Development of novel antibiotics targeting peptidases of non-fermenting gram negative rods.

• Project/Area Number: 16H04902
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Applied microbiology
• Research Institution: Showa University
• Principal Investigator: Tanaka Nobutada 昭和大学, 薬学部, 准教授 (00286866)
• Project Period (FY): 2016-04-01 – 2020-03-31
• Project Status: Completed (Fiscal Year 2019)
• Budget Amount: ¥8,710,000 (Direct Cost: ¥6,700,000、Indirect Cost: ¥2,010,000); Fiscal Year 2018: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000); Fiscal Year 2017: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000); Fiscal Year 2016: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
• Keywords: 糖非発酵性細菌 / ペプチダーゼ / 立体構造 / 抗菌剤 / ドラッグデザイン

Outline of Final Research Achievements

Family S46 peptidases are widely distributed in anaerobic Gram-negative species in the genera Bacteroides, Parabacteroides, and Porphyromonas, but they are not found in mammals. Therefore, S46 peptidases are ideal targets for novel antibiotics. We determined a crystal structure of dipeptidyl peptidase 11 from Porphyromonas gingivalis (PgDPP11) in complex with citrate ions at a 1.50 Å resolution using a high-quality space-grown crystal. The bound citrate ion, a potassium ion, and a water molecule in the active site of PgDPP11 were regarded to mimic the binding of an acidic amino acid and were utilized as a pharmacophore for an in silico inhibitor screening. The screening resulted in the first nonpeptidyl inhibitor of S46 peptidases, SH-5. The binding mode of SH-5 was confirmed by crystal structure analysis at a 2.39 Å resolution. The hit compound SH-5 and a related compound represent promising lead structures for further rational design of potent inhibitors against PgDPP11.

Academic Significance and Societal Importance of the Research Achievements

歯周病原因菌Porphyromonas gingivalisや多剤耐性菌Stenotrophomonas maltophiliaは糖ではなく蛋白質やペプチドをエネルギー源とする「糖非発酵性細菌」である。従って、これらの菌のペプチド代謝経路を阻害するような化合物は新規抗生物質と成り得る。従って、本研究の学術的意義は、糖非発酵性細菌を標的とした新規抗生物質開発に繋がるものである。また、本研究の社会的意義として、製薬企業は感染症関連研究に対して消極的なため大学研究者による抗生物質開発に繋がる基盤研究は社会的に極めて重要であることを強調したい。

Research Products

• [Journal Article] The Crystal Structure of Peptidase Toward Drug Discovery (2019)
  • Author(s): 阪本泰光、六本木沙織、鈴木義之、石原司、日高興士、中村彰宏、本間宣行、小笠原渉、田中信忠
  • Journal Title: International journal of microgravity science and application Volume: 36 Issue: 1 Pages: 360106
  • DOI: 10.15011//jasma.36.360106
  • NAID: 130007842629
  • ISSN: 2188-9783
  • Year and Date: 2019-01-31
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues (2018)
  • Author(s): Roppongi Saori、Suzuki Yoshiyuki、Tateoka Chika、Fujimoto Mayu、Morisawa Saori、Iizuka Ippei、Nakamura Akihiro、Honma Nobuyuki、Shida Yosuke、Ogasawara Wataru、Tanaka Nobutada、Sakamoto Yasumitsu、Nonaka Takamasa
  • Journal Title: Scientific Reports Volume: 8 Issue: 1 Pages: 2714-2714
  • DOI: 10.1038/s41598-018-21056-y
  • Peer Reviewed / Open Access
• [Journal Article] RNaseLにおける酵素活性化機構解明を目指した構造生物学的研究 (2017)
  • Author(s): 田中信忠
  • Journal Title: SAR News Volume: 32 Pages: 10-18
  • Peer Reviewed
• [Journal Article] Periplasmic form of dipeptidyl aminopeptidase IV from Pseudoxanthomonas mexicana WO24: purification, kinetic characterization, crystallization and X‐ray crystallographic analysis (2017)
  • Author(s): Saori Roppongi Chika Tateoka Mayu Fujimoto Ippei Iizuka Saori Morisawa Akihiro Nakamura Nobuyuki Honma Yoshiyuki Suzuki Yosuke Shida Wataru Ogasawara Nobutada Tanaka Yasumitsu Sakamoto Takamasa Nonaka
  • Journal Title: Acta Crystallographica Section F Volume: 73 Issue: 11 Pages: 501-606
  • DOI: 10.1107/s2053230x17014911
  • Peer Reviewed / Open Access
• [Journal Article] 糖非発酵グラム陰性細菌由来新規ジペプチド産生酵素の構造と機能 (2016)
  • Author(s): 阪本泰光、野中孝昌、鈴木義之、小笠原渉、田中信忠
  • Journal Title: 日本結晶学会誌 Volume: 58 Pages: 221-227
  • NAID: 130005267922
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Crystal Structure of Dipeptidyl Peptidase 11 from Porphyromonas gingivalis: The Molecular Basis of Substrate Specificity among the Family S46 Peptidases (2016)
  • Author(s): Sakamoto, Y. and Tanaka, N.
  • Journal Title: Photon Factory Highlights 2015 Volume: - Pages: 56-57
  • Peer Reviewed
• [Presentation] クスリ創りの新時代へ ～宇宙実験・アカデミア創薬・ロボット創薬のコラボレーションによる新薬創製への挑戦～ (2019)
  • Author(s): 阪本泰光、田中信忠、石原司
  • Organizer: 「きぼう」利用シンポジウム
• [Presentation] ジペプチジルアミノペプチダーゼ4ファミリーの立体構造比較研究 (2019)
  • Author(s): 六本木沙織、鈴木義之、館岡千佳、藤本真友、森澤さおり、飯塚一平、中村彰宏、本間宣行、伊藤康広、志田洋介、小笠原渉、田中信忠、阪本泰光、野中孝昌
  • Organizer: 量子ビームサイエンスフェスタ
• [Presentation] Elucidation of substrate recognition mechanism of dipeptidyl aminopeptidase IV from Gram-negative bacteria Pseudoxanthomonas mexicana WO24 (2018)
  • Author(s): Akihiro Nakamura, Nobuyuki Honma, Saori Roppongi, Yoshiyuki Suzuki, Yosuke Shida, Yasumitsu Sakamoto, Koji Inaka, Hiroaki Tanaka, Kiyoito Kihira, Mitsugu Yamada, Izumi Yoshioka, Hiroaki Gouda, Takamasa Nonaka, Nobutada Tanaka, Wataru Ogasawara
  • Organizer: 7th International GIGAKU conference in Nagaoka
  • Int'l Joint Research
• [Presentation] 微生物Dipeptidyl aminopeptidase IVの結晶構造解析 (2018)
  • Author(s): 六本木沙織、鈴木義之、館岡千佳、藤本真友、森澤さおり、飯塚一平、中村彰宏、本間宣行、伊藤康広、志田洋介、小笠原渉、田中信忠、阪本泰光、野中孝昌
  • Organizer: 2017年度量子ビームサイエンスフェスタ
• [Presentation] Pseudoxanthomonas mexicana WO24由来Dipeptidyl aminopeptidase IVの構造・機能解析 (2018)
  • Author(s): 中村彰宏、本間宣行、六本木沙織、鈴木義之、志田洋介、阪本泰光、飯塚一平、伊中浩治、田仲広明、木平清人、山田貢、吉崎泉、合田浩明、野中孝昌、田中信忠、小笠原渉
  • Organizer: 第12回 日本ゲノム微生物学会年会
• [Presentation] Pseudoxanthomonas mexicana WO24由来Dipeptidyl aminopeptidase IVの基質認識機構の解明 (2018)
  • Author(s): 中村彰宏、本間宣行、六本木沙織、鈴木義之、志田洋介、阪本泰光、飯塚一平、伊中浩治、田仲広明、木平清人、山田貢、吉崎泉、合田浩明、野中孝昌、田中信忠、小笠原渉
  • Organizer: 日本農芸化学会2018年度大会
• [Presentation] 部位特異的変異導入解析によるFamily S46ペプチダーゼの基質認識残基の同定 (2018)
  • Author(s): 本間宣行、中村彰宏、六本木沙織、鈴木義之、志田洋介、阪本泰光、飯塚一平、伊中浩治、田仲広明、木平清人、山田貢、吉崎泉、合田浩明、野中孝昌、田中信忠、小笠原渉
  • Organizer: 日本農芸化学会2018年度大会
• [Presentation] X線結晶構造に基づく多剤耐性菌由来DPP-7阻害剤の設計と評価 -国際宇宙ステーションで抗菌薬を開発する- (2018)
  • Author(s): 関拓海、奥野優香、櫻井有紀、日高興士、宮崎杏奈、北條恵子、六本木沙織、阪本泰光、伊藤康広、鈴木義之、小笠原渉、田中信忠、木平清人、山田貢、吉崎泉、田仲広明、伊中浩治、津田裕子
  • Organizer: 日本薬学会第138年会
• [Presentation] 微生物ジペプチジルアミノペプチダーゼIVの結晶構造解析 (2018)
  • Author(s): 六本木沙織、鈴木義之、館岡千佳、藤本真友、森澤さおり、飯塚一平、中村彰宏、本間宣行、伊藤康広、志田洋介、小笠原渉、田中信忠、阪本泰光、野中孝昌
  • Organizer: 日本薬学会第138年会
• [Presentation] Family S46ペプチダーゼの新規基質認識残基の同定 (2017)
  • Author(s): 中村彰宏、伊藤康広、鈴木義之、六本木沙織、飯塚一平、阪本泰光、田中信忠、小笠原渉
  • Organizer: 第17回日本蛋白質科学会
• [Presentation] Enzymatic characterization of S46 peptidase from pathogenic bacteria (2017)
  • Author(s): Nobuyuki Honma, Yasuhiro Ito, Akihiro Nakamura, Saori Roppongi, Yuki Sakurai, Yoshiyuki Suzuki, Koushi Hidaka, Yuko Tsuda, Yasumitsu Sakamoto, Nobutada Tanaka, Wataru Ogasawara
  • Organizer: 2017 1st STI-Gigaku
  • Int'l Joint Research
• [Presentation] Crystal structures of dipeptidyl aminopeptidase IV from non-fermenting gram negative rods. (2017)
  • Author(s): Roppongi, S., Tateoka, C., Suzuki, Y., Ito, Y., Fujimoto, M., Morisawa, S., Iizuka, I., Ogasawara, W., Tanaka, N., Sakamoto, Y., and Nonaka, T.
  • Organizer: International Union of Microbiological Societies 2017
  • Int'l Joint Research
• [Presentation] S46 family bacterial dipeptidyl aminopeptidases as novel antibiotics targets. (2017)
  • Author(s): Sakamoto, Y., Suzuki, Y., Iizuka, I., Tateoka, C., Roppongi, S., Fujimoto, M., Ito, Y., Inaka, K., Tanaka, H., Yamada, M., Ohta, K., Gouda, H., Nonaka, T., Ogasawara, W., and Tanaka, N.
  • Organizer: International Union of Microbiological Societies 2017
  • Int'l Joint Research
• [Presentation] Identification of substrate recognition residues in family S46 peptidase from pathogenic non-fermenting gram-negative bacteria. (2017)
  • Author(s): Nakamura, A., Ito, Y., Suzuki, Y., Roppongi, S., Hidaka, K., Sakamoto, Y., Tanaka, N., and Ogasawara, W.
  • Organizer: International Union of Microbiological Societies 2017
  • Int'l Joint Research
• [Presentation] Identification of Substrate Recognition Residues in Family S46 Peptidase from Gram-Negative Bacteria (2017)
  • Author(s): Nakamura, A., Ito, Y., Suzuki, Y., Roppongi, S., Hidaka, K., Sakamoto, Y., Tanaka, N., and Ogasawara, W.
  • Organizer: 6th International GIGAKU conference in Nagaoka
  • Int'l Joint Research
• [Presentation] Analysis of Substrate Recognition Residues in Family S46 Peptidase from Gram-Negative Bacteria (2017)
  • Author(s): Nakamura, A., Ito, Y., Suzuki, Y., Roppongi, S., Hidaka, K., Sakamoto, Y., Tanaka, N., and Ogasawara, W.
  • Organizer: 2017 2nd STI-Gigaku
  • Int'l Joint Research
• [Presentation] Identification of dipeptidic inhibitors targeting DPP7 derived from multiple drug resistant bacteria Stenotrophomonas maltophilia (2017)
  • Author(s): Yuki Sakurai, Koushi Hidaka, Anna Miyazaki, Keiko Hojo, Saori Roppongi, Yasumitsu Sakamoto, Yasuhiro Ito, Yoshiyuki Suzuki, Wataru Ogasawara, Nobutada Tanaka, and Yuko Tsuda
  • Organizer: The 54th Japanese Peptide Symposium
  • Int'l Joint Research
• [Presentation] Structural Analysis of Dipeptidyl Peptidase 11 (DPP11) from Porphyromonas gingivalis. (2016)
  • Author(s): Sakamoto, Y., Suzuki, Y., Iizuka, I., Tateoka, C., Roppongi, S., Fujimoto, M., Inaka, K., Tanaka, H., Yamada, M., Ohta, K., Gouda, H., Nonaka, T., Ogasawara, W. and Tanaka, N.
  • Organizer: AsCA 2016
  • Place of Presentation: Hanoi, Socialist Republic of Vietnam
  • Year and Date: 2016-12-05
  • Int'l Joint Research
• [Presentation] Structure and Fuctions of Dipeptidyl Peptidase 11 (DPP11) from Porphyromonas gingivalis. (2016)
  • Author(s): Sakamoto, Y., Suzuki, Y., Iizuka, I., Tateoka, C., Roppongi, S., Fujimoto, M., Inaka, K., Tanaka, H., Yamada, M., Ohta, K., Gouda, H., Nonaka, T., Ogasawara, W. and Tanaka, N.
  • Organizer: 2nd International Symposium on Space Science of High Quality Protein Crystallization
  • Place of Presentation: Tokyo, Japan
  • Year and Date: 2016-10-21
  • Int'l Joint Research
• [Presentation] Crystal structure of dipeptidyl amino peptidase 11 from Porphyromonas gingivalis. (2016)
  • Author(s): Sakamoto, Y., Suzuki, Y., Iizuka, I., Tateoka, C., Roppongi, S., Fujimoto, M., Inaka, K., Tanaka, H., Yamada, M., Ohta, K., Gouda, H., Nonaka, T., Ogasawara, W. and Tanaka, N.
  • Organizer: 42nd Naito Conference on In the Vanguard of Structural Biology
  • Place of Presentation: Sapporo, Japan
  • Year and Date: 2016-10-06
  • Int'l Joint Research
• [Presentation] Enzymatic characterization of S46 peptidase from pathogenic bacteria. (2016)
  • Author(s): Ito, Y., Nakamura, A., Roppongi, S., Sakurai, Y., Suzuki, Y., Hidaka, K., Tsuda, Y., Sakamoto, Y., Tanaka, N. and Ogasawara, W.
  • Organizer: The 5th International GIGAKU Conference in Nagaoka
  • Place of Presentation: Nagaoka, Japan
  • Year and Date: 2016-10-06
  • Int'l Joint Research
• [Presentation] Crystal structure of dipeptidyl amino peptidase 11 (DPP11) from periodontal pathogen. (2016)
  • Author(s): Sakamoto, Y., Suzuki, Y., Iizuka, I., Tateoka, C., Roppongi, S., Fujimoto, M., Inaka, K., Tanaka, H., Yamada, M., Ohta, K., Gouda, H., Nonaka, T., Ogasawara, W. and Tanaka, N.
  • Organizer: ISS R&D 2016
  • Place of Presentation: San Diego, USA
  • Year and Date: 2016-07-14
  • Int'l Joint Research
• [Presentation] Crystal Structure analaysis of dipeptidyl peptidase 11 from Porphyromonas gingivalis. (2016)
  • Author(s): Sakamoto, Y., Suzuki, Y., Iizuka, I., Tateoka, C., Roppongi, S., Fujimoto, M., Inaka, K., Tanaka, H., Yamada, M., Ohta, K., Gouda, H., Nonaka, T., Ogasawara, W. and Tanaka, N.
  • Organizer: 16th International Conference on the Crystallization of Biological Macromolecules
  • Place of Presentation: Prague, Czech Republic
  • Year and Date: 2016-07-05
  • Int'l Joint Research
• [Presentation] Structure-Function Relationships of S46 Peptidases from Non-Fermenting Gram-Negative Rods. (2016)
  • Author(s): Roppongi, S., Suzuki, Y., Iizuka, I., Inaka, K., Tanaka, H., Yamada, M., Ohta, K., Nonaka, T., Ogasawara, W., Tanaka, N. and Sakamoto, Y.
  • Organizer: 116th The American Society for Microbiology General meeting
  • Place of Presentation: Boston, USA
  • Year and Date: 2016-06-17
  • Int'l Joint Research
• [Remarks] International Space Station Award
  • URL: http://iss.jaxa.jp/topics/2016/07/160715.html