Synthesis of 3'-deoxynucleosides with 2-oxabicyclo[3.1.0]hexane sugar moieties: addition of difluorocarbene to a 3',4'-unsaturated uridine derivative and 1,2-dihydrofurans derived from D- and L-xylose1

Syntheses of 3'-deoxy analogues of adenosine, cytidine, and uridine with a 2,2-difluorocyclopropane ring fused at C3'-C4' are described. Treatment of a 2',5'-protected-3',4'-unsaturated derivative of uridine with difluorocarbene [generated from (CF3)2Hg and NaI] gave a diastereomeric mixture of the 3',4'-difluoromethylene compounds (alpha-L-arabino/beta-D-ribo, approximately 5:4). The limited stereoselectivity for addition at the beta face results from competitive steric hindrance by an allylic 4-methoxybenzyloxy group at C2' on the alpha face and a homoallylic nucleobase at C1' on the beta face. Protected uracil derivatives were converted into their cytosine counterparts via 4-(1,2,4-triazol-1-yl) intermediates. Treatment of 1,2-dihydrofurans derived from D- and L-xylose with difluorocarbene resulted in stereospecific addition at the beta face (anti to the 1,2-O-isopropylidene group on the alpha face). Glycosylations with activated enantiomeric sugar derivatives with the fused difluorocyclopropane ring on the beta face gave protected adenine nucleosides, whereas attempted glycosylation with an alpha-fused derivative gave multiple products. Removal of base- and sugar-protecting groups gave new difluoromethylene-bridged nucleoside analogues.     

Addition of difluorocarbene to 3',4'-unsaturated nucleosides: synthesis of 2'-deoxy analogues with a 2-oxabicyclo[3.1.0]hexane framework

Treatment of protected 2'-deoxy-3',4'-unsaturated nucleosides derived from adenosine and uridine with difluorocarbene [generated from bis(trifluoromethyl)mercury and sodium iodide] gave fused-ring 2,2-difluorocyclopropane compounds. Stereoselective alpha-face addition to the dihydrofuran ring resulted from hindrance by the protected beta-anomeric nucleobases. A protected uracil compound was converted smoothly into the cytosine derivative via a 4-(1,2,4-triazol-1-yl) intermediate. Removal of the protecting groups gave new difluorocyclopropane-fused nucleoside analogues. The solid-state conformation of the nearly planar furanosyl ring in the uracil compound had a shallow 2E pucker, and a more pronounced 1E conformation was present in the furanosyl ring of the cytosine derivative.     

Chemical alteration of nucleic acids and their components—XIII: Reaction of nucleosides with diacyl peroxides

Diacyl peroxides reacted at room tempt with cytidine and adenosine. The former gave 4-acyl and 3-oxido derivatives and the latter gave 6-acyl and 1-oxido derivatives. At 90°, diacetyl peroxide reacted with guanosine, adenosine, cytidine, and uridine by a homolytic process to give their C-methylated derivatives. The latter reaction was accelerated by the presence of a ferrous ion.     

Phenylsulfanylation of 3',4'-unsaturated adenosine employing thiophenol-N-iodosuccinimide leads to 4'-phenylsulfanylcordycepin: synthesis of 4'-substituted cordycepins on the basis of substitution of the phenylsulfanyl leaving group

Upon reaction of the 3',4'-unsaturated adenosine derivative 2 with N-iodosuccinimide (NIS) and thiophenol, an unexpected electrophilic hydrophenylsulfanylation proceeded to provide 4'-phenylsulfanylcordycepin 7 in 79% yield with the ratio 7a/7b = 6.6/1. A study of the reaction mechanism revealed that hydrogen iodide (HI) generated from NIS and PhSH acted as an active species. On the basis of a deuterium experiment using PhSD, initial protonation occurred at the β face of the double bond to furnish the β-π complex III, which underwent anti addition of PhSH as a major pathway. Nucleophilic substitution of N(6)-pivaloylated 9 with various alcohols in the presence of N-bromosuccinimide (NBS) gave the respective 4'-α-alkoxycordycepins 15a-21a as the major stereoisomers. Use of DAST in place of an alcohol gave the 4'-α-fluoro analogue 23a stereoselectively. Radical-mediated carbon-carbon bond construction was also applicable to 7, giving 4'-α-allylcordycepin (24a) and 4'-α-cyanoethylcordycepin (25) derivatives.     

Nucleoside 5''-phosphordiamidates

A one-flask method is reported for the preparation of the 5'-phosphordiamidate of adenosine (3a), cytidine (3b), guanosine (3c), uridine (3d) and thymidine (3e), and also for that of adenosine 5'-(N,N'-dimethyl) phosphordiamidate (4a), adenosine 5'-(N,N,N',N'-tetramethyl) phosphordiamidate (5a) and adenosine 5'-phosphor-dimorpholidate (6a). The method is based on the aminolysis of nucleoside 5'-phosphordichloridates performed in situ by NH₄OH, or aqueous amine solutions, respectively.     

Nucleophilic addition of benzenethiol to 1',2'-unsaturated nucleosides: 1'-C-phenylthio-2'-deoxynucleosides as anomeric radical precursors

The addition reaction of benzenethiol to the glycal portion of 1',2'-unsaturated uridine proceeds efficiently in the presence of Et(3)N. The mechanism involves nucleophilic attack of thiolate at the anomeric position in the rate-determining step, wherein conjugation between the nucleobase and the glycal portion is crucial. The derivative having a methyl group either at the 2'- or 6-position did not undergo this addition reaction, due to their sterically prohibited coplanarity. The 1',2'-unsaturated derivatives of thymine and adenine can also be used as substrates for this addition reaction. It was also shown that the resulting 1'-C-phenylthio-2'-deoxynucleosides serve as precursors for radical-mediated C-C bond formation at the anomeric position.     

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.     

Ring opening of nucleoside 1',2'-epoxides with organoaluminum reagents: stereoselective entry to ribonucleosides branched at the anomeric position

Epoxidation of 3',5'-O-(di-tert-butylsilylene)-1',2'-unsaturated uridine (11) with dimethyldioxirane proceeded from the alpha-face to give the 1',2'-alpha-epoxide 12. Upon reacting with organoaluminum reagents, the 1',2'-alpha-epoxide 12 underwent preferential syn-opening of the epoxide ring to yield the beta-anomers of 1'-methyl- (13beta), 1'-ethyl- (14beta), 1'-isobutyl- (15beta), 1'-ethynyl- (16beta), 1'-vinyl- (17beta), and 1'-phenyl- (18beta) uridine derivatives, although the corresponding alpha-anomers were also formed except for the reaction with triphenylaluminum. It was found, however, that protection of the N(3)-position of 11 either with a benzyloxymethyl or benzoyl group led to the exclusive formation of the desired beta-anomers. A possible explanation for the observed stereochemical outcome is presented. A similar strategy was found to be applicable to the synthesis of 1'-branched adenosine analogues, which include protected angustmycin C (37).     

Bismethylene triphosphate nucleotides of uridine 4-phosphate analogues: a new class of anionic pyrimidine nucleotide analogues

Cytidine-5'-triphosphate synthase (CTPS) catalyzes the formation of cytidine triphosphate (CTP) from glutamine, uridine 5'-triphosphate (UTP), and adenosine 5'-triphosphate (ATP). This reaction proceeds via formation of the high-energy intermediate UTP-4-phosphate (UTP-4-P). Stable analogues of UTP-4-P may be potent inhibitors of CTPS and useful as lead structures for the development of anticancer and antiviral agents. Several bismethylene triphosphate (BMT) nucleotides of uridine 4-phosphate (U-4-P) analogues have been prepared. A key step was the selective methanolysis, with the aid of a tin catalyst, of the 5' ester moiety of 2',3',5'-tri-O-acetyl or tri-O-benzoyl U-4-P analogues. We believe this represents the first general approach to the selective cleavage of 5' benzoyl esters in benzoylated nucleosides. Mitsunobu coupling of these 5'-deprotected U-4-P analogues to an unsymmetrical, protected BMT bearing a free phosphonic acid moiety at one of the terminal positions gave fully protected BMT-U-4-P analogues. Global deprotection of these species was achieved using TMSBr followed by treatment with NH4OH-MeOH or NH4OH-pyridine. The resulting BMT nucleotides represent a new class of anionic pyrimidine nucleotide analogues.     

Synthesis of 2-(N-Acetylamino)-2-deoxy-C-glucopyranosyl nucleosides as potential inhibitors of chitin synthases

The C-glucopyranosyl nucleosides (1-4) containing the N-acetyl glucosaminyl and uridine units have been synthesized as nonhydrolyzable substrate analogues of UDP-GlcNAc aimed to inhibit the chitin synthases. The key intermediate, 4-(2'-(N-acetylamino)-3', 4',6'-tri-O-benzyl-2'-deoxy-alpha-D-glucopyranosyl)but-2-enoic acid (5), was prepared from the perbenzylated (N-acetylamino)-alpha-C-allylglucoside (7), by successive oxidative cleavage, Wittig olefination, and ester deprotection. The coupling of the acid 5 with the hydroxyl or amine function of the uridine derivatives (6a or 6b) afforded, respectively, the ester 12 and amide 14. The dihydroxylation of the conjugated double bond in ester 12 or amide 14 was better achieved with osmium tetraoxide/barium chlorate, leading to the expected diols 13 and 15 as a mixture of two diastereoisomers. The desired compounds 1-4 were obtained after catalytic hydrogenation of compounds 12-15.     

Mononucleotide gas-phase proton affinities as determined by the kinetic method

The goal of this work is to determine the proton affinities of (deoxy)nucleoside 5'- and 3'-monophosphates (mononucleotides) using the kinetic method with fast atom bombardment mass spectrometry. The proton affinities of the (deoxy)nucleoside 5'- and 3'-monophosphates yielded the following trend: (deoxy)adenosine monophosphates > (deoxy)guanosine monophosphates > (deoxy)cytidine monophosphates > deoxythymidine/uridine monophosphates. In all cases the proton affinity decreases or remains the same with the addition of the phosphate group from those values reported for nucleosides. The proton affinity is dependent on the location of the phosphate backbone (5'-vs. 3'-phosphates): the 3'-monophosphates have lower proton affinities than the 5'-monophosphates except for the thymidine/uridine monophosphates where the trend is reversed. Molecular modeling was utilized to determine if multiple protonation sites and intramolecular hydrogen bond formation would influence the proton affinity measurements. Semiempirical calculations of the proton affinities at various locations on each mononucleotide were performed and compared to the experimental results. The possible influence of intramolecular hydrogen bonding between the nucleobases and the phosphate group on the measured and calculated proton affinities is discussed.     

Intrinsic electrophilic properties of nucleosides: photoelectron spectroscopy of their parent anions

The nucleoside parent anions 2(')-deoxythymidine(-), 2(')-deoxycytidine(-), 2(')-deoxyadenosine(-), uridine(-), cytidine(-), adenosine(-), and guanosine(-) were generated in a novel source, employing a combination of infrared desorption, electron photoemission, and a gas jet expansion. Once mass selected, the anion photoelectron spectrum of each of these was recorded. In the three cases in which comparisons were possible, the vertical detachment energies and likely adiabatic electron affinities extracted from these spectra agreed well with the values calculated both by Richardson et al. [J. Am. Chem. Soc. 126, 4404 (2004)] and by Li et al. [Radiat. Res. 165, 721 (2006)]. Through the combination of our experimental results and their theoretical calculations, several implications emerge. (1) With the possible exception of dG(-), the parent anions of nucleosides exist, and they are stable. (2) These nucleoside anions are valence anions, and in most cases the negative charge is closely associated with the nucleobase moiety. (3) The nucleoside parent anions we have generated and studied are the negative ions of canonical, neutral nucleosides, similar to those found in DNA.     

N-oxides of adenosine-type nucleosides undergo pyrimidine ring opening and closure to give 5-amino-4-(1,2,4-oxadiazol-3-yl)imidazole derivatives

Treatment of acylated adenosine N-oxides with carboxylic anhydrides and thiophenol resulted in pyrimidine ring opening followed by exocyclic ring closure. Ammonolysis gave 5-amino-4-(5-substituted-1,2,4-oxadiazol-3-yl)-1-(beta-d-ribofuranosyl)imidazole derivatives, whereas iodine in methanol selectively unmasked the 5-amino group. Related flexible nucleoside analogues can be prepared from adenine-type precursors.     

Enantiomeric syntheses of conformationally restricted D- and L-2', 3'-dideoxy-2',3'-endo-methylene nucleosides from carbohydrate chiral templates

D- and L-2',3'-dideoxy-2',3'-endo-methylene nucleosides were synthesized as potential antiviral agents. The key intermediates 5-O-tert-butyldiphenylsilyl-D- and L-2,3-dideoxy-2, 3-endo-methylenepentofuranoses (20 and 33, respectively) were obtained by selective protection of the D- and L-2,3-dideoxy-2, 3-endo-methylenepentose derivatives 19 and 32 which were prepared from 1,2:5,6-di-O-isopropylidene-D-mannitol and L-gulonic gamma-lactone, respectively, and converted to 5-O-tert-butyldiphenylsilyl-D- and L-2,3-dideoxy-2, 3-endo-methylenepentofuranosyl acetates (21 and 34, respectively) or the chlorides 22 and 35. The acetates and chlorides were condensed with pyrimidine and purine bases by Vorbrüggen conditions or S(N)2-type condensation. Vorbrüggen conditions using the acetates gave mostly alpha-isomers. In contrast, S(N)2-type condensation using the chlorides greatly improved the beta/alpha ratio. From the synthesis, several D- and L-2',3'-dideoxy-2',3'-endo-methylene nucleoside analogues have been obtained, and their structures have been elucidated by NMR spectroscopy and X-ray crystallography. The synthesized D- and L-adenine derivatives were tested as substrates of adenosine deaminase, which indicated that the D-adenosine derivative 4a was a good substrate of a mammalian adenosine deaminase from calf intestinal mucosa (EC 3.5.4.4) while its L-enantiomer 10a was a poor substrate. Either the D-adenine derivative 4a or its L-enantiomer 10a did not serve as an inhibitor of the enzyme.     

Stereoselective synthesis of 1'-C-branched arabinofuranosyl nucleosides via anomeric radicals generated by 1,2-acyloxy migration

Stereoselective C-C bond formation at the anomeric position of uracil and adenine nucleoside has been accomplished through reaction of the anomeric radical, generated by 1,2-acyloxy migration, with a radical acceptor. The present method consists of the following steps: (1) electrophilic addition (bromo-pivaloyloxylation) to 3',5'-O-(1,1,3,3-tetraisopropyldisiloxane-1,3-diyl)-protected 1',2'-unsaturated nucleoside, (2) tin radical-mediated reaction of the resulting adduct with a radical acceptor. The use of allyl(tributyl)tin gave the 1'-C-allylated uracil nucleoside 14 in 66% yield together with the unrearranged 2'-C-allylated product 15 (6%). Radical acceptors such as styryl(tributyl)tin and 3-bromo-2-methylacrylonitrile can also be used in the reaction of 5, giving 16 (70%) and 17 (76%) without the formation of unrearranged product. The radical-mediated C-C bond formation of the adenine counterpart 12 was also investigated.     

Reactions of trimethylsilyl fluorosulfonyldifluoroacetate with purine and pyrimidine nucleosides

Difluorocarbene, generated from trimethylsilyl fluorosulfonyldifluoroacetate (TFDA), reacts with the uridine and adenosine substrates preferentially at the enolizable amide moiety of the uracil ring and the 6-amino group of the purine ring. 2′,3′-Di-O-benzoyl-3′-deoxy-3′-methyleneuridine reacts with TFDA to produce 4-O-difluoromethyl product derived from an insertion of difluorocarbene into the 4-hydroxyl group of the enolizable uracil ring. Reaction of the difluorocarbene with the adenosine substrates having the unprotected 6-amino group in the purine ring produced the 6-N-difluoromethyl derivative, while reaction with 6-N-benzoyl protected adenosine analogues gave the difluoromethyl ether product derived from the insertion of difluorocarbene into the enol form of the 6-benzamido group. Treatment of the 6-N-phthaloyl protected adenosine analogues with TFDA resulted in the unexpected one-pot conversion of the imidazole ring of the purine into the corresponding N-difluoromethylthiourea derivatives. Treatment of the suitably protected pyrimidine and purine nucleosides bearing an exomethylene group at carbons 2′, 3′ or 4′ of the sugar rings with TFDA afforded the corresponding spirodifluorocyclopropyl analogues but in low yields.     

Synthesis and conformational analysis of new cyclobutane-fused nucleosides

[structure: see text]. A stereselective synthesis of 3-oxabicyclo[3.2.0]heptane nucleoside analogues, which were designed as conformational mimics of the anti-HIV agents 2',3'-didehydro-2',3'-dideoxythimidine (stavudine, d4T) and 2',3'-didehydro-2',3'-dideoxyadenosine (d4A), is described. The target compounds were prepared by condensation of a common intermediate bicyclic acetate, derived from a homochiral 2(5H)-furanone, with pyrimidine and purine bases under modified Vorbrüggen conditions. The conformational behavior of the synthesized nucleoside analogues was studied by NMR spectroscopy and X-ray crystallography.     

Synthesis of 2'-C-alpha-(hydroxyalkyl) and 2'-C-alpha-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.     

Nucleosides and nucleotides. 186. Synthesis and biological activities of pyrimidine carbocyclic nucleosides with a hydroxyamino group instead of a hydroxymethyl group at the 4'-position of the sugar moiety.

Pyrimidine carbocyclic nucleosides with a hydroxyamino group instead of a hydroxymethyl group at the 4'-position of the sugar moiety were designed as potential antitumor and/or antiviral agents. Pd (O)-catalyzed reactions of enantiomerically pure (+)-(1R,4S)-4-[(tert-butyldiphenylsilyl)oxy]-1-(ethoxycarbonylo xy)-2- cyclopentene (9) with N3-benzoylthymine and -uracil gave carbocyclic nucleosides 10 and 11. Subsequent Pd (O)-catalyzed reactions of N3-benzoyl-1-[(1R,4S)-4-(ethoxycarbonyloxy)-2-cyclopenten-1- yl]thymine (14) and -uracil (15) with O-benzylhydroxylamine smoothly gave the hydroxyamino-substituted carbocyclic nucleosides 16 and 17. From these nucleosides, the target compounds were prepared after deprotection or further reactions. The 2',3'-didehydro-2',3'-dideoxythymidine (D4T) analogue 20 was the most effective compound, with IC50 values of 27.3 and 34.5 microM against KB and L1210 cells in vitro. Carbocyclic analogues of uridine and cytidine (29 and 32) were less effective than 20 against both cell lines.     

TiO2纳米颗粒对钌(II)三联吡啶配合物光损伤小牛胸腺DNA能力的影响

由于极短的激发态寿命, 钌(II)三联吡啶配合物对脱氧核糖核酸(DNA)的光损伤能力低下. 设计合成了三个钌(II)三联吡啶配合物[Ru(ttp)(tpy)]^2＋ (1), [Ru(ttp-COOH)(tpy)]^2＋ (2)和[Ru(ttp-COOH)(tpy-pyr)]^2＋ (3), 其中tpy为2,2':6',2"-三联吡啶, ttp为4′-(4-甲苯基)-2,2':6',2"-三联吡啶, ttp-COOH为4′-(4-羧基苯基)-2,2':6',2"-三联吡啶, tpy-pyr为4'-(1-芘基)-2,2':6',2"-三联吡啶. 比较了TiO₂纳米颗粒对它们光损伤小牛胸腺DNA的影响. 发现TiO₂纳米颗粒在空气和氩气条件下均可显著提高配合物3光损伤DNA的能力. TiO₂纳米颗粒和配合物3间的光诱导电子转移作用及其该作用生成的钌(III)物种可能是促进配合物3对DNA光损伤的主要原因.