Stereoselective synthesis of novel analogues of 2′-deoxy- and 2′,3′-dideoxynucleosides with potential antiviral activity

Synthesis of nucleosides with additional nucleobases

The syntheses of two nucleosides with additional nucleobases in the 2'-position are presented. The nucleosides have two- and one-carbon linkers to the additional nucleobase, respectively. The two nucleosides are synthesized from different strategies. The nucleoside with two carbons in the linker has been incorporated into oligonucleotides and showed stabilization of a tree-way junction.

Analogues of a locked nucleic acid with three-carbon 2',4'-linkages: synthesis by ring-closing metathesis and influence on nucleic acid duplex stability and structure

Two bicyclic 2'-deoxynucleoside analogues containing a saturated and an unsaturated three-carbon 2',4'-linkage, respectively, have been synthesized using a ring-closing metathesis-based linear strategy starting from uridine. Both analogues have been incorporated into oligodeoxynucleotide sequences and increased the stability of DNA:RNA hybrid duplexes (DeltaT(m) approximately 2.5-5.0 degrees C per modification) and decreased the stability of dsDNA duplexes (DeltaT(m) approximately 2.5-1.0 degrees C per modification). CD spectroscopy revealed that the bicyclic nucleosides induced formation of A-type-like duplexes albeit to a lesser degree than found for locked nucleic acid (LNA) monomers. From the CD data and UV melting analysis, we propose that the 2'-oxygen atom of the bicyclic moiety is essential for the formation of stabilized A-type-like dsDNA but not for the formation of a stabilized A-type DNA:RNA hybrid.

Synthesis of 2‘-C-α-(Hydroxyalkyl) and 2‘-C-α-Alkylcytidine Phosphoramidites: Analogues for Probing Solvent Interactions with RNA

Nucleoside analogues bearing 2'-C-alpha-(hydroxyalkyl) and 2'-C-alpha-alkyl substitutes have numerous applications in RNA chemistry and biology. In particular, they provide a strategy to probe the interaction between the 2'-hydroxyl group of RNA and water. To incorporate these nucleoside analogues into oligonucleotides for studies of the group II intron (Gordon, P. M.; Fong, R.; Deb, S.; Li, N.-S.; Schwans, J. P.; Ye, J.-D.; Piccirilli, J. A. Chem. Biol. 2004, 11, 237), we synthesized six new phosphoramidite derivatives of 2'-deoxy-2'-C-alpha-(hydroxyalkyl)cytidine (36: R = -(CH2)2OH; 38: R = -(CH2)3OH; 40: R = -(CH2)4OH) and 2'-deoxy-2'-C-alpha-alkylcytidine (37: R = -CH2CH3; 39: R = -(CH2)2CH3; 41: R = -(CH2)3CH3) from cytidine or uridine via 2'-C-alpha-allylation, followed by alkene and alcohol transformations. Phosphoramidites 36 and 37 were prepared from cytidine in overall yields of 14% (10 steps) and 7% (11 steps), respectively. Phosphoramidites 38 and 39 were prepared from uridine in overall yields of 30% (10 steps) and 13% (11 steps), respectively. Phosphoramidites 40 and 41 were synthesized from uridine in overall yields of 21% (13 steps) and 25% (14 steps), respectively.

Synthesis of conformationally restricted nucleic acid fragments using ring-closing alkene and enyne metathesis reactions

In the aim of constructing conformationally restricted nucleic acid fragments for the recognition of secondary RNA structures, we have synthesized different mono- and dinucleotides containing extra rings. These rings were prepared by ring-closing alkene or enyne metathesis reactions from nucleotide substrates in which double or triple bonds have been introduced.

Stabilisation of nucleic acid secondary structures by oligonucleotides with an additional nucleobase; synthesis and incorporation of 2'-deoxy-2'-C-(2-(thymine-1-yl)ethyl)uridine

A nucleoside with two nucleobases is incorporated into oligonucleotides. The synthetic building block, 2'-deoxy-2'-C-(2-(thymine-1-yl)ethyl)uridine, 2, is prepared from uridine via 5',3'-TIPDS-protected 2'-deoxy-2'-C-allyluridine by an oxidative cleavage of the allyl group, a Mitsunobu reaction for the introduction of thymine and appropriate deprotection reactions. This compound is converted into a DMT-protected phosphoramidite and incorporated once into a 13-mer oligodeoxynucleotide sequence, once in an isosequential LNA-modified oligodeoxynucleotide and four times in the middle of a 12-mer oligodeoxynucleotide. These sequences are mixed with different complementary DNA and RNA sequences in order to study the effect of the additional nucleobase in duplexes, in bulged duplexes and in three-way junctions. The first additional thymine is found to be well-accommodated in a DNA-RNA duplex, whereas a DNA-DNA duplex was slightly destabilised. A three-way junction with the additional thymine in the branching point is found to be stabilised in both a DNA-DNA and a DNA-RNA context but destabilised where the modified LNA-sequence is used. In a Mg2+-containing buffer, however, the relative stability of the three-way junctions is found to be opposite with especially the LNA-modified DNA-DNA complex being significantly stabilised by the additional nucleobase.

Stabilisation of a nucleic acid three-way junction by an oligonucleotide containing a single 2'-C to 3'-O-phosphate butylene linkage prepared by a tandem RCM-hydrogenation method

A cyclic dinucleotide with a butylene linker between the upper 2'-C position and the 3'-O-phosphate linkage was synthesised from simple nucleoside building blocks via a tandem ring-closing metathesis and hydrogenation procedure. The major of two phosphorus epimers was incorporated into an oligodeoxynucleotide, as well as into an LNA-DNA mixmer oligonucleotide. These were evaluated as parts in three different secondary structures, a duplex, a bulged duplex and a three-way junction, with both DNA and RNA complements. In the DNA:RNA hybrid molecule, the oligodeoxynucleotide containing this single 2'-C to 3'-O-phosphate butylene linkage was found to stabilise a three-way junction.

Synthesis of the Phosphoramidite Derivatives of 2‘-Deoxy-2‘-C-α-methylcytidine and 2‘-Deoxy-2‘-C-α-hydroxymethylcytidine: Analogues for Chemical Dissection of RNA's 2‘-Hydroxyl Group

Oligonucleotides containing 2'-C-alpha-methyl and 2'-C-alpha-hydroxymethyl modifications enable strategies for delineation of the distinctive role fulfilled by the 2'-hydroxyl group in RNA structure and function. Synthetic routes to the phosphoramidite derivatives of 2'-deoxy-2'-C-alpha-methylcytidine (14%, 15 steps) and 2'-deoxy-2'-C-alpha-hydroxymethylcytidine (19%, 10 steps) from methyl 3,5-di-O-(4-chlorobenzyl)-alpha-d-ribofuranoside are developed.

Synthesis of the phosphoramidite derivative of 2'-deoxy-2'-C-beta-methylcytidine

2'-Deoxy-2'-C-beta-methylnucleosides elicit interest as potential therapeutic agents and as analogues for the analysis of nucleic acid structure and function. An efficient route for the synthesis of 2'-deoxy-2'-C-methyluridine (11), 2'-deoxy-2'-C-methylcytidine (12), and the phosphoramidite derivative of 2'-deoxy-2'-C-beta-methylcytidine (10, 46% overall yield) from 1,2,3,5-tetra-O-benzoyl-2-C-beta-methylribofuranose (1) is described.

New method for the preparation of 3'- and 2'-O-phosphoramidites of 2'- and 3'-difluoromethyluridine derivatives

Hydrogenation of 2'-deoxy-2'-difluoromethylene-5'-O-dimethoxytrityluridine (1) and 3'-deoxy-3'-difluoromethylene-5'-O-dimethoxytrityluridine (7), gave the corresponding 2'- and 3'-difluoromethyluridine derivatives 2a and 8a. Detritylation of compounds 2a, 2b and 8a, 8b resulted in the formation of 1-(2-deoxy-2-C-difluoromethyl-beta-D-arabino-pentofuranosyl)uracil (3a) and 1-(3-deoxy-3-C-difluoromethyl-beta-D-xylo-pento furanosyl)- uracil (9a) as well as corresponding minor isomers 3b and 9b. Compounds 3a and 3b were also obtained from 2'-deoxy-2'-difluoromethylene-3',5'-O-(tetraisopropyldisiloxane-1,3-diyl)uridine (4). Finally, phosphitylation of 2a and 8a provided the title 2'- and 3'-O-phosphoramidites 6 and 10.

Nucleosides and Nucleotides. 156. Chelation-Controlled and Nonchelation-Controlled Diastereofacial Selective Thiophenol Addition Reactions at the 2'-Position of 2'-[(Alkoxycarbonyl)methylene]-2'-deoxyuridines: Conversion of (Z)-2'-[(Alkoxycarbonyl)methylene]-2'-deoxyuridines into Their (E)-Isomers(1)

The Wittig reaction of 1-[3,5-O-(1,1,3,3-tetraisopropyldisiloxane-1,3-diyl)-beta-D-erythro-pentofuranos-2-ulosyl]uracil (4) with Ph(3)P=CHCO(2)R (R = ethyl or tert-butyl) exclusively gave (Z)-2'-[(alkoxycarbonyl)methylene] derivatives 5 and 13, respectively, in high yields. An unusual beta-facial selectivity of thiophenol addition to the 2'-[(alkoxycarbonyl)methylene] moiety of 5 and 13 was observed, and this facial selectivity was found to be influenced by both the thiolate counter cation and the bulkiness of the alkoxy moiety. Treatment of 2'-[(ethoxycarbonyl)methylene] derivative 5with LiSPh (1.5 equiv) in the presence of PhSH in THF selectively gave 2'beta-(phenylthio) derivative 11 in high yield along with a trace of 2'alpha-(phenylthio) derivative 10. On the other hand, when 2'-[(tert-butoxycarbonyl)methylene] derivative13 was treated with KSPh in the presence of PhSH in dioxane/DMF, the facial selectivity was reversed to selectively give the 2'alpha-(phenylthio) adduct14 (alpha:beta, 77:23) in 90% yield. Oxidation of 14 with m-chloroperbenzoic acid in CH(2)Cl(2) and subsequent pyrolysis of the resulting sulfoxides exclusively gave the (Z)-isomer 13 in 92% yield. The oxidativesyn-elimination of the (2'R)-2'-[(tert-butoxycarbonyl)methyl]-2'-deoxy-2'-thiophenoxy-5'-O-(triisopropylsilyl)uridine (17), which was obtained from 14 in two steps, exclusively gave the desired (E)-[(tert-butoxycarbonyl)methylene] derivatives 18 in 90% yield. Deprotection of 18 gave the (E)-(carboxymethylene)-2'-deoxyuridine (3). The (Z)-(carboxymethylene)-2'-deoxyuridine (2) was synthesized from 13 in a similar manner.