How a Flagship Pioneering biotech is using artificial intelligence to unlock new cancer drugs and reshape protein chemistry
For decades, scientists have faced a frustrating problem: thousands of proteins known to cause disease remain “undruggable.” Their surfaces are too smooth or too shallow for medicines to latch onto—leaving many illnesses, especially cancers, beyond the reach of modern drugs.
Now, Expedition Medicines, a biotech startup backed by Flagship Pioneering, believes it has found a way to change that.
Using artificial intelligence and quantum chemistry, the Cambridge, Massachusetts–based company has developed a platform that learns nature’s own rules for how small molecules bind to proteins—even those long considered impossible to target.
And with a strategic cancer research alliance with Pfizer, Expedition is wasting no time putting its discovery engine to work.
Decoding Nature’s Chemistry Through AI
“Nature already knows how to bind to these elusive proteins—we just haven’t been able to understand it,” said Molly Gibson, Expedition’s co-founder and CEO.
Expedition’s proprietary chemoproteomics platform studies how small molecules interact with more than 20,000 protein sites across the human proteome. By analyzing those interactions, the platform generates detailed chemical data—how and where a small molecule forms a covalent bond with a specific amino acid on a protein.
Then, using generative AI and quantum chemistry models, Expedition translates that data into a deeper understanding of how molecules naturally form bonds—effectively “learning” the language of chemistry that governs protein binding.
“By learning from nature,” Gibson said, “we’ve identified latent catalytic sites across the proteome that, when viewed from a new chemical perspective, can form bonds that were previously thought impossible.”
Beyond Discovery: Building Drugs for the Undruggable
Traditional drug discovery often relies on screening massive libraries of molecules to see what sticks to a protein target. The problem is, the easy targets are already hit, and scaling up those libraries becomes costly and inefficient.
Expedition flips that process on its head. Instead of screening blindly, its AI-driven approach predicts how and where a molecule can bind, even on smooth or featureless protein surfaces.
The company’s technology produces a quantitative “target engagement score”, showing exactly how strongly a molecule bonds with a specific protein site—data that feeds back into its learning models to improve predictions over time.
According to Gibson, this creates a “virtuous cycle” of discovery, enabling faster, smarter drug design.
Flagship’s Next Big Bet
Founded three years ago, Expedition Medicines joins an elite roster of Flagship Pioneering companies that explore the frontiers of the proteome. Flagship’s portfolio also includes ProFound Therapeutics, which searches for previously unknown proteins, and Prologue Medicines, which explores the viral proteome.
But Expedition’s focus is distinct. Instead of discovering new biology, it targets known disease-causing proteins where the biology is clear but the chemistry is not.
The startup’s founding team includes scientists behind Vividion Therapeutics, a company acquired by Bayer in 2021 for $1.5 billion upfront for its groundbreaking proteome analysis platform.
Like Vividion, Expedition aims to create small molecule drugs that can reach targets previously considered unreachable. But Gibson says Expedition’s edge lies in learning from nature through data-driven chemistry rather than brute-force experimentation.
A Powerful Partnership with Pfizer
Expedition’s potential has already caught the attention of industry giant Pfizer. Under a multi-target collaboration that began through Flagship’s 2023 partnership with the pharma company, Pfizer and Expedition are working together on prostate cancer research.
“They brought the targets to us,” Gibson explained. “We’re generating the chemistry.”
The partnership underscores the growing confidence major drugmakers have in AI-driven drug discovery, especially for cancer and immunology, which are Expedition’s primary focus areas.
The Future of Drug Discovery
Backed by $50 million in initial funding from Flagship, Expedition is now emerging from stealth and planning to expand its pipeline. The company’s AI and quantum chemistry platform is indication-agnostic, meaning it could eventually apply to diseases far beyond cancer—potentially reshaping how scientists design inhibitors, activators, and protein degraders.
“Our mission,” said Gibson, “isn’t just to discover new drugs—it’s to rewrite the chemistry playbook for how we make them.”
With its mix of cutting-edge science, bold vision, and big-name backing, Expedition Medicines may be charting a new era in AI-powered drug discovery, one where even the most stubborn proteins are finally within reach.
The Takeaway
By fusing AI technology with nature’s chemistry, Expedition Medicines is venturing into uncharted biological territory—transforming what once seemed impossible into a new frontier for medicine.
If successful, this AI startup could open the door to treatments for countless diseases that science has struggled to touch—proving that sometimes, the smartest way forward is to learn from nature itself.
