Synthesis of novel 4′-C-methyl-1′,3′-dioxolane pyrimidine nucleosides and evaluation of its anti-HIV-1 activity

The key glycosyl donor for the target molecule 12 was prepared by two-step sequences; (1) acetalization of tert-butyldimethylsilyloxyacetaldehyde with 3-bromopropanediol, (2) DBN-initiated β-elimination of the resulting 2-(tert-butyldimethylsilyloxy)methyl-4-bromomethyl-1,3-dioxolane 11. Electrophilic glycosidation between 12 and silylated pyrimidine nucleobase proceeded efficiently to provide a mixture of β- and α-anomers of the respective glycosides 14 and 15. Tin radical-mediated reduction of the bromomethyl functional group of 14 and 15 gave protected 4′-C-methyl-dioxorane uracil- 16 and thymine nucleoside 17. The respective cytosine nucleoside 18 was synthesized from 16. De-silylation of 4′-methyl-1′,3′-dioxolane pyrimidine nucleosides 16–18 gave the target molecules. Evaluation of the anti-HIV-1 activity of the β- and α-anomers of the novel 4′-C-methyl-1′,3′-dioxolane nucleosides 22β,α–24β,α revealed that none of the nucleoside derivatives possess anti-viral activity against HIV-1 and show cytotoxicity against MT-4 cells at 100 μM.     

Syntheses of nucleosides with 2′-spirolactam and 2′-spiropyrrolidine moieties as potential inhibitors of hepatitis C virus NS5B polymerase

To discover novel nucleosides as potential antiviral agents, 2′-spirolactam and 2′-spiropyrrolidine-containing nucleoside analogs were envisioned. Efficient synthetic routes were developed with an epoxide opening as the key step to establish the quaternary center at the 2′ position, leading to the design and synthesis of uridine analogs 8 and 21, prodrugs 13–16, and cytidine analog 11.     

An efficient synthesis of 4,4′,5,5′-tetraiododibenzo-24-crown-8 and its highly conjugated derivatives

4,4′,5,5′-Tetraiododibenzo-24-crown-8 (9), a practical building block, was prepared under efficient and mild reaction conditions starting from the simple starting material, catechol (1). Highly conjugated 4,4′,5,5′-tetraethynyldibenzo-24-crown-8 (10a,b) were prepared via a Sonogashira coupling reaction from tetraiodocrown ether 9. These highly conjugated crown ethers form complexes in CD₂Cl₂ with dibenzylammonium hexafluorophosphate in a 1:1 ratio. Emission spectrum of pseudorotaxane 11 shows a dramatic shift from the non-complexed precursor.     

Synthesis of 2′,3′-dideoxy-6′,6′-difluoro-3′-azanucleosides

The straightforward synthesis of four novel 2′,3′-dideoxy-6′,6′-difluoro-3′-azanucleosides 1a-d is described. Efficient construction of the fluorine-containing pyrrolidine ring through two different ways and installation of pyrimidine rings using the amino groups in the intermediates 12, 26 were the key steps of our synthesis.     

Synthesis of a series of novel 2′,3′-dideoxy-6′,6′-difluoro-3′-thionucleosides

A series of novel 2′,3′-dideoxy-6′,6′-difluoro-3′-thionucleosides 1a-d, analogues of 3TC that has high biological activities against HIV and HBV, have been synthesized from the gem-difluorohomoallyl amine 7 in a straightforward fashion. Our synthesis featured the construction of thiofuranose skeleton through ring closure of key intermediates and installation of pyrimidine ring with amino group in compounds 13a,b.     

Synthesis of (±)-9-[c-4, t-5-bis(hydroxymethyl)cyclopent-2-en-r-1-yl]-9H-adenine (BCA) derivatives branched at the 4′-position based on intramolecular SH2′ cyclization

Synthesis of 4′-branched BCA analogues (5) was carried out. Stereospecific construction of the cis-disposed 4′-carbon-substituents and 5′-hydroxymethyl group was secured by employing the bicyclo[3.3.0]lactone 16 as a key intermediate, which was prepared by radical-mediated intramolecular S_H2′ cyclization of the phenylselenomethyl ester 15. After manipulation of the double bond of 16, bis(Boc)adenine was introduced based on the Mitsunobu reaction of the allyl alcohol 24. Transformation of the lactone function of 27 allowed preparation of the 4′-hydroxymethyl (31), the 4′-vinyl (32), the 4′-cyano (34), and the 4′-ethynyl (35) derivatives. Anti-HIV and anti-HCV activities of the free nucleosides 36-38 were also examined.     

Syntheses of 4′-spirocyclic phosphono-nucleosides as potential inhibitors of hepatitis C virus NS5B polymerase

To discover novel nucleosides as potential antiviral agents, 4′-spirocyclic phosphono-nucleosides were designed to mimic the monophosphate of R-1479, a known nucleoside inhibitor of HCV NS5B. Bypassing the first kinase step to nucleoside monophosphate is viewed as advantageous since this phosphorylation is often observed as the rate-limiting transformation to the active NTP for many nucleosides. Efficient synthetic routes were developed with a triphenylphosphine–iodine cyclization reaction as the key step to form the tetrahydrofuran 4′-spirocycle. The desired 4′-spirocyclic phosphono-cytidine analogs 12a, 12b, and 16 were prepared in 11 steps.     

A short and novel synthesis of carbocyclic nucleosides and 4′-epi-carbocyclic nucleosides from 2-cyclopenten-1-ones

Carbocyclic nucleoside analogues remain interesting target molecules having the potential to combine biological activity with greater metabolic stability than their sugar counterparts. This paper describes a rapid and versatile synthetic approach to such compounds based on commercial cyclopentenones (e.g., 1) that has been developed in our laboratory. Carbocyclic nucleosides like 2′-methyl-aristeromycin 6 were synthesized in racemic form in 5 steps via key intermediate 4. The procedure was also adapted to the preparation of 4′-epi-carbocyclic nucleosides using epoxide 17 instead of 4 and employing the same methodology.     

Syntheses of nucleosides with a 1′,2′-β-lactam moiety as potential inhibitors of hepatitis C virus NS5B polymerase

To discover novel nucleosides as potential anti-HCV agents, nucleosides with a 1′,2′-β-lactam moiety were designed as a hybrid scaffold of MK-608 and GS-6620. Synthetic strategies were successfully developed to prepare two series of C-nucleosides with a 1′,2′-β-lactam moiety: a 7-deaza-purine C-nucleoside analog 11 was prepared in 10 steps with an overall yield of 3.7%; a purine C-nucleoside analog 22 was prepared in 9 steps with an overall yield of 9.7%.     

3′-Selective modification of a 4′,5′-didehydro-5′-deoxy-2′,3′-epoxyuridine using nucleophiles

1-(2,3-Anhydro-5-deoxy-4,5-didehydro-α-l-erythro-pent-4-enofuranosyl)uracil 4 was obtained by the treatment of 5′-iodo-2′,3′-epoxyuridine 5 with LiHMDS in excellent yield. The pyrimidine nucleoside 4 possesses quite unique vinyl epoxide moiety within the molecules. The reactions of 4 with a variety of nucleophiles gave 3′-substituted pyrimidine nucleosides without the formation of the corresponding 2′-substituted isomers. In the case of NaN₃ or PhSH, the corresponding 5′-adduct was obtained as a minor product together with the expected 3′-adduct.     

Synthesis and crystal structure of 2′-deoxy-2′-fluoro-4′-thioribonucleosides: substrates for the synthesis of novel modified RNAs

We report herein the synthesis of appropriately protected 2′-deoxy-2′-fluoro-4′-thiouridine (5), -thiocytidine (7), and -thioadenosine (35) derivatives, substrates for the synthesis of novel modified RNAs. The synthesis of 5 and 7 was achieved via the reaction of 2,2′-O-anhydro-4′-thiouridine (3) with HF/pyridine in a manner similar to that of its 4′-O-congener whereas the synthesis of 35 from 4′-thioadenosine derivatives was unsuccessful. Accordingly, 35 was synthesized via the glycosylation of the fluorinated 4-thiosugar 25 with 6-chloropurine. The X-ray crystal structural analysis revealed that 2′-deoxy-2′-fluoro-4′-thiocytidine (8) adopted predominately the same C3′-endo conformation as 2′-deoxy-2′-fluorocytidine.     

Application and details of photoinduced oxidative cyclization of 5-(4′,9′-methanocycloundeca-2′,4′,6′,8′,10′-pentaenylidene)pyrimidine-2,4,6(1,3,5H)-triones and related compounds

As novel methodology for synthesizing the furan ring, a photoinduced oxidative cyclization of 5-(4′,9′-methanocycloundeca-2′,4′,6′,8′,10′-pentaenylidene)pyrimidine-2,4,6(1,3,5H)-triones (7a-c) and related compounds 9a-c was accomplished to give 5,10-methanocycloundeca[4,5]furo[2,3-d]pyrimidine-2,4(1,3H)-dionylium tetrafluoroborates (8a-c⁺·BF₄⁻) and related compounds 2a-c⁺·BF₄⁻, respectively. In the photoinduced oxidative cyclization, the molecular oxygen in air is used as oxidant and the reaction proceeds under mild conditions to give desired products without byproducts, and thus, it is interesting from the viewpoint of the green chemistry. On the reactions of the mono-substituted derivatives 7d,e and 9e,f, the selectivity of the photoinduced cyclizations were reversed as compared with those of the DDQ-promoted oxidative cyclizations. By the NMR monitoring of the reactions of 7a and deuterated compound 7a-D₂ under degassed conditions, the details of the reaction pathway were clarified and rationalized on the basis of the MO calculation by the 6-31G^∗ basis set of the MP2 levels as well.     

Synthesis of 3′-azido-4′-ethynyl-3′,5′-dideoxy-5′-norarabinouridine: a new anti-HIV nucleoside analogue

3′-Azido-4′-ethynyl-3′,5′dideoxy-5′-norarabinouridine 10 was synthesized from commercial uridine 1 in which the key step is the opening of protected 2′,3′-epoxyuridine derivative 7 by sodium azide and the hydroxymethyl at 4-position of the ribose ring are replaced by ethynyl group.     

A new synthetic procedure to spiro[cyclohexane-1,3′-indoline]-2′,4-diones

A new synthetic pathway to spiro[cyclohexane-1,3′-indoline]-2′,4-diones was found starting from 3-chloromethylene-2-indolones 1 and Danishefsky's diene 2. Their synthesis consists of several steps involving the formation of the cycloadducts, the 6-chloro-4-trimethylsilyloxy-2-methoxyspiro[cyclohex-3-en-1,3′-indolin]-2′-one derivatives, transformed into spiro[cyclohexa-2,5-dien-1,3′-indoline]-2′,4-diones via 6-chloro-spiro[cyclohex-2-en-1,3′-indoline]-2′,4-dione intermediates. The reduction of spiro[cyclohexa-2,5-dien-1,3′-indoline]-2′,4-diones gave spiro[cyclohexane-1,3′-indoline]-2′,4-diones 7. Using a ‘one pot reaction’, starting from 1 and 2, compounds 7 were obtained in satisfactory overall yield.     

SnCl4-mediated oxidative biaryl coupling reaction of 1-naphthol and subsequent ring closure of 2,2′-binaphthol to the dinaphthofuran framework

A simple method for the direct synthesis of 2,2′-binaphthols 2 and dinaphtho[1,2-b;2′,1′-d]furans 3 under mild conditions was developed, utilizing a biaryl coupling reaction via electron donor-acceptor complexes of 1-naphthols with SnCl₄. Heating of the complex in a sealed tube for (18-24 h) afforded the corresponding o-o coupled product 2 in excellent yield. Prolonged reaction (56-65 h) under the same conditions afforded 3 in high yield in one step. We also found that in the case of α-naphthol without substituents other than a hydroxyl group at the C-1 position, regioselective o-o coupling reaction proceeded. The products 2a, 2b and 2g should be useful as synthetic intermediates for naturally occurring 3,3′-bijuglone, 3,3′-biplumbagin and elliptinone.     

Synthesis of 1′-fluorouracil nucleosides as potential antimetabolites

The first synthesis of 1′-fluoronucleosides, which has long been synthetic targets as the potential antimetabolites, was achieved. Electrophilic fluorination of the 1′-position occurred to form an anomeric mixture of 1′-fluorouridine derivatives, when the lithium enolate, prepared from 3′,5′-O-tetraisopropyldisiloxane-1,3-diyl (TIPDS)-protected 2′-ketouridine (10) and LiHMDS, was treated with an electrophilic fluorinating agent such as NFSI (13). Subsequent reduction of the 2′-keto-moiety of the resulting β-nucleoside gave the protected 1′-fluorouridine 16 and its arabino-type congener 17. Alternatively, nucleophilic fluorination was also successful. Thus, treatment of 2′,3′,5′-tri-O-acetyl-1′-phenylselenouridine (20) with DAST/NBS produced the 1′-fluorouridine triacetate (21) and its α-anomer 22.     

The novel transition metal free synthesis of 1,1′-biazulene

Reaction of 1-azulenyl methyl sulfoxide (1) under acidic conditions gave the 1,1′-biazulene derivative 3. Methylmercapt groups of 3 were readily converted to formyl groups by Vilsmeier reaction to afford 3,3′-diformyl-1,1′-biazulene (4), which reacted with pyrrole in the presence of acetic acid to give the parent 1,1′-biazulene (5). Reaction of 5 with pyridine in the presence of Tf₂O gave 3,3′-dihydropyridyl-1,1′-biazulene derivative 6. 3,3′-(4-Pyridyl)-1,1′-biazulene (7) was obtained by the reaction of 3 with KOH in EtOH at room temperature in good yield.     

Synthesis of unnatural 3′-phospha-2′-deoxyfuranose nucleoside analogues

This Letter describes the synthesis of racemic analogues of unnatural 2′-deoxy nucleoside with a phosphorus atom replacing the carbon atom in the 3′-position. A seven-step sequence was developed in racemic series to afford unnatural 3′-phospha-2′-deoxyfuranose nucleosides. The phospha nucleoside analogues were tested against HCV, but did not show any antiviral activity at a 10 μM maximum concentration used for the inhibition assays of analogues 2-T, 2-C and 4-Tα.     

A simple and stereodivergent strategy for the synthesis of 3′-C-branched 2′,3′-dideoxynucleosides exploiting (Z)-but-2-en-1,4-diol and (R)-2,3-cyclohexylideneglyceraldehyde

Barbier type additions of allylic bromide 4, derived from (Z)-but-2-en-1,4-diol 2 to (R)-2,3-cyclohexylideneglyceraldehyde 1 were performed through mediation with Zn employing Luche’s procedure and also with low valent Cu, Co, and Fe which were produced via bimetal redox strategy in THF to afford 5c,d as the major products. From these, 5a,b were prepared following an oxidation-reduction protocol. Compound 5c was exploited as a representative starting material to develop a simple and inexpensive strategy toward the synthesis of 3′-C-branched 2′,3′-dideoxynucleosides having stereodiversity at 3′- and 4′-positions.     

Studies on bis(1′-ortho-carboranyl)benzenes and bis(1′-ortho-carboranyl)biphenyls

Reactions between the C,C′-dicopper(I) derivative of ortho-carborane and ortho-, meta- and para-diiodobenzene are reported. The reaction with 1,2-C₆H₄I₂ unexpectedly afforded 2,2′-bis(1′-ortho-carboranyl)biphenyl, [HCB₁₀H₁₀CC₆H₄]₂2, whereas reactions with 1,3- or 1,4-C₆H₄I₂ provided alternative routes to 1,3-bis(1′-ortho-carboranyl)benzene 3 and 1,4-bis(1′-ortho-carboranyl)benzene 4, respectively. The crystal structure of the biphenyl derivative 2 revealed significant distortions in the biphenylene framework attributable to the proximity of the two bulky carborane cages. UV absorption spectra and electrochemical data on 2 and 3 showed little electronic communication between the two carborane cages in either, and negligible π-conjugation between the two ortho-phenylene rings in 2. However, substantial evidence was found of electronic communication between the carborane cages via the para-phenylene bridge in 4. B3LYP/6-31G^∗ computations have been carried out on compounds 2 and 4, on 4,4′-bis(ortho-carboranyl)biphenyl 6 and on 1,2-bis(1′-ortho-carboranyl)benzene 7. Those on 2, 4 and 6 show the computed geometries to be in very good agreement with the experimental geometries: those on 7 allowed the reported molecular geometry of this compound to be revised and revealed a long cage C–C bond of 1.725(3) Å.