A novel synthesis of deoxy phospha sugar-sugar disaccharides

A novel and facile synthetic method is described in the synthesis of several deoxy phospha sugar-sugar disaccharides, analogs of normal sugar disaccharides by treatment of (±)-2-bromo-3-methoxy-1-phenylphospholane 1-oxide with several pentose and hexose sugar acetonides.     

Synthesis of N-methyl-d-ribopyranuronamide nucleosides

The synthesis of N-methyl-d-ribopyranuronamide nucleosides is described. The key route is the rearrangement of a 1,2-O-isopropylidene protected furanose sugar with a carboxamide function in the 4-position to a ribopyranuronamide ring. The Lewis acid catalyzed condensation of adenine and thymine nucleobases with the per-O-acetylated N-methyl-d-ribopyranuronamide sugar is used to give the target nucleosides as a mixture of the α and β anomers. The mixture was separated and the final compounds were obtained by deacetylation in basic conditions.     

5′-substituted-5′-deoxy nucleosides

The methyl esters of the uronic acids derived from uridine, 5-fluorodeoxyuridine, 6-aza-2′-deoxyuridine and 2′,3′-o-isopropylideneadenosine were converted to the amides with aqueous d0·88 ammonia. After protection of the sugar hydroxyls each 5′-carboxamide was dehydrated with phosphoryl chloride at ?5° to yield, after deprotection, the respective novel 5′-nitrile nucleosides. Treatment of the protected 5′-nitrile nucleosides with ammonium azide in DMF gave, after deprotection, the novel 5′-C-tetrazole nucleosides.     

cis-Fused bicyclic sugar thiocarbamates. Reactivity towards amines

1,2-cis-Fused bicyclic sugar thiocarbamates of gluco and manno configurations have been prepared by treatment of the corresponding O-unprotected amino sugars and glycopyranosyl amines with thiophosgene. The reactivity of these compounds towards amines has been studied in order to determine whether these compounds could act as latent isothiocyanates; it is shown that 1,2-cis-fused bicyclic sugar thiocarbamates are more stable than their trans analogues, and are not transformed into thioureas upon treatment with amines. An unprecedented isomerization of a peracetylated glucopyranoso[2,1-d]oxazolidine-2-thione into a glucopyranoso[2,1-d]thiazolidin-2-one in DMF is also reported. The structure of this thiazolidin-2-one was confirmed by X-ray crystallography.     

Deoxyfluorination of alcohols using N,N-diethyl-α,α-difluoro-(m-methylbenzyl)amine

Deoxyfluorination of alcohols was carried out using N,N-diethyl-α,α-difluoro-(m-methylbenzyl)amine (DFMBA). Primary alcohols were effectively converted to fluorides under microwave irradiation or conventional heating. Deoxyfluorination of an anomeric hydroxy group in sugars by DFMBA proceeded at below room temperature and glycosyl fluorides could be obtained in good yields. The deoxyfluorination reaction chemoselectively proceeded and various protecting groups on the sugar can survive under the reaction conditions.     

Direct glycosylation: synthesis of alpha-indoline ribonucleosides

A selective synthesis of α-anomers of indoline nucleosides is described. Ribonucleosides of indoline, dimethylindoline and 5-bromoindoline are readily prepared in good yield by reacting indoline bases directly with the protected sugar, 2,3-O-(1-methylethylidene) 5-O-(triphenylmethyl)-D-ribofuranose in dry ethanol or methylene chloride in presence of molecular sieves at 40-60 °C.     

Evaluation of molecularly imprinted polymers using 2′,3′,5′-tri-O-acyluridines as templates for pyrimidine nucleoside recognition

In this paper, we describe the synthesis and evaluation of molecularly imprinted polymers (MIPs), prepared using 2′,3′,5′-tri-O-acyluridines as ‘dummy’ templates, for the selective recognition of uridine nucleosides. The MIPs were synthesised using a non-covalent approach with 2,6-bis-acrylamidopyridine (BAAPy) acting as the binding monomer and ethylene glycol dimethacrylate (EGDMA) as the cross-linking agent. The MIPs were evaluated in terms of capacity, selectivity and specificity by analytical and frontal liquid chromatography measurements. The results obtained in organic mobile phases suggest that the nucleosides are specifically bound to the polymer by the complementary hydrogen bonding motifs of the binding monomer and the nucleoside bases. The MIPs exhibited relatively high imprinting factors for 2′,3′,5′-tri-O-acyluridines, while they did not show any binding capacity for other nucleosides lacking the imide moiety on their base. Moreover, the presence of ester-COO groups in the EGDMA cross-linker may lead to the formation of additional hydrogen bonds with the 2′,3′ and/or 5′-OH of sugar part, allowing enhancement of the recognition of the uridine nucleosides. In aqueous media, results show that the binding is driven by hydrophobic interactions.     

Characterization of blocked nucleosides by mass spectrometry. Benzyl derivatives

The mass spectra of eleven model monobenzylated nucleosides were studied using low and high resolution mass spectrometry. Structural assignments to the major ions were made and several decomposition mechanisms proposed, with the goal of establishing the uses and limitations of mass spectrometry for the characterization of benzylaled nucleosides. Mass spectra generally permit determination of the extent and site of benzylation, with particular regard to base vs. sugar substitution, 0–2′ vs. 0–3′ or 0–5′, and in some cases 0–5′ vs. other isomers.     

A strategy to access fused triazoloquinoline and related nucleoside analogues

Fused triazoloquinolines have been prepared starting from (E)-3-(2-nitrophenyl)-1-aryl-prop-2-en-1-ones and sugar or benzyl azides in a sequential [3+2] cycloaddition reaction, followed by one pot Pd–C assisted reduction, cyclization and aromatization. The triazolyl fused quinolines with N¹-glycosyl substituents as unnatural nucleosides have inherent potential to generate a library of compounds for bioevaluations.     

Direct SNAr amination of fluorinated imidazo[4,5-c]pyridine nucleosides: efficient syntheses of 3-fluoro-3-deazaadenosine analogs

This paper describes the ready preparation of 3,6-difluoro-3-deazapurine (4,7-difluoroimidazo[4,5-c]pyridine). This novel base was glycosylated under mild conditions using three different ribose sugar analogs. 3,6-Difluoro-3-deazapurine ribonucleoside analogs underwent direct S_NAr amination reactions with liquid ammonia to give 3-fluoro-3-deazaadenosine analogs in excellent yield; in contrast, 6-chloro-3-fluoro-3-deazapurine nucleosides were inert under similar reaction conditions.     

The effect of storage temperature on interactions between dehydrated sugars and phosphatidylcholine

We studied the effects of storage temperature on the stability of dehydrated POPC (1-palmitoyl-2-oleoyl-phosphatidylcholine) mixed with sucrose, trehalose, or a sucrose/raffinose mixture. We used DSC to measure the gel-to-fluid phase transition temperature (T _m) of POPC after incubation either below or near the glass transition temperature (T _g) of the sugars in the mixture. Glass formation by the sugars around fluid-phase POPC led to the lowering ofT _m below that of the fully hydrated lipid. Phospholipid phase behavior did not change during storage belowT _g. In some samples stored aboveT _g, trehalose crystallized completely; in these samples, theT _g of POPC increased to that of the partially dehydrated phospholipid. Melting the crystalline sugar re-established its ability to lower POPC'sT _m. We conclude that prevention of complete sugar crystallization was important for stability in the dry state, and that storage belowT _g conferred long-term stability to the dehydrated sugar-lipid mixtures.     

Optimizing ammonia pressurization/depressurization processing conditions to enhance enzymatic susceptibility of dwarf elephant grass

An ammonia pressurization/depressurization process was investigated to evaluate the potential of producing reducing sugars from dwarf elephant grass, a warm-season forage. Moisture, temperature, and ammonia loading affected sugar yield (p<0.0001). At optimal conditions, ammonia processing solubilized 50.9% of the hemicellulose and raised the sugar yield (percentage of theoretical) from 18 to 83%. Glucose and xylose production were increased 3.2-and 8.2-fold, respectively. The mild processing conditions of the ammonia treatment (90–100°C, 5 min), the low enzyme loading (2 international filter paper units/g), and the short hydrolysis time (24 h), greatly enhance the potential of using for ages to produce sugars valuable for several applications.     

Application of 2,4,6-trioxo-pyrimidin-5-ylidene alditols in the synthesis of pyrano[2,3-d]pyrimidines containing a sugar moiety by hetero-Diels–Alder reactions and by conjugate Michael addition–cyclizations

A convenient and efficient procedure for the preparation of 3,4-dihydro-2H-pyran derivatives containing a sugar moiety is described. The reaction sequence is: Knoevenagel condensation of unprotected sugars and CH acids, acetylation of C-glycosides and hetero-Diels–Alder reaction. O-Acetylated 1,3-dimethyl-2,4,6-trioxo-pyrimidin-5-ylidene derivatives were used as new heterodienes in the synthesis of fused uracils—pyrano[2,3-d]pyrimidines with a sugar moiety. Solvent-free hetero-Diels–Alder cycloadditions of O-acetylated pyrimidin-5-ylidene alditols with enol ethers and cyclic enol ether were investigated at room temperature. New, enantiomerically pure cis and trans diastereoisomers of pyrano[2,3-d]pyrimidines and cis–cis, trans–cis diastereoisomers of pyrano[3′,2′:5,6]pyrano[2,3-d]pyrimidines with alditol moiety were obtained. The same pyrimidin-5-ylidene alditols underwent conjugate Michael addition–cyclizations with malononitrile at room temperature to afford optically active diastereoisomers of pyrano[2,3-d]pyrimidine-6-carbonitriles with a sugar moiety.     

Triazolyl C-nucleosides via the intermediacy of β-1′-ethynyl-2′-deoxyribose derived from a Nicholas reaction: Synthesis,photophysical properties and interaction with BSA

We report the design and synthesis of triazolyl donor/acceptor unnatural C-nucleosides via alkyne (sugar)—azide (aromatic) 1, 3-dipolar cyclo-addition reaction as a key step and studies on their photophysical properties. We have chosen β-1′-ethynyl-2′-deoxyribose as a precursor to synthesize triazolyl-C-nucleosides. Overcoming the difficulties, we obtain β-1′-ethynyl-2′-deoxyribose as a major product following a Co₂(CO)₈ catalyzed intramolecular Nicholas reaction. The 1,3-diaxial interaction is the driving force for the α to β-anomeric conversion while performing cobalt complexation followed by oxidation to afford β-1′- ethynyl-2′-deoxyribose as the major product. A Cu(I)-catalyzed click reaction between different aromatic donor/acceptor azides and β-1′- ethynyl-2′-deoxyribose generates the desired unnatural triazolyl donor-acceptor aromatic C-nucleosides (^cTB_Do/Ac) within 30 min. Single crystal X-ray structure shows the puckered conformation of sugar as C3′-exo. Studies on the photophysical properties suggests good fluorophoric as well as solvatochromic characteristics of these nucleosides. Two of the synthesised nucleosides, ^cTAnthB_Do and ^cTPyB_Do, are found to interact with BSA as the only tested protein with quenching of fluorescence signal. The designed bases, thus, might find applications in stabilizing a DNA and in the biophysical study thereof, if a pair of such donor acceptor C-nucleosides could be incorporated into a DNA sequence.     

Microwave synthesis,anti-oxidant and anti-tumor activity of some nucleosides derived 2-oxonicotinonitrile

Abstract

A facile and convenient synthesis of novel cyclic and acyclic nucleoside derivatives incorporating 2-oxo-1,2-dihydropyridine-3-carbonitrile moiety has been described. The aglycons 3a,b were coupled with different activated halosugars such as glucosyl, galactosyl, lactosyl bromides and peracetylated ribose, in addition to, acyclic sugar as 4-bromobutylacetate and 2-acetoxyethoxymethyl bromide in basic medium under conventional and microwave irradiation. Deprotection of the synthesized nucleosides was obtained in presence of Et₃N/MeOH and few drops of water. The structures of the synthesized compounds have been deduced from their elemental analyses and spectral data (IR, ¹H NMR, and ¹³C NMR). Some of the synthesized compounds were screened as antioxidant and anticancer agents. Good and moderate anticancer activities against HepG-2, PC-3 and HCT116 were observed in vitro for some compounds.     

Synthesis and NMR characterization of a novel crown-ether ring-fused uridine analogue

The chemical synthesis and ¹H NMR analysis of a novel bicyclic uridine derivative, with a 18-crown-6 ether moiety fused at the ribose 2- and 3-positions, as first example of a hitherto unknown class of ribose-modified nucleosides, are here described. NMR-based conformational analysis studies showed for the modified nucleoside a marked preference for an N-type sugar puckering and the nucleobase in the anti conformation, with the uracil favouring the coordination of a sodium ion hosted in the crown ether.     

CZE and ESI-MS of Borate-Sugar Complexes

Capillary zone electrophoresis (CZE) with electrospray ionization (ESI) mass spectrometry (MS) was used to study borate (B^?1) and sugar (L) complexes (L _x B^?1). Boric acid was adjusted to pH 10 with ammonium hydroxide to create an ESI-MS compatible CZE background electrolyte. We show for the first time that the electrophoretic peaks for each injected sugar contained both the substrates (i.e., sugar and/or multimers) and products (i.e., L _x B^?1). The effects of sheath liquid, temperature, and borate concentration were studied. The molecular mass information obtained from the ESI-MS provided new evidence on the mechanisms of borate-sugar complexation. Direct infusion ESI-MS and CZE-ESI-MS experiments strongly suggest that the formation of L _x B^?1 was from the direct reaction of a sugar or sugar multimer (L _x ) and B^?1. Larger L _x B^?1, where x > 2 were observed. Separation in the CZE dimension allows for the simultaneous analysis of a sugar mixture and simplified the ESI-MS analysis of sugars of the same molecular mass. The increase in sugar electrophoretic mobility caused by the increase in borate concentration was discussed in terms of the formation of L _x B^?1 complexes. In addition, the separation of five nucleosides by CZE using a borate electrolyte and detection using ESI-MS is demonstrated.     

Secondary ion mass spectrometry of sugar nucleotides

Secondary ion mass spectra of fifteen sugar nucleotide sodium salts were investigated. In the negative-ion mode. deprotonated free acid molecules, desodiated sodium salts and some structurally significant fragment ion swere obtained. The linked scan at constant B/E gave information on the characteristics of the sugar, nucleosides and base moieties in the sugar nucleotides.     

PROSIT: pseudo-rotational online service and interactive tool, applied to a conformational survey of nucleosides and nucleotides

A Pseudo-Rotational Online Service and Interactive Tool (PROSIT) designed to perform complete pseudorotational analysis of nucleosides and nucleotides is described. This service is freely available at http://cactus.nci.nih.gov/prosit/. Files containing nucleosides/nucleotides or DNA/RNA segments, isolated or bound to other molecules (e.g., a protein) can be uploaded to be processed by PROSIT. The service outputs the pseudorotational phase angle P, puckering amplitude numax, and other related information for each nucleoside/nucleotide detected. The service was implemented using the chemoinformatics toolkit CACTVS. PROSIT was used for a survey of nucleosides contained in the Cambridge Structural Database and nucleotides in high-resolution crystal structures from the Nucleic Acid Database. Special cases discussed include nucleosides having constrained sugar moieties with extreme puckering amplitudes, and several specific DNA/RNA helices and protein-bound DNA oligonucleotides (Dickerson-Drew dodecamer, RNA/DNA hybrid viral polypurine tract, Z-DNA enantiomers, B-DNA containing (L)-alpha-threofuranosyl nucleotides, TATA-box binding protein/TATA-box complex, and DNA (cytosine C5)-methyltransferase complexed with an oligodeoxyribonucleotide containing transition state analogue 5,6-dihydro-5-azacytosine). When the puckering amplitude decreases to a small value, the sugar becomes increasingly planar, thus reducing the significance of the phase angle P. We introduce the term "central conformation" to describe this part of the pseudorotational hyperspace in contrast to the conventional north and south conformations.     

Synthesis and structure of novel conformationally constrained 1',2'-azetidine-fused bicyclic pyrimidine nucleosides: their incorporation into oligo-DNAs and thermal stability of the heteroduplexes

[structures: see text] The synthesis of novel 1',2'-aminomethylene bridged (6-aza-2-oxabicyclo[3.2.0]heptane) "azetidine" pyrimidine nucleosides and their transformations to the corresponding phosphoramidite building blocks (20, 39, and 42) for automated solid-phase oligonucleotide synthesis is reported. The novel bicyclonucleoside "azetidine" monomers were synthesized by two different strategies starting from the known sugar intermediate 6-O-benzyl-1,2:3,4-bis-O-isopropylidene-D-psicofuranose. Conformational analysis performed by molecular modeling (ab initio and MD simulations) and NMR showed that the azetidine-fused furanose sugar is locked in a North-East conformation with pseudorotational phase angle (P) in the range of 44.5-53.8 degrees and sugar puckering amplitude (phi(m)) of 29.3-32.6 degrees for the azetidine-modified T, U, C, and 5-Me-C nucleosides. Thermal denaturation studies of azetidine-modified oligo-DNA/RNA heteroduplexes show that the azetidine-fused nucleosides display improved binding affinities when compared to that of previously synthesized North-East sugar constrained oxetane fused analogues.