Design, synthesis, and evaluation of a novel bridged nucleic acid, 2′,5′-BNA, with S-type sugar conformation fixed by N-O linkage

We designed a novel 2′-O,5′-N bridged nucleic acid, 2′,5′-BNA^ON, whose sugar puckering was fixed to S-type conformation by an N-O linkage. A dimer unit formed from 2′,5′-BNA^ON-U and thymidine was synthesized via a coupling reaction between a protected 2′,5′-BNA^ON-U monomer and a thymidine derivative. Introduction of 2′,5′-BNA^ON-U into DNA was carried out using conventional phosphoramidite chemistry with a DNA synthesizer. The hybridization abilities of 2′,5′-BNA^ON-U-modified oligonucleotides against DNA or RNA complement were evaluated.     

Synthesis of 3′-azido-4′-ethynyl-3′,5′-dideoxy-5′-norarabinouridine: a new anti-HIV nucleoside analogue

3′-Azido-4′-ethynyl-3′,5′dideoxy-5′-norarabinouridine 10 was synthesized from commercial uridine 1 in which the key step is the opening of protected 2′,3′-epoxyuridine derivative 7 by sodium azide and the hydroxymethyl at 4-position of the ribose ring are replaced by ethynyl group.     

Synthesis of a novel bridged nucleoside bearing a fused-azetidine ring, 3′-amino-3′,4′-BNA monomer

A novel bridged nucleic acid monomer, 3′-amino-3′-deoxy-5-methyl-3′-N,4′-C-methyleneuridine, was successfully synthesized via a useful and convenient azetidine ring formation under Staudinger's conditions. A ¹H NMR experiment and a PM3 calculation revealed that the sugar moiety of the novel bridged nucleic acid monomer, 3′-amino-3′,4′-BNA, was restricted to S-type conformation.     

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.     

Synthesis of a series of novel 2′,3′-dideoxy-6′,6′-difluoro-3′-thionucleosides

A series of novel 2′,3′-dideoxy-6′,6′-difluoro-3′-thionucleosides 1a-d, analogues of 3TC that has high biological activities against HIV and HBV, have been synthesized from the gem-difluorohomoallyl amine 7 in a straightforward fashion. Our synthesis featured the construction of thiofuranose skeleton through ring closure of key intermediates and installation of pyrimidine ring with amino group in compounds 13a,b.     

Synthesis of a 4′,4′-spirothietane-2′, N-cycloadenosine as a highly constrained analogue of 5′-deoxy-5′-methylthioadenosine (MTA)

The synthesis of the highly constrained adenosine derivative 7 featuring at spirothietane at C-4′, which may be considered as a rigid analogue of MTA, is described.     

Synthesis of (±)-4′-ethynyl-5′,5′-difluoro-2′,3′-dehydro-3′-deoxy- carbocyclic thymidine: a difluoromethylidene analogue of promising anti-HIV agent Ed4T

Synthesis of (±)-4′-ethynyl-5′,5′-difluoro-2′,3′-dehydro-3′-deoxy-carbocyclic-thymidine (8) was carried out. The difluoromethylylidene group of 8 was constructed by the electrophilic fluorination to the cyclopentenone 11 by using Selectfluor^®. Introduction of thymine base was investigated based on the Mitsunobu reaction by employing cyclopentenyl allyl alcohols variously substituted at the 4-position. It was found the 4-methoxycarbonyl derivative 14 gave the highest selectivity both in terms of regio- and stereochemistry.     

Study on disulfur-backboned nucleic acids: Part IV.Efficient synthesis of 3′,5′-dithio-2′-deoxyguanosine

An efficient and novel method for synthesizing 3′,5′-dithio-2′-deoxyguanosine was described. In this method normal guanosine was used as the strating materials. A very efficient procedure was used to synthesize 2´-O-tosylguanosine 1, which used 0.1eq DBTO instead of 2eq. 1 was treated with LTBH to give 9-(2-deoxy-β-D-threo-pentofuranosyl)guanine 2. 2 could be easily truned to the target compound.     

2′,3′,4′,5′-Tetraacetyl-N(3)-carboxymethylriboflavin derivatives: synthesis and fluorescence studies

The hitherto not described 2′,3′,4′,5′-tetraacetyl-N(3)-carboxymethylriboflavin (1) could be prepared starting from 2′,3′,4′,5′-tetraacetylriboflavin by alkylation with tert-butyl α-bromoacetate and benzyl α-bromoacetate, followed by deprotection reaction. The results of fluorescence studies are described.     

Synthesis and conformation of a novel bridged nucleic acid having a trans-fused 3,5,8-trioxabicyclo[5.3.0]decane structure

A novel bridged nucleic acid analogue, 2′-deoxy-trans-3′,4′-BNA thymine monomer, was successfully synthesized. An ab initio calculation and X-ray structure analysis revealed that the trans-fused bicyclo[5.3.0]decane structure of the 2′-deoxy-trans-3′,4′-BNA effectively constrained the sugar puckering in C_2^′-endo with appropriate γ, δ and χ angles.     

3′-Selective modification of a 4′,5′-didehydro-5′-deoxy-2′,3′-epoxyuridine using nucleophiles

1-(2,3-Anhydro-5-deoxy-4,5-didehydro-α-l-erythro-pent-4-enofuranosyl)uracil 4 was obtained by the treatment of 5′-iodo-2′,3′-epoxyuridine 5 with LiHMDS in excellent yield. The pyrimidine nucleoside 4 possesses quite unique vinyl epoxide moiety within the molecules. The reactions of 4 with a variety of nucleophiles gave 3′-substituted pyrimidine nucleosides without the formation of the corresponding 2′-substituted isomers. In the case of NaN₃ or PhSH, the corresponding 5′-adduct was obtained as a minor product together with the expected 3′-adduct.     

1,15-Bis-(2′,2′,4′-trimethyl-3′-pentoxy)phthalocyanine, a trans-form nonperipheral di-substituted phthalocyanine synthesized by the ‘cross condensation’ method

The crystal structure of 1, 15-bis-(2′,2′,4′-trimethyl-3′-pentoxy)phthalocyanine was determined what confirmed the ‘cross condensation’ method for the ABAB type phthalocyanine and the trans-form arrangement of the two substituents suggested that the alkoxy group also affected the condensation mechanism.     

Highly efficient synthesis of 2′,3′-didehydro-2′,3′-dideoxy-β-nucleosides through a sulfur-mediated reductive 2′,3′-trans-elimination. From iodomethylcyclopropanes to thiirane analogs

Taking into account the thiophilic properties of iodine, a very simple methodology to achieve 2′,3′-didehydro-2′,3′-dideoxy-β-nucleosides in high yield was performed, using mild, and inexpensive conditions, by means of the treatment of 2′-deoxy-3′,5′-dibenzoyl-2′-iodo-β-nucleoside derivatives with NaHS. The process has shown to be highly dependent of the relative geometry between the iodine atom and the adjacent leaving group. In this way, different essays carried out with pyranose derivatives have concluded in no reaction when the vicinal groups to eliminate do not adopt a trans-diaxial disposition. In addition, the treatment of 2-iodomethyl-cyclopropane-1,1-dicarboxylic acid diethyl ester under the same conditions softly and readily leads to the obtention of a mixture of the expected 2-allyl-malonic acid diethyl ester (as the minor product) and the thiirane derivative 2-thiiranylmethyl-malonic acid diethyl ester (as the major product). In this case, the responsible of the reaction progress are the nucleophilic properties of the sulfur atom rather than the thiophilic character of the iodine atom.     

Synthesis, properties and molecular structure of a novel dicyanoheptafulvene derivative, 4′-dicyanomethylidenedispiro[cyclohexane-1, 1′-(1′,4′,7′-trihydrocyclopenta[f]azulene)-7′,1″-cyclohexane]

A novel dicyanoheptafulvene 9 annulated by two spiro[4,5]deca-1,3-dienes was synthesized by the reaction of dispirocyclopentaazulenium cation 8 with bromomalononitrile. Although 9 was found to have a nonplanar heptafulvene structure by its X-ray crystallographic analysis, it is still capable of π-conjugation and thus shows appreciable contribution of the dipolar resonance form 9B based on its spectroscopic data. The degree of the contribution was further evaluated for various dicyanoheptafulvenes in terms of the partial sum of atomic charges of the dicyanomethylene group in the calculated structures besides the interplanar angles of the heptafulvene part and the length of the exocyclic double bond in the crystal structures.     

Fine tuning of folded conformation by change of substituents: H NMR and crystallographic evidence for folded conformation due to arene interactions in pyrazolo[3,4-d]pyrimidine core based ‘propylene linker’ compounds

Proton NMR and X-ray crystallographic analysis of two newly synthesized ‘trimethylene linker,’ (Leonard linker) compounds 1,3-bis(4-ethoxy-6-methylsulfanyl-lH-pyrazolo[3,4-d]pyrimidin-1-yl)propane (4c) and 1,3-bis(4-isopropoxy-6-methylsulfanyl-1H-pyrazolo[3,4-d]pyrimidin-1-yl)propane (4d) show intramolecularly stacked conformations both in solution and solid state. Robustness of the unusual U-motif formed due to intramolecular stacking in earlier related compounds (1, n=3 and 3, n=3) is not only confirmed but additional fine tuning is also achieved in new compounds (4) formed by replacement of remote 4-alkylsulfanyl group in 1a by 4-alkoxy substituents.     

An efficient synthesis of new 1-H-4′-methyl-3′,4′-dihydrospiro[piperidine-4,2′(1′H)quinoline] scaffolds

Efficient synthesis of new 3′,4′-dihydrospiro[piperidine-4,2′(1′H)quinolines] by a four step synthetic route based on 1-benzyl-4-piperidone reactivity is reported.     

Reaction of 3,3′,4,4′-tetramethyl-1,1′-diphosphaferrocene with [Re2(CO)8(CH3CN)2]: Novel coordination modes of the 1,1′-diphosphaferrocene ligand

Reaction of 3,3′,4,4′-tetramethyl-1,1′-diphosphaferrocene (1) with [Re₂(CO)₈(CH₃CN)₂] afforded two trimetallic complexes in which the heterometallocene is ligated across the Re-Re bond. The structure of the complex having 1 bridging the Re₂(CO)₈ moiety through two P atoms was determined by X-ray diffraction and compared with those of analogous complexes with organic bridging bis-phosphines. The second complex obtained in this reaction presumably contains 1 acting as a (P,Fe) bridging ligand.     

Syntheses and properties of complexes with bis(2,2′-bipyridyl)ruthenium(II) moieties coordinated to 4,4′:2′,2′′:4′′,4′′′-quaterpyridinium ligands

Eleven new complexes of the form cis-[Ru^II(bpy)₂(L^A)]⁴⁺ (bpy = 2,2′-bipyridyl; L^A = a pyridinium-substituted bpy derivative) have been prepared and isolated as their PF₆⁻ salts. Characterisation involved various techniques including ¹H NMR spectroscopy and MALDI mass spectrometry. The UV-Vis spectra show intense intraligand π → π^∗ absorptions and metal-to-ligand charge-transfer (MLCT) bands with two distinct maxima in the visible region. Small shifts in the MLCT bands correlate with the electron-withdrawing strength of the ligand L^A. Cyclic voltammograms show quasi-reversible or reversible Ru^III/II oxidation waves, and two or more ligand-based reductions with varying degrees of reversibility. The variations in the redox potentials correlate with changes in the structure of L^A, and also with the MLCT energies. Differential pulse voltammetry allows the first reduction process for two of the complex salts to be resolved into two peaks. Single-crystal X-ray structures have been solved for three of the new complex salts and also for a pro-ligand salt. Two carboxylate-functionalised compounds have been tested as photosensitizers on TiO₂-coated electrodes, but show only negligible efficiencies, in accord with expectations.     

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.     

Novel chiral C1-1′,2′,3′,4′-tetrahydro-1,1′-bisisoquinolines: synthesis, resolution, and applications in catalytic enantioselective reactions

A straightforward synthesis of a structurally constrained C₁-1′,2′,3′,4′-tetrahydro-1,1′-bisisoquinoline 1 is described. Resolution of this compound has been achieved successfully. The preparation of chiral N-alkyl, urea, and thiourea derivatives as potential new chiral ligands, based on the parent compound 1, is reported. Chiral compound 1 induced very good selectivity and yield in the addition of either Et₂Zn (85% ee, 96% yield) or nitromethane (85% ee, 60% yield) to benzaldehyde.