The role of bisulfite in the debromination of 5-bromouracil. The debromination of 5-bromo-5,6-dihydrouracil-6-sulfonate

5-Bromouracil is dehalogenated in the presence of bisulfite buffers to yield uracil which subsequently adds bisulfite to form 5,6-dihydrouracil-6-sulfonate. Presumably, 5-bromo-5,6-dihydrouracil-6-sulfonate is an intermediate in uracil formation. Kinetic data indicate that the disappearance of 5-bromouracil in the presence of bisulfite buffers is second order with respect to total bisulfite concentration, thus indicating the participation of 2 moles of either sulfite or bisulfite in the overall reaction, Iodometric titrations of total bisulfite combined with spectral analysis of the various pyrimidine and dihydropyrimidine species present indicate that, in addition to the total bisulfite required to form 5,6-dihydrouracil-6-sulfonate, an additional mole of sulfite is consumed per mole of 5-bromouracil dehalogenated. These data combined with the finding that sulfate is generated during dehalogenation are indicative of a pathway for the dehalogenation of the intermediate 5-bromo-5,6-dihydro-uracil-6-sulfonate which involves the attack of sulfite either directly or via an intervening molecule of water to yield uracil. Subsequent reactions of halogen-containing intermediates yield sulfate and bromide as final products of the reaction.     

The dehalogenation of the 5-halo-5,6-dihydrouracils: Uracil formation from 5-iodo- and 5-bromo-5,6-dihydrouracil

The elimination of halide ion from either 5-bromo- or 5-iodo-5,6-dihydrouracil to yield uracil is a slow reaction which, in the case of 5-iodo-5,6-dihydrouracil, is 400 times slower than the enzymatic release of ¹²⁵I^? from 5-[¹²⁵I]iodouracil. The elimination of HBr from 5-bromo-5,6-dihydrouracil is subject to general base catalysis by tris(hydroxymethyl)aminomethane (k₂^{Tris base} = 11 × 10^?4M^?1 min^?1, 37°C, ionic strength 1.0 M). At pH values near and above physiological, both the bromo- and iododihydropyrimidines are subject to hydrolysis of the dihydropyrimidine ring, a reaction which parallels halide elimination to yield uracil. The resulting 2-halo-3-ureidopropionate then cyclizes via intramolecular attack of the ureido oxygen atom to yield halide ion and 2-amino-2-oxazoline-5-carboxylic acid as final products. In dilute hydroxide ion, the kinetics of 5-bromo-5,6-dihydrouracil hydrolysis (25°C, ionic strength 1.0 M) show a change in rate-determining step as a function of increasing hydroxide ion concentration, a result which, as in the case of 5,6-dihydrouracil, can be explained in terms of the formation of a tetrahedral addition intermediate. The data are discussed relative to enzymatically catalyzed halopyrimidine dehalogenation.     

The effect of bisulfite on the dehalogenation of 5-chloro-, 5-bromo-, and 5-iodouracil

The 5-chloro-, bromo-, and iodo-analogs of uracil are dehalogenated in the presence of sodium bisulfite to yield 5,6 dihydrouracil-6-sulfonate as the final product. Under similar conditions, 5-fluorouracil adds bisulfite to yield 5-fluoro-5,6 dihydrouracil-6-sulfonate but is not dehalogenated. Ultraviolet absorption spectra of 5-bromouracil and 5-iodouracil reacting under pseudo first-order conditions with bisulfite indicate that dehalogenation proceeds via a pathway which has 5-halo-5,6-dihydrouracil-6-sulfonate and uracil as intermediates. In the case of 5-chlorouracil, the rate of bisulfite attack on the 6-position of the chlorouracil ring system is very slow relative to the rate of bisulfite addition to uracil. Hence, although dechlorination does occur, ultraviolet absorption spectra of reaction mixtures containing bisulfite and 5-chlorouracil do not reveal the uracil absorption peak observed with both 5-iodouracil and 5-bromouracil. Fluorine and proton nmr spectra indicate that bisulfite addition to 5-fluorouracil is stereoselective as is the case of bisulfite addition to uracil.     

Synthesis of 5-Arylthiouridines via Electrophilic Substitution of 5-Bromouridines with Diaryl Disulfides

Abstract

Novel synthetic method of 5-arylthiouridine derivatives is described. Treatment of 5-bromo-2′,3′-O-isopropylideneuridine (1a) with diaryl disulfides in the presence of sodium hydride at ambient temperature gave the 5-arylthiouridines (2) in moderate yields. The present method is devised by virtue of a combination of efficient participation of the 5′-hydroxy group onto the uracil ring and the electrophilic nature of diaryl disulfide, which was applied to the synthesis of 5-arylthio-1-β-D-arabinofuranosyl-uracils (8).     

Thymidylate synthetase. Catalysis of dehalogenation of 5-bromo- and 5-iodo-2'-deoxyuridylate.

Tymidylate synthetase catalyzes the facile dehalogenation of 5-bromo-2'-deoxyuridylate (BrdUMP) and 5-iodo-2'-deoxyuridylate )IdUMP) to give 2'-deoxyuridylate (dUMP), the natural substrate of the enzyme. The reaction does not require folate cofactors and stoichiometrically consumes 2 equiv of thiol. In addition to dUMP, a minor product is formed during the debromination of BrdUMP which has been identified as a 5-alkylthio derivative formed by displacement of bromide ion by thiolate. The reaction has been found to proceed with a substantial alpha-secondary inverse tritium isotope effect (kT/kH = 1.212--1.258) with [2-14C,6-3H]-BrdUMP as the substrate. Similarly, an inverse tritiumisotope effect of 1.18 was observed in the nonenzymatic chemical counterpart of this reaction, the cysteine-promoted dehalogenation of [2-14C,6-3H]-5-bromo-2'-deoxyuridine. Previous evidence for the mechanism of action of this enzyme has rested largely on chemical model studies and on information obtained from its stoichiometric interaction with the inhibitor 5-fluoro-2'-deoxyuridylate. The magnitude of the secondary isotope effect during the enzymatic dehalogenation described here provides direct proof for nucleophilic catalysis and formation of 5,6-dihydroprimidine intermediates in a reaction catalyzed by thymidylate synthetase.     

The dehalogenation of halouracils by hydroxylamine buffers.

At room temperature, hydroxylamine dehalogenates 5-Br-and 5-I-uracil. 5-Cl-uracil reacts to a much less extent. Reaction with 5-F-uracil yields the 6-hydroxyamino-adduct as a product. Kinetics monitored spectrally indicate that dehalogenation involves the formation of a 5-halo-6-hydroxyamino-5, 6-dihydrouracil intermediate which then slowly dehalogenates. 5-Bromo-6-methoxy-5,6-dihydrothymine, a model for the above intermediate, also dehalogenates yielding thymine as a product.Hydroxylamine (NH₂OH), a mutagenic agent (1,2) reacts with pyrimidine rings promoting such reactions as the formation of 5,6-dihydro-N⁴-hydroxy-6-hydroxyaminocytosine from cytosine (3,4) and both urea and isoxazoles from uracil derivatives (2,5,6). It is believed to be unreactive toward 5-substituted uracil derivatives (2,5,6) but has been reported to cause the dehalogenation of 5-bromouracil derivatives yielding Br^? and uracil as products (2,7,8). The object of this report is to demonstrate the generality of NH₂OH addition to the 5-halouracils with the subsequent dehalogenation of both 5-Br-and 5-I-uracil; reactions which appear to proceed via pathways similar to bisulfite buffer mediated halouracil dehalogenation (9–13). A preliminary report of this work has appeared (14).     

Efficient Synthesis of 2′-Bromo-2′-Deoxy-3′,5′-O-TPDS-pyrimidine Nucleosides by Boron Trifluoride Catalyzed Reaction of O2,2′-Anhydro-(1-β-D-Arabinofuran0Syl)pyrimidine Nucleosides with Lithium Bromide

Abstract

Efficient syntheses of 2′-bromo-2′-deoxy-3′,5′-O-TPDS-uridine (5a) and 1-(2-bromo-3,5-O-TPDS-β-D-ribofuranosyl)thymine (5b) from uridine and 1-(β-D-ribofuranosyl)thymine are described, respectively. The key step is a treatment of 3′,5′-O-TPDS-O²,2′-anhydro-1-(β-D-ardbinofuranosyl)uracil (4a) and -thymine (4b) with LiBr in the presence of BF₃-OEt₂ in 1,4-dioxane at 60°C to give 5a and 5b in 98%, and 96% yield, respectively.

     

Thymidylate synthetase catalyzed dehalogenation of 5-bromo-and 5-iodo-2′-deoxyuridylate

Thymidylate synthetase catalyzes a facile dehalogenation of 5-bromo-and 5-iodo-2′-deoxyuridylate in the presence of dithiothreitol. The chloro and fluoro nucleotides are not dehalogenated under similar conditions. A mechanism for this reaction is proposed which is in complete accord with previously ascertained features of the catalytic mechanism as well as model chemical reactions. This reaction is likely an important pathway in the biological dehalogenation of 5-halogenated uracil derivatives.     

The dehalogenation of iodouracil by cysteine. Intramolecular general-acid catalysis of cysteine addition to 5-iodouracil

The rate-determining step of the cysteine-catalyzed deiodination of 5-iodouracil is the formation of 5-iodo-6-cysteinyl-5,6-dihydrouracil. The rate of the reaction depends upon the concentration of un-ionized 5-iodouracil and the following ionic species of cysteine; ^?OOC(NH₃⁺)CHCH₂S^?. Unlike the reaction of 2-mercapto-ethanol with 5-iodouracil, the cysteine reaction is not subject to catalysis by imidazolium ion and tris(hydroxymethyl)aminomethane hydrochloride. When the rates of cysteine reacting with 5-iodouracil are measured in both H₂O and D₂O, a large kinetic isotope effect is observed ($\text{k}{}_2{}^{\mathrm{<mtext>H</mtext><mtext>20</mtext>}}\text{k}{}_2{}^{\mathrm{<mtext>D</mtext><mtext>20</mtext>}}\text{= 4.10}$), thus implicating the protonated α amino group of cysteine as an intramolecular general acid catalyst for the reaction. These results and possible mechanisms for the actual dehalogenation of the intermediate 5-iodo-6-cysteinyl-5,6-dihydrouracil are discussed in terms of a possible mechanism for enzymatic halopyrimidine dehalogenation.     

Synthesis,In Vitro Biological Stability,and Anti-HIV Activity of 5-Halo (or Methoxy)-6-Alkoxy (Azido or Hydroxy)-5,6-Dihydro-2′,3′-Didehydro-3′-Deoxythymidine Diastereomers as Potential Prodrugs of 2′,3′-Didehydro-3′-deoxythymidine (D4T)

Abstract

A new class of 5-halo (or methoxy)-6-alkoxy (azido or hydroxy)-5,6-dihydro-2′,3′-didehydro-3′-deoxythymidines (4–17) were investigated as potential anti-AIDS drugs. These 5,6-dihydro derivatives, which are also potential prodmgs of 2′,3′-didehydro-3′-deoxythymidine (D4T) were designed to have properties which would enhance their duration of action, lipophilicity and cephalic delivery to the central nervous system. The 5,6-dihydro derivatives of D4T (4–15), which differ in configuration at the C-5 and C-6 positions, were synthesized by the regiospecific addition of XR (X = Br, Cl, I; R = OMe, OEt, N₃, OH) to the 5,6-olefinic bond of D4T. These 5,6-disubstituted-5,6-dihydro analogs of D4T are more lipophilic (P = 0.70 – 4.0 range) than D4T (P = 0.12) and are stable to E. coli thymidine phosphorylase. Regeneration of the 5,6-olefinic bond to give D4T, upon incubation of the 5-bromo- and 5-iodo-6-methoxy-5,6-dihydro derivatives (6, 7, 10, 11) with glutathione or a mouse liver soluble enzyme fraction, was extensive (50–95%). The most potent anti-HIV-1 agents, 5-iodo-6-methoxy (10, 11), 5-bromo-6-azido (14, 15) and 5-methoxy-6-hydroxy (16, 17) derivatives of D4T, exhibited anti-HIV activities comparable to D4T.

     

The dehalogenation of halocytosines by bisulfite buffers

Both 5-bromo- and 5-iodocytosine are rapidly dehalogenated in dilute bisulfite buffers to yield cytosine. With 5-bromocytosine, but not with 5-iodocytosine, extrapolation of semilogarithmic plots of extent reaction versus time indicates the bisulfite buffer concentration-dependent formation of an intermediate which subsequently reacts to control the rate of 5-bromocytosine dehalogenation. The disappearance of both halocytosines has a second-order dependence on bisulfite buffer concentration. Both imidazole and acetate buffers catalyze the reaction of 5-iodocytosine, but not that of 5-bromocytosine, with bisulfite. In the case of acetate buffer catalysis of the reaction of 5-iodocytosine with bisulfite, the dependence of the observed rate constants changes from first order to zero order as a function of increasing buffer concentration. The observed rate constants for 5-bromocytosine dehalogenation increase, reach a maximum at about 4.5, and then decrease as a function of pH. Iodometric titration of sulfite utilization coupled with spectrophotometric analysis of pyrimidine reactants and products indicates that 1 mole of sulfite is consumed per mole of halocytosine dehalogenated. The spectrophotometrically determined pK_a values for the conjugate acids of 5-bromo- and 5-iodocytosine at 25°C and ionic strength 1.0 M are 3.25 and 3.56, respectively. These results are discussed in terms of a multistep reaction pathway which is analogous to the bisulfite-catalyzed dehalogenation of the 5-halouracils.     

Synthesis of 5-Formyluridines

Abstract

5-Formyl-2′,3′-O-isopropylideneuridine and 5-formyl-2′,3′,5′-tri-O-acetyluridine were prepared by a new procedure involving palladium-catalyzed coupling of 5-iodouridine with styrene, followed by reaction with acetic anhydride or acetone and ozonolysis of the resulting 5-styryluridine derivatives.     

Nucleosides and Nucleotides. 104. Radical and Palladium-Catalyzed Deoxygenation of the Allylic Alcohol Systems in the Sugar Moiety of Pyrimidine Nucleosides§,1

Abstract

New methods for the synthesis of 2′,3′-didehydro-2′,3′-dideoxy-2′ (and 3′)-methyl-5-methyluridines and 2′,3′-dideoxy-2′ (and 3′)-methylidene pyrimidine nucleosides have been developed from the corresponding 2′ (and 3′)-deoxy-2′ (and 3′)-methylidene pyrimidine nucleosides. Treatment of a 3′-deoxy-3′-methylidene-5-methyluridine derivative 8 with 1,1′-thiocarbonyldiimidazole gave the allylic rearranged 2′,3′-didehydro-2′,3′-dideoxy-3′-[(imidazol-1-yl)carbonylthiomethyl] derivative 24. On the other hand, reaction of 8 with methyloxalyl chloride afforded 2′-O-methyloxalyl ester 25. Radical deoxygenation of both 24 and 25 gave 26 exclusively. Palladium-catalyzed reduction of 2′,5′-di-O-acetyl-3′-deoxy-3′-methylidene-5-methyluridine (32) with triethylammonium formate as a hydride donor regioselectively afforded the 2′,3′-dideoxy-3′-methylidene derivative 35 and 2′,3′-didehydro-2′,3′-dideoxy-3′-methyl derivative 34 in a ratio of 95:5 in 78% yield. These reactions were used on the corresponding 2′-deoxy-2′-methylidene derivatives. An alternative synthesis of 2′,3′-dideoxy-2′-methylidene pyrimidine nucleosides (43, 52, and 54) was achieved from the corresponding 1-(3-deoxy-β-D-thero-pentofuranosyl)pyrimidines (44 and 45). The cytotoxicity against L1210 and KB cells and inhibitory activity of the pathogenicity of HIV-1 are also described     

SYNTHESIS OF 5-METHYLAMINO-2′-DEOXYURIDINE DERIVATIVES

Reductive amination of 3′,5′-O-(tetraisopropyldisilyloxane-1,3-diyl)-2′-deoxy-5-formyluridine with several aliphatic and aromatic amines, in various solvents, is described. In the case of aliphatic amines, the expected C-5 substituted methylamino pyrimidine nucleosides are formed along with by-products deriving from opening of the pyrimidine ring. Relative amounts of the by-products depend upon the polarity of the solvent employed.     

Synthesis and Binding Properties of a Homopyrimidine 2′,5′-Linked Xylose Nucleic Acid (2′,5′-XNA)

Abstract

The synthesis and hybridization properties of pyrimidine 2′,5′-RNA and 2′,5′-Xylose Nucleic Acid (2′,5′-XNA) are described.     

Some reactions of 1,6-di-O-p-tolylsulphonyl-D-mannitol and its derivatives

Nucleophilic displacement of 4,4′-di-O-mesyl-α,α-trehalose hexabenzoate occurred very readily to give, by a double inversion, the thermodynamically more stable 4,4′-di-iodide in 93% yield with overall retention of configuration. Reductive dehalogenation of the 4,4′-di-iodide with hydrazine hydrate—Raney nickel followed by debenzoylation afforded 4,4′-dideoxytrehalose in high, overall yield. Alternatively, treatment of trehalose with sulphuryl chloride afforded 4,6-dichloro-4,6-dideoxy-α-D-galactopyranosyl 4,6-dichloro-4,6-dideoxy-α-D-galactopyranoside, which underwent selective dehalogenation at the secondary positions on treatment with hydrazine hydrate—Raney nickel. Subsequent nucleophilic displacement of the primary chlorine substituents with sodium acetate in N,N-dimethylformamide gave, after deacetylation, 4,4′-dideoxy-α,α-trehalose. Repeated treatment of the 4,4′,6,6′-tetrachlorotrehalose derivative with hydrazine hydrate—Raney nickel gave 4,4′,6,6′-tetradeoxy-α,α-trehalose. An alternative route to the tetradeoxy derivative was via thiocyanate displacement of the 4,4′,6,6′-tetramethanesulphonate. The tetrathiocyanate, formed in poor yield, was desulphurized with Raney nickel to give the tetradeoxytrehalose. Treatment of 4,6-dichloro-4,6-dideoxy-α-D-galactopyranosyl 4,6-dichloro-4,6-dideoxy-α-D-galactopyranoside with methanolic sodium methoxide yielded, initially, 3,6-anhydro-4-chloro-4-deoxy-α-D-galactopyranosyl 4,6- dichloro-4,6-dideoxy-α-D-galactopyranoside which was transformed into the 3,6:3′,6′-dianhydro derivative. Reductive dechlorination of the dianhydride proceeded smoothly to give the 3,6:3′,6′-dianhydride of 4,4′-dideoxytrehalose.     

Synthesis of 6-substituted uridines. synthesis of (R or S)-6-(3-amino-2-carboxypropyl)uridine

Addition of 5-bromo-2′,3′-O-isopropylidene-5′-O-trityluridine (2) in pyridine to an excess of 2-lithio-1,3-dithiane (3) in oxolane at 78° gave (6R)-5,6-dihydro-(1,3-dithian-2-yl)-2′,3′-O-isopropylidene -5′-O-trityluridine (4), (5S,6S)-5-bromo-5,6-dihydro-(1,3-dithian-2-yl)-2′,3′-O-isopropylidene-5′-O-trityluridine (5), and its (5R) isomer 6 in yields of 37, 35, and 10%, respectively. The structure of 4 was proved by Raney nickel desulphurization to (6S)-5,6-dihydro-2′,3′-O-isopropylidene-6-methyl-5′-O-trityluridine (7) and by acid hydrolysis to give D-ribose and (6R)-5,6-dihydro-6-(1,3-dithian-2-yl)uracil (9). Treatment of 4 with methyl iodide in aqueous acetone gave a 30&%; yield of (R,S)-5,6-dihydro-6-formyl-2′,3′-O-isopropylidene-5′-O-trityl-uridine (10), characterized as its semicarbazone 11. Both 5 and 6 gave 4 upon brief treatment with Raney nickel. Both 5 and 6 also gave 6-formyl-2′,3′-O-isopropylidene-5′- O-trityluridine (12) in ～41%; yield when treated with methyl iodide in aqueous acetone containin- 10%; dimethyl sulfoxide. A by-product, identified as the N-methyl derivative (13) of 12 was also formed in yields which varied with the amount of dimethyl sulfoxide used. Reduction of 12 with sodium borohydride, followed by deprotection, afforded 6-(hydroxymethyl)uridine (17), characterized by hydrolysis to the known 6-(hydroxymethyl)uracil (18). Knoevenagel condensation of a mixture of the aldehydes 12 and 13 with ethyl cyanoacetate yielded 38%; of E- (or Z-)6-[(2-cyano-2-ethoxycarbonyl)ethylidene]-2′,3′-O-isopropylidene-5′-O-trityluridine (19) and 10%; of its N-methyl derivative 20. Hydrogenation of 19 over platinum oxide in acetic anhydride followed by deprotection gave R (or S)-6-(3-amino-2-carboxypropyl)uridine (23).     

An efficient synthesis of 3-fluoro-5-thio-xylofuranosyl nucleosides of thymine, uracil, and 5-fluorouracil as potential antitumor or/and antiviral agents

1,2:5,6-Di-O-isopropylidene-alpha-D-glucofuranose by the sequence of mild oxidation, reduction, fluorination, periodate oxidation, borohydride reduction, and sulfonylation gave 3-deoxy-3-fluoro-1,2-O-isopropylidene-5-O-p-toluenesulfonyl-alpha-D-xylofuranose (5). Tosylate 5 was converted to thioacetate derivative 6, which after acetolysis gave 1,2-di-O-acetyl-5-S-acetyl-3-deoxy-3-fluoro-5-thio-D-xylofuranose (7). Condensation of 7 with silylated thymine, uracil, and 5-fluorouracil afforded nucleosides 1-(5-S-acetyl-3-deoxy-3-fluoro-5-thio-beta-D-xylofuranosyl) thymine (8), 1-(5-S-acetyl-3-deoxy-3-fluoro-5-thio-beta-D-xylofuranosyl) uracil (9), and 1-(5-S-acetyl-3-deoxy-3-fluoro-5-thio-beta-D-xylofuranosyl) 5-fluorouracil (10). Compounds 8, 9, and 10 are biologically active against rotavirus infection and the growth of tumor cells.     

Addition of 1-nitroalkanes to methyl 2,3-O-isopropylidene-β-d-ribo-pentodialdo-1,4-furanoside and N6-benzoyl-2′,3′-O-isopropylideneadenosine-5′-aldehyde

Various 1-nitroalkanes reacted with methyl 2,3-O-isopropylidene-β-d-ribo-pentodialdo-1,4-furanoside to yield methyl 6-alkyl-6-deoxy-2,3-O-isopropylidene-6-nitro-β-d-ribofuranosides in 64–79% yield. Similarly, nitromethane and 1-nitropentane reacted with N⁶-benzoyl-2′,3′-O-isopropylideneadenosine-5′-aldehyde, to yield the corresponding 9-[6-alkyl-6-deoxy-2,3-O-isopropylidene-6-nitro-α-l-talo(β-d-allo)furanosyl]-N⁶-benzoyladenines in 74 and 44% yield, respectively. The potential utility of this nitroalkane addition for the synthesis of nucleosides having a C-5′C-6′ bond is discussed.     

Reaction of 5-Carboxypyrimidine Derivatives with Sodium Bisulfite

5-Carboxyuracil derivatives were shown to react with aqueous sodium bisulfite in mild condition resulting in facile decarboxylation to give corresponding 5-decarboxy-5,6-dihydrouracil-6-sulfonates and uracils in good yield. The former compounds were quantitatively transformed to the latter in alkaline condition. Mechanistic feature of this reaction was discussed, which implied the initial nucleophilic addition of bisulfite across the 5,6-double bond. 5-Carboxycytosine was also shown to react similarly, however, accompanied by hydrolytic deamination.