Japan and AI Drug Discovery Innovation
Japan and AI Drug Discovery Innovation
Revolutionizing Drug Development
Welcome back to another edition of MetaphysicalCells.
Today is all about Japan and AI Drug Discovery innovation.
AI Drug Discovery in Japan
👘 On April 22, 2024, Takeda, Astellas and Sumitomo Mitsui Banking (a subsidiary of Sumitomo Mitsui Financial Group, Inc) Announced a Master Agreement to Establish Joint Venture Company. The new company will be dedicated to the incubation of early drug discovery programs, primarily originating from Japan and toward the creation of innovative therapeutics. The name of the new venture is to be determined, the CEO is going to be Toshio Fujimoto, MD, MBA and will be located at the Shonan Health Innovation Park in Fujisawa, Kanagawa, Japan. The initial capital of the new venture is approximately 600 million yen (including capital reserve) with capital structure: Astellas 33.4%, SMBC 33.2%, Takeda 33.4%.
Few words about Astella, SMBC, Takeda and Toshio Fujimoto:
Astellas Pharma Inc (TYO: 4503) is a Japanese multinational pharmaceutical company, formed on 1 April 2005 from the merger of Yamanouchi Pharmaceutical Co., Ltd and Fujisawa Pharmaceutical Co., Ltd. Astellas has been driving forward digital transformation initiatives throughout its value chain, combining the capabilities of AI and robots with the skills and experience of people, and creating a state-of-the-art drug discovery platform that enables the development of high-quality drugs in a shorter time (A Human-in-the-Loop Drug Discovery Platform Integrating Humans, AI, and Robots).
On November 17, 2023, the Japan-based University of Tsukuba and Astellas announced a strategic partnership to accelerate the digitalization of the drug discovery research field, as well as the development of the life science ecosystem in Tsukuba and Kashiwa-no-ha, and to further accelerate innovative drug discovery research and development (medicine, biotechnology and AI/digital analytics).
Sumitomo Mitsui Banking Corporation/SMBC (TYO: 8316) is a Japanese multinational banking financial services institution owned by Sumitomo Mitsui Financial Group, Inc. It is headquartered in Yurakucho, Chiyoda, Tokyo, Japan. The group operates in retail, corporate and investment banking segments worldwide. SMBC was established in 2001 through the merger of The Sakura Bank, which originated from the Mitsui zaibatsu that was founded as Mitsui Bank in 1876, and The Sumitomo Bank, which originated from the Sumitomo zaibatsu and was founded in 1895.
On November 29, 2018, Sumitomo Mitsui Financial Group, Inc, Sumitomo Corporation (TYO: 8053), Sumitomo Mitsui Banking Corporation, Sumitomo Mitsui Finance and Leasing Company, Limited (“SMFL”), and SMBC Aviation Capital Limited executed a part of the Reorganization of the Sumitomo Mitsui Financial Group and Sumitomo Corporation Joint Leasing Partnership stipulated in the final agreement concluded on March 30, 2018. By transforming SMFL into an entity in which both companies have equal ownership, Sumitomo Mitsui Financial Group and Sumitomo Corp will further strengthen their collaborative framework so that they can realize both a material increase in the competitiveness and the sustainable growth of their general leasing business through the strategic joint partnership.
Summit Pharmaceuticals International, the drug research and development arm of Sumitomo Corporation one of the world's biggest general trading firms, entered in 2021 in collaboration with the AI drug discovery platform CytoReason from Israel. CytoReason develops computational disease models for drug discovery and development using AI and these models simulate human disease on a cellular level, in this way reducing the need for animal trials and making human trials "more focused and accurate".
Toshio Fujimoto, MD. MBA. is a founding CEO of iPark Institute Co. Ltd, which has spun out from Takeda Pharmaceutical (NYSE: TAK) in April 2023 to operate Shonan Health Innovation Park (iPark). Shonan iPark is the biggest science park in Japan established in 2018 to foster open innovation.
For more about Takeda (TYO: 4502): Takeda and AI Drug Discovery.
Notable Acquisition: On February 08, 2023, Nimbus Therapeutics, LLC, a clinical-stage company in US using a powerful computational drug discovery engine, announced the closing of Takeda’s acquisition of Nimbus Lakshmi, Inc, a wholly-owned subsidiary of Nimbus, and its tyrosine kinase 2 (TYK2) inhibitor program, which includes the oral, selective allosteric TYK2 inhibitor NDI-034858, now known as TAK-279.
The completion of this acquisition triggered a $4 billion upfront payment from Takeda to Nimbus, which is also eligible to receive up to $2 billion total in sales-based milestone payments.
🎴 On January, 24, 2024, RevolKa has signed a contract research agreement with Sekisui Chemical. RevolKa is a venture-backed biotech company based in Japan providing a game-changing protein engineering technology platform that is creating highly functional proteins by using its AI-driven platform (aiProtein).
On February 1, 2024, RevolKa announced that Norio Hamamatsu, Ph.D. has been named President & CEO and closed a 150 million JPY (US$1.0M) Series A extension financing. D3 LLC (Tomoya Nagata, Managing Partner, CEO) co-led the Series A extension round along with DEEPCORE Inc (Katsumasa Niki, President & CEO) and the existing investor, TOHOKU University Venture Partners Co., Ltd (Tetsuro Higuchi, President & CEO):
D3 LLC is a healthcare-focused investment, business and consulting company in Japan,
DEEPCORE Inc in Japan is a venture capital focused on companies in the fields of AI and advanced technologies and
TOHOKU University Venture Partners (THVP) is a wholly owned subsidiary of Tohoku University.
On April 19, 2024, RevolKa and La Jolla Institute for Immunology (LJI) agreed to start a research collaboration to create antigens for the next-generation vaccines. LJI and RevolKa will synergize LJI’s deep knowledge of immunology and RevolKa’s power of AI-driven protein engineering.
🇯🇵 On August 8, 2023, Japan unveiled its latest development on its “Startup Development Five-year Plan”, that started in November 2022. The program comes through a collaboration with Deep Tech Valley Kansai and aims to boost the Japanese startup ecosystem by investing 10 trillion yen, creating 100,000 new startups and nurturing 100 unicorns by 2027.
A standout among Kansai’s aspiring startups is NUProtein, distinguished for its expertise in the large-scale production of recombinant proteins, across various industries, including cultivated meat, drug discovery and biomass energy.
🏯 Elix is an AI drug discovery company (CEO: Shinya Yuki/Headquarters: Tokyo Japan) that launched the “Elix Discovery” an all-in-one platform that provides everything needed for AI drug discovery, from models for property prediction and molecular design to AI consulting and implementation support. The key modules of Elix Discovery are: Elix Predict (activity against a target, physicochemical properties and ADMET properties), Elix Create (molecular design with desired properties: target activity, physicochemical properties, ADMET and ease of synthesis) and
Elix Assist (methods for efficiently training AI models).
In 2022, Elix started providing AI consulting and implementation support to Kaken Pharmaceutical Co Ltd (TYO: 4521) by using the Elix Discovery. Kaken Pharmaceutical (President and Representative Director: Hiroyuki Horiuchi/ Headquarters: Tokyo) was established in 1948 with its roots in the Riken Foundation, which has produced many extremely important scientists in the history of Japanese science, including Yoshio Nishina, considered the father of modern physics, as well as Nobel Prize winners Hideki Yukawa and Shinichiro Tomonaga.
On March 24, 2022, Elix commenced a joint research on the retrosynthetic analysis module "Elix Synthesise" with Shionogi & Co., Ltd (TYO: 4507)(President and CEO: Isao Teshirogi/Headquarters: Osaka, Japan 🍜) a Japanese pharmaceutical company best known for developing Crestor for the purpose of verifying retrosynthetic analysis using chemical reaction data from Shionogi.
💴 Healx (Cambridge UK, 2014) uses AI to match existing drugs with rare diseases. Their AI platform uses NL processing to extract disease knowledge from published sources and to complement biomedical databases and proprietary curated data. Healx’s data is integrated in the form of the largest, rare disease-focused Knowledge Graph, that shows prioritized hidden and novel connections between drugs and diseases.
On August 5, 2021, it was announced that Healx will work with Ono Pharmaceutical Co Ltd (TYO: 4528), one of the largest pharmaceutical companies in Japan, to find multiple new therapeutic indications for Ono’s proprietary assets.
🎎 ThinkCyte (with offices in Tokyo, Japan and San Carlos, California with a $ 3.2M/ JPY 350M seed-financing round in 2018) pioneered the Ghost Cytometry, a proprietary AI-based, label-free cell sorting technology with partners in major global biopharmaceutical companies and leading academic research institutes.
On Jul 1, 2020, Hitachi Ltd (TYO: 6501) and ThinkCyte (CEO: Waichiro Katsuda) announced a collaboration to develop an AI-driven Cell Analysis and Sorting System.
On May 12, 2021, Sysmex Corporation (TYO: 6869) (Kobe, Japan; Chairman and CEO: Hisashi Letsugu) and ThinkCyte, announced the signing of joint development and investment agreements for the commercialisation of an AI-based cell analysis technology.
On May 19, 2021, ThinkCyte secured a $26M in Series B Financing. And on Jun 23, 2022, ThinkCyte established its presence in the Bay Area and strengthened the senior management team with industry veterans.
In 2023, Toyoda Gosei Co., Ltd invested in ThinkCyte.
🎌 On May 17, 2022, Fujitsu Ltd (TYO: 6702) and RIKEN (Japan’s largest comprehensive research institution) launched a joint research project on next-generation IT drug discovery technology utilizing the supercomputer Fugaku, aiming to accelerate digital transformation in drug discovery. The supercomputer Fugaku (used to accelerate molecular simulations) combines Fujitsu’s DeepTwin AI technology, which accurately acquires quantitative features from complex data by unsupervised learning, with molecular dynamics simulation using RIKEN’s AI drug discovery simulation technology.
On October 10, 2023, Fujitsu Limited and the “High Performance Computing and AI-driven Drug Development Platform Division” of the RIKEN Center for Computational Science, have developed an AI drug discovery technology that can predict structural changes of proteins from electron microscope images as a 3D density map in wide range by utilizing generative AI. Fujitsu also plans to make its prediction technology for protein structural changes available as an AI innovation component of the Fujitsu Kozuchi. Fujitsu Kozuchi is a cloud-based AI platform that enhances the productivity and creativity of your business and supports Sustainability Transformation.
🎍Chugai Pharmaceutical Co Ltd (TYO: 4519) (a drug manufacturer operating in Japan controlled by Hoffmann-La Roche (Roche and AI Drug Discovery) created a self-made AI-based antibody discovery technology named ‘Malexa-Li’ which optimizes the antibody discovery process with training data of a ML model that was provided by analyzing sequence information accumulated from the company’s research conducted over many years.
Moreover, in 2022 Chugai Pharmaceutical and IBM Japan Ltd announced that they have established a digital infrastructure to support new operations of Chugai's production function, with the aim of realizing a digital plant.
On July, 17, 2023, Chugai Pharma and Omron announced that they will be focusing on automation for drug discovery research. In particular, Chugai Pharmaceutical Co., Ltd (President and CEO: Osamu Okuda), OMRON Corporation (Shimogyo-Ku, Kyoto, Japan; President and CEO: Junta Tsujinaga) and OMRON SINIC X Corporation (Bunkyo-ku, Tokyo; President and CEO: Masaki Suwa) have been conducting joint research toward the realization of a flexible lab automation system with greater human compatibility than existing systems, and they are now embarking on a verification testing of the system at Chugai’s new research center, Chugai Life Science Park Yokohama.
🎋 On April 05, 2022, the French AI drug discovery company Iktos announced a strategic collaboration agreement with Teijin Pharma Ltd based in Japan, in order to apply Iktos's generative modeling technology (Computer Aided Drug Design, CADD) to several Teijin Pharma’s small molecule preclinical drug discovery programs. Teijin Pharma is committed to providing healthcare solutions in the priority fields of bone, joint, rehabilitation, neurology, respiratory, cardiovascular and metabolic diseases. Teijin’s Pharma parent organization is Teijin (TYO: 3401), a Japanese chemical, pharmaceutical and information technology company.
Iktos also signed a collaboration agreement on 30rd March of 2022 with Ono Pharmaceutical Co Ltd from Japan with a focus on oncology, immunology and neurology research. Under this agreement, Iktos will apply its de novo ligand and structure-based generative modeling technologies and software Makya and its AI-based retrosynthesis analysis and planning tool Spaya to complement Ono’s drug discovery capabilities.
Iktos also has a collaboration with Curreio, Inc, a Japanese company specializing in structural analysis of biomolecules using cryo-electron microscopy.
🍱 On Nov. 11, 2021, Mitsui & Co., Ltd (TYO: 8031) one of the largest sogo shosha (general trading companies) in Japan (President and CEO: Kenichi Hori) has established a new company, Xeureka Inc, to engage in early drug discovery research. Xeureka uses the latest computational technology, including cutting-edge AI and simulations, in order to improve the efficiency and success rate of drug discovery research (Target Analysis, Ultra Large Scale Virtual Screening, and Large Scale Binding Free Energy Calculation).
On March, 22, 2023, Mitsui and NVIDIA have joined forces to develop what they say is the world’s first generative AI supercomputer, the Tokyo-1 supercomputer, operated by Mitsui’s Xeureka subsidiary will provide clients with access to 16 NVIDIA DGX H100 nodes supporting molecular dynamics simulations, large language model training, quantum chemistry, generative AI models that create novel molecular structures for potential drugs, and more.
Mitsui & Co., Ltd (三井物産, Mitsui Bussan) it is part of the Mitsui Group (三井グループ, Mitsui Gurūpu) that is a Japanese corporate group and keiretsu (a set of companies with interlocking business relationships and shareholdings that have dominated the Japanese economy since the second half of the 20th century) that traces its roots to the zaibatsu groups that were dissolved after World War II.
🍡 Back in 2019, the Japan-based NEC Corporation (a Japanese multinational information technology and electronics corporation, headquartered in Minato, Tokyo) announced that it would expand the application of its AI technologies to drug development and also acquired at the time Norway-based OncoImmunity (NOI), an AI company for immunotherapy.
On March 31, 2023, NEC and NOI announced that NOI will be realigned as a subsidiary of NEC Bio B.V. (NB) in Hilversum, Netherlands, a newly established wholly owned subsidiary of NEC. At the same time, NEC has established another new company, NEC Bio Therapeutics (NBT) in Mannheim, Germany (Japan's NEC establishes European subsidiaries for strengthening global AI drug development biz).
🍜 SyntheticGestalt in Tokyo, Japan is a company developing ML models for drug discovery and software for facilitating and automating research in the life-sciences industry. Its AI platform has a cloud-based, scalable structure and can make predictions on large libraries, making it possible to predict physicochemical and ADME/ Tox properties and early toxicity, as well as enzyme functions.
On January 12, 2024, SyntheticGestalt and Enamine announced the start of a joint effort to create a suite of AI models that will enable the generation of synthetically accessible biologically active compounds with optimized physicochemical and ADME/ Tox properties. Enamine has developed the world’s largest reputable collection of chemical compounds, carefully designed and produced for Life Science industries.
SyntheticGestalt will enhance its pre-trained AI model using the data provided by Enamine. It is expected to become the largest pre-trained model in the world based on the 3D structures of the compounds, to improve the predictive accuracy of SyntheticGestalt’s ML models.
SyntheticGestalt founded in 2018 by Atsuhiro Hagiwara has raised a total of $11M so far.
🍙 Based in Oxford, UK, Exscientia established in 2019 a subsidiary, Exscientia K.K., headquartered in Osaka, Japan and led by Dr Daisuke Tanaka, an experienced medicinal chemist who previously was director of the Innovative Chemistry Group at Sumitomo Dainippon Pharma/DSP. This resulted in the successful delivery by Exscientia to DSP of a completely novel candidate DSP-1181 that was ready for application for US clinical trials in just 12 months. The establishment of Exscientia K.K. will enable the company to target Japan’s many pharma companies.
Unfortunately, during 2021 DSP-1181 was discontinued for development in Japan since the Phase I study did not reach its expected criteria. Despite this, they produced two more compounds, DSP-0038 and DSP-2342, still continuing in phase 1 studies.
Sumitomo Dainippon Pharma (Hiroshi Nomura, CEO) was formed in 2005 from the merger of Dainippon Pharmaceutical Co. and Sumitomo Pharmaceuticals.
On April 1, 2022, the company was renamed from Sumitomo Dainippon Pharma to Sumitomo Pharma Co Ltd (TYO: 4506).
🎴 Based in Tokyo in Japan Modulus Discovery Inc changed its name to Alivexis Inc on March 11, 2024 and is a preclinical-stage drug discovery company developing small-molecule treatments for conditions such as cancer, inflammatory disorders, and rare genetic conditions. Alivexis (S. Roy Kimura, PhD Co-founder & CEO) is utilizing a supercomputer for simulating target proteins. Their intelligent supercomputing platform comprises cutting-edge technologies including GPU-accelerated physics-based simulations, ultra large-scale virtual screening algorithms and specialized ML algorithms built for specific discovery programs.
On August, 03, 2023, Alivexis (at the time still Modulus Discovery, Inc) and PeptiDream Inc, a public Kanagawa, Japan-based biopharmaceutical company (President and CEO: Patrick C. Reid, (Tokyo: 4587) announced the nomination of the first clinical development candidate arising from the companies’ strategic drug discovery partnership.
Founded in 2006, PeptiDream employs its proprietary Peptide Discovery Platform System (PDPS) technology that includes key disciplines required in preclinical research including discovery biology, medicinal chemistry, structural biology, bioinformatics, molecular modeling and pharmacological profiling. PDPS
enables the production of highly diverse (trillions) non-standard peptide libraries with high efficiency, for the identification of highly potent and selective macrocyclic peptide candidates, which then can be developed into peptide-based, small molecule-based, peptide-drug conjugate and multi-functional peptide conjugates based therapeutics and diagnostics.
Until next time 🌸,