Research Summary

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.

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