Deprotonation and hydride shifts in nitrenium and iminium forms of aminoimidazole-azaarene mutagens

An investigation into pharmaceutically relevant mutagenicity data and the influence on Ames predictive potential

Background

In drug discovery, a positive Ames test for bacterial mutation presents a significant hurdle to advancing a drug to clinical trials. In a previous paper, we discussed success in predicting the genotoxicity of reagent-sized aryl-amines (ArNH₂), a structure frequently found in marketed drugs and in drug discovery, using quantum mechanics calculations of the energy required to generate the DNA-reactive nitrenium intermediate (ArNH:+). In this paper we approach the question of what molecular descriptors could improve these predictions and whether external data sets are appropriate for further training.

Results

In trying to extend and improve this model beyond this quantum mechanical reaction energy, we faced considerable difficulty, which was surprising considering the long history and success of QSAR model development for this test. Other quantum mechanics descriptors were compared to this reaction energy including AM1 semi-empirical orbital energies, nitrenium formation with alternative leaving groups, nitrenium charge, and aryl-amine anion formation energy. Nitrenium formation energy, regardless of the starting species, was found to be the most useful single descriptor. External sets used in other QSAR investigations did not present the same difficulty using the same methods and descriptors. When considering all substructures rather than just aryl-amines, we also noted a significantly lower performance for the Novartis set. The performance gap between Novartis and external sets persists across different descriptors and learning methods. The profiles of the Novartis and external data are significantly different both in aryl-amines and considering all substructures. The Novartis and external data sets are easily separated in an unsupervised clustering using chemical fingerprints. The chemical differences are discussed and visualized using Kohonen Self-Organizing Maps trained on chemical fingerprints, mutagenic substructure prevalence, and molecular weight.

Conclusions

Despite extensive work in the area of predicting this particular toxicity, work in designing and publishing more relevant test sets for compounds relevant to drug discovery is still necessary. This work also shows that great care must be taken in using QSAR models to replace experimental evidence. When considering all substructures, a random forest model, which can inherently cover distinct neighborhoods, built on Novartis data and previously reported external data provided a suitable model.

The food mutagen 2-amino-9H-pyrido[2,3-b]indole (AalphaC) but not its methylated form (MeAalphaC) increases intestinal tumorigenesis in neonatally exposed multiple intestinal neoplasia mice

The heterocyclic amines 2-amino-9H-pyrido[2,3-b]indole (AalphaC) and 2-amino-3-methyl-9H-pyrido[2,3-b]indole (MeAalphaC) are carcinogenic in several organs in rodents, but not in the intestinal tract. However, AalphaC induces DNA adducts, mutations and preneoplastic aberrant crypt foci (ACF) in rodent colons. The purpose of this study was to examine whether AalphaC and MeAalphaC could affect intestinal tumorigenesis in C57BL/6J-Min/+ (multiple intestinal neoplasia) mice. These mice are heterozygous for a germline nonsense mutation in codon 850 of the tumor suppressor gene adenomatous polyposis coli (Apc), producing a truncated non-functional Apc protein. They develop multiple intestinal adenomas, and are particularly susceptible to intestinal carcinogens that affect the Apc gene, especially when exposed neonatally. Whole litters consisting of Min/+ and +/+ (wild-type) mice of both sexes were given a single s.c. injection of 0.22 mmol/kg AalphaC (40.3 mg/kg) or MeAalphaC (43.4 mg/kg) or the vehicle 1:1 dimethylsulfoxide:0.9% NaCl on days 3-6 after birth, and were terminated at 11 weeks. AalphaC increased the number and diameter of small intestinal tumors, but not the number of colonic tumors or dysplastic ACF, in female and male Min/+ mice separately. In pooled data from females and males, colonic tumors and ACF found after AalphaC exposure appeared to be smaller than the spontaneous lesions, indicating later induction, slower growth or both. In contrast to AalphaC, MeAalphaC did not affect intestinal tumorigenesis in Min/+ mice. No effects were found by any of the amino-alpha-carbolines in the +/+ mice. AalphaC was less potent than the heterocyclic amine 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine.

Elements in abasic site recognition by the major human and Escherichia coli apurinic/apyrimidinic endonucleases

Sites of base loss in DNA arise spontaneously, are induced by damaging agents or are generated by DNA glycosylases. Repair of these potentially mutagenic or lethal lesions is carried out by apurinic/apyrimidinic (AP) endonucleases. To test current models of AP site recognition, we examined the effects of site-specific DNA structural modifications and an F266A mutation on incision and protein-DNA complex formation by the major human AP endonuclease, Ape. Changing the ring component of the abasic site from a neutral tetrahydrofuran (F) to a positively charged pyrrolidine had only a 4-fold effect on the binding capacity of Ape. A non-polar 4-methylindole base analog opposite F had a <2-fold effect on the incision activity of Ape and the human protein was unable to incise or specifically bind 'bulged' DNA substrates. Mutant Ape F266A protein complexed with F-containing DNA with only a 6-fold reduced affinity relative to wild-type protein. Similar studies are described using Escherichia coli AP endonucleases, exonuclease III and endonuclease IV. The results, in combination with previous findings, indicate that the ring structure of an AP site, the base opposite an AP site, the conformation of AP-DNA prior to protein binding and the F266 residue of Ape are not critical elements in targeted recognition by AP endonucleases.

Chemical and biological factors affecting mutagen potency

This review surveys the chemical and biological factors that are correlated with the mutagenic activity of the aromatic and heterocyclic amines. Particular attention is given to the predicted quantum chemical properties of the parent amines and their metabolites. A number of chemical properties have been found to correlate well with measured mutagenic potency, including log P, the energies of the frontier orbitals of the parent amines, and the thermodynamic stability of the nitrenium ion, possibly the ultimate DNA-binding species. These correlations are intriguing clues to the mutagenic activity of the aromatic amines; however, many factors still await final explanation, including the exact mechanisms of the metabolic enzymes, the identity(s) of the ultimate DNA-binding species, the reaction mechanism in the DNA-adduction, the role of sequence context in the covalent and non-covalent binding of the adducts, and the role of DNA repair.