TLDR: Flagship Pioneering has unveiled Expedition Medicines, a new company dedicated to transforming small molecule drug discovery through generative covalent chemistry and an AI-powered platform. Backed by an initial $50 million commitment from Flagship, Expedition aims to tackle previously ‘undruggable’ disease-driving proteins and has already initiated a multi-target research agreement with Pfizer for prostate cancer.
CAMBRIDGE, Mass. – October 22, 2025 – Flagship Pioneering, a leading scientific innovation enterprise, today announced the launch of Expedition Medicines, a groundbreaking company focused on expanding the frontiers of small molecule therapeutics through generative covalent chemistry. The new venture emerges from three years of intensive in-house development by Flagship and is supported by an initial commitment of $50 million.
Expedition Medicines is poised to address a significant challenge in drug discovery: the vast majority of disease-related proteins that have long been considered ‘undruggable’ due to their smooth surfaces, which lack the traditional binding pockets for small molecules. By integrating generative artificial intelligence (AI) with quantum covalent chemistry, Expedition aims to transform these intractable targets into viable therapeutic opportunities.
Noubar Afeyan, Ph.D., Founder and CEO of Flagship Pioneering and Co-Founder and board director of Expedition Medicines, emphasized the company’s ambitious mission. “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 Dr. Afeyan. He added that Expedition’s ability to explore novel territory stems from a unique understanding of quantum chemistry in protein-small molecule interactions, generative AI, and a multidisciplinary team spanning medicinal chemistry, artificial intelligence, and therapeutic development.
Molly Gibson, Ph.D., Co-Founder, CEO, and board director of Expedition Medicines, and an Origination Partner at Flagship Pioneering, highlighted the transformative role of AI. “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,” stated Dr. Gibson. She further explained that the company’s models are designed to learn the intricate rules of how molecules react and bind to any protein surface, thereby making small molecule programmability a reality.
Expedition Medicines has already established a pipeline of potential first-in-class therapies across various therapeutic areas, including oncology, immunology, and other well-defined diseases. In a significant development, the company has initiated a multi-target exploration agreement with Pfizer to identify novel therapeutic candidates for prostate cancer. This collaboration falls under Flagship’s broader strategic partnership with Pfizer, aiming to create a robust pipeline of innovative medicines.
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Flagship Pioneering, founded in 2000, has a rich history of inventing and building platform companies with the potential to revolutionize human health and sustainability. With over 100 scientific ventures launched and $14 billion in assets under management, Flagship’s ecosystem currently comprises more than 40 biotechnology and health companies. Dr. Gibson brings extensive experience to her role, having previously co-founded Generate Biomedicines and served as its chief strategy and chief innovation officer for five years.
