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Integrated analysis of biological interaction of small molecules at the molecular level of living organisms

Planned Research

Project AreaEstablishment of Integrative Multi-level Systems Biology and its Applications
Project/Area Number 23136102
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Complex systems
Research InstitutionKyoto University

Principal Investigator

YAMASHITA Fumiyoshi  京都大学, 薬学研究科(研究院), 准教授 (30243041)

Co-Investigator(Kenkyū-buntansha) NIIJIMA Satoshi  京都大学, 薬学研究科, 助教 (30456834)
INOGUCHI Akihiro  関西学院大学, 理工学部, 准教授 (70452456)
Co-Investigator(Renkei-kenkyūsha) OKUNO Yasushi  京都大学, 医学研究科, 教授 (20283666)
ITOH Takayuki  お茶の水女子大学, 人間文化創成科学研究科, 教授 (80401595)
Project Period (FY) 2011-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥30,420,000 (Direct Cost: ¥23,400,000、Indirect Cost: ¥7,020,000)
Fiscal Year 2014: ¥9,620,000 (Direct Cost: ¥7,400,000、Indirect Cost: ¥2,220,000)
Fiscal Year 2013: ¥10,140,000 (Direct Cost: ¥7,800,000、Indirect Cost: ¥2,340,000)
Fiscal Year 2012: ¥10,660,000 (Direct Cost: ¥8,200,000、Indirect Cost: ¥2,460,000)
Keywords生体生命情報学 / 薬物動態 / 構造活性相関 / 薬剤反応性 / 酵素誘導 / 生理学的モデル / テキストマイニング / モデル化 / 分子間相互作用
Outline of Final Research Achievements

A disposition behavior of small molecules is integration of their interactions with biological organisms comprising of multi layers. in which the lowest events are molecular interactions. In this study, we established methods for systematically collecting information on interaction between small molecule drugs and ADME-related functional proteins and for analyzing their structure-activity relationship. Being exemplified by the prediction of enzyme induction-associated drug-drug interaction, a method for predicting effect of small molecule drugs on pharmacokinetics of other or its own molecules was also developed. We succeeded in reproducing the biological phenomena on an open platform for multi-level modeling and simulation of physiological system.

Report

(5 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • Research Products

    (34 results)

All 2015 2014 2013 2012 2011

All Journal Article (11 results) (of which Peer Reviewed: 10 results,  Open Access: 3 results,  Acknowledgement Compliant: 2 results) Presentation (22 results) (of which Invited: 4 results) Book (1 results)

  • [Journal Article] Multiple linear regression analysis indicates association of P-glycoprotein substrate or inhibitor character with bitterness intensity, measured with a sensor2015

    • Author(s)
      Kentaro Yano, Suzune Mita, Kaori Morimoto, Tamami Haraguchi, Hiroshi Arakawa, Miyako Yoshida, Fumiyoshi Yamashita, Takahiro Uchida, Takuo Ogihara
    • Journal Title

      Journal of Pharmaceutical Sciences

      Volume: 104 Issue: 9 Pages: 2789-2794

    • DOI

      10.1002/jps.24232

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Artificial neural network analysis for predicting human percutaneous absorption taking account of vehicle properties2015

    • Author(s)
      Tomomi Atobe, Masaaki Mori, Fumiyoshi Yamashita, Mitsuru Hashida, Hirokazu Kouzuki
    • Journal Title

      The Journal of Toxicological Sciences

      Volume: 40 Issue: 2 Pages: 277-294

    • DOI

      10.2131/jts.40.277

    • NAID

      130004904033

    • ISSN
      0388-1350, 1880-3989
    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Self-assembling lipid modified glycol-split heparin nanoparticles suppress lipopolysaccharide-induced inflammation through TLR4-NF-κB signaling2014

    • Author(s)
      Hasan Babazada, Fumiyoshi Yamashita, Shinya Yanamoto, Mitsuru Hashida
    • Journal Title

      Journal of Controlled Release

      Volume: 194 Pages: 332-340

    • DOI

      10.1016/j.jconrel.2014.09.011

    • NAID

      120005512273

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Suppression of experimental arthritis with self-assembling glycol-split heparin nanoparticles via inhibition of TLR4-NF-κB signaling2014

    • Author(s)
      Hasan Babazada, Fumiyoshi Yamashita, Mitsuru Hashida
    • Journal Title

      Journal of Controlled Release

      Volume: 194 Pages: 295-300

    • DOI

      10.1016/j.jconrel.2014.09.015

    • NAID

      120005512274

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] 薬物代謝酵素の誘導に基づく薬物間相互作用の予測2014

    • Author(s)
      吉田秀哉、山下富義
    • Journal Title

      Drug Delivery System

      Volume: 29 Pages: 417-425

    • NAID

      130004874241

    • Related Report
      2014 Annual Research Report
  • [Journal Article] Bilinear Model for the Size-Dependency of the CYP3A4 Inhibitory Activity of Structurally Diverse Compounds2014

    • Author(s)
      Peter Buchwald, Fumiyoshi Yamashita
    • Journal Title

      Molecular Informatics

      Volume: 33 Issue: 1 Pages: 8-14

    • DOI

      10.1002/minf.201300132

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Modeling of rifampicin-induced CYP3A4 activation dynamics for the prediction of clinical drug-drug interactions from in vitro data2013

    • Author(s)
      Fumiyoshi Yamashita, Yukako Sasa, Shuya Yoshida, Akihiro Hisaka, Yoshiyuki Asai, Hiroaki Kitano, Mitsuru Hashida, Hiroshi Suzuki
    • Journal Title

      PLoS One

      Volume: 8(9) Issue: 9 Pages: 1-11

    • DOI

      10.1371/journal.pone.0070330

    • NAID

      120005343920

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Automated extraction of information on chemical-P-glycoprotein interactions from the literature2013

    • Author(s)
      Shuya Yoshida, Fumiyoshi Yamashita, Atsushi Ose, Kazuya Maeda, Yuichi Sugiyama, Mitsuru Hashida
    • Journal Title

      Journal of Chemical Information and Modeling

      Volume: 53 Issue: 10 Pages: 2506-2510

    • DOI

      10.1021/ci4003188

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The Role of Inter-segmental Differences in P-glycoprotein Expression and Activity along the Rat Small Intestine in Causing the Double-peak Phenomenon of Substrate Plasma Concentration2013

    • Author(s)
      Sho Wada, Takashi Kano,Suzune Mita, Yoko Idota, Kaori Morimoto, Fumiyoshi Yamashita, Takuo Ogihara
    • Journal Title

      Drug Metabolism and Pharmacokinetics

      Volume: 28 Issue: 2 Pages: 98-103

    • DOI

      10.2133/dmpk.DMPK-12-RG-005

    • NAID

      130004933523

    • ISSN
      1347-4367, 1880-0920
    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structure-Activity Relationship Modeling for Predicting Interactions with Pregnane X Receptor by Recursive Partitioning2012

    • Author(s)
      Shuya Yoshida, Fumiyoshi Yamashita, Takayuki Itoh, Mitsuru Hashida
    • Journal Title

      Drug Metabolism and Pharmacokinetics

      Volume: 27 Issue: 5 Pages: 506-512

    • DOI

      10.2133/dmpk.DMPK-11-RG-159

    • NAID

      130004463279

    • ISSN
      1347-4367, 1880-0920
    • Related Report
      2012 Annual Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Chemogenomic approach to comprehensive predictions of ligand-target interactions: a comparative study2012

    • Author(s)
      J.B. Brown, S. Niijima, A. Shiraishi, M. Nakatsui, Y. Okuno
    • Journal Title

      Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2012), Workshop on Pharmaco-informatics for Drug Discovery (PIDD 2012)

      Volume: 1 Pages: 136-142

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Presentation] In vitro-in vivo補外予測によりin vivo動態試験のサンプリングコストを低減できるか?2015

    • Author(s)
      山下富義、酒井千賀、橋田 充
    • Organizer
      日本薬学会第135年会
    • Place of Presentation
      神戸サンボーホール(神戸)
    • Year and Date
      2015-03-26
    • Related Report
      2014 Annual Research Report
  • [Presentation] 2 型リアノジン受容体の不整脈原性変異はCICR 活性と細胞内Ca2+動態にどのような影響を及ぼすか?2015

    • Author(s)
      呉林なごみ、村山尚、太田亮作、山下富義、鈴木純二、金丸和典、飯野正光、櫻井隆
    • Organizer
      第88回日本薬理学会年会
    • Place of Presentation
      名古屋国際会議場(名古屋)
    • Year and Date
      2015-03-20
    • Related Report
      2014 Annual Research Report
  • [Presentation] 薬物動態学的相互作用の予測を目指した多階層生体モデリング2015

    • Author(s)
      山下富義
    • Organizer
      第88回日本薬理学会年会
    • Place of Presentation
      名古屋国際会議場(名古屋)
    • Year and Date
      2015-03-19
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 自己組織化ヘパリン誘導体の抗炎症作用と構造活性相関2014

    • Author(s)
      山下富義、Hasan Babazada、酒井千賀、橋田充
    • Organizer
      第42回構造活性相関シンポジウム
    • Place of Presentation
      くまもと森都心プラザ (熊本)
    • Year and Date
      2014-11-14
    • Related Report
      2014 Annual Research Report
  • [Presentation] Computer-aided full-automatic construction of covariate models in population pharmacokinetic analysis2014

    • Author(s)
      Fumiyoshi Yamashita, Shuya Yoshida, Mitsuru Hashida
    • Organizer
      Joint Scientific Meeting: 29th JSSX Meeting and 19th North American ISSX Meeting
    • Place of Presentation
      Hilton San Francisco Union Square (San Francisco)
    • Year and Date
      2014-10-22
    • Related Report
      2014 Annual Research Report
  • [Presentation] Modeling and prediction of cytochrome P450 induction-mediated drug-drug interaction2014

    • Author(s)
      Fumiyoshi Yamashita
    • Organizer
      11th France-Japan DDS Symposium
    • Place of Presentation
      淡路夢舞台国際会議場(淡路)
    • Year and Date
      2014-10-06
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Automated information extraction and structure-activity relationship analysis of cytochrome P450 substrates2013

    • Author(s)
      Fumiyoshi Yamashita
    • Organizer
      9th Retrometabolism Based Drug Design and Targeting Conference
    • Place of Presentation
      The Villas of Grand Cypress Orlando, Orlando
    • Related Report
      2013 Annual Research Report
  • [Presentation] Impact and application of data mining in ADME researches2013

    • Author(s)
      山下富義
    • Organizer
      日本薬物動態学会第28回年会
    • Place of Presentation
      タワーホール船堀(東京)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 遺伝的数式プログラミング法を用いたCYP3A4阻害活性に対する構造活性相関解析2013

    • Author(s)
      吉田秀哉、藤田淳人、山下富義、橋田 充
    • Organizer
      日本薬物動態学会第28回年会
    • Place of Presentation
      タワーホール船堀(東京)
    • Related Report
      2013 Annual Research Report
  • [Presentation] 多階層生体機能モデリング・シミュレーションプラットフォームを利用した酵素誘導型薬物間相互作用シミュレータの開発2013

    • Author(s)
      山下富義、笹 友香子、吉田秀哉、樋坂章博、浅井義之、北野宏明、橋田 充、鈴木洋史
    • Organizer
      第29回Population Pharmacokinetics研究会
    • Place of Presentation
      慶応大学日吉キャンパス(横浜)
    • Related Report
      2013 Annual Research Report
  • [Presentation] 情報科学的アプローチによる薬物動態の予測2013

    • Author(s)
      山下富義
    • Organizer
      第57回日本薬学会関東支部大会
    • Place of Presentation
      帝京大学板橋キャンパス(東京)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 遺伝的数式プログラミング法によるCYP3A4阻害活性予測モデルの構築2012

    • Author(s)
      藤田淳人、山下富義、橋田 充
    • Organizer
      日本動物実験代替法学会第25回大会
    • Place of Presentation
      慶應義塾大学薬学部(東京都)
    • Year and Date
      2012-12-07
    • Related Report
      2012 Annual Research Report
  • [Presentation] P-glycoprotein輸送基質に関する構造活性相関解析2012

    • Author(s)
      吉田秀哉、山下富義、尾瀬淳、前田和也、杉山雄一、橋田充
    • Organizer
      日本動物実験代替法学会第25回大会
    • Place of Presentation
      慶應義塾大学薬学部(東京都)
    • Year and Date
      2012-12-07
    • Related Report
      2012 Annual Research Report
  • [Presentation] Dissecting kinase profiling data to predict activity and understand cross-reactivity of kinase inhibitors2012

    • Author(s)
      S. Niijima, A. Shiraishi, Y. Okuno
    • Organizer
      3rd Strasbourg Summer School in Chemoinformatics
    • Place of Presentation
      Universite de Strasbourg (Strasbourg, France)
    • Year and Date
      2012-06-25
    • Related Report
      2012 Annual Research Report
  • [Presentation] Chemical genomic analysis of cross-reactivity in endogenous GPCR-mediated pathways2012

    • Author(s)
      A. Shiraishi, S. Niijima, Y. Okuno
    • Organizer
      3rd Strasbourg Summer School in Chemoinformatics
    • Place of Presentation
      Universite de Strasbourg (Strasbourg, France)
    • Year and Date
      2012-06-25
    • Related Report
      2012 Annual Research Report
  • [Presentation] 再帰分割法を用いた化合物/Pregnane X receptor間相互作用に関する構造活性相関解析2012

    • Author(s)
      吉田秀哉、山下富義、橋田 充
    • Organizer
      日本薬剤学会第27年会
    • Place of Presentation
      神戸国際会議場(兵庫県)
    • Year and Date
      2012-05-24
    • Related Report
      2012 Annual Research Report
  • [Presentation] In Silico Pharmacokinetics : from QSAR to PK Modeling2012

    • Author(s)
      Fumiyoshi Yamashita
    • Organizer
      1st HD Physiology International Symposium : Integrative Multi-level Systems Biology for In silico Cardiology and Pharmacokinetics
    • Place of Presentation
      東京大学(東京都)
    • Year and Date
      2012-01-21
    • Related Report
      2011 Annual Research Report
  • [Presentation] Prediction of drug-drug interactions with rifampicin based on dynamics of induction of cytochrome P450 3A42012

    • Author(s)
      Y. Sasa, F. Yamashita, M. Hashida
    • Organizer
      第28回Population Pharmacokinetics研究会
    • Place of Presentation
      臨床研究情報センター(兵庫県)
    • Related Report
      2012 Annual Research Report
  • [Presentation] Chemoinformatic Modeling for Discriminating Pregnane X Receptor Activators2012

    • Author(s)
      Shuya Yoshida, Fumiyoshi Yamashita
    • Organizer
      1st HD Physiology International Symposium : Integrative Multi-level Systems Biology for In silico Cardiology and Pharmacokinetics
    • Place of Presentation
      東京大学(東京都)
    • Related Report
      2011 Annual Research Report
  • [Presentation] Pharmacokinetic Modeling Considering Dynamics of Induction of Drug Metabolizing Enzymes2012

    • Author(s)
      Yukako Sasa, Fumiyoshi Yamashita
    • Organizer
      1st HD Physiology International Symposium : Integrative Multi-level Systems Biology for In silico Cardiology and Pharmacokinetics
    • Place of Presentation
      東京大学(東京都)
    • Related Report
      2011 Annual Research Report
  • [Presentation] In Silico Prediction of Pregnane X Receptor Activators by Classification Tree Model2011

    • Author(s)
      Fumiyoshi Yamashita, Shuya Yoshida, Mitsuru Hashida
    • Organizer
      The 8th AFMC International Medicinal Chemistry Symposium
    • Place of Presentation
      京王プラザホテル(東京都)
    • Year and Date
      2011-12-01
    • Related Report
      2011 Annual Research Report
  • [Presentation] 進化的アルゴリズムを利用した母集団薬物動態モデル構築の自動化2011

    • Author(s)
      笹友香子、山下富義、橋田充
    • Organizer
      第4回日本ファーマコメトリクス研究会
    • Place of Presentation
      昭和大学(東京都)
    • Year and Date
      2011-09-03
    • Related Report
      2011 Annual Research Report
  • [Book] Dr. 北野のゼロから始めるシステムバイオロジー 第10講 PhysioDesignerによる生理機能の多階層モデル構築とシミュレーション2015

    • Author(s)
      浅井義之、山下富義
    • Publisher
      羊土社
    • Related Report
      2014 Annual Research Report

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Published: 2013-05-15   Modified: 2019-07-29  

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