Structural analysis of in vivo protein-ligand interactions by 19F-NMR and PRE

• Project/Area Number: 17K07298
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Structural biochemistry
• Research Institution: Tohoku University
• Principal Investigator: Koshiba Seizo 東北大学, 未来型医療創成センター, 教授 (70332301)
• Project Period (FY): 2017-04-01 – 2023-03-31
• Project Status: Completed (Fiscal Year 2022)
• Budget Amount: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000); Fiscal Year 2019: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000); Fiscal Year 2018: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2017: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
• Keywords: NMR / クライオ電子顕微鏡 / 動的構造 / Keap1 / PAH / In-Cell NMR / 19F-NMR / 酵素

Outline of Final Research Achievements

For Keap1-Nrf2 system, we investigated the mechanism of Nrf2 activation by NMR and found that Nrf2 is dissociated from Keap1 by non-electrophilic inhibitors (Nrf2 inducers) or p62, but is not by electrophilic inhibitors, such as CDDO-Im. While there are two Keap1-binding sites (DLGex and ETGE motifs) in Nrf2, these non-electrophilic inhibitors preferentially inhibit the interaction of DLGex, resulting to the intermediate state in which only one binding site, ETGE motif, interacts with Keap1. These results indicate that there are several Nrf2-activation mechanisms and non-electrophilic inhibitors activate Nrf2 by using "Hinge-Latch mechanism". This study provides significant insights for the pharmacological development of new Nrf2 inducers.

Academic Significance and Societal Importance of the Research Achievements

本研究では、生体内におけるストレス応答システムKeap1-Nrf2経路を対象に、各種化合物によるNrf2の活性化のメカニズムの詳細を高次構造変化の視点から明らかにした。Keap1-Nrf2は生体内において様々な疾患に関わることが報告されており、創薬ターゲットとして世界中で研究開発が進められている。本研究成果は今後の創薬開発において重要な情報を提供するものである。

Research Products

• [Journal Article] Transcription factor c-Maf deletion improves streptozotocin-induced diabetic nephropathy by directly regulating Sglt2 and Glut2 (2023)
  • Author(s): Fujino Mitsunori、Morito Naoki、Hayashi Takuto、Ojima Masami、Ishibashi Shun、Kuno Akihiro、Koshiba Seizo、Yamagata Kunihiro、Takahashi Satoru
  • Journal Title: JCI Insight Volume: 8 Issue: 6
  • DOI: 10.1172/jci.insight.163306
  • Peer Reviewed / Open Access
• [Journal Article] Decreased β-hydroxybutyrate and ketogenic amino acid levels in depressed human adults (2023)
  • Author(s): Sato Shiho、Yu Zhiqian、Sakai Mai、Motoike Ikuko N.、Saigusa Daisuke、Hirayama Ryo、Kikuchi Yoshie、Abe Takaaki、Kinoshita Kengo、Koshiba Seizo、Tomita Hiroaki
  • Journal Title: European Journal of Neuroscience Volume: 57 Issue: 6 Pages: 1018
  • DOI: 10.1111/ejn.15931
  • Peer Reviewed / Open Access
• [Journal Article] Maternal Baseline Characteristics and Perinatal Outcomes: The Tohoku Medical Megabank Project Birth and Three-Generation Cohort Study (2022)
  • Author(s): Sugawara, J.,et al., Koshiba, S., et al., Yamamoto, M.（合計32名、本研究者は21番目）
  • Journal Title: Journal of Epidemiology Volume: 32 Issue: 2 Pages: 69-79
  • DOI: 10.2188/jea.JE20200338
  • NAID: 130008157950
  • ISSN: 0917-5040, 1349-9092
  • Year and Date: 2022-02-05
  • Peer Reviewed / Open Access
• [Journal Article] Genome-wide association study of the risk of chronic kidney disease and kidney-related traits in the Japanese population: J-Kidney-Biobank (2022)
  • Author(s): Sugawara Yuka、Hirakawa Yosuke、Nagasu Hajime、Narita Akira、Katayama Akihiro、Wada Jun、Shimizu Miho、Wada Takashi、Kitamura Hiromasa、Nakano Toshiaki、Yokoi Hideki、Yanagita Motoko、Goto Shin、Narita Ichiei、Koshiba Seizo、Tamiya Gen、Nangaku Masaomi、Yamamoto Masayuki、Kashihara Naoki
  • Journal Title: Journal of Human Genetics Volume: 68 Issue: 2 Pages: 55-64
  • DOI: 10.1038/s10038-022-01094-1
  • Peer Reviewed / Open Access
• [Journal Article] Plasma metabolic disturbances during pregnancy and postpartum in women with depression (2022)
  • Author(s): Z Yu, N Matsukawa, D Saigusa, I. N. Motoike, C Ono, Y Okamura, T Onuma, Y Takahashi, M Sakai, H Kudo, T Obara, K Murakami, M Shirota, S Kikuchi, N Kobayashi, Y Kikuchi, J Sugawara, N Minegishi, S Ogishima, K Kinoshita, M Yamamoto, N Yaegashi, S Kuriyama, S Koshiba, H Tomita
  • Journal Title: iScience Volume: 25 Issue: 12 Pages: 105666-105666
  • DOI: 10.1016/j.isci.2022.105666
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Study Profile of the Tohoku Medical Megabank Community-Based Cohort Study (2021)
  • Author(s): Hozawa A, Tanno K, Nakaya N, Nakamura T, Tsuchiya N, Hirata T, Narita A, Kogure M, Nochioka K, Sasaki R, Takanashi N, Otsuka K, Sakata K, Kuriyama S, Kikuya M, 13名略, Kobayashi T, 53名略, Yamamoto M.
  • Journal Title: Journal of Epidemiology Volume: 31 Issue: 1 Pages: 65-76
  • DOI: 10.2188/jea.JE20190271
  • NAID: 130007966030
  • ISSN: 0917-5040, 1349-9092
  • Year and Date: 2021-01-05
  • Peer Reviewed / Open Access
• [Journal Article] Molecular basis for the disruption of Keap1?Nrf2 interaction via Hinge & Latch mechanism (2021)
  • Author(s): Horie Yuta、Suzuki Takafumi、Inoue Jin、Iso Tatsuro、Wells Geoffrey、Moore Terry W.、Mizushima Tsunehiro、Dinkova-Kostova Albena T.、Kasai Takuma、Kamei Takashi、Koshiba Seizo、Yamamoto Masayuki
  • Journal Title: Communications Biology Volume: 4 Issue: 1 Pages: 576-576
  • DOI: 10.1038/s42003-021-02100-6
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Identification of biomarkers to diagnose diseases and find adverse drug reactions by metabolomics (2021)
  • Author(s): Saigusa Daisuke、Matsukawa Naomi、Hishinuma Eiji、Koshiba Seizo
  • Journal Title: Drug Metabolism and Pharmacokinetics Volume: 37 Pages: 100373-100373
  • DOI: 10.1016/j.dmpk.2020.11.008
  • NAID: 210000172800
  • Peer Reviewed / Open Access
• [Journal Article] Comparison of kit-based metabolomics with other methodologies in a large cohort, towards establishing reference values (2021)
  • Author(s): Saigusa D*, Hishinuma E, Matsukawa N, Takahashi M, Inoue J, Tadaka S, Motoike I N, Hozawa A, Izumi Y, Bamba T, Kinoshita K, Ekroos K, Koshiba S, Yamamoto M.
  • Journal Title: Metabolites Volume: 11 Issue: 10 Pages: 652-652
  • DOI: 10.3390/metabo11100652
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Nrf2 plays a critical role in the metabolic response during and after spaceflight (2021)
  • Author(s): Uruno A、Saigusa D、Suzuki T、Yumoto A、Nakamura T、Matsukawa N、Yamazaki T、Saito R、Taguchi K、Suzuki M、Suzuki N、Otsuki A、Katsuoka F、Hishinuma E、Okada R、Koshiba S、Tomioka Y、Shimizu R、Shirakawa M、Kensler TW.、Shiba D、Yamamoto M
  • Journal Title: Communications Biology Volume: 4 Issue: 1 Pages: 1381
  • DOI: 10.1038/s42003-021-02904-6
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Design and Progress of Oral Health Examinations in the Tohoku Medical Megabank Project (2020)
  • Author(s): Tsuboi, A., et al., Koshiba, S., et al., Yamamoto, M.（合計33名、本研究者は20番目）
  • Journal Title: The Tohoku Journal of Experimental Medicine Volume: 251 Issue: 2 Pages: 97-115
  • DOI: 10.1620/tjem.251.97
  • NAID: 130007858973
  • ISSN: 0040-8727, 1349-3329
  • URL: https://pure.teikyo.jp/en/publications/62d8f028-92aa-4584-9ae4-a57a88ed1675
  • Peer Reviewed / Open Access
• [Journal Article] O-Glycan-Altered Extracellular Vesicles: A Specific Serum Marker Elevated in Pancreatic Cancer (2020)
  • Author(s): Yokose, T., et al., Koshiba, S., et al., Kitagawa, Y.（合計32名、本研究者は26番目）
  • Journal Title: Cancers Volume: 12 Issue: 9 Pages: 2469-2469
  • DOI: 10.3390/cancers12092469
  • Peer Reviewed / Open Access
• [Journal Article] Nrf2 contributes to the weight gain of mice during space travel (2020)
  • Author(s): Suzuki, T., et al., Koshiba, S. et al., Yamamoto, M.（合計37名、本研究者は18番目）
  • Journal Title: Communications Biology Volume: 3 Issue: 1 Pages: 496
  • DOI: 10.1038/s42003-020-01227-2
  • NAID: 120007161347
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Identification of critical genetic variants associated with metabolic phenotypes of the Japanese population (2020)
  • Author(s): Koshiba Seizo、Motoike Ikuko N.、Saigusa Daisuke、Inoue Jin、Aoki Yuichi、Tadaka Shu、Shirota Matsuyuki、Katsuoka Fumiki、Tamiya Gen、Minegishi Naoko、Fuse Nobuo、Kinoshita Kengo、Yamamoto Masayuki
  • Journal Title: Communications Biology Volume: 3 Issue: 1 Pages: 662-662
  • DOI: 10.1038/s42003-020-01383-5
  • Peer Reviewed / Open Access
• [Journal Article] jMorp updates in 2020: Large enhancement of multi-omics data resources on the general Japanese population (2020)
  • Author(s): Tadaka Shu、Hishinuma Eiji、Komaki Shohei、Motoike Ikuko N、Kawashima Junko、Saigusa Daisuke、Inoue Jin、Takayama Jun、Okamura Yasunobu、Aoki Yuichi、Shirota Matsuyuki、Otsuki Akihito、Katsuoka Fumiki、Shimizu Atsushi、Tamiya Gen、Koshiba Seizo、Sasaki Makoto、Yamamoto Masayuki、Kinoshita Kengo
  • Journal Title: Nucleic Acids Research Volume: 49 Issue: D1 Pages: D536-D544
  • DOI: 10.1093/nar/gkaa1034
  • Peer Reviewed / Open Access
• [Journal Article] Amino-acid selective isotope labeling enables simultaneous overlapping signal decomposition and information extraction from NMR spectra (2020)
  • Author(s): Takuma Kasai, Shunsuke Ono, Seizo Koshiba, Masayuki Yamamoto, Toshiyuki Tanaka, Shiro Ikeda & Takanori Kigawa
  • Journal Title: Journal of Biomolecular NMR Volume: 74 Issue: 2-3 Pages: 125-137
  • DOI: 10.1007/s10858-019-00295-9
  • Peer Reviewed / Open Access
• [Journal Article] Metabolic Profiling of the Cerebrospinal Fluid in Pediatric Epilepsy (2020)
  • Author(s): Akiyama T, Saigusa D, Hyodo Y, Umeda K, Saijo R, Koshiba S, Kobayashi K
  • Journal Title: Acta Medica Okayama Volume: 74 Issue: 1 Pages: 65-72
  • DOI: 10.18926/AMO/57955
  • NAID: 120006795622
  • URL: https://ousar.lib.okayama-u.ac.jp/57955
  • Peer Reviewed / Open Access
• [Journal Article] Cohort Profile: Tohoku Medical Megabank Project Birth and Three-Generation Cohort Study (TMM BirThree Cohort Study): Rationale, progress and perspective (2020)
  • Author(s): Kuriyama S, Metoki H, Kikuya M, Obara T, Ishikuro M, Yamanaka C, Nagai M, Matsubara H, Kobayashi T, 57名略, Yamamoto M.
  • Journal Title: Int J Epidemiol. Volume: 49 Issue: 1 Pages: 18
  • DOI: 10.1093/ije/dyz169
  • Peer Reviewed / Open Access
• [Journal Article] Identification of novel biomarkers of hepatocellular carcinoma by high-definition mass spectrometry: Ultrahigh-performance liquid chromatography quadrupole time-of-flight mass spectrometry and desorption electrospray ionization mass spectrometry imaging (2020)
  • Author(s): Nagai, K. et al. Koshiba S. et al. Tomioka Y.（合計１７名、本研究者は１４番目）
  • Journal Title: Rapid Commun Mass Spectrom. Volume: 34 Issue: S1
  • DOI: 10.1002/rcm.8551
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] 3.5KJPNv2: an allele frequency panel of 3552 Japanese individuals including the X chromosome (2019)
  • Author(s): Tadaka S. et al. Koshiba S. et al. Kinoshita K.（合計２５名、本研究者は１４番目）
  • Journal Title: Hum Genome Var Volume: 6 Issue: 1 Pages: 28-28
  • DOI: 10.1038/s41439-019-0059-5
  • Peer Reviewed / Open Access
• [Journal Article] ドーピング分析の最前線 日本アンチ・ドーピング研究コンソーシアムの挑戦 (2019)
  • Author(s): 小柴生造，山本雅之
  • Journal Title: 体育の化学 Volume: 69 Pages: 504-509
• [Journal Article] Biallelic GALM pathogenic variants cause a novel type of galactosemia (2019)
  • Author(s): Wada, Y.,（途中略）,Koshiba, S., （途中略）, Kure, S.（合計２４名、本研究者は２２番目）
  • Journal Title: Genet. Med. Volume: 印刷中 Issue: 6 Pages: 1286-1294
  • DOI: 10.1038/s41436-018-0340-x
  • Peer Reviewed
• [Journal Article] Value of global metabolomics in association with diagnosis and clinicopathological factors of renal cell carcinoma (2019)
  • Author(s): Sato, T. （途中略）,Koshiba, S., （途中略）, Arai, Y.（合計１５名、本研究者は１３番目）
  • Journal Title: Int. J. Cancer Volume: 145 Issue: 2 Pages: 484
  • DOI: 10.1002/ijc.32115
  • Peer Reviewed / Open Access
• [Journal Article] Maternity Log study: A longitudinal lifelog monitoring and multiomics analysis for the early prediction of complicated pregnancy (2019)
  • Author(s): Sugawara J, Ochi D, Yamashita R, Yamauchi T, Saigusa D, Wagata M, Obara T, Ishikuro M, Tsunemoto Y, 18名略, Hiyama S, Nagasaki M
  • Journal Title: BMJ Open Volume: 9 Issue: 2 Pages: e025939-e025939
  • DOI: 10.1136/bmjopen-2018-025939
  • Peer Reviewed / Open Access
• [Journal Article] Estimating carrier frequencies of newborn screening disorders using a whole-genome reference panel of 3552 Japanese individuals (2019)
  • Author(s): Yamaguchi-Kabata, Y.,（途中略）,Koshiba, S., （途中略）, Tohoku Medical Megabank Project Study Group.（合計１9名、本研究者は５番目）
  • Journal Title: Hum. Genet. Volume: 印刷中 Issue: 4 Pages: 389-409
  • DOI: 10.1007/s00439-019-01998-7
  • Peer Reviewed / Open Access
• [Journal Article] Omics research project on prospective cohort studies from the Tohoku Medical Megabank Project (2018)
  • Author(s): Koshiba, S., （途中略）, Yamamoto, M.（合計２１名、本研究者は１番目）
  • Journal Title: Genes Cells Volume: 23 Issue: 6 Pages: 406
  • DOI: 10.1111/gtc.12588
  • Peer Reviewed / Open Access
• [Journal Article] Metabolomic changes in the mouse retina after optic nerve injury (2018)
  • Author(s): Sato K, Saigusa D, Saito R, Fujioka A, Nakagawa Y, Nishiguchi KM, Kokubun T, Motoike IN, Maruyama K, Omodaka K, Shiga Y, Uruno A, Koshiba S, Yamamoto M, Nakazawa T.
  • Journal Title: Sci Rep Volume: 8 Issue: 1 Pages: 11930-11930
  • DOI: 10.1038/s41598-018-30464-z
  • Peer Reviewed / Open Access
• [Journal Article] Genome analyses for the Tohoku Medical Megabank Project towards establishment of personalized healthcare (2018)
  • Author(s): Yasuda Jun、Kinoshita Kengo、et al.,
  • Journal Title: The Journal of Biochemistry Volume: 165 Issue: 2 Pages: 139
  • DOI: 10.1093/jb/mvy096
  • NAID: 40021809939
  • Peer Reviewed / Open Access
• [Journal Article] JMorp: Japanese Multi Omics Reference Panel (2018)
  • Author(s): Tadaka S, Saigusa D, Motoike, I.N, Aoki Y, Shirota M, Koshiba S, Yamamoto M, and Kinoshita K.
  • Journal Title: Nucleic Acids Res. Volume: 46 Issue: D1 Pages: D551-D557
  • DOI: 10.1093/nar/gkx978
  • URL: https://pure.teikyo.jp/en/publications/d91494df-d7be-4ad7-8407-c4aa3c4b66c9
  • Peer Reviewed / Open Access
• [Journal Article] Evaluation of reported pathogenic variants and their frequencies in a Japanese population based on a whole-genome reference panel of 2049 individuals article (2018)
  • Author(s): Y Yamaguchi-Kabata, J Yasuda, O Tanabe, Y Suzuki, H Kawame, N Fuse, M Nagasaki, Y Kawai, K Kojima, F Katsuoka, S Saito, I Danjoh, I Motoike, R Yamashita, S Koshiba, D Saigusa, G Tamiya, S Kure, N Yaegashi, Y Kawaguchi, F Nagami, S Kuriyama, J Sugawara, N Minegishi, A Hozawa, T Takai-Igarashi, K Kinoshita, M Yamamoto.
  • Journal Title: Journal of Human Genetics. Volume: 63 Issue: 2 Pages: 213
  • DOI: 10.1038/s10038-017-0347-1
  • Peer Reviewed / Open Access
• [Presentation] 遺伝・生活習慣が日本人の血中代謝プロファイルに与える影響の解析 (2022)
  • Author(s): 小柴生造、元池育子、井上仁、菱沼英史、青木裕一、櫻井美由紀、佐藤允治、七谷圭、田高周、城田松之、木下賢吾、山本雅之.
  • Organizer: 第９５回日本生化学会大会
• [Presentation] 東北大学の最新クライオ電子顕微鏡の活用と共同利用について (2021)
  • Author(s): 小柴生造、木下賢吾、山本雅之
  • Organizer: 第59回日本生物物理学会大会
• [Presentation] 東北メディカル・メガバンク計画におけるメタボローム解析 (2021)
  • Author(s): 小柴生造
  • Organizer: 第３１回日本疫学会
  • Invited
• [Presentation] Metabolic phenotyping of individuals in baseline and repeat surveys of Tohoku Medical Megabank Cohort Project (2019)
  • Author(s): Koshiba S., Saigusa D., Motoike I., Inoue, J., Shirota M., Aoki Y., Tadaka S., Kinoshita K., Yamamoto M
  • Organizer: Metabolomics 2019
  • Int'l Joint Research
• [Presentation] コホート調査における代謝プロファイルの経時変化の解析 (2019)
  • Author(s): 小柴生造，元池育子，三枝大輔，井上仁，菱沼英史，青木裕一，田高周，城田松之，木下賢吾，山本雅之
  • Organizer: 第92回 日本生化学会大会
• [Presentation] Multi Omics Research Project in Tohoku Medical Megabank Organizatio (2018)
  • Author(s): S. Koshiba, I. Motoike, D. Saigusa, J. Inoue, M. Shirota, Y. Aoki, S. Tadaka, S. Tomo, K. Kinoshita, M. Yamamoto
  • Organizer: 日本質量分析学会・日本プロテオーム学会 ２０１８合同大会
  • Invited
• [Presentation] ゲノム情報と連携した日本人多層オミックス参照パネルの意義 (2018)
  • Author(s): 小柴生造，元池育子，三枝大輔，井上仁，城田松之，青木裕一，田高周，斎藤智，木下賢吾，山本雅之
  • Organizer: 第61回日本糖尿病学会年次学術集会
  • Invited
• [Presentation] Metabolic phenotyping in the population based cohort studies of Tohoku Medical Megabank Project (2018)
  • Author(s): Seizo Koshiba, Daisuke Saigusa, Ikuko Motoike, Jin Inoue, Matsuyuki Shirota, Yuichi Aoki, Shu Tadaka, Kengo Kinoshita, Masayuki Yamamoto
  • Organizer: Metabolomics 2018
  • Int'l Joint Research
• [Presentation] Structural and functional analyses of oxidative stress response by Keap1-Nrf2 system (2018)
  • Author(s): Seizo Koshiba, Tatsuro Iso, Jin Inoue, Aki Muramatsu, Takafumi Suzuki, Takanori Kigawa, and Masayuki Yamamoto
  • Organizer: ICMRBS 2018
  • Int'l Joint Research
• [Presentation] メタボロームGWASによる日本人の代謝プロファイルの解析 (2018)
  • Author(s): 小柴生造，元池育子，三枝大輔，井上仁，青木裕一, 田高周, 城田松之，木下賢吾，山本雅之
  • Organizer: 第９１回 日本生化学会大会
• [Presentation] コホート研究におけるオミックス解析 (2017)
  • Author(s): 小柴生造
  • Organizer: 日本人類遺伝学会
  • Invited
• [Presentation] Metabolomics Approach in Tohoku Medical Megabank Project Prospective Cohort Studies. (2017)
  • Author(s): Seizo Koshiba, Daisuke Saigusa, Ikuko Motoike, Natsuyuki Shirota, Jun Yasuda, Kenga Kinoshita, Masayuki Yamamoto.
  • Organizer: Metabolomics 2017
  • Int'l Joint Research
• [Presentation] 東北メディカル・メガバンク機構のオミックス解析 (2017)
  • Author(s): 小柴生造
  • Organizer: 第11回メタボロームシンポジウム
• [Presentation] 酸化ストレス応答におけるKeap1の構造・相互作用解析 (2017)
  • Author(s): 井上仁, 村松亜紀, 鈴木隆史, 磯達朗, 小柴生造, 山本雅之
  • Organizer: 第56回NMR討論会
• [Presentation] 高精度日本人多層オミックス参照パネルの提供 (2017)
  • Author(s): 小柴生造
  • Organizer: 第90回日本生化学会大会
• [Presentation] メタボローム解析による血液検体保管条件の検討 (2017)
  • Author(s): 井上仁, 三枝大輔, 工藤久智, 峯岸直子, 小柴生造, 山本雅之.
  • Organizer: 第90回日本生化学会大会
• [Book] 最新医学 74巻2号 特集 バイオインフォマティクスの進展・臨床応用 (2019)
  • Author(s): 小柴生造
  • Total Pages: 312
  • Publisher: 最新医学社
• [Book] 遺伝子医学MOOK(32) 難病研究up-to-date (2017)
  • Author(s): 小柴生造、山本雅之
  • Total Pages: 280
  • Publisher: メディカルドゥ
  • ISBN: 9784944157624
• [Remarks] 日本人多層オミックス参照パネル
  • URL: https://jmorp.megabank.tohoku.ac.jp/