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Identification of nanaomycin A and its analogs by a newly established screening method for functional inhibitors of the type IX secretion system in Porphyromonas gingivalis

The Journal of Antibiotics volume 78, pages 90–105 (2025)Cite this article

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Abstract

Porphyromonas gingivalis, a Gram-negative anaerobic bacterium, is a key pathogen in chronic periodontitis. P. gingivalis has a type IX secretion system (T9SS) that secretes highly hydrolytic proteinases called gingipains for obtaining peptides as an energy source. Although most T9SS-related proteins have been identified, no specific inhibitor of T9SS has been reported. To screen T9SS inhibitors, we focused on and characterized a minimal liquid medium called mC medium that contains milk casein as the sole protein source. We found that P. gingivalis wild-type strain ATCC 33277 caused cloudiness of mC medium without growth. In mC medium, an alkylating agent, iodoacetamide (IAM) that is an inhibitor of gingipains, and a protonophore, carbonyl cyanide 3-chlorophenylhydrazone (CCCP) that dissipates the proton motive force required for T9SS-mediated secretion, clearly inhibited the increase in turbidity. Moreover, neither the gingipain-null mutant nor the T9SS-deficient mutant caused mC medium cloudiness, suggesting that mC medium cloudiness is dependent on gingipain activity and T9SS. These results indicated that mC medium can be used to assess P. gingivalis gingipain activity and its functional T9SS. Using an assay system with mC medium, we discovered that OM-173αA and OM-173βA in the Ōmura Natural Compound Library and nanaomycin A were probable T9SS inhibitors. The compounds need to be further investigated as tools for analyzing T9SS and as potential therapeutic agents for periodontal disease.

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Acknowledgements

The enormous contribution of MS to this research, including the planning, execution, and paper preparation of this study, should be deeply emphasized. He had a great passion for science throughout his life. The authors thank H. Yukitake for discussions and continuous advice on experimental techniques and K. Nakayama for his support in preparing the revised manuscript. This work was supported by grants from Nagasaki University WISE Program Application Guidance for the Grant for Global Health Research Collaboration to MN, and the Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)) from the Japan Agency for Medical Research & Development (AMED) under Grant Numbers JP19am0101096 (Phase I) to MI. We would like to thank Editage (http://www.editage.com) for English language editing.

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  1. Deceased 16 September 2024: Mikio Shoji

Authors and Affiliations

  1. Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki, Nagasaki, 852-8588, Japan

    Yuko Sasaki, Takehiro Matsuo, Mariko Naito & Mikio Shoji

  2. Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan

    Yoshihiro Watanabe, Masato Iwatsuki & Yuki Inahashi

  3. Department of Microbiology and Immunology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605, Japan

    Satoshi Nishida

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Sasaki, Y., Matsuo, T., Watanabe, Y. et al. Identification of nanaomycin A and its analogs by a newly established screening method for functional inhibitors of the type IX secretion system in Porphyromonas gingivalis. J Antibiot 78, 90–105 (2025). https://doi.org/10.1038/s41429-024-00790-8

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