Novel and efficient syntheses of 3′,5′-diamino derivatives of 2′,3′,5′-trideoxycytidine and 2′,3′,5′-trideoxyadenosine. Protonation behavior of 3′,5′-diaminonucleosides

High yielding synthetic routes to 3′,5′-diamino-2′,3′,5′-trideoxycytidine and 3′,5′-diamino-2′,3′,5′-trideoxyadenosine are described. In addition, the protonation behavior of 3′,5′-diamino-2′,3′,5′-trideoxycytidine, 3′,5′-diamino-2′,3′,5′-trideoxyadenosine, 3′,5′-diamino-3′,5′-dideoxythymidine, and 3′,5′-diamino-2′,3′,5′-trideoxyuridine has been studied by means of pH-metric measurements and NMR spectroscopy. The ionization constants and the sequence of protonation sites have been determined.     

A versatile reagent for the synthesis of 5′-phosphorylated, 5′-thiophosphorylated or 5′-phosphoramidate-conjugated oligonucleotides

We report the synthesis of a new phosphorylating reagent that is easily accessible and allows not only the chemical synthesis of 5′-phosphorylated and 5′-thiophosphorylated oligonucleotides but also the 5′-conjugation through a phosphoramidate linkage. 5′-Amino-linker and 5′-alkyne oligonucleotides were obtained and the latter was conjugated by a 1,3-dipolar cycloaddition (click chemistry) with a galactosylated azide derivative to afford 5′-galactosyl oligonucleotide with high efficiency.     

New and efficient synthesis of 5′-amino-5′-(S)-methyl-2′,5′-dideoxynucleosides

A short, efficient synthesis of 5′-amino-5′-(S)-methyl-2′,5′-dideoxynucleosides 1 has been developed through the diastereoselective addition of methylmagnesium bromide or methyllithium to an intermediate tert-butylsulfinimide.     

Practical synthesis of adenosine 3′,5′-cyclic monophosphorodithioate

Adenosine 3′,5′-cyclic monophosphorodithioate (cAMPS₂), which has two exocyclic sulfurs directly attached to phosphorus, was synthesized from adenosine phosphoramidite by intramolecular cyclization employing the phosphotriester method as a key step.     

An efficient synthesis of highly functionalized dinucleotide cap analogs

An efficient synthesis of new cap analogs containing aminoallyl linkers such as m⁷G[5′]pppp[5′]U-aminoallyl and m₂^7,3′OG[5′]pppp[5′]U-aminoallyl is reported. The final cap analog has been isolated with high purity (>99.8%) after ion-exchange column purification.     

Straightforward synthesis of 3′-deoxy-3′,4′-didehydronucleoside-5′-aldehydes via 2′,3′-O-orthoester group elimination: a simple route to 3′,4′-didehydronucleosides

Straightforward, high-yielding syntheses of 3′-deoxy-3′,4′-didehydronucleoside-5′-aldehydes and 3′-deoxy-3′,4′-didehydronucleosides starting from 2′,3′-O-orthoester derivatives of ribonucleosides are described.     

New reagent for the preparation of oligonucleotides involving a 5′-thiophosphate or a 5′-phosphate group

We report here a novel, simple reagent enabling the chemical incorporation of a thiophosphate or a phosphate group at the 5′-end of oligonucleotides using very mild basic deprotection conditions. This method can be useful in the case of alkali sensitive modified oligonucleotides. This reagent also gives access to the preparation of bifunctional oligonucleotides with either a thiophosphate group at the 5′-end and a phosphate at the 3′-end, or two thiophosphate groups at both the 5′- and the 3′-ends, or a 5′-thiophosphate group and a 3′-amino-containing linker.     

Synthesis and crystal structure of 2′-deoxy-2′-fluoro-4′-thioribonucleosides: substrates for the synthesis of novel modified RNAs

We report herein the synthesis of appropriately protected 2′-deoxy-2′-fluoro-4′-thiouridine (5), -thiocytidine (7), and -thioadenosine (35) derivatives, substrates for the synthesis of novel modified RNAs. The synthesis of 5 and 7 was achieved via the reaction of 2,2′-O-anhydro-4′-thiouridine (3) with HF/pyridine in a manner similar to that of its 4′-O-congener whereas the synthesis of 35 from 4′-thioadenosine derivatives was unsuccessful. Accordingly, 35 was synthesized via the glycosylation of the fluorinated 4-thiosugar 25 with 6-chloropurine. The X-ray crystal structural analysis revealed that 2′-deoxy-2′-fluoro-4′-thiocytidine (8) adopted predominately the same C3′-endo conformation as 2′-deoxy-2′-fluorocytidine.     

2,2′,3,4-Tetrahydroxy-3′-sulpho-5′-nitroazobenzene for spectrophotometric determination of aluminium in pharmaceutical suspensions and granite

A selective and sensitive new spectrophotometric method has been developed for the determination of aluminium. 2,2′,3,4-Tetrahydroxy-3′-sulpho-5′-nitroazobenzene (tetrahydroxyazon SN) formed an orange chelate with aluminium at pH 4. Molar absorptivity of the complex in 1:2 is 5.46 × 10⁴ l mol⁻¹ cm⁻¹ at 479 nm. The method obeys Beer's law in the range of 0.005-1.079 μg ml⁻¹. The determination of aluminium is not interfered with by earth alkaline, alkaline elements, rare earth elements, halides, phosphates, sulphates, urea, ascorbic acid, Sn²⁺, Sr²⁺, Cr³⁺, Cd²⁺, Hg²⁺, or Mn²⁺. The proposed method is rapid and simple, and it has been successfully applied to the determination of aluminium in certified pharmaceutical suspension and granite.     

Application and details of photoinduced oxidative cyclization of 5-(4′,9′-methanocycloundeca-2′,4′,6′,8′,10′-pentaenylidene)pyrimidine-2,4,6(1,3,5H)-triones and related compounds

As novel methodology for synthesizing the furan ring, a photoinduced oxidative cyclization of 5-(4′,9′-methanocycloundeca-2′,4′,6′,8′,10′-pentaenylidene)pyrimidine-2,4,6(1,3,5H)-triones (7a-c) and related compounds 9a-c was accomplished to give 5,10-methanocycloundeca[4,5]furo[2,3-d]pyrimidine-2,4(1,3H)-dionylium tetrafluoroborates (8a-c⁺·BF₄⁻) and related compounds 2a-c⁺·BF₄⁻, respectively. In the photoinduced oxidative cyclization, the molecular oxygen in air is used as oxidant and the reaction proceeds under mild conditions to give desired products without byproducts, and thus, it is interesting from the viewpoint of the green chemistry. On the reactions of the mono-substituted derivatives 7d,e and 9e,f, the selectivity of the photoinduced cyclizations were reversed as compared with those of the DDQ-promoted oxidative cyclizations. By the NMR monitoring of the reactions of 7a and deuterated compound 7a-D₂ under degassed conditions, the details of the reaction pathway were clarified and rationalized on the basis of the MO calculation by the 6-31G^∗ basis set of the MP2 levels as well.     

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.     

A concise synthesis of 3′-α-fluoro-2′,3′-dideoxyguanosine (FddG) via 3′-α-selective fluorination of 8,2′-thioanhydronucleoside

The antiviral nucleoside 3′-α-fluoro-2′,3′-dideoxyguanosine (FddG) was synthesized via 3′-α-selective fluorination of 8,2′-thioanhydronucleoside as the key step. Desulfurization of 3′-α-fluoro-3′-deoxy-8,2′-thioanhydronucleoside could be achieved by the treatment with Raney Ni in toluene. This method provides a concise route to 3′-α-fluoro-2′,3′-dideoxynucleosides that avoids the use of explosive and expensive SF₄-related fluorinating reagents.     

Synthesis,chemical reactivity,and photophysical properties of 2′,7′ phenylated rhodamine dyes

While exploring water soluble rhodamine based fluorescent polymeric systems for biological imaging applications we came across new rhodamine derivatives that possess interesting optical properties. We report the synthesis of three different 2′,7′-diphenylated rhodamine derivatives (1–3) with distinct photophysical properties. The three rhodamine derivatives differ by the number of methyl groups present on the nitrogens and their absorption maxima are red-shifted on increased methylation. We observed an unusual inertness of these compounds toward traditional DCC–DMAP esterification conditions, which we attribute to the ease of lactonization in the presence of even minute amounts of the nucleophile/base DMAP (pK_a = 9.2). Synthesis of acrylate esters was successfully accomplished using MSNT (1-(Mesitylene-2-sulfonyl)-3-nitro-1,2,4-triazole) coupling conditions using a much milder nucleophile/base, for example, N-methyl imidazole (pK_a = 6.95).     

A practical synthesis of 2′-aminoacylamino-2′-deoxyadenosines

A practical and efficient synthesis of 2′-aminoacylamino-2′-deoxyadenosine derivatives is reported. EDCI/HOBt-mediated coupling of a 3′,5′-diprotected 2′-amino-2′-deoxyadenosine derivative to various N-Cbz-l-amino acid derivatives followed by global deprotection affords analytically pure 2′-aminoacylamino-2′-deoxyadenosine derivatives without the necessity for preparative HPLC purification. These compounds are non-hydrolysable isosteres of 2′-aminoacyladenosines, which are of use in X-ray studies for the elucidation of the editing mechanism of various tRNA synthetases.     

5′-Noraristeromycin derivatives isomeric to aristeromycin and 2′-deoxyaristeromycin

A straightforward synthesis of (1S,2R,3R,4R)-4-(6-aminopurin-9-yl)-2-hydroxymethylcyclopentane-1,3-diol (2), an isomer of aristeromycin, and its 2′-deoxy derivative 3 from readily available disubstituted cyclopentenes is presented. An antiviral analysis of 2 showed it to have significant activity versus Epstein-Barr virus (IC₅₀ 0.62 μg/mL in the Elisa assay) and to be free of cytotoxicity effects against the host cells. In a much less comprehensive antiviral analysis, 3 also was active towards Epstein-Barr (IC₅₀ 7.58 μg/mL in the Elisa assay) but this was accompanied by cellular toxicity.     

A colormetric and fluorescent chemosensor for adenosine-5′-triphosphate based on rhodamine derivative

A rhodamine spirolactam derivative (1) was developed as a colormetric and fluorescent chemosensor for adenosine-5′-triphosphate (ATP) via hydrogen bonds interaction. As far as we know, this is the first case to explore ATP-induced ring-opening of spirolactam in rhodamine derivatives. It exhibited a highly sensitive “turn-on” fluorescent response toward ATP with a 47-fold fluorescence intensity enhancement under 20 equiv. of ATP added. The chemosensor can be applied to the quantification of ATP with a linear range covering from 1.0 × 10⁻⁷ to 2.0 × 10⁻⁴ M and a detection limit of 2.5 × 10⁻⁸ M. The experiment results show that the response behavior of 1 toward ATP is pH independent in medium condition (pH 6.0–8.0). Most importantly, the novel chemosensor has well solved the problem of serious interferences from other nucleoside polyphosphates such as ADP and AMP generally met by previously reported typical fluorescent chemosensors for ATP. Moreover, the response of the chemosensor toward ATP is fast (response time less than 3 min). In addition, the chemosensor can be used for the fluorescence assay for protein kinase activity with satisfactory results. The chemosensor for ATP based on hydrogen bonds interaction provided a novel strategy for the design of colormetric and ratiometric fluorescent probes for other target anions with high sensitivity and selectivity.     

Synthesis of (3′R,5′S)-3′-hydroxycotinine using 1,3-dipolar cycloaddition of a nitrone

To synthesize (3′R,5′S)-3′-hydroxycotinine [(+)-1], the main metabolite of nicotine (2), cycloaddition of C-(3-pyridyl)nitrones 3a, 3c, and 15 with (2R)- and (2S)-N-(acryloyl)bornane-10,2-sultam [(2R)- and (2S)-8] was examined. Among them, l-gulose-derived nitrone 15 underwent stereoselective cycloaddition with (2S)-8 to afford cycloadduct 16, which was elaborated to (+)-1.     

In vitro binding studies of organotin(IV) complexes of 1,2-bis(1H-benzimidazol-2-yl)ethane-1,2-diol with CT-DNA and nucleotides (5′-GMP and 5′-TMP): Effect of the ancillary ligand on the binding propensity

The chiral benzimidazole ligand, 1,2-Bis(1H-benzimidazol-2-yl)ethane-1,2-diol, L, exhibiting coordination mode with an oxygen atom of alcohol group directed towards the metal ion and another -OH group with different molecular axis directed away from the metal center was utilized as a building block for organotin complexes [C₁₈H₁₉N₄O₂SnCl], [C₂₈H₂₃N₄O₂SnCl] and [C₅₂H₄₂N₄O₂Sn₂] (1-3). Complexes 1 and 3 exhibit a pentacoordinate geometry while the complex 2 reveals hexacoordinated environment around the Sn(IV) metal ions as evidenced by ¹¹⁹Sn NMR studies. The DNA binding ability of benzimidazole ligand and their organotin(IV) complexes 1-3 were examined by employing different biophysical methods. The absorption titration of the complexes with CT-DNA reveal significant hyperchromic effect together with strong bathochromic shift of 4-5 nm which infer substantial binding of the complexes with CT-DNA. The intrinsic binding constant K_b values of the complexes 1-3 were found to be 2.16 ± 0.04 × 10⁴, 3.47 ± 0.04 × 10⁴ and 4.60 ± 0.04 × 10³ M⁻¹, respectively, suggesting pronounced binding of complex 2 with DNA double helix. The mechanism of binding of the complexes was further ascertained by the interaction studies of these complexes with nucleotides (5′-GMP and 5′-TMP) using absorption spectroscopy suggesting a clear preference for 5′-GMP binding which was further authenticated by NMR (¹H and ³¹P NMR) studies.     

Difluorocarbene chemistry: synthesis of gem-difluorocyclopropenylalkynes and 3,3,3′,3′-tetrafluorobicyclopropyl-1,1′-dienes

A series of gem-difluorocyclopropenylalkynes are easily obtained in good yields by the Sonogashira reaction of 3,3-difluoro-1-iodocyclopropenes with terminal alkynes. Onto these new alkynes addition of difluorocarbene, generated from the decomposition of FSO₂CF₂COOTMS in diglme in the presence of 10 mol% anhydrous NaF at 120 °C, gives 3,3,3′,3′-tetrafluorobicyclopropyl-1,1′-dienes. Acid hydrolysis of gem-difluorocyclopropenylalkynes in refluxing CH₃OH affords the corresponding methoxycarbonylenynes.     

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.