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Development of in silico transition state analogue molecular design method based on large-scale electronic structure calculations

Research Project

Project/Area Number 16KT0168
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section特設分野
Research Field Transition State Control
Research InstitutionInstitute of Physical and Chemical Research

Principal Investigator

Otsuka Takao  国立研究開発法人理化学研究所, 生命機能科学研究センター, 研究員 (30465968)

Project Period (FY) 2016-07-19 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2018: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2017: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2016: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Keywords遷移状態アナログ / 大規模電子状態計算 / Nudged Elastic Band法 / order-N / ヒストン / シトクロムP450 / 遷移状態探索 / 大規模電子状態 / インシリコ創薬 / 反応性部位 / 反応部位予測 / 分子設計
Outline of Final Research Achievements

In order to develop the transition state analogue molecular design in the field of drug discovery, we introduced a large-scale electronic structure calculations combined with transition state search method. With the detailed studies for the transition state structures, environmental effects, and the practical computational conditions, we have obtained the information for designing new transition state analogue molecules. We also applied the methodology to the Cytochrome P450 systems.

Academic Significance and Societal Importance of the Research Achievements

創薬分野の実験技法である「遷移状態アナログ」分子の設計思想を、大規模電子状態計算と遷移状態探索法を組み合わせることで、インシリコ創薬技術の開拓に向けて取り組み、実験と理論の両思想を相補的に活用し、実験技術を理論計算技術化していくことは将来の分子設計に非常に役立つと考える。

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

    (8 results)

All 2019 2018 2017 2016

All Journal Article (4 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 4 results,  Open Access: 4 results) Presentation (4 results) (of which Int'l Joint Research: 2 results)

  • [Journal Article] Quantum chemical analysis of reaction indices and reaction path for drug molecules2019

    • Author(s)
      Takao Otsuka、Noriaki Okimoto、Hiroaki Saito、Makoto Taiji
    • Journal Title

      Journal of Physics: Conference Series

      Volume: 1290 Issue: 1 Pages: 012021-012021

    • DOI

      10.1088/1742-6596/1290/1/012021

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Quantum chemical analysis of reaction indices and reaction path for drug molecules2019

    • Author(s)
      Takao Otsuka, Noriaki Okimoto, Hiroaki Saito, Makoto Taiji
    • Journal Title

      Journal of Physics: Conference Series

      Volume: 印刷中

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Application of order-N first-principles DFT calculations with temperature controlled molecular dynamics to biomolecular system2018

    • Author(s)
      Takao Otsuka, Makoto Taiji
    • Journal Title

      Journal of Physics: Conference Series

      Volume: 1136 Pages: 012025-012025

    • DOI

      10.1088/1742-6596/1136/1/012025

    • Related Report
      2018 Research-status Report 2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Linear-scaling first-principles molecular dynamics of complex biological systems with the CONQUEST code2016

    • Author(s)
      Takao Otsuka, Makoto Taiji, David R. Bowler, Tsuyoshi Miyazaki
    • Journal Title

      Japanese Journal of Applied Physics

      Volume: 55

    • NAID

      210000147203

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] 量子化学計算による薬物分子の代謝反応性部位と初期反応過程に関する考察2019

    • Author(s)
      大塚教雄、沖本憲明、齋藤大明、泰地真弘人
    • Organizer
      第13回分子科学討論会2019名古屋
    • Related Report
      2019 Annual Research Report
  • [Presentation] Quantum chemical analysis of reaction indices and reaction path for drug molecules2018

    • Author(s)
      Takao Otsuka, Noriaki Okimoto, Hiroaki Saito, Makoto Taiji
    • Organizer
      XXX IUPAP Conference on Computational Physics
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] Application of order-N first-principles DFT calculations with temperature controlled molecular dynamics to biomolecular system2017

    • Author(s)
      Takao Otsuka, Makoto Taiji, David R. Bowler, Tsuyoshi Miyazaki
    • Organizer
      XXIX IUPAP Conference on Computational Physics, CCP2017, Paris
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Constant temperature order-N first-principles molecular dynamics calculations of biomolecular system and short-time behavior2016

    • Author(s)
      Takao Otsuka, Makoto Taiji, David R. Bowler, Tsuyoshi Miyazaki
    • Organizer
      第54回日本生物物理学会大会
    • Place of Presentation
      つくば国際会議場、つくば
    • Year and Date
      2016-11-25
    • Related Report
      2016 Research-status Report

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Published: 2016-07-20   Modified: 2023-03-08  

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