Centers & Labs

RIKEN Center for Life Science Technologies

Structure-Based Molecular Design Team

Team Leader: Teruki Honma (Ph.D.)
Teruki  Honma(Ph.D.)

We plan to develop methods for designing novel small molecules, nucleic acids, and proteins, in order to help to accelerate drug development and the elucidation of living systems, and also develop an FBDD (Fragment based Drug Discovery) method for targeting biomolecules currently difficult to make susceptible of binding to small molecules.

Main Research Field

Computer Science

Related Research Fields

Chemistry / Pharmacology & Toxicology

Research Subjects

  • Development of new technologies for in silico screening and the applications
  • Construction of FBDD platform for difficult drug discovery targets
  • Development of simulation/design technologies for unnatural nucleic acid/protein

Selected Publications

Papers with an asterisk(*) are based on research conducted outside of RIKEN.
  1. Okada-Iwabu, M.; Yamauchi, T.; Iwabu, M.; Honma, T.; Hamagami, K. I.; Matsuda, K.; Yamaguchi, M.; Tanabe, H.; Kimura-Someya, T.; Shirouzu, M.; Ogata, H.; Tokuyama, K.; Ueki, K.; Nagano, T.; Tanaka, A.; Yokoyama, S.; Kadowaki, T.:
    “A small-molecule AdipoR agonist for type 2 diabetes and short life in obesity.”
    Nature, 503, 493-499, 2013.
  2. Saito, Y.; Yuki, H.; Kuratani, M.; Hashizume, Y.;Takagi, S.; Honma, T.; Tanaka, A.; Shirouzu, M.; Mikuni, J.; Handa, N.; Ogahara, I.; Sone, A.; Najima, Y.; Tomabechi, Y.; Wakiyama, M.; Uchida, N.; Tomizawa-Murasawa, M.; Kaneko, A.; Tanaka, S.; Suzuki, N.; Kajita, H.; Aoki, Y.; Ohara, O.; Shultz, L.D.; Fukami, T.; Goto, T.; Taniguchi, S.; Yokoyama, S.; Ishikawa, F.:
    “A pyrrolo-pyrimidine derivative targets human primary AML stem cells in vivo.”
    Sci Transl Med 5(181): 181ra152, 2013.
  3. Shiba, T.; Kido, Y.; Sakamoto, K.; Inaoka, D. K.; Tsuge, C.; Tatsumi, R.; Takahashi, G.; Balogun, E. O.; Nara, T.; Aoki, T.; Honma, T.; Tanaka, A.; Inoue, M.; Matsuoka, S.; Saimoto, H.; Moore, A. L.; Harada, S.; Kita, K.:
    “Structure of the trypanosome cyanide-insensitive alternative oxidase.”
    Proc Natl Acad Sci U S A, 110(12), 4580-5, 2013.
  4. Takaya, D.; Sato, T.; Yuki, H.; Sasaki, S.; Tanaka, A.; Yokoyama, S.; Honma, T.
    “Prediction of Ligand-Induced Structural Polymorphism of Receptor Interaction Sites Using Machine Learning.”
    J Chem Inf Model, 53 (3), 704–716, 2013.
  5. Sato, T.; Watanabe, H.; Tsuganezawa, K.; Yuki, H.; Mikuni, J.; Yoshikawa, S.; Kukimoto-Niino, M.; Fujimoto, T.; Terazawa, Y.; Wakiyama, M.; Kojima, H.; Okabe, T.; Nagano, T.; Shirouzu, M.; Yokoyama, S.; Tanaka, A.; Honma, T.:
    “Identification of novel drug-resistant EGFR mutant inhibitors by in silico screening using comprehensive assessments of protein structures.”
    Bioorg. Med. Chem., 20(12), 3756-67, 2012.
  6. Tsuganezawa, K.; Watanabe, H.; Parker, L.; Yuki, H.; Taruya, S.; Nakagawa, Y.; Kamei, D.; Mori, M.; Ogawa, N.; Tomabechi, Y.; Handa, N.; Honma, T.; Yokoyama, S.; Kojima, H.; Okabe, T.; Nagano, T.; Tanaka, A.:
    “A novel Pim-1 kinase inhibitor targeting residues that bind the substrate peptide.”
    J Mol Biol, 417(3), 240-52, 2012.
  7. Yuki, H.; Honma, T.; Hata, M.; Hoshino, T.:
    “Prediction of sites of metabolism in a substrate molecule, instanced by carbamazepine oxidation by CYP3A4.”
    Bioorg Med Chem, 20(2), 775-83, 2011.
  8. Sato, T.; Honma, T.; Yokoyama, S.:
    “Combining Machine Learning and Pharmacophore-based Interaction Fingerprint for in silico Screening.”
    J Chem Inf Model, 50(1), 170-85, 2010.
  9. Sato, T.; Matsuo Y.; Honma, T.; Yokoyama, S.:
    “In silico functional profiling of small molecules and its applications.”
    J Med Chem, 51(24), 7705-16, 2008.
  10. *Sakiyama Y.; Yuki, H.; Moriya, T.; Hattori, K.; Suzuki, M.; Shimada, K.; Honma, T.:
    “Predicting human liver microsomal stability with machine learning techniques.”
    J Mol Graph Model 26(6), 907-915, 2008.

Contact information

1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
Tel: +81-(0)45-503-9433
Fax: +81-(0)45-503-9432

Email: honma [at] gsc.riken.jp