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Search and design of compounds with synergistic effects by AI

Planned Research

Project AreaSynergy pharmaceutical science: understanding and design of compound combination effects by integrating information, material, and life sciences
Project/Area Number 20H05797
Research Category

Grant-in-Aid for Transformative Research Areas (B)

Allocation TypeSingle-year Grants
Review Section Transformative Research Areas, Section (IV)
Research InstitutionKyushu Institute of Technology

Principal Investigator

Yamanishi Yoshihiro  九州工業大学, 大学院情報工学研究院, 教授 (60437267)

Co-Investigator(Kenkyū-buntansha) 天池 一真  名古屋大学, 物質科学国際研究センター, 助教 (00866600)
竹下 潤一  国立研究開発法人産業技術総合研究所, エネルギー・環境領域, 主任研究員 (60574390)
味八木 茂  広島大学, 病院(医), 講師 (10392490)
Project Period (FY) 2020-10-02 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥79,040,000 (Direct Cost: ¥60,800,000、Indirect Cost: ¥18,240,000)
Fiscal Year 2022: ¥25,870,000 (Direct Cost: ¥19,900,000、Indirect Cost: ¥5,970,000)
Fiscal Year 2021: ¥25,870,000 (Direct Cost: ¥19,900,000、Indirect Cost: ¥5,970,000)
Fiscal Year 2020: ¥27,300,000 (Direct Cost: ¥21,000,000、Indirect Cost: ¥6,300,000)
Keywords化合物群 / シナジー効果 / AI / 組み合わせ / 最適化
Outline of Research at the Start

複数の薬剤の組み合わせによる相乗効果(薬剤シナジー)を活用した化学療法が、がんや神経変性疾患など多因子疾患に対する有効な治療法として注目されている。本研究では、疾患状態の生体情報を入力とし、シナジー効果を有する薬剤群を予測するAIを開発する。さらに、より高いシナジー効果を有する新しい化合物群を設計するAIを開発する。有機化合物の組み合わせ数は膨大であり、実験的に全ての可能性を検証することは不可能である。生体情報から複数の薬剤群(または化合物群)を最適化できないか?という問いに対し、物質・生命科学のビッグデータと情報科学のAI技術を融合し、新たな方法論を創生する。

Outline of Final Research Achievements

Chemotherapy that utilizes the synergistic effect of a combination of multiple drugs (drug synergy) has been recognized as an effective method for treatment of multifactorial diseases such as cancer and neurodegenerative diseases. This research group develops statistical methods for predicting drug combinationss with synergistic effects, and machine learning methods for outputting structures of new compounds with stronger effects. Specifically, the research will proceed in the following three stages. 1) Development of a method for predicting drug combinations with synergistic effects by fusion analysis of omics data. 2) Network analysis of the mechanism of drug synergy. 3) Developing methods for generating and designing chemical structures of new compounds with higher synergistic effects.

Academic Significance and Societal Importance of the Research Achievements

これまで臨床研究での偶発的発見や限られた薬剤ペアに対する実験的検証に留まっていた薬剤シナジーに対し、本研究では、薬剤全ての組合せをAIで探索することで、これまでのボトルネックであった組合せ爆発の問題の解決に寄与する。本研究の特色は、疾患特異的な発現異常遺伝子群と薬剤に応答する発現異常遺伝子群を考慮して薬剤シナジーを解析する点にある。薬剤シナジーは、生命システムの動的反応の結果であるため、オミックスデータの活用によって、薬剤シナジーの正確な理解や予測につながることが期待できる。

Report

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

    (35 results)

All 2023 2022 2021

All Journal Article (12 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 12 results,  Open Access: 7 results) Presentation (23 results) (of which Int'l Joint Research: 5 results,  Invited: 19 results)

  • [Journal Article] Revisiting PFA-mediated tissue fixation chemistry: FixEL enables trapping of small molecules in the brain to visualize their distribution changes2023

    • Author(s)
      Nonaka Hiroshi、Mino Takeharu、Sakamoto Seiji、Oh Jae Hoon、Watanabe Yu、Ishikawa Mamoru、Tsushima Akihiro、Amaike Kazuma、Kiyonaka Shigeki、Tamura Tomonori、Radu Aricescu A.、Kakegawa Wataru、Miura Eriko、Yuzaki Michisuke、Hamachi Itaru
    • Journal Title

      Chem

      Volume: 9 Issue: 2 Pages: 523-540

    • DOI

      10.1016/j.chempr.2022.11.005

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Discovery of 2,6-Dihalopurines as Stomata Opening Inhibitors: Implication of an LRX-Mediated H<sup>+</sup>-ATPase Phosphorylation Pathway2023

    • Author(s)
      Ueda Ayaka、Aihara Yusuke、Sato Shinya、Kano Keiko、Mishiro-Sato Emi、Kitano Hiroyuki、Sato Ayato、Fujimoto Kazuhiro J.、Yanai Takeshi、Amaike Kazuma、Kinoshita Toshinori、Itami Kenichiro
    • Journal Title

      ACS Chemical Biology

      Volume: 18 Issue: 2 Pages: 347-355

    • DOI

      10.1021/acschembio.2c00771

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Regulome-based characterization of drug activity across the human diseasome2022

    • Author(s)
      Iwata Michio、Kosai Keisuke、Ono Yuya、Oki Shinya、Mimori Koshi、Yamanishi Yoshihiro
    • Journal Title

      npj Systems Biology and Applications

      Volume: 8 Issue: 1 Pages: 44-44

    • DOI

      10.1038/s41540-022-00255-4

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Small compound-based direct cell conversion with combinatorial optimization of pathway regulations2022

    • Author(s)
      Nakamura Toru、Iwata Michio、Hamano Momoko、Eguchi Ryohei、Takeshita Jun-ichi、Yamanishi Yoshihiro
    • Journal Title

      Bioinformatics

      Volume: 38 Issue: Supplement_2 Pages: ii99-ii105

    • DOI

      10.1093/bioinformatics/btac475

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Transformer-based Objective-reinforced Generative Adversarial Network to Generate Desired Molecules2022

    • Author(s)
      Li Chen、Yamanaka Chikashige、Kaitoh Kazuma、Yamanishi Yoshihiro
    • Journal Title

      Proceedings of the 31st International Joint Conference on Artificial Intelligence and the 25th European Conference on Artificial Intelligence (IJCAI-ECAI 2022)

      Volume: - Pages: 3884-3890

    • DOI

      10.24963/ijcai.2022/539

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach2022

    • Author(s)
      Eguchi Ryohei、Hamano Momoko、Iwata Michio、Nakamura Toru、Oki Shinya、Yamanishi Yoshihiro
    • Journal Title

      Bioinformatics

      Volume: 38 Issue: 10 Pages: 2839-2846

    • DOI

      10.1093/bioinformatics/btac209

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Inflammogenic effect of polyacrylic acid in rat lung following intratracheal instillation2022

    • Author(s)
      Nishida Chinatsu、Tomonaga Taisuke、Izumi Hiroto、Wang Ke-Yong、Higashi Hidenori、Ishidao Toru、Takeshita Jun-ichi、Ono Ryohei、Sumiya Kazuki、Fujii Shota、Mochizuki Shinichi、Sakurai Kazuo、Yamasaki Kei、Yatera Kazuhiro、Morimoto Yasuo
    • Journal Title

      Particle and Fibre Toxicology

      Volume: 19 Issue: 1 Pages: 1-17

    • DOI

      10.1186/s12989-022-00448-z

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] C?H arylation enables synthesis of imidazole-4-carboxamide (ICA) based fairy chemicals with plant growth-promoting activity2022

    • Author(s)
      Ueda Ayaka、Amaike Kazuma、Shirotani Yoko、Warstat Robin、Ito Hideto、Choi Jae-Hoon、Kawagishi Hirokazu、Itami Kenichiro
    • Journal Title

      Canadian Journal of Chemistry

      Volume: - Issue: 7 Pages: 449-452

    • DOI

      10.1139/cjc-2022-0256

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Synthesis, properties, and material hybridization of bare aromatic polymers enabled by dendrimer support2022

    • Author(s)
      Fujiki Shusei、Amaike Kazuma、Yagi Akiko、Itami Kenichiro
    • Journal Title

      Nature Communications

      Volume: 13 Issue: 1 Pages: 5358-5358

    • DOI

      10.1038/s41467-022-33100-7

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Scaffold-Retained Structure Generator to Exhaustively Create Molecules in an Arbitrary Chemical Space2022

    • Author(s)
      Kaitoh Kazuma、Yamanishi Yoshihiro
    • Journal Title

      Journal of Chemical Information and Modeling

      Volume: - Issue: 9 Pages: 2212-2225

    • DOI

      10.1021/acs.jcim.1c01130

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] TRIOMPHE: Transcriptome-Based Inference and Generation of Molecules with Desired Phenotypes by Machine Learning2021

    • Author(s)
      Kaitoh Kazuma、Yamanishi Yoshihiro
    • Journal Title

      Journal of Chemical Information and Modeling

      Volume: 61 Issue: 9 Pages: 4303-4320

    • DOI

      10.1021/acs.jcim.1c00967

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] CLASSIFICATION OF CHEMICAL COMPOUNDS BASED ON THE CORRELATION BETWEEN IN VITRO GENE EXPRESSION PROFILES2021

    • Author(s)
      Takeshita Jun-ichi、Toyoda Akinobu、Tani Hidenori、Endo Yasunori、Miyamoto Sadaaki
    • Journal Title

      Bulletin of informatics and cybernetics

      Volume: 53 Issue: 4 Pages: 1-14

    • DOI

      10.5109/4476055

    • NAID

      120007039341

    • ISSN
      0286-522X, 2435-743X
    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Presentation] AIによるデータ駆動型研究が拓く創薬と医療2022

    • Author(s)
      山西芳裕
    • Organizer
      第96回日本薬理学会年会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] AIによるデータ駆動型研究が拓く創薬と医療2022

    • Author(s)
      山西芳裕
    • Organizer
      日本動物実験代替法学会第35 回大会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] AIによるデータ駆動型研究が拓く創薬と医療2022

    • Author(s)
      山西芳裕
    • Organizer
      日本薬物動態学会 第37回年会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] Developing a network-based combination therapy approach for complex diseases2022

    • Author(s)
      Midori Iida, Yurika Kuniki, Kenta Yagi, Mitsuhiro Goda, Satoko Namba, Jun-ichi Takeshita, Ryusuke Sawada, Michio Iwata, Yoshito Zamami, Keisuke Ishizawa, and Yoshihiro Yamanishi
    • Organizer
      情報計算化学生物学会(CBI学会)2022年大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] AIによるデータ駆動型創薬と医療2022

    • Author(s)
      山西芳裕
    • Organizer
      第81回日本癌学会学術総会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] AIによるデータ駆動型研究が拓く創薬と医療2022

    • Author(s)
      山西芳裕
    • Organizer
      日本化学会関東支部 2022年度講演会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] AIによるデータ駆動型研究が拓く創薬と医療2022

    • Author(s)
      山西芳裕
    • Organizer
      日本オミックス医学会シンポジウム『AI創薬の最新の展開』
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 生薬比率を考慮した漢方薬の作用機序や効能のin silico予測2022

    • Author(s)
      島田祐樹, 江副晃洋, 澤田隆介, 柴田友和, 門脇真, 山西芳裕
    • Organizer
      第39回和漢医薬学会学術大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] AIによるデータ駆動型研究が拓く生命医科学と創薬2022

    • Author(s)
      山西芳裕
    • Organizer
      第95回日本内分泌学会学術総会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] AIによるデータ駆動型研究が拓く創薬と医療2022

    • Author(s)
      山西芳裕
    • Organizer
      第25回ケムステVシンポ「データサイエンスが導く化学の最先端」
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] AIによるデータ駆動型研究が拓く創薬と医療2022

    • Author(s)
      山西芳裕
    • Organizer
      第765回新潟医学会例会シンポジウム「メディカルAIの最前線」
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] Data-driven drug discovery and molecular design by machine learning2022

    • Author(s)
      Yamanishi, Y.
    • Organizer
      Inserm/JSPS joint seminar on artificial intelligence and big data approaches in precision medicine and health science
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Data-driven drug discovery and molecular design by machine learning2022

    • Author(s)
      Yamanishi, Y.
    • Organizer
      The 7th Autumn School of Chemoinformatics in Nara 2022
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Small compound-based direct cell conversion with combinatorial optimization of pathway regulations2022

    • Author(s)
      Nakamura, T., Iwata, M., Hamano, M., Eguchi, R., Takeshita, J., and Yamanishi, Y.
    • Organizer
      The 21st European Conference on Computational Biology (ECCB2022)
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Data-driven drug discovery and healthcare by machine learning2022

    • Author(s)
      Yamanishi, Y.
    • Organizer
      The Eighteenth International Conference on Intelligent Computing (ICIC2022)
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Transformer-Based Objective-Reinforced Generative Adversarial Network to Generate Desired Molecules2022

    • Author(s)
      Li, C., Yamanaka, C., Kaitoh, K. and Yamanishi, Y.
    • Organizer
      The 31st International Joint Conference on Artificial Intelligence and the 25th European Conference on Artificial Intelligence (IJCAI-ECAI 2022) (IJCAI-ECAI 2022)
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] AIによるデータ駆動型創薬と分子設計2022

    • Author(s)
      山西芳裕
    • Organizer
      日本薬学会 第142年会, シンポジウム「創薬・医療における人工知能の活用」
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] AIによるデータ駆動型研究が拓く医薬品・食品開発2022

    • Author(s)
      山西芳裕
    • Organizer
      生物資源と触媒技術に基づく食・薬・材創生コンソーシアム 第5回シンポジウム
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] in silico解析(BD/機械学習)をつかった創薬/ドラッグリポジショニング2021

    • Author(s)
      山西芳裕
    • Organizer
      サイエンス&テクノロジーセミナー
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] AIによるデータ駆動型研究が拓く創薬と医療2021

    • Author(s)
      山西芳裕
    • Organizer
      第80回日本癌学会学術総会, Symposia「AIによる創薬・診断の強化」
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] 機械学習によるデータ駆動型研究が拓くヘルスケア2021

    • Author(s)
      山西芳裕
    • Organizer
      第10回生命医薬情報学連合大会, ワークショップ「人工知能と生命誌に基づく生命医科学のためのバイオインフォマティクス」
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] AI創薬開発-データ駆動型創薬の最新技術動向と今後の展望2021

    • Author(s)
      山西芳裕
    • Organizer
      情報機構セミナー
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] AIによるデータ駆動型研究が拓く創薬と医療2021

    • Author(s)
      山西芳裕
    • Organizer
      第 25 回日本がん分子標的治療学会学術集会日本薬学会, シンポジウム「AI」
    • Related Report
      2021 Annual Research Report
    • Invited

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Published: 2020-10-30   Modified: 2024-01-30  

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