Nucleotides. Part XXXI. Modified Oligomeric 2′–5′ A Analogues: Synthesis of 2′–5′ oligonucleotides with 9-(3′-azido-3′-deoxy-β-D-xylofuranosyl)adenine and 9-(3′-amino-3′-deoxy-β-D-xylofuranosyl)adenine as modified nucleosides

A series of new 2′–5′ oligonucleotides carrying the 9-(3′-azido-3′deoxy-β-D-xylofuranosyl)adenine moiety as a building block has been synthesized via the phosphotriester method. The use of the 2-(4-nitrophenyl)ethyl (npe) and 2-(4-nitrophenyl)ethoxycarbonyl (npeoc) blocking groups for phosphate, amino, and hydroxy protection guaranteed straightforward syntheses in high yields and easy deblocking lo form the 2′–5′ trimers 21 , 22 , and 25 and the tetramer 23 . Catalytic reduction of the azido groups in [9-(3′-azido-3′-deoxy-β-D-xylofuranosyl)adenine]2′-yl-[2′-(O^p-ammonio)→ 5′]-[9-(3′-azido-3′-deoxy-β-D-xylofuranosyl)adenin]-2′-yl-[2′-(O^p-ammonio)→ 5′]-9-(3′-azido-3′-deoxy-β-D-xylofuranosyl)adenine ( 21 ) led to the corresponding 9-(3′-amino-3′-deoxy-β-D-xylofuranosyl)-adenine 2′–5′ trimer 26 in which the two internucleotidic linkages are formally neutralized by intramolecular betaine formation.     

Protonated canthaxanthins as models for blue carotenoproteins

It has been suggested that astaxanthin (3,3'-dihydroxy-beta,beta-carotene-4,4'-dione) in the carotenoprotein alpha-crustacyanin occurs in the diprotonated form. As a model system for protonated astaxanthin in [small alpha]-crustacyanin the reactions of canthaxanthin ([small beta],[small beta]-carotene-4,4[prime or minute]-dione) with Bronsted acids (CF(3)COOH and CF(3)SO(3)H) and the Lewis acid BF(3)-etherate have been investigated. Structures of C-5 protonated, C-7 protonated, enolised O-4 protonated and O-4,4[prime or minute], C-7 triprotonated canthaxanthin have been established by VIS-NIR and NMR spectroscopy. The charge distribution in the cations has been considered by comparison of the (13)C chemical shift difference relative to neutral relevant carotenoid models. The experimental evidence for protonated canthaxanthins differs significantly from previous AM1 calculations. Experimental data for O-4,4[prime or minute], C-7 triprotonated canthaxanthin relative to C-7 protonated canthaxanthin is considered a relevant model for O-4,4[prime or minute] diprotonated canthaxanthin, in comparison with neutral canthaxanthin. The positive charge was mainly located at C-6/6[prime or minute][dbl greater-than] C-8/8[prime or minute] > C-10/10[prime or minute] > C-12/12[prime or minute] > C-14/14[prime or minute][similar] C-15/15[prime or minute] in the polyene chain. Moreover, it was inferred that only 14% of the positive charge is delocalised to the polyene chain, the remaining charge must therefore be located at the protonated carbonyl moiety. The results are discussed in relation to previous solid state NMR studies of (13)C labelled astaxanthin in [small alpha]-crustacyanin and recent X-ray analysis of [small beta]-crustacyanin.     

Synthesis of Methyl 2-Acetamido-4,6-di-O-acetyl-3-S-acetyl-2-deoxy-3-thio-α-D-mannopyranoside

Methyl-2-acetamido-4,6-di-O-acetyl-3-S-acetyl-2-deoxy-3-thio-α-D-mannopy-ranoside has been synthesized by conversion of methyl 2-amino-2-deoxy-4,6-O-benzylidene-α-D-altropyranoside into the corresponding 3-O-methanesulfony1-2-N-[(methylthio)thiocarbonyl]derivative followed by intramolecular displacement of the 3-O-methanesulfonyloxy group with the (methylthio)thiocarbamoyl group.     

A facile synthesis of 2-deoxy-2,3-didehydroneuraminic acid derivatives

The 2-thio- or 2-selenoglycosides of N-acetylneuraminic acid methyl ester were transformed by successive treatment with dimethyl(methylthio)sulfonium triflate (DMTST) and 1,8-diazabicyclo[5.4.0]-7-undecene (DBU) to give the corresponding methyl 2-deoxy-2,3-didehydroneuraminates in excellent yields. Their acids and their analogues are sialidase inhibitors of pharmaceutical interest.     

Synthesis of 2-amino-3-carbethoxy-4,5,6,7-tetrahydrobenzo[b]selenophene and some transformations based on it

A new method for the synthesis of 2-amino-3-carbethoxy-4,5,6,7-tetrahydrobenzo[b]selenophene was developed. The reaction of the latter with allyl isothiocyanate gave 2-(N-allylthioureido)-3-carbethoxy-4,5,6,7-tetrahydrobenzo[b]selenophene, which is cyclized to the potassium salt of 3-allyl-4-oxo-2-thio-3,4,5,6,7,8-hexahydrobenzo[b]selenopheno[2,3-d]pyrimidine on treatment with potassium hydroxide.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 3, pp. 326–328, March, 1973.     

3-Bromopyrazolo[3,4-d]pyrimidine 2'-deoxy-2'-fluoro-beta-D-arabinonucleosides: modified DNA constituents with an unusually rigid sugar N-conformation

The nucleobase anion glycosylation of 3-bromo-4-isopropoxy-1H-pyrazolo[3,4-d]pyrimidin-6-amine (6) with 3,5-di-O-benzoyl-2-deoxy-2-fluoro-alpha-d-arabinofuranosyl bromide (5) furnished the protected N(1)-beta-d-nucleosides 7 (60%) and 8 (ca. 2%) along with the N(2)-beta-d-regioisomer 9 (9%). Debenzoylation of compounds 7 and 9 yielded the nucleosides 10 (81%) and 11 (76%). Compound 10 was transformed to the 2'-deoxyguanosine derivative 1 [6-amino-3-bromo-1-(2-deoxy-2-fluoro-beta-d-arabinofuranosyl)-1H-pyrazolo[3,4-d]pyrimidin-4-one] (85% yield) and the purine-2,6-diamine analogue 2 [3-bromo-1-(2-deoxy-2-fluoro-beta-d-arabinofuranosyl)-1H-pyrazolo[3,4-d]pyrimidin-4, 6-diamine] (78%). Both nucleosides form more than 98% N-conformer population (P(N) ca. 358 degrees and psi(m) ca. 37 degrees ) in aqueous solution. Single-crystal X-ray analysis of 1 showed that the sugar moiety displays also the N-conformation [P = 347.3 degrees and psi(m) = 34.4 degrees ] in the solid state. The remarkable rigid N-conformation of the pyrazolo[3,4-d]pyrimidine 2'-deoxy-2'-fluoro-beta-d-arabinonucleosides 1 and 2 observed in solution is different from that of the parent purine 2'-deoxy-2'-fluoro-beta-d-arabinonucleosides 3 and 4, which are in equilibrium showing almost equal distribution of the N/S-conformers.     

First total synthesis of a naturally occurring nucleoside disulfide:9-(5’-Deoxy-5’-thio-β-D-xylofuranosyl)adenine disulfide

A naturally occurring nucleoside disulfide,9-(5’-deoxy-5’-thio-β-D-xylofuranosyl)adenine disulfide,was first synthesized from D-xylose over 7 steps in 20%overall yield.The key step involved Vorbriiggen glycosylation of silylated N~6-benzoyladenine with xylose diacetate moiety.     

Hydrolytic reactions of 3'-N-phosphoramidate and 3'-N-thiophosphoramidate analogs of thymidylyl-3',5'-thymidine

The diastereomeric thiophosphoramidate analogs [(R(P))- and (S(P))-3[prime or minute],5[prime or minute]-Tnp(s)T] and the phosphoramidate analog [3[prime or minute],5[prime or minute]-TnpT] of thymidylyl-3[prime or minute],5[prime or minute]-thymidine were prepared and their hydrolytic reactions over the pH-range 1-8 at 363.2 K were followed by RP HPLC. At pH < 6, an acid-catalyzed P-N3[prime or minute] bond cleavage (first-order in [H(+)]) takes place with both 3[prime or minute],5[prime or minute]-Tnp(s)T and 3[prime or minute],5[prime or minute]-TnpT, the former being about 12 fold more stable than the latter. At pH > 4, Tnp(s)T undergoes two competing pH-independent reactions, desulfurization (yielding TnpT) and depyrimidination (cleavage of the N-glycosidic bond) the rates of which are of the same order of magnitude. Also with 3[prime or minute],5[prime or minute]-TnpT the pH-independent depyrimidination competes with P-N3[prime or minute] cleavage at pH > 5.     

Conversion of 2-deoxy-D-ribose into 2-amino-5-(2-deoxy-beta-D-ribofuranosyl)pyridine, 2'-deoxypseudouridine, and other C-(2'-deoxyribonucleosides)

The synthesis of 2-amino-5-(2-deoxy-beta-D-ribofuranosyl)pyridine 2a, 2-amino-5-(2-deoxy-alpha-D-ribofuranosyl)-pyridine 23, 2-amino-5-(2-deoxy-beta-D-ribofuranosyl)-3-methylpyridine 2b, 2-amino-5-(2-deoxy-alpha-D-ribofuranosyl)-3-methylpyridine 29 and 5-(2-deoxy-beta-D-ribofuranosyl)-2,4-dioxopyrimidine [2'-deoxypseudouridine] 30a is described. These C-nucleosides are prepared either from 2-deoxy-3,5-O-(1,1,3,3-tetraisopropyldisiloxan-1,3-diyl)-D-ribofuranose 15 or from 2-deoxy-3,5-O-(1,1,3,3-tetraisopropyldisiloxan-1,3-diyl)-D-ribono-1,4-lactone 16, which are themselves prepared from 2-deoxy-D-ribose 13. The sugar derivatives are first allowed to react with the appropriate 5-lithio-pyridine or 5-lithio-pyrimidine derivatives, which are prepared from 5-bromo-2-(dibenzylamino)pyridine 12a, 5-bromo-2-[bis(4-methoxybenzyl)amino]pyridine 12b, 5-bromo-2-dibenzylamino-3-methylpyridine 25 and 5-bromo-2,4-bis(4-methoxybenzyloxy)pyrimidine 33. The products from the reactions between the lithio-derivatives and the lactol 15 are cyclized under Mitsunobu conditions; the products from the reactions between the lithio-derivatives and the lactone 16 are first reduced with L-Selectride before cyclization, also under Mitsunobu conditions. In all cases, the beta-anomers of the protected C-nucleosides are the predominant products. Finally, the separation of the alpha- and beta-anomers and the removal of all of the protecting groups are described.     

Investigation of reactions postulated to occur during inhibition of ribonucleotide reductases by 2′-azido-2′-deoxynucleotides

Model 3′-azido-3′-deoxynucleosides with thiol or vicinal dithiol substituents at C2′ or C5′ were synthesized to study reactions postulated to occur during inhibition of ribonucleotide reductases by 2′-azido-2′-deoxynucleotides. Esterification of 5′-(tert-butyldiphenylsilyl)-3′-azido-3′-deoxyadenosine and 3′-azido-3′-deoxythymidine (AZT) with 2,3-S-isopropylidene-2,3-dimercaptopropanoic acid or N-Boc-S-trityl-L-cysteine and deprotection gave 3′-azido-3′-deoxy-2′-O-(2,3-dimercaptopropanoyl or cysteinyl)adenosine and the 3′-azido-3′-deoxy-5′-O-(2,3-dimercaptopropanoyl or cysteinyl)thymidine analogs. Density functional calculations predicted that intramolecular reactions between generated thiyl radicals and an azido group on such model compounds would be exothermic by 33.6–41.2 kcal/mol and have low energy barriers of 10.4–13.5 kcal/mol. Reduction of the azido group occurred to give 3′-amino-3′-deoxythymidine, which was postulated to occur with thiyl radicals generated by treatment of 3′-azido-3′-deoxy-5′-O-(2,3-dimercaptopropanoyl)thymidine with 2,2′-azobis-(2-methyl-2-propionamidine) dihydrochloride. Gamma radiolysis of N₂O-saturated aqueous solutions of AZT and cysteine produced 3′-amino-3′-deoxythymidine and thymine most likely by both radical and ionic processes.     

Oligodeoxynucleotides containing alpha-L-ribo configured LNA-type C-aryl nucleotides

Synthesis of 2[prime or minute]-O,4[prime or minute]-C-methylene-[small alpha]-l-ribofuranosyl derivatives containing phenyl and 1-pyrenyl aglycons, i.e., novel [small alpha]-l-ribo configured LNA-type C-aryl nucleosides, has been accomplished. Key synthetic steps included stereoselective Grignard reactions on tetrahydrofuran aldehyde, configurational inversion of the resulting alcohol into alcohol, and concomitant Mitsonobu cyclization furnishing the desired bicyclic furanosyl skeleton with a locked conformation. The phosphoramidite derivatives and were used for automated synthesis of 9-mer DNA and [small alpha]-L-LNA oligonucleotides containing the [small alpha]-L-LNA-type C-aryl monomers ([small alpha]L)Ph(L) and ([small alpha]L)Py(L) containing a phenyl and pyrenyl aglycon, respectively. Thermal denaturation studies showed universal base pairing behavior for the pyrenyl monomer ([small alpha]L)Py(L) when incorporated into a DNA or an [small alpha]-L-LNA oligonucleotide.     

Photochromism of triangle terthiophene derivatives as molecular re-router

2,2[prime or minute]-3,3[double prime]-Terthiophene derivatives undergo photochemically reversible cyclization and cycloreversion reactions. The absorption peak wavelength changed systematically with substitution of the phenyl rings at 5-, 5[prime or minute]- and 5[double prime]-positions of the thiophene rings, which indicates re-routing of the [small pi]-conjugation system.     

A stereoselective synthesis of 9-(3-O-benzyl-5-O-tetrahydropyranyl-β-d-arabinofuranosyl)adenine, a potentially useful intermediate for ribonucleoside synthesis

A novel synthesis for preparing 9-(3-O-benzyl-5-O-tetrahydropyranyl-β-d-arabinofuranosyl)adenine (6) has been developed which does not require sub zero temperatures or exotic reagents. A key step in this synthesis is the selective protection of the 3′-OH of ara-A with a benzyl group. The 5′-OH is then selectively protected with DHP to yield 6, a potentially useful intermediate. A synthesis of 9-(2,3-dideoxy-2-fluoro-β-d-threo-pentofuranosyl)adenine (1, FddA), an anti-viral compound, is given to illustrate the utility of this new approach.     

Nucleic acid related compounds. 81. Syntheses of 9-(3-deoxy-β-D-threo-pentofuranosyl)adenine,the core nucleoside of the extraordinarily selective antibiotic agrocin 84, and simplified structural component analogues

Alternative syntheses of 9-(3-deoxy-β-D-threo-pentofuranosyl)adenine ( 4 ), the core nucleoside of agrocin 84 [and its 2′-deoxy threo isomer 5 ] were devised: (1) direct conversion of 9-(β-D-arabinofuranosyl)adenine into 9-(2,3-anhydro-β-D-lyxofuranosyl)adenine and regioselective opening of its oxirane ring with sodium borohy-dride to give 4 and 5 (?7.5:1); (2) treatment of adenosine with sodium hydride and 2,4,6-triisopropylbenzene-sulfonyl chloride, and subjection of the resulting 2′(3′)-sulfonates to the reductive [1,2]-hydride shift rearrangement with lithium triethylborohydride to give 4 and 5 (? 2:1); and (3) subjection of the phenoxythiocar-bonyl esters of 9-[2(3),5-bis-O-(tert-butyldimethylsilyl)-β-D-arabinofuranosyl]adenine to Barton deoxygenation, and deprotection to give 4 and 2′-deoxyadenosine (?5:1). Methods (2) and (3) gave lower yields. Syntheses of simplified 6-N- and 5′-O-adenosine phosphoramidate model compounds were explored to examine potential access to such features in the structure proposed for agrocin 84.     

Synthesis, structure, and biological evaluation of C-2 sulfonamido pyrimidine nucleosides

The C-2 sulfonamido pyrimidine nucleosides were prepared by opening the 2,2′- or 2,3′-bond in anhydronucleosides under nucleophilic attack of sulfonamide anions. Reaction of the sodium salt of p-toluenesulfonamide or 2-(aminosulfonyl)-N,N-dimethylnicotinamide with 2,2′-anhydro-1-(β-d-arabinofuranosyl)cytosine gave the C-2 sulfonamido derivatives in excellent yields. Ring opening of the less reactive 2,2′-anhydrouridine and 2,3′-anhydrothymidine could be accomplished with DBU/CH₃CN activation of p-toluenesulfonamide, giving moderate yields for C-2 sulfonamido derivatives. The action of acetic acid or ZnBr₂/CH₂Cl₂ on 5-methyl-N²-tosyl-1-(2-deoxy-5-O-trityl-β-d-threo-pentofuranosyl)isocytosine led to the cleavage of both the protection group and the nucleoside bond, yielding 5-methyl-N²-tosylisocytosine as the major product. Structures of the prepared C-2 sulfonamido nucleosides were confirmed by the 1D and 2D NMR experiments, and X-ray structural analysis of 4-imino-N²-tosylamino-1-(β-d-arabinofuranosyl)pyrimidine. Both methods confirmed β-configuration and anti-conformation of the 2-sulfonamido nucleosides. The investigated compounds displayed moderate inhibition of tumor cell growth in vitro, as determined by the MTT assay using six different human tumor cell lines.     

Halogenated 7-deazapurine nucleosides: stereoselective synthesis and conformation of 2'-deoxy-2'-fluoro-beta-D-arabinonucleosides

The stereoselective syntheses of 5-halogenated 7-(2-deoxy-2-fluoro-beta-D-arabinofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine nucleosides 3b-d, 4a-c as well as 7-deaza-2'-deoxyisoguanosine are described. Nucleobase anion glycosylation of 2-amino-4-chloro-7H-pyrrolo[2,3-d]pyrimidine (5) with 3,5-di-O-benzoyl-2-deoxy-2-fluoro-alpha-D-arabinofuranosyl bromide (6) exclusively gave the beta-D-anomer, which was deblocked (--> 8), aminated at C4 (--> 3a) and selectively deaminated at C2 to yield 2'-deoxy-2'-fluoro-beta-D-arabinofuranosyl 7-deazaisoguanine (2). Condensation of the 5-halogenated 4-chloro-2-pivaloylamino-7H-pyrrolo[2,3-d]pyrimidines 9a-c with 6 furnished the N7-nucleosides 10a-c together with N2,N7-bisglycosylated compounds 11a-c. The former was converted to the corresponding 2,4-diamino-compounds 3b-d, and the latter was deblocked by NaOMe/MeOH to yield the 4-methoxy-nucleosides 4a-c. Conformational analysis of the sugar moiety of the nucleosides 2 and 3a-d was performed on the basis of vicinal [1H,1H] coupling constants. The fluorine atom in the sugar moiety shifts the sugar conformation from S towards N by about 10%, while the halogen substituents in the base moiety increase the hydrophobicity and polarizability of the nucleobases.     

Selective Protecting Method for the Individual Hydroxyl Groups of Kdn

ABSTRACT

Selective protection for the individual hydroxyl groups of methyl (phenyl 3-deoxy-2-thio-β-D-glycero-D-galacto-2-nonulopyranosid)onate (2) was examined. The 4-, 5-, and 7-hydroxyl groups of methyl (phenyl 3-deoxy-8,9-O-isopropylidene-2-thio-β-D-glycero-D-galacto-2-nonulopyranosid)onate (3) were found selectively to be protected by t-butyldimethylsilyl, methoxymethyl, and benzoyl groups, respectively. In order to obtain the 8- and 9-hydroxyl derivatives selectively, methyl (phenyl 4,5,7-tri-O-acetyl-9-O-t-butyldimethylsilyl-3-deoxy-2-thio-β-D-glycero-D-galacto-2-nonulopyranosid)onate (12) and methyl (phenyl 4,5,7,8-tetra-O-benzyl-9-O-triphenylmethyl-3-deoxy-2-thio-β-D-glycero-D-galacto-2-nonulopyranosid)onate (19) were prepared in moderate yields.     

Synthesis of S-5-pyrrolo[2,3-b]pyridinemethyl and S-5- and S-6-pyrrolo[2,3-d]pyridinemethyl derivatives of 5′-deoxy-5′-thioadenosine

Reaction of 5-dimethylaminomethylpyrrolo[2,3-b]pyridine methiodide or 5-dimethylaminomethylpyrrolo[2,3-d]pyrimidin-4-one methiodide with 5′-deoxy-5′-S-thioacetyl-N⁶-formyl-2′,3′-O-isopropylideneadenosine in ethanolic sodium hydroxide solution, followed by deprotection of the resulting thioether in 80% formic acid, afforded 5′-deoxy-5′-(5-pyrrolo[2,3-b]pyridinemethylthio)adenosine or 5′-deoxy-5′-[5-(pyrrolo[2,3-d]pyrimidin-4-one)methylthio]adenosine, respectively. Similarly, the metiodide salt of the iso-gramine analog, 2-amino-6-dimethylaminomethylpyrrolo[2,3-d]pyrimidin-4-one afforded 5′-deoxy-5′-[6-(2-aminopyrrolo[2,3-d]pyrimidin-4-one)methylthio]adenosine.     

Intramolecular S(N)2' cyclization of an alkyllithium species onto a methoxy allyl ether is syn selective

The preference for syn- or anti-addition of an intramolecular S(N)2[prime or minute] cyclization of an alkyllithium species onto a methoxy allyl ether has been proven unequivocally to take place by a syn S(N)2[prime or minute] mechanism.     

Unidirectional α-cyclodextrin-based [2]rotaxanes bearing viologen unit on axle

1-(2-Carboxyethyl)-1′-(10-carbazole-9-yl-decyl)-4,4′-bipyridinium dibromide 2 forms a unidirectional [2]pseudorotaxane with α-cyclodextrin (α-CD) in water. Condensation of 2/α-CD [2]pseudorotaxane with 4-amino-1-naphthalenesulfonate or 6-amino-β-CD provided the unidirectional [2]rotaxanes 3 and 4, in which the secondary face of α-CD is oriented toward the viologen moiety. The structures were elucidated from two-dimensional ROESY and circular dichroism spectra.