Article Cite This: J. Phys. Chem. A 2019, 123, 6229−6240
pubs.acs.org/JPCA
DFT and MD Studies of Formaldehyde-Derived DNA Adducts: Molecular-Level Insights into the Differential Mispairing Potentials of the Adenine, Cytosine, and Guanine Lesions Published as part of The Journal of Physical Chemistry virtual special issue “Leo Radom Festschrift”. Katie A. Wilson, Josh L. Garden, Natasha T. Wetmore, Lindey R. Felske, and Stacey D. Wetmore*
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Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4 S Supporting Information *
ABSTRACT: 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone is a potent nicotine-based carcinogen that generates many DNA lesions, including the HOCH2−C, HOCH2−G, and HOCH2-A hydroxymethyl adducts. Despite all lesions containing an altered exocyclic amino group, which allows the hydroxymethyl group to be directed away from the Watson−Crick binding face, only the most persistent adenine adduct is mutagenic. As a first step toward understanding this differential mutagenicity, density functional theory (DFT) and molecular dynamics (MD) simulations were used to gain atomic-level structural details of these DNA damage products. DFT calculations reveal that all three lesions exhibit conformational diversity. However, regardless of the hydroxymethyl−nucleobase orientation, both DFT and MD simulations highlight that HOCH2−C and HOCH2−G form pairs with the canonical complementary base (G and C, respectively) that are structural and energetically preferred over mispairs. In contrast, depending on the hydroxymethyl−nucleobase orientation, the Watson−Crick HOCH2-A:T pair can become significantly destabilized relative to undamaged A:T. As a result, HOCH2-A mispairs with G, C, and A are energetically accessible and maintain key geometrical features of canonical DNA. Overall, our data directly correlate with the reported differential mutagenicity of the hydroxylmethyl lesions and will encourage future studies to further uncover the cellular impact of the most persistent adenine lesion.
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lesion identified to date is formed at the O6 site of guanine,15 and this adduct has been shown to be highly mutagenic.16 However, there is mounting evidence that suggests that POB adducts can form at many other nucleobase sites including O2 and O4 of thymine,17 N6 of adenine,18 and O2, N3, and N4 of cytosine.19 POB lesions at the DNA phosphate backbone have also been more recently reported.20 Both experimental16,21−29 and computational studies30−32 have been performed to understand the structural impact of these lesions and their associated mutagenicity. In addition to 4-(3-pyridyl)-4-oxobutanediazohydroxide, methyl hydroxylation of NNK generates a metabolite that can decompose to yield formaldehyde and 4-(3-pyridyl)-4oxobutanediazohydroxide.7,8 Formaldehyde reacts with the exocyclic amino groups of the cytosine, guanine, and adenine nucleobases to form hydroxymethyl adducts (denoted HOCH 2 −C, HOCH 2 −G, and HOCH 2 −A). 33−38 The HOCH2−A lesion has been detected in the lung tissue of rats in comparable levels to the POB−G lesion.39 Furthermore, formaldehyde has been shown to be mutagenic in several cell
INTRODUCTION DNA lesions are generated upon exposure to a variety of compounds in our environment,1−6 including carcinogens found in tobacco.7,8 DNA damage associated with tobacco exposure is of particular interest because it has been estimated that over 46 million Americans and over 1 billion people worldwide are exposed to tobacco on a daily basis.9 One of the most potent carcinogens found in tobacco is 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (commonly abbreviated as NNK, which stands for nicotine-derived nitrosamine ketone). It has been proposed that NNK is the only tobacco carcinogen that has the specificity to cause lung cancer, and NNK has been shown to be a potent lung carcinogen in every species tested regardless of the route of exposure.10,11 As a result, NNK has been classified as a Group 1 human carcinogen by the International Agency for Research on Cancer (IRAC).12 Previous research has established that NNK is metabolized in the human body by cytochrome P450 enzymes.10,11,13,14 Specifically, these enzymes catalyze methyl hydroxylation of NNK to generate 4-(3-pyridyl)-4-oxobutanediazohydroxide, which in turn yields a 4-(3-pyridyl)-4-oxobutanediazonium ion that can react with the DNA nucleobases to give rise to various 4-(3-pyridyl)-4-oxobutyl (POB) adducts.7,8 The first POB © 2019 American Chemical Society
Received: April 25, 2019 Revised: June 26, 2019 Published: June 26, 2019 6229
DOI: 10.1021/acs.jpca.9b03899 J. Phys. Chem. A 2019, 123, 6229−6240
Article
The Journal of Physical Chemistry A lines, including human cells.40−44 Specifically, the hydroxymethyl lesions predominantly result in A → T mutations in hamster ovary cells42 and human lymphoblasts41 but have also been shown to lead to A → C in hamster ovary cells42 and A → G mutations in human lymphoblasts.41 Although a few G → T mutations were detected in hamster ovary cells, the authors report that this observation may have arisen due to experimental error.42 Experimental evidence also suggests that formaldehyde-derived lesions can subsequently lead to DNA−DNA33,34,38 and DNA−protein cross-links.45 Overall, the data reveal that the HOCH2−A lesion is strongly mutagenic. In addition to being the most mutagenic lesion, experimental evidence indicates that the adenine adduct is the most prevalent hydroxymethyl lesion.38 Because all three formaldehyde-derived adducts are formed upon addition of the hydroxymethyl moiety to an exocyclic amino group, the damaging hydroxymethyl moiety could be directed away from the lesion Watson−Crick hydrogenbonding face and as such have no effect on canonical complementary base-pairing (Figure 1). Therefore, it is curious
information regarding the preferred conformation about the hydroxymethyl−nucleobase linkage, as well as within the hydroxymethyl group. Subsequently, 2′-deoxyribose is added to the most stable nucleobase conformations to determine the effects of the sugar group on the hydroxymethyl conformation, as well as the preferred orientation about the nucleobase− sugar (glycosidic) bond. To understand potential base-pairing combinations, DFT-predicted hydrogen-bonding interactions between different adduct conformations and each canonical nucleobase are compared to those for the corresponding canonical base pairs. Finally, to examine the influence of the DNA environment on the adduct structure and base-pairing abilities, as well as the effects of the lesion on the double helix, MD simulations are used to investigate the preferred base pairs within DNA duplexes. Together, our multipronged computational approach reveals key structural features that rationalize the experimentally observed mutagenicity associated with the formaldehyde adenine adduct and the absence of harmful effects for the cytosine and guanine lesions.
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COMPUTATIONAL DETAILS DFT Calculations. The inherent flexibility about the hydroxymethyl−nucleobase bond was initially examined using a usage-directed conformational search (Hyperchem) about the α′, β′, and γ′ dihedral angles (Figure 1),61 with a maximum of 100 000 iterations or 1000 optimizations. Each adduct was modeled using AMBER ff99 (Tables S1−S3). Structures were considered to be duplicates when the energy was
