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2023 Fiscal Year Annual Research Report

新たな創薬資源の採集調査と新奇天然物生合成マシナリーの探索と解明

Research Project

Project/Area Number 20KK0173
Research InstitutionThe University of Tokyo

Principal Investigator

阿部 郁朗  東京大学, 大学院薬学系研究科(薬学部), 教授 (40305496)

Co-Investigator(Kenkyū-buntansha) 淡川 孝義  国立研究開発法人理化学研究所, 環境資源科学研究センター, チームリーダー (80609834) [Withdrawn]
森 貴裕  東京大学, 大学院薬学系研究科(薬学部), 准教授 (60734564)
牛丸 理一郎  東京大学, 大学院薬学系研究科(薬学部), 助教 (10873648)
Project Period (FY) 2020-10-27 – 2024-03-31
Keywords創薬資源採集調査 / 天然物生合成 / 生合成マシナリー / 生物多様性
Outline of Annual Research Achievements

以下の4つの項目を2020年度から4年間の計画で遂行した。
(1)植物内生菌、土壌微生物の最終単離(中国側が主導)長鎖対象地域として、未開拓薬用資源の宝庫、生物多様性ホットスポットとされる、中国南西部を選択した。(2)低分子化合物の単離構造決定、生物活性評価(中国側が主導)上述したカルチャー・コレクションについて、異なる培養条件下で二次代謝産物生産を詳細に検討し、微生物が生産する二次代謝産物とその生物活性を網羅的に解析した。(3)生合成マシナリーの解明と物質生産系の構築(日本側と中国側で同時進行)上述したカルチャー・コレクションで、有用な生物活性物質生産能を示した微生物について、バイオインフォマティクスの技術を駆使したゲノムマイニングにより、テルペン、ポリケタイド、ペプチドなど、生物間相互作用に重要な役割を演ずる可能性が予想される創薬シード合物の新奇生合成酵素遺伝子を網羅的に探索し、その生合成マシナリーの詳細を解明る。大腸菌や酵母、麹菌などを宿主として、これら遺伝子の異種発現による物質生産系を構築する。有機化学を基盤として、生合成反応機構の詳細を酵素遺伝子レベルで明らかにする。(4)酵素結晶構造解析、機能改変と生合成リデザイン(日本側が主導)X線結晶構造解析により、酵素反応の立体構造基盤を明らかにするとともに、結晶構造に基づく酵素触媒機能の拡張と最適化をめざす。さらなる構造多様性の拡大と物質生産系の構築を実現し、所望の構造を有する、天然物を凌ぐ新規有用活性物質の安定供給をめざした。

最終年度も、質量ともに充実した研究成果をあげることに成功した。また、Enfumafungin抗生物質の生合成マシナリーの解明(JACS2024)、生薬クコの実(枸杞子)有効成分の生合成に関わる新奇配糖化酵素の構造機能解析(Nat Commun, in revision)など、共同研究成果が着実に多くの優れた共著論文に実りつつある。

  • Research Products

    (31 results)

All 2024 2023 Other

All Int'l Joint Research (6 results) Journal Article (19 results) (of which Int'l Joint Research: 9 results,  Peer Reviewed: 19 results,  Open Access: 6 results) Presentation (5 results) (of which Int'l Joint Research: 5 results,  Invited: 5 results) Remarks (1 results)

  • [Int'l Joint Research] ジ南大学/中国科学院/浙江大学(中国)

    • Country Name
      CHINA
    • Counterpart Institution
      ジ南大学/中国科学院/浙江大学
    • # of Other Institutions
      3
  • [Int'l Joint Research] チェコ科学アカデミー(チェコ)

    • Country Name
      CZECH
    • Counterpart Institution
      チェコ科学アカデミー
  • [Int'l Joint Research] ノースカロライナ大/テキサス大/カーネギーメロン大(米国)

    • Country Name
      U.S.A.
    • Counterpart Institution
      ノースカロライナ大/テキサス大/カーネギーメロン大
  • [Int'l Joint Research] マンチェスター大(英国)

    • Country Name
      UNITED KINGDOM
    • Counterpart Institution
      マンチェスター大
  • [Int'l Joint Research] オークランド大(ニュージーランド)

    • Country Name
      NEW ZEALAND
    • Counterpart Institution
      オークランド大
  • [Int'l Joint Research]

    • # of Other Countries
      1
  • [Journal Article] Unusual cysteine modifications in natural product biosynthesis2024

    • Author(s)
      Gao Yaojie、Zhu Yuhao、Awakawa Takayoshi、Abe Ikuro
    • Journal Title

      RSC Chemical Biology

      Volume: 5 Pages: 299~311

    • DOI

      10.1039/D4CB00020J

    • Peer Reviewed / Open Access
  • [Journal Article] Characterization of Aziridine-Forming α-Ketoglutarate-Dependent Oxygenase in L-Isovaline Biosynthesis2024

    • Author(s)
      Zhou Lu、Awakawa Takayoshi、Ushimaru Richiro、Kanaida Masahiro、Abe Ikuro
    • Journal Title

      Organic Letters

      Volume: 26 Pages: 724~727

    • DOI

      10.1021/acs.orglett.3c04185

    • Peer Reviewed
  • [Journal Article] Lincosamide Antibiotics: Structure, Activity, and Biosynthesis2024

    • Author(s)
      Mori Takahiro、Abe Ikuro
    • Journal Title

      ChemBioChem

      Volume: 25 Pages: e202300840

    • DOI

      10.1002/cbic.202300840

    • Peer Reviewed
  • [Journal Article] Biosynthesis of enfumafungin-type antibiotic reveals an unusual enzymatic fusion pattern and unprecedented C-C bond cleavage2024

    • Author(s)
      Cao, Z.-Q., Wang, G.-Q., Luo, R., Gao, Y.-H., Lv, J.-M., Qin, S.-Y., Chen, G.-D., Awakawa, T., Bao, X.-F., Mei, Q.-H., Yao, X.-S., Hu, D., Abe, I., Gao, H.
    • Journal Title

      J. Am. Chem. Soc.

      Volume: 146 Pages: in press

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Discovery of (±)-penindolenes reveals an unusual indole ring cleavage pathway catalyzed by P450 monooxygenase2024

    • Author(s)
      Meng, L.-H.,# Awakawa, T.,# Li, X.-M., Quan, Z., Yang, S.-Q., Wang, B.-G., Abe, I.
    • Journal Title

      Angew. Chem. Int. Ed.

      Volume: 63 Pages: in press

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Functional and structural dissection of glycosyltransferases underlying the glycodiversity of wolfberry-derived bioactive ingredients lycibarbarspermidines2024

    • Author(s)
      Shao-Yang Li, Gao-Qian Wang, Liang Long, Jia-Ling Gao, Zheng-Qun Zhou, Yong-Heng Wang, Jian-Ming Lv, Guo-Dong Chen, Dan Hu, Ikuro Abe & Hao Gao
    • Journal Title

      Nature Communications

      Volume: 15 Pages: in press

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Molecular basis for carrier protein-dependent amide bond formation in the biosynthesis of lincosamide antibiotics2023

    • Author(s)
      Mori Takahiro、Kadlcik Stanislav、Lyu Shuang、Kamenik Zdenek、Sakurada Kosuke、Mazumdar Aninda、Wang Huibin、Janata Jiri、Abe Ikuro
    • Journal Title

      Nature Catalysis

      Volume: 6 Pages: 531~542

    • DOI

      10.1038/s41929-023-00971-y

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Back-to-back cycloadditions in nature2023

    • Author(s)
      Ushimaru Richiro、Abe Ikuro
    • Journal Title

      Nature Chemistry

      Volume: 15 Pages: 1056~1057

    • DOI

      10.1038/s41557-023-01282-2

    • Peer Reviewed
  • [Journal Article] Mechanistic Analysis of Stereodivergent Nitroalkane Cyclopropanation Catalyzed by Nonheme Iron Enzymes2023

    • Author(s)
      Ushimaru Richiro、Cha Lide、Shimo Shotaro、Li Xiaojun、Paris Jared C.、Mori Takahiro、Miyamoto Kazunori、Coffer Lindsay、Uchiyama Masanobu、Guo Yisong、Chang Wei-chen、Abe Ikuro
    • Journal Title

      Journal of the American Chemical Society

      Volume: 145 Pages: 24210~24217

    • DOI

      10.1021/jacs.3c08413

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Structural and Mechanistic Insights into the C-C Bond-Forming Rearrangement Reaction Catalyzed by Heterodimeric Hinokiresinol Synthase2023

    • Author(s)
      Ushimaru Richiro、Ding Yiling、Mori Takahiro、Miyamoto Kazunori、Uchiyama Masanobu、Abe Ikuro
    • Journal Title

      Journal of the American Chemical Society

      Volume: 145 Pages: 21966~21973

    • DOI

      10.1021/jacs.3c06762

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Multiple C-C Bond Cleavage Reactions Catalyzed by Tolyporphin Tetrapyrrole Biosynthetic Enzymes2023

    • Author(s)
      Ushimaru Richiro、Lyu Jiaqi、Ling Meiqi、Abe Ikuro
    • Journal Title

      Journal of the American Chemical Society

      Volume: 145 Pages: 9834~9839

    • DOI

      10.1021/jacs.3c01993

    • Peer Reviewed
  • [Journal Article] Assembling neuroactive alkaloids2023

    • Author(s)
      Ushimaru Richiro、Abe Ikuro
    • Journal Title

      Nature Plants

      Volume: 9 Pages: 1946~1947

    • DOI

      10.1038/s41477-023-01586-8

    • Peer Reviewed
  • [Journal Article] Structure‐Function Analysis of the S‐Glycosylation Reaction in the Biosynthesis of Lincosamide Antibiotics2023

    • Author(s)
      Mori Takahiro、Sun Xin、Kadlcik Stanislav、Janata Jiri、Abe Ikuro
    • Journal Title

      Angewandte Chemie International Edition

      Volume: 62 Pages: e202304989

    • DOI

      10.1002/anie.202304989

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Catalytic Mechanism of Nonglycosidic C-N Bond Formation by the Pseudoglycosyltransferase Enzyme VldE2023

    • Author(s)
      Tsunoda Takeshi、Abuelizz Hatem A.、Samadi Arash、Wong Chin Piow、Awakawa Takayoshi、Brumsted Corey J.、Abe Ikuro、Mahmud Taifo
    • Journal Title

      ACS Catalysis

      Volume: 13 Pages: 13369~13382

    • DOI

      10.1021/acscatal.3c02404

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] C-N and C-S bond formation by cytochrome P450 enzymes2023

    • Author(s)
      Ushimaru Richiro、Abe Ikuro
    • Journal Title

      Trends in Chemistry

      Volume: 5 Pages: 526~536

    • DOI

      10.1016/j.trechm.2023.04.008

    • Peer Reviewed
  • [Journal Article] Unusual Dioxygen-Dependent Reactions Catalyzed by Nonheme Iron Enzymes in Natural Product Biosynthesis2023

    • Author(s)
      Ushimaru Richiro、Abe Ikuro
    • Journal Title

      ACS Catalysis

      Volume: 13 Pages: 1045~1076

    • DOI

      10.1021/acscatal.2c05247

    • Peer Reviewed
  • [Journal Article] Genomic and Spectroscopic Signature-Based Discovery of Natural Macrolactams2023

    • Author(s)
      Shin Yern-Hyerk、et al., Abe Ikuro、Moore Bradley S.、Fenical William、Yoon Yeo Joon、Cho Jang-Cheon、Lee Sang Kook、Oh Ki-Bong、Oh Dong-Chan
    • Journal Title

      Journal of the American Chemical Society

      Volume: 145 Pages: 1886~1896

    • DOI

      10.1021/jacs.2c11527

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Structure-based engineering of α-ketoglutarate dependent oxygenases in fungal meroterpenoid biosynthesis2023

    • Author(s)
      Awakawa Takayoshi、Mori Takahiro、Ushimaru Richiro、Abe Ikuro
    • Journal Title

      Natural Product Reports

      Volume: 40 Pages: 46~61

    • DOI

      10.1039/D2NP00014H

    • Peer Reviewed
  • [Journal Article] Diverse enzymatic chemistry for propionate side chain cleavages in tetrapyrrole biosynthesis2023

    • Author(s)
      Ushimaru Richiro、Lyu Jiaqi、Abe Ikuro
    • Journal Title

      Journal of Industrial Microbiology and Biotechnology

      Volume: 50 Pages: kuad016

    • DOI

      10.1093/jimb/kuad016

    • Peer Reviewed / Open Access
  • [Presentation] Unusual Enzyme Reactions in Natural Product Biosynthesis2023

    • Author(s)
      Ikuro Abe
    • Organizer
      4th International Conference on Natural Product Discovery and Development in the Genomic Era, San Diego, USA
    • Int'l Joint Research / Invited
  • [Presentation] Unusual Enzyme Reactions in Natural Product Biosynthesis2023

    • Author(s)
      Ikuro Abe
    • Organizer
      PSJ-PSK Joint Symposium: Natural Products in Drug Discovery, the 143rd Annual Meeting of the Pharmaceutical Society of Japan, Sapporo, Japan
    • Int'l Joint Research / Invited
  • [Presentation] Unusual Enzyme Reactions in Natural Product Biosynthesis2023

    • Author(s)
      Ikuro Abe
    • Organizer
      Gordon Research Conference, Enzymes, Coenzymes and Metabolic Pathways, Waterville Valley, NH, USA
    • Int'l Joint Research / Invited
  • [Presentation] b-NAD as a Building Block in Natural Product Biosynthesis2023

    • Author(s)
      Ikuro Abe
    • Organizer
      Enzyme Engineering XXVII, Singapore, Singapore
    • Int'l Joint Research / Invited
  • [Presentation] Unusual Enzyme Reactions in Natural Product Biosynthesis2023

    • Author(s)
      Ikuro Abe
    • Organizer
      New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) 50th Anniversary Conference, Canterbury, New Zealand
    • Int'l Joint Research / Invited
  • [Remarks] 東京大学大学院薬学系研究科天然物化学教室

    • URL

      https://tennen.f.u-tokyo.ac.jp/head.htm

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Published: 2024-12-25  

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