1
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Minko IG, Kellum AH, Stone MP, Lloyd RS. The aflatoxin B 1-induced imidazole ring-opened guanine adduct: High mutagenic potential that is minimally affected by sequence context. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024; 65 Suppl 1:9-13. [PMID: 37303259 PMCID: PMC10711146 DOI: 10.1002/em.22556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/25/2023] [Accepted: 06/08/2023] [Indexed: 06/13/2023]
Abstract
Dietary exposure to aflatoxin B1 (AFB1) is a recognized risk factor for developing hepatocellular carcinoma. The mutational signature of AFB1 is characterized by high-frequency base substitutions, predominantly G>T transversions, in a limited subset of trinucleotide sequences. The 8,9-dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxyaflatoxin B1 (AFB1-FapyGua) has been implicated as the primary DNA lesion responsible for AFB1-induced mutations. This study evaluated the mutagenic potential of AFB1-FapyGua in four sequence contexts, including hot- and cold-spot sequences as apparent in the mutational signature. Vectors containing site-specific AFB1-FapyGua lesions were replicated in primate cells and the products of replication were isolated and sequenced. Consistent with the role of AFB1-FapyGua in AFB1-induced mutagenesis, AFB1-FapyGua was highly mutagenic in all four sequence contexts, causing G>T transversions and other base substitutions at frequencies of ~80%-90%. These data suggest that the unique mutational signature of AFB1 is not explained by sequence-dependent fidelity of replication past AFB1-FapyGua lesions.
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Affiliation(s)
- Irina G. Minko
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239
| | | | | | - R. Stephen Lloyd
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239
- Department of Molecular and Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239
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2
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Dabbaghi MM, Fadaei MS, Soleimani Roudi H, Baradaran Rahimi V, Askari VR. A review of the biological effects of Myrtus communis. Physiol Rep 2023; 11:e15770. [PMID: 37464095 PMCID: PMC10354007 DOI: 10.14814/phy2.15770] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/03/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
The World Health Organization stated that 1.6 million deaths worldwide were caused by contact with chemicals and toxins in 2019. In the same year, the Centers for Disease Control and Prevention stated that natural toxins caused 3960 deaths. Myrtus communis, also known as common Myrtle, is a flowering plant native to the Mediterranean region. Myrtle has been traditionally used to treat diarrhea, inflammation, bleeding, headache, pulmonary and skin diseases. This review was performed to assess Myrtle's protective and therapeutic efficacy against various chemical, natural, and radiational noxious. Multiple databases such as PubMed, Web of Sciences, and Scopus were investigated without publication time limitation. Recent studies have demonstrated its potential as a protective agent against both natural and chemical toxins. One of Myrtle's most significant protective properties is its high antioxidant content. Studies have shown that the antioxidant properties of Myrtle can protect against harmful substances such as heavy metals, pesticides, and other environmental toxins. Additionally, Myrtle has anti-inflammatory properties that can help reduce the damage caused by long-term exposure to toxins. The anti-inflammatory and antimicrobial properties of Myrtle have also proven effective in alleviating gastrointestinal conditions such as gastric ulcers.
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Affiliation(s)
- Mohammad Mahdi Dabbaghi
- International UNESCO Center for Health-Related Basic Sciences and Human Nutrition, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Saleh Fadaei
- International UNESCO Center for Health-Related Basic Sciences and Human Nutrition, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hesan Soleimani Roudi
- International UNESCO Center for Health-Related Basic Sciences and Human Nutrition, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Vafa Baradaran Rahimi
- Department of Cardiovascular Diseases, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Vahid Reza Askari
- International UNESCO Center for Health-Related Basic Sciences and Human Nutrition, Mashhad University of Medical Sciences, Mashhad, Iran
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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3
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Jaruga P, Tomar R, Kant M, Vartanian V, Sexton B, Rizzo CJ, Turesky RJ, Stone MP, Lloyd RS, Dizdaroglu M. Synthesis and Characterization of 15N 5-Labeled Aflatoxin B 1-Formamidopyrimidines and Aflatoxin B 1-N7-Guanine from a Partial Double-Stranded Oligodeoxynucleotide as Internal Standards for Mass Spectrometric Measurements. ACS OMEGA 2023; 8:14841-14854. [PMID: 37125130 PMCID: PMC10134230 DOI: 10.1021/acsomega.3c01328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
Aflatoxin B1 (AFB1) exposure through contaminated food is a primary contributor to hepatocellular carcinogenesis worldwide. Hepatitis B viral infections in livers dramatically increase the carcinogenic potency of AFB1 exposures. Liver cytochrome P450 oxidizes AFB1 to the epoxide, which in turn reacts with N7-guanine in DNA, producing the cationic trans-8,9-dihydro-8-(N7-guanyl)-9-hydroxyaflatoxin B1 adduct (AFB1-N7-Gua). The opening of the imidazole ring of AFB1-N7-Gua under physiological conditions causes the formation of the cis- and trans-diastereomers of 8,9-dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxyaflatoxin B1 (AFB1-FapyGua). These adducts primarily lead to G → T mutations, with AFB1-FapyGua being significantly more mutagenic than AFB1-N7-Gua. The unequivocal identification and accurate quantification of these AFB1-Gua adducts as biomarkers are essential for a fundamental understanding and prevention of AFB1-induced hepatocellular carcinogenesis. Among a variety of analytical techniques used for this purpose, liquid chromatography-tandem mass spectrometry, with the use of the stable isotope-labeled analogues of AFB1-FapyGua and AFB1-N7-Gua as internal standards, provides the greatest accuracy and sensitivity. cis-AFB1-FapyGua-15N5, trans-AFB1-FapyGua-15N5, and AFB1-N7-Gua-15N5 have been synthesized and used successfully as internal standards. However, the availability of these standards from either academic institutions or commercial sources ceased to exist. Thus, quantitative genomic data regarding AFB1-induced DNA damage in animal models and humans remain challenging to obtain. Previously, AFB1-N7-Gua-15N5 was prepared by reacting AFB1-exo-8,9-epoxide with the uniformly 15N5-labeled DNA isolated from algae grown in a pure 15N-environment, followed by alkali treatment, resulting in the conversion of AFB1-N7-Gua-15N5 to AFB1-FapyGua-15N5. In the present work, we used a different and simpler approach to synthesize cis-AFB1-FapyGua-15N5, trans-AFB1-FapyGua-15N5, and AFB1-N7-Gua-15N5 from a partial double-stranded 11-mer Gua-15N5-labeled oligodeoxynucleotide, followed by isolation and purification. We also show the validation of these 15N5-labeled standards for the measurement of cis-AFB1-FapyGua, trans-AFB1-FapyGua, and AFB1-N7-Gua in DNA of livers of AFB1-treated mice.
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Affiliation(s)
- Pawel Jaruga
- Biomolecular
Measurement Division, National Institute
of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Rachana Tomar
- Department
of Chemistry, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Melis Kant
- Biomolecular
Measurement Division, National Institute
of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Vladimir Vartanian
- Oregon
Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Benjamin Sexton
- Department
of Chemistry, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Carmelo J. Rizzo
- Department
of Chemistry, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Robert J. Turesky
- Masonic
Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Michael P. Stone
- Department
of Chemistry, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - R. Stephen Lloyd
- Oregon
Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Miral Dizdaroglu
- Biomolecular
Measurement Division, National Institute
of Standards and Technology, Gaithersburg, Maryland 20899, United States
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Yahyazadeh R, Baradaran Rahimi V, Yahyazadeh A, Mohajeri SA, Askari VR. Promising effects of gingerol against toxins: A review article. Biofactors 2021; 47:885-913. [PMID: 34418196 DOI: 10.1002/biof.1779] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/04/2021] [Indexed: 12/11/2022]
Abstract
Ginger is a medicinal and valuable culinary plant. Gingerols, as an active constituent in the fresh ginger rhizomes of Zingiber officinale, exhibit several promising pharmacological properties. This comprehensive literature review was performed to assess gingerol's protective and therapeutic efficacy against the various chemical, natural, and radiational stimuli. Another objective of this study was to investigate the mechanism of anti-inflammatory, antioxidant, and antiapoptotic properties of gingerol. It should be noted that the data were gathered from in vivo and in vitro experimental studies. Gingerols can exert their protective activity through different mechanisms and cell signaling pathways. For example, these are mitogen-activated protein kinase (MAPK), nuclear factor-kappa B (NF-kB), Wnt/β-catenin, nuclear factor erythroid 2-related factor 2/antioxidant response element (Nrf2/ARE), transforming growth factor beta1/Smad3 (TGF-β1/Smad3), and extracellular signal-related kinase/cAMP-response element-binding protein (ERK/CREB). We hope that more researchers can benefit from this review to conduct preclinical and clinical studies, treat cancer, inflammation, and attenuate the side effects of drugs and industrial pollutants.
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Affiliation(s)
- Roghayeh Yahyazadeh
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Vafa Baradaran Rahimi
- Department of Cardiovascular Diseases, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ahmad Yahyazadeh
- Department of Histology and Embryology, Faculty of Medicine, Karabuk University, Karabuk, Turkey
| | - Seyed Ahmad Mohajeri
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Vahid Reza Askari
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Pharmaceutical Sciences in Persian Medicine, School of Persian and Complementary Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Persian Medicine, School of Persian and Complementary Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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5
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Tomar R, Minko IG, Kellum AH, Voehler MW, Stone MP, McCullough AK, Lloyd RS. DNA Sequence Modulates the Efficiency of NEIL1-Catalyzed Excision of the Aflatoxin B 1-Induced Formamidopyrimidine Guanine Adduct. Chem Res Toxicol 2021; 34:901-911. [PMID: 33595290 DOI: 10.1021/acs.chemrestox.0c00517] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dietary exposure to aflatoxins is a significant risk factor in the development of hepatocellular carcinomas. Following bioactivation by microsomal P450s, the reaction of aflatoxin B1 (AFB1) with guanine (Gua) in DNA leads to the formation of stable, imidazole ring-opened 8,9-dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxyaflatoxin B1 (AFB1-FapyGua) adducts. In contrast to most base modifications that result in destabilization of the DNA duplex, the AFB1-FapyGua adduct increases the thermal stability of DNA via 5'-interface intercalation and base-stacking interactions. Although it was anticipated that this stabilization might make these lesions difficult to repair relative to helix distorting modifications, prior studies have shown that both the nucleotide and base excision repair pathways participate in the removal of the AFB1-FapyGua adduct. Specifically for base excision repair, we previously showed that the DNA glycosylase NEIL1 excises AFB1-FapyGua and catalyzes strand scission in both synthetic oligodeoxynucleotides and liver DNA of exposed mice. Since it is anticipated that error-prone replication bypass of unrepaired AFB1-FapyGua adducts contributes to cellular transformation and carcinogenesis, the structural and thermodynamic parameters that modulate the efficiencies of these repair pathways are of considerable interest. We hypothesized that the DNA sequence context in which the AFB1-FapyGua adduct is formed might modulate duplex stability and consequently alter the efficiencies of NEIL1-initiated repair. To address this hypothesis, site-specific AFB1-FapyGua adducts were synthesized in three sequence contexts, with the 5' neighbor nucleotide being varied. DNA structural stability analyses were conducted using UV absorbance- and NMR-based melting experiments. These data revealed differentials in thermal stabilities associated with the 5'-neighbor base pair. Single turnover kinetic analyses using the NEIL1 glycosylase demonstrated corresponding sequence-dependent differences in the repair of this adduct, such that there was an inverse correlation between the stabilization of the duplex and the efficiency of NEIL1-mediated catalysis.
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Affiliation(s)
- Rachana Tomar
- Department of Chemistry and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, VU Station B, Box 351822, Nashville, Tennessee 37235, United States
| | - Irina G Minko
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Andrew H Kellum
- Department of Chemistry and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, VU Station B, Box 351822, Nashville, Tennessee 37235, United States
| | - Markus W Voehler
- Department of Chemistry and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, VU Station B, Box 351822, Nashville, Tennessee 37235, United States
| | - Michael P Stone
- Department of Chemistry and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, VU Station B, Box 351822, Nashville, Tennessee 37235, United States
| | - Amanda K McCullough
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States.,Department of Molecular and Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - R Stephen Lloyd
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States.,Department of Molecular and Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
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6
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Aflatoxin B₁⁻Formamidopyrimidine DNA Adducts: Relationships between Structures, Free Energies, and Melting Temperatures. Molecules 2019; 24:molecules24010150. [PMID: 30609733 PMCID: PMC6337653 DOI: 10.3390/molecules24010150] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 12/21/2018] [Accepted: 12/26/2018] [Indexed: 12/02/2022] Open
Abstract
Thermal stabilities of DNA duplexes containing Gua (g), α- (a) or β-anomer of formamidopyrimidine-N7-9-hydroxy-aflatoxin B1 (b) differ markedly (Tm: a<g<b), but the underlying molecular origin of this experimentally observed phenomenon is yet to be identified and determined. Here, by employing explicit-solvent molecular dynamics simulations coupled with free-energy calculations using a combined linear-interaction-energy/linear-response-approximation approach, we explain the quantitative differences in Tm in terms of three structural features (bulkiness, order, and compactness) and three energetical contributions (non-polar, electrostatic, and preorganized-electrostatic), and thus advance the current understanding of the relationships between structures, free energies, and thermal stabilities of DNA double helices.
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7
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Minko IG, Christov PP, Li L, Stone MP, McCullough AK, Lloyd RS. Processing of N 5-substituted formamidopyrimidine DNA adducts by DNA glycosylases NEIL1 and NEIL3. DNA Repair (Amst) 2018; 73:49-54. [PMID: 30448017 DOI: 10.1016/j.dnarep.2018.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/02/2018] [Accepted: 11/02/2018] [Indexed: 12/29/2022]
Abstract
A variety of agents cause DNA base alkylation damage, including the known hepatocarcinogen aflatoxin B1 (AFB1) and chemotherapeutic drugs derived from nitrogen mustard (NM). The N7 site of guanine is the primary site of alkylation, with some N7-deoxyguanosine adducts undergoing imidazole ring-opening to stable mutagenic N5-alkyl formamidopyrimidine (Fapy-dG) adducts. These adducts exist as a mixture of canonical β- and unnatural α-anomeric forms. The β species are predominant in double-stranded (ds) DNA. Recently, we have demonstrated that the DNA glycosylase NEIL1 can initiate repair of AFB1-Fapy-dG adducts both in vitro and in vivo, with Neil1-/- mice showing an increased susceptibility to AFB1-induced hepatocellular carcinoma. Here, we hypothesized that NEIL1 could excise NM-Fapy-dG and that NEIL3, a closely related DNA glycosylase, could excise both NM-Fapy-dG and AFB1-Fapy-dG. Product formation from the reaction of human NEIL1 with ds oligodeoxynucleotides containing a unique NM-Fapy-dG followed a bi-component exponential function under single turnover conditions. Thus, two adduct conformations were differentially recognized by hNEIL1. The excision rate of the major form (∼13.0 min-1), presumed to be the β-anomer, was significantly higher than that previously reported for 5-hydroxycytosine, 5-hydroxyuracil, thymine glycol (Tg), and AFB1-Fapy-dG. Product generation from the minor form was much slower (∼0.4 min-1), likely reflecting the rate of conversion of the α anomer into the β anomer. Mus musculus NEIL3 (MmuNEIL3Δ324) excised NM-Fapy-dG from single-stranded (ss) DNA (turnover rate of ∼0.4 min-1), but not from ds DNA. Product formation from ss substrate was incomplete, presumably because of a substantial presence of the α anomer. MmuNEIL3Δ324 could not initiate repair of AFB1-Fapy-dG in either ds or ss DNA. Overall, the data suggest that both NEIL1 and NEIL3 may protect cells against cytotoxic and mutagenic effects of NM-Fapy-dG, but NEIL1 may have a unique role in initiation of base excision repair of AFB1-Fapy-dG.
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Affiliation(s)
- Irina G Minko
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States
| | - Plamen P Christov
- Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Vanderbilt University, Nashville, TN 37235, United States
| | - Liang Li
- Department of Chemistry and Biochemistry, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, United States
| | - Michael P Stone
- Department of Chemistry and Biochemistry, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, United States
| | - Amanda K McCullough
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, United States
| | - R Stephen Lloyd
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, United States; Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, OR 97239, United States.
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8
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Bamberger SN, Malik CK, Voehler MW, Brown SK, Pan H, Johnson-Salyard TL, Rizzo CJ, Stone MP. Configurational and Conformational Equilibria of N 6-(2-Deoxy-d-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5- N-methylformamidopyrimidine (MeFapy-dG) Lesion in DNA. Chem Res Toxicol 2018; 31:924-935. [PMID: 30169026 DOI: 10.1021/acs.chemrestox.8b00135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The most common lesion in DNA occurring due to clinical treatment with Temozolomide or cellular exposures to other methylating agents is 7-methylguanine (N7-Me-dG). It can undergo a secondary reaction to form N6-(2-deoxy-d-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5- N-methylformamidopyrimidine (MeFapy-dG). MeFapy-dG undergoes epimerization in DNA to produce either α or β deoxyribose anomers. Additionally, conformational rotation around the formyl bond, C5- N5 bond, and glycosidic bond may occur. To characterize and quantitate the mixture of these isomers in DNA, a 13C-MeFapy-dG lesion, in which the CH3 group of the MeFapy-dG was isotopically labeled, was incorporated into the trimer 5'-TXT-3' and the dodecamer 5'-CATXATGACGCT-3' (X = 13C-MeFapy-dG). NMR spectroscopy of both the trimer and dodecamer revealed that the MeFapy-dG lesion exists in single strand DNA as ten configurationally and conformationally discrete species, eight of which may be unequivocally assigned. In the duplex dodecamer, the MeFapy-dG lesion exists as six configurationally and conformationally discrete species. Analyses of NMR data in the single strand trimer confirm that for each deoxyribose anomer, atropisomerism occurs around the C5- N5 bond to produce R a and S a atropisomers. Each atropisomer exhibits geometrical isomerism about the formyl bond yielding E and Z conformations. 1H NMR experiments allow the relative abundances of the species to be determined. For the single strand trimer, the α and β anomers exist in a 3:7 ratio, favoring the β anomer. For the β anomer, with respect to the C5- N5 bond, the R a and S a atropisomers are equally populated. However, the Z geometrical isomer of the formyl moiety is preferred. For the α anomer, the E- S a isomer is present at 12%, whereas all other isomers are present at 5-7%. DNA processing enzymes may differentially recognize different isomers of the MeFapy-dG lesion. Moreover, DNA sequence-specific differences in the populations of configurational and conformational species may modulate biological responses to the MeFapy-dG lesion.
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Affiliation(s)
- Stephanie N Bamberger
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Chanchal K Malik
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Markus W Voehler
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Summer K Brown
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Hope Pan
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Tracy L Johnson-Salyard
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Carmelo J Rizzo
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Michael P Stone
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
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9
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Fedeles BI, Essigmann JM. Impact of DNA lesion repair, replication and formation on the mutational spectra of environmental carcinogens: Aflatoxin B 1 as a case study. DNA Repair (Amst) 2018; 71:12-22. [PMID: 30309820 DOI: 10.1016/j.dnarep.2018.08.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In a multicellular organism, somatic mutations represent a permanent record of the past chemical and biochemical perturbations experienced by a cell in its local microenvironment. Akin to a perpetual recording device, with every replication, genomic DNA accumulates mutations in patterns that reflect: i) the sequence context-dependent formation of DNA damage, due to environmental or endogenous reactive species, including spontaneous processes; ii) the activity of DNA repair pathways, which, depending on the type of lesion, can erase, ignore or exacerbate the mutagenic consequences of that DNA damage; and iii) the choice of replication machinery that synthesizes the nascent genomic copy. These three factors result in a richly contoured sequence context-dependent mutational spectrum that, from appearances, is distinct for most individual forms of DNA damage. Such a mutagenic legacy, if appropriately decoded, can reveal the local history of genome-altering events such as chemical or pathogen exposures, metabolic stress, and inflammation, which in turn can provide an indication of the underlying causes and mechanisms of genetic disease. Modern tools have positioned us to develop a deep mechanistic understanding of the cellular factors and pathways that modulate a mutational process and, in turn, provide opportunities for better diagnostic and prognostic biomarkers, better exposure risk assessment and even actionable therapeutic targets. The goal of this Perspective is to present a bottom-up, lesion-centric framework of mutagenesis that integrates the contributions of lesion replication, lesion repair and lesion formation to explain the complex mutational spectra that emerge in the genome following exposure to mutagens. The mutational spectra of the well-studied hepatocarcinogen aflatoxin B1 are showcased here as specific examples, but the implications are meant to be generalizable.
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Affiliation(s)
- Bogdan I Fedeles
- Departments of Biological Engineering, Chemistry and The Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - John M Essigmann
- Departments of Biological Engineering, Chemistry and The Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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10
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Li W, Liu X, Muhammad S, Shi J, Meng Y, Wang J. Computational investigation of TGF-β receptor inhibitors for treatment of idiopathic pulmonary fibrosis: Field-based QSAR model and molecular dynamics simulation. Comput Biol Chem 2018; 76:139-150. [PMID: 30015175 DOI: 10.1016/j.compbiolchem.2018.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/29/2018] [Accepted: 07/03/2018] [Indexed: 10/28/2022]
Abstract
The discovery of drugs relevant to transforming growth factor β (TGF-β) receptor inhibitors have been considered as a considerable challenge during therapy idiopathic pulmonary fibrosis diseases. For the first time, herein we illustrate a field-based quantitative structure-activity relationship (QSAR) model and molecular dynamics (MD) simulations for novel 7-substituted-pyrazolo [4, 3-b] pyridine derivatives with biological activity for the TGF-β receptor, with an attempt of elucidating the 3D structural features that are essential for the activity. Results demonstrate that the field-based model (Q2 = 0.548, R2training = 0.840, R2test = 0.750) are acceptable with good predictive capabilities. In addition, MD studies were also carried out on the training set with the aim of exploring their binding modes in the active pocket of TGF-β receptor, resulting in some of the crucial structural fragments which are responsible for inhibitory activity. Therefore, we summarized the following features required for TGF-β receptor inhibition: electronegative in region1, bulky groups in region2 and smaller groups in region3. Based on the model and related information, we hope the above information provides an important insight for understanding the interactions of the inhibitors and TGF-β receptor, which may be useful in discovering novel potent inhibitors.
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Affiliation(s)
- Wei Li
- Department of Pharmaceutical Engineering, Shenyang University of Chemical Technology, Shenyang, China
| | - Xue Liu
- Department of Pharmaceutical Engineering, Shenyang University of Chemical Technology, Shenyang, China
| | - Suleiman Muhammad
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - JiYue Shi
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - YanQiu Meng
- Department of Pharmaceutical Engineering, Shenyang University of Chemical Technology, Shenyang, China.
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China.
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Toxicology of DNA Adducts Formed Upon Human Exposure to Carcinogens. ADVANCES IN MOLECULAR TOXICOLOGY 2016. [DOI: 10.1016/b978-0-12-804700-2.00007-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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