Thymine Nucleosides Research Articles

A concise synthesis of 3-fluoro-5-thio-xylo- and glucopyranoses, useful precursors towards their corresponding pyranonucleoside derivatives

The chemical synthesis of 1,2,4-tri- O-acetyl-3-deoxy-3-fluoro-5-thio- d-xylopyranose, 1,2,4,6-tetra- O-acetyl-3-deoxy-3-fluoro-5-thio-α- d-glucopyranose and their corresponding nucleosides of thymine is described. Treatment of 3-fluoro-5- S-acetyl-5-thio- d-xylofuranose, obtained by hydrolysis of the isopropylidene group of 3-fluoro-1,2- O-isopropylidene-5- S-acetyl-5-thio- d-xylofuranose, with methanolic ammonia and direct acetylation, led to triacetylated 3-deoxy-3-fluoro-5-thio- d-xylopyranose. Condensation of acetylated 3-fluoro-5-thio- d-xylopyranose with silylated thymine afforded the corresponding nucleoside. Selective benzoylation and direct methanesulfonylation of 3-fluoro-1,2- O-isopropylidene-α- d-glucofuranose gave the 6- O-benzoyl-5- O-methylsulfonyl derivative, which on treatment with sodium methoxide afforded the 5,6-anhydro derivative. Treatment of the latter with thiourea, followed by acetolysis, gave the 3-fluoro-5- S-acetyl-6- O-acetyl-1,2- O-isopropylidene-5-thio-α- d-glucofuranose. 3-Fluoro-5- S-acetyl-6- O-acetyl-5-thio- d-glucofuranose, obtained after hydrolysis of 5-thiofuranose isopropylidene, was treated with ammonia in methanol and directly acetylated, giving tetraacetylated 3-deoxy-3-fluoro-5-thio-α- d-glucopyranose. Condensation of the latter with silylated thymine afforded the desired 3-deoxy-3-fluoro-5-thio-β- d-glucopyranonucleoside analogue.

The excited states of adenine and thymine nucleoside and nucleotide in aqueous solution: a comparative study by time-dependent DFT calculations

The effect substitutions at nitrogen atom 1 of thymine and nitrogen atom 9 of adenine have on lowest energy excited electronic states has been studied by means of time-dependent PBE0 calculations in aqueous solution. In agreement with the experimental indications, the vertical excitation energy of the bright state of 1,methyl-thymine, thymine nucleoside and thymine nucleotide is red-shifted with respect to that of thymine. Deoxyribose and deoxyribose-phosphate substituents affect mainly the lowest energy dark state of adenine and thymine, slightly increasing their oscillator strength. The excited states of 9, methyl-adenine and 1, methyl-thymine have also been studied by using the recently developed M052X, CAM-B3LYP and LC-ωPBE density functionals. The computed VEE are in good agreement with those obtained by using PBE0, which, however, provides values closer to the experimental band maximum.

Synthesis and Properties of Oligonucleotides Containing A 7-Membered (Oxepane) Sugar Ring

Herein we describe the synthesis of novel 7-membered ring (oxepane) thymine and adenine nucleosides (oT and oA) and their corresponding 5′-O-phosphoramidite derivatives. Two homopolymeric sequences (oT 15 and oA 15 ) were prepared via conventional solid-phase synthesis. The mutually complementary strands had the ability to form a duplex (oT 15 :oA 15 ) exhibiting a transition temperature of 12°C. The oxepane oligonucleotides were also found to associate with their respective complementary RNA strands thus forming oT 15 :rA 15 (13°C) and oA 15 :rU 15 (12°C) hybrids. The corresponding native duplexes, namely dT 15 :dA 15 , dT 15 :rA 15 and dA 15 :rU 15 had melting temperatures of 37°C, 32°C and 16°C, respectively. The CD spectrum of oT 15 :rA 15 closely resembled that of the native dT 15 :rA15 hybrid and, in fact, both were found to be substrates for E. Coli RNase H. Thus the oxepane nucleic acids reported here are one of only a handful of DNA mimics capable of activating RNase H when bound to RNA.

Chemical and Structural Implications of 1‘,2‘- versus 2‘,4‘- Conformational Constraints in the Sugar Moiety of Modified Thymine Nucleosides

In order to understand how the chemical nature of the conformational constraint of the sugar moiety in ON/RNA(DNA) dictates the duplex structure and reactivity, we have determined molecular structures and dynamics of the conformationally constrained 1',2'-azetidine- and 1',2'-oxetane-fused thymidines, as well as their 2',4'-fused thymine (T) counterparts such as LNA-T, 2'-amino LNA-T, ENA-T, and aza-ENA-T by NMR, ab initio (HF/6-31G** and B3LYP/6-31++G**), and molecular dynamics simulations (2 ns in the explicit aqueous medium). It has been found that, depending upon whether the modification leads to a bicyclic 1',2'-fused or a tricyclic 2',4'-fused system, they fall into two distinct categories characterized by their respective internal dynamics of the glycosidic and the backbone torsions as well as by characteristic North-East type sugar conformation (P = 37 degrees +/- 27 degrees , phi(m) = 25 degrees +/- 18 degrees ) of the 1',2'-fused systems, and (ii) pure North type (P = 19 degrees +/- 8 degrees , phi(m) = 48 degrees +/- 4 degrees ) for the 2',4'-fused nucleosides. Each group has different conformational hyperspace accessible, despite the overall similarity of the North-type conformational constraints imposed by the 1',2'- or 2',4'-linked modification. The comparison of pK(a)s of the 1-thyminyl aglycon as well as that of endocyclic sugar-nitrogen obtained by theoretical and experimental measurements showed that the nature of the sugar conformational constraints steer the physicochemical property (pK(a)) of the constituent 1-thyminyl moiety, which in turn can play a part in tuning the strength of hydrogen bonding in the basepairing.

Racemic Synthesis and Antiviral Evaluation of 4′(α)-Hydroxymethyl and 6′(α)-Methyl Substituted Apiosyl Nucleosides

This article reports the novel synthesis of substituted apiosyl nucleosides. The key apiosyl intermediate 9 was constructed by sequential ozonolysis, reductions, and acetylation from the ester derivative 6. The nucleosides of uracil, thymine, cytosine, and adenine were synthesized using the glycosyl condensation procedure (silyated base and TMSOTf). The antiviral activities of the synthesized compounds against the HIV-1, HSV-1, HSV-2, and HCMV viruses were evaluated. The adenine derivative 26 showed weak anti-HIV activity (EC50 = 10.1 μg/ml) without exhibiting any cytotoxicity up to a concentration of 100 μM.

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-α- 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-α- 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-β- d-xylofuranosyl) thymine ( 8), 1-(5- S-acetyl-3-deoxy-3-fluoro-5-thio-β- d-xylofuranosyl) uracil ( 9), and 1-(5- S-acetyl-3-deoxy-3-fluoro-5-thio-β- d-xylofuranosyl) 5-fluorouracil ( 10). Compounds 8, 9, and 10 are biologically active against rotavirus infection and the growth of tumor cells.

Synthesis of Novel Carbocyclic Nucleosides and Pro-Tides Derived from 4-Oxatricyclo[4.2.1.03,7]nonane-9-methanol

(1R*,2R*,3R*,6R*,7S*)-2-Amino-4-oxatricyclo[4.2.1.03,7]nonane-9-methanol (9) was prepared from (1R*,2R*,3R*,4S*)-bicyclo[2.2.1]hept-5-ene-2,3-dimethanol by treatment with benzyl azidoformate followed by hydrogenolysis. The amine9was transformed to thymine and purine nucleoside analogues. The prepared analogues were converted to corresponding Pro-Tides by treatment with methylN-[chloro(phenoxy)phosphoryl]-L-alaninate in the presence of 1-methylimidazole ortert-butylmagnesium chloride.

Synthesis and properties of nicked dumbbell and dumbbell DNA conjugates having stilbenedicarboxamide linkers

The synthesis and properties of nicked dumbbell and dumbbell DNA conjugates having A-tract base pair domains connected by rod-like stilbenedicarboxamide linkers are reported. The nicked dumbbells have one to eight dA-dT base pairs and are missing a sugar-phosphate bond either between the linker and a thymine nucleoside residue or between two thymine residues. Chemical ligation of all of the nicked dumbbells with cyanogen bromide affords the dumbbell conjugates in good yield, providing the smallest mini-dumbbells prepared to date. The dumbbells have exceptionally high thermal stability, whereas the nicked dumbbells are only marginally more stable than the hairpin structures on either side of the nick. The structures of the nicked dumbbells and dumbbells have been investigated using a combination of circular dichroism spectroscopy and molecular modeling. The base pair domains are found to adopt normal B'-DNA geometry and thus provide a helical ruler for studies of the distance and angular dependence of electronic interactions between the chromophore linkers.

Asymmetric synthesis of thymine nucleoside analogues based on the isochroman core

Diastereoisomeric analogues of d4T having an isochroman core as the glycone moiety have been prepared in seven steps. Starting from phthalaldehyde, two chiral centres analogous to the α/β anomers of D/L sugars were created. The first was obtained enantiomerically pure via asymmetric dihydroxylation and the second via cyclisation of an aldehyde group with a primary hydroxyl group. Retention of chiral integrity at the C 4 site enabled enantiomerically pure nucleoside analogues to be obtained.

An alternative method suitable for a large scale synthesis of 4'-ethynyl-2',3'-didehydro-3'-deoxythymidine

Reaction of 4', 5'-unsaturated thymine nucleoside 1 with Pb(OBz)4 gave the 4'-benzoyloxy derivative 9 as a diastereomeric mixture in 79% yield. When 9 was treated with Me3Al in CH2Cl2 at 0 degrees C, spiro-derivative 10 was formed as the major product in 76% yield. On the other hand, the use of Me2AlCl led to the formation of the 4'-chlorinated product 11, which was subjected to in situ treatment with Me3Al to give the 4'-alpha-methyl derivative 12 (15%) as well as the 4'-beta-methyl counterpart 13 (38%). Formation of 11 was also observed during the reaction between 9 and EtAl(Cl)C[triple bond]CTMS, prepared from EtAlCl2 and LiC[triple bond]CTMS. From this reaction, the 4'-ethynyl nucleoside 14 was obtained stereoselectively in 56% yield.

Self-assembling of cytosine nucleoside into triply-bound dimers in acid media. a comprehensive evaluation of proton-bound pyrimidine nucleosides by electrospray tandem mass spectrometry, x-rays diffractometry, and theoretical calculations

Electrospray tandem mass spectrometry (ESI-MS/MS) is used to evaluate the assembling of cytosine and thymine nucleosides in the gas phase, through the formation of hydrogen bonded supermolecules. Mixtures of cytidine analogues and homologues deliver in the gas phase proton-bound heterodimers stabilized by multiple interactions, as proven by the kinetics of their dissociation into the corresponding protonated monomers. Theoretical calculations, performed on initial structures of methylcytosine homodimers available in the literature, converged to a minimized structure whereby the two pyrimidine rings interact through the formation of three hydrogen bonds of similar energy. The crystallographic data here reported show the equivalency of the two interacting pyrimidines which is attributable to the presence of an inversion center. Thymine and uracil pyrimidyl nucleosides form, by ESI, gaseous proton-bound dimers. The kinetic of their dissociation into the related protonated monomers shows that the nucleobases are weekly interacting through a single hydrogen bond. The minimized structure of the protonated heterodimer formed by thymine and N-1-methylthymine confirmed the existence of mainly one hydrogen bond which links the two nucleobases through the O4 oxygens. No crystallographic data exists on thymine proton-bound species, nor have we been able to obtain these aggregates in the solid phase. The gaseous phase, under high vacuum conditions, seems therefore a suitable environment where vanishing structures produced by ESI can be studied with a good degree of approximation.

Synthesis and Biological Evaluation of Thymine Nucleosides Fused with 3′,4′‐Tetrahydrofuran Ring.

AbstractFor Abstract see ChemInform Abstract in Full Text.

Synthesis and antiviral activity of monofluorinated cyclopropanoid nucleosides.

Diastereopure monofluorinated cyclopropanoid nucleosides were synthesized for biological studies. As key intermediates cis- and trans-(+/-)-[1-fluoro-2-(acetoxymethyl)cyclopropyl]methanol were prepared starting from diastereopure fluorinated cyclopropanecarboxylates. The latter were synthesized by copper(i)-catalyzed cyclopropanation of [small alpha]-fluorostyrene with ethyl diazoacetate. After reduction and O-acetylation the diastereomeric (2-fluoro-2-phenylcyclopropyl)methyl acetates were obtained. Oxidative degradation using RuO(4) and reduction of the formed carboxyl group with borane gave the fluorinated alcohols, which were coupled with different nucleobases. After deprotection, the corresponding cyclopropanoid nucleosides of adenine, cytosine, guanine, thymine and uracil were obtained. Antiviral tests revealed for the cis-configured guanosine a low, but specific activity against HSV-1 and HSV-2. In addition low affinities of the adenine derivatives to adenosine receptors were detected.

Synthesis and biological evaluation of thymine nucleosides fused with 3',4'-tetrahydrofuran ring.

The pyrimidine nucleosides fused with 3',4'-tetrahydrofuran ring were successfully synthesized, starting from 1,2;5,6-di-O-isopropylidene-D-glucose and assayed for antiviral activities against HIV-1, HIV-2, EMCV, Cox. B3 and VSV. Thymine analogue (5) and its corresponding 2'-deoxy analogue (6) exhibited high cytotoxicity instead of giving antiviral activities.

2'-chloro-2',3'-dideoxy-3'-fluoro-d-ribonucleosides: synthesis, stereospecificity, some chemical transformations, and conformational analysis.

The synthesis of methyl 5-O-benzoyl-2-chloro-2,3-dideoxy-3-fluoro-beta-d-ribofuranoside (5) and its use as a glycosylating agent for persilylated thymine, N(6)-benzoyladenine, and N(4)-benzoylcytosine are described (Scheme 1). The 2'-chloro-2',3'-dideoxy-3'-fluoro-d-ribonucleosides 10-12 synthesized were transformed to 2',3'-dideoxy-3'-fluoro-alpha- and -beta-d-erythro-pentofuranoside nucleosides of thymine (13a,b), adenine (14a,b), and cytidine (15a,b) by treatment with tributyltin hydride in the presence of alpha,alpha'-azobisisobutyronitrile (Scheme 2). Treatment of 2'-chloro-2',3'-dideoxy-3'-fluoro-d-ribonucleosides with 1 M MeONa/MeOH under reflux for 1-5 h afforded 2',3'-didehydro-2',3'-dideoxy-2'-chloro-d-pentofuranosyl nucleosides as the principal products (47-81%) of the reaction, along with recovered starting nucleoside (11-33%) (Scheme 3). Easy HF elimination was also observed in the case of the 2'-azido-2',3'-dideoxy-3'-fluoro-beta-d-ribofuranosides of thymine (17) and adenine (20) (Scheme 3). The role of conformational peculiarities of 2'-chloro-2',3'-dideoxy-3'-fluoro-d-ribonucleosides as well as of 17 and 20 in the observed exclusive elimination of HF is discussed. The conformational analysis of a rather broad palette of 2,3-dideoxy-3-fluoro-2-(X-substituted)-d-ribofuranosides was performed with the aid of the PSEUROT (version 6.3) program, using (i) the recently reparametrized Karplus-type relation (Chattopadhyaya and co-workers. J. Org. Chem. 1998, 63, 4967) and (ii) empirical bond angle correction terms suggested by us. The predictive power of the Brunck and Weinhold model (J. Am. Chem. Soc. 1979, 101, 1700) of the gauche effect between atoms and groups as a conformational driving force acting upon the pentofuranose ring is explored. Their model invokes maximum antiperiplanar sigma <--> sigma stabilization when the donating bond is the least polar one and the acceptor orbital is at the most polarized bond and is found at least as satisfactory, and in various specific cases more so than, as rationalizations on the basis of the preference of the gauche vs the trans conformation of two vicinal electronegative substituents (Wolfe. Acc. Chem. Res. 1972, 5, 102).

Thymidylate synthase inhibitors.

Thymidylate synthase (TS, EC 2.1.1.45) is an ?#1 essential enzyme in pyrimidine biosynthesis. TS catalyses the methylation of deoxyuridine monophosphate (dUMP) to form deoxythymidine monophosphate (dTMP), using 5,10-methylenetetrahydrofolate as a co-substrate to donate methyl groups. TS is a cytoplasmic enzyme which consists of a dimer of two identical subunits of MW 38.5 kDa [1]. Two binding sites on the enzyme are recognized — the pyrimidine binding site and a pocket of the surface of the enzyme in which the folate co-substrate binds. The enzyme transfers a methyl group from the bound folate to the pyrimidine to form dTMP, followed by release of both products into the cytoplasm. This reaction provides the only endogenous source of dTMP available to cells and is the rate-limiting enzyme for the de novo synthesis of thymine nucleosides and nucleotides. Thus, TS plays an essential role in the synthesis and repair of DNA. The TS gene is located on chromosome 18p11.32 and consists of seven exons and eight introns. The expression of this gene is cell cycle dependent, in that the level increases sharply as cells enter S-phase, but it may also be proliferation dependent [2]. Thus, tumor cells have TS activities much above the level found in nonmalignant cells (see below). A high percentage of monosomic loss of the TS gene has been shown in some cancers, most notably colon carcinoma [3]. Because of its pivotal role in DNA metabolism TS, has long been a target for anticancer chemotherapy. Inhibition of TS leads to major disturbances in pyrimidine and folate metabolism. The desire to exploit this axis has led to the development of a number of TS inhibitors over several decades, which are either analogues of the pyrimidine substrate dUMP, or analogues of the folate cofactor. 5-Fluorouracil (5FU) is the classical pyrimidine analogue, which for several decades has been the mainstay of the treatment of various types of cancer including gastrointestinal (GI), breast and head and neck cancers [4]. Increasing investigation and development of these agents has occurred in recent years, which has maintained this group of drugs in the forefront of anticancer drug pharmacology and therapeutics. There are now a large range of TS inhibitors undergoing evaluation and clinical development (Figs. 1, 2 and 5). This chapter reviews recent developments in the understanding and clinical applications of FP and folate-based TS inhibitors. Readers requiring more background and historical data are referred to previous reviews of these agents [4–6].

Synthesis of Racemic 2-Hydroxy-4- and 2-Hydroxy-5-(hydroxymethyl)cyclohexane Nucleoside Analogues

New racemic 2-hydroxy-4- and 2-hydroxy-5-(hydroxymethyl)cyclohexane analogues of adenine (10b and 16b) and thymine nucleosides (13b and 19b) were prepared by alkylation of 1,8-diazabicyclo[5.4.0]undec-7-ene salt of adenine and/or thymine with 3-vinyl-7-oxabicyclo[4.1.0]heptane followed by cis hydroxylation with osmium(VIII) oxide and sodium chlorate, oxidation with sodium periodate, and borohydride reduction.

α- l-RNA (α- l- ribo Configured RNA): Synthesis and RNA-Selective Hybridization of α- l-RNA/α- l-LNA Chimera

Synthesis of the novel α- l-ribofuranosyl phosphoramidite derivative 7 was accomplished via the α- l-ribofuranosyl thymine nucleoside 4 . Amidite 7 was used in automated syntheses of chimeric oligonucleotides composed of mixtures of the novel α- l-RNA nucleotide monomer ( αL T, α- l- ribo configured RNA), and DNA, LNA ( T L , locked nucleic acid) or α- l-LNA ( αL T L , α- l- ribo configured locked nucleic acid) nucleotide monomers. For α- l-RNA/DNA and α- l-RNA/α- l-LNA chimeras, RNA-selective hybridization was obtained, for α- l-RNA/α- l-LNA chimera we found increased binding affinity compared to the corresponding DNA:RNA reference duplex. In addition, α- l-RNA/α- l-LNA chimera displayed significant stabilization towards 3′-exonucleolytic degradation. These results indicate that α- l-RNA/α- l-LNA chimeras deserve further evaluation as antisense molecules.

ChemInform Abstract: Synthesis and Evaluation of anti‐HIV‐1 Activity of 3′‐Azido‐3′‐deoxy‐2′‐O,4′‐C‐methylene‐Linked Bicyclic Thymine Nucleosides.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Glutarimide: a carrier transporting drug through cell membranes

It is suggested that glutarimide moiety (2,6-piperidinedione) with the intact imide group (OC-NH-CO) and substituted at α or β position in the ring, is acting as the carrier molecule (vector), which transports biologically active substituents (functional groups) through cell membranes. The results obtained from quantum chemical calculations and experimental studies indicate that structural features and physicochemical properties of glutarimide moiety are remarkably similar with those of uracil derivatives. Therefore, glutarimide drug may interact with specific receptors involved in transport of uracil and thymine nucleosides and it may easily cross biological membranes.