Dinucleotides of 4′-C-vinyl- and 5′-C-allylthymidine as substrates for ring-closing metathesis reactions

Thymidine derivatives containing a 4′-C-vinyl group or a 5′-C-allyl group are synthesized and used as building blocks for three different dinucleotides. These are evaluated as substrates for ring-closing metathesis cyclisations, and a protected 5′-C-allylthymidine homo-dimer is found to be the most reactive. A protected precursor for a conformationally restricted cyclic dinucleotide with a four carbon 5′-C to 5′-C connection is hereby efficiently obtained, whereas a corresponding three carbon 4′-C to 5′-C connection is obtained in a lower yield.     

Dinucleotides containing two allyl groups by combinations of allyl phosphotriesters, 5-allyl-, 2′-O-allyl- and 2′-arabino-O-allyl uridine derivatives as substrates for ring-closing metathesis

Five different dinucleotides, each containing two allyl groups in various positions, were prepared and studied as substrates for ring-closing metathesis reactions. These dinucleotides were designed from appropriate nucleoside building blocks combining four different positions for the allyl group; the allyl phosphotriester linkage, 5-allyl-2′-deoxyuridine, and ribo- as well as arabino-configured 2′-O-allyluridine. Thus, convenient procedures for these building blocks were developed. From the dinucleotides, two new cyclic nucleotide structures were obtained; one connecting two adjacent nucleobase moieties and the other forming an unsaturated four-carbon linkage between the phosphate moiety and the adjacent pyrimidine nucleobase. The latter cyclic dinucleotide was also prepared with a saturated four-carbon linkage using a tandem ring-closing metathesis-hydrogenation procedure. This compound was found to be significantly more stable towards a nucleophilic ring-opening than its unsaturated counterpart.     

Synthesis and anti-HIV activity of l-β-3′-C-cyano-2′,3′-unsaturated nucleosides and l-3′-C-cyano-3′-deoxyribonucleosides

An efficient synthetic method was developed for l-β-3′-C-cyano-2′,3′-unsaturated nucleosides and l-3′-C-cyano-3′-deoxyribonucleosides. The key intermediate 11 was obtained from l-xylose, from which a series of pyrimidine and purine nucleosides were prepared in high yield by the coupling of 11 and various silyl-protected bases in the presence of TMSOTf. These nucleosides were eliminated, followed by deprotecting to give l-β-3′-C-cyano-2′,3′-unsaturated nucleosides. When selectively deprotected by hydrazine hydrate in buffered acetic acid-pyridine followed by treatment with potassium carbonate in methanol, l-3′-C-cyano-3′-deoxyribonucleosides were obtained. The synthesized nucleosides were tested for anti-HIV activity.     

Synthesis and anti-HCV activity of 1-(1′,3′-O-anhydro-3′-C-methyl-β-d-psicofuranosyl)uracil

Synthesis of a novel 1′,2′-oxetane-uridine bearing a 2′-C-methyl substituent, [1-(1′,3′-O-anhydro-3′-C-methyl-β-d-psicofuranosyl)uracil], is described. Key to its construction was the use of 6-O-(p-toluoyl)-1,2:3,4-di-O-isopropylidene-3-C-methyl-d-psicofuranose as a nucleosidation substrate, which itself was derived from d-fructose. Anti-HCV activity was examined for the corresponding triphosphate which was not found to be an inhibitor of HCV NS5B 1b wild type polymerase in vitro. The 1′,2′-oxetane uridine triphosphate without 2′-C-methyl substitution was similarly inactive, however, the guanosine analog displayed modest inhibition (IC₅₀ = 10 μM).     

1-C-(2′-Oxoalkyl) glycosides as latent α,β-unsaturated conjugates. Synthesis of aza-C-glycosides by an intramolecular hetero-Michael addition

1-C-(2′-Oxoalkyl)-5-azido-5-deoxy-glycofuranosides were used as latent substrates for intramolecular hetero-Michael addition. Reduction of the azido groups by catalytic hydrogenation followed by base treatment produced 2′-ester and 2′-ketone aza-C-glycopyranosides. The conjugation addition was stereoselective in favor of aza-C-glycosides with equatorial substitutions at the pseudo anomeric center.     

Practical synthetic routes to carbon-substituted nucleosides

Robust practical routes to three different carbon-substituted nucleosides are described. Short synthetic procedures for preparing 1′-homonucleosides, 2′-C-methyl-carbanucleosides and 2′-C-methyl-cyclopropyl/cyclopentyl fused bicyclic ribose analogues are described starting from readily available building blocks.     

Oxidative cleavage of ribofuranose 5-(α-hydroxyphosphonates): a route to erythrofuranose-based nucleoside phosphonic acids

We report here an oxidative cleavage of (5R)- and (5S)-ribofuranosyl-5-C-phosphonate derivatives with periodate anion under both strong acidic and neutral conditions. In both cases, only (5R)-configured compound underwent the expected oxidation reaction and afforded the desired (4R)-erythrofuranosylphosphonate, whereas the second epimer, (5S)-ribofuranosyl-5-C-phosphonate did not provide the corresponding (4S)-erythrofuranosylphosphonate derivative. This different behavior of epimers toward oxidative cleavage is an important phenomenon. The obtained (4R)-erythrofuranosylphosphonate was used for the preparation of phosphonate mimic of adenosine 5′-phosphate via classical nucleosidation reaction. Condensation of the protected shortened AMP analogue with adenosine derivatives, however, provided only the 2′,5′-linked ApA analogue. Study on hybridization of the modified 2′-5′ ApA with polyU revealed its ability to form stable triplex-like complex, similar to natural 2′-5′ r(ApA) and 3′-5′ r(ApA). NMR spectroscopy study showed that the erythrofuranose part of the phosphonate nucleotide unit of modified 2′-5′ ApA was predominantly in the C2′-endo conformation, which is characteristic for B-DNA.     

Anomeric stereospecific synthesis of 2′-C-methyl β-nucleosides; the Holy reaction of cyanamide with 2-C-methyl-d-arabinose

The sequential reactions of 2-C-methyl-d-arabinose with cyanamide and methyl propiolate afford an anhydronucleoside, which may be opened under acid conditions with inversion at C2′, to give 2′-C-methyl uridine; ring opening with sodium hydroxide gave 2′-C-methyl arabino-uridine with retention of configuration at C2′. This gives complete stereospecific control to yield only β-nucleosides.     

Development of a novel nucleoside analogue with S-type sugar conformation: 2′-deoxy-trans-3′,4′-bridged nucleic acids

Two novel trans-3′,4′-bridged nucleic acid (trans-3′,4′-BNA) monomers, one with a 3,5,8-trioxabicyclo[5.3.0]decane structure and the other with a 4,7-dioxabicyclo[4.3.0]nonane structure, were successfully synthesized from thymidine. The locked trans-fused ring structures of the nucleoside analogues were confirmed by X-ray crystallography, which also indicated that their furanose rings had a typical S-type conformation involving C_2′-endo or C_3′-exo sugar puckering, respectively, and the same ring conformation as that observed in the B-type helical structure of the DNA duplex.     

Syntheses of 2′-C-amidoalkyl and 2′-C-cyanoalkyl containing oligodeoxyribonucleotides and assessment of their hybridisation affinity for complementary DNA and RNA

Oligodeoxynucleotides containing 2′-C-branched nucleosides with an amide or nitrile appended to either a one or two carbon alkyl chain have been synthesised. The phosphoramidites of the 2′-C-modified nucleosides were prepared and incorporated into the oligonucleotides using automated DNA synthesis. The duplex stability with complementary RNA and DNA was measured by UV melting experiments, in order to assess whether the amide/nitrile function could induce any duplex stability without the presence of the 2′-oxygen. The duplex stabilities of the oligonucleotides containing the 2′-C-modifications were decreased in the absence of the 2′-oxygen.     

Applications of NHC-mediated O- to C-carboxyl transfer: synthesis of (±)-N-benzyl-coerulescine and (±)-horsfiline

NHC-promoted O- to C-carboxyl transfer of 3-allyl indolyl phenyl carbonates generates 3-allyl-3-phenoxycarbonyl-oxindoles with good catalytic efficiency, which are readily converted into (±)-N-benzyl-coerulescine and (±)-horsfiline.     

Synthesis of 4′,4′-C-diaminomethyl nucleoside derivative as a building block for constructing libraries via amide bond formation

Preparation of the 4′,4′-C-diaminomethyl uridine analog starting from the commercial uridine via 4′,4′-C-dihydroxymethyl uridine, 4′,4′-C-bis-trifluoromethanesulfonyloxymethyl uridine, and 4′,4′-C-diazidomethyl uridine in total eight steps was achieved in 8% yield. Steric hindrance between 3′-O-TBDMS and 5′-O-triflate prevented the undesired ring closure which made the synthesis of target compound feasible.     

Synthesis of thio-C-glycosides from 2′-carbonylalkyl C-glycosides by a tandem β-elimination and intramolecular hetero-Michael addition

2′-Carbonyl 5-S-acetyl-C-glycofuranosides and 2′-carbonyl 4-S-acetyl-C-glycopyranosides were converted in good yields to respective 5-thio-C-glycopyranosides and 4-thio-C-glycofuranosides under base treatment. The transformation was resulted from β-elimination on 2′-carbonyl C-glycoside to form α,β-conjugated aldehyde (or ketone) and following intramolecular hetero-Michael addition by the thiol group.     

Glucose ferrocenyl-oxazolines: Coordination behavior toward [Pd(η-allyl)Cl]2 studied by ESI-MS

Several new oxazolin-2-yl-substituted ferrocenes based on 2-amino-2-deoxy-α-d-glucose were synthesized via the corresponding amides followed by closing the oxazoline-ring with SnCl₄.Coordination properties of representatives of the group of mono- and bis-oxazolinyl ferrocenes, 2-ferrocenyl-4,5-(3,4,6-tri-O-acetyl-1,2-dideoxy-d-glucopyrano)-[2,1-d]-oxazoline and 1,1′-bis{4,5-(3,4,6-tri-O-acetyl-1,2-dideoxy-d-glucopyrano)-[2,1-d]-oxazolin-2-yl}ferrocene, respectively, toward [Pd(η³-allyl)Cl]₂ were investigated by electrospray ionization mass spectrometry in positive ion mode and by MS/MS technique.With the monooxazoline derivative mainly a 1:1 complex with the Pd-moiety was found in the mass spectrum while the bisoxazoline yields a stoichiometry of 2:1 (oxazoline:Pd). The latter result is attributed to steric hindrance of the coordination of a second Pd-moiety to the bulky bisoxazolinyl-ferrocene.In the case of 1,1′-bis{4,5-(3,4,6-tri-O-acetyl-1,2-dideoxy-d-glucopyrano)-[2,1-d]-oxazolin-2-yl}ferrocene 9 overlapping of two signals in the m/z range from 955-965 was found which can be assigned to the singly charged adduct [C₃₆H₄₀FeN₂O₁₆ + Pd(η³-C₃H₅)]⁺ and a doubly charged Pd-ligand cluster with the general formula Pd₂[L(9)]₂.In addition, the molecular structure of 1,1′-bis{4,5-(3,4,6-tri-O-acetyl-1,2-dideoxy-d-glucopyrano)-[2,1-d]-oxazolin-2-yl}ferrocene was determined by X-ray diffraction analysis.     

Palladium(II) complexes containing a bulky pyridinyl N-heterocyclic carbene ligand: Preparation and reactivity

Coordination chemistry of a pyridine imidazole-2-ylidene ligand (pyN ˆC) with sterically hindered substituents toward palladium(II) metal ions has been investigated. The palladium carbene complex [(C-pyN ˆC)Pd(η³-allyl)Cl] (3) is prepared via the transmetallation from the corresponding silver carbene complexes with [ClPd(η³-allyl)]₂. Upon the abstraction of chloride, coordination of pyridinyl-nitrogen becomes feasible to form [C,N-(pyN ˆC)Pd(η³-allyl)](BF₄) (4). Ligand substitution reaction of 4 with triphenylphosphine results in the formation of [(C-pyN ˆC)Pd(PPh₃)(η³-allyl)](BF₄)], which the pyridinyl-nitrogen donor is substituted by the phosphine. This palladium complex appears to be base sensitive. Treatment of 4 with t-butoxide causes the decomposition to yield the metal nano-particles. Furthermore, de-complexation of 4 takes place under hydrogen atmosphere to generate the carbene precursor, 1-(6-mesityl-2-picolyl)-3-mesitylimidazolium salt. Nevertheless, the palladium complex 4 shows good catalytic activity on the Suzuki-Miyaura and Mizoroki-Heck reactions.     

Copper(I) catalysis: Synthesis of N,N′-diarylated and N-aryl,N′-formylated chiral C2-symmetric diamines

Chiral N,N′-diaryl C₂-symmetric diamines and N-aryl,N′-formyl-trans-(1R,2R)-diaminocyclohexane are readily accessed by copper catalyzed N,N′-diarylation and N-aryl,N′-formylation of trans-(1R,2R)-diaminocyclohexane with aryl bromides. N,N′-diarylation using (R)-1,1′-binaphthyl-2,2′-diamine and iodobenzene gave the corresponding (R)-N,N′-diphenyl-1,1′-binaphthyl-2,2′-diamine derivative in 83% yield.     

Efficient conjugation and preferential DNA binding of oligonucleotides containing 2′-O-(2-oxoethyl)arabinouridine

Oligodeoxyribonucleotides were synthesized that contain a novel nucleoside, 2′-O-(2-oxoethyl)arabinouridine. Whereas such oligonucleotides showed only a slight reduction in the T_M values of their complexes with complementary DNA, a significant destabilization was observed in the case of duplexes formed with RNA. This may be explained by the C_2′-endo conformation of 2′-O-(2,3-dihydroxypropyl)arabinouridine as demonstrated by NMR experiments in D₂O. The modified oligonucleotides were used to synthesize a number of conjugates with dyes, biotin and a N-modified laminin peptide, by hydrazone and oxime formation. We suggest that the 2′-arabinoaldehyde-containing DNA duplexes may be valuable tools for affinity modification of DNA-binding proteins.     

The synthesis of R-3-alkoxy-1-(1′-hydroxyethyl)-4-methoxy-2-(1″-propenyl)benzenes utilizing Corey-Bakshi-Shibata asymmetric reductions

Pyrolysis of the 3-O-allyl derivative 7 of isovanillin followed by alkylation of the derived allylphenol 8 afforded a series of benzaldehyde derivatives 9-11 each of which was transformed by initial treatment with methylmagnesium bromide followed by oxidation of the corresponding alcohols with activated manganese dioxide into a series of ketones 15-17. Palladium(0) catalysed isomerization of the double bond in the prop-2′-enyl side-chain afforded ketones 36-38 which were subjected to the Corey-Bakshi-Shibata asymmetric reduction protocol to afford the R-3-alkoxy-1-(1′-hydroxyethyl)-4-methoxy-2-(1″-propenyl) benzenes 42-44 in yields of approximately 60% and with ee's of 75%.     

5′-Epimeric 3′-deoxy-3′,4′-didehydronucleoside-5′-C-phosphonates: synthesis and structural assignment by NMR and X-ray analyses

Epimeric 5′-(RS) dialkyl 3′-deoxy-3′,4′-didehydro-5′-C-phosphonates were prepared by nucleophilic addition of various dialkyl phosphites to 3′-deoxy-3′,4′-didehydronucleoside-5′-aldehydes. Whereas direct NMR configuration assignment for the C5′ atom bearing the phosphoryl and hydroxy groups using the J (P,H4′) and J (H5′,H4′) coupling constants is impossible due to the absence of the H4′ atom, successful separation, crystallisation and X-ray crystallographic analysis of a pair of epimeric 5′-C-phosphonates, followed by correlation with a series of NMR parameters, led to efficacious configuration assignment of individual epimers in the mixtures.     

Recoverable cationic Pd-catalyzed Heck reaction under thermomorphic mode

The reaction of allylpalladium chloride dimer and 4,4′-bis(R_fCH₂OCH₂)-2,2′-bpy, 1a-c, in the presence of AgOT_f resulted in the synthesis of cationic complex, [Pd(η³-allyl)(4,4′-bis-(R_fCH₂OCH₂)-2,2′-bpy)](OT_f), 2a-c where R_f = C₉F₁₉ (a), C₁₀F₂₁ (b), C₁₁F₂₃ (c), respectively. The solubility curves of 2a-c which began from virtually zero below −40 °C and increased dramatically at slightly higher temperature were quantitatively measured. Upon changing from −40-90 °C there was several orders of magnitude increase of solubility for 2a-c. The cationic Pd-catalyzed Heck arylation of methyl acrylate was selected to demonstrate the feasibility of recycling usage with 2b,c as the catalyst using DMF as the solvent at 140 °C for 3 h in each run. At the end of each cycle, the product mixtures were cooled to −30 °C, and then catalysts were recovered by decantation. The products were quantified by GC analysis or by the isolated yield. The Heck reaction of C₆H₅I with methyl acrylate could be catalyzed by 2b with good recycling results for a total of 15 times and also with a 100% selectivity favoring the trans product. To our knowledge, this is the first example of cationic Pd-catalyzed Heck reaction under the thermomorphic mode.