PhD (Tokyo)

Assistant Professor of Department of Chemistry

Contact Information

Office: YEUNG-B6606
Phone: +852 3442-7839
Fax: +852 3442-0522
Email: ymatsuda@cityu.edu.hk
Web: Personal Homepage
ORCID ID: 0000-0001-5650-4732
Author ID:

Research Interests

  • Bioorganic Chemistry
  • Natural Products Chemistry and Biosynthesis
  • Enzymatic Chemistry

Dr. Yudai Matsuda received his B.Sc. in 2010 and M.Sc. in 2012 from The University of Tokyo under the direction of Professor Ikuro Abe. After a short period of experience in industry, he moved back to The University of Tokyo as a Project Researcher (2012-2013) and was then appointed as an Assistant Professor at the same university (2013-2015). Meanwhile, he obtained his Ph.D. in Pharmaceutical Sciences in 2015 from The University of Tokyo. After obtaining his Ph.D. degree, he moved to the Department of Biotechnology and Biomedicine at Technical University of Denmark to work with Professor Thomas O. Larsen as a Postdoc (2015-2017) and subsequently again worked as a Project Researcher at The University of Tokyo (2017-2018). He joined the City University of Hong Kong as an Assistant Professor in April 2018, where he is working on biosynthesis and biosynthetic engineering of natural products.


Research Interest:

Natural products exhibit a wide range of biological activities and have been an attractive and rich source of compounds for drug discovery, providing many important pharmaceuticals. Recent advances in genome sequencing technologies and development of various molecular biological tools have allowed the access to many microbial genomes and provided opportunities to “bioengineer” natural products. By utilizing these state-of-the-art technologies, the Matsuda lab aims to further expand the diversity of natural products and seek to design metabolic pathways to afford useful compounds, which could potentially serve as future drug leads. The group’s current research topics include:

  1. Elucidation of the biosynthesis of complex/bioactive natural products

  2. Genomics-driven discovery and derivatization of natural products

  3. Generation and evolution of “unnatural” natural product pathways


Selected Publications: († equal contribution, * corresponding author)

(Full publication list is available here: https://scholar.google.co.jp/citations?user=E44nwkIAAAAJ&hl=en)

  • Matsuda, Y.,* Bai, T., Phippen, C.B.W., Nødvig, C.S., Kjærbølling, I., Vesth, T.C., Andersen, M.R., Mortensen, U.H., Gotfredsen, C.H., Abe, I.,* Larsen, T.O.* “Novofumigatonin biosynthesis involves a non-heme iron-dependent endoperoxide isomerase for orthoester formation.” Nat. Commun. 9, 2587 (2018).
  • Nakashima, Y., Mitsuhashi, T., Matsuda, Y., Senda, M., Sato, H., Yamazaki, M., Uchiyama, M., Senda, T., Abe, I. “Structural and computational bases for dramatic skeletal rearrangement in anditomin biosynthesis.” J. Am. Chem. Soc. 140, 9743–9750 (2018).
  • Nakamura, H., Matsuda, Y.,* Abe, I.* “Unique chemistry of non-heme iron enzymes in fungal biosynthetic pathways.” Nat. Prod. Rep. 35, 633-645 (2018).
  • Kjærbølling, I., Vesth, T.C., Frisvad, J.C., Nybo, J.L., Theobald, S., Kuo, A., Bowyer, P., Matsuda, Y., Mondo, S., Lyhne, E.K., Kogle, M.E., Clum, A., Lipzen, A.M., Salamov, A.A., Ngan, C.Y., Daum, C.G., Chiniquy, J., Barry, K.W., LaButti, K.M., Haridas, S., Simmons, B.A., Magnuson, J.K., Mortensen, U.H., Larsen, T.O., Grigoriev, I.V., Baker, S.E., Andersen, M.R. “Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species.” Proc. Natl. Acad. Sci. USA 115, E753-E761 (2018).
  • Mori, T., Iwabichi, T., Hoshino, S., Wang, H., Matsuda, Y., Abe, I. “Molecular basis for the unusual ring reconstruction in fungal meroterpenoid biogenesis.” Nat. Chem. Biol. 13, 1066-1073 (2017).
  • Matsuda, Y., Iwabuchi, T., Fujimoto, T., Awakawa, T., Nakashima, Y., Mori, T., Zhang, H., Hayashi, F., Abe, I. “Discovery of key dioxygenases that diverged the paraherquonin and acetoxydehydroaustin pathways in Penicillium brasilianum.” J. Am. Chem. Soc. 138, 12671-12677 (2016).
  • Okada, M., Matsuda, Y., Mitsuhashi, T., Hoshino, S., Mori, T., Nakagawa, K., Quan, Z., Qin, B., Zhang, H., Hayashi, F., Abe, I. “Genome-based discovery of an unprecedented cyclization mode in fungal sesterterpenoid biosynthesis.” J. Am. Chem. Soc. 138, 10011-10018 (2016).
  • Matsuda, Y., Mitsuhashi, T., Lee, S., Hoshino, M., Mori, T., Okada, M., Zhang, H., Hayashi, F., Fujita, M., Abe, I. “Astellifadiene: Structure determination by NMR spectroscopy and crystalline sponge method, and elucidation of its biosynthesis.” Angew. Chem. Int. Ed. 55, 5785-5788 (2016).
  • Qin, B., Matsuda, Y., Mori, T., Okada, M., Quan, Z., Mitsuhashi, T., Wakimoto, T., Abe, I. “An unusual chimeric diterpene synthase from Emericella variecolor and its functional conversion to a sesterterpene synthase by domain swapping.” Angew. Chem. Int. Ed. 55, 1658-1661 (2016).
  • Matsuda, Y., Iwabuchi, T., Wakimoto, T., Awakawa, T., Abe, I. “Uncovering the unusual D-ring construction in terretonin biosynthesis by collaboration of a multifunctional cytochrome P450 and a unique isomerase.” J. Am. Chem. Soc. 137, 3393–3401 (2015).
  • Matsuda, Y., Wakimoto, T., Mori, T., Awakawa, T., Abe, I. “Complete biosynthetic pathway of anditomin: Nature’s sophisticated synthetic route to a complex fungal meroterpenoid.” J. Am. Chem. Soc. 136, 15326-15336 (2014).
  • Matsuda, Y., Awakawa, T., Wakimoto, T., Abe, I. “Spiro-ring formation is catalyzed by a multifunctional dioxygenase in austinol biosynthesis.” J. Am. Chem. Soc. 135, 10962-10965 (2013).