Study on the reaction mechanism of type II NADH dehydrogenase by structural and biochemical analyses of the enzyme-inhibitor interaction.

• Project/Area Number: 15K07005
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Functional biochemistry
• Research Institution: Kagawa University
• Principal Investigator: Yamashita Tetsuo 香川大学, 医学部, 助教 (80444727)
• Co-Investigator(Renkei-kenkyūsha): KITA Kiyoshi 長崎大学, 熱帯医学・グローバルヘルス研究科, 教授 (90134444) ; HARADA Shigeharu 京都工芸繊維大学, 工芸科学研究科, 教授 (80156504) ; SHIBA Tomoo 京都工芸繊維大学, 工芸科学研究科, 准教授 (80401206) ; Inaoka Daniel K 長崎大学, 熱帯医学・グローバルヘルス研究科, 助教 (10623803)
• Project Period (FY): 2015-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000); Fiscal Year 2017: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2016: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2015: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000)
• Keywords: NADH dehydrogenase / ユビキノン結合部位 / X線結晶構造解析 / 共結晶 / 阻害剤 / 基質結合部位 / ユビキノン / 酵素の触媒機構 / フラボプロテイン / 薬剤標的分子 / 結晶構造解析

Outline of Final Research Achievements

Type II NADH dehydrogenase (NDH-2) has emerged as a potential therapeutic target for drugs targeting human pathogenic bacteria and parasites, because mammals have only proton-pumping NADH dehydrogenase (complex I) but not NDH-2. In order to develop highly selective effectiveness inhibitors, it is necessary to understand the reaction mechanism of NDH-2 and its structural basis and investigate the interaction between protein and inhibitor at the level of a molecule. Furthermore, the binding sites of the substrates, NADH and ubiquinone, have to be identified. A crystal structure of yeast NDH-2 (Ndi1) in complex with ubiquinone has already been revealed, but there has been controversy regarding the physiological ubiquinone binding site. In the present study, the inherent ubiquinone-binding site of yeast Ndi1 was identified by structures binding novel competitive- and mixed-type inhibitors, and biochemical analysis.

Research Products

• [Int'l Joint Research] The Scripps Research Institute(米国)
• [Journal Article] Ubiquinone binding site of yeast NADH dehydrogenase revealed by structures binding novel competitive- and mixed-type inhibitors (2018)
  • Author(s): Yamashita Tetsuo, Inaoka Daniel Ken, Shiba Tomoo, Oohashi Takumi, Iwata So, Yagi Takao, Kosaka Hiroaki, Miyoshi Hideto, Harada Shigeharu, Kita Kiyoshi, Hirano Katsuya
  • Journal Title: Scientific Reports Volume: 8 Issue: 1 Pages: 2427-2427
  • DOI: 10.1038/s41598-018-20775-6
  • NAID: 120006532084
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Presentation] 競合および混合阻害剤との共結晶構造解析により明らかとなった出芽酵母由来Type II NADH脱水素酵素のユビキノン結合部位 (2018)
  • Author(s): 山下哲生，稲岡健ダニエル，志波智生，大橋匠，岩田想，矢木隆雄，三芳秀，原田繁春，北潔，平野勝也
  • Organizer: 日本農芸化学会中四国支部第51回講演会
• [Presentation] 出芽酵母由来Type II NADH dehydrogenase (NDH-2)のユビキノン競合阻害剤との高分解能複合体構造解析 (2015)
  • Author(s): 大橋拓未、稲岡ダニエル健、山下哲生、志波智生、岩田想、原田繁春、北潔
  • Organizer: 日本生体エネルギー研究会 第41回討論会
  • Place of Presentation: 東京大学医学部1号館講堂
  • Year and Date: 2015-12-23
• [Remarks] 呼吸鎖酵素NDH-2の反応機構の解明
  • URL: http://www.med.kagawa-u.ac.jp/~cardiovasc-physiol/custom72.html