Derivatives of 1-(2-Deoxy-2-fluoro-β-D-arabinofuranosyl)-5-phenyluracil and 5-Benzyluracil. Synthesis and Biological Properties

Abstract

A number of 1-(2-deoxy-2-fluoro-β-D-arabinofuranosyl)uracil and -cytosine nucleosides substituted at the 5 position with a nitrophenyl or nitrobenzyl group were synthesized from 5-phenyl- and 5-benzyluracil via condensation of the fluorinated sugar, followed by nitration. The corresponding amino analogues were also prepared by reduction of the nitro nucleosides. The uracil nucleosides were converted into the corresponding cytosine nucleosides by way of the triazole intermediates. None of these nucleosides exhibited significant activity against herpes simplex virus type 1 in Vero cells. However, cytosine nucleosides containing the o-nitrophenyl, p-nitrophenyl, p-nitrobenzyl or p-aminobenzyl substituent were found to be toxic (even at 1 μM) to uninfected Vero cells, although they were essentially nontoxic in HL-60 cells. The 5′-monophosphates of the uracil nucleosides were inhibitors of the reaction catalyzed by purified Ehrlich ascites carcinoma thymidylate synthase, the 5-phenyluracil nucleotides causing a strong inhibition, competitive vs dUMP, described by the K_i value of 0.01 μM.     

The Synthesis of Novel Transition State Analogues Related to Imidazole and Purine Nucleotides Involved in the De novo Biosynthesis of Purines

Abstract

5-Amino-4-sulphonamidoimidazole ribofuranosyl nucleosides and a related imidazothiadiazine dioxide nucleoside have been synthesized as potential inhibitors of enzymes involved in the de novo biosynthesis of purine nucleotides.     

The Synthesis of Deuterionucleosides

Abstract

The synthesis of deuterionucleosides for site-specific incorporation into oligo-DNA or -RNA is herein reviewed for NMR or biological studies. The review covers the following aspects: (i) deuteration of the aglycone; (ii) single-site chemical deuteration of the sugar residues; (iii) multiple-site chemical deuteration of the sugar residues; (iv) enzymatic synthesis of deuterated nucleosides or nucleotides; and (v) synthesis of labelled nucleosides with multiple isotopes.     

The occurrence of the syn-C3′ endo conformation and the distorted backbone conformations for C4′-C5′ and P-O5′ in oligo and polynucleotides

Abstract

The nucleoside constituents of nucleic acids prefer the anti conformation (1). When the sugar pucker is taken into account the nucleosides prefer the C2′endo-anti conformation. Of the nearly 300 nucleosides known, about 250 are in the anti conformation and 50 are in the syn-conformation, i.e., anti to syn conformation is 5:1. The nucleotide building blocks of nucleic acids show the same trend as nucleosides. Both the deoxy-guanosine and ribo- guanosine residues in nucleosides and nucleotides prefer the syn-C2′endo conformation with an intra-molecular hydrogen bond (for nucleosides) between the O5′- H and the N3 of the base and, a few syn-C3′endo conformations are also observed. Evidence is presented for the occurrence of the C3′endo-syn conformation for guanines in mis-paired double helical right-handed structures with the distorted sugar phosphate C4′-C5′ and P-O5′ bonds respectively, from g+ (gg) and g- to trans. Evidence is also provided for guanosine nucleotides in left-handed double-helical (Z-DNA) oligo and polynucleotides which has the same syn-C3′endo conformation and the distorted backbone sugar-phosphate bonds (C4′-C5′ and P- O5′) as in the earlier right-handed case.     

Commentary: Metabolic Impediments to the use of Nucleotide Derivatives to Circumvent Resistance to Purine and Pyrimidine Analogs

Abstract

Many attempts have been made to design derivatives of analog nucleotides that might circumvent resistance due to deficiency of enzymes that convert analogs of purines, pyrimidines and nucleosides to nucleotides. None of these prodrugs that have been evaluated has been active against resistant tumor cells in vivo. The probable reason for this failure is that host cells, but not the resistant cells, have the capacity to form toxic nucleotides from bases or nucleosides resulting from degradation of the prodrugs. These considerations indicate that this strategy for circumvention of resistance will be successful only if the prodrug has some property, other than ability to enter the cell and be converted to toxic nucleotide, that will result in selective toxicity to resistant cells.     

Synthesis of 3′-C-Phosphono Nucleosides from α,β-Unsaturated Lactone

Abstract

The reaction of 5-protected α,β-unsaturated γ-lactone 4 with trialkylphosphite gave 3′-C-dialkylphosphono-erythro lactone 5 in high yields. The lactone 5 was reduced with DIBAL to the corresponding lactol, which was converted to the acetate 6 by treatment with acetic anhydride in pyridine. The acetate 6 was coupled with silylated thymine in the presence of TMS-triflate and the resulting anomeric mixture of nucleotides could be separated chromatographically and after desilylation using TBAF in THF the 3′-C-dialkylphosphono nucleosides 7 and 8 were obtained.     

Electroanalytical Study on Nicotinamide 7-Methylguanine Dinucleotide (Nm7GD+), Analog of Coenzyme NAD+ and Related Compounds

Abstract

Electrochemical methods (direct-current polarography, cyclic voltammetry and differential pulse polarography) were used for analysis of 7-methylguanine nucleosides and nucleotides.     

Synthesis of 2′-Spiro Ribo- and Arabinonucleosides

Abstract

Four conformationally restricted bicyclic 2′-spiro nucleosides were synthesised and incorporated into oligonucleotides. These spiro nucleotides induced decreased duplex thermostabilities.     

Electrochemical Removal of Allylic Protecting Groups in Nucleotide Synthesis a

Abstract

Electrochemical, palladium(0)-mediated removal of allylic protecting groups of nucleosides and nucleotides is described. This method required no chromatographic treatment for isolation of the products.

     

C-5 Substituted Pyrimidine Nucleosides,Synthesis of 5-Alkylglycoside Deoxyuridine and Uridine Analogs VIA Organopalladium Intermediates

Abstract

In this communication, we report a chemical synthesis of 5-alkyl glycoside (αD-2-acetamido-2-deoxyglucopyranoside and a D-manno pyranoside) uridine derivatives. These compounds could have importance in molecular genetics as affinity reagents, since it is expected that these modified nucleosides and nucleotides have strong non-bonding interactions with lectins and thus could be selectively retained on such a column.     

Possibility for the Existence of a General Conformational Motif in the Active Sites of Enzymes Which are Involved in Nucleic Acids Metabolism

Abstract

Many different modified nucleosides and nucleotides with conformationally restricted partly flattened sugar residues are analyzed as substrates or inhibitors of several groups of enzymes of nucleic acid metabolism. A detailed examination of the sugar moiety of large group of modified nucleosides showed that there is a striking conformational similarity, i.e., they are flattened. We propose herein a hypothesis which can represent a general conformational elements in the structure of the active sites of several different groups of enzymes. This proposal envisions that during the enzymatic process natural substrates should reflect these flattened conformations. This hypothesis allows computation of conformational analyses of the enzyme actives centers as well as the design of new actively metabolized modified nucleosides.     

HPLC as a Tool to Study the Kinetics of Parallel and Consecutive Reactions: Competitive Interconversion,Dephosphorylation, Deamination and Depyrimidination of Cytidine 2′- and 3′-Monophosphates in Aqueous Acid

Abstract

The applicability of HPLC as a method to study the kinetics of complicated reaction systems of nucleosides and nucleotides has been demonstrated by using the hydrolytic reactions of cytidine 2′- and 3′-monophosphates as an example.     

Mass Spectrometry: Applications in the Analysis of Nucleosides,Nucleotides and Oligonucleotides

Abstract

The past ten years have been an exciting time in mass spectrometry as a number of important instrumental developments have revolutionized the field, including the analysis of nucleic acid components.^1,2 The focus of this talk will be on the impact that new ionization methods, e.g., plasma desorption(PD) and fast atom bombardment(FAB), and new magnet technology (expanded mass range and scan speed capability) have had on the analysis of nucleosides and nucleotides. Results from the speaker's laboratory will be used to illustrate the significance of capillary GC/MS techniques for the separation and analysis of complex mixtures of nucleosides derived from a biological source. In addition, some approaches being developed to overcome current limitations in the FAB analysis of nucleosides and nucleotides will be described. Unfortunately, time does not permit a discussion of other new areas of interest, i.e., LC/MS³ and MS/MS.⁴     

The Acidic Hydrolysis of Nucleosides and Nucleotides

Abstract

The influence of sugar and base substitutions on the stability of the N-glycosidic bond of nucleosides in acidic medium is examined in detail. Then the mechanistic aspect of the phenomenon is described. The last part is devoted to the acidic hydrolysis of nucleotides.     

Conformational Studies on Nucleosides with Furanose Ring Modifications. 1.

Abstract

Conformational energy calculations have been presented on adenine and thymine nucleosides in which the furanose ring is replaced by 2′,3′-dideoxy-2′,3′-didehydrofuran using molecular mechanics and conformational analysis. Conformational energies have been evaluated using the MM2 and AMBER94 force field parameters at two different dielectric constants. The results are presented in terms of isoenergy contours in the conformational space of the glycosidic (χ) and C4′-C5′ (γ) bonds torsions. In general, the χ-γ interrelationships exhibit similarities with the corresponding plots for unmodified nucleosides and nucleotides, reported previously. Consistency of the calculated preferred conformations with the X-ray data is sensitive to the force field employed.     

Fast atom Bombardment Mass Spectrometry of Nucleosides,Nucleotides and Oligonucleotides

Abstract

Fast atom bombardment (FAB) mass spectrometry, a new ionization technique, has been applied to a variety of polar, nonvolatile compounds with considerable success. Current literature regarding the analysis of nucleosides, nucleotides and oligonucleotides using FAB is reviewed.     

2′-Deoxycoformycin: Biosynthesis and Enzymatic Conversion of 8-Keto-Deoxycoformycin to 2′-Deoxycoformycin by Streptomyces Antibioticus

Abstract

Studies on t h e biosynthesis o f the N-nucleoside antibiotics have established that the purine and pyrimidine nucleosides/nucleotides serve as the carbon and nitrogen skeleton, whereas with the C-nucleoside antibioticus, the C-N precursor forthe aglycon is either acetate or glutamate. With the pyrrolopyrimidine nucleoside antibiotics (toyocamycin, tubercidin, and sangi vamycin), either two or three carbons of the N-riboside/ribotide of GTP contribute to carbons 5 and 6 of the pyrrolering and the cyano or carboxamide group. With the naturally occurring nucleoside antibiotic containing the 1,3-diazepine seven-membered ring,2′-deoxycoformycin (dCF)(I), the precursor is not immediately obvious.     

Bacterial Synthesis of Nucleotides

5′-Phosphoribosyl 5-amino-4-imidazole carboxamide was prepared by incubating 5-amino-4-imidazole carboxamide riboside and a phosphate compound with the bacteria characterized to phosphorylate at C_5′ via the phosphoryl transfer reaction. Aromatic phosphate compounds and 5′-nucleotides were able to act as the phosphate donor. This material was isolated chromatographically and its properties were studied. The other bacteria characterized to phosphorylate at C_{3′ (or 2′)} also phosphorylated a little probably at C_{3′ (or 2′)} of 5-amino-4-imidazole carboxamide riboside.

The phosphoryl interconversion between nucleotides and nucleosides was studied to be carried out via the phosphoryl transfer reaction observed in bacteria. The phosphotransferase activity of Ps. trifolii mediated reversibly the phosphoryl transfer between 5′-nucleotides and nucleosides, and its optimal pH was at around 8.5, whereas that of Prot. mirabilis did transfer the phosphoryl radical from 2′- and 3′-nucleotide to nucleoside at its optimal pH, around 5.0.

These donor- and product-isomer specificities of both bacteria were evident to be invariable, regardless of reaction pH and cultural conditions. These reactions, especially using the bacteria characterized to phosphorylate at C_5′ of nucleoside, were demonstrated to catalyze the phosphoryl interconversion between 5′-purine nucleotides and pyrimidine nucleosides or vice versa.     

A Systematic Study of Patterns of Hydration in Nucleic Acids:(I) Guanine and Cytosine

Abstract

The hydration sites of guanine and cytosine are defined by examination of the crystal structures of bases, nucleosides, nucleotides, and three dinucleoside phosphate salts. The patterns of hydration for two guanine and cytosine containing oligonucleotides are then predicted. The relationship between these structural motifs and thermodynamic parameters is discussed.     

Temporal variations of nucleosides and nucleotides in rabbit milk

Abstract

Nucleotides and nucleosides have a preeminent role in physiological and biochemical processes for newborns, the major source of these during early development is the breast milk. Different biomolecules exhibit daily fluctuations in maternal milk that could transfer temporal information that synchronize newborn circadian system. As a first approach, we characterized the diurnal profile of nucleotides and nucleosides contained in maternal milk of rabbits during the first week of lactation. It is possible that some nucleosides, such as adenosine, play a relevant role in setting up the emerging circadian rhythmicity, whereas uridine and guanosine could participate in the maintenance of rhythmicity.