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

Development of the prediction method of ligand binding affinity in SBDD

Research Project

Project/Area Number 18590096
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Drug development chemistry
Research InstitutionKinki University (2008)
Kyoto University (2006-2007)

Principal Investigator

NAKANISHI Isao  Kinki University, 薬学部, 教授 (10362576)

Co-Investigator(Kenkyū-buntansha) KITAURA Kazuo  京都大学, 大学院薬学研究科, 教授 (30132723)
Project Period (FY) 2006 – 2008
Project Status Completed (Fiscal Year 2008)
Budget Amount *help
¥3,540,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥240,000)
Fiscal Year 2008: ¥390,000 (Direct Cost: ¥300,000、Indirect Cost: ¥90,000)
Fiscal Year 2007: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2006: ¥2,500,000 (Direct Cost: ¥2,500,000)
Keywords医薬分子設計 / フラグメント分子軌道法 / 結合エネルギー / 溶媒和エネルギー / 構造最適化 / FKBP / HIV-1プロテアーゼ / タンパク質 / SBDD / 溶媒和カネルギー / HIV-1
Research Abstract

フラグメント分子軌道(FMO)法による相互作用エネルギーを用いた薬物活性予測法の開発を行った。水和エネルギーにPCM法用いたFMO/PCM法は、パラメータを用いないab initioな活性(結合自由エネルギー)予測法にもかかわらず、実験値のオーダーの再現性には非常に優れていた。今後、分子運動やエントロピー等を考慮することにより、実用レベルでの予測精度を達成できるものと期待される。

Report

(4 results)
  • 2008 Annual Research Report   Final Research Report ( PDF )
  • 2007 Annual Research Report
  • 2006 Annual Research Report
  • Research Products

    (55 results)

All 2009 2008 2007 2006 Other

All Journal Article (32 results) (of which Peer Reviewed: 26 results) Presentation (23 results)

  • [Journal Article] Binding free energy calculations of adenosine deaminase inhibitor and the effect of methyl substitution in inhibitors2009

    • Author(s)
      Takahiro Kosugi, Isao Nakanishi, Kazuo Kitaura
    • Journal Title

      J. Chem. Inf. Model. 49

      Pages: 618-622

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Cluster hydration model for binding energy calculations of protein-ligand complexes.2009

    • Author(s)
      Murata Katsumi
    • Journal Title

      J. Phys. Chem. B 113

      Pages: 809-817

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Binding free energy calculations of adenosine deaminase inhibitor and the effect of methyl substitution in inhibitors.2009

    • Author(s)
      Kosugi Takahiro
    • Journal Title

      J. Chem. Info. Model. (in press)

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Amide-πinteractions between formamide and benzene.2009

    • Author(s)
      Imai Nakamura-Yumi
    • Journal Title

      J. Comp. Chem. (in press)

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Fragment molecular orbital study of the electronic excitations in the photosynthetic reaction center of Blastochloris viridi2009

    • Author(s)
      Ikegami Tsutomu
    • Journal Title

      J. Comp. Chem. (in press)

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Covalent Bond fragmentation suitable to descnbe solids in the fragment molecular orbital method2008

    • Author(s)
      Dmitri G Fedorov, Jensen JH, Deka RC, Kazuo Kitaura
    • Journal Title

      J. Phys. Chem. A 112

      Pages: 11808-11816

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Ab lnitio fragment molecular orbital study of ligand binding to human progesterone receptor ligand-binding domain2008

    • Author(s)
      T Harada, K Yamagishi, T Nakano, Kazuo Kitaura, H Tokiwa
    • Journal Title

      Naunyn-Schmiedeberg's Arch Pharmacol. 377

      Pages: 607-615

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Polarizable continuum model with the fragment molecular orbital based time-dependent density functional theory2008

    • Author(s)
      M Chiba, DG Fedorov, Kazuo Kitaura
    • Journal Title

      J. Comp. Chem. 29

      Pages: 2667-2676

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Cl-π interactions in protein-ligand complexes2008

    • Author(s)
      Imai N-Y, Inoue Y, Isao Nakanishi, Kazuo Kitaura
    • Journal Title

      Protein Science 17

      Pages: 1129-1137

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] C1-π interactions in protein-ligand complexes.2008

    • Author(s)
      Imai Nakamura-Yumi
    • Journal Title

      Protein Science 17

      Pages: 1129-1137

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Polarizable continuum model with the fragment molecular orbital based time-dependent density functional theory.2008

    • Author(s)
      Chiba Mahito
    • Journal Title

      J. Comp. Chem. 29

      Pages: 2667-2676

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Ab initio fragment molecular orbital study of ligand binding to human progesterone receptor ligand-binding domain.2008

    • Author(s)
      Harada Takanori
    • Journal Title

      Naunyn-Schmiedeberg's Arch Pharmacol. 377

      Pages: 607-615

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Covalent Bond fragmentation suitable to describe solids in the fragment molecular orbital method.2008

    • Author(s)
      Fedorov Dmitri
    • Journal Title

      J. Phys. Chem. A 112

      Pages: 11808-11816

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The fragment molecular orbital method for geometry optimizations of polypeptides and proteins2007

    • Author(s)
      D. G. Fedorov, T. Ishida, M. Uebayasi, Kazuo Kitaura
    • Journal Title

      J. Phys. Chem. A 111

      Pages: 2722-2732

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Change in a protein's electronic structure induced by an explicit solvent : an ab initio Fragment Molecular Orbital (FMO) study of ubiquitin2007

    • Author(s)
      Y. Komeiji, T. Ishida, D. G. Fedorov, Kazuo Kitaura
    • Journal Title

      J. Comp. Chem. 28

      Pages: 1759-1762

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Accuracy of the three-body fragment molecular orbital method (FMO) applied to Moller-Plesset perturbation theory2007

    • Author(s)
      D. G. Fedorov, K. Ishimura, T. Ishida, Kazuo Kitaura, P. Pulay, S. Nagase
    • Journal Title

      J. Comp. Chem. 28

      Pages: 1476-1484

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Pair interaction energy decomposition analysis2007

    • Author(s)
      D. G. Fedorov, Kazuo Kitaura
    • Journal Title

      J. Comp. Chem. 28

      Pages: 222-237

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular recognition mechanism of FK506 binding protein : An all-electron fragment molecular orbital study2007

    • Author(s)
      Isao Nakanishi, D. G. Fedorov, Kazuo Kitaura
    • Journal Title

      Proteins 68

      Pages: 145-158

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular recognition mechanism of FK506 binding protein: An all-electron fragment molecular orbital study2007

    • Author(s)
      I. Nakanishi, D. G. Fedorov and K. Kitaura
    • Journal Title

      PROTEINS: Structure, Function, and Bioinformatics 68

      Pages: 145-158

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Pair interaction energy decomposition analysis2007

    • Author(s)
      D. G. Fedorov and K. Kitaura
    • Journal Title

      J. Comp. Chem. 28

      Pages: 222-237

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Change in a protein's electronic structure induced by an explicit solvent: an ab initio Fragment Molecular Orbital (FMO) study of ubiquitin2007

    • Author(s)
      Y. Komeiji, T. Ishida, D. G. Fedorov, and K. Kitaura
    • Journal Title

      J. Comp. Chem. 28

      Pages: 1750-1762

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Accuracy of the three-body fragment molecular orbital method (FMO) applied to Moller-Plesset perturbation theory2007

    • Author(s)
      D. G. Fedorov, K. Ishimura, T. Ishida, K. Kitaura, P. Pulay, and S. Nagase
    • Journal Title

      J. Comp. Chem. 28

      Pages: 1476-1484

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The fragment molecular orbital method for geometry optimizations of polypeptides and proteins2007

    • Author(s)
      D. G. Fedorov, T. Ishida, M. Uebayasi, and K. Kitaura
    • Journal Title

      J. Phys. Chem. A 111

      Pages: 2722-2732

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular recognition mechanism of FK506 binding protein : An all-electron fragment molecular orbital study2007

    • Author(s)
      Isao Nakanishi, Dmitri G. Fedorov, Kazuo Kitaura
    • Journal Title

      Protein : Structure, Function, and Bioinformatics 68(in press)

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Pair interaction energy decomposition analysis2007

    • Author(s)
      Dmitri G.Fedorov, Kazuo Kitaura
    • Journal Title

      Journal of Computational Chemistry 28・1

      Pages: 222-237

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Change in a protein s electronic structure induced by an explicit solvent : an ab initio Fragment Molecular Orbital (FMO) study of ubiquitin2007

    • Author(s)
      Yuto Komeiji, Kazuo Kitaura, et al.
    • Journal Title

      Journal of Computational Chemistry 28(in press)

    • Related Report
      2006 Annual Research Report
  • [Journal Article] The fragment molecular orbital method for geometry optimizations of polypeptides and proteins2007

    • Author(s)
      Dmitri G.Fedorov, Kazuo Kitaura, et al.
    • Journal Title

      Journal of Physical Chemistry A(in press)

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Molecular interactions between estrogen receptor and its ligand studied by ab lnito fragment molecular orbital method2006

    • Author(s)
      Kaori Fukuzawa, Kazuo Kitaura, et al.
    • Journal Title

      J. Phys. Chem. B 110

      Pages: 16102-16110

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO)2006

    • Author(s)
      Dmitri G. Fedorov, Kazuo Kitaura, et al.
    • Journal Title

      J. Comp. Chem. 27

      Pages: 976-985

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO)2006

    • Author(s)
      Dmitri G.Fedorov, Kazuo Kitaura, et al.
    • Journal Title

      Journal of Computational Chemistry 27・8

      Pages: 976-985

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Molecular interactions between estrogen receptor and its ligand studied by ab inito fragment molecular orbital method2006

    • Author(s)
      Kaori Fukuzawa, Kazuo Kitaura, et al.
    • Journal Title

      Journal of Physical Chemistry B・110

      Pages: 16102-16110

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Amide-π interactions between formamide and benzene

    • Author(s)
      Imai N-Y, Inoue Y, Isao Nakanishi, Kazuo Kitaura
    • Journal Title

      J. Comp. Chem. (in press)

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Presentation] Development and applications of the fragment molecular orbital method2009

    • Author(s)
      Kitaura Kazuo
    • Organizer
      50th Sanibel Symposium
    • Place of Presentation
      St. Simons, Island
    • Year and Date
      2009-02-28
    • Related Report
      2008 Annual Research Report 2008 Final Research Report
  • [Presentation] フラグメントMO法による構造最適化に対する電子相関の影響2009

    • Author(s)
      中村真也
    • Organizer
      日本薬学会第129年会
    • Place of Presentation
      京都
    • Related Report
      2008 Annual Research Report 2008 Final Research Report
  • [Presentation] FMO法によるカゼインキナーゼ2の分子認識機構解析2009

    • Author(s)
      浅田直也
    • Organizer
      日本薬学会第129年会
    • Place of Presentation
      京都
    • Related Report
      2008 Annual Research Report 2008 Final Research Report
  • [Presentation] フラグメント分子軌道法の開発と応用2009

    • Author(s)
      北浦和夫
    • Organizer
      第3回次世代ナノ統合ソフト公開シンポジウム
    • Place of Presentation
      岡崎
    • Related Report
      2008 Final Research Report
  • [Presentation] フラグメント分子軌道法の開発と応用2009

    • Author(s)
      北浦和夫
    • Organizer
      第3回次世代ナノ統合ソフト公開シンポジウム
    • Place of Presentation
      岡崎市
    • Related Report
      2008 Annual Research Report
  • [Presentation] Theoretical study of geometry and molecular recognition mechanism of Casein Kinase 2α (CK2α) with the FMO-MP2 method2008

    • Author(s)
      Asada Naoya
    • Organizer
      第38回構造活性相関シンポジウム
    • Place of Presentation
      神戸
    • Year and Date
      2008-11-03
    • Related Report
      2008 Final Research Report
  • [Presentation] Theoretical study of geometry and molecular recognition mechanism of Casein Kinase 2α (CK2α) with the FM0-MP2 method.2008

    • Author(s)
      Asada Naoya
    • Organizer
      第38回構造活性相関シンポジウム
    • Place of Presentation
      神戸
    • Year and Date
      2008-11-03
    • Related Report
      2008 Annual Research Report
  • [Presentation] Electronic structure calculations of proteins using fragment molecular orbital method2008

    • Author(s)
      Kitaura Kazuo
    • Organizer
      Telluride Workshop on Many Body Interactions : From Quantum Mechanics to Force Field
    • Place of Presentation
      Telluride, USA
    • Related Report
      2008 Final Research Report
  • [Presentation] Quantum Chemical Calculations of Protein-ligand Interactions with Fragment Molecular Orbital Method2008

    • Author(s)
      Kitaura Kazuo
    • Organizer
      World Association of Theoretical and Computational Chemists 2008
    • Place of Presentation
      Sydney, Australia
    • Related Report
      2008 Final Research Report
  • [Presentation] Cl-π interactions in protein-ligand complexes2008

    • Author(s)
      Imai Nakamura-Yumi
    • Organizer
      XVIIth European symposium on QSARs and Molecular Modeling
    • Place of Presentation
      Uppsara, Sweden
    • Related Report
      2008 Final Research Report
  • [Presentation] Analysis of interactions between Casein Kinase 2α (CK2α) and its ligand using Fragment Molecular Orbital method2008

    • Author(s)
      Asada Naoya
    • Organizer
      XVIIth European symposium on QSARs and Molecular Modeling
    • Place of Presentation
      Uppsara, Sweden
    • Related Report
      2008 Final Research Report
  • [Presentation] Quantum chemical calculation of protein-ligand interaction2008

    • Author(s)
      Nakanishi Isao
    • Organizer
      XXth Iinternational Symposium of Medicinal Chemistry
    • Place of Presentation
      Vienna, Austria
    • Related Report
      2008 Final Research Report
  • [Presentation] Quantum chemical calculation of protein-ligand calculation.2008

    • Author(s)
      Nakanishi Isao
    • Organizer
      XXth Iinternational Symposium of Medicinal Chemistry
    • Place of Presentation
      Vienna, Austria
    • Related Report
      2008 Annual Research Report
  • [Presentation] Analysis of interactions between Casein Kinase 2α (CK2α) and its ligand using Fragment Molecular Orbital method.2008

    • Author(s)
      Asada Naoya
    • Organizer
      XVIIth European symposium on QSARs and Molecular Modeling
    • Place of Presentation
      Uppsara, Sweden
    • Related Report
      2008 Annual Research Report
  • [Presentation] C1-π interactions in protein-ligand complexes.2008

    • Author(s)
      Imai Nakamura-Yumi
    • Organizer
      XVIIth European symposium on QSARs and Molecular Modeling
    • Place of Presentation
      Uppsara, Sweden
    • Related Report
      2008 Annual Research Report
  • [Presentation] Quantum Chemical Calculations of Protein-ligand Interactions with Fragment Molecular Orbital Method.2008

    • Author(s)
      Kitaura Kazuo
    • Organizer
      World Association of Theoretical and Computational Chemists 2008 (WATOC2008)
    • Place of Presentation
      Sydney, Australia
    • Related Report
      2008 Annual Research Report
  • [Presentation] Electronic structure calculations of proteins using fragment molecular orbital method.2008

    • Author(s)
      Kitaura Kazuo
    • Organizer
      Telluride Workshop on Many Body Interactions : From Quantum Mechanics to Force Field
    • Place of Presentation
      Telluride, USA
    • Related Report
      2008 Annual Research Report
  • [Presentation] フラグメント分子軌道法を用いたcasein kinase 2aと阻害剤の相互作用解析2007

    • Author(s)
      浅田直也
    • Organizer
      第35回構造活性相関シンポジウム
    • Place of Presentation
      京都
    • Year and Date
      2007-11-15
    • Related Report
      2008 Final Research Report
  • [Presentation] フラグメント分子軌道法を用いたcase in kinase 2aと阻害剤の相互作用解析2007

    • Author(s)
      浅田 直也, 仲西 功, 北浦 和夫
    • Organizer
      第35回構造活性相関シンポジウム
    • Place of Presentation
      京都
    • Year and Date
      2007-11-15
    • Related Report
      2007 Annual Research Report
  • [Presentation] 、フラグメント分子軌道法によるポリアラニン配座異性体の相対安定性の解析2007

    • Author(s)
      浅田直也
    • Organizer
      第1回分子科学討論会
    • Place of Presentation
      仙台
    • Year and Date
      2007-09-18
    • Related Report
      2008 Final Research Report
  • [Presentation] フラグメント分子軌道法によるポリアラニン配座異性体の相対安定性の解析2007

    • Author(s)
      浅田 直也, 仲西 功, D.G. Fedorov, 北浦 和夫
    • Organizer
      第1回分子科学討論会
    • Place of Presentation
      仙台
    • Year and Date
      2007-09-18
    • Related Report
      2007 Annual Research Report
  • [Presentation] フラグメント分子軌道法による蛋白質-リガンド複合体の分極エネルギーの解析2007

    • Author(s)
      仲西功
    • Organizer
      日本薬学会第127年会
    • Place of Presentation
      富山
    • Related Report
      2008 Final Research Report
  • [Presentation] Fragment法を用いたHIVプロテアーゼ阻害剤の活性評価2006

    • Author(s)
      中村真也
    • Organizer
      日本薬学会第126回年会
    • Place of Presentation
      仙台
    • Related Report
      2008 Final Research Report

URL: 

Published: 2006-04-01   Modified: 2016-04-21  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi