Supercomputers On The Hunt For Middle Molecules

Making use of the Tsubame supercomputer at the Tokyo Institute of Technology, Kawasaki City aims to accelerate the discovery and testing of middle molecule drugs.

AsianScientist (Aug. 17, 2017) – Tokyo Institute of Technology (Tokyo Tech) and Kawasaki City have embarked on a unique industry-academia-government partnership to use supercomputers to identify new drug molcules. Called the Program to Industrialize an Innovative Middle Molecule Drug Discovery Flow through Fusion of Computational Drug Design and Chemical Synthesis Technology, the partnership will see both sides jointly conduct R&D and construct infrastructure.

Conventional drug discovery mainly consists of synthesizing small molecules with a molecular weight under 500 daltons (Da), a strategy known as small molecule drug discovery. In recent years, drug discovery has turned to large molecules such as antibodies that have therapeutic properties. However, industrial synthesis of large molecules is difficult and poses numerous issues such as the extremely high cost incurred for creation using animal cells under advanced control conditions.

On the other hand, middle molecules—peptides, nucleic acids and other molecules with a molecular weight of about 500 to 30,000 Da—can be chemically synthesized and may offer benefits that are similar to large molecules. Machine learning, molecular simulation and computational analysis can support and accelerate decision-making for middle molecule drug discovery can help in the selection of candidate compounds for further testing of bio-stability, membrane permeability and toxicity.

The Program will leverage molecular simulation and machine learning by the Tsubame supercomputer of Tokyo Tech for drug design. Through industry-academia-government partnerships including corporations in Kawasaki City, the Program seeks to form an innovation ecosystem that bridges fundamental research and the drug discovery business, thus dramatically improving the efficiency of developing middle molecule drugs.

To implement this research project, the Middle Molecule IT-based Drug Discovery Laboratory (MIDL) will be opened in Tonomachi King Skyfront, an international strategic zone located in Kawasaki City. The MIDL will possess enhanced research functions for middle molecules and will be the world’s first dedicated facility in this field with state-of-the-art computational approaches.

Tokyo Tech will also open a MIDL core facility within its university campus and establish a system to facilitate the cooperation of faculty across different research fields.

“Computational prediction for the bio-stability and cell membrane permeability of middle molecules is very challenging,” said Professor Yutaka Akiyama of the School of Computing at Tokyo Tech. “By using Tokyo Tech’s world-leading supercomputing techniques and extensive experience in machine learning, and by cooperating with many related corporations, I hope that MIDL will provide the world with practical technology for accelerating middle molecule drug discovery.”


Source: Tokyo Institute of Technology; Photo: Shutterstock.
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