Synthesis of 2-ethyl-3-Hydroxy-4-Pyridone Nucleosides

The hydroxypyridones were found to have wide biological activities such as they can be used as iron chelators for the treatment of iron overload of transfusion-dependant patients^[1]. Some hydroxypyridones were discovered to possess moderate reproducible activity against murine P-388 leukemia^[2] and showed antimalarial activity^[3]. Besides some nucleoside of hydroxypyridones exhibit antitumor activity^[4]. The 2-ethyl-3-hydroxy-4-pyridone nucleosides were synthesized by direct condensation of the silylated 2-ethyl-3-hydroxy-4-pyridone with 1,2,3,5-tetra-o-acetyl-β-D-ribofuranose using trimethylsilyl triflate(Me₃SiOTf) as catalyst. Deblocking of the protected ribofuranosyl nucleosides was performed by the standard methods.     

Synthesis and Characterization of Non-standard Nucleosides and Nucleotides Bearing the Acceptor-Donor-Donor Pyrimidine Analog 6-Amino-3-methylpyrazin-2(1H)-one

6-Aminopyrazin-2(1H)-one, when incorporated as a pyrimidine-base analog into an oligonucleotide chain, presents a H-bond acceptor-donor-donor pattern to a complementary purine analog. When paired with the corresponding donor-acceptor-acceptor purine in oligonucleotides, the heterocycle selectively contributes to the stability of the duplex, presumably by forming a base pair of Watson-Crick geometry joined by a non-standard H-bonding pattern. Aspects of the nucleoside chemistry, including syntheses of the β-furanosyl ribonucleoside 1 , the ribonucleoside triphosphate 2 and the ribonucleoside bisphosphate 3 of 6-aminopyrazin-2(1H)-one are reported here. In aqueous solution, the ribonucleoside 1 was found to undergo acid- and base-catalyzed rearrangement with an apparent half-life of ca. 63 h at neutral pH and 30°. The rearrangement appears to be specific acid- and base-catalyzed. The thermodynamically most stable compound formed during this rearrangement reaction was isolated by HPLC and shown to be the β-pyranosyl form 4 of the 6-aminopyrazin-2(1H)-one nucleoside in its ⁴C₁ chair conformation. This reactivity of 1 under physiological conditions may explain why Nature does not use this particular heterocyclic system to implement an acceptor-donor-donor H-bonding pattern in the genetic alphabet.     

Nucleosides and Nucleotides. Part 19. On Detritylation with Zinc Bromide in Oligonucleotide Synthesis

Zinc bromide has been shown by several groups of workers to be a useful reagent in the removal of trityl protecting groups from nucleotides. An attempt is made here to establish optimum conditions for the reaction, a strange observation is reported, and a novel workup via a soluble, lipophilic zinc complex is described.     

Nucleosides and nucleotides. Part 8. Synthesis of dinucleotides with thymidine and 1-(deoxy-beta-D-ribofuranosyl)-2(1H)-pyridone as building blocks]

In order to investigate the stability of 1-(2′-deoxy-β-D-ribofuranosyl)-2(1H)-pyridone (Π_d, 3 ) under the conditions of oligonucleotide synthesis, the dinucleoside monophosphates (MeOTr)Π_d-T_d ( 9 ) and Π_d-T_d ( 11 ), and the dinucleotides Π_d-T_dp ( 15 ) and pII_d-T_d ( 19 ) were prepared, using various procedures. The N-glycosidic bond between the deoxyribose and the 2(1H)-pyridone proved to be much more labile than the one in the naturally occuring nucleosides. It was partially cleaved in condensation reactions with TPS or MS, but no cleavage was observed when DCC was used. Similarly, the glycosidic linkage was attacked by hot 80% acetic acid, the usual reagent for the removal of a p-methoxytrityl group in thymidine oligonucleotides. Milder treatment with acetic acid/pyridine 7:3 at 100° removed this protecting group and left the N-glycoside intact. The compounds prepared were characterized by paper and thin layer chromatography as well as by enzymatic degradation.     

Synthesis and Conformational Studies of Unnatural Pyrimidine Nucleosides

ABSTRACT

Starting from 3,4-di-O-acetyl-L-rhamnal (6) and thymine (7) the unsaturated nucleosides 1-(2′,3′,6′-trideoxy-4′-O-acetyl-α- and β-L-erythro-hex-2′-enopyranosyl)-thymine (8a and 8b) were prepared in anomerically pure form. In solution 8a was shown to be present in the ⁵ H _o and ⁰ H ₅ conformations, whereas the predominant conformation of 8b was ⁵ H _o. Chemical transformation of 8a and 8b led to the saturated nucleosides 1-(2′,3′,6′-trideoxy-α- and β-L-erythro-hexopyranosyl)thymine (10a and 10b, respectively), which were converted into 1-(4′-azido-2′,3′,4′,6′-tetradeoxy-α- and β-L-threo-hexopyranosyl)thymine (12a and 12b). Preliminary biological studies showed that 9b was inactive against the HIV-1 and HIV-2 viruses.     

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.     

Nucleosides and Nucleotides. Part 13. Synthesis and spectral properties of 1- (3′-O-Phosphoryl-2′-deoxy-β -D-ribofuranosyl)-2(1H)-pyridone-(3′-5′)-1-(2′-deoxy-β-D-ribofuranosyl)-2 (1H)-pyridone

The dinucleoside phosphate Π_dpΠ_d ( 4 ) was synthesized from the monomers 1-(5′-O-monomethoxytrityl - 2′ - deoxy - β - D - ribofuranosyl) - 2 (1 H) - pyridone ((MeOTr) Π_d, 2 ) and 1-(5′-O-phosphoryl-3′-O-acetyl-2′-deoxy-β-D -ribofuranosyl)-(1H)-pyridone (pΠ_d(Ac), 3 ). Its 6.4% hyperchromicity and an analysis of the ¹H-NMR. spectra indicate that the conformation and the base-base interactions in 4 are similar to those in natural pyrimidine dinucleoside phosphates.     

Nucleosides and Nucleotides. Part 17. A simple preparation of protected deoxynucleoside-3'-phosphates

A simple method for the preparation of fully protected 2′-deoxynucleoside-3′-phosphates is described. The main step, phosphorylation of partially protected deoxynucleosides, is performed with the monofunctional reagent p-chlorophenyl (2-cyanoethyl) phosphochloridate³) ( 2 ) in dioxane. This reagent is quickly prepared from readily accessible p-chlorophenyl phosphodichloridate by reaction with 3-hydroxypropionitrile and triethylamine in dioxane or ether. The crude reagent is used directly for phosphorylation. After chromatography, protected deoxynucleoside-3′-phosphates were isolated in yields of 80–87%. The method described here, which has been optimized in detail, represents a simple alternative to published methods.     

Nucleosides and Nucleotides. Part 18. p-nitrobenzenesulfonyl nitroimidazole as a new condensing agent in the triester synthesis of oligonucleotides

p-Nitrobenzenesulfonyl nitroimidazole (p-NBSNI) ( 5 ) has been shown to be an efficient and convenient condensing agent in the coupling of protected nucleotide fragments. Its utility has been demonstrated by a direct comparison with previously-described condensing agents in the synthesis of various di- and tetradeoxy-nucleotides.     

Synthesis of 1(2H)-Isoquinolones. (Review)

Methods published over the last 10 years for the production of substituted 1(2H)-isoquinolones, including those involving the use of organometallic compounds, are discussed.     

Enzymatic Synthesis of a DNA Triblock Copolymer that is Composed of Natural and Unnatural Nucleotides

DNA molecules have come under the spotlight as potential templates for the fabrication of nanoscale products, such as molecular‐scale electronic or photonic devices. Herein, we report an enhanced approach for the synthesis of oligoblock copolymer‐type DNA by using the Klenow fragment exonuclease minus of E. coli DNA polymerase I (KF^?) in a multi‐step reaction with natural and unnatural nucleotides. First, we confirmed the applicability of unnatural nucleotides with 7‐deaza‐nucleosides—which was expected because they were non‐metalized nucleotides—on the unique polymerization process known as the “strand‐slippage model”. Because the length of the DNA sequence could be controlled by tuning the reaction time, analogous to a living polymerization reaction on this process, stepwise polymerization provided DNA block copolymers with natural and unnatural bases. AFM images showed that this DNA block copolymer could be metalized sequence‐selectively. This approach could expand the utility of DNA as a template.     

1,8-Naphthyridines. Part III. Synthesis of some 6-substituted-1,8-naphthyridin-2(1H)ones

The syntheses of some 1,8-naphthyridines substituted in the 6-position with heterocyclic groups are described. A synthetic route to 6-amino-5,7-dimethyl-1,8-naphthyridin-2(1H)one is also presented.     

Nucleosides. Part L.. Structure of lumazine N1-(2′-deoxy-D-ribonucleosides) ( = 1-(2′-deoxy-D-ribofuranosyl)pteridine-2,4(1H,3H)-diones): A revision of the anomeric configuration

The anomeric configuration of the glycosidic bond in lumazine N¹-(2′-deoxy-D -ribonucleosides) 1–6 was investigated by NOE difference spectroscopy. The former configurational assignment of the α - and β -D -anomers 1 and 2, 3 and 4 , and 5 and 6 , respectively, has to be reversed to be in agreement with the physical data. Additional proof is presented by X-ray analysis of 3 and 6 . Chemical interconversions of 1-(2′-deoxy-β-D -ribofuranosyl)-6,7-diphenyllumazine ( 6 ) into 2,3′ -anhydrolumazine 2′-deoxyribonucleosides 16 and 17 are also in agreement with the revised anomeric configuration.     

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.     

Nucleotides. Part XXXIX Synthesis of arabinonucleoside phosphoramidite building blocks

High-yield chemical syntheses of phosphoramidite building blocks of the four arabinonucleosides aUrd ( 1 ), aCyd ( 2 ), aAdo ( 3 ), and aGuo ( 4 ), suitable for (3′–5′)oligoarabinonucleotide synthesis are described. The problem of 2′-hydroxy group protection was solved by introduction of the versatile 2-(4-nitrophenyl)ethoxycarbonyl (npeoc) residue, which was also used for aglycon protection.     

Nucleosides and Nucleotides. 151. Conversion of (Z)-2'-(Cyanomethylene)-2'-deoxyuridines into Their (E)-Isomers via Addition of Thiophenol to the Cyanomethylene Moiety Followed by Oxidative Syn-elimination Reactions(1)

The Wittig reaction of 1-[3,5-O-(1,1,3,3-tetraisopropyldisiloxane-1,3-diyl)-beta-D-erythro-pentofuranos-2-ulosyl]uracil (6) with Ph(3)P=CHCN afforded (Z)-2'-cyanomethylene derivative 7 exclusively. The (E)-isomer was accessed from its (Z)-isomer through a sequence of addition of thiophenol to the 2'-cyanomethylene moiety of the (Z)-isomer from the alpha-face, selectively, and stereoselective oxidative syn-elimination of the resulting adduct. The diastereofacial selectivity of the benzenethiolate addition to the cyanomethylene moiety was found to be influenced by participation of the 2-carbonyl group at the base moiety and steric hindrance of the sugar protecting groups. Although nucleophilic addition reactions at the 2'-position of 6 have been well-known to occur from the alpha-face selectively, treatment of 7 with LiSPh in THF unexpectedly afforded a mixture of alpha- and beta-phenylthio derivatives 8 and 9 in almost equal ratio. Furthermore, an unusual beta-facial selective addition was observed on treatments of 7 with PhSAlMe(2) in CH(2)Cl(2) or with LiSPh in the presence of Mg(ClO(4))(2) in THF. On the other hand, when (Z)-2'-(cyanomethylene)-5'-O-triisopropylsilyl derivative 10 was treated with LiSPh, the alpha-phenylthio derivative 13 was obtained predominantly (89:11). Oxidation of 8 with m-chloroperbenzoic acid (m-CPBA) in CH(2)Cl(2) and pyrolysis of the resulting sulfoxides afforded the (Z)-isomer 7 exclusively. Treatment of 13 with m-CPBA under the same conditions afforded the desired (E)-cyanomethylene derivatives 18 as a major product (E:Z = 14:1) in good yield. Deprotection of 18 by the standard procedures furnished (E)-2'-(cyanomethylene)-2'-deoxyuridine (5).     

1,8-naphthyridines. Part II. Synthesis of some 3-pyridyl-5,7-di(trifluoromethyl)-1,8-naphthyridin-2(1H)ones

Ethyl 2-amino-4,6-di(trifluoromethyl)nicotinate was prepared and its use as an intermediate in the synthesis of two 3-pyridyl-5,7-di(trifluoromethyr)-1,8-naphthyridin-2(1H)ones is presented. A dimer of 2-amino-4,6-di(trifluoromethyl)nieotinaldehyde is described.     

Synthesis of 3-S-hetaryl-substituted pyridin-2(1H)-ones and 5,6-dihydropyridin-2(1H)-ones*

A method has been developed for the synthesis of 3-S-hetaryl-substituted pyridin-2(1H)-ones and 5,6-dihydropyridin-2(1H)-ones based on the base catalyzed cyclization of N-(3-oxoalkyl)- and N-(3-oxoalkenyl)amides which contain a divalent sulfur atom in an α-position to a carbamoyl group and bound to the heterocycle.