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Orbital interaction based binding energy analysis for designing molecular targeted drugs

Research Project

Project/Area Number 16K08321
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Drug development chemistry
Research InstitutionKyushu University

Principal Investigator

ORIMOTO Yuuichi  九州大学, 総合理工学研究院, 学術研究員 (00398108)

Project Period (FY) 2016-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000)
Fiscal Year 2018: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Fiscal Year 2017: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2016: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Keywords分子標的薬 / 結合エネルギー / 分子認識 / タンパク質 / 電子状態 / 構造最適化(エネルギー勾配法) / スルースペース/ボンド軌道相互作用 / オーダーN Elongation法 / 蛋白質
Outline of Final Research Achievements

In vivo molecular recognition causes with concerted structural changes. The aim here is to develop a new binding energy analysis method for designing the recognition ability in molecular targeted drugs, by which the relationship between the structural changes and binding energy can be obtained from the orbital interaction viewpoint. For the purpose, the through-space/bond (TS/TB) interaction analysis method was combined with geometrical optimization algorism to predict optimized geometries under cutting off the specific interactions and its contribution to the binding energy on recognition reaction. As the first step towards huge bio-systems, the TS/TB method was developed so as to analyze orbital interactions in the unit of region localized molecular orbitals generated by O(N) elongation method. As a related work, the DNA-molecule interaction was investigated and machine learning was adopted to find hidden rules among numerous interaction dataset.

Academic Significance and Societal Importance of the Research Achievements

電子相関効果を含めて実行可能な軌道相互作用解析法と構造最適化を結合した本手法は、分子認識時の構造変化や結合エネルギーへの寄与を相互作用単位で高精度評価できる世界に類のないアプローチである。超高精度O(N) Elongation(ELG)法との完全な結合は現在まだ開発中だが、完成すれば創薬分野に貢献しうる新規結合エネルギー評価法として世界をリードできる。ELG法はあらゆる計算設備(PC~スパコン)に対応可能であり、誰もが身近なPC上で分子標的薬の高精度設計が可能となり、広く難病の原因解明や迅速な薬剤開発に貢献できる。創薬の他、材料・触媒開発等、基礎研究から産業分野まで広く波及効果が期待できる。

Report

(5 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Research-status Report
  • 2017 Research-status Report
  • 2016 Research-status Report
  • Research Products

    (32 results)

All 2020 2019 2018 2017 2016

All Journal Article (6 results) (of which Peer Reviewed: 6 results,  Acknowledgement Compliant: 1 results) Presentation (25 results) (of which Int'l Joint Research: 11 results) Book (1 results)

  • [Journal Article] Extent of Structural Change during the Reaction and Its Relationship to Isoselectivity in Polypropylene Polymerization with ansa-Zirconocene/Borate Catalyst: A Computational Study2019

    • Author(s)
      Y. Orimoto, S. Shirane, and Y. Aoki
    • Journal Title

      J. Comput. Chem.

      Volume: 40 Issue: 30 Pages: 2622-2635

    • DOI

      10.1002/jcc.26040

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Extraction of One-Handed Helical Frontier Orbital in Even [n]Cumulenes by Breaking Mirror Images of Right- and Left-Handed Helical Orbitals: Theoretical Study2019

    • Author(s)
      Orimoto Yuuichi、Aoki Yuriko、Imamura Akira
    • Journal Title

      The Journal of Physical Chemistry C

      Volume: 印刷中 Issue: 17 Pages: 11134-11139

    • DOI

      10.1021/acs.jpcc.9b01829

    • Related Report
      2019 Annual Research Report 2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] One-Handed Helical Orbitals in Conjugated Molecules2018

    • Author(s)
      Aoki Yuriko、Orimoto Yuuichi、Imamura Akira
    • Journal Title

      ACS Central Science

      Volume: 4 Issue: 6 Pages: 664-665

    • DOI

      10.1021/acscentsci.8b00228

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] Role of Pyridinium Groups and Iodide Ions in Photoelectrochromism in Viologen-Based Ion-Pair Charge-Transfer Complexes: Molecular Orbital Analysis2018

    • Author(s)
      Orimoto Yuuichi、Ishimoto Kosuke、Aoki Yuriko
    • Journal Title

      The Journal of Physical Chemistry C

      Volume: 122 Issue: 8 Pages: 4546-4556

    • DOI

      10.1021/acs.jpcc.7b10281

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Importance of Through-Space Interaction of [2,2′]-Paracyclophane-oligo(p-phenylenevinylene) Molecular Wires for Photovoltaic Application and Effective Wire Design by Chemical Substitution2017

    • Author(s)
      Yuuichi Orimoto, Kohei Kato, and Yuriko Aoki
    • Journal Title

      The Journal of Physical Chemistry C

      Volume: 121 Issue: 33 Pages: 17703-17711

    • DOI

      10.1021/acs.jpcc.7b05730

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Theoretical Study of Cu Intercalation Through a Defect in Zero-Layer Graphene on SiC Surface2017

    • Author(s)
      Yuuichi Orimoto, Kohei Otsuka, Kazuma Yagyu, Hiroshi Tochihara,Takayuki Suzuki, and Yuriko Aoki
    • Journal Title

      The Journal of Physical Chemistry C

      Volume: 121 Issue: 13 Pages: 7294-7302

    • DOI

      10.1021/acs.jpcc.7b00314

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] Nonlinear optical properties of push-pull π-conjugated molecules via elongation-FF method2020

    • Author(s)
      Mariia V. Ivonina, Yuuichi Orimoto and Yuriko Aoki
    • Organizer
      The 2nd R-CCS international symposium, Kobe, Japan
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Computer-aided molecular design for DNA bulge recognition ligands by order-N elongation method2019

    • Author(s)
      Yuuichi Orimoto, Anna Pomogaeva, Keisuke Hisama, Ayaka Yano, Koichi Miyagawa, Kazuhiko Nakatani, Yuriko Aoki
    • Organizer
      the 46th International Symposium on Nucleic Acids Chemistry, the 3rd Annual Meeting of Japan Society of Nucleic Acid Chemistry (ISNAC 2019), Tokyo, Japan
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] A Linear Scaling Approach for Efficient Geometry Optimization in Perturbed DNAs2019

    • Author(s)
      Yuriko Aoki, Yuuichi Orimoto, Anna Pomogaeva
    • Organizer
      Asia-Pacific Association of Theoretical and Computational Chemists (APATCC 2019), Sydney, Australia
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Linear-scaling two-ways elongation method for local perturbation on nanotubes/DNA2019

    • Author(s)
      Y. Aoki, Y. Orimoto, A. Pomogaeva
    • Organizer
      Current Trends in Theoretical Chemistry VIII, Krakow, Poland
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Elongation法によるDNA損傷修復解明のための見える化システムの構築2019

    • Author(s)
      青木 百合子、折本 裕一
    • Organizer
      2019年度九州大学オープンイノベーションワークショップ(福岡)
    • Related Report
      2019 Annual Research Report
  • [Presentation] 直線炭素鎖分子Cumuleneの特異な螺旋状分子軌道―化学修飾による左右螺旋の分離と機能設計―2019

    • Author(s)
      折本 裕一,大川 育子,青木 百合子
    • Organizer
      第13回分子科学討論会(名古屋)
    • Related Report
      2019 Annual Research Report
  • [Presentation] 特異的な構造特性と電子状態を示す有限ナノリボンと有機太陽電池ワイヤへの応用2019

    • Author(s)
      青木 百合子,折本 裕一
    • Organizer
      第13回分子科学討論会(名古屋)
    • Related Report
      2019 Annual Research Report
  • [Presentation] High throughput molecular design/exploration for DNA bulge/mismatch recognition: computational approach by elongation method2018

    • Author(s)
      Yuuichi Orimoto, Anna Pomogaeva, Ayaka Yano, Kazuhiko Nakatani, Yuriko Aoki
    • Organizer
      The 45th International Symposium on Nucleic Acids Chemistry (ISNAC2018), Kyoto(JAPAN)
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] Ab initio MO study of propylene polymerization by zirconocene/borate catalyst2018

    • Author(s)
      Yuuichi Orimoto, Satoru Shirane, Yuriko Aoki
    • Organizer
      16-th V.A. Fock Meeting on Theoretical, Quantum and Computational Chemistry, Sochi(Russia)
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] Development of efficient elongation method toward locally perturbed aperiodic nano/bio systems2018

    • Author(s)
      Yuriko Aoki, Anna Pomogaeva, Yuuichi Orimoto
    • Organizer
      7th JCS SYMPOSIUM, PRAGUE (Czech Republic)
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] メタロセン触媒の高イソ選択的オレフィン重合反応の量子化学的機構解明 -遷移状態構造における歪と緩和-2018

    • Author(s)
      折本裕一、白根聡、青木百合子
    • Organizer
      シンポジウム「化学反応経路探索のニューフロンティア2018」、福岡
    • Related Report
      2018 Research-status Report
  • [Presentation] ナノリボン末端修飾による構造転移に関する量子化学的研究 -有機太陽電池ワイヤー設計に向けて-2018

    • Author(s)
      青木百合子、折本裕一
    • Organizer
      シンポジウム「化学反応経路探索のニューフロンティア2018」、福岡
    • Related Report
      2018 Research-status Report
  • [Presentation] 高精度かつ効率的ナノチューブ表面反応の電子状態解析法2018

    • Author(s)
      Pomogaeva Anna,折本 裕一,青木 百合子
    • Organizer
      第12回分子科学討論会、福岡
    • Related Report
      2018 Research-status Report
  • [Presentation] リパーゼのエナンチオ選択性の発現に関する量子化学的反応機構解析2018

    • Author(s)
      汐見 彩花,折本 裕一,青木 百合子
    • Organizer
      第12回分子科学討論会、福岡
    • Related Report
      2018 Research-status Report
  • [Presentation] 多階層Elongation構造最適化法によるDNAバルジ/ミスマッチ認識分子の効率探索と理論設計2018

    • Author(s)
      折本 裕一,Pomogaeva Anna, 矢野 綾香,中谷 和彦,青木 百合子
    • Organizer
      第12回分子科学討論会、福岡
    • Related Report
      2018 Research-status Report
  • [Presentation] 光学スイッチ設計に向けたビオロゲン含有ポリマーのフォトエレクトロクロミズムに関する量子化学的研究2018

    • Author(s)
      石本 晃佑,折本 裕一,青木 百合子
    • Organizer
      第12回分子科学討論会、福岡
    • Related Report
      2018 Research-status Report
  • [Presentation] Mechanism of highly selective olefin polymerization by metallocene catalyst: computational approach2018

    • Author(s)
      Yuuichi Orimoto, Satoru Shirane and Yuriko Aoki
    • Organizer
      IRCCS-JST CREST Joint Symposium, Fukuoka
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Elongation method for efficient quantum chemistry calculations toward functional designs of bio/nano materials2018

    • Author(s)
      Yuriko Aoki, Wataru Mizukami, Ikuko Okawa, Yuuichi Orimoto
    • Organizer
      第一回 九州大学女性研究者ダイバーシティーシンポジウム、福岡
    • Related Report
      2017 Research-status Report
  • [Presentation] Selectivity of olefin polymerization with metallocene catalyst and the effects of producted polymers on its mechanism2017

    • Author(s)
      Satoru Shirane, Yuuichi Orimoto and Yuriko Aoki
    • Organizer
      The 19th Cross Straits Symposium on Energy and Environmental Science and Technology (CSS-EEST19), Fukuoka
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Computational design of DNAs: property control via elongation method2017

    • Author(s)
      Yuuichi Orimoto and Yuriko Aoki
    • Organizer
      The 44th International Symposium on Nucleic Acids Chemistry (ISNAC2017), Tokyo
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] 生体分子の反応機構解明と機能設計を目指した量子化学的手法開発とその応用2017

    • Author(s)
      折本 裕一、汐見 彩花、青木 百合子
    • Organizer
      第11回分子科学討論会、仙台
    • Related Report
      2017 Research-status Report
  • [Presentation] Elongation法による生体高分子の効率的構造最適化および反応解析法2017

    • Author(s)
      青木 百合子、水上 渉、伊藤 正浩、折本 裕一
    • Organizer
      第11回分子科学討論会、仙台
    • Related Report
      2017 Research-status Report
  • [Presentation] メタロセン触媒重合の構造制御機構の解明と超効率的計算手法によるポリマー特性の解析2017

    • Author(s)
      白根 聡、折本 裕一、青木 百合子
    • Organizer
      第11回分子科学討論会、仙台
    • Related Report
      2017 Research-status Report
  • [Presentation] Theoretical approach to the property and reaction design of DNA/proteins by through-space/bond interaction analysis and elongation method2016

    • Author(s)
      Yuuichi Orimoto and Yuriko Aoki
    • Organizer
      The 43th International Symposium on Nucleic Acids Chemistry (ISNAC2016)
    • Place of Presentation
      Kumamoto(JAPAN)、熊本大学 工学部百周年記念館
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] 酵素反応機構解明のための軌道相互作用解析法の開発と応用2016

    • Author(s)
      折本 裕一、青木 百合子
    • Organizer
      第10回分子科学討論会
    • Place of Presentation
      神戸、神戸ファッションマート
    • Related Report
      2016 Research-status Report
  • [Book] “Quantum chemical approach for organic ferromagnetic material design”, SPRINGER BRIEFS IN MOLECULAR SCIENCE, ELECTRICAL AND MAGNETIC PROPERTIES OF ATOMS, MOLECULES, AND CLUSTERS2017

    • Author(s)
      Yuriko Aoki, Yuuichi Orimoto and Akira Imamura
    • Total Pages
      138
    • Publisher
      Springer International Publishing
    • ISBN
      9783319498270
    • Related Report
      2017 Research-status Report

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Published: 2016-04-21   Modified: 2021-02-19  

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