Synthesis of hapten-phosphoramidites from 2′-deoxyuridine

A total of 11 novel phosphoramidites, 3a-d, 4a-d and 14a-c were prepared from 2′-deoxyuridine functionalized at 5 and 6-position of the pyrimidine ring with hapten reporter groups, e.g. adamantane, carbazole, dansyl and dabsyl, suitable for use in immunodetection nucleic acid testing assays.     

Efficient synthesis of terminal 4-methylumbelliferyl labeled 5-fluoro-2′-deoxyuridine-5′-O-tetraphosphate (Um-PPPP-FdU): a potential probe for homogenous fluorescent assay

Efficient synthesis of 5-fluoro-2′-deoxyuridine-5′-O-tetraphosphate bearing 4-methylumbelliferyl label on the terminal phosphate is reported. This compound has the potential as a promising probe molecule for homogenous fluorescent polymerase assay. This class of compounds will aid in quantification of cellular internalization and DNA incorporation of nucleotide based chemotherapeutic agents to offer mechanistic insights.     

High quality drug screening by capillary electrophoresis: A review

High quality assays are needed in drug discovery to reduce the high attrition rate of lead compounds during primary screening. Capillary electrophoresis (CE) represents a versatile micro-separation technique for resolution of enzyme-catalyzed reactions, including substrate(s), product(s), cofactor(s) and their stereoisomers, which is needed for reliable characterization of biomolecular interactions in free solution. This review article provides a critical overview of new advances in CE for drug screening over the past five years involving biologically relevant enzymes of therapeutic interest, including transferases, hydrolases, oxidoreductases, and isomerases. The basic principles and major configurations in CE, as well as data processing methods needed for rigorous characterization of enzyme inhibition are described. New developments in functional screening of small molecules that modulate the activity of disease-related enzymes are also discussed. Although inhibition is a widely measured response in most enzyme assays, other important outcomes of ligand interactions on protein structure/function that impact the therapeutic potential of a drug will also be highlighted, such as enzyme stabilization, activation and/or catalytic uncoupling. CE offers a selective platform for drug screening that reduces false-positives while also enabling the analysis of low amounts of complex sample mixtures with minimal sample handling.     

The Trypanosoma cruzi TcrNT2 Nucleoside Transporter Is a Conduit for the Uptake of 5-F-2′-Deoxyuridine and Tubercidin Analogues

Among the scarce validated drug targets against Chagas disease (CD), caused by Trypanosoma cruzi, the parasite’s nucleoside salvage system has recently attracted considerable attention. Although the trypanocidal activity of tubercidin (7-deazapurine) has long been known, the identification of a class of 7-substituted tubercidin analogs with potent in vitro and in vivo activity and much-enhanced selectivity has made nucleoside analogs among the most promising lead compounds against CD. Here, we investigate the recently identified TcrNT2 nucleoside transporter and its potential role in antimetabolite chemotherapy. TcrNT2, expressed in a Leishmania mexicana cell line lacking the NT1 nucleoside transporter locus, displayed very high selectivity and affinity for thymidine with a K_m of 0.26 ± 0.05 µM. The selectivity was explained by interactions of 2-oxo, 4-oxo, 5-Me, 3′-hydroxy and 5′-hydroxy with the transporter binding pocket, whereas a hydroxy group at the 2′ position was deleterious to binding. This made 5-halogenated 2′-deoxyuridine analogues good substrates but 5-F-2′-deoxyuridine displayed disappointing activity against T. cruzi trypomastigotes. By comparing the EC₅₀ values of tubercidin and its 7-substituted analogues against L. mexicana Cas9, Cas9^ΔNT1 and Cas9^ΔNT1+TcrNT2 it was shown that TcrNT2 can take up tubercidin and, at a minimum, a subset of the analogs.     

Preparation of 5-Hydroxymethyl-pyrimidine Based Nucleosides: A Reinvestigation

5-Hydroxymethyl-pyrimidine-based nucleobases have attracted attention in the last years due to their important role in gene regulation. It prompted the development of efficient routes to the corresponding nucleoside building blocks for further incorporation into oligonucleotides. Several pathways have been employed in recent years to access properly protected 5-hydroxymethyl-pyrimidine based nucleosides, including hydroxymethylation of 2’-deoxyuridine, radical bromination of thymidine followed by bromine substitution, or carbonylative coupling through Stille conditions starting from 5-iodo-2’-deoxyuridine. In this study, we review the different approaches currently used to introduce the 5-hydroxymethyl moiety, we reinvestigate some of them, and finally, we propose an alternative route based on the oxidation of the methyl of thymidine followed by its reduction that allows access to protected 5-hydroxymethyl-2’-deoxyuridine in a simple way with good yields. Finally, we present some examples of application including the synthesis of base J and 5-azidomethyl-2’-deoxyuridine.     

Parallel G-quadruplex Structures Increase Cellular Uptake and Cytotoxicity of 5-Fluoro-2′-deoxyuridine Oligomers in 5-Fluorouracil Resistant Cells

Fluoropyrimidines, such as 5-fluorouracil (5-FU) and related prodrugs have been considered first-line chemotherapy agents for the treatment of colorectal cancer. However, poor specificity and tumor cell resistance remain major limiting bottlenecks. G-quadruplexes, have been suggested as preferred nanostructures for enhancing cellular uptake mediated by G-quadruplex binding proteins which are abundant at the membranes of some tumor cells. In the current study, we propose a new strategy to deliver 5-fluoro-2′-deoxyuridine (5-FdU) monophosphate, the main active drug from 5-FU derivatives that may circumvent the cellular mechanisms of FU-resistant cancer cells. Two G-quadruplexes delivery systems containing four and six G-tetrads ((TG₄T) and (TG₆T)) linked to a FdU oligonucleotide were synthesized. Biophysical studies show that the G-quadruplex parallel structures are not affected by the incorporation of the 5 units of FdU at the 5’-end. Internalization studies confirmed the ability of such G-quadruplex nanostructures to facilitate the transport of the FdU pentamer and increase its cytotoxic effect relative to conventional FU drug in FU-resistant colorectal cancer cells. These results suggest that FdU oligomers linked to G-quadruplex parallel sequences may be a promising strategy to deliver fluoropyrimidines to cancer cells.     

One-step to get 5-azidomethyl-2′-deoxyuridine from 5-hydroxymethyl-2′-deoxyuridine and detection of it through click reaction

Nowadays a few ways to synthesize 5-azidomethyl-2′-deoxyuridine from 5-hydroxymethyl-2′-deoxyuridine have been reported. But none of them was one-step. And many of them need to protect the hydroxyl group on the pentose ring. The detection of 5-hydroxymethyl-2′-deoxyuridine is also very important in many biological processes. However few fluorescence detection strategies have been tried to do this. Herein, we reported a one-step protocol to synthesize 5-azidomethyl-2′-deoxyuridine, which was then used for detecting 5-hydroxymethyl-2′-deoxyuridine through a click reaction.     

Uracil ring opening in the reaction of 5-formyl-2′-deoxyuridine with primary alkyl amines

Treatment of 5-formyl-2′-deoxyuridine (f⁵dU) with stoichiometric amounts of strongly nucleophilic, non-hindered primary alkyl amines led to fast and quantitative formation of the corresponding Schiff bases. In the presence of excess amines, novel nucleosides with ring opened pyrimidine bases were formed as a result of the Michael addition of a second amine to the pre-formed imines. In the reaction of f⁵dU with aromatic amines, the formation of Schiff base derivatives was slower and even under prolonged treatment with an excess of amine the uracil ring remained intact.     

Synthesis,cytotoxicity and antiviral activity studies of the conjugates of cobalt bis(1,2-dicarbollide)(-I) with 5-ethynyl-2′-deoxyuridine and its cyclic derivatives

A series of novel conjugates of cobalt bis(1,2-dicarbollide)(-I) with 5-ethynyl-2′-deoxyuridine and its cyclic derivatives were synthesized. Conjugates with 5-ethynyl-2-deoxyuridine were prepared by the direct Sonogashira coupling of a series of cobalt bis(1,2-dicarbollide)(-I) terminal alkynes and 5-iodo-2′-deoxyuridine. Their furo[2,3-d]pyrimidin-2(3H)-one isomers were obtained either by intermolecular cyclization of the above conjugates or by Sonogashira coupling using Pd/C as a catalyst. Action of ammonia on these furo[2,3-d]pyrimidin-2(3H)-one conjugates resulted in pyrrolo[2,3-d]pyrimidin-2(3H)-one conjugates. Most of the designed compounds have shown low cytotoxicity in several cell lines. Some 5-ethynyl-2-deoxyuridine and furo[2,3-d]pyrimidin-2(3H)-one conjugates have also presented antiviral activity.