Google DeepMind has unveiled an AI system called AlphaProteo that can design novel proteins that successfully bind to target molecules, potentially revolutionising drug design and disease research.
AlphaProteo can generate new protein binders for diverse target proteins, including VEGF-A, which is associated with cancer and diabetes complications. Notably, this is the first time an AI tool has successfully designed a protein binder for VEGF-A.
The system’s performance is particularly impressive, achieving higher experimental success rates and binding affinities that are up to 300 times better than existing methods across seven target proteins tested:
Trained on vast amounts of protein data from the Protein Data Bank and over 100 million predicted structures from AlphaFold, AlphaProteo has learned the intricacies of molecular binding. Given the structure of a target molecule and preferred binding locations, the system generates a candidate protein designed to bind at those specific sites.
To validate AlphaProteo’s capabilities, the team designed binders for a diverse range of target proteins, including viral proteins involved in infection and proteins associated with cancer, inflammation, and autoimmune diseases. The results were promising, with high binding success rates and best-in-class binding strengths observed across the board.
For instance, when targeting the viral protein BHRF1, 88% of AlphaProteo’s candidate molecules bound successfully in wet lab testing. On average, AlphaProteo binders exhibited 10 times stronger binding than the best existing design methods across the targets tested.
The system’s performance suggests it could significantly reduce the time required for initial experiments involving protein binders across a wide range of applications. However, the team acknowledges that AlphaProteo has limitations, as it was unable to design successful binders against TNFɑ (a protein associated with autoimmune diseases like rheumatoid arthritis.)
To ensure responsible development, Google DeepMind is collaborating with external experts to inform their phased approach to sharing this work and contributing to community efforts in developing best practices—including the NTI’s new AI Bio Forum.
As the technology evolves, the team plans to work with the scientific community to leverage AlphaProteo on impactful biology problems and understand its limitations. They are also exploring drug design applications at Isomorphic Labs.
While AlphaProteo represents a significant step forward in protein design, achieving strong binding is typically just the first step in designing proteins for practical applications. There remain many bioengineering challenges to overcome in the research and development process.
Nevertheless, Google DeepMind’s advancement holds tremendous potential for accelerating progress across a broad spectrum of research, including drug development, cell and tissue imaging, disease understanding and diagnosis, and even crop resistance to pests.
You can find the full AlphaProteo whitepaper here (PDF)
See also: Paige and Microsoft unveil next-gen AI models for cancer diagnosis
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