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X-ray crystallographic analysis of penicillin-recognizing enzyme for the search of non-covalent inhibitors

Research Project

Project/Area Number 20K07484
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Review Section Basic Section 49050:Bacteriology-related
Research InstitutionJosai International University

Principal Investigator

NUKAGA Michiyoshi  城西国際大学, 薬学部, 教授 (20251150)

Project Period (FY) 2020-04-01 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2023: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000)
Fiscal Year 2022: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2021: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2020: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Keywordsβ-ラクタマーゼ / ペニシリン結合タンパク質 / 抗生物質 / X線結晶解析 / 分子動力学計算 / 耐性菌 / 抗菌薬 / カルバペネマーゼ / メチシリン耐性黄色ブドウ球菌 / バークホルデリア・セパシア細菌群 / カルバペネム / 第五世代セフェム / 薬剤耐性 / ARM / 抗生物質耐性 / X線結晶解析 / MRSA / PBP / 構造生物学 / 細胞壁合成阻害剤
Outline of Research at the Start

β-ラクタム系抗生物質は、ペニシリン結合タンパク質(PBP)に対する優れた阻害剤であり、中でもカルバペネム系薬は耐性要因であるセリンβ-ラクタマーゼにも優れた結合性を示す。しかしながら、これらは、活性中心と共有結合で結ばれたアシル中間体を阻害形態としており、アミノ酸置換などの変異により、耐性菌が生まれやすい。
本研究では、MRSAの耐性要因であるPBP2aと代表的カルバペネマーゼであるBurkholderia multiviorans由来PenAを材料にしてX線結晶構造解析、分子動力学計算、化合物データベース検索などを行い、既知阻害剤の阻害メカニズム研究と新規阻害剤探索を行う。

Outline of Final Research Achievements

Antibiotic resistance is a major medical problem. In this study, we focused on β-lactam resistance and investigated PBP2a (penicillin-binding protein) from MRSA and PenA carbapenemase from Burkholderia multiviorans, mainly by X-ray crystallographic analysis and molecular dynamics calculations.
For the MRSA-derived PBP2a, the crystallisation conditions have been investigated on the basis of the known ceftaroline complex (PDB:3ZG0) and the possibility of allosteric inhibitors was explored.
For PenA carbapenemase, a mutant enzyme was generated and the 3D structure and its motion predicted, providing insight into carbapenem resistance and inhibitor resistance.

Academic Significance and Societal Importance of the Research Achievements

抗生物質耐性菌は世界的な問題で、新しい抗菌剤の開発は急務である。本研究では、最後の切り札的に利用されているカルバペネム系薬耐性の主要因であるカルバペネマーゼの保存性アミノ酸R220とE166の変異酵素の研究を通して、PenAカルバペネマーゼの反応機構におけるタンパク質の動きの重要性を示すとともに、これまで一般的だったツールとしてのE166の問題点を提唱することができた。MRSAのPBP2aの研究では、アロステリック阻害剤の可能性を示した。完了していない部分が多いのではあるが、今後、研究を完成させ発表していきたい。

Report

(5 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Research-status Report
  • 2021 Research-status Report
  • 2020 Research-status Report
  • Research Products

    (8 results)

All 2024 2021 2020 Other

All Int'l Joint Research (3 results) Journal Article (3 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 3 results,  Open Access: 2 results) Presentation (2 results) (of which Int'l Joint Research: 1 results)

  • [Int'l Joint Research] CWRU-Cleveland VAMC Center(米国)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] Louis Stokes Cleveland VAMC(米国)

    • Related Report
      2021 Research-status Report
  • [Int'l Joint Research] Louis Stokes Cleveland VAMC Cleveland(米国)

    • Related Report
      2020 Research-status Report
  • [Journal Article] Development of Inhibitory Compounds for Metallo-beta-lactamase through Computational Design and Crystallographic Analysis2024

    • Author(s)
      Kamo Taichi、Kuroda Keiichi、Nimura Saki、Guo Yan、Kondo Shota、Nukaga Michiyoshi、Hoshino Tyuji
    • Journal Title

      Biochemistry

      Volume: - Issue: 10 Pages: 1278-1286

    • DOI

      10.1021/acs.biochem.4c00069

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Identification of the Inhibitory Compounds for Metallo-β-lactamases and Structural Analysis of the Binding Modes2021

    • Author(s)
      Kamo T, Kuroda K, Kondo S, Hayashi U, Fudo S, Yoneda T, Takaya A, Nukaga M, Hoshino T.
    • Journal Title

      Chemical and Pharmaceutical Bulletin

      Volume: 69 Issue: 12 Pages: 1179-1183

    • DOI

      10.1248/cpb.c21-00611

    • NAID

      130008123292

    • ISSN
      0009-2363, 1347-5223
    • Year and Date
      2021-12-01
    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Assessing the Potency of β-Lactamase Inhibitors with Diverse Inactivation Mechanisms against the PenA1 Carbapenemase from Burkholderia multivorans.2021

    • Author(s)
      Nukaga M, Yoon MJ, Taracilia MA, Hoshino T, Becka SA, Zeiser ET, Johnson JR, Papp-Wallace KM
    • Journal Title

      ACS Infect Dis.

      Volume: 7 Issue: 4 Pages: 826-837

    • DOI

      10.1021/acsinfecdis.0c00682

    • Related Report
      2021 Research-status Report 2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] Burkholderia multivorans由来の薬剤耐性因子PenRのX線結晶構造解析2024

    • Author(s)
      渋谷 明日香、坂本 翔、星野 忠次、Maria F Mojica、額賀 路嘉
    • Organizer
      日本薬学会
    • Related Report
      2023 Annual Research Report
  • [Presentation] Characterizing the resistance mechanisms present in an unusually, highly multi-drug resistant isolate of Burkholderia multivorans(ASM Microbe online, ePoster)2020

    • Author(s)
      M. Nukaga, S. A. Becka, E. T. Zeiser, J. J. LiPuma, K. M. Papp-Wallace
    • Organizer
      5th ASM Microbe Meeting
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research

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Published: 2020-04-28   Modified: 2025-01-30  

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