RIKEN Center for Life Science Technologies


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To let you know about our research, this area contains 4 types of information about CLST; “Article”, “Videos”, “Event” and “Study”.
At “Article”, you can read articles on interviews and lectures, and you can enjoy the videos about CLST at “Videos”. If you want to meet and talk directly with the researcher, “Visit” give you some information of such events. You can find more difficult contents to know about our research deeply at “Study”.
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Labs & Technologies

Structure-based Molecular Design Team

* Due to the reorganization starting as new centers in April 2018, this laboratory is now belong to the Center for Biosystems Dynamics Research. As for the latest information, please see the following URL below.
> The webpage of Laboratory for Structure-Based Molecular Design, Center for Biosystems Dynamics Research

Team Leader
Teruki Honma  Ph.D.

1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 JAPAN
Tel: 045-503-9433


Research Area

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 Publications List


A small-molecule AdipoR agonist for type 2 diabetes and short life in obesity.

Okada-Iwabu M, Yamauchi T, Iwabu M, Honma T, Hamagami K, 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.
Nature, 503(7477), 493-499 (2013).

A Pyrrolo-Pyrimidine Derivative Targets Human Primary AML Stem Cells in Vivo

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 LD, Fukami T, Goto T, Taniguchi S, Yokoyama S, Ishikawa F.
Sci Transl Med, 5(181), 181ra52 (2013).

Structure of the trypanosome cyanide-insensitive alternative oxidase.

Shiba T, Kido Y, Sakamoto K, Inaoka DK, Tsuge C, Tatsumi R, Takahashi G, Balogun EO, Nara T, Aoki T, Honma T, Tanaka A, Inoue M, Matsuoka S, Saimoto H, Moore AL, Harada S, Kita K.
Proc Natl Acad Sci U S A, 110(12), 4580-4585 (2013).

Prediction of ligand-induced structural polymorphism of receptor interaction sites using machine learning.

Takaya D, Sato T, Yuki H, Sasaki S, Tanaka A, Yokoyama S, Honma T.
J Chem Inf Model, 53(3), 704-716 (2013).

Identification of novel drug-resistant EGFR mutant inhibitors by in silico screening using comprehensive assessments of protein structures.

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.
Bioorg Med Chem, 20(12), 3756-3767 (2012).

A novel Pim-1 kinase inhibitor targeting residues that bind the substrate peptide.

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.
J Mol Biol, 417(3), 240-252 (2012).

Prediction of sites of metabolism in a substrate molecule, instanced by carbamazepine oxidation by CYP3A4.

Yuki H, Honma T, Hata M, Hoshino T.
Bioorg Med Chem, 20(2), 775-783 (2012).

Combining machine learning and pharmacophore-based interaction fingerprint for in silico screening.

Sato T, Honma T, Yokoyama S.
J Chem Inf Model, 50(1), 170-185 (2010).

In silico functional profiling of small molecules and its applications.

Sato T, Matsuo Y, Honma T, Yokoyama S.
J Med Chem, 51(24), 7705-7716 (2008).

Predicting human liver microsomal stability with machine learning techniques.

Sakiyama Y, Yuki H, Moriya T, Hattori K, Suzuki M, Shimada K, Honma T.
J Mol Graph Model, 26(6), 907-915 (2008).

>>>ALL Publications

Member  *concurrent

CLST was reorganized into three centers according to the RIKEN 4th Medium-Term Plan from April 1, 2018. For the latest information of Structure-based Molecular Design Team, please visit the following websites.

> The webpage of Laboratory for Structure-Based Molecular Design, Center for Biosystems Dynamics Research [http://www.bdr.riken.jp/en/research/labs/honma-t-labo/index.html]