Sugar-modified nucleosides in past 10 years, a review

From the chemistry of epoxy-sugar nucleosides to the discovery of anti-HIV agent 4'-ethynylstavudine-Festinavir

Branched sugar nucleosides have attracted much attention due to their biological activities. We have demonstrated that epoxysugar nucleosides serve as versatile precursor for the stereo-defined synthesis of these nucleoside derivatives on the basis of its ring opening with organoaluminum or organosilicon reagents. In this review article, novel methods for the synthesis of nucleoside analogues branched at the 1' and 4'-position will be described. During this study, we could discover an anti-HIV agent, 4'-ethynylstavudine (Festinavir). Festinavir showed more potent anti-HIV activity than the parent compound stavudine (d4T). Other significant properties of Festinavir are as follows: 1) much less toxic to various cells and also to mitochondorial DNA synthesis than d4T, 2) better substrate for human thymidine kinase than d4T, 3) resistant not only to chemical glycosidic bond cleavage but also to catabolism by thymidine phosphorylase, 4) the activity improves in the presence of a major mutation, K103N, associated with resistance to non-nucleoside reverse transcriptase inhibitors. Detailed profile of the antiviral activities, biology and pharmacology of Festinavir are also described.

Synthesis of novel aza-analogues of tiazofurin with 2-[5,5-bis(hydroxymethyl)pyrrolidin-2-yl] framework as sugar mimic

The novel aza-analogues of tiazofurin (TZF) with 2-[5,5-bis(hydroxymethyl)pyrrolidin-2-yl] moiety, as sugar mimic, were synthesized from O,O-cyclohexylidene derivative of 4,4-bis(hydroxymethyl)-4-nitrobutanal in multi-gram scale. The synthetic route consisted of three stages: (i) the synthesis of corresponding derivative of 5,5-bis(hydroxymethyl)pyrrolidine-2-carbonitrile, (ii) the construction of ethyl thiazole-2-carboxylate part by the conversion of the pyrrolidine-2-carbonitrile into the N-trifluoroacetyl derivative followed by cyclocondensation with L-cysteine ethyl ester and then by dehydrogenation, and (iii) the final transformation of the ethyl thiazole-4-carboxylate into the aza-analogues of TZF. The TZF aza-analogues were evaluated for their antiviral activities in cell-culture-based assays.

Practical biocatalytic desymmetrization of meso-N-heterocyclic dicarboxamides and their application in the construction of aza-sugar containing nucleoside analogs

Amidase-catalyzed desymmetrization of meso-N-heterocyclic dicarboxamides under very mild conditions provided a highly efficient and practical method for the preparation of enantiomerically pure carbamoyl-substituted heterocyclic amino acids that were unique and versatile platforms for the construction of both antipodes of aza-sugar containing nucleoside analogs.

Ethyl 4-acetamido-3-acetoxy-2-benzyl-3-methylbutanoate

The crystal structure of the title compound, C₁₈H₂₅NO₅, is stabilized by inter­molecular N—H⋯O hydrogen bonds, which form inversion dimers. The ethyl group is disordered over two positions in a 0.651 (12):0.349 (12) ratio.

Selection of a new whole cell biocatalyst for the synthesis of 2-deoxyribose 5-phosphate

2-deoxyribose 5-phosphate (DR5P) is a key intermediate in the biocatalyzed preparation of deoxyribonucleosides. Therefore, DR5P production by means of simpler, cleaner, and economic pathways becomes highly interesting. One strategy involves the use of bacterial whole cells containing DR5P aldolase as biocatalyst for the aldol addition between acetaldehyde and D: -glyceraldehyde 3-phosphate or glycolytic intermediates that in situ generate the acceptor substrate. In this work, diverse microorganisms capable of synthesizing DR5P were selected by screening several bacteria genera. In particular, Erwinia carotovora ATCC 33260 was identified as a new biocatalyst that afforded 14.1-mM DR5P starting from a cheap raw material like glucose.

Synthesis and antiviral evaluation of the 2′-C-methyl branched derivative of a nucleoside analog inhibitor of RNA viral infections, T-1106

An example of a 2′-C-methyl branched nucleoside analogue bearing 3,4-dihydro-3-oxopyrazine-2-carboxamide as the base, namely 4-(2-C-methyl-β-D-ribofuranosyl)-3-oxo-3,4-dihydropyrazine-2-carboxamide, is reported. This compound was synthesized following a Vorbrüggen’s glycosylation procedure in a few steps. When evaluated in cell culture experiments against a broad range of viruses, this compound did not exhibit any significant antiviral effect or cytotoxicity.

Synthesis of 4'-Ethynyl-2'-deoxy-4'-thioribonucleosides and Discovery of a Highly Potent and Less Toxic NRTI

The synthesis of 4'-ethynyl-2'-deoxy-4'-thioribonucleosides was carried out utilizing an electrophilic glycosidation in which 4-ethynyl-4-thiofuranoid glycal 16 served as a glycosyl donor. Electrophilic glycosidation between 16 and the silylated nucleobases (N⁴-acetylcytosine, N⁶-benzoyladenine and N²-acetyl-O⁶-diphenylcarbamoylguanine) was carried out in the presence of N-iodosuccinimide (NIS) leading to the exclusive formation of the desired β-anomers 29, 33 and 36. Anti-HIV studies demonstrated that these 4'-thio nucleosides were less cytotoxic to T-lymphocyte (i.e. MT-4 cells) than the corresponding 4'-ethynyl derivatives of 2'-deoxycytidine (44), 2'-deoxyadenosine (45) and 2'-deoxyguanosine (46). Comparison of the selectivity indices (SI) was made between 4'-thionucleosides (32, 41 and 43) and the corresponding 4'-oxygen analogues 44-46 by using the reported CC₅₀ and EC₅₀ values. In the case of cytosine and adenine nucleosides, comparable SI values were obtained: 32 (545) and 45 (458); 41 (>230) and 45 (1,630). In contrast, 4'-ethynyl-2'-deoxy-4'-thioguanosine 43 was found to possess a SI value of >18,200, which is twenty times better than that of 46 (933).

Synthesis of a Novel Benzoyl Adenosine Analog Containing a 1, 4-Dioxane Sugar Analog and the Synthesis of a Corresponding Uracil Adenine Dinucleotide

Adenosine analogs in which the sugar unit was replaced by a 1,4-dioxane sugar equivalent, were prepared by coupling the 1,4-dioxane sugar analog as its anomeric acetates, with N6-benzoyl protected adenine. The 1,4-dioxane system was obtained in an enantioselective synthesis from (R,R)-dimethyl tartrate. Using standard phosphorimidite methodology, the adenine analog was further reacted with a 1,4-dioxane uridine analog to give the corresponding, protected dinucleotide, set-up for further condensation into larger oligonucleotides.

Palladium-Catalyzed Aryl Amination Reactions of 6-Bromo- and 6-Chloropurine Nucleosides

Palladium‐catalyzed C—N bond forming reactions of 6‐bromo‐ as well as 6‐chloropurine ribonucleosides and the 2′‐deoxy analogues with arylamines are described. Efficient conversions were observed with palladium(II) acetate/Xantphos/cesium carbonate, in toluene at 100 °C. Reactions of the bromonucleoside derivatives could be conducted at a lowered catalytic loading [5 mol% Pd(OAc)₂/7.5 mol% Xantphos], whereas good product yields were obtained with a higher catalyst load [10 mol% Pd(OAc)₂/15 mol% Xantphos] when the chloro analogue was employed. Among the examples evaluated, silyl protection for the hydroxy groups appears better as compared to acetyl. The methodology has been evaluated via reactions with a variety of arylamines and by synthesis of biologically relevant deoxyadenosine and adenosine dimers. This is the first detailed analysis of aryl amination reactions of 6‐chloropurine nucleosides, and comparison of the two halogenated nucleoside substrates.

D-Arabinose-based synthesis of homo-C-d4T and homo-C-thymidine

2,3,5-Tri-O-benzyl-D-arabinofuranosyl halides (chloride, bromide) were reacted with AllMgBr, MeMgBr, and VinMgBr to furnish anomeric mixtures of the C-glycosyl products. The factors that influenced the beta/alpha ratio are discussed. The alpha,beta-C-vinyl derivative was transformed into 1-deoxy-1-C-hydroxymethyl-beta- and -alpha-D-arabinofuranoses (2,5-anhydro-D-glucitol and -mannitol, respectively), separable after isopropylidenation step. 2,5-Anhydro-1,3-O-isopropylidene-D-glucitol was converted into 2,5-anhydro-6-O-triphenylmethyl-D-erythro-hex-3,4-enitol and 2,5-anhydro-4,6-di-O-benzoyl-3-deoxy-D-ribo-hexitol, which were coupled with N-3-benzoylthymine under the Mitsunobu conditions to furnish two analogs of nucleosides with a -CH(2)- insert between sugar moieties and thymine.

Complete assignment of the (1)H and (13)C NMR spectra of cis and trans isonucleoside derivatives of purine with a tetrahydropyran ring

(1)H and (13)C NMR chemical shifts of cis and trans isonucleoside analogues of purine in which the furanose moiety is substituted by a tetrahydropyran ring were completely assigned using one- and two-dimensional NMR experiments that include NOE, DEPT, COSY and HSQC. The significant (1)H and (13)C NMR signals differentiating between the cis and trans stereoisomers were compared.

Lactobacillus reuteri 2'-deoxyribosyltransferase, a novel biocatalyst for tailoring of nucleosides

A novel type II nucleoside 2'-deoxyribosyltransferase from Lactobacillus reuteri (LrNDT) has been cloned and overexpressed in Escherichia coli. The recombinant LrNDT has been structural and functionally characterized. Sedimentation equilibrium analysis revealed a homohexameric molecule of 114 kDa. Circular dichroism studies have showed a secondary structure containing 55% alpha-helix, 10% beta-strand, 16% beta-sheet, and 19% random coil. LrNDT was thermostable with a melting temperature (T(m)) of 64 degrees C determined by fluorescence, circular dichroism, and differential scanning calorimetric studies. The enzyme showed high activity in a broad pH range (4.6 to 7.9) and was also very stable between pH 4 and 7.9. The optimal temperature for activity was 40 degrees C. The recombinant LrNDT was able to synthesize natural and nonnatural nucleoside analogues, improving activities described in the literature, and remarkably, exhibited unexpected new arabinosyltransferase activity, which had not been described so far in this kind of enzyme. Furthermore, synthesis of new arabinonucleosides and 2'-fluorodeoxyribonucleosides was carried out.

Synthesis of a novel, optically active uridine analog containing a 1,4-dioxane sugar moiety. Synthesis of the corresponding dinucleotide

A new optically active uridine nucleoside analogue in which a substituted 1,4-dioxane ring functioned as the sugar analogue was prepared from L-tartaric acid. The nucleoside analogue was further converted into the corresponding protected dinucleotide.

Enantioselective synthesis of homo-N-nucleosides containing a 1,4-dioxane sugar analog

A dioxane homo-sugar analog, (2S,5S)-and (2R,5S)-5-[(4S)-2,2-dimethyl-1,3-dioxolan-4-yl]-2-iodomethyl-1,4-dioxane was prepared from (2R,3R)-dimethyl tartrate, and further elaborated into the corresponding homo-N-nucleoside analogs by its reactions with uracil and adenine, respectively.

Synthesis of N-methyl-d-ribopyranuronamide nucleosides

The synthesis of N-methyl-d-ribopyranuronamide nucleosides is described. The key route is the rearrangement of a 1,2-O-isopropylidene protected furanose sugar with a carboxamide function in the 4-position to a ribopyranuronamide ring. The Lewis acid catalyzed condensation of adenine and thymine nucleobases with the per-O-acetylated N-methyl-d-ribopyranuronamide sugar is used to give the target nucleosides as a mixture of the α and β anomers. The mixture was separated and the final compounds were obtained by deacetylation in basic conditions.

Low-temperature synthesis of 2'-deoxyadenosine using immobilized psychrotrophic microorganisms

Selective biocatalyzed synthesis of 2'-deoxyadenosine from 2'-deoxypyrimidine nucleosides was carried out using free or immobilized whole cells. The reaction was performed at 57 degrees C without secondary reactions. Two psychrotrophic microorganisms, Bacillus psychrosaccharolyticus and Psychrobacter immobilis, are described for the first time as active and specific strains for the synthesis of 2'-deoxyadenosine. Adenosine deaminase activity was not detected. Whole cells were immobilized in different matrixes. Calcium alginate and calcium pectate gave the best biocatalysts. The synthesis of 2'-deoxyadenosine follows an apparent first order kinetic expression. External mass transfer control was negligible as deduced from k(s), N(A), and Omega values. Internal mass transfer was the rate controlling step according to eta(T) and phi values.