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).

Member *concurrent

Teruki Honma
Team Leader
Tomohiro Sato
Research Scientist
Daisuke Takaya
Research Scientist
Hitomi Yuki
Research Scientist

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Labs & Technologies

Structure-based Molecular Design Team

Research Area

Main Publications List

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

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

Structure of the trypanosome cyanide-insensitive alternative oxidase.

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

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

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

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

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

In silico functional profiling of small molecules and its applications.

Predicting human liver microsomal stability with machine learning techniques.

Member *concurrent