Laboratory of in silico design

Members

Project Leader	Suyong Re
Deputy Project Leader	Yi-An Chen
Senior Research Fellow	Kaushik Rahul
Postdoctoral Research Associate	Jelang Muhammad Dirgantara, Mochammad Arfin
Trainee	Firoozeh Piroozmand, YOSHIYAMA Hayato, Chih-Yang Cheng
Administrative Assistant	TOJO Mitsuyo
Former member	NISHIMA Wataru

Background and objectives

This project promotes a rational drug discovery approach grounded in the fundamental principles of life science. This is achieved by integrating informatics technology, which utilizes large-scale data analysis, with structural simulation technology, which elucidates the molecular recognition mechanisms between disease-related proteins and drug candidates from their molecular structure and dynamics.

Under close collaboration with internal teams, external research institutions, and universities, we aim to establish a drug design platform capable of addressing diverse modalities, including medium and large molecules, in addition to conventional small molecule compounds. The ultimate goal is the high-precision and rapid design of drug candidate molecules for any therapeutic targets.

Overview of our research

Development of Data Integration Infrastructure and Application to Drug Discovery

We develop a platform that collects and analyzes publicly available life science data to conquer attractive drug targets currently unaddressed due to ineffective drug discovery strategies. By enabling detailed exploratory network analysis of disease-related target candidates, this platform aims to both accelerate drug design and significantly expand the drug discovery space.

Development of Structural Modeling Infrastructure and Application to Drug Discovery

We promote computational structure-based drug discovery (SBDD) technology by leveraging Artificial Intelligence (AI) and molecular simulation techniques to develop structural modeling technology that accurately visualizes the complex binding dynamics within biological systems, such as protein-protein interactions and other molecular recognition mechanisms between disease-related molecules. We aim to achieve a profound understanding of biomolecular recognition and, based on that knowledge, realize rational and innovative drug design.

References:　

Yi-An Chen, Hitoshi Kawashima, Jonguk Park, et al. “NIBN Japan Microbiome Database, a Database for Exploring the Correlations between Human Microbiome and Health.” Scientific Reports 15, (2025): 19640. https://doi.org/10.1038/s41598-025-04339-z
Yi-An Chen, Rodolfo S Allendes Osorio, and Kenji Mizuguchi. “TargetMine 2022: A New Vision into Drug Target Analysis.” Bioinformatics 38, (2022): 4454–56. https://doi.org/10.1093/bioinformatics/btac507
Yuhi Hosoe, Yohei Miyanoiri, Suyong Re, et al. “Structural Dynamics of the N‐terminal SH2 Domain of PI3K in Its Free and CD28 ‐bound States.” The FEBS Journal, 290, (2022): 2366-2378. https://doi.org/10.1111/febs.16666
Daiki Yamane, Satsuki Onitsuka, Suyong Re, et al. “Selective Covalent Targeting of SARS-CoV-2 Main Protease by Enantiopure Chlorofluoroacetamide.” Chemical Science 13, (2022): 3027–34. https://doi.org/10.1039/D1SC06596C
Taro Tsuji, Kayoko Hashiguchi, Mana Yoshida, et al. “α-Amino Acid and Peptide Synthesis Using Catalytic Cross-Dehydrogenative Coupling.” Nature Synthesis 1, (2022): 304–12. https://doi.org/10.1038/s44160-022-00037-0
Suyong Re, and Kenji Mizuguchi. “Glycan Cluster Shielding and Antibody Epitopes on Lassa Virus Envelop Protein.” The Journal of Physical Chemistry B 125, (2021): 2089–97. https://doi.org/10.1021/acs.jpcb.0c11516

Contact information

E-mail

suyongre[at]nibn.go.jp