Structure of an Unusual Tetracyclic Deoxyguanosine Adduct: Implications for Frameshift Mutagenicity of ortho-Cyano Nitroanilines

Abstract

Nitroaromatic compounds represent a major class of industrial chemicals that are also found in nature. Polycyclic derivatives are regarded as potent mutagens and carcinogens following bioactivation to produce nitrenium electrophiles that covalently modify DNA to afford N-linked C8-2′-deoxyguanosine (C8-dG) lesions that can induce frameshift mutations, especially in CpG repeat sequences. In contrast, their monocyclic counterparts typically exhibit weak mutagenicity or a lack thereof, despite also undergoing bioactivation to afford N-linked C8-dG adducts. Recently, it has been reported that cyano substitution can greatly increase the mutagenicity of nitroaniline derivatives that are components of azo dyes. The basis of this "cyano effect" may be rooted in the formation of a novel polycyclic adduct arising from initial formation of the N-linked C8-dG adduct followed by a cyclization process involving N7 of dG and the ortho-CN group of the attached C8aryl moiety to generate a quinazolinimine ring as part of a fused tetracyclic C8,N7-dG adduct structure. The present work structurally characterizes this novel cyclic adduct using a combination of optical spectroscopies, NMR analysis, density functional theory (DFT) calculations, and molecular dynamics (MD) simulations. Our data indicate that this highly fluorescent cyclic adduct adopts the promutagenic syn conformation and can stabilize the slipped mutagenic intermediate (SMI) within the CpG repeat of the NarI sequence, which is a hotspot for frameshift mutagenesis mediated by polycyclic N-linked C8-dG adducts. In contrast, the open para-CN (4-aminobenzontrile-derived) N-linked C8-dG adduct is less likely to disrupt the canonical B-form. Together, our results provide a rationale for the potent mutagenicity of cyano-substituted nitroaniline derivatives recently reported in frameshift-sensitive tester strains.

Effects of a Second Local DNA Damage Event on the Toxicity of the Human Carcinogen 4-Aminobiphenyl: A Molecular Dynamics Study of a Damaged DNA Structure

“…General Structural Features of ABP dG Monoadducted DNA Suggest Minimal Distortion upon Lesion Incorporation. When ABP dG adopts the anti glycosidic orientation at any G site in the NarI recognition sequence, the damaged DNA maintains a B conformation with the bulky group in the major groove and canonical WC hydrogen bonding at the lesion site (Figure 3, Tables S4, S6, S8, S11, and S12), as previously seen for other C8-dG adducts, [12][13][14][15][16][17][18][19][20][21][22]56,61 including AA-derived lesions. 13,31,57 In terms of the lesion conformation, the relative nucleobase−bulky moiety orientation is consistent across the trajectories (θ and ϕ dihedral angles, Table S9), likely due to hydrogen bonding between the N−H linker (N10−H) and O4′ of the damaged nucleotide or O3′ of the 5′ nucleotide (Figure 3, Table S10).…”

“…Each duplex was solvated in a TIP3P water box and neutralized with Na + ions. Each system then underwent an extensive minimization, heating, and equilibration protocol. , Finally, 0.5 μs MD production simulations were performed in quintuplicate using different initial velocities in the PMEMD module of Amber18. − The backbone root-mean-square deviations (RMSDs) with respect to the first frame of the production simulation verify system stability for each replica (Table S1). The dynamic data obtained by analyzing the five replicas for each system are discussed throughout the main text, with standard deviations reported over all frames unless otherwise specified.…”

“…Each system then underwent an extensive minimization, heating, and equilibration protocol. 56,61 Finally, 0.5 μs MD production simulations were performed in quintuplicate using different initial velocities in the PMEMD module of Amber18. 62−64 The backbone root-mean-square deviations (RMSDs) with respect to the first frame of the production simulation verify system stability for each replica (Table S1).…”

Impact of DNA Adduct Size, Number, and Relative Position on the Toxicity of Aromatic Amines: A Molecular Dynamics Case Study of ANdG- and APdG-Containing DNA Duplexes

“…Based on the previous work, it is expected that the key structural features of the damaged DNA around the lesion site will be relatively independent of the monovalent ion concentration under typical salt conditions. Subsequently, minimization, heating, and equilibration steps were completed following the comprehensive protocol previously used to study other N-linked adducts . Specifically, minimization was conducted over four stages that consisted of 2500 steps of steepest descent followed by 2500 steps of conjugate gradient minimization.…”

“…Subsequently, minimization, heating, and equilibration steps were completed following the comprehensive protocol previously used to study other N-linked adducts. 61 Specifically, minimization was conducted over four stages that consisted of 2500 steps of steepest descent followed by 2500 steps of conjugate gradient minimization. The first stage was completed with a restraint on the solute atoms, while the second stage was performed with a restraint on the heavy atoms.…”