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Asamitsu S, Yabuki Y, Matsuo K, Kawasaki M, Hirose Y, Kashiwazaki G, Chandran A, Bando T, Wang DO, Sugiyama H, Shioda N. RNA G-quadruplex organizes stress granule assembly through DNAPTP6 in neurons. Sci Adv 2023; 9:eade2035. [PMID: 36827365 PMCID: PMC9956113 DOI: 10.1126/sciadv.ade2035] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Consecutive guanine RNA sequences can adopt quadruple-stranded structures, termed RNA G-quadruplexes (rG4s). Although rG4-forming sequences are abundant in transcriptomes, the physiological roles of rG4s in the central nervous system remain poorly understood. In the present study, proteomics analysis of the mouse forebrain identified DNAPTP6 as an RNA binding protein with high affinity and selectivity for rG4s. We found that DNAPTP6 coordinates the assembly of stress granules (SGs), cellular phase-separated compartments, in an rG4-dependent manner. In neurons, the knockdown of DNAPTP6 diminishes the SG formation under oxidative stress, leading to synaptic dysfunction and neuronal cell death. rG4s recruit their mRNAs into SGs through DNAPTP6, promoting RNA self-assembly and DNAPTP6 phase separation. Together, we propose that the rG4-dependent phase separation of DNAPTP6 plays a critical role in neuronal function through SG assembly.
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Affiliation(s)
- Sefan Asamitsu
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan
- Center for Biosystems Dynamics Research (BDR), RIKEN, Kobe, Japan
| | - Yasushi Yabuki
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Kazuya Matsuo
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan
| | - Moe Kawasaki
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yuki Hirose
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Gengo Kashiwazaki
- Major in Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Japan
| | - Anandhakumar Chandran
- Ludwig Cancer Research Oxford, University of Oxford, Old Road Campus Research Building, Oxford, UK
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Dan Ohtan Wang
- Center for Biosystems Dynamics Research (BDR), RIKEN, Kobe, Japan
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
- Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto, Japan
| | - Norifumi Shioda
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
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2
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Kashiwazaki G, Watanabe R, Nishikawa A, Kawamura K, Kitayama T, Hibi T. A selective hybrid fluorescent sensor for fructose detection based on a phenylboronic acid and BODIPY-based hydrophobicity probe. RSC Adv 2022; 12:15083-15090. [PMID: 35693230 PMCID: PMC9116957 DOI: 10.1039/d2ra01569b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/11/2022] [Indexed: 11/21/2022] Open
Abstract
Fructose is widely used in the food industry. However, it may be involved in diseases by generating harmful advanced glycation end-products. We have designed and synthesized a novel fluorescent probe for fructose detection by combining a phenylboronic acid group with a BODIPY-based hydrophobicity probe. This probe showed a linear fluorescence response to d-fructose concentration in the range of 100-1000 μM, with a detection limit of 32 μM, which is advantageous for the simple and sensitive determination of fructose.
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Affiliation(s)
- Gengo Kashiwazaki
- Major in Advanced Bioscience, Graduate School of Agriculture, Kindai University 3327-204, Nakamachi Nara Nara 631-8505 Japan
| | - Ryo Watanabe
- Major in Advanced Bioscience, Graduate School of Agriculture, Kindai University 3327-204, Nakamachi Nara Nara 631-8505 Japan
| | - Akihiro Nishikawa
- Major in Advanced Bioscience, Graduate School of Agriculture, Kindai University 3327-204, Nakamachi Nara Nara 631-8505 Japan
| | - Koyori Kawamura
- Department of Bioscience and Biotechnology, Faculty of Bioscience and Biotechnology, Fukui Prefectural University 4-1-1 Matsuoka-Kenjojima, Eiheiji Fukui 910-1195 Japan
| | - Takashi Kitayama
- Major in Advanced Bioscience, Graduate School of Agriculture, Kindai University 3327-204, Nakamachi Nara Nara 631-8505 Japan
| | - Takao Hibi
- Department of Bioscience and Biotechnology, Faculty of Bioscience and Biotechnology, Fukui Prefectural University 4-1-1 Matsuoka-Kenjojima, Eiheiji Fukui 910-1195 Japan
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Shiohama Y, Fujita R, Sonokawa M, Hisano M, Kotake Y, Krstic-Demonacos M, Demonacos C, Kashiwazaki G, Kitayama T, Fujii M. Elimination of Off-Target Effect by Chemical Modification of 5′-End of Small Interfering RNA. Nucleic Acid Ther 2022; 32:438-447. [DOI: 10.1089/nat.2021.0068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Yasuo Shiohama
- Environmental and Biological Information Group, Tropical Biosphere Research Centre, University of the Ryukyus, Nishihara, Japan
| | - Ryosuke Fujita
- Department of Biological & Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Maika Sonokawa
- Department of Biological & Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Masaaki Hisano
- Department of Biological & Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Yojiro Kotake
- Department of Biological & Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Marija Krstic-Demonacos
- School of Science, Engineering and Environment, University of Salford, Salford, United Kingdom
| | - Constantinos Demonacos
- Division of Pharmacy and Optometry, Faculty of Biology Medicine and Health, School of Health Science, University of Manchester, Manchester, United Kingdom
| | - Gengo Kashiwazaki
- Department of Advanced Bioscience, Faculty of Agriculture, Kindai University, Nara, Japan
| | - Takashi Kitayama
- Department of Advanced Bioscience, Faculty of Agriculture, Kindai University, Nara, Japan
| | - Masayuki Fujii
- Department of Biological & Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
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Kashiwazaki G, Watanabe R, Tsuzuki T, Yamamoto C, Nishikawa A, Ohtomo S, Yoshikawa T, Kitamura Y, Utaka Y, Kawai Y, Tsuchida N, Kitayama T. Brønsted acid-induced transannulation of the phytochemical zerumbone. Org Biomol Chem 2021; 19:10444-10454. [PMID: 34812828 DOI: 10.1039/d1ob01634b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The sesquiterpene zerumbone was treated with HCl in ethyl acetate under the light-protected condition, and the time-dependent conversions were analyzed by gas chromatography. Nine products were isolated, and their structures were revealed by several NMR measurements such as 1H NMR, 13C{1H} NMR, distortionless enhancement by polarization transfer (DEPT)-135, 1H-1H correlation spectroscopy (COSY), 1H-13C heteronuclear multiple quantum coherence (HMQC), and 1H-13C heteronuclear multiple bond coherence (HMBC). The X-ray crystallography determined the stereochemistries of the three products and the two derivatives. After all, this acidic reaction was found to provide the (2Z,6E,10E)-isomer, the two HCl adducts, the two 7,6-bicyclic compounds, the valence isomers cycloheptatriene and norcaradiene, and the two dihydronaphthalenes. Based on the product analyses of the reactions from the isolated intermediates as well as the mechanistic considerations, these products were arranged into two paths: one of the paths ended in the two dihydronaphthalenes the same as previously reported under the Lewis acid condition; the other ended in the 7,6-bicyclic compound, the epimer of which was known. In addition, density functional theory (DFT) calculations indicated that the (2Z,6E,10E)-isomer was more stable than the (2E,6E,10Z)-isomer as well as that the activation energy for the isomerization at the C2-C3 double bond decreased to half by protonation. The closely examined reaction mechanisms under the simple acidic condition were established upon the intensive characterization of the intermediates and products, and these findings would add to the attractive value of zerumbone and would help understand the unknown biosynthetic pathway around sesquiterpenoids.
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Affiliation(s)
- Gengo Kashiwazaki
- Major in Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Nara 631-8505, Japan.
| | - Ryo Watanabe
- Major in Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Nara 631-8505, Japan.
| | - Terutaka Tsuzuki
- Major in Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Nara 631-8505, Japan.
| | - Chieko Yamamoto
- Major in Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Nara 631-8505, Japan.
| | - Atsuya Nishikawa
- Major in Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Nara 631-8505, Japan.
| | - Satoru Ohtomo
- Major in Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Nara 631-8505, Japan.
| | - Tomomi Yoshikawa
- Major in Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Nara 631-8505, Japan.
| | - Yuto Kitamura
- Major in Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Nara 631-8505, Japan.
| | - Yoshimi Utaka
- Major in Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Nara 631-8505, Japan.
| | - Yasushi Kawai
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Noriko Tsuchida
- Faculty of Medicine, Saitama Medical University, Moroyama, Saitama 350-0495, Japan
| | - Takashi Kitayama
- Major in Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Nara 631-8505, Japan.
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Lee JA, An J, Taniguchi J, Kashiwazaki G, Pandian GN, Parveen N, Kang TM, Sugiyama H, De D, Kim KK. Targeted epigenetic modulation using a DNA-based histone deacetylase inhibitor enhances cardiomyogenesis in mouse embryonic stem cells. J Cell Physiol 2020; 236:3946-3962. [PMID: 33164232 DOI: 10.1002/jcp.30140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 09/25/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022]
Abstract
The epigenome has an essential role in orchestrating transcriptional activation and modulating key developmental processes. Previously, we developed a library of pyrrole-imidazole polyamides (PIPs) conjugated with suberoylanilide hydroxamic acid (SAHA), a histone deacetylase (HDAC) inhibitor, for the purpose of sequence-specific modification of epigenetics. Based on the gene expression profile of SAHA-PIPs and screening studies using the α-myosin heavy chain promoter-driven reporter and SAHA-PIP library, we identified that SAHA-PIP G activates cardiac-related genes. Studies in mouse ES cells showed that SAHA-PIP G could enhance the generation of spontaneous beating cells, which is consistent with upregulation of several cardiac-related genes. Moreover, ChIP-seq results confirmed that the upregulation of cardiac-related genes is highly correlated with epigenetic activation, relevant to the sequence-specific binding of SAHA-PIP G. This proof-of-concept study demonstrating the applicability of SAHA-PIP not only improves our understanding of epigenetic alterations involved in cardiomyogenesis but also provides a novel chemical-based strategy for stem cell differentiation.
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Affiliation(s)
- Jin-A Lee
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Jieun An
- Department of Physiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Junichi Taniguchi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto, Japan
| | - Gengo Kashiwazaki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto, Japan
| | - Ganesh N Pandian
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto, Japan
| | - Nazia Parveen
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Tong Mook Kang
- Department of Physiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto, Japan
| | - Debojyoti De
- Department of Biotechnology, National Institute of Technology, Durgapur, Burdwan, West Bengal, India
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
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Utaka Y, Kashiwazaki G, Tsuchida N, Fukushima M, Takahashi I, Kawai Y, Kitayama T. Remarkable Potential of Zerumbone to Generate a Library with Six Natural Product-like Skeletons by Natural Material-Related Diversity-Oriented Synthesis. J Org Chem 2020; 85:8371-8386. [PMID: 32524816 DOI: 10.1021/acs.joc.0c00689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Diversity-oriented synthesis (DOS) is an effective strategy for the quick creation of diverse and high three-dimensional compounds from simple starting materials. The selection of a starting material is the key to constructing useful, chemically diverse compound libraries for the development of new drugs. Here, we report a novel, general, and facile strategy for the creation of diverse compounds with high structural diversity from readily available natural products, such as zerumbone, as the synthetic starting material. Zerumbone is the major component of the essential oil from wild ginger, Zingiber zerumbet Smith. It is noteworthy that zerumbone has a powerful latent reactivity, partly because of its three double bonds, two conjugated and one isolated, and a double conjugated carbonyl group in an 11-membered ring structure. In fact, zerumbone has been shown to be a successful example of natural material-related DOS (NMRDOS). We will report that zerumbone can be converted in one chemical step from four zerumbone derivatives into rare and markedly different scaffolds by transannulation.
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Affiliation(s)
- Yoshimi Utaka
- Major in Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara 631-8505, Japan
| | - Gengo Kashiwazaki
- Major in Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara 631-8505, Japan
| | - Noriko Tsuchida
- Faculty of Medicine, Saitama Medical University, Saitama 350-0495, Japan
| | - Miyuki Fukushima
- Major in Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara 631-8505, Japan
| | - Issei Takahashi
- Major in Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara 631-8505, Japan
| | - Yasushi Kawai
- Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Takashi Kitayama
- Major in Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara 631-8505, Japan
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Utaka Y, Kashiwazaki G, Tajima S, Fujiwara Y, Sumi K, Itoh T, Kitayama T. Antiproliferative effects of zerumbone-pendant derivatives on human T-cell lymphoid cell line Jurkat cells. Tetrahedron 2019. [DOI: 10.1016/j.tet.2019.01.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Noguchi Y, Wariishi N, Iwai S, Kashiwazaki G, Taniguchi J, Bando T, Baba M, Adachi S, Sugiyama H, Kamikubo Y. Abstract 3357: Genetic regulation of RUNX2 induce apoptotic cell death through regulating the expression of SOX2 in CRPC-NE cells. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Although runt-related transcription factor 2 (RUNX2) is well known for its bone-specific transcriptional regulator in highly metastatic prostate cancer, there is little knowledge about its role of RUNX2 in castration-resistant neuroendocrine prostate cancer (it is named CRPC-NE). It is well known that expression of Androgen Receptor (AR) in CRPC-NE cases is lower than other types and AR suppresses RUNX2 expression by binding it and abrogating its recruitment to DNA. This fact suggests that in CRPC-NE, low expression of AR, the addiction of RUNX2 is relatively higher than that of other prostate cancer types. Extensive analysis of the clinical datasets revealed that RUNX2 is one of the most consistently up-regulated genes in CRPC-NE and the overexpression of SOX2 confers an accelerated disease progression and shortened overall survival periods to CRPC-NE patients. We also found that the silencing RUNX2 induced apoptotic cell death in CRPC-NE cells independent on p53, but through transcriptionally down-regulating SOX2 expressions. Mechanistically, ChIP-qPCR assay and luciferase reporter experiments confirmed that RUNX2 positively regulates SOX2 expression by binding to the consensus RUNX2 binding sequence (5'-TGTGGT-3') located in the proximal promoter region of SOX2. Short hairpin RNA (shRNA)-mediated knockdown of RUNX2 in the CRPC-NE cell line PC-3 induced the decreased expression of SOX2 and the increased expression of cleaved form of caspase-3 and PARP in a p53 independent manner. Silencing of SOX2 in PC-3 cells suppressed the proliferation of these cancer cells and induced apoptosis, which phenotypes were rescued by restoring SOX2 in the cells. These data indicates that inhibition of SOX2-apoptosis axis via RUNX2 could be a better therapeutic choice in CRPC-NE. Lastly, we examined the efficacy of our novel molecule Chlorambucil-conjugated Pyrrole Imidazole Polyamide (we named it as Chb-M'), which specifically binds to the consensus RUNX2 binding sequence and inhibits RUNX2 target gene. Surprisingly, Chb-M' had tremendous inhibitory effect on PC-3 cells (IC50 value at 620 nM) through effective SOX2 inhibition. Additionally, it was exceptionally well-tolerated in mice and exerted excellent efficacy against xenograft mice models of CRPC-NE. Taken together, our work identified a novel interaction of RUNX2 and SOX2-apoptosis axis, offering a new strategy for the management of poor-prognostic advanced stage CRPC-NE cancer patients.
Citation Format: Yuki Noguchi, Natsuki Wariishi, Shiina Iwai, Gengo Kashiwazaki, Junichi Taniguchi, Toshikazu Bando, Masaya Baba, Souichi Adachi, Hiroshi Sugiyama, Yasuhiko Kamikubo. Genetic regulation of RUNX2 induce apoptotic cell death through regulating the expression of SOX2 in CRPC-NE cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3357.
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Kashiwazaki G, Maeda R, Kawase T, Hashiya K, Bando T, Sugiyama H. Evaluation of alkylating pyrrole-imidazole polyamide conjugates by a novel method for high-throughput sequencer. Bioorg Med Chem 2018; 26:1-7. [DOI: 10.1016/j.bmc.2017.08.057] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 12/13/2022]
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Kashiwazaki G, Maeda R, Kawase T, Hashiya K, Bando T, Sugiyama H. WITHDRAWN: Evaluation of alkylating pyrrole-imidazole polyamide conjugates by a novel method for high-throughput sequencer. Bioorg Med Chem 2017:S0968-0896(17)31427-X. [PMID: 29884583 DOI: 10.1016/j.bmc.2017.07.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 07/15/2017] [Indexed: 11/24/2022]
Affiliation(s)
- Gengo Kashiwazaki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo, Kyoto 606-8502, Japan
| | - Rina Maeda
- Graduate School of Advanced Integrated Studies in Human Survivability, Kyoto University, Nakaadachi-cho, Yoshida, Sakyo, Kyoto 606-8306, Japan
| | - Takashi Kawase
- Department of Systems Science, Graduate School of Informatics, Kyoto University, Yoshida-Honmachi 36-1, Sakyo, Kyoto 606-8501, Japan
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo, Kyoto 606-8502, Japan.
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiya-cho, Sakyo, Kyoto 606-8501, Japan.
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Mitsuda Y, Morita K, Maeda S, Suzuki K, Kashiwazaki G, Taniguchi J, Bando T, Sugiyama H, Adachi S, Kamikubo Y. Abstract 1530: RUNX1 positively regulates ErbB2/HER2 signaling pathway through modulating the expression of SOS1 in gastric cancer cells. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-1530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Although runt-related transcription factor 1 (RUNX1) is well known for its context-dependent oncogenic properties in various malignancies, its role in gastric cancers has been poorly defined. Up-regulation of receptor tyrosine kinase (RTK) ErbB2/HER2 signaling pathway is encountered in the vast majority of gastric cancer cases and contributes to the initiation and maintenance of these cancer cells. This signaling cascade is partly yet arbitrary mediated by son of sevenless gene 1 (SOS1), which functions as an adaptor protein in RTK cascades. Herein we report that RUNX1 regulates ErbB2/HER2 signaling pathway in gastric cancer cells through transcriptionally regulating SOS1 expressions, rendering itself an ideal target in anticancer strategies. Mechanistically, RUNX1 interacts with the consensus RUNX1 binding sequence (5’-TGTGGT-3’) located in the proximal promoter region of SOS1 and positively regulates it. Short hairpin RNA (shRNA)-mediated knockdown of RUNX1 in the gastric cancer cell line MKN45 led to the decreased expression of SOS1 and of phosphorylated form of ErbB2/HER2 as well as the deactivation of its downstream targets such as AKT and ERK. RUNX1 knockdown subsequently induced cell cycle arrest at G0/G1 phase and successive apoptotic cell death in MKN45 cells. Silencing of HER2 or SOS1 in MKN45 cells unalterably suppressed the proliferation of these cancer cells, highlighting the importance of this ErbB2/HER2 signaling cascade in the maintenance of gastric cancer cells. We also found that SOS1 is one of the most consistently up-regulated genes in RUNX1-high expressing primary gastric cancer cells derived from previously reported human clinical samples. These data collectively indicates that inhibition of RUNX1 could be a legitimate therapeutic choice in the management of gastric cancers. Lastly, we examined the efficacy of a novel small molecule specifically binds and inhibits RUNX1 (we named it as CM). Intriguingly, CM was exceptionally effective against MKN45 cells (IC50 value at 403.5 nM). Besides, CM was well-tolerated in mice and fabulously suppressed the growth of xenotransplanted MKN45 cells in immunodeficient mice in vivo. Taken together, our work identified a novel interaction of RUNX1 and ErbB2/HER2 signaling pathway, paving a new way for the management of dismal-prognostic advanced stage HER2-positive gastric cancer patients.
Citation Format: Yoshihide Mitsuda, Ken Morita, Shintaro Maeda, Kensho Suzuki, Gengo Kashiwazaki, Junichi Taniguchi, Toshikazu Bando, Hiroshi Sugiyama, Souichi Adachi, Yasuhiko Kamikubo. RUNX1 positively regulates ErbB2/HER2 signaling pathway through modulating the expression of SOS1 in gastric cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1530. doi:10.1158/1538-7445.AM2017-1530
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Morita K, Suzuki K, Maeda S, Matsuo A, Mitsuda Y, Tokushige C, Kashiwazaki G, Taniguchi J, Maeda R, Noura M, Hirata M, Kataoka T, Yano A, Yamada Y, Kiyose H, Tokumasu M, Matsuo H, Tanaka S, Okuno Y, Muto M, Naka K, Ito K, Kitamura T, Kaneda Y, Liu PP, Bando T, Adachi S, Sugiyama H, Kamikubo Y. Genetic regulation of the RUNX transcription factor family has antitumor effects. J Clin Invest 2017; 127:2815-2828. [PMID: 28530640 DOI: 10.1172/jci91788] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 04/06/2017] [Indexed: 12/23/2022] Open
Abstract
Runt-related transcription factor 1 (RUNX1) is generally considered to function as a tumor suppressor in the development of leukemia, but a growing body of evidence suggests that it has pro-oncogenic properties in acute myeloid leukemia (AML). Here we have demonstrated that the antileukemic effect mediated by RUNX1 depletion is highly dependent on a functional p53-mediated cell death pathway. Increased expression of other RUNX family members, including RUNX2 and RUNX3, compensated for the antitumor effect elicited by RUNX1 silencing, and simultaneous attenuation of all RUNX family members as a cluster led to a much stronger antitumor effect relative to suppression of individual RUNX members. Switching off the RUNX cluster using alkylating agent-conjugated pyrrole-imidazole (PI) polyamides, which were designed to specifically bind to consensus RUNX-binding sequences, was highly effective against AML cells and against several poor-prognosis solid tumors in a xenograft mouse model of AML without notable adverse events. Taken together, these results identify a crucial role for the RUNX cluster in the maintenance and progression of cancer cells and suggest that modulation of the RUNX cluster using the PI polyamide gene-switch technology is a potential strategy to control malignancies.
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Affiliation(s)
- Ken Morita
- Department of Human Health Sciences, Graduate School of Medicine.,Department of Pediatrics, Graduate School of Medicine, and
| | - Kensho Suzuki
- Department of Human Health Sciences, Graduate School of Medicine
| | - Shintaro Maeda
- Department of Human Health Sciences, Graduate School of Medicine
| | - Akihiko Matsuo
- Department of Human Health Sciences, Graduate School of Medicine
| | | | - Chieko Tokushige
- Department of Human Health Sciences, Graduate School of Medicine
| | - Gengo Kashiwazaki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Junichi Taniguchi
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Rina Maeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Mina Noura
- Department of Human Health Sciences, Graduate School of Medicine
| | - Masahiro Hirata
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Tatsuki Kataoka
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Ayaka Yano
- Department of Human Health Sciences, Graduate School of Medicine
| | - Yoshimi Yamada
- Department of Human Health Sciences, Graduate School of Medicine
| | - Hiroki Kiyose
- Department of Human Health Sciences, Graduate School of Medicine
| | - Mayu Tokumasu
- Department of Human Health Sciences, Graduate School of Medicine
| | - Hidemasa Matsuo
- Department of Human Health Sciences, Graduate School of Medicine
| | - Sunao Tanaka
- Department of Human Health Sciences, Graduate School of Medicine
| | - Yasushi Okuno
- Department of Human Health Sciences, Graduate School of Medicine
| | - Manabu Muto
- Department of Therapeutic Oncology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kazuhito Naka
- Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Kosei Ito
- Department of Molecular Bone Biology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Toshio Kitamura
- Division of Cellular Therapy and Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yasufumi Kaneda
- Division of Gene Therapy Science, Department of Genome Biology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Paul P Liu
- Oncogenesis and Development Section, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Souichi Adachi
- Department of Human Health Sciences, Graduate School of Medicine.,Department of Pediatrics, Graduate School of Medicine, and
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan
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13
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Heidinger L, Kneuttinger AC, Kashiwazaki G, Weber S, Carell T, Schleicher E. Direct observation of a deoxyadenosyl radical in an active enzyme environment. FEBS Lett 2016; 590:4489-4494. [PMID: 27878994 DOI: 10.1002/1873-3468.12498] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 11/11/2022]
Abstract
5'-deoxyadenosyl radicals have been proposed as the first common intermediate in the molecular reaction mechanism of the family of radical S-adenosyl-l-methionine (SAM) enzymes. However, this radical species has not yet been directly observed in a catalytically active enzyme environment. In a reduced and SAM-containing C140A mutant of the spore photoproduct lyase from Geobacillus thermodenitrificans, a mutant with altered catalytic activity, we were able to identify an organic radical with pronounced hyperfine structure using electron paramagnetic resonance spectroscopy. Guided by quantum-chemical computations at the density functional theory level of theory, this radical could be tentatively assigned to a deoxyadenosyl radical, which provides first experimental evidence for this intermediate in the reaction mechanism of radical SAM enzymes.
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Affiliation(s)
- Lorenz Heidinger
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Andrea C Kneuttinger
- Department für Chemie, Ludwig-Maximilians-Universität München, Germany.,Institute of Biophysics and Physical Biochemistry, University of Regensburg, Germany
| | - Gengo Kashiwazaki
- Department für Chemie, Ludwig-Maximilians-Universität München, Germany
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Thomas Carell
- Department für Chemie, Ludwig-Maximilians-Universität München, Germany
| | - Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
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14
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Guo C, Asamitsu S, Kashiwazaki G, Sato S, Bando T, Sugiyama H. DNA Interstrand Crosslinks by H-pin Polyamide (S
)-seco
-CBI Conjugates. Chembiochem 2016; 18:166-170. [DOI: 10.1002/cbic.201600425] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Chuanxin Guo
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwakecho Sakyo-ku Kyoto Japan
| | - Sefan Asamitsu
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwakecho Sakyo-ku Kyoto Japan
| | - Gengo Kashiwazaki
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwakecho Sakyo-ku Kyoto Japan
| | - Shinsuke Sato
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS); Kyoto University; Yoshida-Ushinomiyacho Sakyo-ku Kyoto Japan
| | - Toshikazu Bando
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwakecho Sakyo-ku Kyoto Japan
| | - Hiroshi Sugiyama
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwakecho Sakyo-ku Kyoto Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS); Kyoto University; Yoshida-Ushinomiyacho Sakyo-ku Kyoto Japan
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15
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Wei Y, Pandian GN, Zou T, Taniguchi J, Sato S, Kashiwazaki G, Vaijayanthi T, Hidaka T, Bando T, Sugiyama H. A Multi-target Small Molecule for Targeted Transcriptional Activation of Therapeutically Significant Nervous System Genes. ChemistryOpen 2016; 5:517-521. [PMID: 28032018 PMCID: PMC5167308 DOI: 10.1002/open.201600125] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Indexed: 12/17/2022] Open
Abstract
An integrated multi‐target small molecule capable of altering dynamic epigenetic and transcription programs associated with the brain and nervous system has versatile applications in the regulation of therapeutic and cell‐fate genes. Recently, we have been constructing targeted epigenetic ON switches by integrating sequence‐specific DNA binding pyrrole‐imidazole polyamides with a potent histone deacetylase inhibitor SAHA. Here, we identified a DNA‐based epigenetic ON switch termed SAHA‐L as the first‐ever multi‐target small molecule capable of inducing transcription programs associated with the human neural system and brain synapses networks in BJ human foreskin fibroblasts and 201B7‐iPS cells. Ingenuity pathway analysis showed that SAHA‐L activates the signaling of synaptic receptors like glutamate and γ‐aminobutyric acid, which are key components of autism spectrum disorders. The long‐term incubation of SAHA‐L in 201B7‐iPS cells induced morphology changes and promoted a neural progenitor state. Our finding suggests that the tunable SAHA‐L could be advanced as a cell‐type‐independent multi‐target small molecule for therapeutic and/or cell‐fate gene modulation.
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Affiliation(s)
- Yulei Wei
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Ganesh N Pandian
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS) Kyoto University Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
| | - Tingting Zou
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Junichi Taniguchi
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Shinsuke Sato
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS) Kyoto University Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
| | - Gengo Kashiwazaki
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Thangavel Vaijayanthi
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Takuya Hidaka
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Toshikazu Bando
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Hiroshi Sugiyama
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto606-8502 Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS) Kyoto University Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
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16
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Kashiwazaki G, Chandran A, Asamitsu S, Kawase T, Kawamoto Y, Sawatani Y, Hashiya K, Bando T, Sugiyama H. Comparative Analysis of DNA-Binding Selectivity of Hairpin and Cyclic Pyrrole-Imidazole Polyamides Based on Next-Generation Sequencing. Chembiochem 2016; 17:1752-8. [DOI: 10.1002/cbic.201600282] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Indexed: 12/23/2022]
Affiliation(s)
- Gengo Kashiwazaki
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawaoiwakecho Sakyo Kyoto 606-8502 Japan
| | - Anandhakumar Chandran
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawaoiwakecho Sakyo Kyoto 606-8502 Japan
| | - Sefan Asamitsu
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawaoiwakecho Sakyo Kyoto 606-8502 Japan
| | - Takashi Kawase
- Department of Systems Science; Graduate School of Informatics; Kyoto University; Yoshida-Honmachi 36-1 Sakyo Kyoto 606-8501 Japan
| | - Yusuke Kawamoto
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawaoiwakecho Sakyo Kyoto 606-8502 Japan
| | - Yoshito Sawatani
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawaoiwakecho Sakyo Kyoto 606-8502 Japan
| | - Kaori Hashiya
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawaoiwakecho Sakyo Kyoto 606-8502 Japan
| | - Toshikazu Bando
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawaoiwakecho Sakyo Kyoto 606-8502 Japan
| | - Hiroshi Sugiyama
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawaoiwakecho Sakyo Kyoto 606-8502 Japan
- Institute for Integrated Cell-Material Sciences (iCeMS); Kyoto University; Yoshida-Ushinomiyacho Sakyo Kyoto 606-8501 Japan
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17
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Sawatani Y, Kashiwazaki G, Chandran A, Asamitsu S, Guo C, Sato S, Hashiya K, Bando T, Sugiyama H. Sequence-specific DNA binding by long hairpin pyrrole-imidazole polyamides containing an 8-amino-3,6-dioxaoctanoic acid unit. Bioorg Med Chem 2016; 24:3603-11. [PMID: 27301681 DOI: 10.1016/j.bmc.2016.05.070] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 05/28/2016] [Accepted: 05/30/2016] [Indexed: 12/13/2022]
Abstract
With the aim of improving aqueous solubility, we designed and synthesized five N-methylpyrrole (Py)-N-methylimidazole (Im) polyamides capable of recognizing 9-bp sequences. Their DNA-binding affinities and sequence specificities were evaluated by SPR and Bind-n-Seq analyses. The design of polyamide 1 was based on a conventional model, with three consecutive Py or Im rings separated by a β-alanine to match the curvature and twist of long DNA helices. Polyamides 2 and 3 contained an 8-amino-3,6-dioxaoctanoic acid (AO) unit, which has previously only been used as a linker within linear Py-Im polyamides or between Py-Im hairpin motifs for tandem hairpin. It is demonstrated herein that AO also functions as a linker element that can extend to 2-bp in hairpin motifs. Notably, although the AO-containing unit can fail to bind the expected sequence, polyamide 4, which has two AO units facing each other in a hairpin form, successfully showed the expected motif and a KD value of 16nM was recorded. Polyamide 5, containing a β-alanine-β-alanine unit instead of the AO of polyamide 2, was synthesized for comparison. The aqueous solubilities and nuclear localization of three of the polyamides were also examined. The results suggest the possibility of applying the AO unit in the core of Py-Im polyamide compounds.
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Affiliation(s)
- Yoshito Sawatani
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan
| | - Gengo Kashiwazaki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan
| | - Anandhakumar Chandran
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan
| | - Sefan Asamitsu
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan
| | - Chuanxin Guo
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan
| | - Shinsuke Sato
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-Ushinomiyacho, Sakyo, Kyoto 606-8501, Japan
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan.
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-Ushinomiyacho, Sakyo, Kyoto 606-8501, Japan.
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18
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Chandran A, Syed J, Taylor RD, Kashiwazaki G, Sato S, Hashiya K, Bando T, Sugiyama H. Deciphering the genomic targets of alkylating polyamide conjugates using high-throughput sequencing. Nucleic Acids Res 2016; 44:4014-24. [PMID: 27098039 PMCID: PMC4872120 DOI: 10.1093/nar/gkw283] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 04/05/2016] [Indexed: 12/17/2022] Open
Abstract
Chemically engineered small molecules targeting specific genomic sequences play an important role in drug development research. Pyrrole-imidazole polyamides (PIPs) are a group of molecules that can bind to the DNA minor-groove and can be engineered to target specific sequences. Their biological effects rely primarily on their selective DNA binding. However, the binding mechanism of PIPs at the chromatinized genome level is poorly understood. Herein, we report a method using high-throughput sequencing to identify the DNA-alkylating sites of PIP-indole-seco-CBI conjugates. High-throughput sequencing analysis of conjugate 2: showed highly similar DNA-alkylating sites on synthetic oligos (histone-free DNA) and on human genomes (chromatinized DNA context). To our knowledge, this is the first report identifying alkylation sites across genomic DNA by alkylating PIP conjugates using high-throughput sequencing.
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Affiliation(s)
- Anandhakumar Chandran
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Junetha Syed
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Rhys D Taylor
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Gengo Kashiwazaki
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Shinsuke Sato
- Institute for Integrated Cell-Materials Science (iCeMS) Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan Institute for Integrated Cell-Materials Science (iCeMS) Kyoto University, Sakyo, Kyoto 606-8502, Japan CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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19
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Taylor RD, Chandran A, Kashiwazaki G, Hashiya K, Bando T, Nagase H, Sugiyama H. Selective Targeting of the KRAS Codon 12 Mutation Sequence by Pyrrole-Imidazole Polyamideseco-CBI Conjugates. Chemistry 2015; 21:14996-5003. [DOI: 10.1002/chem.201501870] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Indexed: 12/16/2022]
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20
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Han L, Pandian GN, Chandran A, Sato S, Taniguchi J, Kashiwazaki G, Sawatani Y, Hashiya K, Bando T, Xu Y, Qian X, Sugiyama H. A Synthetic DNA-Binding Domain Guides Distinct Chromatin-Modifying Small Molecules to Activate an Identical Gene Network. Angew Chem Int Ed Engl 2015; 54:8700-3. [PMID: 26094767 DOI: 10.1002/anie.201503607] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Indexed: 12/20/2022]
Abstract
Synthetic dual-function ligands targeting specific DNA sequences and histone-modifying enzymes were applied to achieve regulatory control over multi-gene networks in living cells. Unlike the broad array of targeting small molecules for histone deacetylases (HDACs), few modulators are known for histone acetyltransferases (HATs), which play a central role in transcriptional control. As a novel chemical approach to induce selective HAT-regulated genes, we conjugated a DNA-binding domain (DBD) "I" to N-(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxy-benzamide (CTB), an artificial HAT activator. In vitro enzyme activity assays and microarray studies were used to demonstrate that distinct functional small molecules could be transformed to have identical bioactivity when conjugated with a targeting DBD. This proof-of-concept synthetic strategy validates the switchable functions of HDACs and HATs in gene regulation and provides a molecular basis for developing versatile bioactive ligands.
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Affiliation(s)
- Le Han
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan).,Shanghai Key Laboratory of Chemical Biology, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237 (China)
| | - Ganesh N Pandian
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University Yoshida-Ushinomiyacho, Sakyo-ku, Kyoto 606-8501 (Japan)
| | - Anandhakumar Chandran
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)
| | - Shinsuke Sato
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University Yoshida-Ushinomiyacho, Sakyo-ku, Kyoto 606-8501 (Japan)
| | - Junichi Taniguchi
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)
| | - Gengo Kashiwazaki
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)
| | - Yoshito Sawatani
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)
| | - Yufang Xu
- Shanghai Key Laboratory of Chemical Biology, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237 (China)
| | - Xuhong Qian
- Shanghai Key Laboratory of Chemical Biology, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237 (China)
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan). .,Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University Yoshida-Ushinomiyacho, Sakyo-ku, Kyoto 606-8501 (Japan).
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21
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Han L, Pandian GN, Chandran A, Sato S, Taniguchi J, Kashiwazaki G, Sawatani Y, Hashiya K, Bando T, Xu Y, Qian X, Sugiyama H. A Synthetic DNA-Binding Domain Guides Distinct Chromatin-Modifying Small Molecules to Activate an Identical Gene Network. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503607] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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22
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Syed J, Chandran A, Pandian GN, Taniguchi J, Sato S, Hashiya K, Kashiwazaki G, Bando T, Sugiyama H. A Synthetic Transcriptional Activator of Genes Associated with the Retina in Human Dermal Fibroblasts. Chembiochem 2015; 16:1497-501. [DOI: 10.1002/cbic.201500140] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Indexed: 01/30/2023]
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23
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Pfaffeneder T, Spada F, Wagner M, Brandmayr C, Laube SK, Eisen D, Truss M, Steinbacher J, Hackner B, Kotljarova O, Schuermann D, Michalakis S, Kosmatchev O, Schiesser S, Steigenberger B, Raddaoui N, Kashiwazaki G, Müller U, Spruijt CG, Vermeulen M, Leonhardt H, Schär P, Müller M, Carell T. Tet oxidizes thymine to 5-hydroxymethyluracil in mouse embryonic stem cell DNA. Nat Chem Biol 2014; 10:574-81. [PMID: 24838012 DOI: 10.1038/nchembio.1532] [Citation(s) in RCA: 219] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 04/17/2014] [Indexed: 12/25/2022]
Abstract
Ten eleven translocation (Tet) enzymes oxidize the epigenetically important DNA base 5-methylcytosine (mC) stepwise to 5-hydroxymethylcytosine (hmC), 5-formylcytosine and 5-carboxycytosine. It is currently unknown whether Tet-induced oxidation is limited to cytosine-derived nucleobases or whether other nucleobases are oxidized as well. We synthesized isotopologs of all major oxidized pyrimidine and purine bases and performed quantitative MS to show that Tet-induced oxidation is not limited to mC but that thymine is also a substrate that gives 5-hydroxymethyluracil (hmU) in mouse embryonic stem cells (mESCs). Using MS-based isotope tracing, we show that deamination of hmC does not contribute to the steady-state levels of hmU in mESCs. Protein pull-down experiments in combination with peptide tracing identifies hmU as a base that influences binding of chromatin remodeling proteins and transcription factors, suggesting that hmU has a specific function in stem cells besides triggering DNA repair.
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Affiliation(s)
- Toni Pfaffeneder
- 1] Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany. [2]
| | - Fabio Spada
- 1] Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany. [2]
| | - Mirko Wagner
- 1] Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany. [2]
| | - Caterina Brandmayr
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Silvia K Laube
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - David Eisen
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Matthias Truss
- Charité Universitätsklinikum, Otto-Heubner-Centrum für Kinder und Jugendmedizin, Klinik für Allgemeine Pädiatrie, Labor für Pädiatrische Molekularbiologie, Berlin, Germany
| | - Jessica Steinbacher
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Benjamin Hackner
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Olga Kotljarova
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - David Schuermann
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Stylianos Michalakis
- Center for Integrated Protein Science at the Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-Universität München, München, Germany
| | - Olesea Kosmatchev
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Stefan Schiesser
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Barbara Steigenberger
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Nada Raddaoui
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Gengo Kashiwazaki
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Udo Müller
- Center for Integrated Protein Science at the Department of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Cornelia G Spruijt
- Department of Molecular Cancer Research, Cancer Genomics Netherlands, Utrecht, The Netherlands
| | - Michiel Vermeulen
- 1] Department of Molecular Cancer Research, Cancer Genomics Netherlands, Utrecht, The Netherlands. [2]
| | - Heinrich Leonhardt
- Center for Integrated Protein Science at the Department of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Primo Schär
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Markus Müller
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Thomas Carell
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
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Han YW, Tsunaka Y, Yokota H, Matsumoto T, Kashiwazaki G, Morinaga H, Hashiya K, Bando T, Sugiyama H, Harada Y. Construction and characterization of Cy3- or Cy5-conjugated hairpin pyrrole–imidazole polyamides binding to DNA in the nucleosome. Biomater Sci 2014; 2:297-307. [DOI: 10.1039/c3bm60202h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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25
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Kneuttinger AC, Kashiwazaki G, Prill S, Heil K, Müller M, Carell T. Formation and Direct Repair of UV-induced Dimeric DNA Pyrimidine Lesions. Photochem Photobiol 2013; 90:1-14. [PMID: 24354557 DOI: 10.1111/php.12197] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 10/17/2013] [Indexed: 12/11/2022]
Abstract
Direct repair of UV-induced DNA lesions represents an elegant method for many organisms to deal with these highly mutagenic and cytotoxic compounds. Although the participating proteins are structurally well investigated, the exact repair mechanism of the photolyase enzymes remains a vivid subject of current research. In this review, we summarize and highlight the recent contributions to this exciting field.
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Affiliation(s)
- Andrea Christa Kneuttinger
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Gengo Kashiwazaki
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Stefan Prill
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Korbinian Heil
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Markus Müller
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Thomas Carell
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
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26
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Schiesser S, Pfaffeneder T, Sadeghian K, Hackner B, Steigenberger B, Schröder AS, Steinbacher J, Kashiwazaki G, Höfner G, Wanner KT, Ochsenfeld C, Carell T. Deamination, oxidation, and C-C bond cleavage reactivity of 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine. J Am Chem Soc 2013; 135:14593-9. [PMID: 23980549 DOI: 10.1021/ja403229y] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Three new cytosine derived DNA modifications, 5-hydroxymethyl-2'-deoxycytidine (hmdC), 5-formyl-2'-deoxycytidine (fdC) and 5-carboxy-2'-deoxycytidine (cadC) were recently discovered in mammalian DNA, particularly in stem cell DNA. Their function is currently not clear, but it is assumed that in stem cells they might be intermediates of an active demethylation process. This process may involve base excision repair, C-C bond cleaving reactions or deamination of hmdC to 5-hydroxymethyl-2'-deoxyuridine (hmdU). Here we report chemical studies that enlighten the chemical reactivity of the new cytosine nucleobases. We investigated their sensitivity toward oxidation and deamination and we studied the C-C bond cleaving reactivity of hmdC, fdC, and cadC in the absence and presence of thiols as biologically relevant (organo)catalysts. We show that hmdC is in comparison to mdC rapidly oxidized to fdC already in the presence of air. In contrast, deamination reactions were found to occur only to a minor extent. The C-C bond cleavage reactions require the presence of high concentration of thiols and are acid catalyzed. While hmdC dehydroxymethylates very slowly, fdC and especially cadC react considerably faster to dC. Thiols are active site residues in many DNA modifiying enzymes indicating that such enzymes could play a role in an alternative active DNA demethylation mechanism via deformylation of fdC or decarboxylation of cadC. Quantum-chemical calculations support the catalytic influence of a thiol on the C-C bond cleavage.
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Affiliation(s)
- Stefan Schiesser
- Center for Integrated Protein Science (CiPSM) at the Department of Chemistry, ‡Chair for Theoretical Chemistry at the Department of Chemistry, §Center for Drug Research at the Department of Pharmacy, Ludwig-Maximilians-Universität München , Butenandtstrasse 5-13, 81377 Munich, Germany
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27
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Kneuttinger AC, Heil K, Kashiwazaki G, Carell T. The radical SAM enzyme spore photoproduct lyase employs a tyrosyl radical for DNA repair. Chem Commun (Camb) 2013; 49:722-4. [PMID: 23228940 DOI: 10.1039/c2cc37735g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The spore photoproduct lyase is a radical SAM enzyme, which repairs 5-(α-thyminyl)-5,6-dihydrothymidine. Here we show that the enzyme establishes a complex radical transfer cascade and creates a cysteine and a tyrosyl radical dyade to establish repair. This allows the enzyme to solve topological and energetic problems associated with the radical based repair reaction.
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Affiliation(s)
- Andrea Christa Kneuttinger
- Center for Integrative Protein Science at the Department for Chemistry, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377 Munich, Germany
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28
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Han YW, Matsumoto T, Yokota H, Kashiwazaki G, Morinaga H, Hashiya K, Bando T, Harada Y, Sugiyama H. Binding of hairpin pyrrole and imidazole polyamides to DNA: relationship between torsion angle and association rate constants. Nucleic Acids Res 2012; 40:11510-7. [PMID: 23042247 PMCID: PMC3526260 DOI: 10.1093/nar/gks897] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
N-methylpyrrole (Py)-N-methylimidazole (Im) polyamides are small organic molecules that bind to DNA with sequence specificity and can be used as synthetic DNA-binding ligands. In this study, five hairpin eight-ring Py-Im polyamides 1-5 with different number of Im rings were synthesized, and their binding behaviour was investigated with surface plasmon resonance assay. It was found that association rate (k(a)) of the Py-Im polyamides with their target DNA decreased with the number of Im in the Py-Im polyamides. The structures of four-ring Py-Im polyamides derived from density functional theory revealed that the dihedral angle of the Py amide carbonyl is 14∼18°, whereas that of the Im is significantly smaller. As the minor groove of DNA has a helical structure, planar Py-Im polyamides need to change their conformation to fit it upon binding to the minor groove. The data explain that an increase in planarity of Py-Im polyamide induced by the incorporation of Im reduces the association rate of Py-Im polyamides. This fundamental knowledge of the binding of Py-Im polyamides to DNA will facilitate the design of hairpin Py-Im polyamides as synthetic DNA-binding modules.
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Affiliation(s)
- Yong-Woon Han
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida Honmachi, Sakyo, Kyoto 606-8501, Japan.
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29
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Yoshidome T, Endo M, Kashiwazaki G, Hidaka K, Bando T, Sugiyama H. Sequence-selective single-molecule alkylation with a pyrrole-imidazole polyamide visualized in a DNA nanoscaffold. J Am Chem Soc 2012; 134:4654-60. [PMID: 22320236 DOI: 10.1021/ja209023u] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We demonstrate a novel strategy for visualizing sequence-selective alkylation of target double-stranded DNA (dsDNA) using a synthetic pyrrole-imidazole (PI) polyamide in a designed DNA origami scaffold. Doubly functionalized PI polyamide was designed by introduction of an alkylating agent 1-(chloromethyl)-5-hydroxy-1,2-dihydro-3H-benz[e]indole (seco-CBI) and biotin for sequence-selective alkylation at the target sequence and subsequent streptavidin labeling, respectively. Selective alkylation of the target site in the substrate DNA was observed by analysis using sequencing gel electrophoresis. For the single-molecule observation of the alkylation by functionalized PI polyamide using atomic force microscopy (AFM), the target position in the dsDNA (∼200 base pairs) was alkylated and then visualized by labeling with streptavidin. Newly designed DNA origami scaffold named "five-well DNA frame" carrying five different dsDNA sequences in its cavities was used for the detailed analysis of the sequence-selectivity and alkylation. The 64-mer dsDNAs were introduced to five individual wells, in which target sequence AGTXCCA/TGGYACT (XY = AT, TA, GC, CG) was employed as fully matched (X = G) and one-base mismatched (X = A, T, C) sequences. The fully matched sequence was alkylated with 88% selectivity over other mismatched sequences. In addition, the PI polyamide failed to attach to the target sequence lacking the alkylation site after washing and streptavidin treatment. Therefore, the PI polyamide discriminated the one mismatched nucleotide at the single-molecule level, and alkylation anchored the PI polyamide to the target dsDNA.
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Affiliation(s)
- Tomofumi Yoshidome
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
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Kashiwazaki G, Bando T, Yoshidome T, Masui S, Takagaki T, Hashiya K, Pandian GN, Yasuoka J, Akiyoshi K, Sugiyama H. Synthesis and Biological Properties of Highly Sequence-Specific-Alkylating N-Methylpyrrole–N-Methylimidazole Polyamide Conjugates. J Med Chem 2012; 55:2057-66. [DOI: 10.1021/jm201225z] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Gengo Kashiwazaki
- Department of Chemistry, Graduate
School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502
| | - Toshikazu Bando
- Department of Chemistry, Graduate
School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502
| | - Tomofumi Yoshidome
- Department of Chemistry, Graduate
School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502
| | - Seiji Masui
- Department of Chemistry, Graduate
School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502
| | - Toshiki Takagaki
- Department of Chemistry, Graduate
School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502
| | - Kaori Hashiya
- Department of Chemistry, Graduate
School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502
| | - Ganesh N. Pandian
- Institute for Integrated Cell-Material
Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho,
Sakyo-ku, Kyoto 606-8501
| | - Junichi Yasuoka
- Institute of Biomaterials and
Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062
| | - Kazunari Akiyoshi
- Institute of Biomaterials and
Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062
- Graduate School of Engineering, Kyoto University, Kyoto daigaku-Katsura, Nishikyo-ku,
Kyoto 615-8530
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate
School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502
- Institute for Integrated Cell-Material
Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho,
Sakyo-ku, Kyoto 606-8501
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Yasuda A, Noguchi K, Minoshima M, Kashiwazaki G, Kanda T, Katayama K, Mitsuhashi J, Bando T, Sugiyama H, Sugimoto Y. DNA ligand designed to antagonize EBNA1 represses Epstein-Barr virus-induced immortalization. Cancer Sci 2011; 102:2221-30. [PMID: 21910783 DOI: 10.1111/j.1349-7006.2011.02098.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Epstein-Barr virus (EBV) transforms human B lymphocytes into immortalized cells in vitro and is associated with various malignancies in vivo. EBNA1, which is expressed in the majority of EBV-infected cells, recognizes specific DNA sequences at the cis-acting latent origin of plasmid replication (oriP) element of the EBV genome. EBNA1 plays a critical role in the viral episome maintenance and transactivates viral transforming genes in latently infected cells. Therefore, DNA-targeting agents that can disrupt the EBNA1-oriP interaction will offer novel functional inhibitors of EBNA1. Pyrrole-imidazole polyamides, sequence-specific DNA ligands, can be designed to interfere with the binding of various transcriptional factors. Here, we synthesized pyrrole-imidazole polyamides targeting EBNA1-bound DNA sequences and developed an inhibitor for the EBNA1-oriP interaction. A pyrrole-imidazole polyamide, designated as DSE-3, bound adjacent to the EBNA1 recognition sequences located in the dyad symmetry element of oriP, and selectively inhibited EBNA1-oriP binding both in vitro and in vivo. DSE-3 also inhibited the proliferation of established lymphoblastoid cell lines by eradicating EBV episomes from the cells. In addition, DSE-3 repressed the expression of viral transforming genes after infecting human peripheral blood mononuclear cells with EBV and, as a consequence, inhibited EBV-mediated B-cell immortalization. These results suggest that EBNA1 functions will be an attractive pharmacological target for EBV-associated diseases.
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Affiliation(s)
- Ai Yasuda
- Division of Chemotherapy, Keio University, Tokyo, Japan
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Takagaki T, Bando T, Kitano M, Hashiya K, Kashiwazaki G, Sugiyama H. Evaluation of PI polyamide conjugates with eight-base pair recognition and improvement of the aqueous solubility by PEGylation. Bioorg Med Chem 2011; 19:5896-902. [PMID: 21903400 DOI: 10.1016/j.bmc.2011.08.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 08/04/2011] [Accepted: 08/05/2011] [Indexed: 11/15/2022]
Abstract
To investigate the effect of elongating base-pair (bp) recognition sequences, we synthesized N-methylpyrrole-N-methylimidazole (PI) polyamide conjugates with eight-bp recognition (3-5). The DNA alkylating activities of conjugates 3-5 were evaluated by high-resolution denaturing polyacrylamide gel electrophoresis with a 208-bp DNA fragment. Conjugates 3-5 showed high alkylating activities at nanomolar concentrations. We then addressed the following issue about PI conjugates. Generally, PI polyamide conjugates hardly dissolve in aqueous solution. To improve the aqueous solubility, by the introduction of hydrophilic groups, we synthesized PI polyamide conjugates that were modified with a seco-CBI moiety (6-11). Conjugates 9-11 that were modified by methoxypolyethylene glycol (PEG) 750 acquired moderate solubility and stability in aqueous solution. In addition, conjugates 10 and 11 had high cytotoxicity against A549 and DU145.
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Affiliation(s)
- Toshiki Takagaki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto 606-8502, Japan
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33
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Kashiwazaki G, Bando T, Shinohara KI, Minoshima M, Kumamoto H, Nishijima S, Sugiyama H. Alkylation of a human telomere sequence by heterotrimeric chlorambucil PI polyamide conjugates. Bioorg Med Chem 2010; 18:2887-93. [DOI: 10.1016/j.bmc.2010.03.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 03/04/2010] [Accepted: 03/05/2010] [Indexed: 12/16/2022]
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Nishijima S, Shinohara KI, Bando T, Minoshima M, Kashiwazaki G, Sugiyama H. Cell permeability of Py–Im-polyamide-fluorescein conjugates: Influence of molecular size and Py/Im content. Bioorg Med Chem 2010; 18:978-83. [DOI: 10.1016/j.bmc.2009.07.018] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Revised: 07/06/2009] [Accepted: 07/07/2009] [Indexed: 10/20/2022]
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35
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Koide T, Kashiwazaki G, Furukawa K, Osuka A. Homo- and Heterobismetal Complexes of 5-Hydroxy-10,15,25,30-tetrakis(pentafluorophenyl)-Substituted [26]Hexaphyrin(1.1.1.1.1.1). Inorg Chem 2009; 48:4595-7. [DOI: 10.1021/ic900084p] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Taro Koide
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan,
| | - Gengo Kashiwazaki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan,
| | - Ko Furukawa
- Institute for Molecular Science, Myodaiji, Okazaki 444-8585, Japan
| | - Atsuhiro Osuka
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan,
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36
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Koide T, Kashiwazaki G, Suzuki M, Furukawa K, Yoon MC, Cho S, Kim D, Osuka A. A Stable Radical Species from Facile Oxygenation of meso-Free 5,10,20,25-Tetrakis(pentafluorophenyl)-Substituted [26]Hexaphyrin(1.1.1.1.1.1). Angew Chem Int Ed Engl 2008; 47:9661-5. [DOI: 10.1002/anie.200804570] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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37
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Koide T, Kashiwazaki G, Suzuki M, Furukawa K, Yoon MC, Cho S, Kim D, Osuka A. A Stable Radical Species from Facile Oxygenation of meso-Free 5,10,20,25-Tetrakis(pentafluorophenyl)-Substituted [26]Hexaphyrin(1.1.1.1.1.1). Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200804570] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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38
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Fujimoto J, Bando T, Minoshima M, Kashiwazaki G, Nishijima S, Shinohara KI, Sugiyama H. Perylene-conjugated pyrrole polyamide as a sequence-specific fluorescent probe. Bioorg Med Chem 2008; 16:9741-4. [DOI: 10.1016/j.bmc.2008.09.073] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Revised: 09/26/2008] [Accepted: 09/26/2008] [Indexed: 10/21/2022]
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39
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Kashiwazaki G, Bando T, Sugiyama H. Sequence-specific alkylation of DNA by pyrrole-imidazole polyamides through cooperative interaction. Nucleic Acids Symp Ser (Oxf) 2008:365-6. [PMID: 18776405 DOI: 10.1093/nass/nrn184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We designed and synthesized an alkylating N-methylpyrrole (Py) -N-methylimidazole (Im) polyamide and l-(chloromethyl)-5-hydroxy-l,2-dihydro-3H benz[e]indole (seco-CBI) conjugate 1. DNA alkylating activities of conjugate 1 were evaluated by high-resolution denaturing polyacrylamide gel electrophoresis with DNA fragment containing human telomere repeat sequence. These results revealed that simultaneous treatment of the DNA fragment with conjugate 1 and Distamycin A (Dist) alkylate at the 5(')-GGTTAGGGTTA-3' sequence effectively due to cooperative interaction. Moreover, this combination has achieved 11-base-pair (bp) recognition. Thus, it is suggested that the utilization of one alkylating agent possessing long Py-Im polyamide moiety and short Py-Im polyamide partner can be an expedient way to attain the extension and precision of the recognition of DNA sequence.
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Affiliation(s)
- Gengo Kashiwazaki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
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40
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Bando T, Minoshima M, Kashiwazaki G, Shinohara KI, Sasaki S, Fujimoto J, Ohtsuki A, Murakami M, Nakazono S, Sugiyama H. Requirement of β-alanine components in sequence-specific DNA alkylation by pyrrole–imidazole conjugates with seven-base pair recognition. Bioorg Med Chem 2008; 16:2286-91. [DOI: 10.1016/j.bmc.2007.11.064] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Accepted: 11/25/2007] [Indexed: 10/22/2022]
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41
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Bando T, Fujimoto J, Minoshima M, Shinohara KI, Sasaki S, Kashiwazaki G, Mizumura M, Sugiyama H. Detection of CAG repeat DNA sequences by pyrene-functionalized pyrrole-imidazole polyamides. Bioorg Med Chem 2007; 15:6937-42. [PMID: 17826098 DOI: 10.1016/j.bmc.2007.07.055] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2007] [Accepted: 07/30/2007] [Indexed: 11/16/2022]
Abstract
Five N-methylpyrrole-N-methylimidazole (Py-Im) polyamides possessing a fluorescent pyrene were synthesized by Fmoc solid-phase synthesis using Py/Im monomers and pyrenylbutyl-pyrrole monomer compound 9. The steady state fluorescence of conjugates 1-5 was examined in the presence and absence of (CAG)(12)-containing oligodeoxynucleotides (ODNs) 1 and 2. Of the conjugates, conjugate 1 showed no background emission around 470 nm in the absence of ODNs, and a clear increase of emission at 475 nm was observed upon addition of ODNs 1 and 2. The emission of conjugate 1 at 475 nm increased linearly with the concentration of ODN and the number of CAG repeats. The results indicate that conjugate 1 efficiently forms a pyrene excimer upon binding in the minor groove of DNA.
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Affiliation(s)
- Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
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