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Structure and dynamics based drug development to obtain highly active compounds

Research Project

Project/Area Number 20H03378
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 47020:Pharmaceutical analytical chemistry and physicochemistry-related
Research InstitutionThe University of Tokyo (2021-2023)
National Institute of Advanced Industrial Science and Technology (2020)

Principal Investigator

Takeuchi Koh  東京大学, 大学院薬学系研究科(薬学部), 教授 (20581284)

Co-Investigator(Kenkyū-buntansha) 徳永 裕二  東京大学, 大学院薬学系研究科(薬学部), 助教 (80713354)
Project Period (FY) 2020-04-01 – 2023-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥17,680,000 (Direct Cost: ¥13,600,000、Indirect Cost: ¥4,080,000)
Fiscal Year 2022: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000)
Fiscal Year 2021: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000)
Fiscal Year 2020: ¥6,630,000 (Direct Cost: ¥5,100,000、Indirect Cost: ¥1,530,000)
KeywordsNMR / 立体構造 / 運動性 / 薬剤設計 / 創薬作用点 / 薬物 / 動的相互作用 / 創薬 / 動的構造 / 創薬基盤技術 / タンパク質 / クリプトサイト
Outline of Research at the Start

本研究においては、化合物と創薬標的タンパク質の運動性を溶液中で評価することで、高活性化合物の創生を加速し、創薬標的の枯渇を解消する「動的構造創薬」の基盤の確立を目指す。その際、溶液中での動的構造解析が可能なNMR法を中心として、化合物の結合時の運動性解析から構造最適化の指針を提示する技術、タンパク質のクリプトサイトを同定し、安定化することで創薬標的の枯渇の解消に貢献する技術を確立する。

Outline of Final Research Achievements

Dynamic properties are extremely important for proteins to perform their functions. The same is true in drug discovery, where protein functions are controlled by compounds. In this study, we examined the possibility of utilization of dynamic information obtained by solution NMR in structure-guided drug discovery. As a result, we established a strategy to quantify the mobility of each site in compounds in the target protein bound state. In addition, we succeeded in developing a strategy to identify and utilize “cryptic sites,” hidden compound binding sites, on the surface of drug-target proteins.

Academic Significance and Societal Importance of the Research Achievements

本研究においては化合物、タンパク質の両面から動的構造創薬という新しい分野の可能性を実験に基づき明確に提示し、生物学および創薬化学における新しい学術基盤を創造することを目指した。その結果、化合物の運動性に着目し高活性化合物の創生を加速する方法、標的にできなかったタンパク質の創薬可能性(ドラッガビリティ)を再評価し創薬において大きな問題となっている創薬標的の枯渇を解消する方策を提示することに成功した。よって本研究の成果は、創薬化学に広く貢献する共に、タンパク質や化合物の機能メカニズムを解明することにも貢献するものである。

Report

(4 results)
  • 2023 Final Research Report ( PDF )
  • 2022 Annual Research Report
  • 2021 Annual Research Report
  • 2020 Annual Research Report
  • Research Products

    (22 results)

All 2023 2022 2021 2020 Other

All Journal Article (12 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 12 results,  Open Access: 7 results) Presentation (8 results) (of which Int'l Joint Research: 2 results,  Invited: 6 results) Remarks (2 results)

  • [Journal Article] Absence of ULK1 decreases AMPK activity in the kidney, leading to chronic kidney disease progression2023

    • Author(s)
      Tomoki Yanagi, Hiroaki Kikuchi, Koichiro Susa, Naohiro Takahashi, Naohiro Takahashi, Hiroki Bamba, Takefumi Suzuki, Yuta Nakano, Tamami Fujiki, Yutaro Mori, Fumiaki Ando, Shintaro Mandai, Takayasu Mori, Koh Takeuchi, Shinya Honda, Satoru Torii, Shigeomi Shimizu, Tatemitsu Rai, Shinichi Uchida, Eisei Sohara
    • Journal Title

      Genes to Cells

      Volume: 28 Issue: 1 Pages: 5-14

    • DOI

      10.1111/gtc.12989

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Functional molecular evolution of a <scp>GTP</scp> sensing kinase: <scp>PI5P4Kβ</scp>2023

    • Author(s)
      Takeuchi Koh、Senda Miki、Ikeda Yoshiki、Okuwaki Koji、Fukuzawa Kaori、Nakagawa So、Sasaki Mika、Sasaki Atsuo T.、Senda Toshiya
    • Journal Title

      The FEBS Journal

      Volume: 290 Issue: 18 Pages: 4419-4428

    • DOI

      10.1111/febs.16763

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Role of the orphan transporter SLC35E1 in the nuclear egress of herpes simplex virus 12022

    • Author(s)
      Fumio Maeda, Akihisa Kato, Kosuke Takeshima, Misato Shibazaki, Ryota Sato, Takuma Shibata, Kensuke Miyake, Hiroko Kozuka-Hata, Masaaki Oyama, Eigo Shimizu, Seiya Imoto, Satoru Miyano, Shungo Adachi, Tohru Natsume, Koh Takeuchi, Yuhei Maruzuru, Naoto Koyanagi, Jun Arii, Yasushi Kawaguchi
    • Journal Title

      Journal of Virology

      Volume: - Issue: 10 Pages: 10-10

    • DOI

      10.1128/jvi.00306-22

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The GTP responsiveness of PI5P4Kβ evolved from a compromised trade-off between activity and specificity2022

    • Author(s)
      Takeuchi Koh、Ikeda Yoshiki、Senda Miki、Harada Ayaka、Okuwaki Koji、Fukuzawa Kaori、Nakagawa So、Yu Hong Yang、Nagase Lisa、Imai Misaki、Sasaki Mika、Lo Yu-Hua、Ito Doshun、Osaka Natsuki、Fujii Yuki、Sasaki Atsuo T.、Senda Toshiya
    • Journal Title

      Structure

      Volume: 30 Issue: 6 Pages: 886-899.e4

    • DOI

      10.1016/j.str.2022.04.004

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] <sup>15</sup>N-Detected TROSY NMR experiments to study large disordered proteins in high-field magnets2022

    • Author(s)
      Dubey Abhinav、Viennet Thibault、Chhabra Sandeep、Takeuchi Koh、Seo Hee-Chan、Bermel Wolfgang、Frueh Dominique P.、Arthanari Haribabu
    • Journal Title

      Chemical Communications

      Volume: 58 Issue: 68 Pages: 9512-9515

    • DOI

      10.1039/d2cc02005j

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Residue-based program of a β-peptoid twisted strand shape via a cyclopentane constraint2022

    • Author(s)
      Kim J, Kobayashi H, Yokomine M, Shiratori Y, Ueda T, Takeuchi K, Umezawa K, Kuroda D, Tsumoto K, Morimoto J, Sando S.
    • Journal Title

      Org. Biomol. Chem.

      Volume: 20 Issue: 35 Pages: 6994-7000

    • DOI

      10.1039/d2ob01300b

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] S. Helix-forming aliphatic homo-δ-peptide foldamers based on the conformational restriction effects of cyclopropane.2022

    • Author(s)
      89.Nagata, M.; Watanabe, M.; Doi, R.; Uemura, M.; Ochiai, N.; Ichinose, W.; Fujiwara, K.; Kameda, T.; Sato, Y.; Takeuchi, K.; Shuto,
    • Journal Title

      Org. Biomol. Chem.

      Volume: - Issue: 5 Pages: 970-980

    • DOI

      10.1039/d2ob01715f

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Oligo(N‐methylalanine) as a Peptide‐Based Molecular Scaffold with a Minimal Structure and High Density of Functionalizable Sites2022

    • Author(s)
      Yokomine Marin、Morimoto Jumpei、Fukuda Yasuhiro、Shiratori Yota、Kuroda Daisuke、Ueda Takumi、Takeuchi Koh、Tsumoto Kouhei、Sando Shinsuke
    • Journal Title

      Angewandte Chemie International Edition

      Volume: 61 Issue: 14 Pages: 6994-7000

    • DOI

      10.1002/anie.202200119

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Function-Related Dynamics in Multi-Spanning Helical Membrane Proteins Revealed by Solution NMR2021

    • Author(s)
      Takeuchi Koh、Kofuku Yutaka、Imai Shunsuke、Ueda Takumi、Tokunaga Yuji、Toyama Yuki、Shiraishi Yutaro、Shimada Ichio
    • Journal Title

      Membranes

      Volume: 11 Issue: 8 Pages: 604-604

    • DOI

      10.3390/membranes11080604

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Targeting the cryptic sites: NMR-based strategy to improve protein druggability by controlling the conformational equilibrium2020

    • Author(s)
      Mizukoshi Yumiko、Takeuchi Koh、Tokunaga Yuji、Matsuo Hitomi、Imai Misaki、Fujisaki Miwa、Kamoshida Hajime、Takizawa Takeshi、Hanzawa Hiroyuki、Shimada Ichio
    • Journal Title

      Science Advances

      Volume: 6 Issue: 40

    • DOI

      10.1126/sciadv.abd0480

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The role of NMR in leveraging dynamics and entropy in drug design2020

    • Author(s)
      Dubey Abhinav、Takeuchi Koh、Reibarkh Mikhail、Arthanari Haribabu
    • Journal Title

      Journal of Biomolecular NMR

      Volume: 74 Issue: 10-11 Pages: 479-498

    • DOI

      10.1007/s10858-020-00335-9

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Role of NMR in High Ordered Structure Characterization of Monoclonal Antibodies2020

    • Author(s)
      Tokunaga Yuji、Takeuchi Koh
    • Journal Title

      International Journal of Molecular Sciences

      Volume: 22 Issue: 1 Pages: 46-46

    • DOI

      10.3390/ijms22010046

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] How does a molecule drive life?2022

    • Author(s)
      竹内恒
    • Organizer
      第22回日本蛋白質科学会年会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] Conformational plasticity defines cell permeabilization activity of cyclic Ras-inhibitor peptides2022

    • Author(s)
      Koh Takeuchi
    • Organizer
      ICMRBS 2022
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Utilization of NMR dynamics information to improve protein druggability2022

    • Author(s)
      Koh Takeuchi
    • Organizer
      The 7th International Symposium on Drug Discovery and Design by NMR
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Affinity-driven H+-coupled transport of a MATE transporter2022

    • Author(s)
      Koh Takeuchi
    • Organizer
      The 61st Annual Meeting of the NMR Society of Japan
    • Related Report
      2022 Annual Research Report
  • [Presentation] Development of inhibitors for the GTP energy system2022

    • Author(s)
      Koh Takeuchi
    • Organizer
      分子生物学会年会2022
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] NMRを用いた動的生命現象の理解と創薬への応用2021

    • Author(s)
      竹内 恒
    • Organizer
      第65回日本薬学会関東支部大会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] 動的生命現象のNMRを用いた理解と創薬への応用2021

    • Author(s)
      竹内 恒
    • Organizer
      日本薬学会東海支部
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] 溶液NMRを用いた動的構造創薬2020

    • Author(s)
      竹内 恒
    • Organizer
      第93回日本生化学会大会
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Remarks] 東京大学大学院薬学系研究科生命物理化学教室ホームページ

    • URL

      https://biophys.f.u-tokyo.ac.jp/

    • Related Report
      2021 Annual Research Report
  • [Remarks] 隠れた薬剤結合部位を発見・活用する技術の確立に成功

    • URL

      https://unit.aist.go.jp/cmb5/topics/topics07.html

    • Related Report
      2020 Annual Research Report

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Published: 2020-04-28   Modified: 2025-01-30  

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