Flagship Pioneering Unveils Expedition Medicines to Expand the Boundaries of Small Molecule Medicines with Generative Design

After three years of internal development, Expedition is building a generative AI platform for covalent drug discovery, supported by a $50M initial commitment from Flagship Pioneering

Multi-target exploration agreement in prostate cancer initiated under Flagship’s strategic partnership with Pfizer

CAMBRIDGE, Mass., October 22, 2025 — Flagship Pioneering, a scientific innovation engine for transformative platforms and products, today unveiled Expedition Medicines™, a company pioneering generative covalent chemistry to expand the boundaries of medicine. Following three years of in-house development, Flagship has committed an initial $50 million to support scaling Expedition’s platform for generating small molecule medicines to any target and to further develop its discovery programs in oncology, immunology, and other well-defined diseases. In addition, Expedition recently initiated a multi-target exploration agreement to identify novel therapeutic candidates for prostate cancer under Flagship’s strategic collaboration with Pfizer.

“Today, the majority of proteins known to be involved in disease have no medicines that can reach them. By harnessing AI and quantum covalent chemistry to rewrite what’s possible in drug design, Expedition is transforming these undruggable proteins into tractable targets,” said Noubar Afeyan, Ph.D., Founder and CEO of Flagship Pioneering and Co-Founder and board director of Expedition Medicines. “Expedition is able to explore entirely new territory thanks to a unique insight from the quantum chemistry of protein-small molecule interactions, generative AI, and a team that bridges medicinal chemistry, artificial intelligence, and therapeutic development to redefine the drug discovery paradigm.”

Proteins with smooth surfaces have been considered undruggable because they lack the features for small molecules to latch onto and reversibly bind. Rather than this traditional “binding-first” approach, Expedition’s approach is driven by its discovery of a “reaction-first” covalent chemical insight, where quantum interactions between small molecules and reactive parts of protein surfaces enable high potency binding even in shallow pockets of proteins.

Grounded in this insight, Expedition is building a quantum chemistry AI platform that is fueled by an industry-leading chemoproteomic screening and data generation engine. The platform has enabled Expedition to access new protein targets, create high-quality quantitative molecular interaction data at scale, and train generative chemistry models to deliver de novo small molecules that effectively interact with the most elusive targets in the proteome, such as transcription factors, adaptor proteins, regulators, and protein-protein interfaces – mechanisms that have been implicated as central regulators of a wide range of diseases.

“AI is transforming biology by learning the grammar of proteins and DNA. At Expedition, we are pioneering the same leap for small molecules grounded in the quantum chemistry of covalent interactions and fueled by unprecedented experimental data,” said Molly Gibson, Ph.D., Co-Founder, CEO, and board director of Expedition and Origination Partner at Flagship Pioneering. “Our models are learning the rules of how molecules react and bind to any protein surface in order to make small molecule programmability a reality.”

Expedition has initiated research to identify new potential therapeutic candidates for prostate cancer as part of Flagship’s strategic partnership with Pfizer, which seeks to create a pipeline of innovative medicines. The research, which is subject to the terms of the 2023 agreement between Flagship and Pfizer, will leverage Expedition’s platform in an effort to identify novel targeted molecules for previously undruggable targets with known correlation to prostate cancer disease progression and treatment resistance.

Together with Afeyan and Gibson, Expedition is led by Nathan Stebbins, Ph.D., Co-Founder and Chief Strategy Officer and Senior Principal at Flagship Pioneering; Dean Stamos, Ph.D., Co-Founder and CSO – Chemistry & Proteomics and Flagship Science Partner; Todd Kinsella, Ph.D., CSO – Drug Discovery and Translation and Flagship Science Partner; Henry van den Bedem, Ph.D., Chief Technology Officer; and Marie Yurkovich, Ph.D., Co-Founder and Head of Strategy and Operations at Expedition and Operating Principal at Flagship. Kinsella and Stamos previously led biology and chemistry innovation, respectively, at Vividion Therapeutics, and van den Bedem previously led Machine Learning at Atomwise. Geoffrey von Maltzahn, Ph.D., Co-Founder of Expedition and General Partner at Flagship Pioneering, will serve on the company’s board.

About Expedition Medicines

Expedition Medicines is building AI to expand the boundaries of medicine. Its quantum chemistry AI platform, powered by an industry-leading chemoproteomics data generation engine, learns the rules of molecular reactivity to generate small molecule drugs against disease-driving proteins that have long been considered undruggable. The platform has enabled the creation of a pipeline of potential first-in-class therapies across oncology, immunology, and other well-defined diseases. Expedition was founded by Flagship Pioneering in 2022. For more, visit www.expeditionmedicines.com and LinkedIn.

About Flagship Pioneering

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, operating with $14 billion of assets under its direction as of its latest capital raise, announced in July 2024. The current Flagship ecosystem comprises more than 40 companies, including Foghorn Therapeutics, Generate Biomedicines, Inari, Indigo Agriculture, Lila Sciences, Moderna, Sana Biotechnology, Tessera Therapeutics and Valo Health.