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.     

Synthesis of acyclic bis-vinyl pyrimidines: a general route to d4T via metathesis

Unsaturated acyclic pyrimidine analogues, 1-{1-[1-(hydroxymethyl)prop-2-enyloxy]prop-2-enyl}uracil, 1-{1-[1-(hydroxymethyl)prop-2-enyloxy]prop-2-enyl}thymine and 1-{1-[1-(hydroxymethyl)prop-2-enyloxy]prop-2-enyl}cytosine having two asymmetric carbon atoms have been prepared in good yield starting from uridine and 5-methyluridine. The bis-vinyl thymine derivative underwent ring closure metathesis to give d4T, thus providing a novel synthesis of this compound.     

Synthesis of purine- and pyrimidine-substituted heptadienes. The stereochemistry of cyclization and cyclopolymerization products

A series of 1,6-heptadienes, substituted in the 4 position with nucleic acid bases 1-6, have been synthesized via Mitsunobu condensations. Guanine, adenine, thymine, and uracil derivatives can be prepared directly by coupling the protected base with 1,6-heptadien-4-ol (7). However, coupling protected cytosine and 7 gives an O-alkylated product. Thus, the cytosine derivative must be prepared from the uracil-substituted heptadienes via the triazole. The free-radical addition of CCl(4) and BrCCl(3) to these adducts was investigated. In all cases, both 1:1 and 1:2 adducts were obtained. The 1:1 adduct was identified as the cyclized product of the initially formed 5-hexen-1-yl radical. The cyclization takes place in a stereospecific manner, with only one of the four possible diastereomers resulting. NMR studies indicate that all substituents are cis in this product. In the case of the addition of CCl(4) to the uracil-substituted heptadiene, this conclusion was confirmed by an X-ray structure determination of the isolated cyclized product. The free-radical-initiated cyclocopolymerizations of 1-6 with SO(2) gave 1:1 copolymers with cis-linked five-membered rings. Two-dimensional NMR studies on poly(2-SO(2)) showed predominately the cis-syn isomer while poly(6-SO(2)) has an approximately equal amount of cis-syn and cis-anti isomers.     

Synthesis of [2-(vinyloxy)ethyl]uracil and [2-(allyloxy)ethyl]uracil

A synthesis is reported for N¹-mono- and N¹,N³-disubstituted uracil derivatives containing a terminal carbon-carbon double bond in the side-chain. Alkylation of vinyl 2-chloroethyl ether by uracil potassium salts leads to a mixture of 1-[2-(vinyloxy)ethyl] and 1,3-di[2-(vinyloxy)ethyl] derivatives while treatment of 2,4-bis(trimethylsilyloxy)pyrimidines by vinyl 2-chloroethyl ether leads exclusively to N¹-monosubstituted products. Alkylation of cytosine by this chloroether gave 1-[2-(vinyloxy)ethyl]cytosine. The synthesis of 1-[2-(allyloxy)ethyl]uracil derivatives was carried out by treatment of uracil potassium salts by 1-(allyloxy)-2-(p-toluenesulfonyloxy)ethane.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 3, pp. 393–397, March, 1993.     

Deamination of the Radical Cation of the Base Moiety of 2′‐Deoxycytidine: A Theoretical Study

Five pathways leading to the deamination of cytosine (to uracil) after formation of its deprotonated radical cation are investigated in the gas phase, at the UB3LYP/6‐311G(d,p) level of theory, and in bulk aqueous solvent. The most favorable pathway involves hydrogen‐atom transfer from a water molecule to the N3 nitrogen of the deprotonated radical cation, followed by addition of the resulting hydroxyl radical to the C4 carbon of the cytosine derivative. Following protonation of the amino group (N4), the C4? N4 bond is broken with elimination of the NH₃^?+ radical and formation of a protonated uracil. The rate‐determining step of this mechanism is hydrogen‐atom transfer from a water molecule to the cytosine derivative. The associated free energy barrier is 70.2 kJ mol^?1.     

Reaction of β-aminocrotonamide with dibasic acid derivatives

Reaction of β-aminocrotonamide ( 1 ) with succinic anhydride gave β-succinaminocrotonamide ( 3a ), which was treated with base to cyclize to 3,4-dihydro-6-methyl-4-oxo-2-pyrimidinepropanoic acid ( 4a ). Similarly, pyrimidinepentanoic acid derivative 4b was prepared from compound 1 and glutaric anhydride. Reaction of compound 1 with glutarate, adipate, and phthalate gave the corresponding pyrimidines 4b, 4c and 4d , while reaction of compound 1 with malonate gave 2-hydroxypyridine derivative 11 and dimethylpyrimidinone 4e . Reaction of dimethyl fumarate with compound 1 in the presence of methoxide gave a poor yield of pyrrolo[3,4-c]pyridine derivative 13 .     

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.     

Nucleotides. Part XLVIII. Synthesis of 2′-amino-2′-deoxyarabinonucleoside phosphoramidite building blocks

Chemical syntheses of 2′-amino-2′-deoxyarabinonucleosides of uracil, thymine, cytosine, adenine, and guanine and their conversion into suitably protected 3′-phosphoramidite building blocks 24–28 for oligonucleotide synthesis are described. The 2-(4-nitrophenyl)ethoxycarbonyl (npeoc) group was used for protection of the aglycon and the 2′-amino functions.     

Exploitation of sugar ring flipping for a hinge-type tether assisting a [2 + 2] cycloaddition

Methyl 3-O-p-methoxybenzyl-beta-D-xylopyranoside (2) was exploited as a novel hinge-type tether for the [2 + 2] cycloaddition of cinnamate. The major ring conformation occupied by the 2,4-dicinnamate derivative of 2 was 4C1, which extends two cinnamates along a diequatorial orientation. However, 3-O-deprotected dicinnamate 5, when in a non-polar solvent, favours the 1C4 conformation, which assists the approach of two cinnamates with the 1,3-diaxial scaffold. Photoirradiation of compound at 313 nm in CHCl3 afforded the intramolecular cycloaddition of cinnamates to give methyl beta-, delta-, and xi-truxinates in a 86 : 8 : 6 ratio after transesterification with methanol. The regio- and stereoselectivities are comparable to those reported by others for tethered cinnamates. The per-deuterated dicinnamate derivative of 5 facilitated the conformation analyses of the pyranoside rings by 1H NMR, indicating that all the products of photoirradiation had 1C4-fixed pyranosides. Excellent beta-selectivity was achieved when m-bromocinnamate was subjected to hinge-tethered [2 + 2] cycloaddition.     

1H,13C 2D NMR and X-ray studies of the products of the reaction between dibenzylidencyclohexanone and 6-amino-1,3-dimethyl uracil

The reaction of the 6-amino-1,3-dimethyl uracil with the dibenzylidencyclohexanone (1), provided three adducts whose structures result from nucleophilic attack yielding the monoadduct 3 and two isomeric bisadducts (4 and 5) in moderate yields (50-60%). The structures obtained in this study were elucidated with 2D high resolution NMR experiments, variable temperature NMR and X-ray crystallographic studies. In compound 3, the tricyclic skeleton is essentially planar and the cyclohexane ring addopts an envelope conformation. The structures 4 and 5 correspond to two isomeric spiro compounds.     

Studies on 2'-alpha-C-carboxyalkyl nucleosides and their application to a stereocontrolled nucleobase exchange process

The ability of 2'-alpha-C-carboxyalkyl nucleosides to undergo an unusual two-step stereocontrolled nucleobase exchange process has been investigated. Upon silylation a protected 2'-deoxy-2'-alpha-C-(carboxymethyl)uridine derivative can undergo intramolecular displacement of the uracil base, by the 2'-carboxylic acid group, to form a pentofuranosyl gamma-lactone. Under identical conditions the homologous 2'-deoxy-2'-alpha-C-(carboxyethyl)uridine derivative does not yield the corresponding delta-lactone, but undergoes elimination of uracil to give the corresponding glycal. The pentofuranosyl gamma-lactone is a good substrate for nucleoside synthesis by the Vorbrüggen procedures and undergoes completely stereoselective ring opening with either pyrimidine or purine silylated nucleobases to give novel 2'-C-carboxymethyl beta-nucleosides in moderate to high yield.     

Stereoselective synthesis of the 5'-hydroxy-5'-phosphonate derivatives of cytidine and cytosine arabinoside

Both the (R)- and (S)-5'-hydroxy 5'-phosphonate derivatives of cytidine and cytosine arabinoside (ara-C) have been prepared via phosphite addition or a Lewis acid mediated hydrophosphonylation of appropriately protected 5'-nucleoside aldehydes. Phosphite addition to a cytosine aldehyde protected as the 2',3'-acetonide gave predominately the 5'R isomer, while phosphite addition to the corresponding 2',3'-bis TBS derivative favored the 5'S stereochemistry. In contrast, phosphite addition to the 2',3'-bis TBS protected aldehyde derived from ara-C gave only the 5'R adduct. However, TiCl(4)-mediated hydrophosphonylation of the same ara-C aldehyde favored the 5'S stereoisomer by a 2:1 ratio. Once all four of the diastereomers were in hand, the stereochemistry of these compounds could be assigned based on their spectral data or that obtained from their O-methyl mandelate derivatives. After hydrolysis of the phosphonate esters and various protecting groups, the four alpha-hydroxy phosphonic acids were tested for their ability to serve as substrates for the enzyme nucleoside monophosphate kinase and for their toxicity to K562 cells.     

Carbocyclic analogs of cytosine nucleosides

The carbocyclic analogs of cytidine, 2′-deoxycytidine, and 3′-deoxycytidine were synthesized from the analogous uracil derivatives. The route consists of complete benzoylation of the uracil derivative, selective removal of a benzoyl group attached to the pyrimidine ring, conversion of the 4-oxo to a 4-chloro group with the dimethylformamide-thionyl chloride reagent, and replacement of the chloro group with an amino group in methanolic ammonia. When the total products of the deoxychlorination reaction were employed, the desired cytosine derivatives were frequently accompanied by small amounts of the corresponding N,N-dimethylcytosine derivatives, which could be removed by ion-exchange chromatography. Carbodine (VIa), the carbocyclic analog of cytidine, was obtained in 84% yield from the pure 4-chloropyrimidinone intermediate, after the latter was prepared by deoxychlorination in carbon tetrachloride. Carbodine has antileukemic, antiviral, and antibacterial activity.     

Synthesis of 1-(3′-deoxy-β-D-glycero-pentofuran-2′-ulosyl)uracil by selective elimination reactions

For the synthesis of y 1-(3′-deoxy-β-D-glycero-pentofuran-2′-ulosyl)uracil (16), the precursor, 5′-O-benzoyl derivative (2),² was elaborated in a variety of ways. 1-(5′-O-Benzoyl-3′-O-tosyl-β-D- lyxofuranosyl)uracil (4)² was benzoylated to N³-benzoyl-1-(2′,5′-di-O-benzoyl-3′-O-tosyl-β-D- lyxofuranosyl)uracil (5), which directly yielded 2 on treatment with sodium benzoate. 1-(3′,5′-Di-O- benzoyl-2′-O-tosyl-β-D-lyxofuranosyl)uracil (8) and its 3′,5′-O-isopropylidene analog (10) resisted elimination reactions, thus proving absolute selectivity in the elimination of the derivatives of 1-β-D- lyxofuranosyl-uracil. Seeking a more economical path to 2, 1-(5′-O-benzoyl-β-D-lyxofuranosyl)uracil (11) was first benzoylated to give 2′,5′-di-O-benzoate (12), accompanied by 3′,5′-di- and 2′,3′,5′-tri-O- benzoate. Mesylation of the major product (12) gave 1-(2′,5′-di-O-benzoyl-3′-O-mesyl-β-D- lyxofuranosyl)uracil (15), which, on treatment with sodium benzoate, gave 2 in an highly improved yield. Basic hydrolysis on 2 gave compound 16.     

Synthesis of 1-(5,6-dihydro-2H-thiopyran-2-yl)uracil by a Pummerer-type thioglycosylation reaction: the regioselectivity of allylic substitution

1-(5,6-Dihydro-2H-thiopyran-2-yl)uracil derivatives, a new 4′-thio-D4-nucleoside analogue, were synthesized by reacting 5,6-dihydro-2H-thiopyran sulfoxide and persilylated uracil in a Pummerer-type thioglycosylation reaction. The reaction of 5-alkyl substituted dihydrothiopyran sulfoxide 7 only gave 1-(dihydrothiopyran-2-yl)uracil 9. On the other hand, the reaction with a 5-siloxy substituted derivative of 7 resulted in a mixture of products with the uracil moiety at either the α- or the γ-position. The use of a prolonged reaction time resulted in the exclusive formation of the 4-substituted dihydrothiopyran derivative 10. The result suggests that an equilibrium is operative in the formation of the α- and γ-adducts and that the latter should be more thermodynamically stable than the former. This conclusion was also supported by theoretical calculations.     

Cyclisation of 4-[2-Cyclofentenyl]-3-Hydroxy [1] Benzopypan-2-One

4-[2-cyclopentenyl]-3-hydroxy [1] bonzopyran-2-one(3) was cyclised to the bicyclie coumar in-1,3-ethano-2-bromo-1,2-dihydro-3H-pyrano [2,3-c] [1] benzopyran-5-one (6) by a sequence of reactions viz. acetylation of 3, addition of bromine to cyclopenteny double bond and treating the resulting acetyldibromo compound (5) with 4% alcoholic KOH, Cyclisation of compound (3) with mercuric acetate in methanol gave condensed furan derivative 7 which on reductive demercuration with zinc borohydride in dimethoxyethane gave the 1,3-propano-1,2-dihydrofuro [2,3-c] [1] benzopyran-4-one, 8. Cyclisation of compound 2 with come. H₂SO₄ furnished a mixture of bicyclic derivative 9 ad furo coumarin derivative 8.     

Synthesis and EPR Studies of 2′‐Deoxyuridines with Alkynyl,Rodlike Linkages

Sonogashira coupling of diacetyl 5‐ethynyl‐2′‐deoxyuridine with diacetyl 5‐iodo‐2′‐deoxyuridine gave the acylated ethynediyl‐linked 2′‐deoxyuridine dimer ( 3 b ; 63 %), which was deprotected with ammonia/methanol to give ethynediyl‐linked 2′‐deoxyuridines ( 3 a ; 79 %). Treatment of 5‐ethynyl‐2′‐deoxyuridine ( 1 a ) with 5‐iodo‐2′‐deoxyuridine gave the furopyrimidine linked to 2′‐deoxyuridine (78 %). Catalytic oxidative coupling of 1 a (O₂, CuI, Pd/C, N,N‐dimethylformamide) gave butadiynediyl‐linked 2′‐deoxyuridines ( 4 ; 84 %). Double Sonogashira coupling of 5‐iodo‐2′‐deoxyuridine with 1,4‐diethynylbenzene gave 1,4‐phenylenediethynediyl‐bridged 2′‐deoxyuridines ( 5 ; 83 %). Cu‐catalyzed cycloisomerization of dimers 4 and 5 gave their furopyrimidine derivatives. One‐electron addition to 1 a , 3 a , and 4 gave the anion radical, the EPR spectra of which showed that the unpaired electron is largely localized at C6 of one uracil ring (17 G doublet) at 77 K. The EPR spectra of the one‐electron‐oxidized derivatives of ethynediyl‐ and butadiynediyl‐linked uridines 3 a and 4 at 77 K showed that the unpaired electron is delocalized over both rings. Therefore, structures 3 a and 4 provide an efficient electronic link for hole conduction between the uracil rings. However, for the excess electron, an activation barrier prevents coupling to both rings. These dimeric structures could provide a gate that would separate hole transfer from electron transport between strands in DNA systems. In the crystal structure of acylated dimer 3 b , the bases were found in the anti position relative to each other across the ethynyl link, and similar anti conformation was preserved in the derived furopyrimidine–deoxyuridine dinucleoside.     

Design and synthesis of a novel ring-expanded 4′-thio-apio-nucleoside derivatives

The synthesis of a ring-expanded 4′-thio-apio-nucleoside derivative 4, designed to serve as a potential anti-HIV agent, is described. The epoxy alcohol derivative 10, prepared from 2-butene-1,4-diol, was converted to an allylsulfide derivative 13 in 3 steps. Ring-closing-metathesis of 13 gave the dihydrothiopyran derivative 20, which was further converted into sulphoxide 24. A Pummerer-type thioglycosylation reaction of 24 with a persilylated uracil derivative, followed by conversion to a cytosine derivative and deprotection, gave a racemic mixture of the ring-expanded 4′-thio-apio-nucleoside derivative 4 in good yield.     

Syntheses of substituted 1-methyl-2-(1,3,4-thiadiazol-2-yl)-4-nitropyrroles and 1-methyl-2-(1,3,4-oxadiazol-2-yl)-4-nitropyrroles

Starting from readily available ethyl-4-nitropyrrole-2-carboxylate ( 1 ), substituted 1-methyl-2-(1,3,4-thiadiazol-2-yl)-4-nitropyrroles and 1-methyl-2-(1,3,4-oxadiazol-2-yl)-4-nitropyrroles were prepared. The reaction of 1 with diazomethane gave ethyl 1-methyl-4-nitropyrrole-2-carboxylate ( 2 ). Reaction of compound 2 with hydrazine hydrate afforded the corresponding hydrazide 3 . The reaction of 3 with formic acid yielded 1-(1-methyl-4-nitropyrrole-2-carboxyl)-2-(formyl)hydrazine ( 7 ). Refluxing of the latter with phosphorus pentasulfide in xylene yielded compound 6 in 40% yield. Reaction of compound 7 with phosphorus pentoxide afforded compound 9 . Reaction of compound 3 with 1,1′-carboxyldiimidazole in the presence of triethylamine yielded 2-(1-methyl-4-nitro-2-pyrrolyl)-1,3,4-oxadiazoline-4(H)-5-one ( 11 ). Refluxing compound 3 with cyanogen bromide in methanol gave compound 12 . Compound 13 could be obtained through the reaction of compound 3 with carbon disulfide in basic medium. Alkylation of compound 13 afforded the correspanding alkylthio derivative 14 . Reaction of 1-methyl-4-nitropyrrole-2-carboxylic acid ( 15 ) with thiosemicarbazide and phosphorus oxychloride gave 2-amino-5-(1-methyl-4-nitro-2-pyrrolyl)-1,3,4-thiadiazole ( 16 ). Sandmeyer reaction of compound 16 yielded 2-chloro-5-(1-methyl-4-nitro-2-pyrrolyl)-1,3,4-thiadiazole ( 17 ). Refluxing of the latter with thiourea afforded 2-(1-methyl-4-nitro-2-pyrrolyl)-1,3,4-thiadiazoline-4(H)-5-thione ( 18 ). Alkylation of compound 18 gave the corresponding alkylthio derivative 19 . Oxidation of the latter with hydrogen peroxide in acetic acid yielded 2-(1-methyl-4-nitro-2-pyrrolyl)-5-methylsulfonyl-1,3,4-thiadiazole ( 20 ).     

Reaction of 1-methyluracil with phenylbenzhydrazonoyl chloride

The ambident anion of 1-methyluracil gives with phenylbenzyhydrazonoyl chloride, depending on the conditions, the N-acylation product (polar solvent, room temperature), or the O-acylation product (nonpolar solvent, heating), which rearranges to a cytosine derivative. Convenient methods have been developed for the preparation of 6-methyl-1,3-diphenyl-5,6-dihydro-5-oxopyrimido[4,3-c]triazolium chloride, a fluorescent derivative of 1-methyluracil, from the N-acylation product, and for the rapid base cleavage of the uracil ring under very mild conditions.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 5, pp. 649–655, May, 1986.