Tokyo Tech News

In Silico Discovery and Development of Constrained Peptides


Published: August 25, 2016

Tokyo Institute of Technology (Tokyo Tech) and PeptiDream Inc. (PeptiDream) announced that both sides had entered into a collaboration for the in silico* discovery and development of constrained peptides using Tokyo Tech's TSUBAME 2.5 supercomputer and related technologies.


PeptiDream has generated and continues to generate a significant amount of information and learnings regarding the discovery and development of the company's constrained peptides as therapeutics, attained across PeptiDream's extensive collaboration partners and internal company programs. These critical learnings have significantly advanced PeptiDream's understanding of the therapeutic properties of constrained peptides, such as the effect of peptide solubility, plasma stability, metabolic stability, plasma protein binding, 2D/3D structure, etc., on the pharmacokinetic and pharmacologic activity of these molecules. PeptiDream has been looking to more systematically and comprehensively leverage these learnings to more efficiently optimize and accelerate the discovery and development of peptide therapeutics. In this collaboration, PeptiDream will provide Tokyo Tech with various experimental data related to these molecules, to which Tokyo Tech will generate powerful in silico prediction and simulation computational technologies that promise to significantly accelerate the optimization and development of peptide candidates identified from PeptiDream's Peptide Discovery Platform Systerm (PDPS) technology.

Professor Yutaka Akiyama at School of Computing (also a member of Advanced Computational Drug Discovery Unit, Institute of Innovative Research) at Tokyo Tech is one of the world leaders in in silico molecular simulation and prediction technologies using supercomputing.

Over the past six years, PeptiDream has established funded discovery collaborations with 16 leading pharmaceutical companies; Amgen, AstraZeneca, Bristol-Myers Squibb, Lilly, GlaxoSmithKline, Novartis, Mitsubishi Tanabe, Daiichi Sankyo, Merck, Sanofi, Teijin, Kyorin, Ipsen, Genentech, Shionogi, and Asahi Kasei Pharma all of which are active and ongoing. In addition, PeptiDream has transferred its PDPS discovery platform for broad use to Bristol-Myers-Squibb, Novartis, Lilly and Genentech.

Comment from Patrick Reid SVP and Keiichi Masuya VP of PeptiDream Inc.

We are very excited about initiating this collaboration with Tokyo Tech, one of the world-leaders in applying supercomputing to in silico drug discovery and development. The essence of this collaboration will be to combine PeptiDream's extensive knowledge of constrained peptide therapeutics with Tokyo Tech's extensive expertise in in silico molecule simulation and prediction methodologies and technologies to better predict, design, discover, and development better constrained peptide therapeutics.

In Silico Discovery and Development of Constrained Peptides

About PeptiDream Inc.

PeptiDream Inc. is a public biopharmaceutical company founded in 2006 employing the proprietary PDPS, a state-of-the-art highly versatile discovery platform which enables the production of highly diverse (trillions) non-standard peptide libraries with high efficiency, for the identification of highly potent and selective hit candidates, which then can be developed into peptide-based or small molecule-based therapeutics. PeptiDream aspires to be a world leader in drug discovery and development to address unmet medical needs and improve the quality of life of patients worldwide.

* in silico

In silico is an expression used widely in scientific studies meaning "performed on computer or via computer simulation." In silico study is one of computational analyses which have the potential to speed the rate of drug discovery and development by predicting how drugs interact with the body and with pathogens.

School of Computing

School of Computing
—Creating the Future Information Society—

Information on School of Computing inaugurated in April 2016

School of Computing

Schools, Departments, and Institute for Liberal Artsouter

Further information

Professor Yutaka Akiyama
School of Computing, Tokyo Institute of Technology

Tel +81-3-5734-3645

SVP Patrick C Reid

PeptiDream Inc.

Tel +81-3-3468-9022


Center for Public Affairs and Communications
Tokyo Institute of Technology

Tel +81-3-5734-2975