452-51-7Relevant academic research and scientific papers
Prebiotic phosphorylation of 2-thiouridine provides either nucleotides or DNA building blocks via photoreduction
Xu, Jianfeng,Green, Nicholas J.,Gibard, Clémentine,Krishnamurthy, Ramanarayanan,Sutherland, John D.
, p. 457 - 462 (2019/04/08)
Breakthroughs in the study of the origin of life have demonstrated how some of the building blocks essential to biology could have been formed under various primordial scenarios, and could therefore have contributed to the chemical evolution of life. Missing building blocks are then sometimes inferred to be products of primitive biosynthesis, which can stretch the limits of plausibility. Here, we demonstrate the synthesis of 2′-deoxy-2-thiouridine, and subsequently 2′-deoxyadenosine and 2-deoxyribose, under prebiotic conditions. 2′-Deoxy-2-thiouridine is produced by photoreduction of 2,2′-anhydro-2-thiouridine, which is in turn formed by phosphorylation of 2-thiouridine—an intermediate of prebiotic RNA synthesis. 2′-Deoxy-2-thiouridine is an effective deoxyribosylating agent and may have functioned as such in either abiotic or proto-enzyme-catalysed pathways to DNA, as demonstrated by its conversion to 2′-deoxyadenosine by reaction with adenine, and 2-deoxyribose by hydrolysis. An alternative prebiotic phosphorylation of 2-thiouridine leads to the formation of its 5′-phosphate, showing that hypotheses in which 2-thiouridine was a key component of early RNA sequences are within the bounds of synthetic credibility.
Enzymatic synthesis of ribo- and 2′-deoxyribonucleosides from glycofuranosyl phosphates: An approach to facilitate isotopic labeling
Zhang, Wenhui,Turney, Toby,Surjancev, Ivana,Serianni, Anthony S.
, p. 125 - 133 (2017/08/08)
Milligram quantities of α-D-ribofuranosyl 1-phosphate (sodium salt) (αR1P) were prepared by the phosphorolysis of inosine, catalyzed by purine nucleoside phosphorylase (PNPase). The αR1P was isolated by chromatography in >95% purity and characterized by 1H and 13C NMR spectroscopy. Aqueous solutions of αR1P were stable at pH 6.4 and 4 °C for several months. The isolated αR1P was N-glycosylated with different nitrogen bases (adenine, guanine and uracil) using PNPase or uridine phosphorylase (UPase) to give the corresponding ribonucleosides in high yield based on the glycosyl phosphate. This methodology is attractive for the preparation of stable isotopically labeled ribo- and 2′-deoxyribonucleosides because of the ease of product purification and convenient use and recycling of nitrogen bases. The approach eliminates the need for separate reactions to prepare individual furanose-labeled ribonucleosides, since only one ribonucleoside (inosine) needs to be labeled, if desired, in the furanose ring, the latter achieved by a high-yield chemical N-glycosylation. 2′-Deoxyribonucleosides were prepared from 2′-deoxyinosine using the same methodology with minor modifications.
A 2-deoxy-D-ribose preparation method
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Paragraph 0067; 0076; 0077, (2019/02/02)
The invention discloses a preparation method of 2-deoxidation-D-ribose. The method comprises the following steps: (1) carrying out a Reformasky reaction on D-glyceraldehyde acetonide and ethyl bromoacetate at an inert atmosphere and under a catalytic action of active zinc powder so as to obtain a compound shown in the formula I; (2) carrying out a substitution reaction on the compound shown in the formula I and an organic silicon protecting agent in the presence of an alkali so as to obtain a compound shown in the formula II; (3) carrying out a reduction reaction on the compound shown in the formula II under the condition of a reducing agent so as to obtain a compound shown in the formula III; (4) carrying out an oxidation reaction on the compound shown in the formula III under the condition of an oxidizing agent so as to obtain a compound shown in the formula IV; (5) carrying out deprotection on the compound shown in the formula IV in the presence of an acid and then carrying out a cyclization reaction so as to obtain the 2-deoxidation-D-ribose. According to the method, the Reformasky reaction is adopted, so that the selectivity is good; the high-yield compound shown in the formula I is obtained. The method is convenient to operate, low in raw material cost and easy to industrialize.
Transition state analysis of thymidine hydrolysis by human thymidine phosphorylase
Schwartz, Phillip A.,Vetticatt, Mathew J.,Schramm, Vern L.
supporting information; experimental part, p. 13425 - 13433 (2010/12/19)
Human thymidine phosphorylase (hTP) is responsible for thymidine (dT) homeostasis, and its action promotes angiogenesis. In the absence of phosphate, hTP catalyzes a slow hydrolytic depyrimidination of dT yielding thymine and 2-deoxyribose (dRib). Its transition state was characterized using multiple kinetic isotope effect (KIE) measurements. Isotopically enriched thymidines were synthesized enzymatically from glucose or (deoxy)ribose, and intrinsic KIEs were used to interpret the transition state structure. KIEs from [1′- 14C]-, [1-15N]-, [1′-3H]-, [2′R-3H]-, [2′S-3H]-, [4′- 3H]-, and [5′-3H]dTs provided values of 1.033 ± 0.002, 1.004 ± 0.002, 1.325 ± 0.003, 1.101 ± 0.004, 1.087 ± 0.005, 1.040 ± 0.003, and 1.033 ± 0.003, respectively. Transition state analysis revealed a stepwise mechanism with a 2-deoxyribocation formed early and a higher energetic barrier for nucleophilic attack of a water molecule on the high energy intermediate. An equilibrium exists between the deoxyribocation and reactants prior to the irreversible nucleophilic attack by water. The results establish activation of the thymine leaving group without requirement for phosphate. A transition state constrained to match the intrinsic KIEs was found using density functional theory. An active site histidine (His116) is implicated as the catalytic base for activation of the water nucleophile at the rate-limiting transition state. The distance between the water nucleophile and the anomeric carbon (rC-O) is predicted to be 2.3 A at the transition state. The transition state model predicts that deoxyribose adopts a mild 3′-endo conformation during nucleophilic capture. These results differ from the concerted bimolecular mechanism reported for the arsenolytic reaction (Birck, M. R.; Schramm, V. L. J. Am. Chem. Soc. 2004, 126, 2447-2453).
A new synthetic strategy for 2-deoxy-D-ribose via palladium(II)-catalyzed cyclization of aldehyde
Miyazawa, Masahiro,Awasaguchi, Ken-Ichiro,Uoya, Ikuyo,Yokoyama, Hajime,Hirai, Yoshiro
, p. 1891 - 1902 (2011/04/12)
We achieved a total synthesis of 2-deoxy-D-ribose through intramolecular Pd(II)-catalyzed cyclization of aldehyde via an unstable hemiacetal intermediate as a key step. The Japan Institute of Heterocyclic Chemistry.
α,β-Methylene-2′-deoxynucleoside 5′-triphosphates as noncleavable substrates for DNA polymerases: Isolation, characterization, and stability studies of novel 2′-deoxycyclonucleosides, 3,5′-cyclo-dG, and 2,5′-cyclo-dT
Liang, Fengting,Jain, Nidhi,Hutchens, Troy,Shock, David D.,Beard, William A.,Wilson, Samuel H.,Chiarelli, M. Paul,Cho, Bongsup P.
experimental part, p. 6460 - 6470 (2009/10/23)
We report synthesis and characterization of a complete set of α,β-methylene-2′-dNTPs (α,β-m-dNTP; N = A, C, T, G, 12-15) in which the α,β-oxygen linkage of natural dNTP was replaced by a methylene group. These nucleotides were designed to be noncleavable substrates for DNA polymerases. Synthesis entails preparation of 2′-deoxynucleoside 5′-diphosphate precursors, followed by an enzymatic γ-phosphorylation. All four synthesized α,β-m-dNTPs were found to be potent inhibitors of polymerase β, with Ki values ranging 1-5 μM. During preparation of the dG and dT derivatives of α,β-methylene diphosphate, we also isolated significant amounts of 3,5′-cyclo-dG (16) and 2,5′-cyclo-dT (17), respectively. These novel 2′-deoxycyclonucleosides were formed via a base-catalyzed intramolecular cyclization (N3 → C5′ and O2 → C5′, respectively). In acidic solution, both 16 and 17 underwent glycolysis, followed by complete depurination. When exposed to alkaline conditions, 16 underwent an oxidative deamination to produce 3,5′-cyclo-2′-deoxyxanthosine (19), whereas 17 was hydrolyzed exclusively to dT.
Efficient production of 2-deoxyribose 5-phosphate from glucose and acetaldehyde by coupling of the alcoholic fermentation system of baker's yeast and deoxyriboaldolase-expressing Escherichia coli
Horinouchi, Nobuyuki,Ogawa, Jun,Kawano, Takako,Sakai, Takafumi,Saito, Kyota,Matsumoto, Seiichiro,Sasaki, Mie,Mikami, Yoichi,Shimizu, Sakayu
, p. 1371 - 1378 (2008/02/11)
2-Deoxyribose 5-phosphate production through coupling of the alcoholic fermentation system of baker's yeast and deoxyriboaldolase-expressing Escherichia coli was investigated. In this process, baker's yeast generates fructose 1,6-diphosphate from glucose and inorganic phosphate, and then the E. coli convert the fructose 1,6-diphosphate into 2-deoxyribose 5-phosphate via D-glyceraldehyde 3-phosphate. Under the optimized conditions with toluene-treated yeast cells, 356 mM (121 g/l) fructose 1,6-diphosphate was produced from 1,111 mM glucose and 750 mM potassium phosphate buffer (pH 6.4) with a catalytic amount of AMP, and the reaction supernatant containing the fructose 1,6-diphosphate was used directly as substrate for 2-deoxyribose 5-phosphate production with the E. coli cells. With 178 mM enzymatically prepared fructose 1,6-diphosphate and 400 mM acetaldehyde as substrates, 246 mM (52.6 g/l) 2-deoxyribose 5-phosphate was produced. The molar yield of 2-deoxyribose 5-phosphate as to glucose through the total two step reaction was 22.1%. The 2-deoxyribose 5-phosphate produced was converted to 2-deoxyribose with a molar yield of 85% through endogenous or exogenous phosphatase activity.
Azacytosine analogs and derivatives
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Page/Page column 4; sheet 3, (2008/06/13)
Compounds and compositions of azacytosine analogs and derivatives are provided. In one aspect of the invention, analogs or derivatives of decitabine and azacitidine are provided with modification at the 4- and 6-position of the triazine ring, at the 1′-6′position of the ribose ring, or combinations thereof. Methods of synthesizing and manufacturing these analogs and derivatives are also provided. These compounds can be formulated into pharmaceutical compositions that can be used for treating any disease that is sensitive to the treatment with decitabine or azacitidine, such as hematological disorders and cancer.
Glycosidic Bond Cleavage of Thymidine by Low-Energy Electrons
Zheng, Yi,Cloutier, Pierre,Hunting, Darel J.,Wagner, J. Richard,Sanche, Leon
, p. 1002 - 1003 (2007/10/03)
Thymidine was exposed to low-energy electrons (LEE) as a thin solid film under a high vacuum. Nonvolatile radiation products, remaining on the irradiated surface, were analyzed by HPLC/UV and GC/MS. Here, we show that exposure of thymidine to 3-100 eV electrons gives thymine as a major product with a yield of 3.2 × 10-2 per electron (about one-third of the total decomposition of thymidine). The formation of thymine indicates that LEE induces cleavage of the glycosidic bond separating the base and sugar moieties, suggesting a nonionizing resonant process involving dissociative attachment (a new mechanism of DNA damage involving the interaction of LEE. Copyright
Persistence of N7-(2,3,4-trihydroxybutyl)guanine adducts in the livers of mice and rats exposed to 1,3-butadiene
Oe, Tomoyuki,Kambouris, Sara J.,Walker, Vernon E.,Meng, Quanxin,Recio, Leslie,Wherli, Suzanne,Chaudhary, Ajai K.,Blair, Ian A.
, p. 247 - 257 (2007/10/03)
Liquid chromatography (LC) in combination with tandem mass spectrometry (MS/MS) and stable isotope methodology was employed for the analysis of the N7-guanine (Gua) adducts derived from 1,2:3,4-diepoxybutane (BDO2) a reactive metabolite of 1,3-butadiene (BD). Two diastereomeric forms of N7- (2,3,4-trihydroxybutyl)guanine (THBG) were identified in the livers of both mice and rats. One of the diastereomers [(±)-THBG] was formed by reaction of DNA with (±)-BDO2, and the other diastereomer (meso-THBG) was formed by reaction of DNA with meso-BDO2. There was significantly more (±)-THBG and meso-THBG in the liver DNA of the mice when compared with those of the rats during the 10 days of exposure to BD and the 6 days of postexposure that were monitored. There was a 2-fold excess of (±)-THBG over meso-THBG in the rat liver at all the time points. In the mouse liver after 10 days of exposure to BD, the (±)-THBG (3.9 adducts/106 normal bases) was also present in an almost 2-fold excess over meso-THBG (2.2 adducts/106 normal bases). However, 6-days after exposure to BD, (±)THBG (1.2 adducts/106 normal bases) and meso-THBG (1.0 adduct/106 normal bases) were present in almost equal amounts in the mouse liver. Furthermore, there was an almost 5-fold excess of the two THBG diastereomers in the mouse liver DNA 6 days after exposure to BD when compared with rat liver DNA. The half-lives of (±)-THBG and meso-THBG appeared to be slightly longer in mouse liver (4.1 and 5.5 days, respectively) than in rat liver (3.6 and 4.0 days, respectively). The apparent persistence of these adducts in the mouse may contribute to the increased susceptibility of this species to BD-induced carcinogenesis. It is possible that (±)-THBG and meso-THBG could have also been derived from the reaction of DNA with the hydrolysis product of BDO2, 1,2-dihydroxy-3,4- epoxybutane (DHEB). Surprisingly, a vast majority of the studies in which the mutagenic and carcinogenic potential of BDO2 have been examined have only employed the commercially available (±)-BDO2. In light of the present findings, additional studies will be required to determine the potency of meso-BDO2 and the DHEB that is the precursor to meso-THBG as mutagens and carcinogens.
