5-Cyanoamino-4-imidazolecarboxamide and nitrosative guanine deamination: experimental evidence for pyrimidine ring-opening during deamination

Critical Review of Synthesis, Toxicology and Detection of Acyclovir

Acyclovir (ACV) is an effective and selective antiviral drug, and the study of its toxicology and the use of appropriate detection techniques to control its toxicity at safe levels are extremely important for medicine efforts and human health. This review discusses the mechanism driving ACV’s ability to inhibit viral coding, starting from its development and pharmacology. A comprehensive summary of the existing preparation methods and synthetic materials, such as 5-aminoimidazole-4-carboxamide, guanine and its derivatives, and other purine derivatives, is presented to elucidate the preparation of ACV in detail. In addition, it presents valuable analytical procedures for the toxicological studies of ACV, which are essential for human use and dosing. Analytical methods, including spectrophotometry, high performance liquid chromatography (HPLC), liquid chromatography/tandem mass spectrometry (LC-MS/MS), electrochemical sensors, molecularly imprinted polymers (MIPs), and flow injection–chemiluminescence (FI-CL) are also highlighted. A brief description of the characteristics of each of these methods is also presented. Finally, insight is provided for the development of ACV to drive further innovation of ACV in pharmaceutical applications. This review provides a comprehensive summary of the past life and future challenges of ACV.

Importance of phenols structure on their activity as antinitrosating agents: A kinetic study

Objective:

Nitrosative deamination of DNA bases induced by reaction with reactive nitrogen species (RNS) has been pointed out as a probable cause of mutagenesis. (Poly)phenols, present in many food items from the Mediterranean diet, are believed to possess antinitrosating properties due to their RNS scavenging ability, which seems to be related to their structure. It has been suggested that phenolic compounds will react with the above-mentioned species more rapidly than most amino compounds, thus preventing direct nitrosation of the DNA bases and their transnitrosation from endogenous N-nitroso compounds, or most likely from the transient N-nitrosocompounds formed in vivo.

Materials and Methods:

In order to prove that assumption, a kinetic study of the nitroso group transfer from a N-methyl-N-nitrosobenzenesulfonamide (N-methyl-N-nitroso-4-methylbenzenesulfonamide, MeNMBS) to the DNA bases bearing an amine group and to a series of phenols was carried out. In the transnitrosation of phenols, the formation of nitrosophenol was monitored by Ultraviolet (UV) / Visible spectroscopy, and in the reactions of the DNA bases, the consumption of MeNMBS was followed by high performance liquid chromatography (HPLC).

Results:

The results obtained point to the transnitrosation of DNA bases being negligible, as well as that of phenols bearing electron-withdrawing groups. Phenols with methoxy substituents in positions 2, 4, and / or 6, although they seemed to react, did not afford the expected product. Phenols with electron-releasing substituents, unless these blocked the oxygen atom, reacted with our model compound at an appreciable rate. O-nitrosation of the phenolate ion followed by rearrangement of the C-nitrosophenol seemed to be involved.

Conclusion:

This study provided evidence that the above compounds might actually act as antinitrosating agents in vivo.

Ammonia elimination from protonated nucleobases and related synthetic substrates

The results are reported of mass-spectrometric studies of the nucleobases adenine 1h (1, R = H), guanine 2h, and cytosine 3h. The protonated nucleobases are generated by electrospray ionization of adenosine 1r (1, R = ribose), guanosine 2r, and deoxycytidine 3d (3, R = deoxyribose) and their fragmentations were studied with tandem mass spectrometry. In contrast to previous EI-MS studies of the nucleobases, NH(3) elimination does present a major path for the fragmentations of the ions [1h + H](+), [2h + H](+), and [3h + H](+). The ion [2h + H - NH(3)](+) also was generated from the acyclic precursor 5-cyanoamino-4-oxomethylene-dihydroimidazole 13h and from the thioether derivative 14h of 2h (NH(2) replaced by MeS). The analyses of the modes of initial fragmentation is supported by density functional theoretical studies. Conjugate acids 15-55 were studied to determine site preferences for the protonations of 1h, 2h, 3h, 13h, and 14h. The proton affinity of the amino group hardly ever is the substrate's best protonation site, and possible mechanisms for NH(3) elimination are discussed in which the amino group serves as the dissociative protonation site. The results provide semi-direct experimental evidence for the existence of the pyrimidine ring-opened cations that we had proposed on the basis of theoretical studies as intermediates in nitrosative nucleobase deamination.

Nitrosative cytosine deamination. An exploration of the chemistry emanating from deamination with pyrimidine ring-opening

A discussion of nitrosative deamination of cytosine 1 is presented that argues for the formation of 6 by diazotization of 1 to cytosinediazonium ion 2 and its electrostatic complex 3, dediazoniation to 4 <--> 5, and amide-bond cleavage to 6. The reaction channels available to 6 include hydrolytic deglycation to 3-isocyanatoacrylonitrile 7, water addition to carbamic acid 9 with the possibility for re-closure to uracil 13, water addition to carbamic acid 9, and decarboxylation to 3-aminoacrylonitrile 10. With a view to the instability of the carbamic acid 9, the carbamate models ethyl (Z)-2-cyanovinylcarbamate 14 and (Z)-2-cyano-1-tert-butylvinylcarbamate 20 were studied. Acid-catalyzed hydrolysis of 14 leads to 2-amino-carbonylphenylcarbamate 15, and its cyclization yields the benzo-fused uracil quinazoline-2,4-dione 16. In contrast to the aromatic system 14, acid-catalyzed cyclization cannot compete with oligomerization in the case of 20, and 5-tert-butyluracil 22 is accessible only with base-catalysis. It is shown that 23, the parent of 10, also easily polymerizes. The experimental results provide a rationale as to why 9, 10, and 12 would have escaped detection in in vitro studies: they would have oligomerized. In contrast to the in vitro experiments, the oligomerizations of 9, 10, or 12 clearly are not relevant in vivo because of low monomer concentrations. With the exclusion of recyclization and of oligomerization in vivo, attention thus needs to focus on (Z)-3-aminoacrylonitrile 10 as the most likely deamination product of cytosine aside from uracil.

Chemical synthesis and thermodynamic characterization of oxanine-containing oligodeoxynucleotides

Oxanine (Oxa, O), one of the major damaged bases from guanine generated by NO- or HNO₂-induced nitrosative deamination, has been considered as a mutagen-potent lesion. For exploring more detailed properties of Oxa, large-scale preparation of Oxa-containing oligodeoxynucleotide (Oxa-ODN) with the desired base sequence is a prerequisite. In the present study, we have developed a chemical synthesis procedure of Oxa-ODNs and characterized thermodynamic properties of Oxa in DNA strands. First, 2′-deoxynucleoside of Oxa (dOxo) obtained from 2′-deoxyguanosine by HNO₂-nitrosation was subjected to 5′-O-selective tritylation to give 5′-O-(4,4′-dimethoxytrityl)-dOxo (DMT-dOxo) with a maximum yield of 70%. Subsequently, DMT-dOxo was treated with conventional phosphoramidation, which resulted in DMT-dOxo-amidite monomer with a maximum yield of 72.5%. The amidite obtained was used for synthesizing Oxa-ODNs: the coupling yields for Oxa incorporation were over 93%. The prepared Oxa-ODNs were employed for analyzing the thermodynamic properties of DNA duplexes containing base-matches of O:N [N; C (cytosine), T (thymine), G (guanine) or A (adenine)]. Melting temperatures (T_m) and thermodynamic stability (ΔG370) were found to be lower by 6.83∼13.41°C and 2.643∼6.047 kcal mol⁻¹, respectively, compared with those of oligodeoxynucleotides, which had the same base sequence except that O:N was replaced by G:C (wild type). It has also been found that Oxa-pairing with cytosine shows relatively high stability in DNA duplex compared with other base combinations. The orders of ΔΔG370 were O:C > O:T > O:A > O:G. The chemical synthesis procedure and thermodynamic characteristics of Oxa-ODNs established here will be helpful for elucidating the biological significance of Oxa in relation to genotoxic and repair mechanisms.

Cytosine catalysis of nitrosative guanine deamination and interstrand cross-link formation

Effects are discussed of the anisotropic DNA environment on nitrosative guanine deamination based on results of an ab initio study of the aggregate 3 formed by guaninediazonium ion 1 and cytosine 2. Within 3, the protonation of 2 by 1 is fast and exothermic and forms 6, an aggregate between betaine 4 (2-diazonium-9H-purin-6-olate) and cytosinium ion 5. Electronic structure analysis of 4 shows that this betaine is not mesoionic; only the negative charge is delocalized in the pi-system while the positive charge resides in the sigma-system. Potential energy surface exploration shows that both dediazoniation and ring-opening of betaine 4 in aggregate 6 are fast and exothermic and lead irreversibly to E-11, the aggregate between (E)-5-cyanoimino-4-oxomethylene-4,5-dihydroimidazole E-10 and 5. The computed pair binding energies for 3, 6, and E-11 greatly exceed the GC pair binding energy. While 1 can be a highly reactive intermediate in reactions of the "free nucleobase" (or its nucleoside and nucleotide), the cyanoimine 10 emerges as the key intermediate in nitrosative guanine deamination in ds-DNA and ds-oligonucleotides. In essence, the complementary nucleobase cytosine provides base catalysis and switches the sequence of deprotonation and dediazoniation. It is argued that this environment-induced switch causes entirely different reaction paths to products as compared to the respective "free nucleobase" chemistry, and the complete consistency is demonstrated of this mechanistic model with all known experimental results. Products might form directly from 10 by addition and ring closure, or their formation might involve water catalysis via 5-cyanoamino-4-imidazolecarboxylic acid 12 and/or 5-carbodiimidyl-4-imidazolecarboxylic acid 13. The pyrimidine ring-opened intermediates 10, 12, and 13 can account for the formations of xanthosine, the pH dependency and the environment dependency of oxanosine formation, the formation of the classical cross-link dG(N(2)())-to-dG(C2), including the known sequence specificity of its formation, and the formation of the structure-isomeric cross-link dG(N1)-to-dG(C2).

Ab Initio Study of the SN1Ar and SN2Ar Reactions of Benzenediazonium Ion with Water. On the Conception of “Unimolecular Dediazoniation” in Solvolysis Reactions

The nucleophilic substitution of N2 in benzenediazonium ion 1 by one H2O molecule to form protonated phenol 2 has been studied with ab initio (RHF, MP2, QCISD(T)//MP2) and hybrid density functional (B3LYP) methods. Three mechanisms were considered: (a) the unimolecular process SN1Ar with steps 1 --> Ph+ + N2 and Ph+ + H2O --> 2, (b) the bimolecular process SN2Ar with precoordination 1 + H2O --> 1 x H2O, SN reaction 1 x H2O --> [TS]++ --> 2 x N2 and dissociation of the postcoordination complex 2 x N2 --> 2 + N2, and (c) the direct bimolecular process SN2Ar that bypasses precoordination and involves just the SN reaction 1 + H2O --> [TS]++ --> 2 + N2. The SN2Ar reactions proceed by way of a Cs symmetric SN2Ar transition state structure that is rather loose, contains essentially a phenyl cation weakly bound to N2 and OH2, and is analogous to the transition state structures of front-side nucleophilic replacement at saturated centers. In solvolysis reactions, all of these processes follow first-order kinetics, and the electronic relaxation is essentially the same. It is argued that "unimolecular dediazoniations" have to proceed by way of SN2Ar transition state structures because strict SN1Ar reactions cannot be realized in solvolyses, despite the fact that the Gibbs free energy profile favors the strict SN1Ar process over the SN2Ar reaction by 6.7 kcal/mol. It is further argued that the direct SN2Ar process is the best model for the solvolysis reaction for dynamic reasons, and its Gibbs free energy of activation is 19.3 kcal/mol and remains higher than the SN1Ar value. Even though the SN1Ar and SN2Ar models provide activation enthalpies and SKIE values that closely match the experimental data, the analysis leads us to the unavoidable conclusion that this agreement is fortuitous. While the experiments do show that the solvent effect on the activation energy is about the same for all solvents, they do not show the absence of a solvent effect. The ab initio results presented here suggest that the solvent effect on the direct SN2Ar dediazoniation is approximately 12 kcal/mol, and computation of solvent effects with the isodensity polarized continuum model (IPCM) support this conclusion.