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Wu J, Zhang M, Song L, Tan Y, Taniguchi Y, Hipolito CJ, Zhang Y, Yin Y. Implications of N7-hydrogen and C8-keto on the base pairing, mutagenic potential and repair of 8-oxo-2'-deoxy-adenosine: Investigation by nucleotide analogues. Bioorg Chem 2022; 127:106029. [PMID: 35858520 DOI: 10.1016/j.bioorg.2022.106029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/20/2022] [Accepted: 07/12/2022] [Indexed: 11/02/2022]
Abstract
Oxidative lesions, such as 8-oxo-dG and 8-oxo-dA, are continuously generated from exposure to reactive oxygen species. While 8-oxo-dG has been extensively studied, 8-oxo-dA has not received as much attention until recently. Herein, we report the synthesis of duplex DNAs incorporating dA, 8-oxo-dA, 7-deaza-dA, 8-Br-dA, and 8-Br-7-deaza-dA, which have different substitutions at 7- and 8-position, for the investigation into the implications of N7-hydrogen and C8-keto on the base pairing preference, mutagenic potential and repair of 8-oxo-dA. Base pairing study suggested that the polar N7-hydrogen and C8-keto of 8-oxo-dA, rather than the syn-preference, might be essential for 8-oxo-dA to form a stable base pair with dG. Insertion and extension studies using KF-exo- and human DNA polymerase β indicated that the efficient dGTP insertion opposite 8-oxo-dA and extension past 8-oxo-dA:dG are contingent upon not only the stable base pair with dG, but also the flexibility of the active site in polymerase. The N7-hydrogen in 8-oxo-dA or C7-hydrogen in 7-deaza-dA and 8-Br-7-deaza-dA was suggested to be important for the recognition by hOGG1, although the excision efficiencies of 7-deaza-dA and 8-Br-7-deaza-dA were much lower than 8-oxo-dA. This study provides an insight into the structure-function relationship of 8-oxo-dA by nucleotide analogues.
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Affiliation(s)
- Junjie Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Mengmeng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Lulu Song
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yahong Tan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yosuke Taniguchi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | | | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Yizhen Yin
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China.
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Thavoncharoensub N, Maruyama K, Heh CH, Hoong Leong K, Shi H, Shigematsu Y, Sasaki S, Taniguchi Y. Synthesis of γ-N-modified 8-oxo-2'-deoxyguanosine triphosphate and its characterization. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 38:578-589. [PMID: 30929604 DOI: 10.1080/15257770.2019.1586919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
8-OxodGTP is generated by the reaction between dGTP and reactive oxygen species and a considered mutagenic nucleotide. It can be incorporated into the duplex DNA during replication processes by the DNA polymerase, and thus the repair enzyme removes oxodGTP from the nucleotide pools in living cells. On the other hand, the γ-modified triphosphates show interesting properties for use as biological tools. Therefore, the γ-N-pyrenylalkyl-oxodGTP derivatives were synthesized and their effect on the enzymatic reactions were evaluated. The γ-N-pyrenylmethyl-oxodGTP was found to be accepted by the DNA polymerase just like oxodGTP, but showed a competitive inhibition property for the human oxodGTPase.
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Affiliation(s)
- Ninticha Thavoncharoensub
- a Department of Medicinal Sciences , Graduate School of Pharmaceutical Sciences, Kyushu University , Higashi-ku , Fukuoka , Japan.,b Department of Pharmacy , Faculty of Pharmacy, Mahidol University , Bangkok , Thailand
| | - Kento Maruyama
- a Department of Medicinal Sciences , Graduate School of Pharmaceutical Sciences, Kyushu University , Higashi-ku , Fukuoka , Japan
| | - Choon Han Heh
- c Department of Pharmacy, Faculty of Medicine , University of Malaya , Kuala Lumpur , Malaysia
| | - Kok Hoong Leong
- c Department of Pharmacy, Faculty of Medicine , University of Malaya , Kuala Lumpur , Malaysia
| | - Hui Shi
- a Department of Medicinal Sciences , Graduate School of Pharmaceutical Sciences, Kyushu University , Higashi-ku , Fukuoka , Japan
| | - Yoshiharu Shigematsu
- a Department of Medicinal Sciences , Graduate School of Pharmaceutical Sciences, Kyushu University , Higashi-ku , Fukuoka , Japan
| | - Shigeki Sasaki
- a Department of Medicinal Sciences , Graduate School of Pharmaceutical Sciences, Kyushu University , Higashi-ku , Fukuoka , Japan
| | - Yosuke Taniguchi
- a Department of Medicinal Sciences , Graduate School of Pharmaceutical Sciences, Kyushu University , Higashi-ku , Fukuoka , Japan
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Šebera J, Hattori Y, Sato D, Reha D, Nencka R, Kohno T, Kojima C, Tanaka Y, Sychrovský V. The mechanism of the glycosylase reaction with hOGG1 base-excision repair enzyme: concerted effect of Lys249 and Asp268 during excision of 8-oxoguanine. Nucleic Acids Res 2017; 45:5231-5242. [PMID: 28334993 PMCID: PMC5435939 DOI: 10.1093/nar/gkx157] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/24/2017] [Indexed: 12/14/2022] Open
Abstract
The excision of 8-oxoguanine (oxoG) by the human 8-oxoguanine DNA glycosylase 1 (hOGG1) base-excision repair enzyme was studied by using the QM/MM (M06-2X/6-31G(d,p):OPLS2005) calculation method and nuclear magnetic resonance (NMR) spectroscopy. The calculated glycosylase reaction included excision of the oxoG base, formation of Lys249-ribose enzyme–substrate covalent adduct and formation of a Schiff base. The formation of a Schiff base with ΔG# = 17.7 kcal/mol was the rate-limiting step of the reaction. The excision of the oxoG base with ΔG# = 16.1 kcal/mol proceeded via substitution of the C1΄-N9 N-glycosidic bond with an H-N9 bond where the negative charge on the oxoG base and the positive charge on the ribose were compensated in a concerted manner by NH3+(Lys249) and CO2−(Asp268), respectively. The effect of Asp268 on the oxoG excision was demonstrated with 1H NMR for WT hOGG1 and the hOGG1(D268N) mutant: the excision of oxoG was notably suppressed when Asp268 was mutated to Asn. The loss of the base-excision function was rationalized with QM/MM calculations and Asp268 was confirmed as the electrostatic stabilizer of ribose oxocarbenium through the initial base-excision step of DNA repair. The NMR experiments and QM/MM calculations consistently illustrated the base-excision reaction operated by hOGG1.
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Affiliation(s)
- Jakub Šebera
- The Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo námestí 2, 166 10 Praha, Czech Republic
| | - Yoshikazu Hattori
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama-Boji 180, Yamashiro-cho, Tokushima 770 8514, Japan
| | - Daichi Sato
- Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Sendai 980 8578, Japan
| | - David Reha
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Zámek 136, 373 33 Nové Hrady, Czech Republic
| | - Radim Nencka
- The Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo námestí 2, 166 10 Praha, Czech Republic
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute 1-1, Tsukiji 5-chome, Chuo-ku, Tokyo 104 0045, Japan
| | - Chojiro Kojima
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya-ku, Yokohama 240 8501, Japan
| | - Yoshiyuki Tanaka
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama-Boji 180, Yamashiro-cho, Tokushima 770 8514, Japan.,Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Sendai 980 8578, Japan
| | - Vladimír Sychrovský
- The Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Praha, Czech Republic.,Department of Electrotechnology, Electrical Engineering Czech Technical University, Technická 2, 166 27 Praha, Czech Republic
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Boiteux S, Coste F, Castaing B. Repair of 8-oxo-7,8-dihydroguanine in prokaryotic and eukaryotic cells: Properties and biological roles of the Fpg and OGG1 DNA N-glycosylases. Free Radic Biol Med 2017; 107:179-201. [PMID: 27903453 DOI: 10.1016/j.freeradbiomed.2016.11.042] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 11/22/2016] [Accepted: 11/25/2016] [Indexed: 01/23/2023]
Abstract
Oxidatively damaged DNA results from the attack of sugar and base moieties by reactive oxygen species (ROS), which are formed as byproducts of normal cell metabolism and during exposure to endogenous or exogenous chemical or physical agents. Guanine, having the lowest redox potential, is the DNA base the most susceptible to oxidation, yielding products such as 8-oxo-7,8-dihydroguanine (8-oxoG) and 2-6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG). In DNA, 8-oxoG was shown to be mutagenic yielding GC to TA transversions upon incorporation of dAMP opposite this lesion by replicative DNA polymerases. In prokaryotic and eukaryotic cells, 8-oxoG is primarily repaired by the base excision repair pathway (BER) initiated by a DNA N-glycosylase, Fpg and OGG1, respectively. In Escherichia coli, Fpg cooperates with MutY and MutT to prevent 8-oxoG-induced mutations, the "GO-repair system". In Saccharomyces cerevisiae, OGG1 cooperates with nucleotide excision repair (NER), mismatch repair (MMR), post-replication repair (PRR) and DNA polymerase η to prevent mutagenesis. Human and mouse cells mobilize all these pathways using OGG1, MUTYH (MutY-homolog also known as MYH), MTH1 (MutT-homolog also known as NUDT1), NER, MMR, NEILs and DNA polymerases η and λ, to prevent 8-oxoG-induced mutations. In fact, mice deficient in both OGG1 and MUTYH develop cancer in different organs at adult age, which points to the critical impact of 8-oxoG repair on genetic stability in mammals. In this review, we will focus on Fpg and OGG1 proteins, their biochemical and structural properties as well as their biological roles. Other DNA N-glycosylases able to release 8-oxoG from damaged DNA in various organisms will be discussed. Finally, we will report on the role of OGG1 in human disease and the possible use of 8-oxoG DNA N-glycosylases as therapeutic targets.
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Affiliation(s)
- Serge Boiteux
- Centre de Biophysique Moléculaire, CNRS, UPR4301, rue Charles Sadron, 45072 Orléans, France.
| | - Franck Coste
- Centre de Biophysique Moléculaire, CNRS, UPR4301, rue Charles Sadron, 45072 Orléans, France
| | - Bertrand Castaing
- Centre de Biophysique Moléculaire, CNRS, UPR4301, rue Charles Sadron, 45072 Orléans, France.
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Taniguchi Y. Development of Damaged Nucleoside Mimics for Inhibition of Their Repair Enzymes. YAKUGAKU ZASSHI 2017; 137:293-300. [PMID: 28250323 DOI: 10.1248/yakushi.16-00231-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
8-Oxo-2'-deoxyguanosine (8-oxo-dG) is a representative of nucleoside damage, which is generated by the reaction of the 8 position of dG with reactive oxygen species. Abundant 8-oxo-dG in DNA exhibits genotoxicity and has been linked to aging and disease, such as cancer. As the metabolism of cancer cells is much faster than that of normal cells, the oxidized product of the oligonucleotides and the nucleotide pool produces 8-oxo-dG and 8-oxo-2'-deoxyguanosine triphosphate (8-oxo-dGTP), respectively. Human oxoguanine glycosylase (hOGG1) shows base excision activity for 8-oxo-dG in duplex DNA. On the other hand, human mutT homologue protein (hMTH1, also known as NUDT1) is important for oxidized nucleotide removal including 8-oxo-dGTP, and it is reported that the presence of hMTH1 is not essential for normal cells but is required for the survival of cancer cells. Therefore, we designed and synthesized 8-halogenated 7-deaza-2'-deoxyguanosine triphosphate (8-halo-7-deaza-dGTP) derivatives as mimics of 8-oxo-dGTP in order to interact with hMTH1. The 8-halo-7-deaza-dGTP derivatives were poor substrates for but strong binders to hMTH1. Interestingly, they exhibited strong competitive inhibition of hMTH1 in the hydrolysis of 8-oxo-dGTP. This inhibitory effect is caused by the slower rate of hydrolysis due to possible small enzyme structural changes. Although the detailed inhibition mechanism of the hydrolysis activity of hMTH1 is unknown, this result is the first to demonstrate the potential of nucleoside triphosphate derivatives as antitumor agents.
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Effects of 8-halo-7-deaza-2'-deoxyguanosine triphosphate on DNA synthesis by DNA polymerases and cell proliferation. Bioorg Med Chem 2016; 24:3856-61. [PMID: 27372838 DOI: 10.1016/j.bmc.2016.06.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 06/15/2016] [Accepted: 06/15/2016] [Indexed: 01/23/2023]
Abstract
8-OxodG (8-oxo-2'-deoxyguanosine) is representative of nucleoside damage and shows a genotoxicity. To significantly reveal the contributions of 7-NH and C8-oxygen to the mutagenic effect of 8-oxodG by DNA polymerases, we evaluated the effects of the 8-halo-7-deaza-dG (8-halogenated 7-deaza-2'-deoxyguanosine) derivatives by DNA polymerases. 8-Halo-7-deaza-dGTPs were poorly incorporated by both KF(exo(-)) and human DNA polymerase β opposite dC or dA into the template DNA. Furthermore, it was found that KF(exo(-)) was very sensitive to the introduction of the C8-halogen, while polymerase β can accommodate the C8-halogen resulting in an efficient dCTP insertion opposite the 8-halo-7-deaza-dG in the template DNA. These results indicate that strong hydrogen bonding between 7-NH in the 8-oxo-G nucleobase and 1-N in the adenine at the active site of the DNA polymerase is required for the mutagenic effects. Whereas, I-deaza-dGTP shows an antiproliferative effect for the HeLa cells, suggesting that it could become a candidate as a new antitumor agent.
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Yin Y, Sasaki S, Taniguchi Y. Inhibitory Effect of 8-Halogenated 7-Deaza-2'-deoxyguanosine Triphosphates on Human 8-Oxo-2'-deoxyguanosine Triphosphatase, hMTH1, Activities. Chembiochem 2016; 17:566-9. [PMID: 26879218 DOI: 10.1002/cbic.201500589] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Indexed: 12/12/2022]
Abstract
hMTH1 (8-oxo-2'-deoxyguanine triphosphatase) hydrolyzes oxidized nucleoside triphosphates; its presence is non-essential for survival of normal cells but is required for survival of cancer cells. In this study, 8-halogenated-7-deaza-2'-deoxyguanosine triphosphate (8-halogenated-7-deazadGTP) derivatives were synthesized. Interestingly, these triphosphates were poor substrates for hMTH1, but exhibited strong competitive inhibition against hMTH1 at nanomolar levels. This inhibitory effect is attributed to slower rate of hydrolysis, possibly arising from enzyme structural changes, specifically different stacking interactions with 8-halogenated-7-deazadGTP. This is the first example of using nucleotide derivatives to inhibit hMTH1, thus demonstrating their potential as antitumor agents.
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Affiliation(s)
- Yizhen Yin
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yosuke Taniguchi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
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