Thermochemical properties of some vinyl chloride-induced DNA lesions: detailed view from NBO & AIM analysis

Etheno-damaged DNA adducts such as 3,N ⁴-ethenocytosine, N ²,3-ethenoguanine, and 1,N ²-ethenoguanine are associated with carcinogenesis and cell death. These inevitable damages are counteracted by glycosylase enzymes, which cleave damaged nucleobases from DNA. Escherichia coli alkyl purine DNA glycosylase is the enzyme responsible for excising damaged etheno adducts from DNA in humans. In an effort to understand the intrinsic properties of these molecules, we examined gas-phase acidity values and proton affinities (PA) of multiple sites of these molecules as well as equilibrium tautomerization and base pairing properties by quantum mechanical calculations. We also used calculations to compare the acidic and basic properties of these etheno adduct with those of the normal bases—cytosine and guanine nucleobases. We hypothesize that alkyl DNA glycosylase may cleave certain damaged nucleobases as anions and that the active site may take advantage of a nonpolar environment to favor deprotonated cytosine or guanine as a leaving group versus damaged nucleobases.     

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.     

One-pot synthesis of N-alkyl purine and pyrimidine derivatives from alcohols using TsIm: a rapid entry into carboacyclic nucleoside synthesis

A convenient and efficient one-pot N-alkylation of nucleobases from alcohols using N-(p-toluenesulfonyl)imidazole (TsIm) is described. In this method, treatment of alcohols with a mixture of purine or pyrimidine nucleobase, TsIm, K₂CO₃, and triethylamine in refluxing DMF regioselectively furnishes the corresponding N-alkyl nucleobases in good yields. This methodology is highly efficient for various structurally diverse primary alcohols.     

Synthesis of racemic and enantiomeric 3-pyrrolidinyl derivatives of nucleobases

The synthesis of novel 3-pyrrolidinyl derivatives of nucleobases is described. Starting from malic acid, we improved the synthesis of both racemic and optically active N-benzyl-3-hydroxypyrrolidine-2,5-diones, which were transformed in four steps into N-tert-butyloxycarbonyl-3-mesyloxypyrrolidines, the key synthons for the alkylation of purine and pyrimidine nucleobases. Alkylations of cesium salts of purines and sodium salts of pyrimidines with N-tert-butyloxycarbonyl-3-mesyloxypyrrolidines proceeded smoothly, giving high yields of 9-substituted purine derivatives and moderate yields of 1-substituted pyrimidine derivatives. Using (S)-N-tert-butyloxycarbonyl-3-mesyloxypyrrolidine as the same intermediate for the synthesis of both enantiomeric N-Boc-3-pyrrolidinyladenines, and considering the results obtained on chiral HPLC analysis of the products, we proved that nucleophilic displacement of the mesyloxy group proceeded with inversion and not with retention of the configuration. Prepared compounds were tested for cytostatic and antiviral properties, but no significant activity was found.     

Groebke-Blackburn-Bienaymé multicomponent reaction in scaffold-modification of adenine, guanine, and cytosine: synthesis of aminoimidazole-condensed nucleobases

A multicomponent method for scaffold-modification of nucleobases (adenine, guanine, and cytosine) was developed. This modification approach, as an alternative to usual synthetic routes involving protection-deprotection or S_NAr of halo (or leaving group-equivalent)-purines, affords in one step therapeutically-relevant substituted aminoimidazole-[i]-condensed adenine, [b]-condensed guanine, [c]-condensed cytosine. These derived nucleobases possess enhanced lipophilicity and solubility and contain the functionalities useful for further chemical manipulations.     

Diastereo- and enantioselective synthesis of N,O-nucleosides

The diastereo- and enantioselective synthesis of α- and β-3′-hydroxymethyl-N,O-nucleosides is described, based on the 1,3-dipolar cycloaddition of a N-glycosyl nitrone. Two approaches have been evaluated: the one-step procedure, which uses vinyl nucleobases, showed a better stereoselectivity towards β-nucleosides.     

Enantioselective synthesis of homocarbocyclic-2′-oxo-3′-azanucleosides

The enantioselective synthesis of homocarbocyclic-2′oxo-3′-azanucleosides has been performed by cycloaddition reaction of the N-glycosyl nitrones with allyl nucleobases. The use of nitrones originated from two different carbohydrates, the N-ribosyl nitrone and the N-mannosyl nitrone, proceeded in a stereocontrolled and predictable manner with a good degree of enantioselectivity, so allowing an easy entry to both enantiomers.     

Regioselective N‐Arylation of Some Pyrimidine and Purine Nucleobases

N‐Arylation of some pyrimidine and purine nucleobases in the presence of SiO₂ and Cs₂CO₃ under solvent‐free as well as in solution conditions is described. In these conditions, N1‐aryl pyrimidines and N9‐aryl purines have been obtained regioselectively in moderate to high yields with relatively short reaction times.     

Synthesis of aza-analogues of Ganciclovir

Aza-analogues of ganciclovir have been prepared via coupling of nucleobases with N-[2-pivaloyloxy-1-(pivaloyloxymethyl)ethyl]methanesulfonamide or 3-mesyl-4-(benzoyloxymethyl)-1,3-oxazolidine.     

Prolinol-based nucleoside phosphonic acids: new isosteric conformationally flexible nucleotide analogues

trans-4-Hydroxy-l-proline has been used as a starting material for the synthesis of prolinol-based nucleotide analogues with an N-phosphonomethyl moiety attached to the prolinol ring nitrogen atom. The synthetic methodology based on the inversion of configuration at both 1- and 4-position led to all diastereoisomeric O-protected 4-mesyloxyprolinol-N-phosphonates. Alkylation of nucleobases using the synthons in the l-series afforded the nucleotide analogues corresponding to α-l- and β-l-nucleotide. The NMR-based conformational study of these compounds in aqueous solution performed at two different pH values, showing either N-fully protonated or deprotonated forms, revealed the occurrence of the same mostly populated conformer in both cases. All final l-prolinol-based nucleoside phosphonic acids were tested for cytotoxic and antiviral properties, but no significant activity was found.     

Diastereoselective synthesis of homo-N,O-nucleosides

A new class of homo-N,O-nucleosides has been designed, based on the 1,3-dipolar cycloaddition of C-substituted nitrones with allyl nucleobases. The N-methyl-C-ethoxycarbonyl nitrone 1, and the C-α-silyloxymethyl-N-methyl nitrone 7 have been exploited: the stereochemical features of the obtained nucleosides are dependent on the nature of the dipole. The results obtained with DFT calculations fully agree with the experimental results and successfully reproduce the experimentally observed reversal of endo/exo selectivity for nitrones 1 and 7.     

A Mild and Efficient Method for N‐Arylnucleobase Synthesis via the Cross‐Coupling Reactions of Nucleobases with Arylboronic Acids Catalyzed by Simple Copper Salts

A simple and efficient copper‐salt catalyzed N‐arylation of nucleobases is reported. In a mixed solvent of MeOH and H₂O, the coupling products were obtained in moderate to excellent yields at room temperature within a short time. A variety of substituted N‐aryl nucleobases can be prepared through this procedure.     

Synthesis of novel isoxazolidine analogues of homonucleosides

A general method for the synthesis of nucleobase-derived nitrones 4a–e by treatment of N-(2-oxoethyl)nucleobases with N-methylhydroxylamine is reported. The nitrones 4a–e were applied in the synthesis of isoxazolidine homonucleosides. Moderate diastereoselectivities (de 28–82%) were observed for cycloadditions between nitrones 4a–e and allyl alcohol with cis-isoxazolidines predominating. The stereochemistry of the substituted isoxazolidines was established based on an analysis of 2D NOE experiments for uracil-containing cycloadducts 6a and 7a. Cycloadditions of uracil-based nitrone 4a with vinyl-, allyl-, vinyloxymethyl- and allyloxymethylphosphonates gave the respective phosphonylated cis-isoxazolidines as the major adducts.     

Application of chromium‐doped fullerene as a carrier for thymine and uracil nucleotides: Comprehensive density functional theory calculations

The interactions of the nucleobases thymine (C₅H₆N₂O₂) and uracil (C₄H₄N₂O₂) with Cr‐doped C₂₀ fullerene (C₁₉Cr) are investigated by performing density functional theory calculations. The adsorption of these nucleobases on C₁₉Cr leads to two distinct geometries (P1 and P2) differing in the orientation of the nucleobases. The interaction of the nucleobases with the C₁₉Cr nanocluster is highly exothermic, revealing that they are chemically adsorbed on C₁₉Cr. The results show that the binding energy of the thymine–C₁₉Cr complex is slightly higher than that of the uracil–C₁₉Cr complex. In addition, the P2 geometry is more stable compared to P1 due to the higher binding energy in the former configuration. However, based on the results of natural bond orbital and frontier molecular orbitals analyses, the C₁₉Cr nanocage has higher reactivity with the nucleobases in P1 geometry in comparison with P2 due to the larger charge transfer and orbital hybridization in the former geometry. Moreover, the band gap of the C₁₉Cr nanocage decreases after interaction with the nucleobases, and interestingly the impact is more pronounced for P1 geometry, confirming the higher sensitivity of C₁₉Cr to the nucleobases in P1 geometry. Our findings reveal the promising potential of C₁₉Cr as an organometallic carrier for nucleobases thymine and uracil.     

Carboxyalkyl peptoid PNAs: synthesis and hybridization properties

N^γ-Carboxyalkyl modified peptide nucleic acids (PNAs), containing the four canonical nucleobases, were prepared via solid-phase oligomerization. The inserted peptoid monomers 1 and 2 were constructed through simple synthetic procedures, utilizing appropriate glycidol and iodoalkyl electrophiles. Thermal denaturation studies, performed with complementary antiparallel DNA strands, demonstrated that the length of the N^γ-side chain strongly influences the modified PNAs hybridization properties. Moreover, multiple negative charges on the oligoamide backbone, when present on γ-nitrogen C₆ side chains proved to be beneficial for the oligomers’ water solubility and DNA hybridization specificity.     

Theoretical Study on the Photo-Oxidation and Photoreduction of an Azetidine Derivative as a Model of DNA Repair

Photocycloreversion plays a central role in the study of the repair of DNA lesions, reverting them into the original pyrimidine nucleobases. Particularly, among the proposed mechanisms for the repair of DNA (6-4) photoproducts by photolyases, it has been suggested that it takes place through an intermediate characterized by a four-membered heterocyclic oxetane or azetidine ring, whose opening requires the reduction of the fused nucleobases. The specific role of this electron transfer step and its impact on the ring opening energetics remain to be understood. These processes are studied herein by means of quantum-chemical calculations on the two azetidine stereoisomers obtained from photocycloaddition between 6-azauracil and cyclohexene. First, we analyze the efficiency of the electron-transfer processes by computing the redox properties of the azetidine isomers as well as those of a series of aromatic photosensitizers acting as photoreductants and photo-oxidants. We find certain stereodifferentiation favoring oxidation of the cis-isomer, in agreement with previous experimental data. Second, we determine the reaction profiles of the ring-opening mechanism of the cationic, neutral, and anionic systems and assess their feasibility based on their energy barrier heights and the stability of the reactants and products. Results show that oxidation largely decreases the ring-opening energy barrier for both stereoisomers, even though the process is forecast as too slow to be competitive. Conversely, one-electron reduction dramatically facilitates the ring opening of the azetidine heterocycle. Considering the overall quantum-chemistry findings, N,N-dimethylaniline is proposed as an efficient photosensitizer to trigger the photoinduced cycloreversion of the DNA lesion model.     

N-Glycosylation of 2,3-dideoxyfuranose derivatives having a (diethoxyphosphorothioyl)difluoromethyl group at the 3α-position

Lewis acid-mediated N-glycosylation of 2,3-dideoxyribofunanosides having a (diethoxyphosphorothioyl)difluoromethyl group at the 3α-position with silylated nucleobases was examined. The phosphorothioyldifluoromethyl was found to be an effective functional group for the diastereoselective synthesis of β-N¹-pyrimidine-nucleotide analogues 26 and 28-30. However, the method was not useful for the diastereoselective synthesis of adenine nucleotide analogues. The nucleotide analogue 26 was transformed to the difluoromethylenephosphonate analogue 31 of thymidine-3′-phosphate by oxidation with m-CPBA, followed by aqueous work-up.     

Synthesis of a bicyclic double-headed nucleoside

An attempt of preparing a carbocyclic LNA-analogue using different RCM-methods failed. However, a compound with a hemiacetal linker between the C2′ and the C4′-positions was isolated and found to be a suitable substrate for making a conformationally restricted double-headed nucleoside. This contains two uracil nucleobases organized on a bicyclic skeleton and is locked in an N-type conformation.     

Participation of the nucleobases in the regioselective backbone fragmentation of nucleic acids. A molecular dynamics and tandem mass spectrometric investigation on a model dinucleoside phosphotriester

The anions (I–III) obtained from O-methyl 5′-O-(5′-deoxythymidine) 3′-O-(2′,3′-dideoxyuridine) phosphate by the competitive removal of the 3-N-H protons of the nucleobases and of the methyl group from the phosphotriester bond, assume in the gas phase stable conformations as a function of their charge site. The mass-analyzed ion kinetic energy (MIKE) spectra of I and III show that the regioselective backbone cleavage of the internucleotidic linkage is controlled by the 2′-H proton transfer to the nucleobase within the 5′-end nucleoside. Similar pathways are taken by species II when the nucleobase is eliminated as neutral from the 5′-end nucleoside.     

Rapid simultaneous determination of 15 nucleosides and nucleobases in marine medicinal organism Anthopleura lanthogrammica Berkly by micellar electrokinetic capillary chromatography

In this study, a rapid and reliable micellar electrokinetic capillary chromatography (MECC) method has been developed and validated for the separation and quantification of 15 nucleosides and nucleobases in a kind of marine medicinal animal Anthopleura lanthogrammica Berkly. Factors such as micelle concentration, pH, concentration of buffer, etc. were investigated in order to obtain the optimum conditions for the separation. The optimized separation procedure employed 25 mM disodium hydrogen phosphate buffer containing 70 mM sodium dodecyl sulfate (SDS) at pH 8.7 as background electrolyte, 25°C of capillary temperature and 20 kV of separation voltage. UV detection was at 260 nm and injection was hydrodynamic at 50 mbar for 3 s. The whole analysis was completed within 13 min. The relative standard deviations (RSDs) of the peak areas for method precision ranged from 1.4 to 7.6%, and the recovery was between 80.2 and 112.9%. The limit of detection (LOD) for 15 nucleosides and nuleobases was between 0.25 and 0.75 μg/mL. According to the evaluation study, the method was shown to be precise, accurate and reproducible. The proposed MECC method was successfully applied for determination of nucleosides and nucleobases in Chinese Anthopleura lanthogrammica Berkly. The result showed that the species and content of nucleosides and nucleobases in Anthopleura lanthogrammica Berkly samples were abundant.