Synthesis and Studies of 3′-C-Trifluoromethyl-β-D-ribonucleosides Bearing the Five Naturally Occurring Nucleic Acid Bases

Abstract

3′-C-Trifluoromethyl-β-D-ribonucleoside derivatives bearing the five naturally occurring nucleic acid bases have been synthesized. All these derivatives were prepared by glycosylation reactions of purine and pyrimidine bases with a suitable peracylated 3-C-trifluoromethyl ribofuranose precursor. After deprotection, the resulting title nucleoside analogues were tested for their inhibitory properties against the replication of HIV, HBV and several RNA viruses. However, none of these compounds showed significant antiviral activity.     

Synthesis of 2'-deoxy and 2',3'-dideoxynucleoside derivatives from thioglycosides.

The synthesis of both 2'-deoxy and 2',3'-dideoxynucleoside derivatives by the reaction of thioglycosides with nucleoside bases was examined. The stereochemical outcome at the anomeric position was found to depend on the protecting groups and the C-3 configuration in the sugar moiety, the kind of activator, and the reaction temperature. Based on these findings, 2'-deoxy-D-xylo nucleoside and 2',3'-dideoxynucleoside derivatives have been synthesized in beta-selective manner.     

Synthesis of UV-curable chitosan derivatives and palladium (II) adsorption behavior on their UV-exposed films

Novel chitosan derivatives with UV-curable functional groups, such as 3-methoxy-4-(2-hydroxy-3-methacryloyloxypropoxy)benzyl, 3,4-bis(2-hydroxy-3-methacryloyloxypropoxy)benzyl, 3-methoxy-4-methacryloyloxybenzyl, and 3,5-dimethacryloyloxybenzyl groups, were prepared. Introduction of photosensitive functional groups to chitosan was accomplished by reductive N-alkylation via Schiff’s bases using corresponding photosensitive aldehydes. Compared to starting chitosan, UV-curable chitosan derivatives showed better solubility in several organic solvents, such as DMSO and 70% methacrylic acid. The solubility of these compounds increased with an increase in the degree of substitution of the N-alkyl side chains. After UV irradiation for 20 s under a high-pressure mercury lamp at a distance of 15 cm from the samples, acidic methanol solutions of these derivatives were transformed to gels in the presence of photo-initiator, and their dried films adsorbed palladium (II) at pH 1.1 and pH 5.3. The UV-curable chitosan derivatives were successfully used as coating materials for electroless plating on non-conductive substances.     

Polymethylene Derivatives of Nucleic Bases with ω-Functional Groups: V. Pyrimidine- and Purine-Containing γ-Butyrophenones

New polymethylene derivatives of nucleic bases containing a keto function in the ω-position were synthesized by alkylation of nucleic bases with 2-(3-chloropropyl)-2-phenyl-1,3-dioxolane and the subsequent deblocking of the keto group; their physicochemical properties were studied.     

Synthesis of 3'-deoxy-3'-C-methyl nucleoside derivatives

2',3'-Dideoxy-3'-C-methyl nucleosides bearing the five naturally occurring nucleic acid bases were synthesized. Additionally, the 3'-deoxy-3'-C-methyl nucleoside analogues bearing 5-aminoimidazole-4-carboxamide as well as 1,2,4-triazole-3-carboxamide moieties were prepared. The synthesis of the corresponding 2',3'-dideoxy-3'-C-methyl triazole derivative was also accomplished. The dideoxynucleoside derivatives were prepared by radical deoxygenation from their 3'-deoxy-3'-C-methyl parent ribonucleosides. When evaluated for their antiviral activity in cell culture experiments, none of these compounds showed any significant antiviral activity.     

Synthesis of 6-(2-thienyl)purine nucleoside derivatives toward the expansion of the genetic code.

Unnatural bases specifically pairing with pyridin-2-one, 2-amino-6-(2-thienyl) purine and 2-amino-6-(2-furanyl)purine, were newly designed to replace 2-amino-6-(N,N-dimethylamino)purine. It was expected that these novel purine analogues, as compared with 2-amino-6-(N,N-dimethylamino)purine, might reduce the interference in the stacking interactions with the neighboring bases in a duplex and improve the efficiency of the enzymatic incorporation of the nucleoside triphosphate of pyridin-2-one opposite these unnatural bases. The syntheses of these nucleoside derivatives and the DNA fragments were examined.     

High-performance liquid chromatography analysis of molecular species of sphingolipid-related long chain bases and long chain base phosphates in Saccharomyces cerevisiae after derivatization with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate.

The molecular species of dihydrosphingosines and phytosphingosines and their 1-phosphates with carbon chain lengths from 16 to 20 have been tagged with the fluorescent amino group reagent, 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate. All these derivatives could be resolved by reversed phase HPLC on a C18 column. A convenient one-pot method is described whereby lipid extracts from strains of Saccharomyces cerevisiae containing carbon chain length homologs of sphingolipid long chain bases and their phosphorylated derivatives were directly reacted with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate, ester lipids were deacylated, and the reaction mixtures were subjected to liquid chromatography. Five molecular species of both sphingolipid long chain bases and their phosphorylated derivatives are for the first time separated and analyzed. The procedure is quite sensitive, requiring only approximately 10(8) wild-type cells.     

Long-chain bases in the sphingolipids of atherosclerotic human aorta

Long-chain bases were prepared from human aorta sphingomyelin by a combined enzymatic hydrolysis-alkaline hydrolysis procedure and these bases were isolated by thin-layer chromatography. Aldehydes, obtained from the long-chain bases by periodate oxidation, were converted to 1,3-dioxolane derivatives. Dioxolanes were identified and quantified by gas-liquid chromatography before and after catalytic hydrogenation, and before and after separation into saturated, monoene, and diene dioxolane fractions. The monoene dioxolanes were converted to aldehydes by reductive ozonolysis with dimethyl sulfide and these aldehydes were isolated and identified as dioxolane derivatives. The double bond positions in the major diene component were established by reductive ozonolysis and permanganate-periodate oxidation. Sphingenines in the cerebroside-sulfatide and sulfatide fractions of aorta were converted to aldehydes by the reductive ozonolysis of intact sphingolipids and these aldehydes were analyzed as the dioxolanes. Human aorta sphingomyelin contained significant amounts of 4-hexadecasphingenine, 4-heptadecasphingenine, sphinganine, 4-sphingenine, and 4,x14-sphingadienine. Small amounts of hexadecasphinganine, 4-tetradecasphingenine, a sphingadienine isomer, an unknown sphinganine, and two unknown diene long-chain bases were also found in sphingomyelin. The presence of a branched-chain 4-sphingenine was tentatively established and the possible presence of a sphingenine isomer was suggested. The major sphingenines were the same in the sphingomyelin, sulfatide, and cerebroside-sulfatide fractions of human aorta.     

Synthesis and evaluation of some new spiro indoline-based heterocycles as potentially active antimicrobial agents

Several new spiro indoline-based heterocycles were synthesized by prior preparation of the 4-(2'-oxo-indol-3'-ylidene)-oxazol-5-one derivatives and subsequent reaction of the produced indol-3-ylidene based heterocycles with activated nitrile reagents. The obtained products were allowed to react with hydrazine hydrate in alcoholic basic to give the target compounds. Structure of these products was confirmed on the bases of elemental as well as spectral data. Representative compounds of the hitherto synthesized products were tested and evaluated as antimicrobial agents.     

Metabolic pool of purine compounds in erythrocytes of mice during growth of transplanted tumors

The pattern of purine derivatives was studied in the erythrocytes of C3HA and ICR mice during Hepatoma 22 and Ehrlich ascites tumor cells growth. Host erythrocytes purine nucleotides, nucleosides and bases were affected by the implanted tumors. The results indicated that the host erythrocytes markedly concentrated adenine and guanine nucleotides on the 5th and 11th-12th day of tumor growth. By contrast, content of nucleosides and bases were sharply decreased during the log growth phase (5th day) with the restoring of these precursors within the 11th-12th day (plateau phase). These observations indicate that aspects of the purine compounds metabolism in host erythrocytes are linked with tumor development.     

Identification of 10-methylsphinganine in cerebrosides of the guinea pig harderian gland

A large amount of branched long chain bases was detected in the cerebrosides of guinea pig Harderian gland. The long chain bases of cerebrosides were analyzed by GLC as trimethylsilyl derivatives. The branched long chain bases were separated into four peaks (I, II, III, IV) according to the number of carbon atoms and the position of branching. In the present work, the structures of long chain bases in the four peaks were analyzed by GLC and GC-MS after conversion of them to aldehydes, alcohols, and fatty acids. Furthermore the main component of long chain bases (Peak II) was isolated by HPLC as N-acetyl derivatives and analyzed by NMR. The structures of branched long chain bases in Peaks I, II, III, and IV are as follows. Branched long chain bases of Peak I are 2-amino-10- (main component), 2-amino-9-, and 2-amino-8-methylhexadecane-1,3-diol. Branched long chain bases of Peak II also consist of a mixture of 2-amino-10-, 2-amino-9-, and 2-amino-8-methyl-heptadecane-1,3-diol. The branched long chain base of Peak III is 2-amino-10-methyl-octadecane-1,3-diol, while that of Peak IV is 2-amino-16-methyloctadecane-1,3-diol. Among these branched long chain bases, 10-methylsphinganines are dominant though the chain lengths are different. These branched long chain bases, in which the substituted positions exist in the middle part of aliphatic chain (10-, 9-, or 8-methylsphinganine) are novel long chain bases in mammals.     

Application of capillary gas chromatography-mass spectrometry to chemical characterization of radiation-induced base damage of DNA: implications for assessing DNA repair processes

The application of capillary gas chromatography-mass spectrometry (GC-MS) to the chemical characterization of radiation-induced base products of calf thymus DNA is presented. Samples of calf thymus DNA irradiated in N2O-saturated aqueous solution were hydrolyzed with HCOOH, trimethylsilylated, and subjected to GC-MS analysis using a fused-silica capillary column. Hydrolysis conditions suitable for the simultaneous analysis of the radiation-induced products of all four DNA bases in a single run were determined. The trimethylsilyl derivatives of these products had excellent GC properties and easily interpretable mass spectra; an intense molecular ion (M+.) and a characteristic (M-CH3)+ ion were observed. The complementary use of t-butyldimethylsilyl derivatives was also demonstrated. These derivatives provided an intense characteristic (M-57)+ ion, which appeared as either the base peak or the second most intense ion in the spectra. All mass spectra obtained are discussed. Because of the excellent resolving power of capillary GC and the accurate high-sensitivity identification by MS, the capillary GC-MS is suggested as a very suitable technique for identification of altered bases removed from DNA by base excision-repair enzymes such as DNA glycosylases and, thus, as very useful for an understanding of the base excision-repair of DNA.     

Branched long-chain bases from the bivalve Corbicula sandai.

Long-chain bases were liberated from a crude mixture of sphingolipids from whole tissue of the fresh-water bivalve C. sandai, and conversion of the bases into N-acetyl-0-trimethylsily derivatives was accomplished. The derivatized bases were analyzed by combined gas-liquid chromatography and mass spectrometry. A portion of the sphingolipids was subjected to catalytic hydrogenation from whch saturated long-chain bases (sphinganines) were obtained. The saturated bases were oxidized with lead tetra-acetate and the aldehydes produced were analyzed by gas-liquid chromatography. The aldehydes were further oxidized to acids with silver oxide, the resulting fatty acids methylated and also analyzed by gas-liquid chromatography. By these analyses, altogether five long-chain bases were identified, consisting of hexadeca-4-sphingenine (15%), heptadeca-4-sphingenine (2%), iso-octadeca-4-sphingenine (13%), octadeca-4-sphingenine (39%) and anteiso-noadeca-4-sphingenine (31%). So far no branches have been found in shellfish spingolipid long-chain bases.     

Rapid synthesis of 2′,3′-dideoxy-3′β-fluoro-pyrimidine nucleosides from 2′-deoxypyrimidine nucleosides

A rapid synthesis of 2′,3′-dideoxy-3′-fluoro-β-d-threo-nucleosides bearing the pyrimidine canonical bases of nucleic acids has been developed in order to discover new nucleoside derivatives as potential antiviral drugs. However, when evaluated for their antiviral activity in cell culture experiments, none of these compounds showed any significant antiviral activity.     

Quantitative analysis of free sphingoid bases in the brain and spinal cord tissues by high-performance liquid chromatography with a fluorescence detection

The o-phthaldialdehyde precolumn derivatives of psychosine, sphinganine and sphingosine extracted from brain and spinal cord tissues were determined by high-performance liquid chromatography–fluorescence detection. This method was developed with the purpose of detecting an endogenous amount of psychosine, sphingosine and sphinganine using small aliquots of brain tissues and spinal cord in rats. These sphingolipid bases were extracted in various ratios of chloroform–methanol and several pH values. Recovery of the method is about 81% in 12 ng/tube (final volume, 320 μl), 90–95% in 45 ng/tube of sphingosine and sphinganine within 2–12% relative standard deviation. Detection limits of these sphingoid bases were about 0.05 pmol/mg brain tissue. In the forebrain, brainstem and spinal cord of rats at three different ages of postnatal days (PND) 1, PND 13 and 6 months old, the endogenous concentrations of psychosine, sphingosine and sphinganine were determined. From these results, this method is suitable for the determination of sphingoid bases in small aliquot of brain and spinal cord tissues.     

Polymethylene derivatives of nucleic bases with omega-functional groups. V. Pyrimidine- and purine-containing gamma-butyrophenones

New polymethylene derivatives of nucleic bases containing a keto function in the omega-position were synthesized by alkylation of nucleic bases with 2-(3-chloropropyl)-2-phenyl-1,3-dioxolane and the subsequent deblocking of the keto group; their physicochemical properties were studied. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2005, vol. 31, no. 6; see also http://www.maik.ru.     

Carbonic anhydrase inhibitors. Inhibition of cytosolic/tumor-associated carbonic anhydrase isozymes I, II, IX, and XII with Schiff's bases incorporating chromone and aromatic sulfonamide moieties, and their zinc complexes

A series of Schiff's bases was prepared by reaction of 3-formyl-chromone or 6-methyl-3-formyl-chromone with aromatic sulfonamides, such as sulfanilamide, homosulfanilamide, 4-aminoethyl-benzenesulfonamide, a pyrimidinyl-substituted sulfanilamide derivative, sulfaguanidine and 4-amino-6-trifluoromethyl-benzene-1,3-disulfonamide. The zinc complexes of these sulfonamides have also been obtained. The new derivatives and their Zn(II) complexes were investigated for the inhibition of four physiologically relevant isozymes of carbonic anhydrase (CA, EC 4.2.1.1): the cytosolic isoforms I and II, as well as the tumor-associated, transmembrane isozymes CA IX and XII. Except for the sulfaguanidine-derived compounds which were devoid of activity against all isozymes, the other sulfonamides and their metal complexes showed interesting inhibitory activity. Against isozyme CA I, the inhibition constants were in the range of 13-100 nM, against isozyme CA II in the range of 1.9-102 nM, against isozyme CA IX in the range of 6.3-48nM, and against CA XII in the range of 5.9-50nM. Generally, the formyl-chromone derived compounds were better CA inhibitors as compared to the corresponding 6-methyl-chromone derivatives, and for the simple, benzenesulfonamide derivatives activity increased with an increase of the spacer from sulfanilamide to homosulfanilamide and 4-aminoethylbenzenesulfonamide derivatives, respectively. Some of these compounds may show applications for the development of therapies targeting hypoxic tumors in which CA IX and XII are often highly overexpressed.     

Overcoming potassium-mediated triplex inhibition.

Sequence-specific duplex DNA recognition by oligonucleotide-directed triple helix formation is a possible approach to in vivo gene inhibition. However, triple helix formation involving guanine-rich oligonucleotides is inhibited by physiological ions, particularly K+, most likely due to oligonucleotide aggregation via guanine quartets. Three oligodeoxynucleotide (ODN) derivatives were tested for their ability to resist guanine quartet-mediated aggregation, yet form stable triplexes. Electrophoretic mobility shift and dimethyl sulfate footprinting assays were used to analyze the formation of triplexes involving these oligonucleotide derivatives. In the absence of K+, all ODNs had similar binding affinities for the duplex target. Triplexes involving a 14mer ODN derivative containing 7-deazaxanthine substituted for three thymine bases or an 18mer ODN containing two additional thymines on both the 5' and 3' termini were abolished by 50 mM K+. Remarkably, triplexes involving an ODN derivative containing four 6-thioguanine bases substituted for guanine resisted K+ inhibition up to 200 mM. We hypothesize that the increased radius and decreased electronegativity of sulfur in the 6-position of guanine destabilize potential guanine quartets. These results improve the prospects for creating ODNS that might serve as specific and efficient gene repressors in vivo.     

A novel approach to the synthesis of oligodeoxyribonucleotide boranophosphates.

Deoxyribonucleoside 3'-boranophosphate derivatives including adenine, cytosine, guanine, and thymine bases were synthesized in good yields by the use of a new boranophosphorylation reaction. The reaction was found to be effective for the formation of internucleotidic boranophosphate linkages.     

A review of conditions affecting the radiolysis due to40K on nucleic acid bases and their derivatives adsorbed on clay minerals: Implications in prebiotic chemistry

This paper describes the possible effects of ionizing radiation arising from long-lived soluble radionuclides within clays, in particular⁴⁰K, at the epoch of the emergence of life on Earth. The free dispersion of soluble radionuclides constitutes an effectivein situ irradiation mechanism that might have acted upon adsorbed nucleic bases and their derivatives on clays, inducing chemical changes on these organic molecules. Several types of well documented reactions for radiolysis of nucleic acid bases and their derivatives are known, even at low doses (i.e., 0.1 Gy). For example, estimates with a dose rate calculated from⁴⁰K from deep sea clays at 3.8 Ga ago, indicates that over a period of 1000 years the amount of organic material transformated is 1.8 × 10^–7 moles/kg-clay.Although ionizing radiation may also induce synthetic reactions with prebiological interest, all in all these considerations indicate that nucleic acid bases and their derivatives adsorbed on clays were exposed for long periods to degradation conditions. Such situation promotes decomposition of organic molecules rather than protection of them and enhancement of further polymerization, as it has been usually taken for granted.