C-branched Nucleosides Research Articles

An alternative method for the synthesis of 2′-halogeno-1′,2′-unsaturated uridine derivatives through syn-elimination of pivalic acid of 2′-halogeno- 2′-deoxy-1′-pivaloyloxyuracil nucleoside: preparation of its 2′-C-branched nucleosides

An alternative method for the preparation of 2′-bromo- (5b) and 2′-iodo- (5c) 1′,2′-unsaturated uracil nucleosides has been developed. The protocol was on the basis of the syn-elimination of pivalic acid from 2′-bromo-(7a,b) and 2′-iodo-(9a,b) 1′-pivaloyloxy-2′-deoxyuridine derivatives, which were derived from the halo-pivaloyloxylation of 3′,5′-bis-O-TBDMS-1′,2′-unsaturated uridine 1. Compounds 5b and 5c were shown to serve as versatile synthons for the respective 2′-C-branched 1′,2′-unsaturated uracil nucleosides, through palladium-catalyzed cross-coupling or halogen-lithium exchange reactions.

ChemInform Abstract: Synthesis of 2′‐C‐Branched Nucleosides

AbstractReview: 150 refs.

Synthesis of 2′-C-Branched Nucleosides

B = base A = adenine ABz = N 6-benzoyladenine C = cytosine CAc = N 4-acetylcytosine CBz = N 4-benzoylcytosine CMMTr = N 4-(Monomethoxytrityl)cytosine G = guanine GAc = N 2-acetylguanine GCHNMe2 = N...

Synthesis and Antiviral Evaluation of 4′-C-Azidomethyl-β-D-Ribofuranosyl Purine and Pyrimidine Nucleosides

In the search for inhibitors of the replication of RNA viruses, including hepatitis C virus (HCV), the hitherto unknown 4′-C-azidomethyl-β-D-ribofuranosyl nucleosides of the five naturally occurring nucleic acid bases have been synthesized and their antiviral properties examined. These 4′-C-branched nucleosides were stereospecifically prepared by glycosylation of purine and pyrimidine aglycons with a suitable peracylated 4-C-azidomethyl-D-pentofuranose sugar, followed by removal of the protecting groups. The prepared compounds were tested for their activity against several viruses, but they did not show an antiviral effect.

Syntheses of 2′- C-amidoalkyl and 2′- C-cyanoalkyl containing oligodeoxyribonucleotides and assessment of their hybridisation affinity for complementary DNA and RNA

Oligodeoxynucleotides containing 2′- C-branched nucleosides with an amide or nitrile appended to either a one or two carbon alkyl chain have been synthesised. The phosphoramidites of the 2′- C-modified nucleosides were prepared and incorporated into the oligonucleotides using automated DNA synthesis. The duplex stability with complementary RNA and DNA was measured by UV melting experiments, in order to assess whether the amide/nitrile function could induce any duplex stability without the presence of the 2′-oxygen. The duplex stabilities of the oligonucleotides containing the 2′- C-modifications were decreased in the absence of the 2′-oxygen.

Convenient Synthesis of Nucleoside and Isonucleoside Analogues

[reaction: see text]. A very simple methodology to stereoselectively achieve tricyclic isonucleosides (nucleobase = thymine, uracil, and 5-fluoruracil) and 3'-C-branched nucleosides (nucleobase = theophylline) was performed by means of a DBU-mediated addition process using a readily available 2-bromo sugar. The mechanism for these transformations implies the loss of both substituents at C-2 and C-3 on the sugar moiety, and although it seems that DBU is probably involved, its involvement has not yet been ascertained. Cytosine did not react under these conditions.

Syntheses and base-pairing properties of locked nucleic acid nucleotides containing hypoxanthine, 2,6-diaminopurine, and 2-aminopurine nucleobases.

Second generation 2'-O,4'-C-methylene-linked nucleotides 1-3 containing hypoxanthine, 2,6-diaminopurine, and 2-aminopurine nucleobases were synthesized and incorporated into locked nucleic acid (LNA) oligonucleotides by means of the automated phosphoramidite method. The required phosphoramidite monomeric units were efficiently prepared via convergent synthesis. The glycosyl donor 4 was stereoselectively coupled with hypoxanthine and 6-chloro-2-aminopurine to give the 4'-C-branched nucleosides 5 and 17. The methods for conversion of 5 and 17 into phosphoramidites 11, 25, and 29 were developed and described in full details for the first time. Hybridization properties of LNA octamers containing the new LNA nucleotides were assessed against perfect and singly mismatched DNA. The binding studies revealed that all LNA octamers hybridize very efficiently to DNA following Watson-Crick base-pairing rules with increased binding affinity compared to the DNA analogues. The unique properties of the nucleotides 1-3 make them very useful for further strengthening of the LNA technology.

Total synthesis of 3',5'-C-branched nucleosides.

[reaction: see text] A novel total synthesis of 3',5'-C-branched uridine azido acid has been accomplished using stereoselective aldehyde alkynylation, Ireland-Claisen rearrangement, and iodolactonization as the key reactions. Compared to traditional routes that start from carbohydrates, the present methodology is more efficient, flexible for future optimization, and provides access to both enantiomers of the products. Because the key chemistry does not involve the 3'- and 5'-C substituents, our route is a general approach to 3',5'-C alkyl nucleoside analogues.

A simplified and efficient route to 2'-O, 4'-C-methylene-linked bicyclic ribonucleosides (locked nucleic acid).

A novel efficient method for the synthesis of locked nucleic acid (LNA) monomers is described. The LNA 5',3'-diols containing thymine, 4-N-acetyl- and 4-N-benzoylcytosine, 6-N-benzoyladenine, and 2-N-isobutyrylguanine as nucleobases were prepared via convergent syntheses. The method is based on the use of the common sugar intermediate 1,2-di-O-acetyl-3-O-benzyl-4-C-methanesulfonoxymethyl-5-O-methanesulfonyl-D-erythro-pentofuranose (8) that easily can be prepared from D-glucose in multigram scale. Four different nucleobases were stereoselectively coupled to 8 using a modified Vorbrüggen procedure to give the corresponding 4'-C-branched nucleoside derivatives. Subsequent ring closing furnished the protected LNA nucleosides. The 5'-O-mesyl groups were efficiently displaced by nucleophilic substitution using sodium benzoate. Saponification of the 5'-benzoates followed by catalytic removal of the 3'-O-benzyl groups afforded the free LNA diols. The exocyclic amino groups of adenosine and cytidine were selectively acylated to give 4-N-acetyl- or 4-N-benzoyl-LNA-C and 6-N-benzoyl-LNA-A. The isobutyryl group of guanine was retained during the preparation of 2-N-isobutyryl-LNA-G. The LNA-T diol and base-protected LNA diols can be directly converted into LNA-phosphoramidites for automated chemical synthesis of LNA containing oligonucleotides.

Oligonucleotides Containing Novel 4′-C- or 3′-C-(Aminoalkyl)-Branched Thymidines

The synthesis of four novel 3′-C-branched and 4′-C-branched nucleosides and their transformation into the corresponding 3′-O-phosphoramidite building blocks for automated oligonucleotide synthesis is reported. The 4′-C-branched key intermediate 11 was synthesized by a convergent strategy and converted to its 2′-O-methyl and 2′-deoxy-2′-fluoro derivatives, leading to the preparation of novel oligonucleotide analogues containing 4′-C-(aminomethyl)-2′-O-methyl monomer X and 4′-C-(aminomethyl)-2′-deoxy-2′-fluoro monomer Y (Schemes 2 and 3). In general, increased binding affinity towards complementary single-stranded DNA and RNA was obtained with these analogues compared to the unmodified references (Table 1). The presence of monomer X or monomer Y in a 2′-O-methyl-RNA oligonucleotide had a negative effect on the binding affinity of the 2′-O-methyl-RNA oligonucleotide towards DNA and RNA. Starting from the 3′-C-allyl derivative 28, 3′-C-(3-aminopropyl)-protected nucleosides and 3′-O-phosphoramidite derivatives were synthesized, leading to novel oligonucleotide analogues containing 3′-C-(3-aminopropyl)thymidine monomer Z or the corresponding 3′-C-(3-aminopropyl)-2′-O,5-dimethyluridine monomer W (Schemes 4 and 5). Incorporation of the 2′-deoxy monomer Z induced no significant changes in the binding affinity towards DNA but decreased binding affinity towards RNA, while the 2′-O-methyl monomer Z induced decreased binding affinity towards DNA as well as RNA complements (Table 2).

Diastereoselective synthesis of α-substituted-γ-butyrolactones of nucleosides via [1,5]-C,H insertion reactions of α-diazomalonates of nucleosides

Diastereoselective and regioselective [1,5]-C,H insertion reactions of 2′-deoxy-3′-diazomalonate nucleosides afforded τ-butyrolactones of nucleosides as chiral synthons for the preparation of 2′-C-branched nucleosides.

A novel stereo-controlled nucleobase exchange process for the synthesis of 2′-C-branched nucleosides

A novel stereo-controlled process is described which enables the uracil base on a 2′-deoxy-2′-α-C-carboxymethyluridine nucleoside to be exchanged for either a purine or another pyrimidine base, via the intermediacy of an isolable pentofuranosyl butyrolactone.

Synthesis, structure and reactions of uridine 2′-C,3′-O-γ-butyrolactone: versatile intermediate for the synthesis of 2′-C-branched nucleosides

Uridine 2′-C-3′-O-γ-butyrolactone 5a has been prepared by cyclisation of 2′-α-C-carboxymethyl-2′-deoxyuridine 8 in acetic acid–methanol. Detailed 1H NMR studies on compound 5a clearly demonstrate cis fusion between the γ-lactone and the sugar moiety, and determination of conformationally averaged structural descriptors, i.e. the pseudorotation phase angle and the puckering amplitude, suggests that the dominant conformer of the furanose ring is S. The 2′-C,3′-O-lactone 5a and its 5′-protected derivatives (5b and 5c) readily undergo aminolyses to yield a range of amide derivatives. Reaction with 5′-amino-5′-deoxythymidine gave a 2′–5′-amide-linked analogue of a dinucleoside monophosphate. Under acidic conditions the amides slowly relactonised. The 5′-protected lactones were also shown to react with simple organometallic reagents.

Sunthesis of functionalised 2′- C-branched nucleosides via their γ-butyrolactones

Functionalised 2′- C-branched nucleosides that contain either a carboxylic acid ( 2), a primary amide ( 3) or a primary hydroxyl ( 4) group have been prepared and their protection for oligonucleotide synthesis investigated. The 2′- C-3′- O- γ-butyrolactone ( 5) was also shown to be a useful intermediate for the preparation of these analogues.

Stereoselective Synthesis of 1'-C-Branched Uracil Nucleosides from Uridine

Abstract Face-selective electrophilic addition (bromo-pivaloyloxylation) to 1-[3,5-bis-O-(tert-butyldimethylsilyl)-2-deoxy-D-erythro-pent-1-enofurano-syl]uracil (1), when combined with nucleophilic substitution using organosilicon or organoaluminum reagents, provides a new and highly divergent C-C bond forming method at the anomeric position.

Diastereospecific synthesis of 2′- or 3′- c-branched nucleosides through intramolecular free-radical capture by silicon-tethered acetylene

The intramolecular free-radical trapping by a silicon tethered acetylene function in a ribonucleoside 2a, 2b, 2c, 8a, 8b or 8c gave only the [3.3.0]-cis-fused Z-vinylsiloxane 3a, 3b, 3c, 9a, 9b or 9c (&>90%) in a diastereospecific manner. The temporary silicon connection from the Z-vinylsiloxane was removed by the oxidation to give the 2′- or 3′-C-branched α-keto-,β-D-ribonucleoside (∼85%), which was diastereospecifically reduced to give 1,3-syn diol (&>90%, &>97% ee) [2′-or 3′-C-branched-α-substituted R or S-hydroxymethyl-β-D-ribonucleosides 5a, 5b, 5c, 11a, 11b or 11c]. These are the first examples of highly diastereospecific synthesis of 2′-or 3′-C-branched ribonucleosides, through a 5-trig-exo radical cyclization, using the silicon-tethered approach.

How does the steric effect drive the sugar conformation in the 3′-C-branched nucleosides?

The steric effect of 3′-CH2OH group drives the North⇄ South pseudorotational equilibrium of the sugar moiety in the isomeric 1-(2′,3′-dideoxy-3′-hydroxymethyl-β-D-erythro-pentofuranosyl)cytosine 1(80% North at 298 K; ΔH°=+5.9 kJ mol–1, ΔS°=+7.4 J K–1 mol–1), and 1-(2′,3′-dideoxy-3′-hydroxymethyl-β-D-threo-pentofuranosyl)cytosine 2(82% South at 293 K; ΔH°=–0.9 kJ mol–1, ΔS°=+9.5 J K–1 mol–1) and it is found to be three times stronger in 2(ΔH°=–5.9 kJ mol–1) in comparison with that of 1(ΔH°=–2.1 kJ mo–1).

Stereoselective synthesis of 4′- C-branched 2,′3′-didehydro-2′-dideoxy nucleosides based on SnCl 4-promoted allylic rearrangement

Based on SnCl 4-[promoted allylic rearrangement between a 3′,4′-unsaturated uracil nucleoside and organosilicon reagents, stereoselective introduction of carbon functionalities to the 4′-position has been accomplished, disclosing a new entry for a series of 4′-C-branched nucleosides of biological interests.

New stereocontrolled synthesis of isomeric C-branched-β-D-nucleosides by intramolecular free-radical cyclization- opening reactions based on temporary silicon connection

Silicon-bearing allyl group tethered to a 2′ or 3′-hydroxyl group onto the radical generated at the vicinal 2′ or 3′ center in the free-radical precursors 11, 15, 19 and 23 were used to promote intramolecular stereocontrolled free-radical-cyclization to give 12a + 12b, 16, 20 and 24 in 60–70% yields. The configuration at the 2′ or the 3′ center of the allylsiloxane group dictated the stereochemical outcome of the radical cyclization reaction to give cisfused seven-membered rings in compounds 16, 20 and 24 (from 15, 19 and 23, respectively) due to relatively long SiO bond and large CSiO bond angle leading to exclusive 7-endo cyclization. The only exception to this was found in the radical-cyclization of 11 in which both cis-fused and trans-fused seven-membered rings 12a and 12b were formed as inseparable mixture almost in equal amounts. The seven-membered siloxane ring in the radical-cyclized products 12a + 12b, 16, 20 and 24 were then opened up by a simple oxidation reaction to give different 1,5-diols 13a + 13b, 17, 21 and 25 in high yields. The 5′-O-(4-methoxytrityl) group from 13a + 13b, 17, 21 and 25 was then removed to give pure and isomeric C-branched nucleosides 14a, 14b, 18, 22 and 26, respectively. The acid catalyzed isomerization of the pentofuranose ring in 17 to a pyranose system in 18 has been concluded on the basis of comparative structural analysis of 17 and 18 by 500 MHz 1H-NMR spectroscopy. The configurations of triol 18 are C-2′(S), C-4′(R), C-5(R), C-6(S), C-7(S) which are also the configurations of the corresponding chiral centers in the precursors 16 and 17. Note that the acid catalyzed isomerization of furanose in 17 to pyranose ring in 18 has been achieved with full retention of anomeric configuration. The configuration of C-3′ in compounds 14a. 14b, 22, and C-2′ in 26 has been elucidated by 1D differential nOe experiments by 1H-NMR spectroscopy at 500 MHz in D 2O solution at 293K. The estimation of the 3J HH coupling constants led us to calculate dihedral angles of 14a, 14b, 17, 18, 22 and 26 using the Karplus-Altona algorithm which have allowed us to define the conformational parameters of their constituent sugar moieties. Molecular mechanics calculations have been subsequently performed on the initial NMR structures of 17 and 18 to give their energy minimized conformations. The structures of 18 has been finally confirmed by estimating proton-proton distances derived from their nOe build-up rates by 2D NOESY experiments at 293K at different mixing times.

Synthesis of furo[2,3-c]pyran-β-d-nucleosides by radical-cyclization & their conformational analysis by 500 mhz 1h-nmr spectroscopy

Free-radical, generated from the 3′-phenylseleno nucleosides as the radical precursors 2 – 5, was efficiently trapped intramolecularly by an olefin or alkyne funtion anchored from the 5′-end by an ether function to give various [3.4.0]-cis-fused furo[2,3-c]pyrans 6 – 9 (16–34%) along with some reduced products (<10%). Similar intramolecular radical trapping reaction with 5′-O-α,β-ester-linked free radical precursor 10 – 12, under an identical reaction condition, gave [3.4.0]-cis-fused δ-lactones 13 – 15 in 10–53% yields without any trace of reduced products. The synthesis of [3.4.0]-cis-fused furo-pyrans 6 – 9 from 4-oxo-6-heptenyl radical formed from the precursor 2 – 5 and the transformations of 10 – 12 to δ-lactones 13 – 15, respectively, constitute first example of intramolecular 6-exo radical cyclization reaction involving the nucleophilic attack of endocyclic ring-radical to the electron-deficient exocyclic unsaturated chain. Smooth conversion of δ-lactones 14 and 15 to the ring-opened C-branched erythro derivatives 16 (95%) and 17 (94%), respectively, upon treatment with diluted aqueous ammonia have provided a new methodology for diastereospecific synthesis of 3′-C-branched nucleosides through free-radical cyclization and ring-opening sequence. The structures of furo[2′,3-c]pyrans 6 – 9 and δ-lactones 13 – 15 have been firmly established by detailed ID differential nOe experiments. Subsequently, we have also analyzed all 3J HH coupling constants at 500 MHz at 0°, 20° and 40 °C to estimate all endocyclic dihedral angles using the Karplus-Altona algorithm. Temperature-independent 3J HH clearly show that furo[2,3-c]pyrans 6 – 9 and δ-lactones 13 – 15 have rigid conformations. Construction of molecular models using the endocyclic torsions of the pentose unit and various dihedral angles of the pyran or δ-lactone unit shows that the pyran ring in [3.4.0]-cis-fused furo-pyrans 6 – 9 are in chair conformation and the pentofuranose ring is in North conformation (Figs. 1A & 1B), while the δ-lactone ring in [3.4.0]-cis-fused δ-lactones 13 – 15 are in boat conformation and the pentofuranose ring is locked in South conformation (Figs. 1C & 1D). The C *-alkyl substituents in the six-membered ring in both furo[2,3-c]pyrans 6 – 9 and in δ-lactones 13 – 15 are oriented however in an equatorial position. A comparison of interproton distances obtained from molecular models (Fig. 1A – D), based on 3J HH coupling constants, with those obtained from volumes and intensities of nOe and rOe crosspeaks in the NOESY and ROESY spectra supports the molecular models shown in Fig. 1.