Unit Leader
Teruki Honma
Ph.D.
Drug Discovery Computational Chemistry Platform Unit
[Affiliation has changed to RIKEN Center for Integrated Medical Sciences (IMS) as of April 2025]
LocationYokohama
E-mailhonma.teruki@riken.jp
Our unit realizes highly accurate in silico screening from the latest modeling and statistical theory based on three-dimensional structures of target proteins and known inhibitors through collaboration among other drug discovery platform units. We utilize machine learning prediction by experimental data such as assay results and accurate interaction analysis using quantum chemical calculations based on target protein-compound complex structures to optimize compound design considering both main activity and ADMET.
Selected Publications
Komura H, Watanabe R, Kawashima H, et al.
A public-private partnership to enrich the development of in silico predictive models for pharmacokinetic and cardiotoxic properties.
Drug discovery today
26(5), 1275-1283 (2021)
doi: 10.1016/j.drudis.2021.01.024
Watanabe C, Okiyama Y, Tanaka S, et al.
Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses.
Chemical Science
12(13), 4722-4739 (2021)
Takaya D, Watanabe C, Nagase S, et al.
FMODB: the world's first database of quantum mechanical calculations for biomacromolecules based on the fragment molecular orbital method.
Journal of Chemical Information and Modeling
61(2), 777-794 (2021)
Sato T, Sekimata K, Sakai N, et al.
Structural Basis of Activin Receptor-Like Kinase 2 (R206H) Inhibition by Bis-heteroaryl Pyrazole-Based Inhibitors for the Treatment of Fibrodysplasia Ossificans Progressiva Identified by the Integration of Ligand-Based and Structure-Based Drug Design Approaches.
ACS Omega
5(20), 11411-11423 (2020)
Shirai F, Mizutani A, Yashiroda Y, et al.
Design and Discovery of an Orally Efficacious Spiroindolinone-Based Tankyrase Inhibitor for the Treatment of Colon Cancer.
Journal of Medicinal Chemistry
63(8), 4183-4204 (2020)
Ogura K, Sato T, Yuki H, Honma T.
Support Vector Machine model for hERG inhibitory activities based on the integrated hERG database using descriptor selection by NSGA-II.
Scientific Reports
9(1), 1-12 (2019)
Sato T, Yuki H, Ogura K, Honma T.
Construction of an integrated database for hERG blocking small molecules.
PLoS One
13(7), e0199348/1-e0199348/18 (2018)
Watanabe C, Watanabe H, Fukuzawa K, et al.
Theoretical Analysis of Activity Cliffs among Benzofuranone-Class Pim1 Inhibitors Using the Fragment Molecular Orbital Method with Molecular Mechanics Poisson-Boltzmann Surface Area (FMO+MM-PBSA) Approach.
Journal of Chemical Information and Modeling
57(12), 2996-3010 (2017)
Saito Y, Yuki H, Kuratani M, et al.
A pyrrolo-pyrimidine derivative targets human primary AML stem cells in vivo.
Science Translational Medicine
5(181), 181ra152 (2013)
doi: 10.1126/scitranslmed.3004387
Yuki H, Honma T, Hata M, Hoshino T.
Prediction of sites of metabolism in a substrate molecule, instanced by carbamazepine oxidation by CYP3A4.
Bioorganic & Medicinal Chemistry
20(2), 775-783 (2012)
doi: 10.1016/j.bmc.2011.12.004
