Ribothymidine Research Articles

Analytical method development and validation of related substances by rphplc of sofosbuvir and velpatasvir tablets

The developed method was a simple, accurate, precise, specific and robust method for the validation of Sofosbuvir and Velpatasvir Tablets by reverse phase high pressure liquid chromatography. For Sofosbuvir and Velpatasvir Tablets Chromatography was performed on Agilent 1200 series, UV and PDA Detector, Waters X-bridge C18 (150 mm x 4.6 mm, 3.5 µm) by using Mobile Phase A contains Buffer solution (0.6% Trifluroacetic acid in water adjusted pH to 2.2±0.05) : Acetonitrile (95:5)%v/v and Mobile Phase B contains mixture of purified water, methanol and acetonitrile in the ratio of (20: 30: 50) % v/v/v. at a flow rate of 1.0 mL/min and at 263 nm for Sofosbuvir and 320 nm for Velpatasvir wavelength. The retention times of About 48.0 minutes for Sofosbuvir and About 78.8 minutes for Velpatasvir respectively. Methyl Uridine and Impurity at RRT 0.39 found linear over the range of LOQ - 150 % of target concentration. Method also found precise by spiking impurities at specification level. Accuracy was demonstrate at LOQ - 150 % level by preparing sample in triplicate for each level and found accurate. Hence, the method could be successfully used for the analysis Impurities in Sofosbuvir and Velpatasvir Tablets Tablet.

Synthesis and antisense properties of 2'-O-(2S-methoxypropyl)-RNA-modified gapmer antisense oligonucleotides.

To ascertain whether increasing hydrophobicity can enhance the activity of second-generation antisense oligonucleotides (ASOs) in muscle, we investigated the antisense properties of 2'-O-(2S-methoxypropyl)-RNA (2S-MOP)-modified ASOs. Synthesis of the 2S-MOP 5-methyl uridine phosphoramidite was accomplished on a multi-gram scale by Lewis-acid-catalyzed ring opening of 5'-O-tert-butyldiphenylsilyl ether-protected 2,2'-anhydro-5-methyl uridine with 2S-methoxy-1-propanol. Synthesis of the 2S-MOP 5-methyl cytidine nucleoside from the corresponding 5-methyl uridine nucleoside was accomplished by formation and displacement of a 4-triazolide intermediate with aqueous ammonia. 2S-MOP-modified oligonucleotides were prepared on an automated DNA synthesizer and showed similar enhancements in duplex thermal stability as 2'-O-methoxyethyl RNA (MOE)-modified oligonucleotides. 2S-MOP-containing antisense oligonucleotides were evaluated in Balb-c mice and showed good activity for decreasing the expression levels of scavenger receptor B1 (Srb1) and phosphatase and tensin homologue (PTEN) mRNA in liver and muscle tissue.

A single methyltransferase YefA (RlmCD) catalyses both m5U747 and m5U1939 modifications in Bacillus subtilis 23S rRNA

Methyltransferases that use S-adenosylmethionine (AdoMet) as a cofactor to catalyse 5-methyl uridine (m5U) formation in tRNAs and rRNAs are widespread in Bacteria and Eukaryota, and are also found in certain Archaea. These enzymes belong to the COG2265 cluster, and the Gram-negative bacterium Escherichia coli possesses three paralogues. These comprise the methyltransferases TrmA that targets U54 in tRNAs, RlmC that modifies U747 in 23S rRNA and RlmD that is specific for U1939 in 23S rRNA. The tRNAs and rRNAs of the Gram-positive bacterium Bacillus subtilis have the same three m5U modifications. However, as previously shown, the m5U54 modification in B. subtilis tRNAs is catalysed in a fundamentally different manner by the folate-dependent enzyme TrmFO, which is unrelated to the E. coli TrmA. Here, we show that methylation of U747 and U1939 in B. subtilis rRNA is catalysed by a single enzyme, YefA that is a COG2265 member. A recombinant version of YefA functions in an E. coli m5U-null mutant adding the same two rRNA methylations. The findings suggest that during evolution, COG2265 enzymes have undergone a series of changes in target specificity and that YefA is closer to an archetypical m5U methyltransferase. To reflect its dual specificity, YefA is renamed RlmCD.

Specificity shifts in the rRNA and tRNA nucleotide targets of archaeal and bacterial m5U methyltransferases.

Methyltransferase enzymes that use S-adenosylmethionine as a cofactor to catalyze 5-methyl uridine (m(5)U) formation in tRNAs and rRNAs are widespread in Bacteria and Eukaryota, but are restricted to the Thermococcales and Nanoarchaeota groups amongst the Archaea. The RNA m(5)U methyltransferases appear to have arisen in Bacteria and were then dispersed by horizontal transfer of an rlmD-type gene to the Archaea and Eukaryota. The bacterium Escherichia coli has three gene paralogs and these encode the methyltransferases TrmA that targets m(5)U54 in tRNAs, RlmC (formerly RumB) that modifies m(5)U747 in 23S rRNA, and RlmD (formerly RumA) the archetypical enzyme that is specific for m(5)U1939 in 23S rRNA. The thermococcale archaeon Pyrococcus abyssi possesses two m(5)U methyltransferase paralogs, PAB0719 and PAB0760, with sequences most closely related to the bacterial RlmD. Surprisingly, however, neither of the two P. abyssi enzymes displays RlmD-like activity in vitro. PAB0719 acts in a TrmA-like manner to catalyze m(5)U54 methylation in P. abyssi tRNAs, and here we show that PAB0760 possesses RlmC-like activity and specifically methylates the nucleotide equivalent to U747 in P. abyssi 23S rRNA. The findings indicate that PAB0719 and PAB0760 originated as RlmD-type m(5)U methyltransferases and underwent changes in target specificity after their acquisition by a Thermococcales ancestor from a bacterial source.

Conformationally-2',4'-Locked Aza-ENA and Carbocyclic ribo-Thymidine

Conformationally-2',4'-Locked Aza-ENA and Carbocyclic ribo-Thymidine

Effect of a Water Molecule on the Sugar Puckering of Uridine, 2‘-Deoxyuridine, and 2‘-O-Methyl Uridine Inserted in Duplexes

We used high-level quantum mechanical calculations to determine the pucker (north type or south type) of various compounds: uridine, 2'-deoxyuridine, and 2'-O-methyl uridine. Although the dihedrals of the backbone are set close to their experimental values in double-stranded nucleic acids, calculations using density functional theory show that, in vacuo or in a continuum mimicking the dielectric properties of water, the south puckering conformations of uridine is favored. This contrasts with experimental data: most ribonucleosides inserted into a duplex have the north puckering. We show here that the north puckering is favored when an explicit water molecule is introduced into the calculation. The orientations of the 2' group and of the water molecule have implications for the prevalence of the north puckering. We studied several orientations of the water molecule binding uracil O2 and the 2' group and estimated the energy barriers in the path between the north-to-south conformations. The north puckering is more favored in 2'-OH than in 2'-OCH3 compounds in the presence of the explicit water molecule.

Voltammetry of Osmium End‐Labeled Oligodeoxynucleotides at Carbon, Mercury, and Gold Electrodes

AbstractVoltammetric behavior of oligodeoxynucleotide (ODN) 5′‐T40 (GAA)7–3′ end‐labeled with osmium tetroxide,2,2‐bipyridine [Os(VIII)bipy] was compared with Os(VIII)bipy‐base‐ and with Os(VI)bipy‐sugar‐modified thymine ribosides. Cyclic voltammograms of Os(VIII)bipy‐modified ODN at mercury and carbon electrodes were similar but not identical to those of Os(VIII)bipy‐modified thymine riboside. Treatment of the ODN with Os(VI)bipy did not result in the ODN modification, in agreement with the known specificity of the reagent to the sugar cis‐diols. We show that in addition to mercury and carbon electrodes, the gold electrode can be used to detect Os(VIII)bipy‐labeled ODN. Comparison of voltammetric behavior of end‐labeled ODN using three types of electrodes most frequently used in DNA analysis may help to optimize electrochemical DNA sensors.

Computational and Empirical Trans-hydrogen Bond Deuterium Isotope Shifts Suggest that N1–N3 A:U Hydrogen Bonds of RNA are Shorter than those of A:T Hydrogen Bonds of DNA

Density functional theory calculations of isolated Watson-Crick A:U and A:T base pairs predict that adenine 13C2 trans-hydrogen bond deuterium isotope shifts due to isotopic substitution at the pyrimidine H3, (2h)Delta13C2, are sensitive to the hydrogen-bond distance between the N1 of adenine and the N3 of uracil or thymine, which supports the notion that (2h)Delta13C2 is sensitive to hydrogen-bond strength. Calculated (2h)Delta13C2 values at a given N1-N3 distance are the same for isolated A:U and A:T base pairs. Replacing uridine residues in RNA with 5-methyl uridine and substituting deoxythymidines in DNA with deoxyuridines do not statistically shift empirical (2h)Delta13C2 values. Thus, we show experimentally and computationally that the C7 methyl group of thymine has no measurable affect on (2h)Delta13C2 values. Furthermore, (2h)Delta13C2 values of modified and unmodified RNA are more negative than those of modified and unmodified DNA, which supports our hypothesis that RNA hydrogen bonds are stronger than those of DNA. It is also shown here that (2h)Delta13C2 is context dependent and that this dependence is similar for RNA and DNA.

Application of urinary nucleosides in the diagnosis and surgical monitoring of colorectal cancer

To evaluate the value of urinary normal and modified nucleosides in diagnosis and surgical monitoring of colorectal cancer (CRC). Between October 2002 and July 2003, 52 consecutive patients with pathological confirmed CRC were included in this study. Spontaneous urine samples were collected 1 d before and 8 d after surgery and 14 kinds of urinary nucleosides in the samples were determined by reversed-phase high-performance liquid chromatography (RP-HPLC) method. Another 62 healthy volunteers were also enrolled as controls. The routine clinical tumor markers, including serum CEA, CA199, CA125 and AFP levels of CRC patients were evaluated by electrochemical-luminescence immunoassay simultaneously. The mean levels of pseudouridine (Pseu), adenosine (A), cytidine (C), 1-methyladenosine (m1A), 1-methylinosine (m1I), 3-methyluridine + 5-methyluridine (mU), 2,2-methylguanosine (m22G), inosine (I), 1-methylguanosine (m1G), N4-acetylcytidine (ac4C), N6-methyladenosine (m6A) among 14 kinds of determined urinary nucleosides in CRC group were much higher than those of controls (P < 0.05). Based on principal component analysis, 76.9% of CRC patients were correctly identified, which was much higher than that of CEA (38.5%), CA199 (40.4%), CA125 (15.4%), and AFP (17.3%) (P < 0.01). ROC curve analysis of m1G, and Pseu showed good sensitivity-specificity profiles to CRC. Two classification equations, Y(normal) = -3.009 + 0.0272 x Pseu + 4.918 x m1G and Y(CRC) = -8.057 + 0.0667 x Pseu + 8.258 x m1G, were established by Bayes stepwise discriminate analysis for predicting carcinogenesis of CRC. The elevated levels of Pseu, C, U (uridine), m1A, m1I, m1G, ac4C, A, m22G dramatically decreased after curative resection of 40 cases of CRC. And our data also showed that the preoperative levels of Pseu, m1G, m1A and m22G were positively related with tumor size and the preoperative levels of m1A, m22G and ac4C were positively related with Duke's staging of CRC (P < 0.05). Normal and modified urinary nucleosides may become additional tumor markers which are feasible in the clinical setting and will prove helpful in the diagnosis, management and follow-up of CRC, and Pseu and m1G may be more promising for clinical application.

The synthesis and binding properties of oligonucleotide analogs containing diastereomerically pure conformationally restricted acetal linkages

The synthesis of 5,6-bicyclic thymine:thymine nucleoside containing a conformationally restricted dioxane acetal has been achieved from 2′- O-allyl 5-methyl uridine. The two diastereomers were separated and incorporated in a single position within an oligonucleotide (ON) sequence. The binding properties of these ONs when hybridized to complementary RNA and DNA were evaluated by thermal denaturation (Tm) analysis. Lower Tms for both diastereomers were obtained when compared to the corresponding control phosphodiester ON.

Novelp-Toluenesulfonylation and Thionocarbonylation of Unprotected Thymine Nucleosides

A new procedure involving the use of both dibutyltin oxide and a quaternary ammonium salt along with p-toluenesulfonyl chloride or phenoxythiocarbonyl chloride leads in good yields to the desired monotosylate or to the 2′,3′-O -cyclic thiocarbonate of thymine nucleosides without prior modification of any hydroxyl group. It is noteworthy that with 5-methyl uridine, tosylation occurs regioselectively at the 2′- position, while the 3′-O-tosylate is formed when 5-methyl uridine is substituted on 1′ by a methyl (or cyano) group.

Synthesis and Anticancer Activity of 3-(3-Oxoprop-1-enyl)-Substituted Analogues of Carbocyclic Pyrimidine Nucleosides and 2′,3′-Dideoxy Pyrimidine Nucleosides

Abstract Various 2′, 3′ -dideoxy and carbocyclic pyrimidine nucleosides, and their corresponding 3-(3-oxoprop-1-enyl) derivatives, have been synthesized and evaluated against murine L1210 and P388 leukemias and Sarcoma 180 and human CCRF-CEM lymphoblastic leukemia. Among the compounds tested, 3-(3-oxoprop-1-enyl)-3′ -fluoro-3′ -deoxythymidine (17), 3-(3-oxoprop-1-enyl)-3′ -azido-3′ -deoxythymidine (15) and 3-(3-oxoprop-1-eny!)-(+)-1-[(lα, 3β, 4α)-3-hydroxy-4-(hydroxymethyl)cyclopentyl]-5-methyl-2,4 (lH,3H)pyrimidinedione (6) were found to be the most active with ED50, values of 0.5,0.2,0.1, and 0.3 μM; 1.2, 0.5,1.0 and 1.0 μM; and 0.8,0.7,1.5, and 3.0μM, respectively. Our preliminary findings indicate that the 3-(3-oxoprop-1-enyl) derivative of carbocyclic thymidine is approximately 7 times more active than the 3-(3-oxoprop-1-enyl) derivative of carbocyclic thymine riboside against L1210 leukemia cells in vitro, with ED50 values of 0.8 μM and 5.5 μM, respectively. These findings suggest that the cytotoxicity of these compounds not only is dependent upon the 3-(3-oxoprop-1-enyl)-substituted group, but also may vary with the sugar moiety.

168 MOLECULAR AND KINETIC PROPERTIES OF CYTIDINE DEAMINASE FROM HUMAN SPLEEN

Cytidine deaminase (EC 3.5.4.5) catalyzes the irreversible hydrolytic deamination of both cytidine and its nucleoside analogues including many antineoplastic agents. The enzyme has been purified from human spleen 2000-fold with respect to the crude extract. The procedure consists of heat treatment, anionic exchange on DEAE-52, hydrophobic interaction on TSK-Phenyl-5PW and an anionic exchange on Mono Q. The last two steps were performed using an FPLC system. The final enzyme preparation shows a microheterogeneity. The native molecular weight is about 50,000. Cytidine deaminase is strictly dependent on the presence of reducing agents for its activity. The enzyme displays linear kinetics. It shows the highest affinity for deoxycytidine among the various substrates tested. The enzyme is inhibited by the reaction products uridine and ammonia in a competitive fashion suggesting a rapid equilibrium random Uni-Bi kinetic mechanism. Furthermore, the enzyme is competitively inhibited by various compounds, such as 5, 6-dihydrouridine, deoxyuridine, thymidine, thymine riboside and deoxyadenosine.

Establishment of a nucleoside-specific suppressor T cell line from SLE prone (NZB/NZW)F1 mice.

A long-term cultured suppressor T cell line (GTS-124) was established from an autoimmune mouse strain, (NZB X NZW)F1, by a two-part procedure: a) B/W F1 mice were made tolerant to guanosine (G) by administration of a tolerogen, the G-modified copolymer of D-glutamic acid and D-lysine (G-D-GL); and b) the spleen cells obtained from tolerant mice were repeatedly stimulated with mitomycin C-treated G-modified syngeneic spleen cells. The GTS-124 cells suppressed the secondary in vitro response to G-keyhole limpet hemocyanin (G-KLH) but did not suppress the response to unrelated antigens, sheep erythrocytes (SRBC), or trinitrophenyl-KLH (TNP-KLH). The expression of Thy-1 antigen on the cell surface of GTS-124 was demonstrated by flow cytometry. Growth of GTS-124 cells was dependent on IL 2. To determine whether GTS-124 cells could suppress the response to nucleosides other than G, KLH coupled with four nucleosides (adenosine [A], G, cytidine [C], and thymine riboside [T]) collectively (AGCT-KLH) was first used as the antigen in the assay system. The PFC response to the individual nucleosides (anti-A, -G, -C, and -T PFC) were effectively inhibited by GTS-124 cells, suggesting that the GTS-124 cells mediated cross-suppression toward all four nucleosides. A more stringent cross-suppression test was conducted by using only the T moiety bound to KLH (T-KLH) as antigen. The results showed that GTS-124 cells were capable of suppressing the T-specific response. The cross-suppression could be seen after repeated selection on a G-BSA-coated dish. These results provide direct evidence that the suppressor T cells induced by in vitro stimulation with G-modified self can indeed suppress the response to nucleosides other than G.

Effect of corticosteroids on serum antinuclear antibodies in man

The effect of prednisone on serum levels of IgG antibodies to viral and bacterial antigens was measured and compared to its effect on IgG antibodies to nuclear antigens in 8 patients with systemic lupus erythematosus. Prednisone at 15–80 mg/day (mean 55 mg/day) for 14–30 days (mean 19 days) lowered the serum IgG by an average of 22% (p<0.005). An even greater reduction in IgG antinuclear antibodies occurred (mean 43%, p<0.001) including responses to double stranded DNA, single stranded DNA, and the nucleosides, adenosine, guanosine, cytidine and thymine riboside. In contrast, there was no alteration in serum IgG antibody levels to influenza virus vaccine and pneumococcal vaccine antigens. These results suggest that prednisone has a selective effect on the expression of autoimmunity which may, in part, be responsible for its clinical efficacy in systemic lupus erythematosus.

Crystal structure of O4-methyl uridine: stacking induced changes in the geometry of the pyrimidine ring and its mutagenic role.

The geometric properties of the pyrimidine ring of O4-methyl uridine more closely resemble those of cytidine than diketo uridine. Differences between the independent molecules of O4-methyl uridine are observed in the C(7)-O(4)-C(4)-C(5)-C(6) bond orders and the planarity of the pyrimidine rings. These differences are attributed to the monopole-induced dipole interactions between the ribose ring oxygen atom and a neighboring base of molecule A. A survey of the literature reveals that similar stacking-induced effects occur in other structures, involving both pyrimidine and purines. Finally, two base pairing schemes between O4-methyl uridine and guanosine, in which two hydrogen bonds can form, have been presented. Of these two the mispair with Watson-Crick geometry is favored.

17O and 14N spectroscopy of 17O‐labeled nucleic acid bases

AbstractOxygen‐17 and nitrogen‐14 nuclear magnetic resonance techniques have been utilized in studying liquid‐state hydrogen bonding interactions between nucleic acid bases and between the bases and solvent. The bases uracil and thymine have been labeled with 17O at positions 2 and 4, cytosine at position 2 and thymine riboside at position 4. The 17O chemical shift was found to be a sensitive structural probe and to provide information concerning the resonance forms that contribute to the total wave function. The chemical shift of the oxygen of thymine and uracil at position 2 was detected at a higher field than that of oxygen at position 4, presumably owing to an increased contribution of single bonded‐oxygen valence bond structures at position 2. The 17O and 14N chemical shifts of cytosine were found to be strongly pH dependent, and the results have been interpreted in terms of predominant cytosine resonance structures contributing to the aqueous cation and anion. The 17O line width of cytosine in aqueous solution indicates the presence of hydrogen bonded dimers between neutral and cationic forms.

The fine specificity of immune suppression to individual nucleosides.

The fine specificity of immune suppression was further studied in a murine experimental model in which the induction and expression of suppression by individual nucleoside-bound spleen cells were examined. The experiments were undertaken: a) to determine whether all 4 nucleosides have the ability to elicit suppressor T cells; b) to examine the specificity of cross-suppression induced by individual nucleosides; and c) to establish that nucleoside-specific suppression is mediated by T cells bearing nucleoside-specific receptors. The results show that, of the 4 nucleosides studied, only guanosine and thymine riboside were capable of eliciting immune suppression. Thymine riboside-coupled spleen cells induced cross-suppression to all 4 nucleosides. Furthermore, the nonresponsive state generated by guanosine-spleen cells was found to be transferable and mediated by nucleoside-binding T cells. The ability of only select nucleosides to elicit immune suppression is discussed in the context of recent evidence demonstrating the selective activation of T cell subsets by intramolecular antigenic determinants.

Transport of a nonphosphorylated nucleoside, 5'-deoxyadenosine, by murine leukemia L1210 cells.

The mode of transport of a nonphosphorylated adenosine analog, 5'-deoxyadenosine, was studied in murine leukemia L1210 cells. This compound is not subject to the action of intracellular nucleoside-trapping kinases, and its transport can be examined without regard for effects of experimental conditions on kinase activity. Accumulation of 5'-deoxyadenosine was rapid, and nonconcentrative, with equilibrium attained within 12 s at 37 degrees. Kinetic studies were carried out at 20 degrees. We found both a nonmediated (diffusion) and a mediated transport process. The latter had an apparent Km fo 115 micrometer, Vmax = 105 pmol/10(6) cells/min. Uptake of 5'-deoxyadenosine was inhibited by several heterologous nucleosides including adenosine, 2'-deoxyadenosine, thymine riboside, and inosine. Like 2'-deoxyadenosine, 5'-deoxyadenosine was more lipid-soluble than adenosine (from octanol/water partition studies). Compared with 5'-deoxyadenosine, adenosine had a much lower apparent Km (5 micrometer) and a higher Q10 over the 27-37 degrees range (3.0 versus 1.3). Data obtained with adenosine might, however, reflect properties of intracellular adenosine kinase interacting with a transport process.

Circular dichroism of the nucleic acid monomers

AbstractCircular dichroism spectra of the nucleic acid monomers have been measured in aqueous solution and extended into the vacuum ultraviolet region to about 166 nm. Measurements were made on ribo and deoxyribo derivatives of adenine, guanine, hypoxanthine, cytosine, thymine, and uracil derivatives both with and without the 5′‐phosphate (with the exception of ribosyl thymine 5′‐phosphate). Absorption spectra of the deoxyribonucleotides measured to about 175 nm are also presented. The results demonstrate that both the circular dichroism and absorption spectra observed below 200 nm are no more complicated than the spectra normally recorded above 200 nm. In most cases, the circular dichroism spectra of the various derivatives of a given base are similar, indicating that the conformations are similar. On the other hand, the differences among the circular dichroism spectra of the various derivatives of a given base are sufficient to identify a particular derivative. The average circular dichroism for the deoxyribonucleotides is compared with the circular dichroism of native E. coli DNA. The comparison reveals that the circular dichroism of DNA below 200 nm is due principally to the interaction between the bases rather than the intrinsic circular dichroism of the monomers. The monomer transitions are discussed in relationship to the absorption and circular dichroism spectra presented.