Efficient and selective enzymatic acylation reaction: separation of furanosyl and pyranosyl nucleosides

Candida antarctica lipase-B (CAL-B) immobilized on lewatite selectively acylated the primary hydroxyl group of the furanosyl nucleoside in a mixture of 1-(alpha-D-arabinofuranosyl)thymine and 1-(alpha-D-arabinopyranosyl)thymine. This selective biocatalytic acylation of furanosyl nucleoside has enabled us an easy separation of arabinofuranosyl thymine from an inseparable mixture with arabinopyranosyl thymine. The primary hydroxyl selective acylation methodology of arabinonucleoside has also been successfully used for the separation of 1-(beta-D-xylofuranosyl)thymine and 1-(beta-D-xylopyranosyl)thymine from a mixture of the two, which demonstrate the generality of the enzymatic methodology for separation of furanosyl and pyranosyl nucleosides.     

Boronic acid-based fluorescent receptors for selective recognition of thymine glycol

Thymine glycol is the major oxidation product of thymine. The amount of thymine glycol present within cellular DNA is one marker of the extent of oxidative damage, and chemosensors for thymine glycol have therefore a number of potential applications. In continuation of our studies devoted to the detection of modified nucleosides, we report herein our results toward the fluorescence detection of thymine glycol at both the nucleoside and the oligonucleotide levels using boronic acid sensors. These receptors show significant fluorescence enhancements and high selectivities in aqueous conditions upon binding with thymine glycol.     

Synthesis of hydroxymethyl branched [3.2.0]bicyclic nucleosides using a regioselective oxetane ring-formation

Two [3.2.0]bicyclic nucleosides, 35 and 34, with one and two hydroxymethyl substituents, respectively, have been efficiently synthesized. A protected (3'-C-vinyl-beta-D-allofuranosyl)thymine derivative 28 was easily prepared from diacetone-D-glucose and the thymine moiety was protected with a BOM-group. After the introduction of a leaving group in the 2'-position, the subsequent nucleoside 31 was used as the substrate for a stereoselective dihydroxylation and a regioselective oxetane ring-formation to give after deprotection the bicyclic nucleoside 34. The surprisingly efficient formation of an oxetane was first discovered by serendipity on a corresponding methylfuranoside derivative. The allo-configured bicyclic nucleoside 34 was easily shortened to a ribo-configured analogue 35 by a diol-cleaving reaction and subsequent reduction. Both 34 and 35 are conformationally restricted in the important intermediate 04'-endo conformation.     

Synthesis and properties of purine-type base-discriminating fluorescent (BDF) nucleosides: distinction of thymine by fluorescence-labeled deoxyadenosine derivatives

Novel base-discriminating fluorescent (BDF) nucleoside, 8-fluorescence-labeled adenosine derivative (^8PyA), was developed for the detection of thymine base on a target DNA. The BDF nucleoside was incorporated into oligodeoxynucleotides by post-synthetic modification. BDF probes containing ^8PyA selectively emit fluorescence only when the base opposite BDF nucleoside is thymine and act as effective reporter probes for homogeneous SNP typing.     

Synthesis and Anti-HIV Activity of Triazolo-fused 3',4'-Cyclic and 4'-Spiro Nucleoside Analogues

Triazolo-fused 3',4'-cyclic nucleoside 4'-spiro nucleoside analogues were synthesized by an intramolecular 1,3-dipolar cycloaddition of 4'-azido nucleoside derived azido-alkynes in a regio- and stereo-specific manner. The thymine nucleoside base in these target compounds was transformed into the corresponding 5-methyl cytosine component. The synthesized com­pounds were examined in an MAGI(multinuclear-activation galactosidase indicator) assay for exploring the anti-HIV activity and in a H9 T(human T lymphocytes H9) assay for measuring the cell toxicity.     

Synthesis and Anti‐HIV Activity of Triazolo‐Fused 3′,5′‐Cyclic Nucleoside Analogues Derived from an Intramolecular Huisgen 1,3‐Dipolar Cycloaddition

Triazolo‐fused 3′,5′‐cyclic nucleoside analogues were synthesized by an intramolecular 1,3‐dipolar cycloaddition of nucleoside‐derived azido‐alkynes in a regio‐ and stereospecific manner. The thymine nucleoside base in these target compounds was transformed successfully into the corresponding 5‐methylcytosine component. The synthesized compounds were examined in a MAGI assay for exploring the anti‐HIV activity and in a H9 T lymphocytes assay for measuring the cell toxicity.     

Convenient syntheses of 7-hydroxy-1-(hydroxymethyl)-3-(thymin-1-yl)-2,5-dioxabicyclo

Synthesis of the diastereoisomeric LNA (locked nucleic acid) nucleosides 1-(2-O,4-C-methylene-alpha-L-ribofuranosyl)thymine (6) and 1-(2-O,4-C-methylene-alpha-L-xylofuranosyl)thymine (13) are reported via convenient reaction cascades from di-O-p-toluenesulfonyl and tri-O-methanesulfonyl nucleoside derivatives 3, 7, and 10.     

The excited states of adenine and thymine nucleoside and nucleotide in aqueous solution: a comparative study by time-dependent DFT calculations

The effect substitutions at nitrogen atom 1 of thymine and nitrogen atom 9 of adenine have on lowest energy excited electronic states has been studied by means of time-dependent PBE0 calculations in aqueous solution. In agreement with the experimental indications, the vertical excitation energy of the bright state of 1,methyl-thymine, thymine nucleoside and thymine nucleotide is red-shifted with respect to that of thymine. Deoxyribose and deoxyribose-phosphate substituents affect mainly the lowest energy dark state of adenine and thymine, slightly increasing their oscillator strength. The excited states of 9, methyl-adenine and 1, methyl-thymine have also been studied by using the recently developed M052X, CAM-B3LYP and LC-ωPBE density functionals. The computed VEE are in good agreement with those obtained by using PBE0, which, however, provides values closer to the experimental band maximum.     

Regioselective and enantiospecific rhodium-catalyzed allylic amination with thymine: synthesis of a new conformationally rigid nucleoside

The regioselective and enantiospecific rhodium-catalyzed allylic amination of secondary allylic carbonates with N3-benzoyl thymine in conjunction with a stereoselective free radical cyclization provides a convenient method for the construction of a new conformationally rigid nucleoside.     

Synthesis of nucleoside analogues bearing the five naturally occurring nucleic acid bases built on a 2-oxabicylo[3.1.0]hexane scaffold

Hitherto unknown nucleoside analogues incorporating the five naturally occurring nucleic acid bases built on a 2-oxabicyclo[3.1.0]hexane template were synthesized. The synthesis of these new conformationally restricted nucleoside analogues involved the preparation of a suitable sugar precursor bearing the 2-oxabicyclo[3.1.0]hexane scaffold. This sugar was readily obtained from [(3aS,6aS)-2,2-dimethyl-3a,6a-dihydrofuro[2,3-d][1,3]dioxol-5-yl]methyl benzyl ether (4) following a Simons-Smith-type cyclopropanation reaction. Finally, glycosylation reactions and deprotection provided the nucleoside analogues. Using nucleoside 14 bearing thymine base as a model, we found that the conformation of such nucleoside analogue was restricted toward a (0)T(1) conformation.     

Synthesis of 1-(2'-Alkylthioethoxy)methyl Uracil and Thymine Derivatives

There is a serious need for compounds that are effective in the treatment of cancer and virus (HIV. Human Immunodeficiency Virus,etc.). Among the large number of nucleoside analogs which have been synthesized and evaluated^(1-2) recently several 5'-alkylthio nucleosides have been reported to exhibit good antitumor and antiviral activities^(3-4). Their anticancer mechanism involves blocking cancer cell proliferation and inhibiting the cytoplasmic isozyme(C-TK)⁽⁵⁾, one isozyme of thymine kinase, which predominates in human tumor cell lines⁽⁶⁾. As we know, many acylic nucleoside analogs have appeared good biological activities⁽⁷⁾. It is reported that they can also act on some thymine kinases and end up the propagation of the viral DNA chain⁽⁸⁾.     

Clustering of nucleobases with alkali metals studied by electrospray ionization tandem mass spectrometry: implications for mechanisms of multistrand DNA stabilization

Self-clustering of the five common nucleobases was investigated by electrospray ionization tandem mass spectrometry and shown to provide insight into the non-covalent interactions between identical bases. Alkali and ammonium cations significantly increase self-aggregation of the nucleobases and lead to the formation of uniquely stable magic number clusters. Sodium adducts of guanine, thymine and uracil preferentially take the form of tetrameric (quartet) clusters. This gas-phase result correlates with previously reported solution-phase data on sodium cation stabilized guanosine, thymine and uracil quartet structures believed to be responsible for telomere stabilization. In the presence of potassium, cesium or ammonium cations, pentameric magic number clusters are formed from thymine and uracil, while in solution the nucleoside isoguanosine yields clusters of this favored size. The formation of magic number metaclusters occurs for thymine and uracil in the presence of ammonium cations. These doubly charged 10- and 15-mers are tentatively attributed to the formation of pentamer/ammonium cation/ pentamer sandwich structures.     

Stereoselective synthesis of new bicyclic N,O-iso-homonucleoside analogues

The synthesis of two new bicyclic nucleoside analogues is reported. These compounds are iso-homonucleoside and are synthesised through a 1,3-dipolar cycloaddition of an enantiopure cyclic nitrone to protected allyl acohol and subsequent introduction of thymine by a Mitsunobu reaction.     

Characterization of novel nucleoside analogs by electrospray ionization mass spectra

In this paper, we synthesized a novel nucleoside analog by coupling thymine with dimethyl dicarboxylate biphenyl (DDB). The structure of the target compound was determined using 1H nuclear magnetic resonance (NMR) and electrospray ionization tandem mass spectrometry (ESI-MS/MS). The fragmentation pathways were studied in details through ESI-MS/MS. By comparing with unsubstituted nucleosides, such as AZT, MCI, d4T and DDI, it was found that the nucleoside analog coupled with DDB would not yield the daughter ions corresponding to the fragments of the nucleoside base and arabinofuranose analogs, but would lose a neutral molecule HF and DDB easily. However, the unsubstituted nucleosides could lightly yield the fragment ions of the nucleoside base and sugar ring. Hence, electrospray ionization mass spectrometry combined with tandem mass spectrometry (MS/MS) provides a convenient method to recognize the substituted and unsubstituted nucleosides.     

Synthesis and conformational analysis of 1-[2,4-dideoxy-4-C-hydroxymethyl-alpha-l-lyxopyranosyl]thymine

Previously different types of nucleosides with a six-membered carbohydrate moiety have been evaluated for their potential antiviral and antibiotic properties and as building blocks in nucleic acid synthesis. However, a pyranose nucleoside with a 1,4-substitution pattern like 1-[2,4-dideoxy-4-C-hydroxymethyl-alpha-l-lyxopyranosyl]thymine (4) has not been studied yet. Modeling suggested that this nucleoside would show the (4)C(1) conformation in contrast to anhydrohexitol nucleosides (1) whose most stable conformation is (1)C(4). The key to the synthesis of 4 involves the stereoselective introduction of the hydroxymethyl group onto the C-4 carbon of the pyranose sugar. Attempts to achieve this via hydroboration/oxidation of a C-4'-exocyclic vinylic intermediate selectively yielded the undesired alpha-directed hydroxymethyl group. Therefore, we envisaged another approach in which the C-4 substituent was introduced upon treatment of 2,3-O-isopropylidene-1-O-methyl-4-O-phenoxythiocarbonyl-alpha-l-lyxopyranose with beta-tributylstannyl styrene. This allowed stereoselective beta-directed introduction of a 2-phenylethenyl group at C-4, which was converted via oxidation/reduction (OsO(4), NaIO(4)/NaBH(4)) into the desired 4-hydroxymethyl group (20). The resulting 1-O-methyl-2,3,6-tri-O-acetyl-protected sugar was coupled with silylated thymine, using SnCl(2) as Lewis acid (22). After suitable protection, Barton deoxygenation of the 2'-hydroxyl function of the obtained ribo-nucleoside yielded the desired 2'-deoxynucleoside 4, indeed showing the expected equatorial orientation of the thymine ring ((4)C(1)).     

Metabolism of [2-14C]thymine and [2-14C]thymidine in germinating black gram (Phaseolus mungo) seeds

The metabolism of [2-14C]thymine and [2-14C]thymidine in the cotyledons and embryonic axes of black gram (Phaseolus mungo) seedlings was investigated. Both [2-14C]thymine and [2-14C]thymidine degraded extensively into [14C]CO2. The rate of release of [14C]CO2 from [2-14C]thymine was much greater than that from [2-14C]thymidine. Radioactivity from both precursors was also observed beta-ureidoisobutyric acid. This indicated that thymine was degraded by the reductive pathway of pyrimidine degradation. Small amounts of [2-14C]thymine and [2-14C]thymidine were salvaged for deoxyribonucleotide and DNA synthesis. The highest incorporation of [2-14C]thymine and [2-14C]thymidine into the DNA fraction was observed in 24 hour-old cotyledons where net DNA synthesis was not observed. These precursors seem to be utilised for DNA synthesis of organelles of the cotyledonary cells, probably mitochondria. In embronic axes, [2-14C]thymine is more effectively salvaged for DNA synthesis than [2-14C]thymine. The incorporation rate increased during the early phase of germination and attained its maximum at 48 h after which it decreased. No thymidine kinase activity was detected in either cotyledons or in the embryonic axes. Thymidine salvage seems to be catalysed by nucleoside phosphotransferase which is present both in the cotyledons and in the embryonic axes. This suggests that, in contrast to other pyrimidine and purine bases and nucleosides, no specific salvage system for thymine and thymidine is present in black gram seedlings.     

Synthesis of novel 1,2,3-triazolyl nucleoside analogues bearing uracil, 6-methyluracil, 3,6-dimethyluracil,thymine, and quinazoline-2,4-dione moieties

A series of novel 1,2,3-triazolyl nucleoside analogues was synthesized via the CuAAC reaction of N1-alkynyl uracil, 6-methyluracil, 3,6-dimethyl uracil, thymine and quinazolin-2,4-dione with protected azido β-d-ribofuranose. The obtained compounds differ in both the nature of the pyrimidine-2,4-dione fragment and the length of the polymethylene linker connecting it with the β-d-ribofuranosyl-1,2,3-triazol-4-yl moiety. The 1,2,3-triazolyl nucleoside analogues were evaluated for their cytotoxicity in vitro.     

Synthesis of (Carbo)nucleoside Analogues by [3+2] Annulation of Aminocyclopropanes

(Carbo)nucleoside derivatives constitute an important class of pharmaceuticals, yet there are only few convergent methods to access new analogues. Here, we report the first synthesis of thymine‐, uracil‐, and 5‐fluorouracil‐substituted diester donor–acceptor cyclopropanes and their use in the indium‐ and tin‐catalyzed [3+2] annulations with aldehydes, ketones, and enol ethers. The obtained diester products could be easily decarboxylated and reduced to the corresponding alcohols. The method gives access to a broad range of new (carbo)nucleoside analogues in only four or five steps and will be highly useful for the synthesis of libraries of bioactive compounds.     

Helical supramolecular self-assembly by prolamide thymidine/uridine analogues

This report describes the syntheses of rationally designed non-sugar nucleoside as prolamide nucleosides which contain prolyl ring and pyrimidine nucleobases (uracil/thymine) via acetamide bonds. These nucleosides have propensity to form distinctive self-assembly supramolecular helical structures ubiquitously through Watson-Crick/reverse type of hydrogen bonding with nucleobases. Moreover, the prolyl acetamide backbone groups- carbonyl (-C = O) and hydroxyl (-OH) group, are also involved in strengthening of self-assembled helical structures. Importantly, both prolamide thymidine and prolamide uridine have shown two distinctive helical structural patterns, in spite of containing the same backbone. Hence thymine and uracil moieties of prolamide nucleosides are responsible for unique supramolecular helical structural architectures.     

Synthesis and properties of nicked dumbbell and dumbbell DNA conjugates having stilbenedicarboxamide linkers

The synthesis and properties of nicked dumbbell and dumbbell DNA conjugates having A-tract base pair domains connected by rod-like stilbenedicarboxamide linkers are reported. The nicked dumbbells have one to eight dA-dT base pairs and are missing a sugar-phosphate bond either between the linker and a thymine nucleoside residue or between two thymine residues. Chemical ligation of all of the nicked dumbbells with cyanogen bromide affords the dumbbell conjugates in good yield, providing the smallest mini-dumbbells prepared to date. The dumbbells have exceptionally high thermal stability, whereas the nicked dumbbells are only marginally more stable than the hairpin structures on either side of the nick. The structures of the nicked dumbbells and dumbbells have been investigated using a combination of circular dichroism spectroscopy and molecular modeling. The base pair domains are found to adopt normal B'-DNA geometry and thus provide a helical ruler for studies of the distance and angular dependence of electronic interactions between the chromophore linkers.