Fathom Therapeutics Raises $47M in Series A Funding

The company plans to use the funds to speed up the growth of its lab-in-the-loop technology and expand its internal research programs focused on major diseases.

Microcosmos, the company’s drug design platform, uses its own algorithms to simulate protein motion at the atomic level, generating data that has been hard to capture at scale. These algorithms make protein modeling 10,000 times faster without sacrificing accuracy. Using physics-based simulations, the system helps design small molecules that change protein behavior to achieve the desired therapeutic effect.

Microcosmos has shown strong early results in helping discover and improve molecules across different targets and drug types. In one example, the Fathom team used it to create new degraders for a target once thought “undruggable.” In just six weeks, the platform produced strong, highly selective candidates that are now being refined for clinical development to address a major unmet medical need.

Fathom has set up a Scientific Advisory Board (SAB) to guide its drug design strategy and pipeline development. The board includes Ian Taylor, former Chief Scientific Officer at Arvinas; Dimitris Agrafiotis, Director at Arsenal Capital Partners and former executive at Novartis and Generate Biomedicines; and Bruce Zetter, a Professor of Cancer Biology at Harvard University and Boston Children’s Hospital.

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"Current drug discovery efforts are limited by reliance on static structures of isolated proteins," said Huafeng Xu, PhD, Co Founder and CEO of Fathom Therapeutics. "Microcosmos is a world model of drugs in living cells that surpasses these limitations by translating accurate quantum mechanical calculations to measurable cellular outcomes."

"We backed Huafeng because he wanted to rethink how machines understand molecules, combining the best of physics and machine learning, actually to move the frontier in computational drug design," said Keith Loebner, Managing Director at Sutter Hill Ventures.

"He and the world-class team he's assembled have demonstrated that their approach not only works, but works better than we imagined. We're proud to lead this round, turning Fathom's field-defining molecular design capability into new medicines for patients." Founded in 1962, Sutter Hill Ventures has previously invested in NVIDIA, Snowflake, Pure Storage, Corcept Therapeutics, GRAIL, and Forty Seven.

"Fathom stood out to us as a company tackling one of the most ambitious and technically difficult challenges in biotech — already showing the real ability to translate computational results into molecules with promising therapeutic profiles," said Ethan Kurzweil, Co-Founder and Managing Partner, Chemistry. "We're excited to back Fathom as they work to build medicines that would be impossible to create any other way."

"I welcome this extraordinary team of scientific and business leaders to our internal leadership, board, and SAB, who bring deep expertise and complementary perspectives across biology, technology, partnering, and translational medicine," said Dr. Xu. "Each of these leaders shares our ambitious goal of pushing the molecular frontier to deliver better therapies to patients, and their combined expertise will accelerate the process of taking each idea to regulatory approval."

About Fathom Therapeutics

Founded in 2023 by Huafeng Xu, Jesus Izaguirre, and Yujie Wu, Fathom Therapeutics is based in New York with a second office in Boston. The company designs drugs using AI and physics based simulations to model protein motion and interactions at the atomic level. Its Microcosmos platform simulates protein behavior to generate the data needed to create small molecules with better therapeutic effects and fewer side effects.

Fathom has its own drug pipeline, works with partners on discovery programs, and has moved its lead program into animal studies. The company was started by the team behind the Anton supercomputer and widely used software for predicting protein-drug binding.

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