Effect of ionic state of 2'-deoxyguanosine and solvent on its aralkylation by benzyl bromide

N-4 Alkyl Cytosine Derivatives Synthesis: A New Approach

The selective N-4 alkylation of cytosine plays a critical role in the synthesis of biologically active molecules. This work focuses on the development of practical reaction conditions toward a regioselective synthesis of N-4-alkyl cytosine derivatives. The sequence includes a direct and selective sulfonylation at the N-1 site of the cytosine, followed by the alkylation of the amino site using KHMDS in CH2Cl2/THF mixture, providing a fast and efficient approach consistent with pyrimidine-based drug design.

Synthesis of N2 -Aryl-2'-Deoxyguanosine Modified Phosphoramidites and Oligonucleotides

The N² -position of 2'-deoxyguanosine (N² -position in dG) is well known for forming carcinogenic minor groove DNA adducts, which originate from environmental pollutants, chemicals, and tobacco smoke. The N² -dG DNA adducts have strong implications on biological processes such as DNA replication and repair and may, therefore, result in genomic instability by generating mutations or even cell death. It is crucial to know the role of DNA polymerases when they encounter the N² -dG damaged site in DNA. To get detailed insights on the in vitro DNA damage tolerance or bypass mechanism, there is a need to synthetically access N² -dG damaged DNAs. This article describes a detailed protocol of the synthesis of N² -aryl-dG modified nucleotides using the Buchwald-Hartwig reaction as a main step and incorporation of the modified nucleotides into DNA. In Basic Protocol 1, we focused on the synthesis of five different N² -dG modified phosphoramidites with varying bulkiness (benzyl to pyrenyl). Basic Protocol 2 describes the details of synthesizing N² -dG modified oligonucleotides employing the standard solid phase synthesis protocol. This strategy provides robust synthetic access to various modifications at the N² -position of dG; the modified dGs serve as good substrates to study translesion synthesis and repair pathways. Overall data presented in this article are based on earlier published reports. © 2019 by John Wiley & Sons, Inc.

Synthesis of N2-Deoxyguanosine Modified DNAs and the Studies on Their Translesion Synthesis by the E. coli DNA Polymerase IV

We report the synthesis of N²-aryl (benzyl, naphthyl, anthracenyl, and pyrenyl)-deoxyguanosine (dG) modified phosphoramidite building blocks and the corresponding damaged DNAs. Primer extension studies using E. coli Pol IV, a translesion polymerase, demonstrate that translesion synthesis (TLS) across these N²-dG adducts is error free. However, the efficiency of TLS activity decreases with increase in the steric bulkiness of the adducts. Molecular dynamics simulations of damaged DNA-Pol IV complexes reveal the van der Waals interactions between key amino acid residues (Phe13, Ile31, Gly32, Gly33, Ser42, Pro73, Gly74, Phe76, and Tyr79) of the enzyme and adduct that help to accommodate the bulky damages in a hydrophobic pocket to facilitate TLS. Overall, the results presented here provide insights into the TLS across N²-aryl-dG damaged DNAs by Pol IV.

Nucleoside-Metallacarborane Conjugates for Base-Specific Metal Labeling of DNA

A general approach to the synthesis of nucleoside conjugates between derivatives of thymidine (T), 2'-O-deoxycytidine (dC), 2'-O-deoxyadenosine (dA), and 2'-O-deoxyguanosine (dG), and metallacarborane complexes is described. Metallacarborane-nucleoside derivatives are prepared by reaction of the dioxane-metallacarborane adduct with a base-activated 3',5'-protected nucleoside. In the case of T and dG a mixture of regioisomers, which is easily separable by chromatographic methods, is obtained, thus yielding a series of modifications containing metallacarborane groups at the 2-O, 3-N, 4-O and 1-N, 2-N, 6-O locations, respectively; dC and dA are alkylated at the exo-amino function. The proposed methodology provides a route for the synthesis and study of nucleic acids modified with metallacarboranes at designated locations and a versatile approach to the incorporation of metals into DNA.

Modeling Acid and Cationic Catalysis on the Reactivity of Duocarmycins

Several catalyzed alkylation reactions of 9-methyladenine by a model [CPI, cyclopropa[c]pyrrolo[3,2-e]indol-4(5H)-one (1)] of duocarmycin anticancer drugs have been compared to the uncatalyzed reaction in gas phase and in water solvent bulk, using density functional theory at the B3LYP level with the 6-31+G(d,p) basis set and C-PCM solvation model. The effect on the CPI reactivity induced by water, formic and phosphoric acids (general acid catalysis), H3O+ (specific acid catalysis), sodium, and ammonium cation complexation (cationic catalysis) has been investigated. The calculations indicate that the specific acid catalysis and the catalysis induced by sodium cation complexation are strong in the gas phase, but solvation reduces them dramatically by electrostatic effects. The specific acid catalysis is still operative, but strongly reduced in water solution, where the reaction barrier is reduced by 8.6 kcal mol(-1) in comparison to the uncatalyzed reaction. The general acid catalysis induced by phosphoric acid (-7.3 kcal mol(-1)) and the catalysis induced by Na+ and NH4+ complexation become competitive, with a catalytic effect of -3.6 and -4.1 kcal mol(-1) in water, respectively. With the specific acid catalysis, the high acidity (low pK(a) value) of the conjugated acid of CPI (CPIH+), computed in water solution using both C-PCM (pK(a) = +2.6) and PCM-B3LYP/6-31+G(d,p) (pK(a) = +2.4) solvation models, suggests that the catalytic effects induced by NH4+ complexation could become more important than the specific acid catalysis and the general catalysis by H3PO4 under physiological conditions, due to concentration effects of the catalysts.

Fluorosubstitution and 7-alkylation as prospective modifications of biologically active 6-aryl derivatives of tricyclic acyclovir and ganciclovir analogues

A series of fluorine containing tricyclic analogues of acyclovir (ACV, 1) and ganciclovir (GCV, 2) were synthesized and evaluated for their activity against herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2) and cytostatic activity against HSV-1 thymidine kinase (TK) gene-transduced human osteosarcoma tumour cells. It was found that fluorine substitution reduced the antiviral activity, but most of the new compounds were pronounced cytostatic agents with potency and selectivity similar to those of parental ACV and GCV. Compounds 12, 13 and 16 seem to be promising as labeled substrates for (19)F NMR studies of the HSV TK-ligand interaction and/or monitoring of their metabolites in cells expressing HSV TK.

Modeling Substituent and Conformational Effects on the Reactivity of Antitumor Agents Containing a Cyclopropylcyclohexadienone Subunit

The uncatalyzed alkylation reactions of ammonia by the parent spirocyclopropylcyclohexadienone (6), its 3-amino analogue (7), the cyclic derivative (8), its N-formyl derivative (9), and a closer model (10) of the CPI (1-4) drugs have been investigated in gas phase and in water solvent bulk, using density functional theory at the B3LYP level with several basis sets and the C-PCM solvation model. The effect of several structural key features such as the vinylogous amide conjugation, the acylation of the 2-amino substituent, the ring constraint of the heterocyclic nitrogen atom at C(2) carbon in a ring, and the presence of a condensed pyrrole ring on the reaction activation energy have been investigated. Substrate 7, which is a flexible conformational model of the cyclopropylpyrroloindole moiety (CPI) contained in the duocarmycins, has been used to model the shape-dependent reactivity of these drugs, in gas phase and water solutions. The calculations indicate that shape dependence of reactivity is strongly operative both in gas phase and in polar solvents, since conformational effects are capable of reducing the reaction activation energy by -8.4 and -4.3 kcal mol(-1) in gas phase and in water solution, respectively, that is required to promote "conformational catalysis".

Selectivity of purine alkylation by a quinone methide. Kinetic or thermodynamic control?

The alkylation reaction of 9-methyladenine and 9-methylguanine (as prototype substrates of deoxy-adenosine and -guanosine), by the parent o-quinone methide (o-QM), has been investigated in the gas phase and in aqueous solution, using density functional theory at the B3LYP/6-311+G(d,p) level. The effect of the medium on the reactivity, and on the stability of the resulting adducts, has been investigated by using the C-PCM solvation model to assess which adduct arises from the kinetically favorable path, or from an equilibrating process. The calculations indicate that the most nucleophilic site of the methyl-substituted nucleobases in the gas phase is the guanine oxygen atom (O(6)) (DeltaG()(gas) = 5.6 kcal mol(-)(1)), followed by the adenine N1 (DeltaG)(gas) = 10.3 kcal mol(-)(1)), while other centers exhibit a substantially lower nucleophilicity. The bulk effect of water as a solvent is the dramatic reduction of the nucleophilicity of both 9-methyladenine N1 (DeltaG)(solv) = 14.5 kcal mol(-)(1)) and 9-methylguanine O(6) (DeltaG)(solv) = 17.0 kcal mol(-)(1)). As a result there is a reversal of the nucleophilicity order of the purine bases. While O(6) and N7 nucleophilic centers of 9-methylguanine compete almost on the same footing, the reactivity gap between N1 and N7 of 9-methyladenine in solution is highly reduced. Regarding product stability, calculations predict that only two of the adducts of o-QM with 9-methyladenine, those at NH(2) and N1 positions, are lower in energy than reactants, both in the gas phase and in water. However, the adduct at N1 can easily dissociate in water. The adducts arising from the covalent modification of 9-methylguanine are largely more stable than reactants in the gas phase, but their stability is markedly reduced in water. In particular, the oxygen alkylation adduct becomes slightly unstable in water (DeltaG(solv) = +1.4 kcal mol(-)(1)), and the N7 alkylation product remains only moderately more stable than free reactants (DeltaG(solv) = -2.8 kcal mol(-)(1)). Our data show that site alkylations at the adenine N1 and the guanine O(6) and N7 in water are the result of kinetically controlled processes and that the selective modification of the exo-amino groups of guanine N2 and adenine N6 are generated by thermodynamic equilibrations. The ability of o-QM to form several metastable adducts with purine nucleobases (at guanine N7 and O(2), and adenine N1) in water suggests that the above adducts may act as o-QM carriers.

Modeling H-bonding and solvent effects in the alkylation of pyrimidine bases by a prototype quinone methide: a DFT study

Nucleophilicity of NH(2), N3, and O(2) centers of cytosine toward a model quinone methide (o-QM) as alkylating agent has been studied using DFT computational analysis [at the B3LYP/6-311+G(d,p) level]. Specific and bulk effects of water (by C-PCM model) on the alkylation pathways have been evaluated by analyzing both unassisted and water-assisted reaction mechanisms. An ancillary water molecule, H-bonded to the alkylating agent, may interact monofunctionally with the o-QM oxygen atom (passive mechanisms) or may participate bifunctionally in cyclic hydrogen-bonded structures as a proton shuttle (active mechanisms). A comparison of the unassisted with the water-assisted reaction mechanisms has been made on the basis of activation Gibbs free energies (DeltaG(++)). The gas-phase alkylation reaction at N3 does proceed through a passive mechanism that is preferred over both the active (by -6.3 kcal mol(-1)) and the unassisted process. In contrast, in the gas phase, the active assisted processes at NH(2) and O(2) centers are both favored over their unassisted counterparts by -4.0 and -2.2 kcal mol(-1), respectively. The catalytic effect of a water molecule, in gas phase, reduces the gap between the TSs of the O(2) and NH(2) reaction pathways, but the former remains more stable. Water bulk effect significantly modifies the relative importance of the unassisted and water-assisted alkylation mechanisms, favoring the former, in comparison to the gas-phase reactions. In particular, the unassisted alkylation becomes the preferred mechanism for the reaction at both the exocyclic (NH(2)) and the heterocyclic (N3) nitrogen atoms. By contrast, alkylation at the cytosine oxygen atom is a water-catalyzed process, since in water the active water-assisted mechanism is still favored. As far as competition, among all the possible mechanisms, our calculations unambiguously suggest that the most nucleophilic site both in gas phase (naked reagents: N3 >> O(2) >or= NH(2)) and in water solution (solvated reagents: N3 >> NH(2) >> O(2)) is the heterocyclic nitrogen atom (N3) (DeltaG(++)(gas) = +7.1 kcal mol(-1), and DeltaG(++)(solv) = +13.7 kcal mol(-1)). Our investigation explains the high reactivity and selectivity of the cytosine moiety toward o-QM-like structures both in deoxymononucleoside and in a single-stranded DNA, on the basis of strong H-bonding interactions between reactants and solvent bulk effect. It also offers two general reactivity models in water, uncatalyzed and active water-catalyzed mechanisms (for nitrogen and oxygen nucleophiles, respectively), which should provide a general tool for the planning of nucleic acid modification.

Reaction of the tamoxifen cation and the bis-(4-methoxyphenyl)methyl cation in aqueous solutions containing 2'-deoxyguanosine

The competition between 2'-deoxyguanosine (dG) and water has been quantitatively evaluated for the allylic carbocation derived from tamoxifen and for the stabilized diarylmethyl cation (bis-(4-methoxyphenyl)methyl). Both systems were examined by the competition kinetics method, in which the products were quantitatively analyzed after the SN1 solvolysis of the corresponding acetate esters in aqueous solutions containing the nucleoside. The principal product of the reaction of both cations with dG is the adduct at the NH2 group, a characteristic of delocalized carbocations. The tamoxifen cation was also examined by laser flash photolysis, with absolute rate constants for the reaction with dG and water being obtained and converted into rate constant ratios. The principal result of this study is that there is a three orders of magnitude difference in the reactivity of these cations towards the neutral form of dG and its conjugate base. Under acidic conditions where the reaction occurs with neutral dG, the guanine–water selectivity is low. Even at relatively high concentrations of dG, the majority of the product is alcohol derived from the water reaction. At pH 10 to 11, in contrast, dG is present as the anion and this is highly competitive. Yields of adduct as high as 90% can be attained. A consequence of the large difference in reactivities is that at neutral pH the majority of the reaction of the cation with dG is actually occurring via the small amount of conjugate base present. A further feature of the results is that the NH2 adduct is the predominant stable product from the anion. To explain the high rate constant for the reaction forming this product, a mechanism is proposed whereby one of the protons of the NH2 group is transferred to N1 as the N2-cation bond is forming.Key words: guanine, DNA adduct, carbocation, tamoxifen.

Specific DNA adducts induced by some mono-substituted epoxides in vitro and in vivo

Alkyl epoxides are important intermediates in the chemical industry. They are also formed in vivo during the detoxification of alkenes. Alkyl epoxides have shown genotoxicity in many toxicology assays which has been associated with their covalent binding to DNA. Here aspects of the formation and properties of DNA adducts, induced by some industrially important alkenes and mono-substituted epoxides are discussed. These include propylene oxide, epichlorohydrin, allyl glycidyl ether and the epoxy metabolites of styrene and butadiene. The major DNA adducts formed by epoxides are 7-substituted guanines, 1- and 3-substituted adenines and 3-substituted cytosines. In addition, styrene oxide and butadiene monoepoxide are able to modify exocyclic sites in the DNA bases, the sites being in the case of styrene oxide N(2)- and O(6)-positions of guanine, N(6)-adenine as well as N(4)-and O(2)-cytosine. In vivo the main adduct is the 7-substituted guanines. The 1-substituted adenines have also shown marked levels, and these adducts should also be targets in biomonitoring of human exposures. Due to its low mutagenicity, 7-substituted guanines are considered as a surrogate marker for other mutagenic lesions, e.g. those of 1-adenine or 3-uracil adducts.

Substituent--directed aralkylation and alkylation reactions of the tricyclic analogues of acyclovir and guanosine

Aryl or tert-butyl substituent in the 6 position of 3,9-dihydro-3-[(2-hydroxyethoxy)methyl]-9-oxo-6-R-5H-imidazo[1,2-a]purine (6-R-TACV) 1 partly directs aralkylation reactions into unusual positions: N-4 to give 3 and C-7 to give N-5,7-disubstituted or N-4,7-disubstituted derivatives. In the case of alkylation the effect is limited to aryl substituent and position N-4. Replacement of acyclic moiety of 1 with a ribosyl one like in 7 prevents N-4 substitution. Cleavage of the third ring of 3b to give 3-benzylacyclovir 10 is an example of a new short route to 3-aralkyl-9-substituted guanines.

A one-pot preparation of 1-benzyl-2'-deoxyinosine from ionized 2'-deoxyinosine

A simple and one step synthetic method for the formation of 1-benzyl-2'-deoxyinosine was developed by direct benzylation of ionized 2'-deoxyinosine. Treatment of 2'-deoxyinosine, in the presence of NaOH, with benzyl bromide in 2,2,2-trifluoroethanol (TFE) or N,N-dimethylaetamide (DMA) gave 1-benzyl-2'-deoxyinosine in 35% and 80% yields, respectively.

Synthesis and characterization of oligonucleotides containing site-specific bulky N2-aralkylated guanines and N6-aralkylated adenines

7-Bromomethylbenz[a]anthracene is a known mutagen and carcinogen. The two major DNA adducts produced by this carcinogen, i.e., N2-(benz[a]anthracen-7-ylmethyl)-2'-deoxyguanosine (2, b[a]a2G) and N6-(benz[a]anthracen-7-ylmethyl)-2'-deoxyadenosine (4, b[a]a6A), as well as the simpler benzylated analogs, N2-benzyl-2'-deoxyguanosine (1, bn2G) and N6-benzyl-2'-deoxyadenosine (3, bn6A), were prepared by direct aralkylation of 2'-deoxyguanosine and 2'-deoxyadenosine. To determine the site-specific mutagenicity of these bulky exocyclic amino-substituted adducts, the suitably protected nucleosides were incorporated into 16-base oligodeoxyribonucleotides in place of a normal guanine or adenine residues which respectively are part of the ATG initiation codon for the lac Z' alpha-complementation gene by using an in situ activation approach and automated phosphite triester synthetic methods. The base composition and the incorporation of the bulky adducts into synthetic oligonucleotides were characterized after purification of the modified oligonucleotides by enzymatic digestion and HPLC analysis.

Adenine N3 is a main alkylation site of styrene oxide in double-stranded DNA

Styrene 7,8-oxide (SO), a major metabolite of styrene, is classified as a probable human carcinogen. In the present work, salmon testis DNA was reacted with SO and the alkylation products were analysed after sequential depurination in neutral or acidic conditions followed by HPLC separation and UV-detection. A novel finding was that the N-3 position of adenine was the next most reactive alkylation site in double-stranded DNA, comprising 4% of the total alkylation, as compared to alkylation at the N-7 position of guanine, 93% of the total alkylation. Both alpha- and beta-products of SO were formed at these two sites. Other modified sites were N2-guanine (1.5%, alpha-isomer), 1-adenine (0.4%, both isomers) and N6-adenine (0.7%, both isomers) as well as 1-hypoxanthine (0.1%, alpha-isomer), formed by deamination of the corresponding 1-adenine adduct. The results indicated that in double-stranded DNA N-7 of guanine and N-3 of adenine account for 97% of alkylation by SO. However, these abundant adducts are not stable, the half-life of depurination in DNA for 3-substituted adenines being approximately 10 and approximately 20 h, for alpha- and beta-isomers, respectively, and 51 h for both isomers of 7-substituted guanines.