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Chen YN, Chan CK, Yen CY, Shiau JP, Chang MY, Wang CC, Jeng JH, Tang JY, Chang HW. Antioral Cancer Effects by the Nitrated [6,6,6]Tricycles Compound (SK1) In Vitro. Antioxidants (Basel) 2022; 11:2072. [PMID: 36290795 PMCID: PMC9598307 DOI: 10.3390/antiox11102072] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/13/2022] [Accepted: 10/19/2022] [Indexed: 11/25/2023] Open
Abstract
A novel nitrated [6,6,6]tricycles-derived compound containing nitro, methoxy, and ispropyloxy groups, namely SK1, was developed in our previous report. However, the anticancer effects of SK1 were not assessed. Moreover, SK1 contains two nitro groups (NO2) and one nitrogen-oxygen (N-O) bond exhibiting the potential for oxidative stress generation, but this was not examined. The present study aimed to evaluate the antiproliferation effects and oxidative stress and its associated responses between oral cancer and normal cells. Based on the MTS assay, SK1 demonstrated more antiproliferation ability in oral cancer cells than normal cells, reversed by N-acetylcysteine. This suggests that SK1 causes antiproliferation effects preferentially in an oxidative stress-dependent manner. The oxidative stress-associated responses were further validated, showing higher ROS/MitoSOX burst, MMP, and GSH depletion in oral cancer cells than in normal cells. Meanwhile, SK1 caused oxidative stress-causing apoptosis, such as caspases 3/8/9, and DNA damages, such as γH2AX and 8-OHdG, to a greater extent in oral cancer cells than in normal cells. Siilar to cell viability, these oxidative stress responses were partially diminished by NAC, indicating that SK1 promoted oxidative stress-dependent responses. In conclusion, SK1 exerts oxidative stress, apoptosis, and DNA damage to a greater extent to oral cancer cells than in normal cells.
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Affiliation(s)
- Yan-Ning Chen
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chieh-Kai Chan
- Institute of Chemistry, Academia Sinica, Taipei 115024, Taiwan
| | - Ching-Yu Yen
- School of Dentistry, Taipei Medical University, Taipei 11031, Taiwan
- Department of Oral and Maxillofacial Surgery, Chi-Mei Medical Center, Tainan 71004, Taiwan
| | - Jun-Ping Shiau
- Division of Breast Oncology and Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Meng-Yang Chang
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | | | - Jiiang-Huei Jeng
- School of Dentistry, College of Dental Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Dentistry, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan
- Department of Dentistry, National Taiwan University Hospital, Taipei 100225, Taiwan
| | - Jen-Yang Tang
- Department of Radiation Oncology, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan
- School of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Hsueh-Wei Chang
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Biomedical Science and Environmental Biology, PhD Program in Life Science, College of Life Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
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He F, Yu H, Shi H, Li X, Chu S, Huo C, Liu R. Behavioral, histopathological, genetic, and organism-wide responses to phenanthrene-induced oxidative stress in Eisenia fetida earthworms in natural soil microcosms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:40012-40028. [PMID: 35113383 DOI: 10.1007/s11356-022-18990-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
Phenanthrene (PHE) contamination not only changes the quality of soil environment but also threatens to the soil organisms. There is lack of focus on the eco-toxicity potential of this contaminant in real soil in the current investigation. Here, we assessed the toxic effects of PHE on earthworms (Eisenia fetida) in natural soil matrix. PHE exhibited a relatively high toxicity to E. fetida in natural soil, with the LC50 determined to be 56.68 mg kg-1 after a 14-day exposure. Excessive ROS induced by PHE, leading to oxidative damage to biomacromolecules in E. fetida, including lipid peroxidation, protein carbonylation, and DNA damage. The antioxidant defense system (total antioxidant capacity, glutathione S-transferase, peroxidase, catalase, carboxylesterase, and superoxide dismutase) in E. fetida responded quickly to scavenge excess ROS and free radicals. Exposure to PHE resulted in earthworm avoidance responses (2.5 mg kg-1) and habitat function loss (10 mg kg-1). Histological observations indicated that the intestine, body wall, and seminal vesicle in E. fetida were severely damaged after exposure to high-dose PHE. Moreover, earthworm growth (weight change) and reproduction (cocoon production and the number of juvenile) were also inhibited after exposure to this pollutant. Furthermore, the integrated toxicity of PHE toward E. fetida at different doses and exposure times was assessed by the integrated biomarker response (IBR), which confirmed that PHE is more toxic to earthworms in the high-dose and long-term exposure groups. Our results showed that PHE exposure induced oxidative stress, disturbed antioxidant defense system, and caused oxidative damage in E. fetida. These effects can trigger behavior changes and damage histological structure, finally cause growth inhibition, genotoxicity, and reproductive toxicity in earthworms. The strength of this study is the comprehensive toxicity evaluation of PHE to earthworms and highlights the need to investigate the eco-toxicity potential of exogenous environmental pollutants in a real soil environment.
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Affiliation(s)
- Falin He
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong, 266237, People's Republic of China
| | - Hanmei Yu
- Yanzhou District Branch of Jining Ecological Environment Bureau, No. 159, Wenhua East Road , Yanzhou District, Jining City, Shandong Province, 272100, People's Republic of China
| | - Huijian Shi
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong, 266237, People's Republic of China
| | - Xiangxiang Li
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong, 266237, People's Republic of China
| | - Shanshan Chu
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong, 266237, People's Republic of China
| | - Chengqian Huo
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong, 266237, People's Republic of China
| | - Rutao Liu
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong, 266237, People's Republic of China.
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3
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He F, Wan J, Chu S, Li X, Zong W, Liu R. Toxic mechanism on phenanthrene-triggered cell apoptosis, genotoxicity, immunotoxicity and activity changes of immunity protein in Eisenia fetida: Combined analysis at cellular and molecular levels. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 819:153167. [PMID: 35051481 DOI: 10.1016/j.scitotenv.2022.153167] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 01/05/2022] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Phenanthrene (PHE) is a harmful organic contaminant and exists extensively in the soil environment. The accumulation of PHE would potentially threaten soil invertebrates, including earthworms, and the toxicity is also high. Currently, the possible mechanisms underlying apoptotic pathways induced by PHE and its immunotoxicity and genotoxicity in earthworms remain unclear. Thus, Eisenia fetida coelomocytes and immunity protein lysozyme (LYZ) were chosen as targeted receptors to reveal the apoptotic pathways, genotoxicity, and immunotoxicity triggered by PHE and its binding mechanism with LYZ, using cellular, biochemical, and molecular methods. Results indicated that PHE exposure can cause cell membrane damage, increase cell membrane permeability, and ultimately trigger mitochondria-mediated apoptosis. Increased 8-hydroxy-2-deoxyguanosine (8-OHdG) levels indicated PHE had triggered DNA oxidative damage in cells after PHE exposure. Occurrence of detrimental effects on the immune system in E. fetida coelomocytes due to decreased phagocytic efficacy and destroyed the lysosomal membrane. The LYZ activity in coelomocytes after PHE exposure was consistent with the molecular results, in which the LYZ activity was inhibited. After PHE binding, the protein structure (secondary structure and protein skeleton) and protein environment (the micro-environment of aromatic amino acids) of LYZ were destroyed, forming a larger particle size of the PHE-LYZ complex, and causing a significant sensitization effect on LYZ fluorescence. Molecular simulation indicated the key residues Glu 35, Asp 52, and Trp 62 for protein function located in the binding pocket, suggesting PHE preferentially binds to the active center of LYZ. Additionally, the primary driving forces for the binding interaction between PHE and LYZ molecule are hydrophobicity forces and hydrogen bonds. Taken together, PHE exposure can induce apoptosis by mitochondria-mediated pathway, destroy the normal immune system, and trigger DNA oxidative damage in earthworms. Besides, this study provides a comprehensive evaluation of phenanthrene toxicity to earthworms on molecular and cellular level.
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Affiliation(s)
- Falin He
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Jingqiang Wan
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Shanshan Chu
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Xiangxiang Li
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Wansong Zong
- College of Geography and Environment, Shandong Normal University, 88# East Wenhua Road, Jinan, Shandong 250014, PR China
| | - Rutao Liu
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China.
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Thapa B, Hebert SP, Munk BH, Burrows CJ, Schlegel HB. Computational Study of the Formation of C8, C5, and C4 Guanine:Lysine Adducts via Oxidation of Guanine by Sulfate Radical Anion. J Phys Chem A 2019; 123:5150-5163. [DOI: 10.1021/acs.jpca.9b03598] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Bishnu Thapa
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Sebastien P. Hebert
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Barbara H. Munk
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Cynthia J. Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - H. Bernhard Schlegel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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5
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Hebert SP, Schlegel HB. Computational Study of the pH-Dependent Competition between Carbonate and Thymine Addition to the Guanine Radical. Chem Res Toxicol 2019; 32:195-210. [PMID: 30592213 DOI: 10.1021/acs.chemrestox.8b00302] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
When oligonucleotides are oxidized by carbonate radical, thymine and carbonate can add to guanine radical, yielding either a guanine-thymine cross-link product (G∧T) or 8-oxo-7,8-dehydroguanine (8oxoG) and its further oxidation products such as spiroiminodihydantoin (Sp) and guanidinohydantoin (Gh). The ratio of thymine addition to carbonate addition depends strongly on the pH. Details of the mechanism have been explored by density functional calculations using the ωB97XD/6-31+G(d,p) level of theory with the SMD implicit solvation method, augmented with a few explicit waters. Free energies of intermediates and transition states in aqueous solution have been calculated along the pathways for addition of thymine, CO32-/HCO3- and carbonate radical to guanine radical. The pH dependence was examined by using appropriate explicit proton donors/acceptors as computational models for buffers at pH 2.5, 7, and 10. Deprotonation of thymine is required for nucleophilic addition at C8 of guanine radical, and thus is favored at higher pH. The barrier for carbonate radical addition is lower than for bicarbonate or carbonate dianion addition; however, for low concentrations of carbonate radical, the reaction may proceed by addition of bicarbonate/carbonate dianion to guanine radical. Thymine and bicarbonate/carbonate dianion addition are followed by oxidation by O2, loss of a proton from C8 and decarboxylation of the carbonate adduct. At pH 2.5, guanine radical cation can be formed by oxidization with sulfate radical. Water addition to guanine radical cation is the preferred path for forming 8oxoG at pH 2.5.
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Affiliation(s)
- Sebastien P Hebert
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - H Bernhard Schlegel
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
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Matter B, Seiler CL, Murphy K, Ming X, Zhao J, Lindgren B, Jones R, Tretyakova N. Mapping three guanine oxidation products along DNA following exposure to three types of reactive oxygen species. Free Radic Biol Med 2018; 121:180-189. [PMID: 29702150 PMCID: PMC6858621 DOI: 10.1016/j.freeradbiomed.2018.04.561] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 04/16/2018] [Accepted: 04/18/2018] [Indexed: 12/18/2022]
Abstract
Reactive oxygen and nitrogen species generated during respiration, inflammation, and immune response can damage cellular DNA, contributing to aging, cancer, and neurodegeneration. The ability of oxidized DNA bases to interfere with DNA replication and transcription is strongly influenced by their chemical structures and locations within the genome. In the present work, we examined the influence of local DNA sequence context, DNA secondary structure, and oxidant identity on the efficiency and the chemistry of guanine oxidation in the context of the Kras protooncogene. A novel isotope labeling strategy developed in our laboratory was used to accurately map the formation of 2,2-diamino-4-[(2-deoxy-β-D-erythropentofuranosyl)amino]- 5(2 H)-oxazolone (Z), 8-oxo-7,8-dihydro-2'-deoxyguanosine (OG), and 8-nitroguanine (8-NO2-G) lesions along DNA duplexes following photooxidation in the presence of riboflavin, treatment with nitrosoperoxycarbonate, and oxidation in the presence of hydroxyl radicals. Riboflavin-mediated photooxidation preferentially induced OG lesions at 5' guanines within GG repeats, while treatment with nitrosoperoxycarbonate targeted 3'-guanines within GG and AG dinucleotides. Little sequence selectivity was observed following hydroxyl radical-mediated oxidation. However, Z and 8-NO2-G adducts were overproduced at duplex ends, irrespective of oxidant identity. Overall, our results indicate that the patterns of Z, OG, and 8-NO2-G adduct formation in the genome are distinct and are influenced by oxidant identity and the secondary structure of DNA.
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Affiliation(s)
- Brock Matter
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Christopher L Seiler
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kristopher Murphy
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Xun Ming
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jianwei Zhao
- Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Bruce Lindgren
- Biostatistics Core, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Roger Jones
- Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Natalia Tretyakova
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.
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7
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Sun Y, Zhou W, Moe MM, Liu J. Reactions of water with radical cations of guanine, 9-methylguanine, 2′-deoxyguanosine and guanosine: keto–enol isomerization, C8-hydroxylation, and effects of N9-substitution. Phys Chem Chem Phys 2018; 20:27510-27522. [DOI: 10.1039/c8cp05453c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The reactions of D2O with guanine radical cations in nucleobases and nucleosides were studied in the gas phase using the guided-ion-beam experiment and computational modeling.
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Affiliation(s)
- Yan Sun
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
| | - Wenjing Zhou
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
| | - May Myat Moe
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
| | - Jianbo Liu
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
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Lee CY, Park KS, Park HG. Pyrrolo-dC modified duplex DNA as a novel probe for the sensitive assay of base excision repair enzyme activity. Biosens Bioelectron 2017; 98:210-214. [DOI: 10.1016/j.bios.2017.06.052] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 06/07/2017] [Accepted: 06/25/2017] [Indexed: 01/13/2023]
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9
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Yuan F, Zhao H, Liu M, Quan X. Visible assay for glycosylase based on intrinsic catalytic ability of graphene/gold nanoparticles hybrids. Biosens Bioelectron 2015; 68:7-13. [DOI: 10.1016/j.bios.2014.12.048] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Revised: 12/15/2014] [Accepted: 12/22/2014] [Indexed: 02/04/2023]
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10
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Cerón-Carrasco JP, Requena A, Zúñiga J, Jacquemin D. Mutagenic effects induced by the attack of NO2 radical to the guanine-cytosine base pair. Front Chem 2015; 3:13. [PMID: 25798437 PMCID: PMC4351615 DOI: 10.3389/fchem.2015.00013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 02/16/2015] [Indexed: 12/04/2022] Open
Abstract
We investigate the attack of the nitrogen dioxide radical (NO•2) to the guanine—cytosine (GC) base pair and the subsequent tautomeric reactions able to induce mutations, by means of density functional theory (DFT) calculations. The conducted simulations allow us to identify the most reactive sites of the GC base pair. Indeed, the computed relative energies demonstrate that the addition of the NO•2 radical to the C8 position of the guanine base forms to the most stable adduct. Although the initial adducts might evolve to non-canonical structures via inter-base hydrogen bonds rearrangements, the probability for the proton exchange to occur lies in the same range as that observed for undamaged DNA. As a result, tautomeric errors in NO2-attacked DNA arises at the same rate as in canonical DNA, with no macroscopic impact on the overall stability of DNA. The potential mutagenic effects of the GC–NO•2 radical adducts likely involve side reactions, e.g., the GC deprotonation to the solvent, rather than proton exchange between guanine and cytosine basis.
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Affiliation(s)
| | - Alberto Requena
- Departamento de Química Física, Universidad de Murcia Murcia, Spain
| | - José Zúñiga
- Departamento de Química Física, Universidad de Murcia Murcia, Spain
| | - Denis Jacquemin
- Chimie et Interdisciplinarité, Synthèse, Analyse, Modélisation, UMR Centre National de la Recherche Scientifique, Université de Nantes Nantes, France ; Institut Universitaire de France Paris, France
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11
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Formation of spiroiminodihydantoin due to the reaction between 8-oxoguanine and carbonate radical anion: A quantum computational study. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2013.12.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Modeling the scavenging activity of ellagic acid and its methyl derivatives towards hydroxyl, methoxy, and nitrogen dioxide radicals. J Mol Model 2013; 19:5445-56. [DOI: 10.1007/s00894-013-2023-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 09/25/2013] [Indexed: 02/08/2023]
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13
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Prasad AK, Mishra PC. Study of scavenging action of zingerone towards the OH radical: formation of vanillin and ferulic acid. J PHYS ORG CHEM 2013. [DOI: 10.1002/poc.3200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Ajit Kumar Prasad
- Department of Physics; Banaras Hindu University; Varanasi 221 005 India
| | - P. C. Mishra
- Department of Physics; Banaras Hindu University; Varanasi 221 005 India
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14
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Yadav A, Mishra P. Carbonate radical anion as an efficient reactive oxygen species: Its reaction with guanyl radical and formation of 8-oxoguanine. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2012.06.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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15
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Jena NR, Mishra PC. Formation of ring-opened and rearranged products of guanine: mechanisms and biological significance. Free Radic Biol Med 2012; 53:81-94. [PMID: 22583701 DOI: 10.1016/j.freeradbiomed.2012.04.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 03/30/2012] [Accepted: 04/06/2012] [Indexed: 11/16/2022]
Abstract
DNA damage by endogenous and exogenous agents is a serious concern, as the damaged products can affect genome integrity severely. Damage to DNA may arise from various factors such as DNA base modifications, strand break, inter- and intrastrand crosslinks, and DNA-protein crosslinks. Among these factors, DNA base modification is a common and important form of DNA damage that has been implicated in mutagenesis, carcinogenesis, and many other pathological conditions. Among the four DNA bases, guanine (G) has the smallest oxidation potential, because of which it is frequently modified by reactive species, giving rise to a plethora of lethal lesions. Similarly, 8-oxo-7,8-dihydroguanine (8-oxoG), an oxidatively damaged guanine lesion, also undergoes various degradation reactions giving rise to several mutagenic species. The various products formed from reactions of G or 8-oxoG with different reactive species are mainly 2,6-diamino-4-oxo-5-formamidopyrimidine, 2,5-diamino-4H-imidazolone, 2,2,4-triamino-5-(2H)-oxazolone, 5-guanidino-4-nitroimidazole, guanidinohydantoin, spiroiminodihydantoin, cyanuric acid, parabanic acid, oxaluric acid, and urea, among others. These products are formed from either ring opening or ring opening and subsequent rearrangement. The main aim of this review is to provide a comprehensive overview of various possible reactions and the mechanisms involved, after which these ring-opened and rearranged products of guanine would be formed in DNA. The biological significance of oxidatively damaged products of G is also discussed.
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Affiliation(s)
- N R Jena
- Department of Physics, Indian Institute of Information Technology, Design and Manufacturing, Khamaria, Jabalpur 482005, India.
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17
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Agnihotri N, Mishra PC. Scavenging mechanism of curcumin toward the hydroxyl radical: a theoretical study of reactions producing ferulic acid and vanillin. J Phys Chem A 2011; 115:14221-32. [PMID: 22035040 DOI: 10.1021/jp209318f] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Curcumin is known to be an antioxidant, as it can scavenge free radicals from biological media. A sequence of H-abstraction and addition reactions involving up to eight OH radicals and curcumin or its degradation products leading to the formation of two other antioxidants, namely, ferulic acid and vanillin, was studied. Single electron transfer from curcumin to an OH radical was also studied. All relevant extrema on the potential energy surfaces were located by optimizing geometries of the reactant and product complexes, as well as those of the transition states, at the BHandHLYP/6-31G(d,p) level of density functional theory in the gas phase. Single-point energy calculations were also performed in the gas phase at the BHandHLYP/aug-cc-pVDZ and B3LYP/aug-cc-pVDZ levels of theory. Solvent effects in aqueous media were treated by performing single-point energy calculations at all of the above-mentioned levels of theory employing the polarizable continuum model and the geometries optimized at the BHandHLYP/6-31G(d,p) level in the gas phase. A few reaction steps were also studied by geometry optimization in aqueous media, and the thus-obtained Gibbs free energy barriers were similar to those obtained by corresponding single-point energy calculations. Our calculations show that the hydrogen atom of the OH group attached to the phenol moiety of curcumin would be most efficiently abstracted by an OH radical, in agreement with experimental observations. Further, our study shows that OH addition would be most favored at the C10 site of the heptadiene chain. It was found that curcumin can serve as an effective antioxidant.
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Affiliation(s)
- Neha Agnihotri
- Department of Physics, Banaras Hindu University, Varanasi, India
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18
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Tiwari S, Agnihotri N, Mishra PC. Quantum theoretical study of cleavage of the glycosidic bond of 2'-deoxyadenosine: base excision-repair mechanism of DNA by MutY. J Phys Chem B 2011; 115:3200-7. [PMID: 21384840 DOI: 10.1021/jp1109256] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enzyme adenine DNA glycosylase, also called MutY, is known to catalyze base excision repair by removal of adenine from the abnormal 2'-deoxyadenosine:8-oxo-2'-deoxyguanosine pair in DNA. The active site of the enzyme was considered to consist of a glutamic acid residue along with two water molecules. The relevant reaction mechanism involving different barrier energies was studied theoretically. Molecular geometries of the various molecules and complexes involved in the reaction, e.g., the reactant, intermediate, and product complexes as well as transition states, were optimized employing density functional theory at the B3LYP/6-31G(d,p) level in the gas phase. It was followed by single-point energy calculations at the B3LYP/AUG-cc-pVDZ, BHandHLYP/AUG-cc-pVDZ, and MP2/AUG-cc-pVDZ levels in the gas phase. Single-point energy calculations were also carried out at the B3LYP/AUG-cc-pVDZ and BHandHLYP/AUG-cc-pVDZ levels in aqueous media as well as in the solvents chlorobenzene and dichloroethane. For the solvation calculations, the integral equation formalism of the polarizable continuum model (IEF-PCM) was employed. It is found that glutamic acid along with two water molecules would effectively cleave the glycosidic bond of adenosine by a new two-step reaction mechanism proposed here which is different from the three-step mechanism proposed by other authors earlier regarding the working mechanism of MutY.
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Affiliation(s)
- Saumya Tiwari
- Department of Physics, Banaras Hindu University, Varanasi, India
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Cerón-Carrasco JP, Requena A, Perpète EA, Michaux C, Jacquemin D. Theoretical study of the tautomerism in the one-electron oxidized guanine-cytosine base pair. J Phys Chem B 2011; 114:13439-45. [PMID: 20883043 DOI: 10.1021/jp101711z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Ionizing radiation on DNA mainly generates one-electron oxidized guanine-cytosine base pair (G(+·):C), and in the present paper we study all possible tautomers of G(+·):C by using ab initio approaches. Our calculations reveal that the tautomeric equilibrium follows a peculiar path, characterized by a stepwise mechanism: first the proton in the central hydrogen bond N1(G)-H1-N3(C) migrates from guanine to cytosine, and then the cytosine cation releases one proton from its amino group. During this second step, water acts as a proton acceptor, localizing the positive charge on one of the water molecules interacting with the guanine radical. In agreement with experimental findings, the computed energy barriers show that the deprotonation of the cytosine cation is the speed-limiting step in the tautomeric equilibrium. The influence of the number of water molecules incorporated in the theoretical model is analyzed in detail. The evolution of electronic properties along the reaction path is also discussed on the basis of partial atomic charges and spin density distributions. This work demonstrates that water indeed plays a crucial role in the tautomeric equilibra of base pairs.
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Affiliation(s)
- J P Cerón-Carrasco
- Departamento de Química Física Facultad de Química, Universidad de Murcia, Campus de Espinardo, 30100 Murcia, Spain.
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Reactivities of radicals of adenine and guanine towards reactive oxygen species and reactive nitrogen oxide species: OH and NO2. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.01.042] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Kumar N, Shukla P, Mishra P. Reactions of the OOH radical with guanine: Mechanisms of formation of 8-oxoguanine and other products. Chem Phys 2010. [DOI: 10.1016/j.chemphys.2010.08.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Agnihotri N, Mishra PC. Formation of 8-Nitroguanine Due to Reaction between Guanyl Radical and Nitrogen Dioxide: Catalytic Role of Hydration. J Phys Chem B 2010; 114:7391-404. [DOI: 10.1021/jp9122437] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Neha Agnihotri
- Department of Physics, Banaras Hindu University Varanasi 221 005, India
| | - P. C. Mishra
- Department of Physics, Banaras Hindu University Varanasi 221 005, India
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