NVIDIA and Mitsui Launch Japan’s First Generative AI Supercomputer to Accelerate Drug Discovery

By Bio-IT World Staff  

April 14, 2023 | In collaboration with NVIDIA, Mitsui, Japan, recently launched Tokyo-1, a supercomputer designed to boost Japan’s $100B pharmaceutical industry. The project features 16 NVIDIA DGX H100 AI systems—a part of NVIDIA’s NGX enterprise AI platform—to simulate high-resolution molecular dynamics and generate AI models for accelerated drug discovery. 

Japan commands the world’s third-largest pharmaceutical industry behind the United States and China. Yet, it struggles to produce and approve drug products without significant lags and delays, even for therapeutics already available in other parts of the world. Their pipeline issues were only magnified when many companies raced to develop COVID-19 vaccines during the pandemic. As such, Japanese pharma giants and startups hope to adopt AI on a broader scale, thereby increasing production speed and capacity. 

“Japanese pharma companies are experts in wet lab research, but they have not yet taken advantage of high-performance computing and AI on a large scale,” said Yuhi Abe, general manager of Mitsui's digital healthcare business department, in a press release. “With Tokyo-1, we are creating an innovation hub that will enable the pharma industry to transform the landscape with state-of-the-art tools for AI-accelerated drug discovery.” 

The Tokyo-1 supercomputer comprises 16 multi-nodal NVIDIA DGX H100 systems—complete with eight NVIDIA H100 Tensor Core GPUs each—that support molecular dynamics simulations, large language model training, quantum chemistry, transformer model training, and molecular design. 

Tokyo-1 also includes NVIDIA’s BioNeMo drug discovery software and service, enabling large language models for multi-omics data, allowing researchers to scale their AI models by billions of parameters related to protein structure prediction, small molecule generation, and pose prediction estimation. 

Xeureka—a Mitsui subsidiary—will operate Tokyo-1 and plans to add additional nodes after the project launches later this year. Customers will access Tokyo-1 through a dedicated server and receive technical support directly from Xeureka and NVIDIA, with the option to attend various workshops on accelerated computing. Xeureka will also offer software solutions for molecular dynamics, docking, and free-energy perturbation calculations as add-ons. 

“Tokyo-1 is designed to address some of the barriers to implementing data-driven, AI-accelerated drug discovery in Japan,” said Hiroki Makiguchi, product engineering manager in the science and technology division at Xeureka. “This initiative will uplevel the Japanese pharmaceutical industry with high-performance computing and unlock the potential of generative AI to discover new therapies.” 

Leading pharma companies—such as Astellas Pharma, Daiichi-Sankyo, and Ono Pharmaceutical—are anxious to employ Tokyo-1 to bolster sales, manufacturing, research, and development. Astellas Pharma sees the supercomputer as a versatile tool with the potential to maximize patient outcomes and reduce healthcare costs.  

“AI and large-scale simulations can be used for applications including small molecule compounds, antibodies, gene therapy, cell therapy, targeted protein degradation, engineered phage therapy, and mRNA medicine,” said Kazuhisa Tsunoyama, head of digital research solutions, advanced informatics, and analytics at Astellas. 

Ono Pharmaceutical believes Tokyo-1 to be a powerful key to unlocking oncology, immunology, and neurology discoveries. “Training AI models requires significant computational power, and we believe that the massive GPU resources of Tokyo-1 will solve this problem,” said Hiromu Egashira, director of the Drug Discovery DX Office in the drug discovery technology department at Ono. “We envision our use of the DGX supercomputer to be very broad, including high-quality simulations, image analysis, video analysis, and language models.” 

After its initial launch later this year, Tokyo-1 will be released to Japanese medical-device companies and global healthcare startups in the NVIDIA Inception program, a free resource offering support and exposure to heighten business growth and visibility.