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

2013 Fiscal Year Final Research Report

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

Research Project

  • PDF
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
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
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)).

  • Research Products

    (33 results)

All 2014 2013 2012 2011

All Journal Article (13 results) (of which Peer Reviewed: 12 results) Presentation (18 results) Book (2 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 Pages: 2606-2614

    • DOI

      10.2174/1381612811319140010

    • 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

    • 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

    • DOI

      10.1074/jcb.M113.452623

    • 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, W.-L. Hsu, S. Chiba, T. Furuta, M. Sakurai.
    • Journal Title

      Chem. Phys. Lett.

      Volume: 557 Pages: 145-149

    • DOI

      10.1016/j.cplett.2012.12.040

    • 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

  • [Journal Article] The power stroke driven by ATP binding in CFTR as studied by molecular dynamics simulations2013

    • Author(s)
      T. Furukawa-Hagiya, T. Furuta, S. Chiba, Y. Sohma, M. Sakurai.
    • Journal Title

      J. Phys. Chem. B.

      Volume: 117 Pages: 83-93

    • DOI

      10.1021/jp308315w

    • 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, and A. Kidera.
    • Journal Title

      J. Chem. Phys.

      Volume: 139 Pages: 054117-1-9

    • DOI

      10.1063/1.4817209

    • 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

    • 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 Pages: 999-1009

    • DOI

      10.1021/ja207173p

    • 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

      Sci. Rep. (Nature.com)

      Volume: 2 Pages: 331-1-331-8

    • DOI

      10.1038/srep00331

    • Peer Reviewed
  • [Journal Article] A quantum generalization of intrinsic reaction coordinate using path integral centroid coordinates2012

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

      J. Chem. Phys

      Volume: 136 Pages: 184103-1-11

    • DOI

      10.1063/1.4709723

    • Peer Reviewed
  • [Journal Article] Minimum Free Energy 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 Pages: 1002555-1-12

    • DOI

      10.1371/journal.pcbi.1002555

    • 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

    • 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)
    • Year and Date
      20140200
  • [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)
    • Year and Date
      20131000
  • [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)
    • Year and Date
      20131000
  • [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
    • Year and Date
      20130900
  • [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)
    • Year and Date
      20130700
  • [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
    • Year and Date
      20130300
  • [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
    • Year and Date
      20121200
  • [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)
    • Year and Date
      20120900
  • [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
    • Year and Date
      20120900
  • [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)
    • Year and Date
      20120900
  • [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)
    • Year and Date
      20120800
  • [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
  • [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
  • [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)
    • Year and Date
      20110700
  • [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
  • [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
  • [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
  • [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
  • [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.
    • Total Pages
      103-124
    • Publisher
      de Gruyter (Germany)
  • [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.
    • Total Pages
      365-376
    • Publisher
      Wiley-VCH (Germany)

URL: 

Published: 2015-07-16  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi