- ESI-CID spectral characterization and differentiation of the cross links of thymine formed by one electron oxidation with SO4 ●-
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The analysis of urinary nucleosides is becoming a very good tool in the diagnosis of diseases like AIDS and cancer and consequently the identification of modified nucleosides using mass spectrometry is an area of utmost importance. In this context, there is a high relevance in the understanding of the mechanism of collisionally induced dissociation (CID) of these heterocyclics. The present work characterizes and differentiates the cross-linked products formed by one electron oxidation of thymine (T). Three dimers A, B and C, were analyzed, out of which the dimer A is a C5–C5’ cross link of two T molecules containing a fused tetrahydrofuran ring, while B and C are N–C cross linked products. B and C showed very similar fragmentation pattern but that of A was different. The differentiation between these three were made by monitoring two characteristic peaks, the water loss peak ([M+H]+) and the protonated T fragment ([T + H]+). The probable mechanism of formation of these fragments and their CID mechanism in both positive and negative ionization modes are also explained. The neutral losses of NH3, H2O and NHCO were the prominent mechanism in the positive mode, while in the negative mode, only NHCO and CO losses were observed.
- Chandran, Jisha,Vishnu,Aravind, Usha K.,Aravindakumar
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- Synthesis and mass spectrometry analysis of oligonucleotides bearing 5- formyl-2'-deoxyuridine in their structure
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Two oligonucleotides containing FdU (1) have been synthesized. The use of the 'Pac-amidites' for the natural nucleosides has allowed the incorporation of the oxidized thymine residue without protection of the aldehydic function. The oligonucleotide composition was confirmed by enzymatic digestion and electrospray mass spectrometry.
- Berthod,Petillot,Guy,Cadet,Forest,Molko
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- Molecular basis for the substrate specificity and catalytic mechanism of thymine-7-hydroxylase in fungi
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TET proteins play a vital role in active DNA demethylation in mammals and thus have important functions in many essential cellular processes. The chemistry for the conversion of 5mC to 5hmC, 5fC and 5caC catalysed by TET proteins is similar to that of T to 5hmU, 5fU and 5caU catalysed by thymine-7-hydroxylase (T7H) in the nucleotide anabolism in fungi. Here, we report the crystal structures and biochemical properties of Neurospora crassa T7H. T7H can bind the substrates only in the presence of cosubstrate, and binding of different substrates does not induce notable conformational changes. T7H exhibits comparable binding affinity for T and 5hmU, but 3-fold lower affinity for 5fU. Residues Phe292, Tyr217 and Arg190 play critical roles in substrate binding and catalysis, and the interactions of the C5 modification group of substrates with the cosubstrate and enzyme contribute to the slightly varied binding affinity and activity towards different substrates. After the catalysis, the products are released and new cosubstrate and substrate are reloaded to conduct the next oxidation reaction. Our data reveal the molecular basis for substrate specificity and catalytic mechanism of T7H and provide new insights into the molecular mechanism of substrate recognition and catalysis of TET proteins.
- Li, Wenjing,Zhang, Tianlong,Ding, Jianping
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- New Metal-Free Route towards Imidazole-Substituted Uridine
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Nucleosides with a bi(hetero)aryl nucleobase have unique potential applications as antiviral drugs and molecular probes. The need for transition metal catalysis to synthesize these nucleosides from pre-functionalized building blocks and the use of nucleobase protection groups results in expensive and tedious syntheses. Herein we report that 5-imidazolyl-uracil can be obtained by scalable Van Leusen imidazole synthesis and regioselectively introduced on ribose to obtain the desired nucleoside in a 5 step synthesis (total yield 55 percent). The 5-imidazolyl moiety leads to improved fluorescence properties. The only side-product formed was characterized by 2D-NMR and X-ray crystallography and could be suppressed during synthesis in favor of the desired product.
- Dehaen, Wim,Herdewijn, Piet,Mattelaer, Henri-Philippe,Van Hool, Anne-Sophie,Van Meervelt, Luc,Van der Auweraer, Mark,de Jong, Flip
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- Steric fixation of bromovinyluracil: Synthesis of furo[2,3-d]pyrimidine nucleosides
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A new synthetic proccdure for the preparation of 5,6-dihydrofuro[2,3-d]pyrimidin-2(3H)-one (3) and its deoxyriboside 8 is reported. Compound 3 undergoes nucleophilic reactions with various agents to yield 5-substituted uracil derivatives. The dehydro derivative of 3, furo[2,3-d]pyrimidin-2(3H)-one (18) was synthesized by cyclization of BVU 15, which made us develop a reproducible and high yield method for the synthesis of BV(D)U. Starting from 18, the α-deoxyriboside 20 and the β-riboside 22 were prepared.
- Eger,Jalalian,Schmidt
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- Fluorescent biaryl uracils with C5-dihydro- And quinazolinone heterocyclic appendages in PNA
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There has been much effort to exploit fluorescence techniques in the detection of nucleic acids. Canonical nucleic acids are essentially nonfluorescent; however, the modification of the nucleobase has proved to be a fruitful way to engender fluorescence. Much of the chemistry used to prepare modified nucleobases relies on expensive transition metal catalysts. In this work, we describe the synthesis of biaryl quinazolinone-uracil nucleobase analogs prepared by the condensation of anthranilamide derivatives and 5-formyluracil using inexpensive copper salts. A selection of modified nucleobases were prepared, and the effect of methoxy- or nitro- group substitution on the photophysical properties was examined. Both the dihydroquinazolinone and quinazolinone modified uracils have much larger molar absorptivity (~4-8×) than natural uracil and produce modest blue fluorescence. The quinazolinone-modified uracils display higher quantum yields than the corresponding dihydroquinazolinones and also show temperature and viscosity dependent emission consistent with molecular rotor behavior. Peptide nucleic acid (PNA) monomers possessing quinazolinone modified uracils were prepared and incorporated into oligomers. In the sequence context examined, the nitro-substituted, methoxy-substituted and unmodified quinazolinone inserts resulted in a stabilization (?Tm = +4.0/insert; +2.0/insert; +1.0/insert, respectively) relative to control PNA sequence upon hybridization to complementary DNA. All three derivatives responded to hybridization by the “turn-on” of fluorescence intensity by ca. 3-to-4 fold and may find use as probes for complementary DNA sequences.
- Heidari, Ali,Ghorbani-Choghamarani, Arash,Hajjami, Maryam,Hudson, Robert H.E.
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- The detrimental effect of orotic acid substitution in the peptide nucleic acid strand on the stability of PNA2:NA triple helices
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We have investigated the incorporation of C6 derivatives of uracil into polypyrimidine peptide nucleic acid oligomers. Starting with uracil-6-carboxylic acid (orotic acid), a peptide nucleic acid monomer compatible with Fmoc-based synthesis was prepared. This monomer then served as a convertible nucleobase whereupon treatment of the resin-bound methyl orotate containing hexamers with hydroxide or amines cleanly converted the ester to an orotic acid or orotamide-containing peptide nucleic acid. Peptide nucleic acid hexamers containing the C6-modified nucleobase hybridized to both poly(riboadenylic acid) and poly(deoxyriboadenylic acid) via triplex formation. Complexes formed with poly(riboadenylic acid) were more stable than those formed with poly(dexoyriboadenylic acid), as measured by temperature-dependent UV spectroscopy. However, both of these complexes were destabilized relative to the complexes formed by an unmodified peptide nucleic acid oligomers. Internal or doubly substituted hexamers are destabilized more strongly than a terminally substituted one, and the type of substitution (carboxamide, ester, carboxylic acid) affects the overall triplex stability. These results clearly show that incorporation of a C6-substituted uracil into polypyrimidine PNA is detrimental to triplex formation. We have also extended this chemistry to incorporate uracil-5-methylcarboxylate into a peptide nucleic acid hexamer. After on-resin conversion of the C5 ester to the 3-(N,N-dimethylamino)propylamide, significant stabilization of the triplex formed with poly(riboadenylic acid) was observed, which illustrates the compatibility of C5 substitution with peptide nucleic acid directed triple helix formation.
- Hudson, Robert H. E.,Wojciechowski, Filip
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- The pH-Dependence of the Hydration of 5-Formylcytosine: an Experimental and Theoretical Study
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5-Formylcytosine is an important nucleobase in epigenetic regulation, whose hydrate form has been implicated in the formation of 5-carboxycytosine as well as oligonucleotide binding events. The hydrate content of 5-formylcytosine and its uracil derivative has now been quantified using a combination of NMR and mass spectroscopic measurements as well as theoretical studies. Small amounts of hydrate can be identified for the protonated form of 5-formylcytosine and for neutral 5-formyluracil. For neutral 5-formylcytosine, however, direct detection of the hydrate was not possible due to its very low abundance. This is in full agreement with theoretical estimates.
- Zott, Fabian L.,Korotenko, Vasily,Zipse, Hendrik
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- Preparation method of 2, 4-dichloro-5-pyrimidinecarboxaldehyde and derivative thereof
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The invention discloses a preparation method of 2, 4-dichloro-5-pyrimidinecarboxaldehyde and derivatives thereof. The method comprises the following steps:(1)by taking uracil as a raw material, addingDMF, slowly dropwise adding thionyl chloride at the temperature of 40 DEG C or below, controlling the temperature to be 35-40 DEG C after dropwise adding is finished, tracking by HPLC(High Performance Liquid Chromatography)until the raw material is completely reacted, cooling the system to room temperature, pouring into water, and separating out to generate 2, 4-dyhydroxyl-5-pyrimidinecarboxaldehyde; and(2)reacting the 2, 4-dihydroxy-5-pyrimidinecarboxaldehyde with phosphorus oxychloride to obtain 2, 4-dichloro-5-pyrimidinecarboxaldehyde; the method is good in operability and high in yield, and industrial production can be achieved.
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Paragraph 0013-0021
(2020/04/02)
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- Novel 1H-pyrazolo[3,4-d]pyrimidin-6-amino derivatives as potent selective Janus kinase 3 (JAK3) inhibitors. Evaluation of their improved effect for the treatment of rheumatoid arthritis
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Selective JAK3 inhibitors have been shown to have a potential benefit in the treatment of autoimmune disorders. Here we report the identification of a series of pyrazolopyrimidine derivatives as potent JAK3 inhibitors that exploit a unique cysteine (Cys909) residue in JAK3. Most of these compounds (13k, 13n and 13 t), displayed stronger anti-JAK3 kinase activity and selectivity than tofacitinib. Furthermore, the most active inhibitor 13t (IC50 = 0.1 nM), also exhibited favourable selectivity for JAK3 in a panel of 9 kinases which contain the same cysteine. In a series of cytokinestimulated cellular analysis, compound 13 t, could potently block the JAK3-STAT signaling pathway. Further biological studies, including cellular antiproliferative activity assays and a rat adjuvant-induced arthritis model for in vivo evaluation, also indicated its efficacy and low toxicity in the treatment of rheumatoid arthritis. The results of these experimental explorations suggested that 13t is a promising lead compound for the development of selective JAK3 inhibitor with therapeutic potential in rheumatoid arthritis.
- Chen, Cheng-Juan,Shu, Lei,Wang, Zhi-Jian,Yin, Yuan,Yu, Ru-Nan,Zhang, Da-Yong,Zhang, Tian-Tai
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- RIBOCICLIB INTERMEDIATE AND PROCESS FOR PREPARATION THEREOF
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The present invention relates to the process for the preparation of ribociclib succinate by making use of novel intermediates. The invention also relates to the process for the preparation of novel intermediates.
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Page/Page column 4; 7
(2020/06/10)
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- Synthesis of 5-hetaryluracil derivatives via 1,3-dipolar cycloaddition reaction
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1,3-Dipolar cycloaddition is a convenient method for construction of various heterocyclic systems. We applied this method for the synthesis 5-hetaryluracil derivatives where substituted uracils played the role of 1,3-dipoles or dipolarophiles. Treatment of the nitrile oxide derived from 5-formyluracil and substituted alkenes gave the appropriate 5-(4,5-dihydroisoxazol-3-yl)pyrimidine-2,4(1H,3H)-diones, which by oxidation with N-bromosuccinimide were transformed into appropriate 5-(isoxazol-3-yl)uracils. When 5-cyanouracil was used as a dipolarophile in the reaction with nitrile oxides, generated from aromatic aldoximes, several 5-(1,2,4-oxadiazol-5-yl)uracils were obtained. An alternative reaction of 5-formyluracil with an excess of nitriles in the presence of cerium ammonium nitrate as an oxidant gave 1,2,4-oxadiazol-3-yl derivatives in moderate yields. (Chemical Equation Presented).
- Jakubiec, Dominika,Przypis, ?ukasz,Suwiński, Jerzy W.,Walczak, Krzysztof Z.
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p. 149 - 161
(2017/02/19)
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- Isoxazolidine analogues of pseudouridine: A new class of modified nucleosides
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A new class of modified C-nucleosides has been synthesized according to the 1,3-dipolar cycloaddition methodology. The obtained compounds are structurally related to natural pseudouridine, where the sugar moiety is replaced by an isoxazolidine ring. Different experimental conditions, and the effect of additives on the cycloaddition process, have been examined; the best results were obtained when the cycloaddition reaction was performed under microwave irradiation.
- Chiacchio, Ugo,Corsaro, Antonino,Mates, Juan,Merino, Pedro,Piperno, Anna,Rescifina, Antonio,Romeo, Giovanni,Romeo, Roberto,Tejero, Tomas
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p. 4733 - 4738
(2007/10/03)
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- PYRIMIDINEDIONE, PYRIMIDINETRIONE, TRIAZINEDIONE AND TETRAHYDROQUINAZOLINEDIONE DERIVATIVES AS ALPHA1-ADRENERGIC RECEPTOR ANTAGONISTS
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Compounds of Formula I: STR1 where R 5 is a group selected from Formulae (a), (b), (c) and (d): STR2 and the pharmaceutically acceptable salts and N-oxides thereof, are α 1-adrenergic receptor antagonists useful for the treatment of diseases involving directly or indirectly an obstruction of the lower urinary tract, such as benign prostatic hyperplasia.
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- Measurement of oxidative damage at pyrimidine bases in γ-irradiated DNA
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Oxidized nucleobases represent one of the main classes of damage induced in DNA by ionizing radiation. Emphasis was placed in this work on the measurement of four oxidized pyrimidine bases, including 5- (hydroxymethyl)uracil (5-HMUra), 5-formyluracil (5-ForUra), 5-hydroxy- cytosine (5-OHCyt), and 5-hydroxyuracil (5-OHUra), in isolated DNA upon exposure to γ radiation in aerated aqueous solution. For this purpose, both high performance liquid chromatography associated with electrochemical detection (HPLC-EC) and gas chromatography coupled to mass spectrometry (GC- MS) were used. Conditions of hydrolysis of the N-glycosidic bond were carefully checked in order to achieve a quantitative release of the lesions. We showed that 60% formic acid treatment leads to the decomposition of the four lesions studied. On the other hand, hydrolysis based on the use of either 88% formic acid or 70% hydrogen fluoride in pyridine (HF/Pyr) allowed the quantitative release of the modified bases, with the exception of 5- HMUra when the latter reagent was utilized. A dose course study of the radiation-induced formation of 5-HMUra and 5-ForUra in DNA by using the GC- MS assay showed that the latter lesion was produced in a 2.1-fold higher yield than the former one. HF/Pyr and 88% formic acid hydrolysis provided similar results for 5-ForUra, indicating the reliability of both techniques for the measurement of this lesion. For 5-OHUra and 5-OHCyt, the level of modification determined by GC-MS analysis was higher after 88% formic acid treatment than upon HF/Pyr hydrolysis. When DNA was enzymatically digested and analyzed by HPLC-EC for 5-OHdCyd and 5-OHdUrd, the results were very close to those obtained by GC-MS following HF/Pyr treatment. It was concluded that additional amounts of both 5-OHUra and 5-OHCyt are produced during the 88% formic acid treatment from radiation-induced 5,6-saturated pyrimidine precursors. It is likely that cytosine and uracil diols are involved in this reaction. The radiochemical yields of formation (in μmol · J-1) for the products studied are in the following decreasing order: 5-ForUra (0.0083) > 5-OHCyt (0.0046) > 5-HMUra (0.0039) > 5-OHUra (0.0035).
- Douki, Thierry,Delatour, Thierry,Paganon, Frederique,Cadet, Jean
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p. 1145 - 1151
(2007/10/03)
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- Synthesis of a potential antiviral compound: 5-Bromoethynyl-2'- deoxyuridine
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5-Bromoethynyluracil and its deoxyriboside can be prepared in good yields starting from dibromovinyluracil, which is accesible by literature methods. 5-Bromoethynyl-deoxyuridine is less effective against HSV-1 than E- (bromovinyl)-deoxyuridine but, similar to BVDU, seems to exhibit a certain selectivity toward HSV-1. Molecular calculations prove the spatial similarity of both compounds.
- Eger,Jalalian,Schmidt
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p. 8371 - 8380
(2007/10/02)
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- Oxidation of nucleic acid related compounds by the peroxodisulfate ion
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The treatment of nucleic acid bases, nucleosides, and nucleotides with peroxodisulfate ion in a phosphate buffer solution at pH 7.0 or water at 70-75°C was investigated. The reaction of thymine and 5-methylcytosine nucleosides and nucleotides resulted in the oxidation of the 5-methyl groups. The oxidation products from 1,3-dimethyluracils and the time-course of the reaction of uracils led to two plausible reaction mechanisms for the oxidation of uracils.
- Itahara,Yoshitake,Koga,Nishino
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p. 2257 - 2264
(2007/10/02)
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- Oxidation of Thymines by Peroxosulfate Ions in Water
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Oxidation of thymines by sodium peroxodisulfate in water at 85 deg C gave the corresponding 5-(hydroxymethyl)uracils and 5-formyluracils.The reaction may proceed via thymine cation radicals.On the other hand, oxidation of thymines by potassium peroxomonosulfate in water gave the corresponding cis-5,6-dihydroxy-5,6-dihydrothymines and 5-hydroxy-5-methylbarbituric acids.Furthermore, treatment of thymine with both potassium peroxomonosulfate and hydrogen peroxide in water gave cis-6-hydroperoxy-5-hydroxy-5,6-dihydrothymine.
- Itahara, Toshio,Fujii, Yukiko,Tada, Miki
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p. 3421 - 3424
(2007/10/02)
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- Oxidation of Thymines and Uracils with Sodium Peroxodisulfate
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Reaction of thymines with Na2S2O8 in water resulted in selective oxidation of the methyl group at 5-position of thymines.Oxidation of thymines with Na2S2O8 in hydrochloric acid gave 5-chloro-6-hydroxy-5,6-dihydrothymines and in acetic acid containing NaCl gave 6-acetoxy-5-chloro-5,6-dihydrothymines which were converted to 6-alkoxy-5-chloro-5,6-dihydrothymines with alcohols.The reaction of uracils also gave similar products together with 5-chlorouracils.
- Itahara, Toshio,Ebihara, Reiko,Fujii, Yukiko,Tada, Miki
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p. 1319 - 1322
(2007/10/02)
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