Nucleosides and nucleotides. Part 25.. Synthesis of a protected 1-(2′-deoxy-β-D-ribofuranosyl)-1 H-benzimidazole 3′-phosphate

1-(2′-Deoxy-5′-O-dimethoxytrityl-′-D -ribofuranosyl)-1 H-benzimidazole 3′-[(p-chlorophenyl)(2-cyanoethyl) phosphate] ( 6 ) has been synthesized from 1-(β-D -ribofuranosyl)-1H-benzimidazole ( 3b ) using regiospecific 2′-deoxygenation. The latter compound was obtained by glycosylation of benzimidazole with the D -ribose derivative 2 leading exclusively of the β-D -anomer.     

Nucleoside und Nucleotide. Teil 10. Synthese von Thymidylyl-(3′-5′) -thymidylyl-(3′-5′)-1-(2′-desoxy-β-D-ribofuranosyl)-2(1 H)-pyridon

Nucleosides and Nucleotides. Part 10. Synthesis of Thymidylyl-(3′-5′)-thymidylyl-(3′-5′)-1-(2′-deoxy-β-D - ribofuranosyl)-2(1 H)-pyridone The synthesis of 5′-O-monomethoxytritylthymidylyl-(3′-5′)-thymidylyl-(3′-5′)-1-(2′-deoxy-β-D -ribofuranosyl)-2(1H)-pyridone ((MeOTr)T_dpT_dp∏_d, 5 ) and of thymidylyl-(3′-5′)-thymidylyl-(3′-5′)-1-(2′-deoxy-β-D -ribofuranosyl)-2(1 H)-pyridone (T_dpT_dp∏_d, 11 ) by condensing (MeOTr) T_dpT_d ( 3 ) and p∏_d(Ac) ( 4 ) in the presence of DCC in abs. pyridine is described. Condensation of (MeOTr) T_dpT_dp ( 6 ) with Π_d(Ac) ( 7 ) did not yield the desired product 5 because compound 6 formed the 3′-pyrophosphate. The removal of the acetyl- and p-methoxytrityl protecting group was effected by treatment with conc. ammonia solution at room temperature, and acetic acid/pyridine 7 : 3 at 100°, respectively. Enzymatic degradation of the trinucleoside diphosphate 11 with phosphodiesterase I and II yielded T_d, pT_d and p∏_d, T_dp and Π_d, respectively, in correct ratios.     

Nucleoside und Nucleotide. Teil 16. Verhalten von 1-(2′-Desoxy-β-D-ribofuranosyl)-2(1 H)-pyrimidinon-5′-triphosphat, 1-(2′-Desoxy-β-D-ribofuranosyl)-2(1 H)pyridinon-5′-triphosphat und 4-Amino-1-(2′-Desoxy-β-D-ribofuranosyl)-2(1 H)-pyridinon-5′-triphosphat gegenüber DNA-Polymerase

Nucleosides and Nucleotides. Part 16. The Behaviour of 1-(2′-Deoxy-β-D -ribofuranosyl)-2(1H)-pyrimidinone-5′-triphosphate, 1-(2′-Deoxy-β-D -ribofuranosyl-2(1H))-pyridinone-5′-triphosphate and 4-Amino-1-(2′-desoxy-β-D -ribofuranosyl)-2(1H)-pyridinone-5′-triphosphate towards DNA Polymerase The behaviour of nucleotide base analogs in the DNA synthesis in vitro was studied. The investigated nucleoside-5′-triphosphates 1-(2′-deoxy-β-D -ribofuranosyl)-2(1 H)-pyrimidinone-5′-triphosphate (pppM_d), 1-(2′-deoxy-β-D -ribofuranosyl)-2(1 H)-pyridinone-5′-triphosphate (pppII_d) and 4-amino-1-(2′-deoxy-β-D -ribofuranosyl)-2(1 H)-pyridinone-5′-triphosphate (pppZ_d) can be considered to be analogs of 2′-deoxy-cytidine-5′-triphosphate. However, their ability to undergo base pairing to the complementary guanine is decreased. When pppM_d, pppII_d or pppZ_d are substituted for pppC_d in the enzymatic synthesis of DNA by DNA polymerase no incorporation of these analogs is observed. They exhibit only a weak inhibition of the DNA synthesis. The mode of the inhibition is uncompetitive which shows that these nucleotide analogs cannot serve as substrates for the DNA polymerase.     

Nucleotides. Part LIV. Synthesis of condensed N1-(2′-deoxy-β-D-ribofuranosyl)lumazines,New fluorescent building blocks in oligonucleotide synthesis

Various condensed areno[g]lumazine derivatives 2 , 3 , and 5 – 7 were synthesized as new fluorescent aglycones for glycosylation reactions with 2-deoxy-3, 5-di-O-(p-toluoyl)-α/β-D -erythro-pentofuranosyl chloride ( 10 ) to form, in a Hilbert-Johnson-Birkofer reaction, the corresponding N¹-(2′-deoxyribonucleosides) 15 – 21 . The β-D -anomers 15 , 17 , 19 , and 21 were deblocked to 24 – 27 and, together with N¹-(2′-deoxy-β-D -ribofuranosyl)lumazine ( 22 ) and its 6, 7-diphenyl derivative 23 , dimethoxytritylated in 5′-position to 28–33. These intermediates were then converted into the 3′-(2-cyanoethyI diisopropylphosphoramidites) 34 – 39 which function as monomeric building block in oligonucleotide syntheses as well as into the 3′-(hydrogen succinates) 40 – 45 which can be used for coupling with the solid-support material. A series of lumazine-modified oligonucleotides were synthesized and the influence of the new nucleobases on the stability of duplex formation studied by measuring the T_m values in comparison to model sequences. A substantial increase in the T_m is observed on introduction of areno[g]lumazine moieties in the oligonucleotide chain stabilizing obviously the helical structures by improved stacking effects. Stabilization is strongly dependent on the site of the modified nucleobase in the chain.     

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.     

Nucleotides. Part XXXV. Synthesis of 3′-deoxyadenylyl-(2′–5′)-3′-deoxyadenyIyl-(2′–ω)-9-(ω-hydroxyalkyl)adenines

Via the phosphotriester approach, new structural analogs of (2′–5′)oligoadenyiates, namely 3′-deoxyadenylyl-(2′–5′)-3′-dcoxyadenylyl-(2′–ω)-9-(ω-hydroxyalkyl)adenines 18 – 21 , have been synthesized (see Scheme) which should preserve biological activity and show higher stability towards phosphodiesterases. The newly synthesized oligonucleotides 18 – 21 have been characterized by ¹H-NMR spectra, TLC, and HPLC analysis.     

Nucleosides CIII. Anhydropyrimidine-C-nueleosides. Synthesis of 4,2′-anhydro-5-(β-D-arabinofuranosyl)- and 5-(β-D-arabinofuranosyl)pyrimidine C-nucleosides

4,2′-Anhydro-5-(β-D -arabinofuranosyl)isocytosine and 4,2′-anhydro-5-(β-D -arabinofuranosyl)-uracil were synthesized. Treatment of Ψ-isocytidine with either α-acetoxyisobutyryl chloride or salicyloyl chloride in acetonitrile afforded the acylated anhydronucleoside. Deacylation of the product with methanol-hydrogen chloride afforded 4,2′-anhydro-5-(β-D -arabinofuranosyl)isocylosine hydrochloride in crystalline form. Analogous reaction of Ψ-uridine with the acyl chloride reagents, however, always gave a mixture of the acylated anhydronucleoside and 2′-chloro-2′-deoxy-Ψ-uridine. Treatment of these products either singly or as a mixture with sodium methoxide in methanol afforded 4,2′-anhydro-5-(β-D -arabinofuranosyl)uracil in crystalline form in good yield. 5-(β-D -Arabinofuranosyl)isocytosine was obtained upon treatment of the corresponding 4,2′-anhydronucleoside with 10% sodium hydroxide under reflux for 30 minutes. Treatment of the anhydro uracil nucleoside with a small amount of Dowex 50(H⁺) in water at 50° gave 5-(β-D -arabinofuranosyl)uracil.     

Synthesis of 5-(β-D-ribofuranosyl)-1,2,4-oxadiazole-3-carboxamide

The title compound was synthesized in three steps from ethoxycarbonylformamide oxime (5) and 3,4,6-tri-O-acetyl-2,5-anhydroallonyl chloride (4b) in 62% overall yield. An acid catalyzed de-esterification was required to prevent a facile base catalyzed elimination reaction.     

Nucleotides. Part XXVI.. A new synthesis of 9-(′-D-ribofuranosyl)uric acid and its 5′-monophosphate

Syntheses for 9-(β-D -ribofuranosyl)uric acid ( 16 ) and its 5′-monophosphate 14 have been achieved starting from guanosine and applying the 2-(p-nitrophenyl)ethyl group for protection of the aglycon moiety as well as the phosphate function. A more efficient and direct approach to 14 uses O⁶, O⁸-dibenzyl protection and phosphorylation by the Yoshikawa procedure. The various protected intermediates have been characterized by spectroscopic means and elemental analysis.     

5-(α-Fluorovinyl)tryptamines and 5-(α-Fluorovinyl)-3-(N-methyl-1′,2′,5′,6′,-tetrahydropyridin-3′- and -4′-yl)indoles—5-(α-Fluorovinyl)tryptamines

5-(α-Fluorovinyl)tryptamines 4a, 4b and 5-(α-fluorovinyl)-3-(N-methyl-1′,2′,5′,6′-tetrahydropyridin-3′- and -4′-yl) indoles 5a, 5b were synthesized using 5-(α-fluorovinyl)indole ( 7 ). The target compounds are bioisosteres of 5-carboxyamido substituted tryptamines and their tetrahydropyridyl analogs.     

C-Nucleosides. 8. Synthesis of 5-hydroxy-2-(β-D-ribofuranosyl)pyridine

The synthesis of 5-hydroxy-2-(β-D-ribofuranosyl)pyridine ( 12 ) from 2-(2,3,5-tri-O-benzoyl-β-D-ribofuranosyl)furan ( 1 ) is described. Treatment of 1 with α-methoxycarbamate in the presence of p-toluenesulfonic acid in benzene at reflux temperature afforded furfurylcarbamate ( 2 ) and its α-isomer in a 5/1 ratio. The anomerization was circumvented by treatment of 1 with α-methoxycarbamate in the presence of boron trifluoride in benzene at room temperature. Compound 2 was electrochemically oxidized to give dihydrofuran 4 . However, conversion of 4 into 11 was unsuccessful. Treatment of azide 8 with bromine and methanol afforded 9 . Reduction of 9 with zinc powder gave dihydrofurfurylamine 10 , in 80% yield. Treatment of this with concentrated hydrochloric acid in methanol yielded 11 , which on deblocking with 5% sodium hydroxide aqueous solution gave 12.     

Synthesis of 1-(β-D-ribofuranosyl)indol-3-acetic acid

By condensation of ethyl indolin-3-acetate ( 4 ) and 2,3,5-tri-O-benzoylribofuranosyl-1-acetate ( 5 ), ethyl 1-(2,3,5-tri-O-benzoyl-β-D-ribofuranosyl)indolin-3-acetate ( 6 ) was obtained in good yield. The indoline nucleoside 6 was aromatized to ethyl 1-(2,3,5-tri-O-benzoyl-β-D-ribofuranosyl)indol-3-acetate ( 7 ) with DDQ. The treatment of the indole nucleoside with barium hydroxide and methanol gave the methyl ester 8 , which was further treated in water to give the desired 1-(β-D-ribofuranosyl)indol-3-acetic acid ( 9 ).     

Nucleotides Part LI. Synthesis and biological activities of (2′-5′)adenylate trimer conjugates with 2′-terminal 3′-O(ω-hydroxyalkyl) and 3′-O-(ω-carboxyalkyl) spacers

An efficient strategy for the synthesis of (2′-5′)adenylate trimer conjugates with 2′-terminal 3′-O-(ω-hydroxyalkyl) and 3′-O-(ω-carboxyalkyl) spacers is reported. Npeoc-protected adenosine building blocks 37--40 for phosphoramidite chemistry carrying a 3′-O-[11-(levulinoyloxy)undecyl], 3′-O-{2-[2-(levulinoyloxy)ethoxy]ethyl}, 3′-O-[5-(2-cyanoethoxycarbonyl)pentyl], and 3′-O-{5-[(9H-fluoren-9-ylmethoxy)carbonyl]pentyl} moiety, respectively, were prepared (npeoc = 2-(4-nitrophenyl)ethoxycarbonyl). Condensation with the cordycepin (3′-deoxyadenosine) dimer 1 led to the corresponding trimers 42, 43, 47 , and 48. Whereas the levulinoyl (lev) and 9H-fluoren-9-ylmethyl (fm) blocking groups could be cleaved off selectively from the trimers 42, 43 , and 48 yielding the intermediates 44, 45 , and 49 for the synthesis of the 3′-O-(ω-hydroxyalkyl)trimers 53, 54 and the cholesterol conjugates 59--61 , the 2-cyanoethyl (ce) protecting group of 47 , however, could not be removed in a similar manner from the carboxy function. Trimer 47 served as precursor for the preparation of the trimer 55 with a terminal 3′-O-(5-carboxypentyl)adenosine moiety. The metabolically stable 3′-O-alkyl-(2′--5′)A derivatives were tested regarding inhibition of HIV-1 syncytia formation and HIV-1 RT activity. Only the conjugate 59 showed significant effects, whereas the trimers 53--55 and the conjugates 60 and 61 were less potent inhibitors, even at 100-fold larger concentrations.     

Nucleosides. 117. Synthesis of 4-oxo-8-(β-D-ribofuranosyl)-3H-pyrazolo[1,5-a]-1,3,5-triazine (OPTR) via 3-amino-2N-carbamoyl-4-(β-D-ribofuranosyl)pyrazole (ACPR) derivatives

Reaction of 2-formyl-2-(2,3-O-isopropylidene-5-O-trityl-D-ribofuranosyl)acetonitrile (VII) with semicarbazide hydrochloride followed by sodium ethoxide treatment afforded an α,β-mixture of 3-amino-2N-carbamoyl-4-(2,3-O-isopropylidene-5-O-trityl-D-ribofuranosyl)pyrazole (IX). Conversion of IX to 4-oxo-8-(2,3-O-isopropylidene-5-O-trityl-D-ribofuranosyl)-3H-pyrazolo[1,5-a]-1,3,5-triazine (XIII) was achieved by treatment of IX with ethylorthoformate. The β-isomer IXb gave only the β-isomer XIIIb, and the α-isomer IXa was converted exclusively into the α-isomer XIIIa. Upon deprotection with 3% n-butanolic hydrogen chloride, both IXa and IXb gave the same mixture of the α- and β-isomers of 3-amino-2N-carbamoyl-4-(D-ribosyl)pyrazole, which were separated by chromatography. The syntheses of the hitherto unknown compounds, 3-amino-2N-carbamoylpyrazole (IVa) and its 4-methyl analog (IVb) are also reported. Experimental details of the synthesis of 3-amino-4-(2,3-O-isopropylidene-5-O-trityl-β-D-ribofuranosyl)pyrazole (XIIb), an important intermediate for “purine-like” C-nucleosides, are also described.     

Synthesis of β-D-ribo- and 2′-deoxy-β-D-ribofuranosyl derivatives of 6-aminopyrazolo[4,3-c]pyridin-4(5H)-one by a ring closure of pyrazole nucleoside precursors

6-Amino-1-(2-deoxy-β-D-erthro-pentofuranosyl)pyrazolo[4,3-c]pyridin-4(5H)-one ( 5 ), as well as 2-(β-D-ribofuranosyl)- and 2-(2-deoxy-β-D-ribofuranosyl)- derivatives of 6-aminopyrazolo[4,3-c]pyridin-4(5H)-one ( 18 and 22 , respectively) have been synthesized by a base-catalyzed ring closure of pyrazole nucleoside precursors. Glycosylation of the sodium salt of methyl 3(5)-cyanomethylpyrazole-4-carboxylate ( 6 ) with 1-chloro-2-deoxy-3,5-di-O-p-toluoyl-α-D-erythro-pentofuranose ( 8 ) provided the corresponding N-1 and N-2 glycosyl derivatives ( 9 and 10 , respectively). Debenzoylation of 9 and 10 with sodium methoxide gave deprotected nucleosides 14 and 16 , respectively. Further ammonolysis of 14 and 16 afforded 5(or 3)-cyanomethyl-1-(2-deoxy-β-D-erythro-pentofuranosyl)pyrazole-4-carboxamide ( 15 and 17 , respectively). Ring closure of 15 and 17 in the presence of sodium carbonate gave 5 and 22 , respectively. By contrast, glycosylation of the sodium salt of 6 with 2,3,5-tri-O-benzoyl-D-ribofuranosyl bromide ( 11 ) or the persilylated 6 with 1-O-acetyl-2,3,5-tri-O-benzoyl-β-D-ribofuranose gave mainly the N-2 glycosylated derivative 13 , which on ammonolysis and ring closure furnished 18 . Phosphorylation of 18 gave 6-amino-2-β-D-ribofuranosylpyrazolo[4,3-c]pyridin-4(5H)-one 5′-phosphate ( 19 ). The site of glycosylation and the anomeric configuration of these nucleosides have been assigned on the basis of ¹H nmr and uv spectral characteristics and by single-crystal X-ray analysis of 16 .     

Nucleosides and nucleotides. 2. Synthesis of both anomers of 1-(5'-O-phosphoryl-2'-deoxy-D-ribofuranosyl)-2(1H)-pyridone

The two anomeric 1-(2′-deoxy-D -ribofuranosyl)-2(1H)-pyridones 6 and 7 were synthesized from 2-pyridone and 3,5-di-(O-p-toluoyl)-2-deoxy-D -ribofuranosyl chloride ( 2 ) via the di-O-p-toluoyl derivatives 3 and 4 using the mercuric halide procedure. Phosphorylation of the nucleosides 6 and 7 by bis-(2,2,2-trichloroethyl)-chlorophosphate gave the phosphate esters 8 and 9 together with some 2-(bis-[2,2,2-trichloroethyl]-phosphoryloxy)-pyridine 10 , which proved to be very labile. Structure and configuration of compounds 6 to 9 were established by spectral methods, the configurations being derived from the chemical shifts of the sugar protons and the splitting patterns of the anomeric protons (‘triplet-quartet rule’). The specific rotations of 3 , 4 , 6 , 7 , 8 and 9 show that the three pairs of anomers represent exceptions to Hudson's rule of isorotation. Reductive removal of the trichloroethyl groups in 8 and 9 with zinc proceeds stepwise, yielding the phosphoro-diesters 13 and 14 and the two desired anomeric 5′-nucleotides 15 and 16 . These latter were purified and characterised as the ammonium salts. Enzymatic cleavage by the 5′-nucleotidase of Crotalus adamanteus venom took place only in the ‘natural’ β-series. The ‘unnatural’ α-anomers were resistent to the enzyme. The structure of 10 was established by spectral methods and confirmed by synthesis.     

Nucleotides. Part XXVIII. Chemical syntheses of the 2′-5′-cordycepin-trimer core

The chemical synthesis of 3′-deoxyadenyly-(2′-5′)-3′-deoxyadenylyl-(2′-5′)-3′-deoxyadenosine ( 30 ; trimeric cordycepin) is described by three different routes using various protecting groups and applying the phosphotriester approach. The intermediates have been isolated and characterized by elemental analyses and spectroscopic means. High yields of 30 have been obtained on deprotection making this biologically very active compound available in preparative scale.