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RIKEN Center for Biosystems Dynamics Research Laboratory for Structure-Based Molecular Design

Team Leader: Teruki Honma (Ph.D.)

Research Summary

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 Fields

  • 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.

Related Links

Lab Members

Principal investigator

Teruki Honma
Team Leader

Core members

Tomohiro Sato
Research Scientist
Daisuke Takaya
Research Scientist
Hitomi Yuki
Research Scientist
Chiduru Watanabe
Research Scientist
Mayuko Yasuda
Technical Scientist
Shunpei Nagase
Technical Staff I

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

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