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AI-based drug discovery approach based on biomedical big data and its application to refractory diseases

Research Project

Project/Area Number 18H03334
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 62010:Life, health and medical informatics-related
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) 沖米田 司  関西学院大学, 理工学部, 教授 (90398248)
谷 憲三朗  東京大学, 定量生命科学研究所, 特任教授 (00183864)
土方 康基  東京大学, 医科学研究所, 特任助教 (80460856)
Project Period (FY) 2018-04-01 – 2021-03-31
Project Status Completed (Fiscal Year 2020)
Budget Amount *help
¥17,290,000 (Direct Cost: ¥13,300,000、Indirect Cost: ¥3,990,000)
Fiscal Year 2020: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000)
Fiscal Year 2019: ¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000)
Fiscal Year 2018: ¥6,240,000 (Direct Cost: ¥4,800,000、Indirect Cost: ¥1,440,000)
Keywords機械学習 / ビッグデータ / 創薬 / 人工知能 / 難治性疾患
Outline of Final Research Achievements

In this research, we build information infrastructure technologies to realize drug discovery using pharmaceutical big data and machine learning, a fundamental technology of artificial intelligence (AI). Based on information on compounds such as pharmaceuticals, plants, and food ingredients, information on biomolecules such as genes, proteins, and glycans, and information on intractable diseases such as omics data and genomic data including SNPs, we constructed models for predicting the target of compounds in the framework of graph convolutional neural networks and recursive neural networks. We also constructed algorithms that take into account the applicability domains of chemical structures of compounds. Finally, we comprehensively predicted drug candidate compounds for malignant lymphoma and cystic fibrosis, and validated some of the prediction results.

Academic Significance and Societal Importance of the Research Achievements

疾患治療に有用な化合物の同定は、人類の医療やヘルスケアにとって最重要課題である。現在でも有効な治療法が無い難治性疾患や希少疾患は多く、疾患に苦しむ患者に対する迅速な救済措置が必要である。しかしながら、最近の新薬開発は低迷しており、新薬を一個開発するのに数千億円の研究開発費と10年以上の歳月を要すると云われている。本研究では、医薬ビッグデータと人工知能(AI)の基盤技術である機械学習を用いた創薬「AI創薬」を提唱し、それを実現するための機械学習手法の研究開発を行なった。深層学習の予測モデルを構築し、医薬品候補の化合物を情報化学的にスクリーニングする技術基盤を構築することができた。

Report

(4 results)
  • 2020 Annual Research Report   Final Research Report ( PDF )
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • Research Products

    (31 results)

All 2021 2020 2019 2018

All Journal Article (6 results) (of which Peer Reviewed: 6 results,  Open Access: 1 results) Presentation (25 results) (of which Int'l Joint Research: 3 results,  Invited: 18 results)

  • [Journal Article] Lean-Docking: Exploiting Ligands’ Predicted Docking Scores to Accelerate Molecular Docking2021

    • Author(s)
      Berenger Francois、Kumar Ashutosh、Zhang Kam Y. J.、Yamanishi Yoshihiro
    • Journal Title

      Journal of Chemical Information and Modeling

      Volume: 61 Issue: 5 Pages: 1-12

    • DOI

      10.1021/acs.jcim.0c01452

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Ranking Molecules with Vanishing Kernels and a Single Parameter: Active Applicability Domain Included2020

    • Author(s)
      Berenger, F. and Yamanishi, Y.
    • Journal Title

      Journal of Chemical Information and Modeling

      Volume: 60 Issue: 9 Pages: 43764387-43764387

    • DOI

      10.1021/acs.jcim.9b01075

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Prediction of the Health Effects of Food Peptides and Elucidation of the Mode-of-action Using Multi-task Graph Convolutional Neural Network2020

    • Author(s)
      Fukunaga, I., Sawada, R., Shibata, T., Kaitoh, K., Sakai, Y., and Yamanishi, Y.,
    • Journal Title

      Molecular Informatics

      Volume: 39(1-2) Issue: 1-2

    • DOI

      10.1002/minf.201900134

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Omics-based identification of glycan structures as biomarkers for a variety of diseases2020

    • Author(s)
      Akiyoshi, S., Iwata, M., Berenger, F., and Yamanishi, Y.
    • Journal Title

      Molecular Informatics

      Volume: 39(1-2) Issue: 1-2

    • DOI

      10.1002/minf.201900112

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Chemoinformatics and structural bioinformatics in OCaml.2019

    • Author(s)
      Berenger F, Zhang KYJ, Yamanishi Y.
    • Journal Title

      J Cheminform.

      Volume: 11 Issue: 1 Pages: 10-10

    • DOI

      10.1186/s13321-019-0332-0

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A Distance-Based Boolean Applicability Domain for Classification of High Throughput Screening Data.2019

    • Author(s)
      Berenger F, Yamanishi Y.
    • Journal Title

      J Chem Inf Model.

      Volume: 59 Issue: 1 Pages: 463-476

    • DOI

      10.1021/acs.jcim.8b00499

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Presentation] 機械学習によるデータ駆動型創薬2021

    • Author(s)
      山西芳裕
    • Organizer
      日本薬学会 第141年会
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] AIによるデータ駆動型研究が拓く創薬や医療2021

    • Author(s)
      山西芳裕
    • Organizer
      第58回日本糖尿病学会関東甲信越地方会
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] AIによるデータ駆動型研究が拓く創薬や医療2021

    • Author(s)
      山西芳裕
    • Organizer
      ALDOCKセミナー
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] AIによるデータ駆動型研究が拓く創薬や医療2020

    • Author(s)
      山西芳裕
    • Organizer
      Science Pioneers Consortium (SPC) 2020
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] Multiple omics-based diseasome analysis on gene expression machinery toward understanding disease-disease relationships and drug discovery2020

    • Author(s)
      岩田通夫, 沖真弥, 山西芳裕
    • Organizer
      第43回 日本分子生物学会年会
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] AIによる漢方薬の作用機序解析と効能予測2020

    • Author(s)
      山西芳裕
    • Organizer
      第2回日本東洋医学会福岡県部会
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] 摂動応答トランスクリプトームを用いた創薬標的分子と治療薬の探索2020

    • Author(s)
      難波里子, 岩田通夫, 飯田緑, 山西芳裕
    • Organizer
      第9回生命医薬情報学連合大会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 深層学習による食品ペプチドの健康効果の予測と作用機序の解明2020

    • Author(s)
      Fukunaga, I., Sawada, R., Shibata, T., Kaitoh, K., Sakai, Y., and Yamanishi, Y.
    • Organizer
      第9回生命医薬情報学連合大会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 深層学習を用いた漢方薬リポジショニングと作用機序解析2020

    • Author(s)
      Douke, A., Sawada, R., Iwata, M., Sakai, Y., Kadowaki, M., and Yamanishi, Y.
    • Organizer
      第9回生命医薬情報学連合大会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Data-driven drug discovery and medical treatment by machine learning2019

    • Author(s)
      Yamanishi, Y.
    • Organizer
      ACS Fall 2019 National Meeting & Exposition, Herman Skolnik Symposium
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Data-driven drug discovery and medical treatment by machine learning2019

    • Author(s)
      Yamanishi, Y.
    • Organizer
      The 6th Autumn School of Chemoinformatics in Nara 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Prediction of Health Effects of Food Peptides and Elucidation of The Mode-of-action Using Multi-task Graph Convolutional Neural Networks2019

    • Author(s)
      Fukunaga, I., Sawada, R., Shibata, T., Kaitoh, K., Sakai, Y., and Yamanishi, Y.
    • Organizer
      情報計算化学生物学会2019年大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] AI創薬:化合物の薬効や副作用を予測するデータ駆動型アプローチ2019

    • Author(s)
      山西芳裕
    • Organizer
      第46回日本毒性学会学術年会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] AI創薬:薬効や副作用を予測するデータ駆動型アプローチ2019

    • Author(s)
      山西芳裕
    • Organizer
      第66回日本実験動物学会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] AI創薬:薬効や副作用を予測するデータ駆動型アプローチ2019

    • Author(s)
      山西芳裕
    • Organizer
      第63回日本リウマチ学会総会・学術集会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] AI創薬:化合物の薬効や副作用を予測するデータ駆動型アプローチ2019

    • Author(s)
      山西芳裕
    • Organizer
      ファーマIT&デジタルエキスポ2019
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 機械学習によるデータ駆動型創薬とパスウェイ創薬2019

    • Author(s)
      山西芳裕
    • Organizer
      第92回日本薬理学会年会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] AI創薬:化合物の薬効を予測するデータ駆動型アプローチ2019

    • Author(s)
      山西芳裕
    • Organizer
      第1回日本メディカルAI学会学術集会
    • Related Report
      2018 Annual Research Report
  • [Presentation] AI創薬:薬効や副作用を予測するデータ駆動型アプローチ2018

    • Author(s)
      山西芳裕
    • Organizer
      第31回日本動物実験代替法学会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] ディジーゾーム解析による疾患間の関連性理解と創薬応用2018

    • Author(s)
      山西芳裕
    • Organizer
      第12回メタボロームシンポジウム
    • Related Report
      2018 Annual Research Report
  • [Presentation] AI創薬:薬効や副作用を予測するデータ駆動型アプローチ2018

    • Author(s)
      山西芳裕
    • Organizer
      第39回富山大学和漢医薬学総合研究所特別セミナー
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] AI創薬:薬効や副作用を予測するデータ駆動型アプローチ2018

    • Author(s)
      山西芳裕
    • Organizer
      新学術領域(研究領域提案型)「化学コミュニケーションのフロンティア」第1回若手シンポジウム
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] AI創薬:薬効や副作用を予測するデータ駆動型アプローチ2018

    • Author(s)
      山西芳裕
    • Organizer
      構造活性フォーラム2018
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] AI創薬:薬効や副作用を予測するデータ駆動型アプローチ2018

    • Author(s)
      山西芳裕
    • Organizer
      九州大学-理化学研究所-福岡市 三者連携シンポジウム
    • Related Report
      2018 Annual Research Report
  • [Presentation] Data-driven drug discovery and repositioning by machine learning methods2018

    • Author(s)
      Yamanishi, Y.
    • Organizer
      ACS Skolnik Symposium
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited

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Published: 2018-04-23   Modified: 2022-01-27  

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