D-ribose Moiety Research Articles

Design, synthesis and antiviral evaluation of 2'-C-methyl branched guanosine pronucleotides: the discovery of IDX184, a potent liver-targeted HCV polymerase inhibitor.

Ribonucleoside analogs possessing a β-methyl substituent at the 2'-position of the d-ribose moiety have been previously discovered to be potent and selective inhibitors of hepatitis C virus (HCV) replication, their triphosphates acting as alternative substrate inhibitors of the HCV RdRp NS5B. Results/methodology: In this article, the authors detail the synthesis, anti-HCV evaluation in cell-based replicon assays and structure-activity relationships of several phosphoramidate diester derivatives of 2'-C-methylguanosine (2'-MeG). The most promising compound, namely the O-[S-(hydroxyl)pivaloyl-2-thioethyl]{abbreviated as O-[(HO)tBuSATE)]} N-benzylamine phosphoramidate diester derivative (IDX184), was selected for further in vivo studies, and was the first clinical pronucleotide evaluated for the treatment of chronic hepatitis C up to Phase II trials.

Characterization of [ 3H]LUF5834: A novel non-ribose high-affinity agonist radioligand for the adenosine A 1 receptor

The adenosine A 1 receptor is a promising therapeutic target for neurological disorders such as cognition deficits and is involved in cardiovascular preconditioning. Classically adenosine receptor agonists were all derivatives of adenosine, and thought to require a D-ribose moiety. More recently, however, the discovery of non-adenosine agonists for the human adenosine A 1 receptor (hA 1R) has challenged this dogma (Beukers et al., 2004). In this study we characterize the tritiated form of one of these compounds, [ 3H]LUF5834, as the first non-ribose partial agonist radioligand with nanomolar affinity for the hA 1R. Due to its partial agonist efficacy, [ 3H]LUF5834 labeled both G protein-coupled and uncoupled receptors with a similar high affinity. Using [ 3H]LUF5834 we performed competition binding experiments to characterize a range of A 1R ligands varying in efficacy from the full agonist CPA to the inverse agonist DPCPX. Surprisingly, in the control condition both agonists and inverse agonists displayed biphasic isotherms. With the addition of 1 mM GTP the high affinity isotherm of agonists or the low affinity isotherm of inverse agonists was lost revealing the mechanism of action of such inverse agonists at the A 1R. Consequently, [ 3H]LUF5834 represents a novel high affinity radioligand for the A 1R and may prove a useful tool to provide estimates of inverse agonist efficacy at this receptor.

The lectin-like activity of human C1q and its implication in DNA and apoptotic cell recognition

C1q, the binding subunit of the C1 complex of complement, is an archetypal pattern recognition molecule known for its striking ability to recognize a wide variety of targets, ranging from pathogenic non self to altered self. DNA is one of the C1q ligands, but the precise region of C1q and the DNA motifs that support interaction have not been characterized yet. Here, we report for the first time that the peripheral globular region of the C1q molecule displays a lectin-like activity, which contributes to DNA binding through interaction with its deoxy- d-ribose moiety and may participate in apoptotic cell recognition.

Preparation and XAFS studies of organotin(IV) complexes with adenosine and related compounds and calf thymus DNA

Complexes of adenosine and related compounds (adenosine-5’-monophosphate, adenosine-5’-triphosphate and pyridoxal-5-phosphate) with Bu2SnO and/or BuSnCl2 were prepared in the solid state. The compositions of the complexes were determined by standard analytical methods. It was found that the complexes contain the organotin(IV) moiety and the ligand in a ratio of 1:1. The FT-IR spectra demonstrated that Bu2SnO reacts with the D-ribose moiety of the ligands, while Bu2SnCl2 is coordinated to the deprotonated phosphate group. The basic part of the ligands does not participate directly in complex formation. Comparison of the experimental Mossbauer Δ (quadrupole splitting) values with those calculated on the basis of the pqs concept revealed that the organotin(IV) moiety has Tbp and in some cases also Th geometry. The adenosine complex contains the organotin(IV) cation in two different surroundings (Tbp and Th). The local structures of the complexes were determined by means of EXAFS measurements. At the same time a number of organotin(IV) complexes containing different organo moieties of calf thymus DNA were also prepared. Similarly as above, EXAFS data were obtained for these compounds and analyzed by using multishell models up to 300 pm. These results are the first structural data (bond lengths) on complexes formed with organotin(IV)-DNA and related compounds.

Infrared spectral change in 2-deoxy- d-ribose by irradiation with monochromatic photons around oxygen K-edge

Analyses of chemical changes in DNA by energy deposition from ionizing radiation are quite important to strictly know characteristics of radiobiological effects. Monochromatic photons from synchrotron radiation are one of the powerful probes to investigate the effects. As a step for the aim, chemical analyses by Fourier-transform infrared spectroscopy of the samples irradiated with the monochromatic photons were performed. It appeared that 2-deoxy- d-ribose irradiated around the energy of oxygen K-edge contained CO or CC, which would be responsible for a direct strand break of DNA. These data are noteworthy to find not only the strand scission at 2-deoxy- d-ribose moiety by the direct energy deposition by photon but also the following radiobiological responses such as cell killing or mutation.

Preparation and spectroscopic studies of diorganotin(IV) complexes with adenosine and related compounds

Nine complexes of adenosine and related compounds (adenosine-5'-monophosphate, adenosine-5'-triphosphate, 1-methyl-adenosine, pyridoxal-5-phosphate and β-nicotinamide-adenine-dinucleotide-phosphoric acid) with di-n-butyltin(IV) oxide and/or di-n-butytin(IV) dichloride were prepared in the solid state. The compositions of the complexes were determined by standard analytical methods. It was found that the complexes contain organotin(IV) moiety and the ligand in a ratio of 1:1 or 2:1. The FTIR spectra demonstrated that di-n-butyltin(IV) oxide reacts with the D-ribose moiety of the ligands, while di-n-butyltin(IV) dichloride is co-ordinated to the deprotonated phosphate group. The basic part of the ligands does not participate directly in complex formation. Comparison of the experimental Mossbauer QS values with those calculated on the basis of the PQS concept revealed that the organotin(IV) moiety has trigonal-bipyramidal, octahedral and in some cases tetrahedral geometry also. Some of the complexes contain the organotin(IV) cation in two different surroundings.

Evaluation of biosynthetic pathways to delta-aminolevulinic acid in Propionibacterium shermanii based on biosynthesis of vitamin B12 from D-[1-13C]glucose.

Analysis of the (13)C nuclear magnetic resonance (NMR) spectrum of (13)C-labeled vitamin B(12) biosynthesized from D-[1-(13)C]glucose by Propionibacterium shermanii provided evidence suggesting that delta-aminolevulinic acid (ALA) incorporated in the (13)C-labeled vitamin B(12) may have been synthesized via both the Shemin pathway and the C5 pathway under anaerobic conditions in the ratio of 1 < [(ratio of ALA biosynthesis from the Shemin pathway)/(that from the C5 pathway)] < 1.8. The D-ribose moiety of vitamin B(12) was labeled with (13)C at R-1, R-3, and R-5. The aminopropanol moiety of vitamin B(12) was labeled on Pr-1 and Pr-2, but not Pr-3.

EPR spectroscopic evidence for the mechanism-based inactivation of adenosylcobalamin-dependent diol dehydratase by coenzyme analogs.

EPR spectra were measured upon incubation of the complex of diol dehydratase with coenzyme analogs in the presence of 1,2-propanediol, a physiological substrate. When the analog in which the D-ribose moiety of the nucleotide loop was replaced by a trimethylene group was used as coenzyme, essentially the same EPR spectrum as that with adenosylcobalamin was obtained. The higher-field doublet and the lower-field broad signals derived from an organic radical and low-spin Co(II) of cob(II)alamin, respectively, were observed. With the imidazolyl counterpart, base-on cob(II)alamin-like species accumulated, but signals due to an organic radical quickly disappeared. When a coenzyme analog lacking the nucleotide moiety was incubated with apoenzyme in the presence of substrate, the EPR spectrum resembling cob(II)inamide was obtained, but no signals due to an organic radical were observed. From these results, it was concluded that the extinction of organic radical intermediates results in inactivation of the enzyme by these coenzyme analogs. Upon suicide inactivation with a [15N2]imidazolyl analog, the octet signals due to Co(II) showed superhyperfine splitting into doublets, indicating axial coordination of 5,6-dimethylbenzimidazole to the cobalamin bound to diol dehydratase.

Stereochemistry of nickel(II) complexes with N-glycosylamine ligands from 1,3-diaminopropane and aldopentoses. Correlation between configurational structures and circular dichroism spectra†

Reactions of [Ni(tn)3]X2·2H2O (tn = 1,3-diaminopropane, X = Cl or Br) with aldopentoses afforded a series of mononuclear nickel(II) complexes with N-glycosylamine ligands, [Ni(aldose-tn)2]X2 [aldose-tn = 1-(N-aldosyl)amino-3-aminopropane, aldose = D-xylose (D-Xyl) 1, D-lyxose (D-Lyx) 2, D-ribose (D-Rib) 3, or D-arabinose (D-Ara) 4], which were characterized by elemental analysis, electronic absorption and circular dichroism (CD) spectroscopy, and X-ray crystallography. Compound 4b, [Ni(D-Ara-tn)2]Br2·2H2O, was shown by an X-ray analysis to have a C2 symmetrical mononuclear nickel(II) structure ligated by two tridentate N-glycosylamine ligands, 1-amino-3-(N-D-arabinosyl)propane. The two N-glycosylamines are co-ordinated to the metal through the primary amino and N-glycosidic secondary amino groups and the C-2 hydroxy group of the sugar moiety in a meridional mode, resulting in a Λ-C2-helical configuration around the metal centre. The sugar rings adopt an unusual α-1C4 chair conformation and the sugar–chelate ring conformation is δ. The co-ordination behavior of D-ribose was confirmed by an X-ray analysis of an analogous compound, [Ni(D-Rib-men)2]Br2·2CH3OH 5 [D-Rib-men = 1-methylamino-2-(N-D-ribosyl)aminoethane], derived from the reaction of [Ni(men)3]Br2 with D-ribose [men = 1-amino-2-(N-methylamino)ethane]. The D-ribose moiety forms an α-N-glycosidic bond with the primary amino group of men, and adopts an α-4C1 chair form, the sugar–chelate ring conformation being δ. The CD spectra of 1–4 were measured in the region 9000–50 000 cm–1 and clearly indicated the structural features of the complexes; the Cotton effects at around 10 000 cm–1 (the first absorption band of the d–d transitions) reflected the conformation of the sugar chelate or the absolute configuration of the N-glycosidic nitrogen atom, and those at around 40 000–46 000 cm–1 (charge-transfer bands) demonstrated the C2 chiral configuration around the metal centre. These assignments were also confirmed by the CD spectra of known compounds.

Roles of the D-ribose and 5,6-dimethylbenzimidazole moieties of the nucleotide loop of adenosylcobalamin in manifestation of coenzymic function in the diol dehydrase reaction.

Coenzyme analogs in which the D-ribose moiety of the nucleotide loop was replaced by an oligomethylene group and a trimethylene analog containing imidazole instead of 5,6-dimethylbenzimidazole were synthesized. Coordination of the 5,6-dimethylbenzimidazole to the cobalt atom in these analogs was much weaker than that in cobalamins. The replacement of this base with imidazole did not significantly alter the strength of the coordination to the cobalt atom. 5,6-Dimethylbenzimidazolyl trimethylene and tetramethylene and imidazolyl trimethylene analogs were partially active as coenzymes in the diol dehydrase reaction in this order as judged by kcat, but the others were not active as coenzymes and were weak competitive inhibitors. This indicates that neither the alpha-D-ribofuranose ring nor the functional groups of the ribose moiety are essential for coenzymic function. There was an optimum loop size of the analogs for catalysis and for tight binding to the apoenzyme, which corresponds to the loop size of cobalamins. Therefore, the D-ribose moiety seems important as a spacer to keep the base in the proper position. The reaction with the imidazolyl trimethylene analog as coenzyme was accompanied with concomitant rapid inactivation during catalysis. The inactivation occurred only in the presence of substrate. Upon inactivation with this analog, 5'-deoxyadenosine and a B12r-like species were formed from the adenosyl group and the rest of the analog molecule, respectively, without modification of the apoenzyme. Therefore, it can be concluded that this is a kind of suicide inactivation which occurred from one of the intermediates in the normal catalytic process. The dimethylbenzo moiety of the regular coenzyme thus seems to play an important role in preventing the intermediate complexes from inactivation during catalysis.

Roles of β- d-ribofuranose ring and the functional groups of the d-ribose moiety of adenosylcobalamin in the diol dehydratase reaction

Four analogs of adenosylcobalamin (AdoCbl) modified in the d-ribose moiety of the Coβ ligand were synthesized, and their coenzyme properties were studied with diol dehydratase of Klebsiella pneumoniae ATCC 8724. 2′-Deoxyadenosylcobalamin (2′-dAdoCbl) and 3′-deoxyadenosylcobalamin (3′-dAdoCbl) were active as coenzyme. 2′,3′-Secoadenosylcobalamin (2′,3′-secoAdoCbl), an analog bearing the same functional groups as AdoCbl but nicked between the 2′ and 3′ in the ribose moiety, and its 2′,3′-dialdehyde derivative (2′,3′-secoAdoCbl dialdehyde) were totally inactive analogs of the coenzyme. It is therefore evident that the β- d-ribofuranose ring itself, possibly its rigid structure, is essential and much more important than the functional groups of the ribose moiety for coenzyme function (relative importance; β- d-ribofuranose ring ⪢ 3′-OH ⪢ 2′-OH ⪢ ether group). With 2′-dAloCbl and 3′-dAdoCbl as enzymes. an absorption peak at 478 nm appeared during enzymatic reaction, suggesting homolysis of the CCo bound to form cob(II)alamin as intermediate. In the absence of substrate, the complexes of the enzyme with these active analogs underwent rapid inactivation by oxygen. This suggests that their CCo bond is activated even in the absence of substrate by binding to the apoprotein. No significant spectral changes were observed with 2′,3′-secoAdoCbl upon binding to the apoenzyme. In contrast, spectroscopic observation indicates that 2′,3′-secoAdoCbl dialdehyde, another inactive analog, underwent gradual and irreversible cleavage of the CCo bond by interaction with the apodiol dehydratase, forming the enzyme-bound cob(II)alamin without intermediates.

Mutagenicity of irradiated solutions of nucleic acid bases and nucleosides in Salmonella typhimurium

Solutions of nucleic acid bases, nucleosides and a nucleotide, saturated with either N 2, N 2O or O 2, were irradiated and tested for mutagenicity towards Salmonella typhimurium, with and without pre-incubation. Irradiated solutions of the nucleic acid bases were all non-mutagenic. Irradiated solutions of the nucleosides showed mutagenicity in S. typhimurium TA100 (pre-incubation assay). Generally, the mutagenicity followed the order: N 2O > N 2 > O 2. The results show that the formation of mutagenic radiolytic products is initiated by attack of mainly OH radicals on the 2-deoxy- d-ribose moiety of the nucleosides. With irradiated solutions of the nucleotide, thymidine-5′-monophosphate, no mutagenicity could be detected.

Reaction of the D-ribose moiety of adenosine and AMP with periodate and 5,5-dimethylcyclohexane-1,3-dione (dimedone)

Reaction of the D-ribose moiety of adenosine and AMP with periodate and 5,5-dimethylcyclohexane-1,3-dione (dimedone)