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Development of small molecules that spontaneously oligomerize on trinucleotide repeats

Research Project

Project/Area Number 19K05693
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Review Section Basic Section 37010:Bio-related chemistry
Research InstitutionOsaka University

Principal Investigator

YAMADA Takeshi  大阪大学, 産業科学研究所, 助教 (80633263)

Project Period (FY) 2019-04-01 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥390,000 (Direct Cost: ¥300,000、Indirect Cost: ¥90,000)
Fiscal Year 2021: ¥130,000 (Direct Cost: ¥100,000、Indirect Cost: ¥30,000)
Fiscal Year 2020: ¥130,000 (Direct Cost: ¥100,000、Indirect Cost: ¥30,000)
Fiscal Year 2019: ¥130,000 (Direct Cost: ¥100,000、Indirect Cost: ¥30,000)
Keywords核酸 / 有機合成 / 低分子 / トリヌクレオチドリピート / RNA / DNA / オリゴマー / ミスマッチ塩基対 / 分子認識 / ケミカルバイオロジー
Outline of Research at the Start

本申請研究では、神経変性疾患の原因となる異常伸長した(CXG)nリピートが形成するヘアピン構造をテンプレートとして、ヘアピン構造に結合して自発的にオリゴマー化し、リピートヘアピンを高度に安定化する分子の開発を目指す。(CGG)nリピートヘアピン上で二量化する低分子NCD-CC(論文報告済み)をリード化合物として、リピートヘアピンをテンプレートにオリゴマー化する低分子NCD-SSを開発する。さらに、リピート認識部位、オリゴマー化部位の変更を行い、脆弱X症候群に代表される、リピート病一般への幅広い応用を目指した低分子群を開発する。

Outline of Final Research Achievements

In this study, we tried to achieve selective recognition of long trinucleotide repeat by synthesizing small molecules that bind to the hairpin structure formed by abnormally expanded (CXG) n-repeats and spontaneously become oligomers. As a result, although we could not synthesize such molecules, "selective recognition of expanded repeats" was achieved by the newly synthesized NA dimer.

Academic Significance and Societal Importance of the Research Achievements

本研究の成果であるNAダイマーは、CAGリピートDNA・RNAの両方に結合する、これまでになかったタイプのRNA結合性低分子であり、重篤な神経変性疾患であるCAGリピート関連病の発症・重篤化の機構を明らかにするための分子プローブとして期待される。さらに近年、国内外でRNA標的低分子創薬が急速に進んでいるが、RNA-低分子複合体の具体例が少ないこと、低分子とRNAの複合体構造予測が困難である点が、RNA標的低分子創薬のボトルネックになっている。NAダイマーはその貴重な具体例であり、今後、複合体構造を明らかにしていくことでRNA標的低分子創薬を推進するリード化合物となることが期待される。

Report

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

    (25 results)

All 2022 2021 2020 2019

All Journal Article (3 results) (of which Peer Reviewed: 3 results,  Open Access: 1 results) Presentation (22 results) (of which Int'l Joint Research: 10 results,  Invited: 1 results)

  • [Journal Article] Mismatch binding ligand upregulated back-splicing reaction producing circular RNA in a cellular model2022

    • Author(s)
      Ni Lu、Yamada Takeshi、Murata Asako、Nakatani Kazuhiko
    • Journal Title

      Chemical Communications

      Volume: 58 Issue: 22 Pages: 3629-3632

    • DOI

      10.1039/d1cc06936e

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Chemical Probing of Thymine in the TGG/CGG Triad to Explore the Deamination of 5-Methylcytosine in the CGG Repeat2020

    • Author(s)
      Yagi Yuki、Yamada Takeshi、Nakatani Kazuhiko
    • Journal Title

      Biochemistry

      Volume: 59 Issue: 29 Pages: 2679-2683

    • DOI

      10.1021/acs.biochem.0c00333

    • Related Report
      2020 Research-status Report
    • Peer Reviewed
  • [Journal Article] Assembly of ruthenium complexes on double stranded DNA using mismatch binding ligands2020

    • Author(s)
      Ni Lu、Yamada Takeshi、Nakatani Kazuhiko
    • Journal Title

      Chemical Communications

      Volume: 56 Issue: 39 Pages: 5227-5230

    • DOI

      10.1039/d0cc01863e

    • Related Report
      2019 Research-status Report
    • Peer Reviewed
  • [Presentation] The binding motif of naphthyridine-azaquinolone dimer (NAD) in CAG-repeat RNA2022

    • Author(s)
      ○Qingwen Chen, Takeshi Yamada, Asako Murata, Kazuhiko Nakatani
    • Organizer
      日本化学会第102回春季年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] NMR study on the binding of naphthyridine dimer to d(CGG) triad2022

    • Author(s)
      ○Shuhei Sakurabayashi, Kyoko Furuita, Takeshi Yamada, Toshimichi Fujiwara, Kazuhiko Nakatani, Chojiro Kojima
    • Organizer
      日本化学会第102回春季年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 15N標識ナフチリジン誘導体の合成と性質2022

    • Author(s)
      ○杉浦 徳昭・中谷 和彦・山田 剛史
    • Organizer
      日本化学会第102回春季年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Machine learning-based classification in small molecules targeting CAG-repeat DNA2021

    • Author(s)
      ○Qingwen Chen, Yasuyuki Matsushita, Asako Murata, Takeshi Yamada, Ayako Sugai, Kazuhiko Nakatani
    • Organizer
      FIBER日本核酸化学学会若手フォーラム2021
    • Related Report
      2021 Annual Research Report
  • [Presentation] Regulation of circRNA expression in cell via RNA binding small molecule2021

    • Author(s)
      ○Takeshi YAMADA, Lu Ni, Asako MURATA, Kazuhiko NAKATANI
    • Organizer
      IS3NA-IRT virtual symposium 2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Multiplexing ligands through click chemistry at the anomeric site of sugars for oligonucleotide conjugation2021

    • Author(s)
      ○Dhrubajyoti Datta, Takeshi Yamada, Shigeo Matsuda, Muthiah Manoharan
    • Organizer
      IS3NA-IRT virtual symposium 2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Regulation of circular RNA biogenesis via nucleic acid binding small molecule in cells2021

    • Author(s)
      ○Lu Ni, Takeshi Yamada, Asako Murata, Kazuhiko Nakatani
    • Organizer
      ISNAC2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Computer-aided classification of small molecules targeting CAG-repeat DNA2021

    • Author(s)
      ○Qingwen Chen, Asako Murata, Takeshi Yamada, Ayako Sugai, Yasuyuki Matsushita, Kazuhiko Nakatani
    • Organizer
      ISNAC2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Intermediate structure in the binding of naphthyridine dimer to d(CGG) triad revealed by NMR2021

    • Author(s)
      ○Shuhei Sakurabayashi, Kyoko Furuita, Takeshi Yamada, Toshimichi Fujiwara, Kazuhiko Nakatani, and Chojiro Kojima
    • Organizer
      ISNAC2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Regulation of circular RNA biogenesis using nucleic acid binding small molecule in cellular environment2021

    • Author(s)
      ○Lu Ni, Takeshi Yamada, Asako Murata, Kazuhiko Nakatani
    • Organizer
      Pacificham2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Using machine learning to classify and extract features of small-molecule libraries targeting DNA and RNA2021

    • Author(s)
      ○Qingwen Chen, Yasuyuki Matsushita, Asako Murata, Takeshi Yamada, Ayako Sugai, Kazuhiko Nakatani
    • Organizer
      Pacifichem2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] In-cell NMR to investigate the interactions between a hairpin RNA containing a UGGAA/UGGAA pentad and a synthetic small molecule2021

    • Author(s)
      ○Shuhei Sakurabayashi, Qingci Zhao, Takeshi Yamada, Noritaka Nishida, Gota Kawai, Kazuhiko Nakatani
    • Organizer
      Pacifichem2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] NMR解析のための13C標識ナフチリジン誘導体の合成2021

    • Author(s)
      ○櫻林 修平、山田 剛史、河合 剛太、中谷 和彦
    • Organizer
      日本化学会第101回年会
    • Related Report
      2020 Research-status Report
  • [Presentation] Regulation of circular RNA biogenesis via RNA binding small molecule2021

    • Author(s)
      ○Lu Ni, Takeshi Yamada, Asako Murata, Kazuhiko Nakatani
    • Organizer
      日本化学会第101回年会
    • Related Report
      2020 Research-status Report
  • [Presentation] Synthesis and the properties of naphthyridine-azaquinolone dimer (NAD) tatgeting CAG-repeat RNA2021

    • Author(s)
      ○Qingwen Chen, Takeshi Yamada, Asako Murata, Kazuhiko Nakatani
    • Organizer
      日本化学会第101回年会
    • Related Report
      2020 Research-status Report
  • [Presentation] Structural analysis and functionalization of naphthyridine dimer derivatives bound to CGG repeats2020

    • Author(s)
      ○Takeshi Yamada, Shuhei Sakurabayashi, Kyoko Huruitab, Chojiro Kojima, Kazuhiko Nakatani
    • Organizer
      The 23rd SANKEN INTERNATIONAL SYMPOSIUM
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] NMR structural analysis of naphthyridine dimer derivatives binding to CGG/CGG triplets in DNAs2020

    • Author(s)
      ○YAMADA Takeshi
    • Organizer
      2nd Indo-Japan (NCBS/inStem-ISIR, Osaka University) Meeting: Interfacing Chemistry and Biology
    • Related Report
      2019 Research-status Report
    • Invited
  • [Presentation] Assembly of ruthenium complexes on dsDNA using mismatch binding ligand2020

    • Author(s)
      ○Lu Ni, Takeshi Yamada, Kazuhiko Nakatani,
    • Organizer
      日本化学会第100春季年会
    • Related Report
      2019 Research-status Report
  • [Presentation] Synthesis and the properties of NA Dimer2020

    • Author(s)
      ◯Chen Qingwen, Yamada Takeshi, Murata Asako, Nakatani Kazuhiko
    • Organizer
      日本化学会第100春季年会
    • Related Report
      2019 Research-status Report
  • [Presentation] Synthesis and properties of 13C-labeled naphthyridine derivative2020

    • Author(s)
      ○Shuhei Sakurabayashi, Takeshi Yamada, Gota Kawai, Kazuhiko Nakatani
    • Organizer
      日本化学会第100春季年会
    • Related Report
      2019 Research-status Report
  • [Presentation] XGGリピートDNA中のピリミジン塩基を選択的に酸化するリガンドの開発2019

    • Author(s)
      ◯八木 勇樹、山田 剛史、中谷 和彦
    • Organizer
      日本ケミカルバイオロジー学会 第14回年会
    • Related Report
      2019 Research-status Report
  • [Presentation] The methylation effect for binding of dimeric 2-amino-1,8-naphthyridine derivatives to CGG/CGG triad in DNA2019

    • Author(s)
      ○Takeshi Yamada, Shuhei Sakurabayashi, Kazuhiko Nakatani
    • Organizer
      The Commemorative International Symposium of the Japan Society of Nucleic Acids Chemistry (CISNAC 2019)
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research

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Published: 2019-04-18   Modified: 2023-01-30  

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