role in the regulation of imprinted genes. The differentially methylated state of the imprinting control region is inherited via the gametes at fertilization, and is stably maintained in somatic cells throughout development, influencing the expression of genes across the imprinting cluster. In contrast, DNA methylation patterns are more labile at secondary differentially methylated regions which are established at imprinted loci during post-implantation development...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28648900/tet-catalyzed-5-hydroxymethylation-precedes-hnf4a-promoter-choice-during-differentiation-of-bipotent-liver-progenitors
#16
Pierre-Benoit Ancey, Szilvia Ecsedi, Marie-Pierre Lambert, Fazlur Rahman Talukdar, Marie-Pierre Cros, Denise Glaise, Diana Maria Narvaez, Veronique Chauvet, Zdenko Herceg, Anne Corlu, Hector Hernandez-Vargas
Understanding the processes that govern liver progenitor cell differentiation has important implications for the design of strategies targeting chronic liver diseases, whereby regeneration of liver tissue is critical. Although DNA methylation (5mC) and hydroxymethylation (5hmC) are highly dynamic during early embryonic development, less is known about their roles at later stages of differentiation. Using an in vitro model of hepatocyte differentiation, we show here that 5hmC precedes the expression of promoter 1 (P1)-dependent isoforms of HNF4A, a master transcription factor of hepatocyte identity...
July 11, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28647531/a-rapid-mass-spectrometric-method-for-the-measurement-of-catalytic-activity-of-ten-eleven-translocation-enzymes
#17
Babu Sudhamalla, Debasis Dey, Megan Breski, Kabirul Islam
Enzymatic methylation at carbon five on cytosine (5mC) in DNA is a hallmark of mammalian epigenetic programming and is critical to gene regulation during early embryonic development. It has recently been shown that dynamic erasure of 5mC by three members of the ten-eleven translocation (TET) family plays a key role in cellular differentiation. TET enzymes belong to Fe (II)- and 2-ketoglutarate (2KG) dependent dioxygenases that successively oxidize 5mC to 5-hydroxymethyl cytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxycytosine (5CaC), thus providing a chemical basis for the removal of 5mC which once was thought to be a permanent mark in mammalian genome...
June 21, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28643168/self-aggregation-of-synthetic-zinc-methyl-20-substituted-3-hydroxymethyl-pyropheophorbides-as-models-of-bacteriochlorophyll-c
#18
Ayaka Wada, Hitoshi Tamiaki
Zinc 3-hydroxymethyl-13(1)-oxo-chlorins bearing a variety of primary alkyl groups at the 20-position were prepared as models of bacteriochlorophyll-c by chemical modification of naturally occurring chlorophyll-a. The synthetic chlorophyll-a derivatives self-aggregated in an aqueous Triton X-100 solution to afford large oligomers whose Soret and Qy bands were red-shifted and broadened, compared with the bands of their monomers in tetrahydrofuran. The oligomeric bands are similar to those of bacteriochlorophyll-c self-aggregates in chlorosomes, the main light-harvesting antennae of photosynthetic green bacteria...
June 22, 2017: Photosynthesis Research
https://www.readbyqxmd.com/read/28642635/virtual-screening-following-rational-drug-design-based-approach-for-introducing-new-anti-amyloid-beta-aggregation-agent
#19
Garshasb Rigi, Mohammad Vala Ashdar Nakhaei, Hoda Eidipour, Arshia Najimi, Fahimeh Tajik, Niloufar Taher, Kamran Yarahmadi
Amyloid β (Aβ) sheets aggregations is the main reason of Alzheimer disease. The interacting areas between monomers are residue number 38 to 42. Inhibition of interaction between Aβ molecules prevents plaque formation. In the present study, we have performed a high-throughput virtual screening among ZINC database and top 1000 hits were checked again regarding binding affinity by AutoDock software. Top 4 successive second step screening hits was considered for drug design purpose against aggregation site of Aβ molecules...
2017: Bioinformation
https://www.readbyqxmd.com/read/28642138/molecular-cloning-of-chicken-tet-family-genes-and-role-of-chicken-tet1-in-erythropoiesis
#20
Yuya Okuzaki, Hidenori Kaneoka, Ken-Ichi Nishijima, Seitaro Murakami, Yuki Ozawa, Shinji Iijima
Ten-eleven translocation (TET) methylcytosine dioxygenase has potential as an active eraser to regulate the genomic DNA methylation status. We herein cloned chicken TET (cTET) family genes, and confirmed their functions. Quantitative reverse-transcription PCR showed that cTET1 was strongly expressed in erythrocytes throughout development. This cTET1 expression pattern, together with the results of methylated or hydroxymethylated DNA immunoprecipitation, suggests that cTET1 contributes to demethylation around the promoter region of the definitive-type β-globin gene βΑ in erythroid cells...
June 19, 2017: Biochemical and Biophysical Research Communications
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