Research
Faculty Members
Quantum life science and bioinformatics（Biology）
Takaya DaisukeSpecially Appointed Assosiate Professor / Lecturer
Dr. Daisuke Takaya works as a computational chemist. He has been in charge of ligand-based and structure-based drug design for drug development projects. He has been involved in drug discovery projects conducted by universities, research institutes, and companies. His work focuses on development of molecular modeling, machine learning, protein-ligand docking, database such as FMODB, and their applications for drug design. His latest interest is learning how to construct AI for the targets.
Research theme
Drug discovery research using in silico screening technology
There are two basic approaches to the design of drug candidate compounds: Ligand-Based Drug Design (LBDD), which focuses on the physical properties and structural information of known inhibitors, and Structure-Based Drug Design (SBDD), which focuses on structural complementarity with target proteins. Using these methods, we are searching for molecules that control the actual target molecule on the computer.
Drug discovery research using fragment molecular orbital method
Many methodologies have been proposed for LBDD and SBDD, and new methods are still being actively proposed. For example, features derived from drug information,called descriptors, can be used for various predictions. The Fragment Molecular Orbital method (FMO) is not only useful for analyzing interactions between compounds and target proteins, but are also expected to be used as descriptors for artificial intelligence (AI).
Development of databases related to drug discovery researches
The development of AI requires large amounts of data and learning these data, and this applies to the field of theoretical drug discovery as well. For the purpose of accumulating the data, we are contributing to the development of FMODB (https://drugdesign.riken.jp/FMODB/), a database of FMO computational results. Currently, we are developing this database and developing methods using the data.
Representative achievements
Special Features of COVID-19 in the FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2-Related Proteins, JOURNAL OF CHEMICAL INFORMATION AND MODELING 61(9)
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)
Protein ligand interaction analysis against new CaMKK2 inhibitors by use of X-ray crystallography and the fragment molecular orbital (FMO) method, JOURNAL OF MOLECULAR GRAPHICS & MODELLING 99 107599-107599
Characterization of crystal water molecules in a high-affinity inhibitor and hematopoietic prostaglandin D synthase complex by interaction energy studies, BIOORGANIC & MEDICINAL CHEMISTRY 26(16) 4726-4734
Targeting Ras-Driven Cancer Cell Survival and Invasion through Selective Inhibition of DOCK1, CELL REPORTS 19(5) 969-980 2017
Pyridinone compound and use thereof
