Molecular and Chemical Life Science :
Chemical Biology


Professor ARIMOTO Hirokazu
Campus Katahira campus
Laboratory Analytical Bioorganic Chemistry
Tel +81-22-217-6201
E-mail arimoto@tohoku.ac.jp
Website http://www.agri.tohoku.ac.jp/bunseki/index-j.html

I was educated as a synthetic chemist but am now working in an interdisciplinary field at the chemistry-biology interface. Most of our alumni with Ph. D. degrees continue their research in academic institutions, and those with Master’s degrees work in chemical or pharmaceutical industries.


Keio University: B.S., 1988. Keio University: Ph.D., 1995 (Total synthesis of γ-pyrone-containing marine natural products, eg. Onchitriols; Thesis advisors: Drs. Shosuke Yamamura & Shigeru Nishiyama).

University of Pennsylvania: Postdoctoral Associate, 1996-97 (Postdoctoral advisor: Dr. Amos B. Smith, III: discodermolide project).

Asahi Glass Company, Yokohama: Researcher (1990-1992): F-containing chemicals.

Shizuoka University, Dept. of Chemistry, Shizuoka: Assistant Professor (1994), Associate Professor (1999).

Nagoya University, Dept. of Chemistry, Nagoya: Associate Professor (2001-2005).

Tohoku University, Grad. Sch. of Life Sciences, Sendai: Full Professor (2005- ).

Selected Publications
Book chapter
  1. Important Natural Products, in "Quaternary Stereocenters - Challenges for Organic Synthesis", ed. by J. Christoffers and A. Baro, Wiley (2005)
Recent papers
  1. AUTACs: Cargo-Specific Degraders Using Selective Autophagy, Molecular Cell 2019, 76, in press. https://doi.org/10.1016/j.molcel.2019.09.009
  2. Endogenous Nitrated Nucleotide Is a Key Mediator of Autophagy and Innate Defense against Bacteria, Molecular Cell 2013, 52, 794.
  3. Staphylococcus aureus Penicillin-Binding Protein 2 Can Use Depsi-Lipid II Derived from Vancomycin-Resistant Strains for Cell Wall Synthesis, Chem. Eur. J. 2013, 19, 12104.
  4. Elucidation of the Active Conformation of Vancomycin Dimers with Antibacterial Activity against Vancomycin-resistant Bacteria, Chem. Eur. J. 2012, 18, 12681.
  5. Total Synthesis of Antibiotic Kendomycin: a Macrocyclization Using Tsuji-Trost Etherification/Claisen Rearrangement Sequence, Angew. Chem. Int. Ed. 2014, 53 4213.
Activities in Academic Societies

The Chemical Society of Japan; American Chemical Society; the Society of Synthetic Organic Chemistry, Japan; Japan Society for Bioscience, Biotechnology, and Agrochemistry; Japanese Society for Chemical Biology; Nitric Oxide Society of Japan


Advanced analytical bioorganic chemistry, Analytical bioorganic chemistry (Faculty of Agriculture), Analytical chemistry (Faculty of Agriculture), etc.

Recent Activities

  1. Autophagy is a cytoprotective mechanism that degrades biomolecules, protein aggregates, or damaged organelles. We recently discovered that 8-nitro-cGMP, a nitric oxide signal mediator, is an autophagy inducer. For example, 8-nitro-cGMP modifies invading bacteria via covalent modification (S-guanylation), which accelerates elimination of the modified bacteria via ubiquitin-mediated selective autophagy. We believe that this novel mechanism will be of great importance in creating new medicines for diseases, such as cancer or neurodegenerative diseases.
  2. Vancomycin is the drug of last resort for treatment of serious nosocomial infections, and thus vancomycin-resistant bacteria (VRE, VRSA) are of great concern in clinics. We have chemically modified vancomycin to improve its potency against VRE/VRSA.
  3. Total synthesis of biologically active natural substances such as pinnaic acid, halichlorine, and kendomycin have been accomplished in our laboratory. We also have developed new synthesis techniques that facilitate the preparation of these biologically important substances. For example, we have discovered a very interesting dehomologation reaction that produces 1-carbon shorter carboxylic acids from the corresponding primary alcohols.
  4. Electron paramagnetic resonance (EPR) imaging allows us to investigate live animals without using radio-labeled probes. Working with researchers in Hokkaido University, we are studying useful spin probes for EPR imaging.

Message to Students

Applicants to this laboratory should have a strong background in synthetic organic chemistry from undergraduate study. Theses topics are usually selected from interdisciplinary areas, and thus require the guidance of specialists (often biologists) outside of our laboratory. Therefore, students are requested to be highly self-motivated to seek network opportunities outside of our laboratory.