• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to previous page

The study on the structure-based inhibitor mechanism for xanthine oxidoreductase: beyond a lock-key system

Research Project

Project/Area Number 23570198
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Biophysics
Research InstitutionNippon Medical School

Principal Investigator

KIKUCHI Hiroto  日本医科大学, 医学部, 准教授 (00224907)

Co-Investigator(Kenkyū-buntansha) OKAMOTO Ken  日本医科大学, 医学部, 准教授 (60267143)
FUJISAKI Hiroshi  日本医科大学, 医学部, 准教授 (60573243)
FURUTA Tadaomi  東京工業大学, 准教授, 助教 (10431834)
Project Period (FY) 2011 – 2013
Project Status Completed (Fiscal Year 2013)
Budget Amount *help
¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000)
Fiscal Year 2013: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2012: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2011: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
Keywords酸化還元酵素 / 構造・機能予測 / 分子動力学 / キサンチン / 痛風治療薬 / 阻害剤 / フェブキソスタット / 創薬 / キサンチン
Research Abstract

Xanthine oxidoreductase (XOR) catalyzes the oxidation of hypoxanthine to xanthine followed by oxidation of xanthine to uric acid. Because having too much uric acid in the body causes a disease, gout, human XOR is a target of drugs to treat gout. XOR is found in a wide range of organisms from bacteria to man, and the substrate-binding pockets of mammalian and bacterial XOR are well-conserved as regards catalytically important residues and three-dimensional structure. In this research, we found in terms of the enzymatic experiments that febuxostat, a drug recently developed in Japan inhibits mammalian XOR, but not bacterial XOR. This means that a so-called key-lock system breaks and it is difficult to elucidate this functional differences from the view point of static three-dimensional structure of an inhibitor and an enzyme. However,we succeeded in reproducing the experimental results using MD calculations from the view point of dynamics (Sci. Rep. 2, 331; DOI:10.1038/srep00331 (2012)).

Report

(4 results)
  • 2013 Annual Research Report   Final Research Report ( PDF )
  • 2012 Research-status Report
  • 2011 Research-status Report
  • Research Products

    (48 results)

All 2014 2013 2012 2011

All Journal Article (16 results) (of which Peer Reviewed: 14 results) Presentation (28 results) Book (4 results)

  • [Journal Article] Chemical Nature and Reaction Mechanisms of the Molybdenum Cofactor of Xanthine Oxidoreductase2013

    • Author(s)
      K. Okamoto, T. Kusano, T. Nishino.
    • Journal Title

      Curr. Pham. Des.

      Volume: 19 Issue: 14 Pages: 2606-2614

    • DOI

      10.2174/1381612811319140010

    • Related Report
      2013 Annual Research Report 2013 Final Research Report 2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] A Versatile Method for Making Wilson's B-matrix in silico and a Study of Force Constant Transformation between Internal and Cartesian Coordinates2013

    • Author(s)
      H. Kikuchi.
    • Journal Title

      Bull. Lib. Arts & Sci. Nippon Med. Sch.

      Volume: 42 Pages: 37-85

    • NAID

      40019920401

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] The tryptophan redidue at the active site tunnel entrance of Trichoderma reesei cellobiohydrolase Cel7A is important for initiation of degradation of crystalline cellulose2013

    • Author(s)
      A. Nakamura, T. Tsukada, S. Auer, T. Furuta, M. Wada, A. Koivula, K. Igarashi, M. Samejima.
    • Journal Title

      J. Biol. Chem.

      Volume: 288 Pages: 13403-13510

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Dynamics and structural changes induced by ATP and/or substrate binding in the inward-facing conformation state of P-glycoprotein2013

    • Author(s)
      Y. Watanabe
    • Journal Title

      Chem. Phys. Left

      Volume: 557 Pages: 145-149

    • DOI

      10.1016/j.cplett.2012.12.040

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] キサンチン酸化還元酵素研究110年 ― 酵素蛋白お哺乳類における多面性 ;デヒドロゲナーゼからオキシダーゼへの変換とキサンチン酸化還元酵素が触媒するさまざまな反応 ―2013

    • Author(s)
      岡本研
    • Journal Title

      高尿酸血症と痛風

      Volume: 21 Pages: 69-74

    • Related Report
      2013 Final Research Report
  • [Journal Article] The Power Stroke Driven by ATP Binding in CFTR As Studied by by ATP Binding in CFTR As Studied by Molecular Dynamics Simulations2013

    • Author(s)
      T. Furukawa-Hagiya
    • Journal Title

      J. Phys. Chem. B

      Volume: 117 Issue: 1 Pages: 83-93

    • DOI

      10.1021/jp308315w

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Multiscale enhanced path sampling based on the Onsager-Machlup action: Application to a model polymer2013

    • Author(s)
      H. Fujisaki, M. Shiga, K. Moritsugu, A. Kidera
    • Journal Title

      Journal of Chemical Physics

      Volume: 139 Issue: 5 Pages: 0541171-9

    • DOI

      10.1063/1.4817209

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] タンパク質へのリガンド結合に関する計算物理・化学的アプローチ2013

    • Author(s)
      藤崎弘士
    • Journal Title

      日本医科大学医学会誌

      Volume: 9 Pages: 135-139

    • NAID

      130004942046

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] キサンチン酸化還元酵素研究110年 -酵素蛋白の哺乳類における多面性;デヒドロゲナーゼからオキシダーゼへの変換とキサンチン酸化還元酵素が触媒するさまざまな反応-2013

    • Author(s)
      岡本研
    • Journal Title

      高尿酸血症と痛風

      Volume: 21 Pages: 69-74

    • Related Report
      2013 Annual Research Report
  • [Journal Article] The Tryptophan Residue at the Active Site Tunnel Entrance of Trichoderma reesei Cellobiohydrolase Ce17A Is Important for Initiation of Degradation of Crystalline Cellulose2013

    • Author(s)
      Akihiko Nakamura, Tsukada, T., Auer, S., Furuta, T., Wada, M., Koivula, A., Igarashi, K. and Samejima M.
    • Journal Title

      Journal of Biological Chemistry

      Volume: 288 Issue: 19 Pages: 13503-13510

    • DOI

      10.1074/jbc.m113.452623

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Protein conformational gating of enzymatic activity in xanthine oxidoreductase2012

    • Author(s)
      H. Ishikawa, B. T. Eger, K. Okamoto, T. Nishino, E. F. Pai.
    • Journal Title

      J. Am. Chem. Soc.

      Volume: 134 Issue: 2 Pages: 999-1009

    • DOI

      10.1021/ja207173p

    • Related Report
      2013 Final Research Report 2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Different inhibitory potency of febuxostat towards mammalian and bacterial xanthine oxidoreductases: insight from molecular dynamics2012

    • Author(s)
      H. Kikuchi, H. Fujisaki, T. Furuta, K.Okamoto, S. Leimkuhler, and T. Nishino
    • Journal Title

      Scientific Reports

      Volume: 2 Issue: 1 Pages: 331-331

    • DOI

      10.1038/srep00331

    • Related Report
      2013 Final Research Report 2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] A quantum generalization of intrinsic reactioncoordinate using path integral centroid coordinate2012

    • Author(s)
      M. Shiga and H. Fujisaki
    • Journal Title

      J. Chem. Phys

      Volume: 136 Issue: 18 Pages: 18410-18410

    • DOI

      10.1063/1.4709723

    • Related Report
      2013 Final Research Report 2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase2012

    • Author(s)
      Y. Matsunaga, H. Fujisaki, T. Terada, T. Furuta, K. Moritsugu, and A. Kidera
    • Journal Title

      PLoS Comput. Biol

      Volume: 8 Issue: 6 Pages: 12-12

    • DOI

      10.1371/journal.pcbi.1002555

    • Related Report
      2013 Final Research Report 2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] 理論生物物理と生化学を組み合わせた薬物研究―キサンチン酸化還元酵素と阻害剤フェブキソスタットの結合機序―2012

    • Author(s)
      藤崎弘士, 古田忠臣, 岡本研, 菊地浩人
    • Journal Title

      日本医科大学医学会誌

      Volume: 8 Pages: 222-227

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] 理論生物物理と生化学を組み合わせた薬効研究―キサンチン酸化還元酵素と阻害剤フェブキソスタットの結合機序―2012

    • Author(s)
      藤崎弘士, 古田忠臣, 岡本研, 菊地浩人
    • Journal Title

      日本医科大学医学会誌

      Volume: 8 Pages: 222-227

    • NAID

      130004471511

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Presentation] Time series analysis of molecular dynamics simulation-collective behavior and conformational change-2014

    • Author(s)
      K. Fuji, H. Fujisaki, M. Toda.
    • Organizer
      Biophysical Society 58^<th> Annual Meeting
    • Place of Presentation
      San Francisco (USA)
    • Related Report
      2013 Final Research Report
  • [Presentation] Time series analysis of molecular dynamics simulation -collective behavior and conformational change-2014

    • Author(s)
      K. Fuji, H. Fujisaki, M. Toda
    • Organizer
      Biophysical Society 58th Annual Meeting
    • Place of Presentation
      San Francisco (USA)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Onsager-Machlup作用を用いたペプチドのパスサンプリング2013

    • Author(s)
      藤崎弘士, 松永康佑, 木寺詔紀
    • Organizer
      日本物理学会第68回年次大会
    • Place of Presentation
      広島大学
    • Related Report
      2013 Final Research Report 2012 Research-status Report
  • [Presentation] Molecular Dynamics and Free Energy Analysis of Xanthine Oxidoreductase-Ligand Interactions2013

    • Author(s)
      K. Okamoto, H. Kikuchi, H. Fujisaki, T. Furuta, S. Leimkuhler, and T. Nishino.
    • Organizer
      2013 Molybdenum & Tungsten Enzymes Conference
    • Place of Presentation
      Sintra (Portugal)
    • Related Report
      2013 Final Research Report
  • [Presentation] タンパク質シニョリンの構造変化パスサンプリング2013

    • Author(s)
      藤崎弘士, 冨士香奈, 戸田幹人
    • Organizer
      日本物理学会2013年秋季大会
    • Place of Presentation
      徳島
    • Related Report
      2013 Final Research Report
  • [Presentation] Mutation studies on the mammalian and the bacterial XORs with inhibitors2013

    • Author(s)
      H. Kikuchi, H. Fujisaki, T. Furuta, K. Okamoto, and T. Nishino.
    • Organizer
      The 51^<st> Annual Meeting of the Biophysics society of japan
    • Place of Presentation
      Kyoto (Jpn)
    • Related Report
      2013 Final Research Report
  • [Presentation] Time-series analysis of molecular dynamics : Conformational change and dynamics of collective behavior2013

    • Author(s)
      K. Fuji, M. Sekijima, H. Fujisaki, M. Toda.
    • Organizer
      The 51^<st> Annual Meeting of the Biophysics society of japan
    • Place of Presentation
      Kyoto (Jpn)
    • Related Report
      2013 Final Research Report
  • [Presentation] Mutation studies on the mammalian and the bacterial XORs with inhibitors2013

    • Author(s)
      H. Kikuchi, H. Fujisaki, T. Furuta, K. Okamoto, T. Nishino
    • Organizer
      The 51st Annual meeting of the Biophysics Society of Japan
    • Place of Presentation
      Kyoto
    • Related Report
      2013 Annual Research Report
  • [Presentation] Time-series analysis of molecular dynamics: Conformational change and dynamics of collective behavior2013

    • Author(s)
      K Fuji, M. Sekijima, H. Fujisaki, M. Toda
    • Organizer
      The 51st Annual meeting of the Biophysics Society of Japan
    • Place of Presentation
      Kyoto
    • Related Report
      2013 Annual Research Report
  • [Presentation] タンパク質シニョリンの構造変化パスサンプリング2013

    • Author(s)
      藤崎弘士、冨士香奈、戸田幹人
    • Organizer
      日本物理学会秋季大会
    • Place of Presentation
      徳島
    • Related Report
      2013 Annual Research Report
  • [Presentation] 分子階層モデルを使った生体分子の量子ダイナミクスII2012

    • Author(s)
      藤崎弘士, 菊地浩人, 戸田幹人, 高見利也
    • Organizer
      日本物理学会第67回年次大会
    • Place of Presentation
      関西学院大学
    • Year and Date
      2012-03-26
    • Related Report
      2013 Final Research Report
  • [Presentation] 生体分子の分子動力学時系列データに対する統計解析22012

    • Author(s)
      戸田幹人, 高見利也, 福水健次, 菊地浩人, 藤崎弘士
    • Organizer
      日本物理学会第67回年次大会
    • Place of Presentation
      関西学院大学
    • Year and Date
      2012-03-24
    • Related Report
      2013 Final Research Report
  • [Presentation] Theoretical investigation of vibrational energy transfer using the tier model with ab initio potential energy surfaces2012

    • Author(s)
      H. Fujisaki.
    • Organizer
      Gordon Research Conference on vibrational spectroscopy
    • Place of Presentation
      Biddeford, Maine (USA)
    • Related Report
      2013 Final Research Report 2012 Research-status Report
  • [Presentation] Molecular dynamics and free energy analysis of xanthine oxidoreductase-ligand interactions2012

    • Author(s)
      H. Kikuchi, H. Fujisaki, T. Furuta, K. Okamoto, and T. Nishino.
    • Organizer
      TACC 2012 Theory and Applications of Computational Chemistry
    • Place of Presentation
      Pavia (Italy)
    • Related Report
      2013 Final Research Report 2012 Research-status Report
  • [Presentation] 分子階層モデルを使った量子ダイナミクスIII2012

    • Author(s)
      藤崎弘士, 菊地浩人, 戸田幹人, 高見利也
    • Organizer
      日本物理学会2012年秋季大会
    • Place of Presentation
      横浜国立大学
    • Related Report
      2013 Final Research Report
  • [Presentation] Molecular dynamics simulations and binding free energy analysis of xanthine oxidoreductase-ligand complexes2012

    • Author(s)
      H. Kikuchi, H. Fujisaki, T. Furuta, K. Okamoto, and T. Nishino.
    • Organizer
      The 50^<st> Annual Meeting of the Biophysics society of Japan
    • Place of Presentation
      Nagoya (Japan)
    • Related Report
      2013 Final Research Report
  • [Presentation] 抗痛風薬フェブキソスタットとキサンチン酸化還元酵素との相互作用の解析2012

    • Author(s)
      岡本研, 菊地浩人, 藤崎弘士, 古田忠臣, 西野武士
    • Organizer
      第85回日本生化学会大会
    • Place of Presentation
      福岡国際会議場
    • Related Report
      2013 Final Research Report 2012 Research-status Report
  • [Presentation] 分子階層モデルを使った量子ダイナミクス32012

    • Author(s)
      藤崎弘士,菊地浩人,戸田幹人,高見利也
    • Organizer
      日本物理学会2012年秋季大会
    • Place of Presentation
      横浜国立大学
    • Related Report
      2012 Research-status Report
  • [Presentation] 生体分子の分子動力学時系列データに対する統計解析22012

    • Author(s)
      戸田幹人、高見利也、福水健次、菊地浩人、藤崎弘士
    • Organizer
      日本物理学会第67回年次大会
    • Place of Presentation
      関西学院大学
    • Related Report
      2011 Research-status Report
  • [Presentation] 分子階層モデルを使った量子ダイナミクスII2012

    • Author(s)
      藤崎弘士、菊地浩人、戸田幹人、高見利也
    • Organizer
      日本物理学会第67回年次大会
    • Place of Presentation
      関西学院大学
    • Related Report
      2011 Research-status Report
  • [Presentation] 生体分子の分子動力学時系列データに対する統計解析2011

    • Author(s)
      戸田幹人, 高見利也, 福水健次, 菊地浩人, 藤崎弘士
    • Organizer
      日本物理学会2011年秋季大会
    • Place of Presentation
      富山大学
    • Year and Date
      2011-09-23
    • Related Report
      2013 Final Research Report 2011 Research-status Report
  • [Presentation] キサンチン酸化還元酵素に対するファブキソスタットの阻害作用2011

    • Author(s)
      菊地浩人, 藤崎弘士, 古田忠臣, 岡本研, 西野武士
    • Organizer
      日本物理学会2011年秋季大会
    • Place of Presentation
      富山大学
    • Year and Date
      2011-09-22
    • Related Report
      2013 Final Research Report
  • [Presentation] ミオシンATPaseにおける加水分解の反応経路:QM/MM法による計算2011

    • Author(s)
      香川浩, 藤崎弘士, 菊地浩人, 志賀基之
    • Organizer
      日本物理学会2011年秋季大会
    • Place of Presentation
      富山大学
    • Year and Date
      2011-09-22
    • Related Report
      2013 Final Research Report
  • [Presentation] 分子階層モデルを使った生体分子の量子ダイナミクス2011

    • Author(s)
      藤崎弘士, 菊地浩人, 戸田幹人, 高見利也.
    • Organizer
      日本物理学会2011年秋季大会
    • Place of Presentation
      富山大学
    • Year and Date
      2011-09-21
    • Related Report
      2013 Final Research Report 2011 Research-status Report
  • [Presentation] Structure-based inhibitor mechanism of febuxostat for xanthine oxidoreductase : molecular dynamics study2011

    • Author(s)
      H. Kikuchi, H. Fujisaki, T. Furuta, K. Okamoto, S. Leimkuhler, and T. Nishino.
    • Organizer
      Ninth Triennial Congress of the World Association of Theoretical and Computational Chemists
    • Place of Presentation
      Santiago de Compostela (Spain)
    • Related Report
      2013 Final Research Report
  • [Presentation] Structure-based inhibitor mechanism of febuxostat for xanthine oxidoreductase: molecular dynamics study2011

    • Author(s)
      H. Kikuchi, H. Fujisaki, T. Furuta, K. Okamoto, S. Leimkuhler, and T. Nishino
    • Organizer
      Ninth Triennial Congress of the World Association of Theoretical and Computational Chemists
    • Place of Presentation
      Santiago de Compostela, Spain
    • Related Report
      2011 Research-status Report
  • [Presentation] キサンチン酸化還元酵素に対するフェブキソスタットの阻害作用2011

    • Author(s)
      菊地浩人、藤崎弘士、古田忠臣、岡本研、西野武士
    • Organizer
      日本物理学会2011年秋季大会
    • Place of Presentation
      富山大学
    • Related Report
      2011 Research-status Report
  • [Presentation] ミオシンATPase における加水分解の反応経路:QM/MM法による計算2011

    • Author(s)
      香川浩、藤崎弘士、菊地浩人、志賀基之
    • Organizer
      日本物理学会2011年秋季大会
    • Place of Presentation
      富山大学
    • Related Report
      2011 Research-status Report
  • [Book] The xanthine oxidoreductase enzyme family : xanthine dehydrogenase, xanthine oxidase, and aldehyde oxidase. Hand book of flavoproteins Volume 2 (Hille R, Miller S M, Palfey B editors)2013

    • Author(s)
      T. Nishino, K. Okamoto, B. T. Eger, E. F. Pai.
    • Publisher
      de Gruyter (Germany)
    • Related Report
      2013 Final Research Report
  • [Book] Hand book of flavoproteins Volume 2 (Hille R, Miller S M, Palfey B editors); (分担)The xanthine oxidoreductase enzyme family: xanthine dehydrogenase, xanthine oxidase, and aldehyde oxidase2013

    • Author(s)
      Nishino T, Okamoto K, Eger B T, Pai E F
    • Publisher
      de Gruyter, Germany
    • Related Report
      2013 Annual Research Report
  • [Book] A new-generation uric acid production inhibitor : Febuxostat. In : Fischer J, Ganellin CR, Rotella DP editors. Analogue-based Drug Discovery III.2012

    • Author(s)
      K. Okamoto, S. Kondo, T. Nishino.
    • Publisher
      Wiley-VCH (Germany)
    • Related Report
      2013 Final Research Report
  • [Book] A new-generation uric acid production inhibitor: Febuxostat. In: Fischer J, Ganellin CR, Rotella DP editors. Analogue-based Drug Discovery III.2012

    • Author(s)
      Okamoto K, Kondo S, Nishino T.
    • Total Pages
      12
    • Publisher
      Wiley-VCH (Germany)
    • Related Report
      2012 Research-status Report

URL: 

Published: 2011-08-05   Modified: 2019-07-29  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi