- Use of 13C as an indirect tag in 15N specifically labeled nucleosides. Syntheses of [8-13C-1,7,NH2-15N3]adenosine, -guanosine, and their deoxy analogues.
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We have previously reported the use of a 13C tag at the C2 of 15N-multilabeled purine nucleosides to distinguish the adjacent-labeled 15N atoms from those in an untagged nucleoside. We now introduce the use of an indirect tag at the C8 of 15N7-labeled purine nucleosides. This tag allows unambiguous differentiation between a pair of 15N7-labeled purines in which only one is 13C8 labeled. Although the very small C8-N7 coupling (200 Hz) because H8 is coupled to both N7 and C8. The 13C8 atom is introduced by means of a ring closure of the exocyclic amino groups of a pyrimidinone using [13C]sodium ethyl xanthate. Here, we present methods for the syntheses of [8-13C-1,7,NH2-15N3]adenosine, -guanosine, and their deoxy analogues.
- Shallop, Anthony J,Gaffney, Barbara L,Jones, Roger A
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Read Online
- Use of Nucleoside Phosphorylases for the Preparation of Purine and Pyrimidine 2′-Deoxynucleosides
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Enzymatic transglycosylation – the transfer of the carbohydrate moiety from one heterocyclic base to another – is being actively developed and applied for the synthesis of practically important nucleosides. This reaction is catalyzed by nucleoside phosphorylases (NPs), which are responsible for reversible phosphorolysis of nucleosides to yield the corresponding heterocyclic bases and monosaccharide 1-phosphates. We found that 7-methyl-2′-deoxyguanosine (7-Me-dGuo) is an efficient and novel donor of the 2-deoxyribose moiety in the enzymatic transglycosylation for the synthesis of purine and pyrimidine 2′-deoxyribonucleosides in excellent yields. Unlike 7-methylguanosine, its 2′-deoxy derivative is dramatically less stable. Fortunately, we have found that 7-methyl-2′-deoxyguanosine hydroiodide may be stored for 24 h in Tris-HCl buffer (pH 7.5) at room temperature without significant decomposition. In order to optimize the reagent ratio, a series of analytical transglycosylation reactions were conducted at ambient temperature. According to HPLC analysis of the transglycosylation reactions, the product 5-ethyl-2′-deoxyuridine (5-Et-dUrd) was obtained in high yield (84–93%) by using a small excess (1.5 and 2.0 equiv.) of 7-Me-dGuo over 5-ethyluracil (5-Et-Ura) and 0.5 equiv. of inorganic phosphate. Thymidine is a less effective precursor of α-d-2-deoxyribofuranose 1-phosphate (dRib-1p) compared to 7-Me-dGuo. We synthesized 2′-deoxyuridine, 5-Et-dUrd, 2′-deoxyadenosine and 2′-deoxyinosine on a semi-preparative scale using the optimized reagent ratio (1.5:1:0.5) in high yields. Unlike other transglycosylation reactions, the synthesis of 2-chloro-2′-deoxyadenosine was performed in a heterogeneous medium because of the poor solubility of the initial 2-chloro-6-aminopurine. Nevertheless, this nucleoside was prepared in good yield. The developed enzymatic procedure for the preparation of 2′-deoxynucleosides may compete with the known chemical approaches. (Figure presented.).
- Drenichev, Mikhail S.,Alexeev, Cyril S.,Kurochkin, Nikolay N.,Mikhailov, Sergey N.
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supporting information
p. 305 - 312
(2018/01/15)
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- Structural and biochemical characterization of the nucleoside hydrolase from C. elegans reveals the role of two active site cysteine residues in catalysis
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Nucleoside hydrolases (NHs) catalyze the hydrolysis of the N-glycoside bond in ribonucleosides and are found in all three domains of life. Although in parasitic protozoa a role in purine salvage has been well established, their precise function in bacteria and higher eukaryotes is still largely unknown. NHs have been classified into three homology groups based on the conservation of active site residues. While many structures are available of representatives of group I and II, structural information for group III NHs is lacking. Here, we report the first crystal structure of a purine-specific nucleoside hydrolase belonging to homology group III from the nematode Caenorhabditis elegans (CeNH) to 1.65? resolution. In contrast to dimeric purine-specific NHs from group II, CeNH is a homotetramer. A cysteine residue that characterizes group III NHs (Cys253) structurally aligns with the catalytic histidine and tryptophan residues of group I and group II enzymes, respectively. Moreover, a second cysteine (Cys42) points into the active site of CeNH. Substrate docking shows that both cysteine residues are appropriately positioned to interact with the purine ring. Site-directed mutagenesis and kinetic analysis proposes a catalytic role for both cysteines residues, with Cys253 playing the most prominent role in leaving group activation.
- Singh, Ranjan Kumar,Steyaert, Jan,Versées, Wim
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p. 985 - 996
(2017/05/01)
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- Production, characterization and synthetic application of a purine nucleoside phosphorylase from Aeromonas hydrophila
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Purine nucleoside phosphorylase (PNP) from Aeromonas hydrophila encoded by the deoD gene has been over-expressed in Escherichia coli, purified, characterized about its substrate specificity and used for the preparative synthesis of some 6-substituted purine-9-ribosides. Substrate specificity towards natural nucleosides showed that this PNP catalyzes the phosphorolysis of both 6-oxo- and 6-aminopurine (deoxy)ribonucleosides. A library of nucleoside analogues was synthesized and then submitted to enzymatic phosphorolysis as well. This assay revealed that 1-, 2-, 6- and 7-modified nucleosides are accepted as substrates, whereas 8-substituted nucleosides are not. A few transglycosylation reactions were carried out using 7-methylguanosine iodide (4) as a d-ribose donor and 6-substituted purines as acceptor. In particular, following this approach, 2- amino-6-chloropurine-9-riboside (2c), 6-methoxypurine- 9-riboside (2d) and 2-amino-6-(methylthio)purine- 9-riboside (2g) were synthesized in very high yield and purity.
- Ubiali, Daniela,Serra, Carla D.,Serra, Immacolata,Morelli, Carlo F.,Terreni, Marco,Albertini, Alessandra M.,Manitto, Paolo,Speranzab, Giovanna
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experimental part
p. 96 - 104
(2012/04/11)
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- HETEROCYCLIC GTP CYCLOHYDROLASE 1 INHIBITORS FOR THE TREATMENT OF PAIN
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The present invention relates to the field of small molecule heterocyclic inhibitors of GTP cyclohydrolase (GCH-I), or a tautomer, prodrug, or pharmaceutically acceptable salt thereof. The invention also features pharmaceutical compositions of the compounds and the medical use of these compounds for the treatment or prevention of pain (e.g., inflammatory pain, nociceptive pain, functional pain, or neuropathic pain).
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Page/Page column 48
(2011/04/19)
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- BODIPY-modified 2′-deoxyguanosine as a novel tool to detect DNA damages
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BODIPY-modified 2′-deoxyguanosine was synthesized for use as a detection reagent for genotoxic compounds. BODIPY-FL is a well known fluorescence reagent whose fluorescent light emission diminishes near a guanine base by a photo-induced electron transfer process. We attached BODIPY-Fl to the 5′ position of the deoxyribose moiety of 2′-deoxyguanosine. Although this compound has low fluorescence activity, when depurination by the action of alkylating reagents and dG oxidation by singlet oxygen occurred, the emission of strong fluorescence was observed. BODIPY-dG was found, therefore, to be a very useful tool for selectively detecting DNA damaging activity particularly in natural environmental extracts.
- Takamura-Enya, Takeji,Ishii, Ryoko
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body text
p. 4206 - 4209
(2011/08/10)
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- Kinetic properties of Cellulomonas sp. purine nucleoside phosphorylase with typical and non-typical substrates: Implications for the reaction mechanism
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Phosphorolysis catalyzed by Cellulomonas sp. PNP with typical nucleoside substrate, inosine (Ino), and non-typical 7-methylguanosine (m7Guo), with either nucleoside or phosphate (Pi) as the varied substrate, kinetics of the reverse synthetic reaction with guanine (Gua) and ribose-1-phosphate (R1P) as the varied substrates, and product inhibition patterns of synthetic and phosphorolytic reaction pathways were studied by steady-state kinetic methods. It is concluded that, like for mammalian trimeric PNP, complex kinetic characteristics observed for Cellulomonas enzyme results from simultaneous occurrence of three phenomena. These are sequential but random, not ordered binding of substrates, tight binding of me substrate purine bases, leading to the circumstances that for such substrates (products) rapid-equilibrium assumptions do not hold, and a dual role of Pi, a substrate, and also a reaction modifier that helps to release a tightly bound purine base. Copyright Taylor & Francis, Inc.
- Wielgus-Kutrowska, Beata,Bzowska, Agnieszka
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p. 471 - 476
(2008/02/01)
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- Spectroscopic and kinetic studies of interactions of calf spleen purine nucleoside phosphorylase with 8-azaguanine, and its 9-(2-phosphonylmethoxyethyl) derivative
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Spectroscopic and kinetic studies of interactions of calf spleen purine nucleoside phosphorylase with 8-azaguanine, an excellent fluorescent/fluorogenic substrate for the synthetic pathway of the reaction, and its 9-(2-phosphonylmethoxyethyl) derivative, a bisubstrate analogue inhibitor, were carried out. The goal was to clarify the catalytic mechanism of the enzymatic reaction by identification of ionic/tautomeric forms of these ligands in the complex with PNP. Copyright Taylor & Francis, Inc.
- Wierzchowski, Jacek,Stepniak, Katarzyna,Bzowska, Agnieszka,Shugar, David
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p. 459 - 464
(2008/02/02)
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- 2-Pivalamido-3H-pyrimidin-4-one derivatives: Convenient pivalamide hydrolysis using Fe(NO3)3 in MeOH
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A simple methodology for pivalamide (trimethylacetamide, pivaloylamino) hydrolysis has been discovered using Fe(NO3)3 in MeOH at room temperature. The pivalamido group of 2-pivalamido-3H-pyrimidin-4-ones or fused 2-pivalamido-3H-pyrimidin-4-ones such as 2-pivalamido-3H-quinazolin-4-ones and 2-pivalamido-3H-pteridines have been hydrolysed under these conditions to afford the corresponding amine.
- Bavetsias,Henderson,McDonald
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p. 5643 - 5644
(2007/10/03)
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- The Cu2+-promoted cleavage of mRNA 5'-cap analogs: A kinetic study with p1(7-methylguanosin-5'-yl) p3-(nucleosid-5'-yl) triphospates and p1- (7-methylguanosin-5'-yl) p4-(guanosin-5'-yl) tetraphosphate
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A kinetic study on the cleavage of a number of mRNA 5'-cap analogs, m7GpppN and m7GppppG, with Cu2+ aquo ion has been performed. Time- dependent product distributions at various pH and metal ion concentrations have been determined by capillary zone electrophoresis, and these data have been used to calculate the rate constants for various parallel reactions of the breakdown of the cap analogs.
- Wieczorek, Zbigniew,Darzynkiewicz, Edward,Kuusela, Satu,Loennberg, Harri
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- The mechanism of decomposition of N-methyl-N-nitrosourea (MNU) in water and a study of its reactions with 2'-deoxyguanosine, 2'-deoxyguanosine 5'-monophosphate and d(GTGCAC)
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The carcinogenicity of N-methyl-N-nitrosourea (MNU) arises, from its ability to methylate DNA, This occurs in an aqueous environment and therefore an appreciation of the mode of decomposition of MNU in water is essential to understanding the mechanism of DNA methylation and its base sequence dependence. The kinetics of MNU hydrolyses are shown to be first order in MNU with a steep rise in rate above pH 8. Using NMR for in situ monitoring of reaction intermediates and products from hydrolyses of [13CO]MNU, [15NH2]MNU and [13CH3]MNU, it is proved that base-induced hydrolysis of MNU is initiated by deprotonation at the carbamoyl group. The critical reactive species are shown to be the methyldiazonium ion (Me-N2+) and cyanate (NCO-). Investigations of reactions of [13CH3]MNU with 2'-deoxyguanosine (dGuo) and 2-deoxyguanosine 5'-monophosphate (dGuo-5P) showed that: a) the site of methylation of dGuo is highly pH-dependent (relatively more N-1 and O6-methylation compared to N-7 occurs at higher pH; b) the principal site of methylation of dGuo-5P by MNU is at phosphate; c) incorporation of deuterium into methyl groups occurs in D2O at higher pH. Methylation of the oligonucleotide d(GT[15N]GCAC) by MNU in D2O showed partial deuteriation of the N7-methyl groups of the guanines, whilst methylation by MNU in water indicated no significant preference for either guanine with respect to N7-methylation.
- Golding, Bernard T.,Bleasdale, Christine,McGinnis, Joseph,Mueller, Susanna,Rees, Hue Thu,Rees, Nicholas H.,Farmer, Peter B.,Watson, William P.
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p. 4063 - 4082
(2007/10/03)
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- The in vitro methylation of DNA by a minor groove binding methyl sulfonate ester
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The preparation of sequence and groove specific DNA methylating agents based on N-methylpyrrolecarboxamide subunits appended with an O-methyl sulfonate ester functionality (MeOSO2(CH2)2-Lex) has previously been described [Zhang, Y., Chen, F.-X., Mehta, P., and Gold, B. (1993) Biochemistry 32, 7954-7965]. In contrast to simple methyl sulfonate esters, e.g., methyl methanesulfonate (MMS), which predominantly methylate at 7- guanine, MeOSO2(CH2)2-Lex affords N3-methyladenine (3-MeAde) as its major adduct. Using competitive ELISA determinations, the methylation at major and minor groove sites in calf thymus DNA by MeOSO2(CH2)2-Lex has been precisely quantitated. The yields of N7-methylguanine (7-MeGua), 3-MeAde, and O6-methyldeoxyguanosine (6-Me-dGuo) are 0.424, 3.195, and 0.0027 mmol of adduct/mol of DNA, respectively, using 10 μM MeOSO2(CH2)2-Lex and 100 μM DNA. This compares to 0.773, 0.072, and 0.0033 mmol of adduct/mol of DNA for 7-MeGua, 3-MeAde, and 6-Me-dGuo, respectively, using MMS. The increase in the yield of 3-MeAde due to the minor groove equilibrium binding properties of MeOSO2(CH2)2-Lex is ~40-fold relative to MMS.
- Encell,Shuker,Foiles,Gold
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p. 563 - 567
(2007/10/03)
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- METHYLATION OF DEOXYNUCLEOTIDES WITH TRIMETHYL PHOSPHATE IN AQUEOUS PHASE.
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Action of trimethyl phosphate on thymidine 5 prime -phosphate, deoxycytidine 5 prime -phosphate, deoxyadenosine 5 prime -phosphate, and deoxyguanosine 5 prime -phosphate at 37-60 degree C, and pH 7-10 gave their methyl esters and base-methylated derivatives. Esterification took place in all deoxyribonucleotides to the almost same extent and its rate was enhanced by the reaction temperature, while being independent of pH in the range 7-10. On the other hand, methylation of the base moieties was affected by both the reaction temperature and pH of the reaction medium.
- Tanabe,Yamauchi,Kinoshita
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p. 1826 - 1831
(2007/10/02)
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- Methylation study of ribonucleosides, deoxyribonucleosides, and 2′-O-methylribonucleosides with trimethylsulphonium hydroxide and trimethylsulphonium iodide. Influence of the 2′-hydroxy-groups on the reactivity of the base moieties of ribonucleosides
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Methylations of the naturally occuring ribonucleoside (1), deoxyribonucleoside (2), and 2′-O-methylribonucleoside (3) were carried out using trimethylsulphonium hydroxide (Me3SOH) and trimethylsulphonium iodide (Me3Sl). The base moiety of (2) and (3) are more reactive than the corresponding base moiety of (1). The sites and extent of methylation of (2) are considerably different from those of (1), but are almost identical with those of (3). The reactivities of (1)-(3) are discussed in connection to an intramolecular interaction of the 2′-OH groups with the base moiety of (1). The methylating characteristics of Me 3SOH and Me3Sl are also described. The kinetics indicate an SN2 mechanism for methylation of nucleosides by Me 3S+ ions.
- Yamauchi, Kiyoshi,Nakagima, Toru,Kinoshita, Masayoshi
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p. 2787 - 2792
(2007/10/02)
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