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HIGH ACCURACY PREDICTION OF DRUG-PROTEIN INTERACTION; LINEAR EXPRESSION BY REPRESENTATIVE ENERGY TERMS

Research Project

Project/Area Number 24590051
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Physical pharmacy
Research InstitutionThe University of Tokushima

Principal Investigator

CHUMAN Hiroshi  徳島大学, 大学院ヘルスバイオサイエンス研究部, 教授 (20304545)

Co-Investigator(Renkei-kenkyūsha) YOSHIDA Tatsusada  徳島大学, 大学院ヘルスバイオサイエンス研究部, 助教 (80527557)
Project Period (FY) 2012-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000)
Fiscal Year 2014: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2013: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Fiscal Year 2012: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Keywords創薬理論計算化学 / 情報科学 / 定量的構造活性相関 / 分子科学計算 / 薬物・タンパク質相互作用 / 超精密予測 / 自由エネルギー変化の線形表現 / フラグメント分子軌道法 / トリプシン阻害剤 / MMP阻害剤 / CYP P450 / ノイラミニダーゼ阻害剤
Outline of Final Research Achievements

We have proposed a novel procedure called the Linear Expression by Representative Energy terms (LERE), and further developed LERE by modifying the dispersion, hydration, entropic energy, and other terms. We applied a novel quantitative structure activity relationship combined with the LERE procedure to several cases of ligands-protein interaction system in order to demonstrate the validity of the LERE procedure. As a result, we confirmed that the procedure provides valuable information which cannot be obtained with any other methods and approaches.

Report

(4 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Research-status Report
  • 2012 Research-status Report
  • Research Products

    (44 results)

All 2014 2013 2012 Other

All Journal Article (7 results) (of which Peer Reviewed: 7 results,  Open Access: 4 results,  Acknowledgement Compliant: 3 results) Presentation (35 results) (of which Invited: 12 results) Remarks (2 results)

  • [Journal Article] QSAR Study on the Inhibition Mechanism of Matrix Metalloproteinase-12 by Arylsulfone Analogues Based on Molecular Orbital Calculations2014

    • Author(s)
      S. Hitaoka, H. Chuman, and K. Yoshizawa
    • Journal Title

      Org. Biomol. Chem.

      Volume: 13 Issue: 3 Pages: 793-806

    • DOI

      10.1039/c4ob01843e

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Connecting Classical QSAR and LERE Analyses Using Modern Molecular Calculations, LERE-QSAR (VI): Hydrolysis of Substituted Hippuric Acid Phenyl Esters by Trypsin2014

    • Author(s)
      Akira Mashima, Masahiro Kurahashi, Katsunori Sasahara, Tatsusada Yoshida, Hiroshi Chuman
    • Journal Title

      Mol. Info.

      Volume: 33 Issue: 11-12 Pages: 802-814

    • DOI

      10.1002/minf.201400099

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Binding Free-Energy Calculation is a Powerful Tool for Drug Optimization: Calculation and Measurement of Binding Free Energy for 7-Azaindole Derivatives to Glycogen Synthase Kinase-3β2014

    • Author(s)
      Kunihiro Kitamura, Yunoshin Tamura, Tomokazu Ueki, Koji Ogata, Shigeho Noda, Ryutaro Himeno, Hiroshi Chuman
    • Journal Title

      J. Chem. Inf. Model.

      Volume: 54 Issue: 6 Pages: 1653-1660

    • DOI

      10.1021/ci400719v

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] A Simple and Efficient Dispersion Correction to the Hartree-Fock Theory2014

    • Author(s)
      Tatsusada Yoshida, Akira Mashima, Katsunori Sasahara, Hiroshi Chuman
    • Journal Title

      Bioorganic & Medicinal Chemistry Letters

      Volume: Vol.24 Issue: 4 Pages: 1037-1042

    • DOI

      10.1016/j.bmcl.2014.01.020

    • Related Report
      2014 Annual Research Report 2013 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Revisiting the Hansch–Fujita approach and development of a fundamental QSAR2013

    • Author(s)
      Hitaoka S , et al.
    • Journal Title

      Journal of Pesticide Science

      Volume: 38 Issue: 2 Pages: 60-67

    • DOI

      10.1584/jpestics.D12-082

    • NAID

      130004445303

    • ISSN
      1348-589X, 1349-0923
    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Modeling of Human Neuraminidase-1 and Its Validation by LERE-Correlation Analysis2013

    • Author(s)
      S. Hitaoka, Y. Shibata, H. Matoba, A. Kawano, M. Harada, M.M. Rahman, D. Tsuji D, T. Hirokawa, K. Itoh, T.Yoshida, H. Chuman
    • Journal Title

      Chem-Bio Informatics Journal

      Volume: 13 Issue: 0 Pages: 30-44

    • DOI

      10.1273/cbij.13.30

    • NAID

      130004054117

    • ISSN
      1347-0442, 1347-6297
    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] A Combined QM/MM (ONIOM) and QSAR Approach to the Study of Complex Formation of Matrix Metalloproteinase-9 with a Series of Biphenylsulfonamides - LERE-QSAR Analysis (V)2012

    • Author(s)
      Yoshida T, et al.
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 116 Issue: 34 Pages: 10283-10289

    • DOI

      10.1021/jp305476x

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Presentation] リガンド-タンパク質の複合体形成における分散力相互座用の検討:LERE-QSAR解析における結合相互作用エネルギー項の定量的評価2014

    • Author(s)
      吉田達貞, 林敬久, 倉橋昌大, 馬島彬, 笹原克則, 中馬寛
    • 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, 熊本県・熊本市
    • Year and Date
      2014-11-14
    • Related Report
      2014 Annual Research Report
  • [Presentation] 腫瘍懐死因子α変換酵素(TACE)とεラクタムヒドロキサム酸誘導体のLIE法に基づく解析, LERE-QSAR解析と検証2014

    • Author(s)
      野々下航, 濱野綾那, 岸優作, 吉田達貞, 中馬寛
    • 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, 熊本県・熊本市
    • Year and Date
      2014-11-14
    • Related Report
      2014 Annual Research Report
  • [Presentation] 分子科学計算を用いたチオリダジンのCYP2D6による代謝過程の非経験的解析(Ⅰ)2014

    • Author(s)
      吉田達貞, 笹原克則, 馬島彬, 中馬寛
    • 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, 熊本県・熊本市
    • Year and Date
      2014-11-13
    • Related Report
      2014 Annual Research Report
  • [Presentation] 触媒反応機構に基づいたインフルエンザ・ノイラミニダーゼとシアル酸誘導体との相互作用解析2014

    • Author(s)
      芝田雄登, 吉田達貞, 中馬寛
    • 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, 熊本県・熊本市
    • Year and Date
      2014-11-13
    • Related Report
      2014 Annual Research Report
  • [Presentation] 馬尿酸フェニルエステルのシステインとセリンプロテアーゼの加水分解反応の分子科学計算による詳細解析(Ⅰ)2014

    • Author(s)
      倉橋昌大, 馬島彬, 吉田達貞, 中馬寛
    • 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, 熊本県・熊本市
    • Year and Date
      2014-11-13
    • Related Report
      2014 Annual Research Report
  • [Presentation] 分子科学計算を用いたHIV-1 proteaseとアロフェニルノルスタチン骨格を持つ化合物と複合体の精密相互作用解析2014

    • Author(s)
      林敬久, 野脇静, 吉田達貞, 中馬寛
    • 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, 熊本県・熊本市
    • Year and Date
      2014-11-13
    • Related Report
      2014 Annual Research Report
  • [Presentation] A New Era for Drug Discover: Revisitig Claddical QSAR and Seeking New Ones2014

    • Author(s)
      Hiroshi Chuman
    • Organizer
      Asia Hub for e-Drug Discovery Symposium 2014
    • Place of Presentation
      Chengdu University, Chengdu (China)
    • Year and Date
      2014-11-13
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] High Precision Prediction of Protein-Ligand Binding Free-Energy Change : Linear Expression by Representative Energy Terms2014

    • Author(s)
      Hiroshi Chuman
    • Organizer
      5th French-Japanese Workshop on Computational Methods in Chemistry
    • Place of Presentation
      University of Strasbourg, Strasbourg (France)
    • Year and Date
      2014-06-30
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 生体分子科学計算と定量的構造活性相関2014

    • Author(s)
      中馬寛
    • Organizer
      第41回生体分子討論会
    • Place of Presentation
      九州大学西新プラザ, 福岡市・福岡県
    • Year and Date
      2014-06-06
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Linear Expression by Representative Energy Terms: a Novel QSAR Procedure Using Theoretical Computations on Protein–Ligand Complexes2014

    • Author(s)
      Hiroshi Chuman
    • Organizer
      International Symposium on Compound Design Technology
    • Place of Presentation
      英国大使館 (東京都)
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] 自由エネルギー変化の代表エネルギー項による線形表現を用いた定量的構造活性相関解析の構築とその応用表現

    • Author(s)
      中馬寛
    • Organizer
      構造生物応用研究会
    • Place of Presentation
      アークホテル仙台通り (宮城県)
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] 自由エネルギー変化の線形表現に基づくリガンド―タンパク質結合自由エネルギー変化の超精密予測

    • Author(s)
      中馬寛
    • Organizer
      構造活性相関フォーラム
    • Place of Presentation
      理化学研究所横浜キャンパス交流楝ホール (神奈川県)
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] 大規模分子科学計算を用いる定量的構造活性相関;自由エネルギー変化の線形表現に基づくリガンド―タンパク質結合自由エネルギー変化の超精密予測

    • Author(s)
      中馬寛
    • Organizer
      新学術領域研究「天然ケミカルバイオロジー地区ミニシンポジウム」
    • Place of Presentation
      千葉大学薬学部120周年記念講堂(千葉県)
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] A Novel QSAR Precedure Using Theoretical Computations on Protein-Ligand Complexes

    • Author(s)
      Hiroshi Chuman
    • Organizer
      the 7th International Symposium on Computational Methods in Toxicology and Pharmacology Integrating Internet Resources
    • Place of Presentation
      Grand Hilton Hotel, Seol (Korea)
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] Estimation of Non-covalent Interactions with a New Efficient Dispersion Corrected HF Approach

    • Author(s)
      Tatsusada Yoshida, Akira Mashima, Katsunori Sasahara, Yuto Shibata, MasahiroEguchi, Seiji Hitaoka, and Hiroshi Chuman
    • Organizer
      the 7th International Symposium on Computational Methods in Toxicology and Pharmacology Integrating Internet Resources
    • Place of Presentation
      Grand Hilton Hotel, Seol (Korea)
    • Related Report
      2013 Research-status Report
  • [Presentation] Estimation of Non-covalent Interactions with a New Efficient Dispersion Corrected HF Approach

    • Author(s)
      Tatsusada Yoshida, Akira Mashima, Katsunori Sasahara, Hiroshi Chuman
    • Organizer
      生命医薬情報学連合大会(JSBi2013)
    • Place of Presentation
      タウンホール船堀 (東京都)
    • Related Report
      2013 Research-status Report
  • [Presentation] Binding Mechanism of KNI-272 with HIV-1 Protease

    • Author(s)
      Takahisa Hayashi, Takuya Sugimoto, Shuhei Sakamoto, Akihiro Kawano, Tatsusada Yoshida, Hiroshi Chuman
    • Organizer
      生命医薬情報学連合大会(JSBi2013)
    • Place of Presentation
      タウンホール船堀 (東京都)
    • Related Report
      2013 Research-status Report
  • [Presentation] LERE-QSAR Analysis of Binding of γ-Lactum Hydroxamic Acid Derivatives with Tumor Necrosis Factor-Alpha Converting Enzyme

    • Author(s)
      Tatsusada Yoshida, Koh Nonoshita, Takuya Sugimoto, Ayana Hamano, Akihiro Kawano, Shuhei Sakamoto, Hiroshi Chuman
    • Organizer
      生命医薬情報学連合大会(JSBi2013)
    • Place of Presentation
      タウンホール船堀 (東京都)
    • Related Report
      2013 Research-status Report
  • [Presentation] 分子科学計算によるアゾール系化合物-ヒトCYP2B6複合体における相互作用解析に基づくLERE-QSAR解析

    • Author(s)
      坂本修平, 笹原克則, 吉田達貞, 中馬寛
    • Organizer
      第41回構造活性相関シンポジウム
    • Place of Presentation
      関西学院会館 (兵庫県)
    • Related Report
      2013 Research-status Report
  • [Presentation] ヒドロキサム酸系MMP阻害剤のLERE-QSAR解析

    • Author(s)
      杉本拓弥, 野々下航, 濱野綾那, 林敬久, 吉田達貞, 中馬寛
    • Organizer
      第41回構造活性相関シンポジウム
    • Place of Presentation
      関西学院会館 (兵庫県)
    • Related Report
      2013 Research-status Report
  • [Presentation] インフルエンザ・ノイラミニダーゼとピロリジン系化合物との相互作用解析

    • Author(s)
      河野明大, 芝田雄登, 林敬久, 倉橋昌大, 吉田達貞, 中馬寛
    • Organizer
      第41回構造活性相関シンポジウム
    • Place of Presentation
      関西学院会館 (兵庫県)
    • Related Report
      2013 Research-status Report
  • [Presentation] LERE-QSAR解析の精密化とその検証

    • Author(s)
      吉田達貞, 馬島彬, 笹原克則, 芝田雄登, 江口将大, 比多岡清司, 中馬寛
    • Organizer
      第41回構造活性相関シンポジウム
    • Place of Presentation
      関西学院会館 (兵庫県)
    • Related Report
      2013 Research-status Report
  • [Presentation] Linear Expression by Representative Energy Terms: a Novel QSAR Procedure Using Theoretical Computations on Protein–Ligand Complexes

    • Author(s)
      Hiroshi Chuman
    • Organizer
      International Symposium on Compound Design Technology
    • Place of Presentation
      英国総領事館 (大阪府)
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] LERE-QSAR 解析によるbilinear model の新しい解釈:トリアジン誘導体とジヒドロ葉酸還元酵素との複合体形成

    • Author(s)
      山内 香子
    • Organizer
      第40回構造活性相関シンポジウム
    • Place of Presentation
      岡崎市図書館交流プラザ・りぶら(愛知県)
    • Related Report
      2012 Research-status Report
  • [Presentation] LERE-QSAR 解析の酵素触媒反応への適用:トリプシンによる置換馬尿酸フェニルの加水分解反応のミカエリス・メンテン定数および反応速度定数の定量的解析

    • Author(s)
      馬島 彬
    • Organizer
      第40回構造活性相関シンポジウム
    • Place of Presentation
      岡崎市図書館交流プラザ・りぶら(愛知県)
    • Related Report
      2012 Research-status Report
  • [Presentation] リガンド-タンパク質の複合体形成に及ぼす溶媒効果の検討:LERE-QSAR解析における水和自由エネルギー項の定量的考察

    • Author(s)
      比多岡 清司
    • Organizer
      第40回構造活性相関シンポジウム
    • Place of Presentation
      岡崎市図書館交流プラザ・りぶら(愛知県)
    • Related Report
      2012 Research-status Report
  • [Presentation] β‐セクレターゼ阻害剤のLead Evolution とOptimization:分子化学計算による薬物-タンパク質間相互作用から定量的考察

    • Author(s)
      相原 薫
    • Organizer
      第40回構造活性相関シンポジウム
    • Place of Presentation
      岡崎市図書館交流プラザ・りぶら(愛知県)
    • Related Report
      2012 Research-status Report
  • [Presentation] 非経験的分子軌道法計算を用いたリレンザおよびその誘導体とインフルエンザ・ノイラミニダーゼとの結合自由エネルギー変化のQSAR解析-Fragment Based LERE-QSAR

    • Author(s)
      的場弘
    • Organizer
      第40回構造活性相関シンポジウム
    • Place of Presentation
      岡崎市図書館交流プラザ・りぶら(愛知県)
    • Related Report
      2012 Research-status Report
  • [Presentation] A Combined QM/MM (ONIOM) and QSAR Approach to the Study of Complex Formation of Matrix Metalloproteinase-9 with a Series of Biphenylsulfonamides-LERE QSAR Analysis

    • Author(s)
      杉本 拓弥
    • Organizer
      第40回構造活性相関シンポジウム
    • Place of Presentation
      岡崎市図書館交流プラザ・りぶら(愛知県)
    • Related Report
      2012 Research-status Report
  • [Presentation] A New Efficient Approch to Solvation Energy Change Associated with Complex Formation of Ligand with Protein: CriticalComparison of Various Solvation Energy Calculations

    • Author(s)
      Hitaoka S
    • Organizer
      Joint Conference on Informatics in Biology, Medicine and Pharmacology
    • Place of Presentation
      タワーホール船堀(東京都)
    • Related Report
      2012 Research-status Report
  • [Presentation] A Novel Fragment Based QSAR Using FMO and LERE: Binding Affinity of Relenza and Its Analogues with Influenza Virus Neuraminidase、

    • Author(s)
      Matoba H
    • Organizer
      Joint Conference on Informatics in Biology, Medicine and Pharmacology
    • Place of Presentation
      タワーホール船堀(東京都)
    • Related Report
      2012 Research-status Report
  • [Presentation] A Novel and Consistenet Approach to Enzymatic Reactions Using Ab Initio MO Calculations: Trypsin Catalysis of Series of Substrates

    • Author(s)
      Mashima A
    • Organizer
      Joint Conference on Informatics in Biology, Medicine and Pharmacology
    • Place of Presentation
      タワーホール船堀(東京都)
    • Related Report
      2012 Research-status Report
  • [Presentation] Development of a Novel QSAR using Molecular Calculations:Linear Expression by Representative Energy Terms

    • Author(s)
      Chuman H
    • Organizer
      Joint Conference on Informatics in Biology, Medicine and Pharmacology
    • Place of Presentation
      タワーホール船堀(東京都)
    • Related Report
      2012 Research-status Report
    • Invited
  • [Presentation] New Starting Points toward Construction of Fundamental QSAR : Wonderful Gifts from Hansch and Fujita

    • Author(s)
      中馬寛
    • Organizer
      Hansch-藤田法50周年記念シンポジウム
    • Place of Presentation
      京都大学芝蘭会館稲盛ホール(京都)
    • Related Report
      2012 Research-status Report
    • Invited
  • [Presentation] ノイラミニダーゼ・阻害剤の結合相互作用エネルギーの非経験的分子軌道法による定量構想活性相関解析(LERE‐QSAR)

    • Author(s)
      比多岡清司
    • Organizer
      エミール研究会
    • Place of Presentation
      コープイン・京都 (京都)
    • Related Report
      2012 Research-status Report
    • Invited
  • [Remarks] 徳島大学薬学部・薬科学教育部・創薬理論化学

    • URL

      http://www.tokushima-u.ac.jp/ph/faculty/labo/ana/

    • Related Report
      2014 Annual Research Report
  • [Remarks] 徳島大学・大学院(創薬理論化学)

    • URL

      http://www.tokushima-u.ac.jp/ph/faculty/labo/ana/

    • Related Report
      2012 Research-status Report

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Published: 2013-05-31   Modified: 2019-07-29  

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