Deoxynucleoside Research Articles

The development of β-selective glycosylation reactions with benzyl substituted 2-deoxy-1,4-dithio-D-erythro-pentofuranosides: enabling practical multi-gram syntheses of 4'-Thio-2'-deoxycytidine (T-dCyd) and 5-aza-4’-thio-2’-deoxycytidine (aza-T-dCyd) to support clinical development

The lack of effective methods to perform direct β-selective glycosylation reactions with 2-deoxy-1,4-dithio-D-erythro-pentofuranosides has long been a significant stumbling block for the multi-gram synthesis of 4’-thio-2’-deoxy nucleosides. In addition, previously reported methods for the preparation of appropriately substituted 2-deoxy-1,4-dithio-D-erythro-pentofuranosides have proven problematic for large scale synthesis. To address these issues, herein we describe the modification and optimization of previously reported methods to allow for the convenient large scale synthesis of benzyl substituted 2-deoxy-1,4-dithio-D-erythro-pentofuranosides. Furthermore, we describe the development of reaction conditions for β-selective glycosylation reactions of benzyl substituted 2-deoxy-1,4-dithio-D-erythro-pentofuranosides with both N4-benzoylcytosine and 5-aza-cytosine to enable the practical multi-gram syntheses of the clinical candidates 4'-thio-2'-deoxycytidine (T-dCyd) and 5-aza-4’-thio-2’-deoxycytidine (aza-T-dCyd). Taken together, these new synthetic developments have made possible the preclinical and early clinical development of these important anticancer agents at the National Cancer Institute.

Berichtigung: Pac13 is a Small Dehydratase that Mediates the Formation of the 3′‐Deoxy Nucleoside of Pacidamycins

Berichtigung: Pac13 is a Small Dehydratase that Mediates the Formation of the 3′‐Deoxy Nucleoside of Pacidamycins

The Cupin Protein Pac13 is Suggested by the Data to Be a Homodimer

AbstractCupin proteins share a double‐stranded β‐helix fold, form one of the largest protein superfamilies, and possess remarkable functional diversity. They usually exist in homooligomeric states. Goss and co‐workers recently reported that the cupin protein Pac13, which is a dehydratase that mediates the formation of the 3′‐deoxy nucleoside of pacidamycins, is an unusual small monomer. However, a careful analysis of the biophysical and structural data provided by the authors suggests that Pac13 is in fact a homodimer, similar to many other cupin proteins.

Corrigendum: Pac13 is a Small Dehydratase that Mediates the Formation of the 3'-Deoxy Nucleoside of Pacidamycins.

Our previous gel filtration of Pac13 suggested a monomer.1 Analysis of the crystal structure was inconclusive.1, 2 Therefore based on the gel filtration analyses we concluded this protein to be a monomer in solution. Thanks to the letter of Professor Rundong Zhang4 we revisited these experiments. Although a recent re-run of the gel filtration of a sample of Pac13 that we had in hand was more ambiguous, it remained more consistent with a monomer (Figure 1 of this Corrigendum). We then examined the protein sample using the more definitive technique of multi-angle light scattering (MALS), an analytical technique that we had not used in our initial study. These MALS analyses indicate the protein to have a MW of 27.3 KDa (Table 1 of this Corrigendum). Repeated and annotated gel filtration of a sample of Pac13. a) Raw trace data for Pac13. b) Raw trace data calibration standards. Pac13 was expressed with a His8 tag, and following TEV cleavage, an additional 3 amino acid residues remain. Calculated MW: 14096Da (monomer), 28192 Da (dimer).1, 3 Hydrodynamic radius (Q) moments [nm] Rh(Q)z 3.048 (±4.977 %) Rh(Q)(avg) 2.688 (±1.665 %) Masses Calculated Mass [μg] 56.81 Molar mass moments [g mol−1] Mn 2.726×104 (±0.629 %) Mp 2.709×104 (±0.606 %) Mw 2.726×104 (±0.630 %) rms radius moments [nm] Rz 12.4 (±17.0%) From MALS analysis, we conclude that Pac13 is indeed dimeric. References in the original work to Pac13 being a monomer should thus be removed, along with the term “monomeric” in the original title. The other results, discussion, and conclusions in the Communication are not altered by the revised conclusion of the oligomeric species. We thank Hannes Ludewig and Jag Dhaliwal (University of St Andrews), and Audrey LeBas and Gemma Harris (Research Complex at Harwell, Rutherford Laboratory) for their roles in producing further protein and carrying out gel filtration and MALS analysis.

3'-O-Caged 2'-Deoxynucleoside Triphosphates for Light-Mediated, Enzyme-Catalyzed, Template-Independent DNA Synthesis.

Synthesis, purification, and characterization of 3'-O-caged 2'-deoxyribonucleoside triphosphates (dNTPs), namely 3'-O-(2-nitrobenzyl)-2'-deoxy ribonucleoside triphosphates (NB-dNTPs) and 3'-O-(4,5-dimethoxy-2-nitrobenzyl)-2'-deoxy ribonucleoside triphosphates (DMNB-dNTPs), are discussed in detail. A total of eight 3'-O-caged dNTPs are synthesized with specific protocols depending on the nitrogenous base on the first carbon, i.e., adenine, guanine, thymine, and cytosine, as well as the photo-cleavable group, i.e, 2-nitrobenzyl and 4,5- dimethoxy-2-nitrobenzyl, to be attached in the 3'-O position. The purification of the synthesized compounds is done using ion-exchange and flash chromatography; this is followed by structural confirmation by nuclear magnetic resonance (NMR) and mass spectroscopy (MS). The efficiency of the designed compounds is tested by conducting and evaluating UV-cleaving experiments at 365nm with proton NMR and LC-MS curves. Finally, the application of the 3'-O-cagged dNTPs in template-independent, enzyme-catalyzed, photo-mediated oligonucleotide synthesis is demonstrated. © 2017 by John Wiley & Sons, Inc.

Pac13 is a Small, Monomeric Dehydratase that Mediates the Formation of the 3'-Deoxy Nucleoside of Pacidamycins.

The uridyl peptide antibiotics (UPAs), of which pacidamycin is a member, have a clinically unexploited mode of action and an unusual assembly. Perhaps the most striking feature of these molecules is the biosynthetically unique 3′‐deoxyuridine that they share. This moiety is generated by an unusual, small and monomeric dehydratase, Pac13, which catalyses the dehydration of uridine‐5′‐aldehyde. Here we report the structural characterisation of Pac13 with a series of ligands, and gain insight into the enzyme's mechanism demonstrating that H42 is critical to the enzyme's activity and that the reaction is likely to proceed via an E1cB mechanism. The resemblance of the 3′‐deoxy pacidamycin moiety with the synthetic anti‐retrovirals, presents a potential opportunity for the utilisation of Pac13 in the biocatalytic generation of antiviral compounds.

Pac13 is a Small, Monomeric Dehydratase that Mediates the Formation of the 3′‐Deoxy Nucleoside of Pacidamycins

AbstractThe uridyl peptide antibiotics (UPAs), of which pacidamycin is a member, have a clinically unexploited mode of action and an unusual assembly. Perhaps the most striking feature of these molecules is the biosynthetically unique 3′‐deoxyuridine that they share. This moiety is generated by an unusual, small and monomeric dehydratase, Pac13, which catalyses the dehydration of uridine‐5′‐aldehyde. Here we report the structural characterisation of Pac13 with a series of ligands, and gain insight into the enzyme's mechanism demonstrating that H42 is critical to the enzyme's activity and that the reaction is likely to proceed via an E1cB mechanism. The resemblance of the 3′‐deoxy pacidamycin moiety with the synthetic anti‐retrovirals, presents a potential opportunity for the utilisation of Pac13 in the biocatalytic generation of antiviral compounds.

Mechanism of Roscovitine in inhibiting HBV replication

Objective To investigate the mechanism of Roscovitine, an inhibitor of cyclin-dependent kinase (CDK), in inhibiting HBV replication. Methods Recombiant expression plasmids of SAMHD1 (sterile alpha motif and histidine/aspartic acid domain-containing protein 1) mutants that were defective in dNTPase (deoxynucleoside triphosphate triphosphohydrolase) activity and phosphorylation at the threonine (T) 592 residue were constructed. Huh7.0 cells were respectively co-transfected with different SAMHD1 mutants in combiantion with HBV replication plasmid to analyze whether the retroviral restriction ability of SAMHD1 was regulated by phosphorylation. The cytotoxicity of Roscovitine to Huh7 cells was evaluated by MTT assay. HBV core-associated DNA levels and phosphorylation of SAMHD1 in transfected Huh7.0 cells which were treated with different concentrations of Roscovitine were measured by Southern blot and Western blot assays. Results The SAMHD1 mutant that was defective in the dNTPase active site of D207N lost its ability to restrict HBV replication. Dephosphorylation of SAMHD1 at T592 enhanced its restriction on HBV. The median toxic concentration (TC50) of Roscovitine was 11.20 μmol/L. Both the HBV core-associated DNA levels and the phosphorylation of SAMHD1 were down-regulated by Roscovitine. Conclusion The anti-HBV function of SAMHD1 in dividing cells is regulated by phosphorylation. Roscovitine can inhibit the replication of HBV through reducing the phosphorylation of SAMHD1. Key words: Roscovitine; Hepatitis B virus; SAMHD1; Phosphorylation; Inhibition

Synthesis of 3-Cyano-1H-indolo-2′-deoxy-ribonucleosides

Key words deoxyribo-nucleosides - aldol condensation - Michael addition - copper catalysis - aromatization - cyanoindoles

Synthesis of unnatural 3′-phospha-2′-deoxyfuranose nucleoside analogues

This Letter describes the synthesis of racemic analogues of unnatural 2′-deoxy nucleoside with a phosphorus atom replacing the carbon atom in the 3′-position. A seven-step sequence was developed in racemic series to afford unnatural 3′-phospha-2′-deoxyfuranose nucleosides. The phospha nucleoside analogues were tested against HCV, but did not show any antiviral activity at a 10μM maximum concentration used for the inhibition assays of analogues 2-T, 2-C and 4-Tα.

Synthetic Routes to a Series of Proximal and Distal 2'-Deoxy Fleximers.

Two series of innovative 2'-deoxy nucleoside analogues have been designed where the nucleobase has been split into its imidazole and pyrimidine subunits. This structural modification serves to introduce flexibility into the nucleobase scaffold while still retaining the elements required for recognition. The synthetic efforts to realize these analogues are described within.

Synthesis and biological evaluation of a series of thieno-expanded tricyclic purine 2′-deoxy nucleoside analogues

Introducing structural diversity into the nucleoside scaffold for use as potential chemotherapeutics has long been considered an important approach to drug design. In that regard, we have designed and synthesized a number of innovative 2′-deoxy expanded nucleosides where a heteroaromatic thiophene spacer ring has been inserted in between the imidazole and pyrimidine ring systems of the natural purine scaffold. The synthetic efforts towards realizing the expanded 2′-deoxy-guanosine and -adenosine tricyclic analogues as well as the preliminary biological results are presented herein.

Lipophilic Prodrugs and Formulations of Conventional (Deoxy)Nucleoside and Fluoropyrimidine Analogs in Cancer

Many drugs that are currently used for the treatment of cancer have limitations, such as induction of resistance and/or poor biological half-life, which reduce their clinical efficacy. To overcome these limitations, several strategies have been explored. Chemical modification by the attachment of lipophilic moieties to (deoxy)nucleoside analogs should enhance the plasma half-life, change the biodistribution, and improve cellular uptake of the drug. Attachment of a lipophilic moiety to a phosphorylated (deoxy)nucleoside analog will improve the activity of the drugs by circumventing the rate-limiting activation step of (deoxy)nucleoside analogs. Encapsulating drugs in nanoparticles or liposomes protects the drug against enzymatic breakdown in the plasma and makes it possible to get lipophilic compounds to the tumor site. In this review, we discuss the considerable progress that has been made in increasing the efficacy of classic (deoxy)nucleoside and fluoropyrimidine compounds by chemical modifications and alternative delivery systems.

Determination of the Phosphorylated Metabolites of Gemcitabine and of Difluorodeoxyuridine by LCMSMS

Gemcitabine is an established chemotherapy agent in several solid tumors. Its mechanism of action has been theoretically established and this is supported with strong experimental evidence. However, certain aspects of the resistance mechanism for this agent remain elusive. We present a method of analysis using tandem liquid chromatography and mass spectrometry that provides a broader, yet more focused view of the action of gemcitabine and its primary metabolite, difluorodeoxyuridine in relation to the (deoxy) nucleoside and (deoxy) nucleotide pools in tumor cell lines. Alcoholic cytosole extracts were incubated with alkaline phosphatase reducing the nucleotide pools to their respective nucleosides. Determination of the nucleoside content by a sensitive LCMSMS method before and after incubation enables the calculation of the total amount of phosphorylation of each (deoxy) nucleoside in the cell. Incubation with clinically relevant levels of gemcitabine (dFdC) or difluorodeoxyuridine (dFdU) for 24 hours enabled the determination of the changes in the (deoxy) nucleotide pools in relation to chemotherapeutic and toxicological effects. Confirmation of the presence of dFdC phosphorylation is presented as well as direct evidence of dFdU phosphorylation after both dFdC and dFdU treatment. Differences in the nucleotide pools are presented after dFdC and dFdU incubation, indicating that dFdU might have more chemotherapeutic properties than previously believed.

Synthesis of a Complete Janus-type Guanosine–Cytosine Base and Its 2′-Deoxyribonucleoside

Abstract Novel Janus-type guanosine–cytosine pyrimido[4,5-d]pyrimidine and its 2′-deoxyribonucleoside have been synthesized in a viable route employing the Vorbruggen method.

ChemInform Abstract: The Synthesis and Antiviral Activity of Some 4′-Thio-2′-deoxy Nucleoside Analogues.

Starting from benzyl 3,5-di-O-benzyl-2-deoxy-1,4-dithio-D-erythro- pentofuranoside (4), the following 2'-deoxy nucleoside analogues have been synthesized: 4'-thiothymidine (8), 3'-azido-4'-thio- deoxythymidine (10), and (E)-5-(2-bromovinyl)-4'-thio-2'-deoxyuridine (22). The first compound is toxic, the second is not toxic nor has detectable biological activity, and the third is not toxic and has significant activity against some herpesviruses.

ChemInform Abstract: A Novel Route for the Synthesis of Deoxy Fluoro Sugars and Nucleosides.

The reaction of (diethylamino)sulfur trifluoride (DAST) with methyl 5-O-benzoyl-β-D-xylofuranoside (1) followed by column chromatography afforded the riboside 2 (62%) and the ribo-epoxide 3 (18%) (Scheme 1). Under similar reaction conditions, the α-D-anomer 4 gave the riboside 5 and the difluoride 6 in 60 and 9% yield, respectively. Treatment of the β-D-xyloside 10 with DAST gave, after chromatographic purification, the riboside 11 as the principal product (48%; Scheme 2). These results suggest that the C(3)−O−SF2NEt2 derivatives were initially formed in the case of the xylosides studied. The distinctive feature of the reaction of DAST with the β-D-arabinoside 12 consists in the formation of a 3- or 5-benzylideneoxoniumyl-substituted intermediate on one of the consecutive transformations, which finally give rise to the inversion of the configuration at C(3) affording the xylosides 17 (18%) and 18 (55%); the lyxoside 14 was also isolated from the reaction mixture in a yield of 25% (Scheme 3). In the presence of the non-participating 5-O-trityl group, i.e., from the reaction products of 21 with DAST, the compounds 23 and 24 were isolated in 16 and 52% yield, respectively (Scheme 4). It may be thus reasonable to conclude that, in the case of the β-D-arabinosides 12 and 21, the principal route of the reaction is the formation of the intermediate C(2)−O−SF2NEt2 derivative. Unlike 21, the α-D-arabinoside 26 was converted to the lyxo-epoxide 25 (53%) and the lyxoside 27 (14%), which implies the intermediate formation of the C(3)−O−SF2NEt2 derivative (Scheme 5).

Oligonucleotide N3′→P5′ Phosphoramidates and Thio‐Phoshoramidates as Potential Therapeutic Agents

Nucleic acids analogues, i.e., oligonucleotide N3'-->P5' phosphoramidates and N3'-->P5' thio-phosphoramidates, containing 3'-amino-3'-deoxy nucleosides with various 2'-substituents were synthesized and extensively studied. These compounds resist nuclease hydrolysis and form stable duplexes with complementary native phosphodiester DNA and, particularly, RNA strands. An increase in duplexes' melting temperature, DeltaT(m), relative to their phosphodiester counterparts, reaches 2.2-4.0 degrees per modified nucleoside. 2'-OH- (RNA-like), 2'-O-Me-, and 2'-ribo-F-nucleoside substitutions result in the highest degree of duplex stabilization. Moreover, under close to physiological salt and pH conditions, the 2'-deoxy- and 2'-fluoro-phosphoramidate compounds form extremely stable triple-stranded complexes with either single- or double-stranded phosphodiester DNA oligonucleotides. Melting temperature, T(m), of these triplexes exceeds T(m) values for the isosequential phosphodiester counterparts by up to 35 degrees . 2'-Deoxy-N3'-->P5' phosphoramidates adopt RNA-like C3'-endo or N-type nucleoside sugar-ring conformations and hence can be used as stable RNA mimetics. Duplexes formed by 2'-deoxy phosphoramidates with complementary RNA strands are not substrates for RNase H-mediated cleavage in vitro. Oligonucleotide phosphoramidates and especially thio-phosphoramidates conjugated with lipid groups are cell-permeable and demonstrate high biological target specific activity in vitro. In vivo, these compounds show good bioavailability and efficient biodistribution to all major organs, while exerting acceptable toxicity at therapeutically relevant doses. Short oligonucleotide N3'-->P5' thio-phosphoramidate conjugated to 5'-palmitoyl group, designated as GRN163L (Imetelstat), was recently introduced as a potent human telomerase inhibitor. GRN163L is not an antisense agent; it is a direct competitive inhibitor of human telomerase, which directly binds to the active site of the enzyme and thus inhibits its activity. This compound is currently in multiple Phase-I and Phase-I/II clinical trials as potential broad-spectrum anticancer agent.

Application of Germyldesulfonylation Reactions to the Synthesis of Germanium-Containing Nucleoside Analogues

Treatment of the protected (E)-5′-deoxy-5′-[(p-toluenesulfonyl)methylene]uridine and adenosine derivatives with tributyl- or triphenylgermane hydride (AIBN/toluene/Δ) effected radical-mediated germyldesulfonylations to give 5′-(tributyl- or triphenylgermyl)methylene-5′-deoxyuridine and adenosine derivatives as single (E)-isomers. Analogous treatment of 2′-deoxy-2′-[(phenylsulfonyl)methylene]uridine with Ph3GeH afforded the corresponding vinyl triphenylgermane product. Stereoselective halodegermylation of the (E)-5′-(tributylgermyl)methylene-5′-deoxy nucleosides with N-iodosuccinimide or N-bromosuccinimide provided the Wittig-type (E)-5′-deoxy-5′-(halomethylene) nucleosides quantitatively, while no halodegermylations was observed with the 5′-deoxy-5′-(triphenylgermyl)methylene counterparts. Treatment of the vinyl trialkylgermanes with aqueous trifluoroacetic acid effected protiodegermylation, while vinyl triarylgermanes were stable under the acidic conditions.

Characterization of the Mn2+-stimulated (di)adenosine polyphosphate hydrolase encoded by the Deinococcus radiodurans DR2356 nudix gene

The DR2356 nudix hydrolase gene from Deinococcus radiodurans has been cloned and the product expressed as an 18 kDa histidine-tagged protein. The enzyme hydrolysed adenosine and diadenosine polyphosphates, always generating ATP as one of the initial products. ATP and other (deoxy)nucleoside triphosphates were also substrates, yielding (d)NDP and Pi as products. The DR2356 protein was most active at pH 8.6-9.0 and showed a strong preference for Mn(2+) as activating cation. Mg(2+) ions at 15 mM supported only 5% of the activity achieved with 2 mM Mn(2+). K (m) and k (cat) values for diadenosine tetra-, penta- and hexaphosphates were 2.0, 2.4 and 1.1 microM and 11.4, 28.6 and 12.0 s(-1), respectively, while for GTP they were 20.3 microM and 1.8 s(-1), respectively. The K (m )for adenosine 5'-pentaphosphate was <1 microM. Expression analysis showed the DR2356 gene to be induced eight- to ninefold in stationary phase and in cells subjected to slow dehydration plus rehydration. Superoxide (but not peroxide) treatment and rapid dehydration caused a two-to threefold induction. The Mn-requirement and induction in stationary phase suggest that DR2356 may have a specific role in maintenance mode metabolism in stationary phase as Mn(2+) accumulates.