Fathom Therapeutics announced that it has raised $47 million in an oversubscribed Series A financing to accelerate development of its AI- and physics-driven drug discovery platform and expand its pipeline of next-generation medicines.
The round was led by Sutter Hill Ventures, with participation from Chemistry, Alexandria Venture Investments, and NY Ventures, among others. The company, formerly known as Atommap, is focused on combining quantum chemistry and artificial intelligence to design novel small-molecule therapies.
At the core of Fathom’s platform is Microcosmos, a proprietary drug design engine that simulates protein motion at atomic resolution. The system uses physics-based modeling to generate dynamic data on how proteins behave inside living cells, enabling the design of molecules that can more precisely influence biological processes. The platform is designed to overcome limitations of traditional drug discovery approaches, which often rely on static representations of proteins.
Fathom reports that its technology can accelerate modeling of protein dynamics by up to 10,000 times without sacrificing accuracy. Early results include the generation of novel drug candidates targeting previously “undruggable” proteins, with some candidates produced within weeks and now advancing toward clinical development.
The company was founded by Huafeng Xu, Yujie Wu, and Jesus Izaguirre, who bring deep expertise in computational biology, molecular modeling, and AI-driven drug discovery. The leadership team has collectively advanced 19 drugs into the clinic, including seven that have received FDA approval.
The new capital will be used to scale Fathom’s lab-in-the-loop capabilities, expand its internal discovery programs targeting high-impact diseases, and deepen partnerships with external collaborators. The company also maintains an active pipeline and multiple discovery partnerships.
Alongside the financing, Fathom announced key leadership additions, including the appointment of Mandana Honu as Chief Business Officer and Diala Ezzeddine to its board of directors. The company has also established a Scientific Advisory Board featuring experts from across biotech and pharmaceutical research.
The funding highlights continued investor interest in AI-driven drug discovery platforms, particularly those that integrate physics-based simulations with machine learning to improve the speed and precision of therapeutic development.
KEY QUOTES:
“Current drug discovery efforts are limited by reliance on static structures of isolated proteins. Microcosmos is a world model of drugs in living cells that surpasses these limitations by translating accurate quantum mechanical calculations to measurable cellular outcomes.”
Huafeng Xu, Co-Founder And CEO, Fathom Therapeutics
“We backed Huafeng because he wanted to rethink how machines understand molecules, combining the best of physics and machine learning to actually move the frontier in computational drug design. 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.”
Keith Loebner, Managing Director, Sutter Hill Ventures
“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. We’re excited to back Fathom as they work to build medicines that would be impossible to create any other way.”
Ethan Kurzweil, Co-Founder And Managing Partner, Chemistry
“We started Fathom to build a flywheel for new small molecule medicines that previously seemed impossible.”
Huafeng Xu, Co-Founder And CEO, Fathom Therapeutics
