Synthesis and properties of 2'-deoxy-8,2'-methylene-cyclopurine nucleosides

A method was developed to synthesize 2'-deoxy-8,2'-methylene-cycloadenosine (1) and -cycloguanosine (2) which were new carbon-bridged cyclopurine nucleosides fixed in a high-anti torsional angle region. 3',5'-Di-O-acetyl-8-methanesulfonyl-2'-O-p-toluene-sulfonyladenosine+ ++ (3) or 2-acetamido-9- (3,5-di-O-acetyl-2-O-p-toluenesulfonyl-beta-D-ribofuranosyl)-6- ethoxy-8-methanesulfonyl-purine (9) was treated with sodium salt of ethyl malonate to give the cyclized nucleosides (4 and 10) in good yields, respectively. Subsequent decarboxylation and deblocking of 4 and 10 afforded 1 and 2 in crystalline form, respectively.     

Synthesis of 2'-([1,2,3]triazol-1-yl)-2'-deoxyadenosines

A reliable and efficient protocol for the synthesis of 2 '-([1,2,3]triazol-1-yl)-2 '-deoxyadenosine derivatives from vidarabine is presented. Vidarabine was converted to 2'-azido-2'-deoxy-3',5-O-(tetraisopropyldisiloxane-1,3-diyl)-adenosine. This azide was used as the starting material for the Cu(I)-catalyzed parallel synthesis of 1,2,3-triazoles using a variety of alkynes. The reactions proceeded in good yield and gave almost exclusively the 1,4-disubstituted 1,2,3-triazoles.     

Synthesis and properties of ApU analogues containing 2'-halo-2'-deoxyadenosines. Effects of 2' substituents on oligonucleotide conformation

Five A-U analogues containing deoxyadenosine or 2'-halo-2'-deoxyadenosines, which are known to have widely different C3'-endo conformer populations according to their electronegativities of the halogen substituents, dAfl-U, dAcl-U, dAbr-U, dAio-U, and dA-U, were synthesized chemically. Characterization of these dimers has been performed by UV absorption, circular dichroism, and proton nuclear magnetic resonance spectroscopy. The results show that the dimers containing 2'-halo-2'-deoxyadenosines have stacked conformations with a geometry similar to that of A-U and the degree of stacking decreases in the order dAfl-U greater than dAcl-U greater than dAbr-U greater than dAio-U. dAcl-U is assumed to have the same degree of stacking as A-U. dA-U takes a more stacked conformation than does dAio-U, but the mode of stacking is different from those of the other dimers. The effects of the 2' substituents on dimer conformation are discussed in terms of electronegativity, molecular size, and hydrophobicity.     

An improved synthesis of 5'-fluoro-5'-deoxyadenosines

Synthesis of 5'-fluoro-5'-deoxyadenosine (5'-FDA) and structurally similar compounds is generally a poor yielding process. This is attributed to the instability of the selected synthetic intermediates. Herein, we report a general synthesis of 5'-fluoro-5'-deoxy-N6-substituted adenosines including a high yielding access to 5'-FDA.     

Formation of 2'-deoxy-2-nitroadenosines by reaction of 2'-deoxyadenosines with copper(II) nitrate/acetic anhydride

Nitration of 9-substituted [ethyl, (Ac)2-2'-deoxyribosyl, (Ac)3-ribosyl] N6-acetyladenine derivatives with Cu(NO3)2.3H2O/Ac2O was examined. Nitration proceeded at the 2-position, although the yield was low. Removal of the acetyl groups gave 2'-deoxy-2-nitroadenosine derivatives.     

Dinucleoside monophosphate having a high anti conformation: the crystal structure of 8,2'-S-cycloadenylyl-(3'-5')-8,2'-S-cycloadenosine hydrochloride

The crystal and molecular structure of 8,2'-S-cycloadenylyl-(3'-5')-8,2'-S-cycloadenosine (AspAs) hydrochloride has been determined by X-ray method. The conformation of two independent AspAs molecules found in an asymmetric unit are almost identical to each other. The torsion angles concerning the sugar-phosphate backbone are different from those in crystalline dinucleoside monophosphates so far determined by X-rays. Both AspAs molecules are in the sharp bend conformations, i.e. each rotation around P-O bond (omega', omega) is (g-, t) rather than the preferred (g-, g-) or (g+, g+) conformation. There is no intramolecular base stacking or base-pairing but the intermolecular base stacking was found.     

Pyrrolo[2,3-d]pyrimidine nucleosides: synthesis and antitumor activity of 7-substituted 7-deaza-2'-deoxyadenosines

A one step synthesis, using the nucleoside 7-iodo-2'-deoxytubercidin (2b) in a Pd(0)/Cu(I)-catalyzed cross coupling reaction furnished a series of 7-alkynyl-2'-deoxytubercidin derivatives. The 7-iodo-, 7-chloro- or 7-bromo 2'-deoxytubercidins 2b-d as well as certain 7-alkynyl derivatives show significant activity against several tumor cell lines, with 7-iodo-2'-deoxytubercidin (2b) as the most effective compound.     

Biophysical and antisense properties of oligodeoxynucleotides containing 7-propynyl-, 7-iodo- and 7-cyano-7-deaza-2-amino-2'-deoxyadenosines.

The synthesis of 7-propynyl-, 7-iodo- and 7-cyano-7-deaza-2-amino-2'-deoxyadenosines is described. The nucleosides were synthesized, functionalized into the phosphoramidites and incorporated into oligodeoxynucleotides. Spectroscopic melting experiments against complementary RNA showed increases of 3-4 degreesC per modification for single substitutions and smaller increases per incorporation for multiple substitutions relative to unmodified control sequences. The 7-propyne and 7-iodo nucleosides were incorporated into antisense sequences targeting the 3'-UTR of murine C- raf mRNA. Both nucleosides demonstrated substitution-dependent potency. The sequences with three and four substitutions of the 7-propyne-7-deaza-2-amino-2'-deoxyadenosine exhibited a 2-3-fold increase in potency over unmodifed controls.     

Polynucleotides. XXXII. Further studies on the synthesis of oligonucleotides containing 8,2''-S-cycloadenosine.

A dinucleoside monophosphate, 8,2'-anhydro-8-mercapto-9-beta-D-arabinofuranosyladenine phosphoryl-(3'-5')-inosine (AspI) was synthesized by the condensation of protected 8-mercapto-adenosine 2',3'-cyclic phosphate and 2',3'-isopropylideneinosine with diphenylphosphorochloridate. 8-Mercaptoadenosine 2',3'-cyclic phosphate was polymerized by using tetraphenyl pyrophosphate as the condensing reagent. As oligonucleotides, thus obtained, contained some uncyclized 8-mercaptoadenosine residues and were cleaved at these sites with 0.3N KOH. As 5'-phosphate was synthesized and polymerized with DCC to give oligonucleotides with chain lengths 2 to 9.     

DNA damage products (5'R)- and (5'S)-8,5'-cyclo-2'-deoxyadenosines as potential biomarkers in human urine for atherosclerosis

We hypothesized that DNA damage products (5'R)-8,5'-cyclo-2'-deoxyadenosine (R-cdA) and (5'S)-8,5'-cyclo-2'-deoxyadenosine (S-cdA) may be well-suited biomarkers of risk and diagnosis for atherosclerosis. We tested this hypothesis by measuring the levels of R-cdA and S-cdA and another product, 8-hydroxy-2'-deoxyguanosine (8-OH-dG), in urine of atherosclerosis patients and healthy individuals using liquid chromatography-tandem mass spectrometry with isotope dilution. We showed the presence of these products at significantly greater concentrations in urine of atherosclerosis patients than in that of healthy individuals. Our data suggest that R-cdA and S-cdA can be accurately and reproducibly measured in human urine as potential biomarkers of risk and diagnosis for atherosclerosis.     

Polynucleotides. XXXI1. Synthesis of AUG analogs containing 8,2''-S-cycloadenosine, 8,5''-S-cycloadenosine, 8-bromoadenosin, 8-oxyadenosine and formycin in the first position of the codon.

Five AUG analogs having 8,2'-S-cycloadenosine (I), 8,5'-S-cycloadenosine (II), 8-bromoadenosine (III), 8-oxyadenosine (IV) and formycin (V) in the first position of ApUpG W were synthesized. 3'-Phosphates of I, II and V were synthesized by phosphorylation using cyanoethylphosphate and DCC. In the case of II, 2', 3'-cyclic phosphate was directly obtained. 3'-Phosphates, thus obtained, were properly protected on the 2'-OH and/or the N6-amino group and condensed with U(OBz)pGiBu(iBu)2 using DCC to give ApUpG analogs. Some properties on paper chromatography and electrophoresis, and the UV and CD spectra of these trinucleoside diphosphates are reported.     

Synthesis of 2'-O-substituted ribonucleosides

An efficient synthesis of 2'-O-substituted ribonucleosides, including 2'-O-TBDMS and 2'-O-TOM protected as well as 2'-O-Me and 2'-O-allyl derivatives is presented. Di-t-butylsilylene group was employed for simultaneous protection of 3'- and 5'- hydroxyl functions of nucleoside on the first step. Subsequent silylation or alkylation of free 2'-OH followed by introduction of suitable protection on the base moiety and removal of cyclic silyl protection gave target compounds in a high yield.     

Synthesis of Streptovitacin-C2 Isomers

(2R*,4S*,6S*,αS*)- and (2R,4R,6R,αS)-Streptovitacin-C₂ (STV-C₂) (1a and 1b) were synthesized by an aldol condensation of (2R*,4S*)- or (2R,4R)-2,4-dimethyl-2-trimethylsiloxy-1-cyclohexanone (15a or 15b) with 4-(2-oxoethyl)-2,6-piperidinedione (16), which was followed by desilylation of the products. The stereochemistry of the synthesized STV-C₂ isomers (1a and 1b) was elucidated by NMR. STV-C₂ isomers (1a and 1b) did not show strong antimicrobial activity against Saccharomyces cerevisiae and Pyricularia oryzae.     

Synthesis of 2'-end-modified 2'-5'-oligoadenylates

Analogs of 2'5'-oligiadenylates (2-5As) have been prepared on the basis of the recently developed internucleotide-linkage formation via selective hydroxyl activation of N-unprotected nucleosides. The analogs synthesized include the trimeric cores having 2'-deoxyadenosine, cordycepin (3'-deoxyadenosine), and 2',3'-bisdeoxyadenosine at the 2' termini, and the tetramer with 2'-end 2'-deoxyadenosine.     

Synthesis of p-nitrophenyl 2-acetamido-2-deoxy-O-beta-D-galactopyranosyl-beta-D-glucopyranosides.

Reaction of p-nitrophenyl 2-acetamido-2-deoxy-4,6-O-(p-methoxybenzylidene)-beta-D-glucopyranoside (2) with 2,3,4,6-tetra-O-acetyl-alpha-D-galactopyranosyl bromide (3) under the usual conditions, followed by removal of the p-methoxybenzylidene group and O-deacylation, produced crystalline p-nitrophenyl 2-acetamido-2-deoxy-3-O-beta-D-galactopyranosyl-beta-D-glucopyranoside (6). Starting from p-nitrophenyl 2-acetamido 3,4-di-O-acetyl-2-deoxy-beta-D-glucopyranoside, the synthesis of p-nitrophenyl 2-acetamido-2-deoxy-6-O-beta-D-galactopyranosyl-beta-D-glucopyranoside was also accomplished.