Stereoselective Synthesis of Highly Functionalized Arabinosyl Nucleosides through Application of an N-Nitro Protecting Group

2'-β-Methylselenyl nucleos(t)ide analogs as reverse transcriptase inhibitors against diverse HIV mutants

Nucleoside reverse transcriptase inhibitors (NRTIs) have been extensively studied as drugs targeting HIV RT. However, the practice or use of approved NRTIs lacking the 3'-hydroxy group often promotes frequent HIV mutations and generates drug-resistance. Here, we describe a novel NRTI with 2'-β-methylselenyl modification. We found that this modification inhibited the DNA elongation reaction by HIV-1 RT despite having a 3'-hydroxy group. Moreover, the conformation of this nucleoside analog is controlled at C3'-endo, a conformation that resists excision from the elongating DNA by HIV RT. Accordingly, the designed analogs exhibited activity against both wild-type HIV and multidrug-resistant HIV mutants.

Transient imine as a directing group for the Pd-catalyzed anomeric C(sp3)-H arylation of 3-aminosugars

The first example of Pd(II)-catalyzed anomeric arylation of 3-aminosugars is reported by using an L,X-type transient directing group (TDG) approach combined with an external 2-pyridone ligand. The released free amine was in situ transformed into an azide function, which was then exploited in a CuAAC to increase the molecular complexity and prepare a variety of complex substituted C3-triazolo C-glycosides in good yields.

Two-Factor Fluorogenicity of Tetrazine-Modified Cyanine-Styryl Dyes for Bioorthogonal Labelling of DNA

Two green fluorescent tetrazine-modified cyanine-styryl dyes were synthesized for bioorthogonal labelling of DNA by means of the Diels-Alder reaction with inverse electron demand. With DNA as target biopolymer the fluorescence of these dyes is released by two factors: (i) sterically by their interaction with DNA, and (ii) structurally via the conjugated tetrazine as quencher moiety. As a result, the reaction with bicyclononyne-modified DNA is significantly accelerated up to ≥284,000 M^-1  s^-1 , and the fluorescence turn-on is enhanced up to 560 by the two-factor fluorogenicity. These dyes are cell permeable even in low concentrations and undergo fluorogenic reactions with BCN-modified DNA in living HeLa cells. The two-factor fluorescence release improves the signal-to-noise ratio such that washing procedures prior to cell imaging are not needed, which is a great advantage for live cell imaging of DNA and RNA in the future.

Double-Headed 2'-Deoxynucleotides That Hybridize to DNA and RNA Targets via Normal and Reverse Watson-Crick Base Pairs

Through the use of modified nucleotides, synthetic nucleic acids have found several fields of application within biotechnology and in the pharmaceutical industry. We have previously introduced nucleotides with an additional functional nucleobase linked to C2' of arabinonucleotides (B_X). These double-headed nucleotides fit neatly into DNA·DNA duplexes, where they can replace the corresponding natural dinucleotides and thus condense the molecular information. Here, we introduce a 2'-deoxy version of the B_X design with inversion of the C2' stereochemistry (^dSB_X) with the aim of obtaining improved RNA recognition. Specifically, ^dSB_X analogues with cytosine or isocytosine attached to C2' of 2'-deoxyuridine (^dSU_C and ^dSU_iC) were synthesized and evaluated in duplexes. Whereas the ^dSB_X design did not outperform the B_X design in terms of mimicking dinucleotides in nucleic acid duplexes, it was able to engage in reverse Watson-Crick pairing using its 2'-base. This was evident from the ability of the ^dSU_C cytosine to form stable mis-matching base pairs with opposite cytosines identified as hemiprotonated C·C⁺ pairs. Furthermore, specific base-pairing with guanine was only observed for the isocytosine-bearing ^dSU_iC monomer. Very stable duplexes were obtained with ^dSU_C/iC monomers in each strand indicating that fully modified double-headed nucleic acid sequences could be based on the ^dSB_X design.

Transglycosylation in the Modification and Isotope Labeling of Pyrimidine Nucleosides

Transglycosylation of pyrimidine nucleosides is demonstrated in a one-pot synthesis of uridine derivatives under microwave irradiation. Inductive activation of 2',3',5'-tri-O-acetyl uridine with a 5-nitro group produces a more-reactive glycosyl donor. Under optimized Vorbrüggen conditions, the 5-nitrouridine facilitates a reversible nucleobase exchange with a series of 5-substituted uracils. The protocol is also exemplified in a gram-scale reaction under thermal heating. The strategy provides easy access to isotopically labeled uridine.

Investigation of pyrimidine nucleoside analogues as chemical probes to assess compound effects on the proliferation of Trypanosoma cruzi intracellular parasites

Trypanosoma cruzi parasites utilise de novo pyrimidine biosynthesis to produce DNA and survive within mammalian host cells. This pathway can be hijacked to assess the replication of intracellular parasites with the exogenous addition of a DNA specific probe. To identify suitable probe compounds for this application, a collection of pyrimidine nucleoside analogues was assessed for incorporation into T. cruzi intracellular amastigote DNA using image-based technology and script-based analysis. Associated mammalian cell toxicity of these compounds was also determined against both the parasite host cells (3T3 cells) and HEK293 cells. Incorporation of 5-ethynyl-2′-deoxyuridine (EdU) into parasite DNA was the most effective of the probes tested, with minimal growth inhibition observed following either two or four hours EdU exposure. EdU was subsequently utilised as a DNA probe, followed by visualisation with click chemistry to a fluorescent azide, to assess the impact of drugs and compounds with previously demonstrated activity against T. cruzi parasites, on parasite replication. The inhibitory profiles of these molecules highlight the benefit of this approach for identifying surviving parasites post-treatment in vitro and classifying compounds as either fast or slow-acting. F-ara-EdU resulted in <50% activity observed against T. cruzi amastigotes following 48 hours incubation, at 73 μM. Collectively, this supports the further development of pyrimidine nucleosides as chemical probes to investigate replication of the parasite T. cruzi.

Chagas disease occurs within 21 countries in the Americas, causes over 10, 000 deaths per year and a further 25 million people are at risk of being infected. The cause of Chagas disease is Trypanosoma cruzi, a single celled protozoan parasite, which enters the bloodstream of a host by the bite of a “kissing bug”. In advanced disease stages, the parasite hides in heart and gut tissue and is difficult to treat. Identifying the replicative ability of these parasites is important to understanding Chagas disease progression and the effectiveness of compounds and drugs for treatment. By testing a panel of nucleoside analogues that may incorporate into DNA during synthesis, we developed an image-based method with a fluorescently-labelled DNA probe to identify replicating parasites. This method has effectively shown that drugs used to treat the parasite are able to clear intracellular infection, whilst a compound that was not efficacious in clinical trials leaves replicating T. cruzi behind. This methodology can be used to understand the action of further compounds and supports the identification of new, less toxic probes to assess intracellular parasite replication.

Extension of the 5-alkynyluridine side chain via C-C-bond formation in modified organometallic nucleosides using the Nicholas reaction

Dicobalt hexacarbonyl nucleoside complexes of propargyl ether or esters of 5-substituted uridines react with diverse C-nucleophiles. Synthetic outcomes confirmed that the Nicholas reaction can be carried out in a nucleoside presence, leading to a divergent synthesis of novel metallo-nucleosides enriched with alkene, arene, arylketo, and heterocyclic functions, in the deoxy and ribo series.

Synthesis of 5-Alkynyl Substituted 2'-Arabinosyl 2'-Halogenated Uridine Nucleosides

This unit describes the detailed preparation of 5-alkynyl-2'-halogenated arabinosyl uridine nucleosides (2'-halo-ara-EdU) from uridine. These compounds were synthesized as prospective chemical probes for the detection of DNA synthesis in proliferating cells. Currently, this is the only synthetic methodology reported to access these compounds. The key to success of the synthetic approach was to employ a 3-N-nitro-protecting group to stabilize the required 2'-triflate nucleoside precursor toward nucleophilic substitution. Several synthetic challenges were overcome to accommodate the combination of a 5-alkyne and 3-N-nitro functional group, including facile introduction and removal of the N-nitro group, and removal of the sugar acetyl groups under acidic conditions. © 2019 by John Wiley & Sons, Inc.