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Integrating Computational and Experimental Approaches for New Paradigms in Molecule Synthesis

Research Project

Project/Area Number 19KK0150
Research Category

Fund for the Promotion of Joint International Research (Fostering Joint International Research (B))

Allocation TypeMulti-year Fund
Review Section Medium-sized Section 38:Agricultural chemistry and related fields
Research InstitutionUniversity of Shizuoka

Principal Investigator

Watanabe Kenji  静岡県立大学, 薬学部, 教授 (50360938)

Co-Investigator(Kenkyū-buntansha) 佐藤 道大  静岡県立大学, 薬学部, 講師 (10629695)
恒松 雄太  静岡県立大学, 薬学部, 講師 (30629697)
岸本 真治  静岡県立大学, 薬学部, 助教 (40814330)
Project Period (FY) 2019-10-07 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥18,330,000 (Direct Cost: ¥14,100,000、Indirect Cost: ¥4,230,000)
Fiscal Year 2021: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000)
Fiscal Year 2020: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000)
Fiscal Year 2019: ¥6,630,000 (Direct Cost: ¥5,100,000、Indirect Cost: ¥1,530,000)
Keywords天然物 / 生合成 / Diels-Alder / 反応メカニズム / Diels-Alderase / 生合成酵素 / Diels-Alder反応 / 天然物生合成 / 酵素反応機構 / [4+2]環化反応 / spiro-carbon / monooxygenase / FAD / epoxidation / 天然物化学 / 酸化反応 / 計算化学
Outline of Research at the Start

本研究課題では、非経験的量子化学を基盤とした、反応遷移状態における計算化学、マイクロ秒レベルの分子動力学、タンパク質デザインとそれを用い化合物を生産するための生合成を合理的に構築することを目的とする。その目的の達成による出口として、生物活性を持つ分子を新たに合成/生合成するための新しい方法論の樹立が挙げられる。そのためには、酵素機能の精密な解析が必要不可欠となる。目的とする方法論を確立するために、本研究課題で海外共同研究者としてKendall Houk教授を選んだ。カリフォルニア大学ロサンゼルス校化学部に所属するHouk教授は計算化学分野の世界的権威である。

Outline of Final Research Achievements

Here we show the crystal structure of CghA–product complex at 2.0 resolution. Our result provides the second structural information of eukaryotic Diels–Alderases and adds yet another fold to the family of proteins reported to catalyse [4+2] cycloaddition reactions. Site-directed mutagenesis-coupled kinetic characterization and computational analyses allowed us to identify key catalytic residues and propose a possible catalytic mechanism. Most interestingly, we were able to rationally engineer CghA such that the mutant was able to catalyse preferentially the formation of the energetically disfavoured exon adduct. This work expands our knowledge and understanding of the emerging and potentially widespread class of natural enzymes capable of catalysing stereoselective Diels-Alder reactions, and paves the way toward developing enzymes potentially useful in various bio/synthetic applications.

Academic Significance and Societal Importance of the Research Achievements

リポカリン型の構造を有するDAaseは報告がなく, 天然におけるDAaseの収斂進化を示唆するものであった。またCghA-1の複合体結晶構造解析および変異体の速度論解析からは, 酵素の基質許容に関する知見が得られ, ジエノフィルの電子求引に関わるアミノ酸残基を明らかにすることができた。さらに立体選択性に関しては, 基質のコンフォメーションをendoではなくexo付加に優位となるよう改変することで, 立体選択性の異なる酵素の創製に成功した。また, DAaseの生成物阻害回避機構については, 計算解析による遷移状態の自由エネルギーを算出することで, 合理的な説明が可能となった。

Report

(4 results)
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Research-status Report
  • 2019 Research-status Report
  • Research Products

    (17 results)

All 2021 2020 2019 Other

All Int'l Joint Research (2 results) Journal Article (8 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 7 results,  Open Access: 3 results) Presentation (5 results) (of which Int'l Joint Research: 4 results,  Invited: 1 results) Remarks (2 results)

  • [Int'l Joint Research] UCLA(米国)

    • Related Report
      2020 Research-status Report
  • [Int'l Joint Research] HKI(ドイツ)

    • Related Report
      2020 Research-status Report
  • [Journal Article] Catalytic mechanism and endo-to-exo selectivity reversion of an octalin-forming natural Diels?Alderase2021

    • Author(s)
      Sato Michio、Kishimoto Shinji、Yokoyama Mamoru、Jamieson Cooper S.、Narita Kazuto、Maeda Naoya、Hara Kodai、Hashimoto Hiroshi、Tsunematsu Yuta、Houk Kendall N.、Tang Yi、Watanabe Kenji
    • Journal Title

      Nature Catalysis

      Volume: 4 Issue: 3 Pages: 223-232

    • DOI

      10.1038/s41929-021-00577-2

    • Related Report
      2021 Annual Research Report 2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Discovery and investigation of natural Diels?Alderases2021

    • Author(s)
      Watanabe Kenji
    • Journal Title

      Journal of Natural Medicines

      Volume: 1 Issue: 3 Pages: 1-6

    • DOI

      10.1007/s11418-021-01502-4

    • NAID

      40022591483

    • Related Report
      2021 Annual Research Report 2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] ディールス-アルダラーゼとはどういった酵素なのか2021

    • Author(s)
      佐藤道大, 渡辺賢二
    • Journal Title

      化学

      Volume: 2 Pages: 72-73

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] ディールス-アルダラーゼとはどういった酵素なのか?2020

    • Author(s)
      佐藤道大、渡辺賢二
    • Journal Title

      化学

      Volume: 76 Pages: 72-73

    • Related Report
      2020 Research-status Report
  • [Journal Article] Biosynthesis of the Immunosuppressant (?)-FR9014832020

    • Author(s)
      Zhang Zhuan、Tamura Yui、Tang Mancheng、Qiao Tianzhang、Sato Michio、Otsu Yoshihiro、Sasamura Satoshi、Taniguchi Masatoshi、Watanabe Kenji、Tang Yi
    • Journal Title

      Journal of the American Chemical Society

      Volume: 143 Issue: 1 Pages: 132-136

    • DOI

      10.1021/jacs.0c12352

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Specialized Flavoprotein Promotes Sulfur Migration and Spiroaminal Formation in Aspirochlorine Biosynthesis2020

    • Author(s)
      Tsunematsu Yuta、Maeda Naoya、Sato Michio、Hara Kodai、Hashimoto Hiroshi、Watanabe Kenji、Hertweck Christian
    • Journal Title

      Journal of the American Chemical Society

      Volume: 143 Issue: 1 Pages: 206-213

    • DOI

      10.1021/jacs.0c08879

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Functional and Structural Analyses of trans C-Methyltransferase in Fungal Polyketide Biosynthesis2019

    • Author(s)
      Kishimoto Shinji、Tsunematsu Yuta、Matsushita Takuma、Hara Kodai、Hashimoto Hiroshi、Tang Yi、Watanabe Kenji
    • Journal Title

      Biochemistry

      Volume: 58 Issue: 38 Pages: 3933-3937

    • DOI

      10.1021/acs.biochem.9b00702

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Genomic Mushroom Hunting Decrypts Coprinoferrin, A Siderophore Secondary Metabolite Vital to Fungal Cell Development2019

    • Author(s)
      Tsunematsu Yuta、Takanishi Jun、Asai Shihori、Masuya Takahiro、Nakazawa Takehito、Watanabe Kenji
    • Journal Title

      Organic Letters

      Volume: 21 Issue: 18 Pages: 7582-7586

    • DOI

      10.1021/acs.orglett.9b02861

    • NAID

      40022757906

    • Related Report
      2019 Research-status Report
    • Peer Reviewed
  • [Presentation] Diels-Alderaseのジアステレオ選択性および生成物阻害回避メカニズムの解明2021

    • Author(s)
      佐藤道大、岸本真治、Cooper S. Jamiesonc、原幸大、橋本博、恒松雄太、Houk N. Kendall、Yi Tang、渡辺賢二
    • Organizer
      第62回天然有機化合物討論会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Diels-Alderaseのジアステレオ選択性および生成物阻害回避メカニズムの解明2020

    • Author(s)
      渡辺賢二
    • Organizer
      新学術領域研究「生合成リデザイン」第9回公開シンポジウム
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Diels-Alderase のジアステレオ選択性および生成物阻害回避メカニズムの解明2020

    • Author(s)
      佐藤道大, 岸本真治, Cooper S. Jamieson, 原幸大, 橋本博, 恒松雄太, Houk N. Kendall, Yi Tang, 渡辺賢二
    • Organizer
      第62回天然有機化合物討論会
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research
  • [Presentation] Diels-Alderase CghA の全容解明2020

    • Author(s)
      岸本真治, 佐藤道大, Jamieson Cooper, 横山葵, 成田一仁, 前田直哉, 恒松雄太, 原幸大, 橋本博, Houk Kendall N., 渡辺賢二
    • Organizer
      日本農芸化学会2020年度大会
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research
  • [Presentation] 酵素的Diels-Alder反応におけるジアステレオ選択性の制御機構2020

    • Author(s)
      佐藤道大, 岸本真治, Jamieson Cooper, 成田一仁, 前田直哉, 原幸大, 橋本博, 恒松雄太, Houk N. Kendall, Yi Tang, 渡辺賢二
    • Organizer
      日本薬学会第140年会
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research
  • [Remarks] WATANABE RESEARCH GROUP

    • URL

      https://sweb.u-shizuoka-ken.ac.jp/~kenji55-lab/

    • Related Report
      2021 Annual Research Report
  • [Remarks] https://sweb.u-shizuoka-ken.ac.jp/~kenji55-lab/

    • Related Report
      2020 Research-status Report

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Published: 2019-10-10   Modified: 2023-01-30  

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