Urinary Modified Nucleosides as Tumor Markers

Abstract

Extracts of urinary nucleosides have been sequentially purified and examined by mass spectrometric analysis. Seventeen modified nucleosides have been unequivocally identified and a further five provisionally identified. While several nucleosides were found only in a small number of extracts, the occurrence and levels of others were found to correlate with the tumour type and stage.     

Affinity chromatography using enzymatically synthesized nucleotide-containing DNA binding polymers

A series of nucleotide-containing polyphenols has been synthesized by a simple, two-step enzymatic method. The binding properties of these synthetic polymers to complementary oligonucleotides have been evaluated using a commercially available oligo(dT)cellulose column. Complementary synthetic nucleosides were retained on this column to a greater extent than non-complementary synthetic nucleosides. These results suggest that the synthetic nucleosides prepared via this two-step enzymatic approach may have application as affinity matrices.     

Studies on the synthesis and unusual behavior of vinyl sulfone-modified hexenopyranosylthymines

Although vinyl sulfone-modified- (VSM) pent-2'-enofuranosyl nucleosides 2 and hex-2-enopyranosyl glycoside 4 are easily synthesized from the corresponding mesylated sulfones 1c and 3c, respectively, via an oxidation-mesylation-elimination route, the 3'-C-sulfonyl-hex-2'-enopyranosylthymine 11 is not obtained from 10 and a glycal derivative 12 is formed instead. On the other hand, 3'-C-sulfonyl-hex-3'-enopyranosylthymine 20 is easily synthesized from the mesylated sulfone 19. Again unlike the reaction patterns of VSM-pent-2'-enofuranosyl nucleosides 2 and hex-2-enopyranosyl glycosides 4 as Michael acceptors, the reactions of nucleophiles with 3'-C-sulfonyl-hex-3'-enopyranosylthymine 20 yielded a rearranged product 21 instead of Michael adducts.     

5-alkylvinyl-1,2,4-triazole nucleosides: Synthesis and biological evaluation

Abstract

Some 5-substituted ribavirin analogues have a high antiviral and anticancer activity, but their mechanisms of action are obviously not the same as their parent compound. The SAR studies performed on 3 (5)-substituted 1,2,4-triazole nucleosides have shown a high dependency between the structure of the 3 (5)-substituent and the level of antiviral/anticancer activity. The most active substances of the row contain coplanar with the 1,2,4-triazole ring aromatic substituent which is connected by a rigid ethynyl bond. However, the compounds with the trans-vinyl linker also had antiviral activity. We decided to study the antitumor activity of ribavirin analogues with alkyl/aryl vinyl substituents in the 5th position of the 1,2,4-triazole ring. Protected nucleoside analogues with various 5-alkylvinyl substituents were obtained by Horner-Wadsworth-Emmons reaction from the common precursor and converted to the nucleosides. Arylvinyl nucleosides were synthesised according the reported procedures. All compounds did not show significant antiproliferative activity on several tumour cell lines. Coplanar aromatic motif in the 5-substituent for the anticancer activity manifestation was confirmed.     

Synthesis and Biological Evaluation of Acyclic Phosphonic Acid Nucleoside Derivatives

As part of a project to generate a library of nucleosides as potential antiviral agents, a small subset of novel acyclic phosphonic acid nucleosides was prepared. Practical synthetic routes are described for three targets, which were then tested against HIV, hepatitis C virus (HCV), and Dengue virus.     

Determination of urinary nucleosides by direct injection and coupled-column high-performance liquid chromatography

A coupled-column liquid chromatographic method for the direct analysis of 14 urinary nucleosides is described. Efficient on-line clean-up and concentration of 14 nucleosides from urine samples were obtained by using a boronic acid-substituted silica column (40 mm x 4.0 mm I.D.) as the first column (Col-1) and a Hypersil ODS2 column (250 mm x 4.6 mm I.D.) as the second column (Col-2). The mobile phases applied consisted of 0.25 mol/L ammonium acetate (pH 8.5) on Col-1, and of 25 mmol/L potassium dihydrogen phosphate (pH 4.5) on Col-2, respectively. Determination of urinary nucleosides was performed on Col-2 column by using a linear gradient elution comprising 25 mmol/L potassium dihydrogen phosphate (pH 4.5) and methanol-water (60:40, v/v) with UV detection at 260 nm. Urinary nucleosides analysis can be carried out by this procedure in 50 min requiring only pH adjustment and the protein precipitation by centrifugation of urine samples. Calibration plots of 14 standard nucleosides showed excellent linearity (r > 0.995) and the limits of detection were at micromolar levels. Both of intra- and inter-day precisions of the method were better than 6.6% for direct determination of 14 nucleosides. The validated method was applied to quantify 14 nucleosides in 20 normal urines to establish reference ranges.     

Concentration of Nucleosides and Related Compounds in Cerebral and Cerebellar Cortical Areas and White Matter of the Human Brain

1. Nucleosides potentially participate in the neuronal functions of the brain. However, their distribution and changes in their concentrations in the human brain is not known. For better understanding of nucleoside functions, changes of nucleoside concentrations by age and a complete map of nucleoside levels in the human brain are actual requirements.2. We used post mortem human brain samples in the experiments and applied a recently modified HPLC method for the measurement of nucleosides. To estimate concentrations and patterns of nucleosides in alive human brain we used a recently developed reverse extrapolation method and multivariate statistical analyses.3. We analyzed four nucleosides and three nucleobases in human cerebellar, cerebral cortices and in white matter in young and old adults. Average concentrations of the 308 samples investigated (mean±SEM) were the following (pmol/mg wet tissue weight): adenosine 10.3±0.6, inosine 69.5±1.7, guanosine 13.5±0.4, uridine 52.4±1.2, uracil 8.4±0.3, hypoxanthine 108.6±2.0 and xanthine 54.8±1.3. We also demonstrated that concentrations of inosine and adenosine in the cerebral cortex and guanosine in the cerebral white matter are age-dependent.4. Using multivariate statistical analyses and degradation coefficients, we present an uneven regional distribution of nucleosides in the human brain. The methods presented here allow to creation of a nucleoside map of the human brain by measuring the concentration of nucleosides in microdissected tissue samples. Our data support a functional role for nucleosides in the brain.     

Oligonucleotides Containing Disaccharide Nucleosides: Synthesis,Physicochemical, and Substrate Properties

Abstract

The efficient synthesis of oligonucleotides containing 2′-O-β-D-ribofuranosyl (and β-D-ribopyranosyl)nucleosides, 2′-O-α-D-arabinofuranosyl (and α-L-arabinofuranosyl)nucleosides, 2′-O-β-D-erythrofuranosylnucleosides, and 2′-O-(5′-amino-5-deoxy-β-D-ribofuranosyl)nucleosides have been developed.     

Investigation of Anti‐Fatigue Effect and Simultaneous Determination of Eight Nucleosides in Different Parts of Velvet Antler in Red Deer and Sika Deer

Velvet antler (VA) is crucial and precious nourishment in China and some countries in Southeast Asia and has excellent anti‐fatigue effect. The incidence of fatigue syndrome has increased gradually. VA can be a potential source of anti‐fatigue products. Therefore, we investigated the anti‐fatigue activity of different sections (upper, middle, and basal section) of VA from different species (red deer and sika deer) via loading swimming test in mice. Furthermore, nucleosides are one kind of active components in VA which could considerably reduce fatigue in mice. In order to explore whether the nucleosides are correlated with anti‐fatigue effect, the contents of eight nucleosides (uracil, cytidine, hypoxanthine, xanthine, thymine, inosine, guanosine, and adenosine) were determined simultaneously using high‐performance liquid chromatography. The results indicated that the swimming time in mice was increased from basal to upper section, which was consistent with the change trend of the total contents of eight nucleosides of VA. Therefore, we speculated that the contents of nucleosides in VA may affect its anti‐fatigue effect. Furthermore, the contents of nucleosides were also used as a reference for evaluating the quality of different parts of VA obtained from red and sika deer.     

Subribosomal particle analysis reveals the stages of bacterial ribosome assembly at which rRNA nucleotides are modified

Modified nucleosides of ribosomal RNA are synthesized during ribosome assembly. In bacteria, each modification is made by a specialized enzyme. In vitro studies have shown that some enzymes need the presence of ribosomal proteins while other enzymes can modify only protein-free rRNA. We have analyzed the addition of modified nucleosides to rRNA during ribosome assembly. Accumulation of incompletely assembled ribosomal particles (25S, 35S, and 45S) was induced by chloramphenicol or erythromycin in an exponentially growing Escherichia coli culture. Incompletely assembled ribosomal particles were isolated from drug-treated and free 30S and 50S subunits and mature 70S ribosomes from untreated cells. Nucleosides of 16S and 23S rRNA were prepared and analyzed by reverse-phase, high-performance liquid chromatography (HPLC). Pseudouridines were identified by the chemical modification/primer extension method. Based on the results, the rRNA modifications were divided into three major groups: early, intermediate, and late assembly specific modifications. Seven out of 11 modified nucleosides of 16S rRNA were late assembly specific. In contrast, 16 out of 25 modified nucleosides of 23S rRNA were made during early steps of ribosome assembly. Free subunits of exponentially growing bacteria contain undermodified rRNA, indicating that a specific set of modifications is synthesized during very late steps of ribosome subunit assembly.     

Simultaneous Determination of Purine and Pyrimidine Metabolites in Hprt-Deficient Cell Lines

Genetic mutations in the purine salvage enzyme, hypoxanthine-guanine phosphoribosyltransferase (HPRT), are known to cause Lesch–Nyhan syndrome and Kelley–Seegmiller syndrome. In patients, purine metabolism is different from that of normal persons. We have previously developed a method for simultaneously determining the concentration of purine and pyrimidine nucleosides and nucleotides. This system was applied to determine the concentrations of nucleosides and nucleotides in HPRT-deficient cell lines. The amount of inosine 5′-monophosphate (IMP) was different in Lesch–Nyhan syndrome, Kelley–Seegmiller syndrome, and control cell lines. The difference in the amount of IMP confirmed the mutation of the enzyme.     

Physiological concentrations of purines and pyrimidines

The concentrations of bases, nucleosides, and nucleosides mono-, di- and tri-phosphate are compared for about 600 published values. The data are predominantly from mammalian cells and fluids. For the most important ribonucleotides average concentrations ±SD (M) are: ATP, 3,152±1,698; GTP, 468±224; UTP, 567±460 and CTP, 278±242. For deoxynucleosidestriphosphate (dNTP), the concentrations in dividing cells are: dATP, 24±22; dGTP, 5.2±4.5; dCTP, 29±19 and dTTP 37±30. By comparison, dUTP is usually about 0.2 M. For, the 4 dNTPs, tumor cells have concentrations of 6–11 fold over normal cells, and for the 4 NTPs, tumor cells also have concentrations 1.2–5 fold over the normal cells. By comparison, the concentrations of NTPs are significantly lower in various types of blood cells. The average concentration of bases and nucleosides in plasma and other extracellular fluids is generally in the range of 0.4–6 M; these values are usually lower than corresponding intracellular concentrations. For phosphate compounds, average cellular concentrations are: P_i, 4400; ribose-1-P, 55; ribose-5-P, 70 and P-ribose-PP, 9.0. The metal ion magnesium, important for coordinating phosphates in nucleotides, has values (mM) of: free Mg²⁺, 1.1; complexed-Mg, 8.0. Consideration of experiments on the intracellular compartmentation of nucleotides shows support for this process between the cytoplasm and mitochondria, but not between the cytoplasm and the nucleus.     

Synthesis and Antitumor Activity of N-Sulfonyl Derivatives of Nucleobases and Sulfonamido Nucleoside Derivatives

Abstract

The introduction of sulfonamido group on the C-2 position of pyrimidine nucleosides was achieved by ring opening of 2,2′- and 2,3′-anhydronucleosides. N-sulfonyl derivatives of nucleobases and sulfonamido derivatives of nucleosides were assayed for in vitro antitumor activity.     

Differential reactivity of alpha and beta 2'-deoxyribonucleosides towards protonation and metalation

The reactivity of artificial 2'-deoxyribonucleosides, designed as nucleoside surrogates in metal-mediated base pairs, towards protonation and metalation has been shown to be dependent on the choice of the anomer. The alpha nucleosides comprising the aglycones imidazole, 1,2,4-triazole, benzimidazole and imidazo[4,5-b]pyridine are more basic than the respective beta nucleosides as was shown by a combined experimental and theoretical approach. The DeltapK(a) values observed experimentally are in the range of 0.19+/-0.03 to 0.41+/-0.07 (with the error representing three times the standard deviation of the mean value). An independent confirmation of this differential reactivity was obtained from density functional theory (DFT) calculations using 1,2,4-triazole nucleoside as an example. The result of these calculations is in good agreement with the experimental data (DeltapK(a)=0.16 vs. 0.21+/-0.07). The stability of the respective metal ion complexes of the anomeric 1,2,4-triazole nucleosides follows the same trend as that of the respective protonated nucleosides: Those of the alpha nucleoside are more stable than those of the beta nucleoside (Deltalogbeta(2)=0.6+/-0.2 for the 2:1 complex with Ag(+); Deltalogbeta(1)=0.51+/-0.07 for the 1:1 complex with Hg(2+)). These slightly different reactivities will be useful for fine-tuning the metal-ion binding behavior of oligonucleotides containing metal-mediated base pairs.     

Determination of pseudouridine and other nucleosides in human blood serum by high-performance liquid chromatography

A specific, sensitive, and rapid method to measure pseudouridine in human blood serum is described. The method is based on the following steps: (i) deproteinization of serum samples by filtration on membrane cones or by acetonitrile; (ii) purification of nucleosides and concentration of the sample by affinity chromatography on phenylboronate gel followed by lyophilization; and (iii) separation of nucleosides and their quantitation by reserse-phase high-performance liquid chromatography.The pseudouridine mean value in 30 normal subjects was 2.52 ± 0.28 nmol/ml. The procedure also allows the identification of inosine, uridine, guanosine, and adenosine. Nevertheless, the presence in human blood serum of enzymatic activities which convert adenosine to inosine and cytidine to uridine prevents the precise quantitation of these nucleosides. All the compounds were identified by comparing their retention times and absorbance ratios ($\text{A}{}_{280}\text{A}{}_{254}$) with those of pure compounds, as well as by cochromatography.     

Bicyclic Nucleoside Synthesis—A Photochemical Approach

The synthesis of a series of bicyclic nucleosides using photolytic ring-expansion of cyclobutanones is reported. The cyclobutanone precursors were prepared by [2+2] cycloaddition of a series of cyclic alkenes with chlorinated ketenes, derived from dichloro- and trichloroacetyl chloride. The synthesis of the nucleosides was achieved through photolysis of cyclobutanone precursors with 6-chloropurine by UV irradiation. The generality of this method was investigated and the absolute stereochemistry was assigned by NMR spectroscopy. The photoproducts demonstrated a marked preference for the 2′-exo conformation.     

2‐Azapurine Nucleosides: Synthesis,Properties, and Base Pairing of Oligonucleotides

This review deals with 2‐azapurine (imidazo[4,5‐d] [1,2,3]triazine) nucleosides and closely related analogs. Different routes are described to yield the desired target compounds, including a sequence of ring‐opening and ring‐closure reactions performed on purine nucleosides or direct glycosylation of a 2‐azapurine nucleobase with a sugar halide. Further, physical and spectroscopic properties of 2‐azapurine nucleosides are discussed, including fluorescence, ¹³C‐NMR data, single‐crystal X‐ray analyses, and conformation studies on selected compounds; new biological data are presented. The second part of this review is dedicated to oligonucleotides containing 2‐azapurines, including building‐block (phosphoramidite) preparation and their use in solid‐phase oligonucleotide synthesis. Base‐pairing properties of 2‐azapurine nucleosides as surrogates of canonical constituents of DNA were evaluated.     

Rearrangement Reactions of Guanosine Cyclonucleosides and Their Analogs

Abstract

Under acid-catalyzed transglycosylation conditions 5′,8-cyclo-8-oxoguanine nucleosides undergo a ring-opening reaction to 8-oxoguanine derivatives, instead of the 7–9 isomerization.     

Recombinant photoreactive tRNA molecules as probes for cross-linking studies

Photoreactive tRNA derivatives have been used extensively for investigating the interaction of tRNA molecules with their ligands and substrates. Recombinant RNA technology facilitates the construction of such tRNA probes through site-specific incorporation of photoreactive nucleosides. The general strategy involves preparation of suitable tRNA fragments and their ligation either to a photoreactive nucleotide or to each other. tRNA fragments can be prepared by site-specific cleavage of native tRNAs, or synthesized by enzymatic and chemical means. A number of photoreactive nucleosides suitable for incorporation into tRNA are presently available. Joining of tRNA fragments is accomplished either by RNA ligase or by DNA ligase in the presence of a DNA splint. The application of this methodology to the study of tRNA binding sites on the ribosome is discussed, and a model of the tRNA-ribosome complex is presented.     

Synthesis of new mannosyl, galactosyl and glucosyl theophylline nucleosides with potential activity as antagonists of adenosine receptors. DEMA-induced cyclization of glycosylideneiminouracils

The synthesis of D-mannosyl, D-galactosyl and D-glucosyl theophylline nucleosides by diethoxymethyl acetate (DEMA)-induced cyclization of 4-amino-5-glycosylideneimino-1,3-dimethyluracil is reported. 8-Methyltheophylline derivatives of the same sugars were also prepared by Ac(2)O/H(+)-induced cyclization of their imine precursors. This approach has allowed beta-D-mannopyranosyl-, alpha-D-galactofuranosyl- and beta-D-glucofuranosyltheophylline nucleosides to be synthesized for the first time. The inhibition of specific binding at A(1), A(2A), A(2B) and A(3) adenosine receptors in the mannose derivatives is also reported.