28806-14-6Relevant articles and documents
Synthesis and stability of nucleoside 3a?2,5a?2-cyclic phosphate triesters masked with enzymatically and thermally labile phosphate protecting groups
Sontakke, Vyankat A.,Shinde, Vaishali S.,L??nnberg, Harri,Ora, Mikko
, p. 389 - 394 (2015)
Appropriately protected structurally modified nucleoside 3a?2,5a?2-cyclic monophosphates are known to show antiviral activity. For this reason, a straightforward synthesis of nucleoside 3a?2,5a?2-cyclic phosphates protected with three different enzymatically removable groups, viz. 3-acetyloxy-2,2-bis-(ethoxycarbonyl)propyl (in 1 and 4), 4-acetylthio-2,2-di-methyl-3-oxobutyl (in 2), and 4-(tert-butyldisulfanyl)-2,2-di-methyl-3-oxobutyl (in 3) groups, is described. Removal of these protecting groups at pH 7.5 and 37?°C was monitored by reverse-phase HPLC.
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Kossel,Neumann
, p. 2219 (1894)
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Ulbricht
, p. 225,230 (1959)
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Sources of 2,5-diaminoimidazolone lesions in DNA damage initiated by hydroxyl radical attack
Thomas, Caroline Suzanne,Pollard, Hannah Catherine,Razskazovskiy, Yuriy,Roginskaya, Marina
, p. 517 - 524 (2020)
The present study reports radiation-chemical yields of 2.5-diaminoimidazolone (Iz) derivatives in X-irradiated phosphate-buffered solutions of guanosine and double-stranded DNA. Various gassing conditions (air, N20/O2 (4:1), N2O, vacuum) were employed to elucidate the contribution of several alternative pathways leading to Iz in reactions initiated by hydroxyl radical attack on guanine. In all systems, Iz was identified as the second by abundance guanine degradation product after 8-oxoguanine, formed in 1:5 (guanosine) and 1:3.3 (DNA) ratio to the latter in air-saturated solutions. Experimental data strongly suggest that the addition of molecular oxygen to the neutral guanine radical G(-H)? plays a major in Iz production in oxygenated solutions of double-stranded DNA while in other systems it may compete with recombination of G(-H)? with superoxide and/or alkyl peroxyl radicals. The production of Iz through hydroxyl radical attack on 8-oxoguanine was also shown to take place although the chemical yield of Iz (ca 6%) in this process is too low to compete with the other pathways. The linearity of Iz accumulation with dose also indicates a negligible contribution of this channel to its yield in all systems.
The kinetic mechanism of Human Thymidine Phosphorylase-a molecular target for cancer drug development
Deves, Candida,Rostirolla, Diana Carolina,Martinelli, Leonardo Kras Borges,Bizarro, Cristiano Valim,Santos, Diogenes Santiago,Basso, Luiz Augusto
, p. 592 - 604 (2014)
Human Thymidine Phosphorylase (HTP), also known as the platelet-derived endothelial cell growth factor (PD-ECGF) or gliostatin, catalyzes the reversible phosphorolysis of thymidine (dThd) to thymine and 2-deoxy-α-d-ribose-1- phosphate (2dR1P). HTP is a key enzyme in the pyrimidine salvage pathway involved in dThd homeostasis in cells. HTP is a target for anticancer drug development as its enzymatic activity promotes angiogenesis. Here, we describe cloning, expression, and purification to homogeneity of recombinant TYMP-encoded HTP. Peptide fingerprinting and the molecular mass value of the homogenous protein confirmed its identity as HTP assessed by mass spectrometry. Size exclusion chromatography showed that HTP is a dimer in solution. Kinetic studies revealed that HTP displayed substrate inhibition for dThd. Initial velocity and isothermal titration calorimetry (ITC) studies suggest that HTP catalysis follows a rapid-equilibrium random bi-bi kinetic mechanism. ITC measurements also showed that dThd and Pi binding are favorable processes. The pH-rate profiles indicated that maximal enzyme activity was achieved at low pH values. Functional groups with apparent pK values of 5.2 and 9.0 are involved in dThd binding and groups with pK values of 6.1 and 7.8 are involved in phosphate binding.
Mass spectrometry and theoretical studies on N-C bond cleavages in the N-sulfonylamidino thymine derivatives
Kobeti?, Renata,Kazazi?, Snje?ana,Kova?evi?, Borislav,Glasovac, Zoran,Krstulovi?, Luka,Baji?, Miroslav,?ini?, Biserka
, p. 833 - 842 (2015)
Abstract The reactivity of new biologically active thymine derivatives substituted with 2-(arylsulfonamidino)ethyl group at N1 and N3 position was investigated in the gas phase using CID experiments (ESI-MS/MS) and by density functional theory (DFT) calculations. Both derivatives show similar chemistry in the negative mode with a retro-Michael addition (Path A-) being the most abundant reaction channel, which correlate well with the fluoride induced retro-Michael addition observed in solution. The difference in the fragmentation of N-3 substituted thymine 5 and N-1 substituted thymine 1 in the positive mode relates to the preferred cleavage of the sulfonyl group (m/z 155, Path B) in N-3 isomer and the formation of the acryl sulfonamidine 3 (m/z 309) via Path A in N-1 isomer. Mechanistic studies of the cleavage reaction conducted by DFT calculations give the trend of the calculated activation energies that agree well with the experimental observations. A mechanism of the retro-Michael reaction was interpreted as a McLafferty type of fragmentation, which includes Hβ proton shift to one of the neighboring oxygen atoms in a 1,5-fashion inducing N1(N3)-Cα bond scission. This mechanism was found to be kinetically favorable over other tested mechanisms. Significant difference in the observed fragmentation pattern of N-1 and N-3 isomers proves the ESI-MS/MS technique as an excellent method for tracking the fate of similar sulfonamidine drugs. Also, the observed N-1 and/or N-3 thymine alkylation with in situ formed reactive acryl sulfonamidine 3 as a Michael acceptor may open interesting possibilities for the preparation of other N-3 substituted pyrimidines.
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Sevilla et al.
, p. 3577,3579 (1972)
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Disposition of [1′-14C]stavudine after oral administration to humans
Zhou, Lian,Kaul, Sanjeev,Liu-Kreyche, Peggy,Tran, Scott B.,Espina, Robert R.,Warrack, Bethanne M.,Roongta, Vikram A.,Iyer, Ramaswamy A.
, p. 655 - 666 (2010)
The disposition of stavudine, a potent and orally active nucleoside reverse transcriptase inhibitor, was investigated in six healthy human subjects. Before dosing humans with [1′-14C]stavudine, a tissue distribution study was performed in Long-Evans rats. Results from this study showed no accumulation of radioactivity in any of the tissues studied, indicating that the position of the 14Clabel on the molecule was appropriate for the human study. After a single 80-mg (100 μCi) oral dose of [1′- 14C]stavudine, approximately 95% of the radioactive dose was excreted in urine with an elimination half-life of 2.35 h. Fecal excretion was limited, accounting for only 3% of the dose. Unchanged stavudine was the major drug-related component in plasma (61% of area under the plasma concentration-time curve from time zero extrapolated to infinite time of the total plasma radioactivity) and urine (67% of dose). The remaining radioactivity was associated with minor metabolites, including mono- and bis-oxidized stavudine, glucuronide conjugates of stavudine and its oxidized metabolite, and an N-acetylcysteine (NAC) conjugate of the ribose (M4) after glycosidic cleavage. Formation of metabolite M4 was shown in human liver microsomes incubated with 2′,3′-didehydrodideoxyribose, the sugar base of stavudine, in the presence of NAC. In addition, after similar microsomal incubations fortified with GSH, two GSH conjugates, 3′-GS-deoxyribose and 1′-keto-2′,3′-dideoxy-3′-GS-ribose, were observed. This suggests that 2′,3′-didehydrodideoxyribose underwent cytochrome P450-mediated oxidation leading to an epoxide intermediate, 2′,3′- ribose epoxide, followed by GSH addition. In conclusion, absorption and elimination of stavudine were rapid and complete after oral dosing, with urinary excretion of unchanged drug as the predominant route of elimination in humans. Copyright
Selective hydrolysis of nucleotides to nucleosides and free bases
Chmielowiec, Urszula,Kruszewska, Hanna,Cybulski, Jacek
, p. 611 - 614 (1999)
The kinetics of the hydrolysis of 2'-deoxyadenosine-5'-monophosphoric acid (dAMP), 2'-deoxycytidine-5'-monophosphoric acid (dCMP), 2'-deoxyguanosine-5'-monophosphoric acid (dGMP) and tymidine-5'-monophosphoric acid (dTMP) was studied in the presence of Xanthomonas maltophilia [1]. The reaction products are nucleosides: 2'-deoxyadenosine (dA), 2'-deoxycytidine (dC), 2'-deoxyguanosine (dG) and tymidine (dT), respectively, or the respective free bases. Hydrolysis of dTMP and dGMP proceeded stepwise according to the sequence: nucleotide→nucleoside→free base, whereas no accumulation of the free base was observed during the hydrolysis of dAMP and dCMP. Copyright (C) 1999 Elsevier Science S.A.
N2-amination of guanine to 2-hydrazinohypoxanthine, a novel in vivo nucleic acid modification produced by the hepatocarcinogen 2-nitropropane
Sodum, Rama S.,Fiala, Emerich S.
, p. 1453 - 1459 (1998)
2-Nitropropane, an industrial chemical and a hepatocarcinogen in rats, induces aryl sulfotransferase-mediated liver DNA and RNA base modifications [Sodum, R. S., Sohn, O. S., Nie, G., and Fiala, E. S. (1994) Chem. Res. Toxicol. 7, 344-351]. Two of these modifications were previously identified as 8-aminoguanine and 8-oxoguanine. We now report that the base moiety of the so far unidentified third nucleic acid modification, namely RX1 in RNA and DX1 in DNA, is 2-hydrazinohypoxanthine (N2-aminoguanine). 2-Hydrazinoinosine and 2-hydrazinodeoxyinosine, synthesized by adapting published procedures, cochromatographed with RX1 and DX1 of liver RNA and DNA, respectively, from 2-nitropropane-treated rats. 2-Hydrazinoinosine and 2-hydrazinodeoxyinosine are unstable in solution like the in vivo products RX1 and DX1. At neutral pH, hypoxanthine nucleoside is the major product of decomposition, while at pH 10 or above, xanthine nucleoside is also formed. RX1 and DX1 could be generated in the anaerobic reactions of hydroxylamine-O-sulfonic acid, an intermediate in the proposed activation pathway of 2-nitropropane, with guanine nucleosides. These results provide further evidence for the activation of 2-nitropropane and other carcinogenic secondary nitroalkanes to a reactive species capable of aminating nucleic acids and proteins.
Lipase catalyzed diastereoselective deacetylations of anomeric mixtures of peracetylated 2'-deoxynucleosides
Damkjaer,Petersen,Wengel
, p. 1801 - 1807 (1994)
Lipase catalyzed deacetylations of anomeric mixtures of peracetylated 2'- deoxyribofuranosyl- and 2'-deoxyribopyranosyl thymine nucleosides 1 and 5 have been investigated. Generally, the diastereoselectivity was more pronounced in pure phosphate buffer than in phosphate buffer containing 10% DMF. Wheat Germ Lipase and Porcine Liver Esterase catalyzed diastereoselective deacetylation of 1 affording the pure β-anomer thymidine (4β) as the only completely deprotected nucleoside product.
Kinetics and mechanism of the oxidation of sugars and nucleotides by oxoruthenium(IV): Model studies for predicting cleavage patterns in polymeric DNA and RNA
Neyhart,Cheng,Thorp
, p. 1463 - 1471 (1995)
Kinetic parameters for the oxidation of D-ribose, 2-deoxy-D-ribose, adenosine 5'-monophosphate (AMP), adenosine 5'-diphosphate (ADP), 2'-deoxyadenosine 5'-monophosphate (dAMP), cytidine 5'-monophosphate (CMP), 2'-deoxycytidine 5'-monophosphate (dCMP), and thymidine 5'-monophosphate (TMP) by Ru(tpy)(bpy)O2+ were determined in pH 7 phosphate buffer (tpy = 2,2',2''-terpyridine, bpy = 2,2'-bipyridine). Plots of k(obs) vs [substrate] were linear for the oxidation of ribose, 2-deoxyribose, TMP, and dCMP, yielding second-order rate constants of 0.029, 0.082, 0.38, and 0.46 M-1 s-1, respectively. From the temperature dependence of the rate constant, activation parameters consistent with the oxidation of other organic molecules by hydride transfer were found. For GMP, AMP, and dAMP, k(obs) vs [substrate] plots were curved due to electrostatic binding of Ru(tpy)(bpy)O2+ to the dianionic nucleotides, and the data were treated using double-reciprocal plots, yielding effective second-order rate constants of 0.10, 0.39, and 2.5 M-1 s-1, respectively. Product analysis by HPLC shows that a quantitative yield of free cytosine is obtained upon oxidation of dCMP based on nucleotide consumed. In TMP oxidations, an 80% yield of free thymine is observed based on Ru(tpy)(bpy)O2+ consumed. The kinetics and product analyses are consistent with sugar oxidation at the 1' position, and the increased reactivity of DNA compared to RNA can be understood on the basis of deactivation of the sugar oxidation product by the polar effect of the 2'-hydroxyl. The oxidation of the guanine base in GMP by Ru(tpy)(bpy)O2+ proceeds via an oxo transfer mechanism where the initial step is formation of a bound Ru(III)OR2+ intermediate. The ratio of the rate-determining rate constant for oxidation of guanine nucleotides to the average rate constant of sugar oxidation predicts the relative yields of base and sugar oxidation on sequencing gels.
Acyl Migration in the Production of Thymine Propenal from 3'-O-Benzoyl-5'-deoxy-4'-hydroperoxythymidine: A Reinterpretation of a Putative Model for Bleomycin-Mediated DNA Degradation
McGall, Glenn H.,Stubbe, JoAnne,Kozarich, John W.
, p. 48 - 55 (1991)
Studies of Saito et al. (Saito, I.; Morii, T.; Matsuura, T.J.Org.Chem. 1987, 52, 1008) analyzing the decomposition of 3'-O-benzoyl-5'-deoxy-4'-hydroperoxythymidine (7) claimed to model the decomposition of the putative 4'-hydroxyperoxynucleotide intermediate in the bleomycin (BLM) mediated production of base propenal, 3'-phosphoglycolate, and 5'-phosphate termini from double-stranded DNA.A number of puzzling observations reported in this paper prompted a reinvestigation of this model system in detail. 18O2>-7 and its 4'-epimer 8 were prepared and their fate in aqueous solution as a function of pH was examined.Compound 7 decompos ed in aqueous solution to produce thymine propenal accompanied by stoichiometric formation of benzoate containing 1 atom of 18O.In addition, thymine accompanied by stoichiometric amounts of malondialdehyde and 18O>benzoate was also observed.Acetate containing 1 atom of 18O accompanied production of both thymine and thymine propenal.The ratio of thymine propenal to thymine varied as a function of pH and temperature.Production of 18O>benzoate and a detailed kinetic analysis of the decomposition of 7 unequivocally demonstrated that conversion of 7 to thymine propenal required the intermediacy of a 4'-perbenzoate ester.This perester produced by migration of the 3'-benzoyl blocking group of 7 to the terminal oxygen of its 4'-hydroperoxy moiety would then greatly facilitate heterolytic cleavage of the oxygen-oxygen bond.For stereochemical reasons a similar intramolecular benzoyl migration cannot occur with 8, explaining its lack of reactivity.These results call into question the relevance of the Model proposed by Saito et al. to understanding the base propenal pathway in the BLM-catalyzed degradation of DNA.In addition, preparation of a second model of a putative intermediate in the base propenal pathway, oxy>-3-oxopropyl>thymine (12) is reported.The detailed kinetics of its decomposition as well as identification of the products accompanying ist decomposition are reported.The relevance of these two model systems to the mechanism of degradation of DNA by BLM is discussed.
The photochemistry of thymine in frozen aqueous solution: Trimeric and minor dimeric products
Shetlar, Martin D.,Basus, Vladimir J.
, p. 631 - 639 (2013)
Early work identified three compounds, namely the c,s cyclobutane dimer, the so-called (6-4) photoproduct (5-hydroxy-6-4′-(5-methylpyrimidin- 2′-one)-5,6-dihydrothymine) and a trimer hydrate, as products formed upon UV irradiation of thymine in frozen aqueous solution. More recent work has shown that an (α-4) product, namely α-4′-(5′- methylpyrimidine-2′-one)-thymine, is a likely product formed under these reaction conditions. During a thorough reinvestigation of the photochemistry of Thy in ice at -78.5°C, we found that a variety of other products could be detected. In addition to the c,s dimer, the other three known cyclobutane dimers, namely the c,a, t,s and t,a forms, are produced, although in considerably smaller amounts. The so-called spore product of thymine (5,6-dihydro-5-(α-thyminyl)thymine) is likewise formed. Two other dimers have been identified as minor products; one of these has been determined to be 5-(thymin-3-yl)-5,6-dihydrothymine and the other has been tentatively assigned to be a (5-4) adduct (6-hydroxy-5-4′-(5-methylpyrimidin-2′-one)-5,6- dihydrothymine). Compounds with the behavior expected of true trimeric compounds have been isolated via HPLC and characterized by mass spectrometry and photochemical behavior. One of these materials, putatively containing an oxetane ring, decomposes thermally to a secondary trimeric product that is then converted into the known trimer hydrate.
Solid-phase synthesis and structural characterisation of phosphoroselenolate-modified DNA: A backbone analogue which does not impose conformational bias and facilitates SAD X-ray crystallography
Conlon, Patrick F.,Eguaogie, Olga,Wilson, Jordan J.,Sweet, Jamie S. T.,Steinhoegl, Julian,Englert, Klaudia,Hancox, Oliver G. A.,Law, Christopher J.,Allman, Sarah A.,Tucker, James H. R.,Hall, James P.,Vyle, Joseph S.
, p. 10948 - 10957 (2019)
Oligodeoxynucleotides incorporating internucleotide phosphoroselenolate linkages have been prepared under solid-phase synthesis conditions using dimer phosphoramidites. These dimers were constructed following the high yielding Michaelis-Arbuzov (M-A) reaction of nucleoside H-phosphonate derivatives with 5′-deoxythymidine-5′-selenocyanate and subsequent phosphitylation. Efficient coupling of the dimer phosphoramidites to solid-supported substrates was observed under both manual and automated conditions and required only minor modifications to the standard DNA synthesis cycle. In a further demonstration of the utility of M-A chemistry, the support-bound selenonucleoside was reacted with an H-phosphonate and then chain extended using phosphoramidite chemistry. Following initial unmasking of methyl-protected phosphoroselenolate diesters, pure oligodeoxynucleotides were isolated using standard deprotection and purification procedures and subsequently characterised by mass spectrometry and circular dichroism. The CD spectra of both modified and native duplexes derived from self-complementary sequences with A-form, B-form or mixed conformational preferences were essentially superimposable. These sequences were also used to study the effect of the modification upon duplex stability which showed context-dependent destabilisation (-0.4 to-3.1 °C per phosphoroselenolate) when introduced at the 5′-Termini of A-form or mixed duplexes or at juxtaposed central loci within a B-form duplex (-1.0 °C per modification). As found with other nucleic acids incorporating selenium, expeditious crystallisation of a modified decanucleotide A-form duplex was observed and the structure solved to a resolution of 1.45 ?. The DNA structure adjacent to the modification was not significantly perturbed. The phosphoroselenolate linkage was found to impart resistance to nuclease activity.
Anion exchange resins in phosphate form as versatile carriers for the reactions catalyzed by nucleoside phosphorylases
Artsemyeva, Julia N.,Buravskaya, Tatiana N.,Esipov, Roman S.,Konstantinova, Irina D.,Litvinko, Natalia M.,Mikhailopulo, Igor A.,Miroshnikov, Anatoly I.,Remeeva, Ekaterina A.
, p. 2607 - 2622 (2020/11/26)
In the present work, we suggested anion exchange resins in the phosphate form as a source of phosphate, one of the substrates of the phosphorolysis of uridine, thymidine, and 1-(β-D-arabinofuranosyl)uracil (Ara-U) catalyzed by recombinant E. coli uridine (UP) and thymidine (TP) phosphorylases. α-D-Pentofuranose-1-phosphates (PF-1Pis) obtained by phosphorolysis were used in the enzymatic synthesis of nucleosides. It was found that phosphorolysis of uridine, thymidine, and Ara-U in the presence of Dowex 1X8 (phosphate; Dowex-nPi) proceeded smoothly in the presence of magnesium cations in water at 20-50 °C for 54-96 h giving rise to quantitative formation of the corresponding pyrimidine bases and PF-1Pis. The resulting PF-1Pis can be used in three routes: (1) preparation of barium salts of PF-1Pis, (2) synthesis of nucleosides by reacting the crude PF-1Pi with an heterocyclic base, and (3) synthesis of nucleosides by reacting the ionically bound PF-1Pi to the resin with an heterocyclic base. These three approaches were tested in the synthesis of nelarabine, kinetin riboside, and cladribine with good to excellent yields (52-93%).
Thermodynamic Reaction Control of Nucleoside Phosphorolysis
Kaspar, Felix,Giessmann, Robert T.,Neubauer, Peter,Wagner, Anke,Gimpel, Matthias
supporting information, p. 867 - 876 (2020/01/24)
Nucleoside analogs represent a class of important drugs for cancer and antiviral treatments. Nucleoside phosphorylases (NPases) catalyze the phosphorolysis of nucleosides and are widely employed for the synthesis of pentose-1-phosphates and nucleoside analogs, which are difficult to access via conventional synthetic methods. However, for the vast majority of nucleosides, it has been observed that either no or incomplete conversion of the starting materials is achieved in NPase-catalyzed reactions. For some substrates, it has been shown that these reactions are reversible equilibrium reactions that adhere to the law of mass action. In this contribution, we broadly demonstrate that nucleoside phosphorolysis is a thermodynamically controlled endothermic reaction that proceeds to a reaction equilibrium dictated by the substrate-specific equilibrium constant of phosphorolysis, irrespective of the type or amount of NPase used, as shown by several examples. Furthermore, we explored the temperature-dependency of nucleoside phosphorolysis equilibrium states and provide the apparent transformed reaction enthalpy and apparent transformed reaction entropy for 24 nucleosides, confirming that these conversions are thermodynamically controlled endothermic reactions. This data allows calculation of the Gibbs free energy and, consequently, the equilibrium constant of phosphorolysis at any given reaction temperature. Overall, our investigations revealed that pyrimidine nucleosides are generally more susceptible to phosphorolysis than purine nucleosides. The data disclosed in this work allow the accurate prediction of phosphorolysis or transglycosylation yields for a range of pyrimidine and purine nucleosides and thus serve to empower further research in the field of nucleoside biocatalysis. (Figure presented.).
