UF Researchers Use Generative AI to Engineer Enzymes and Advance Biotechnology

Wenjun Xie, Ph.D., an assistant professor of medicinal chemistry at the UF College of Pharmacy, has received $100,000 in funding from the Defense Advanced Research Projects Agency (DARPA) to explore AI and machine learning’s role in designing proteins and biomolecules to improve health outcomes. DARPA supports research with transformative potential, and this funding will accelerate efforts in enzyme engineering. Xie is collaborating with Jing Pan, Ph.D., an assistant professor of electrical and computer engineering at the UF Herbert Wertheim College of Engineering, to advance this research.  

By engineering enzymes, scientists can develop therapeutics to treat genetic diseases and design small molecules to target enzymes for various medical applications. Generative AI plays a key role in this process, enabling researchers to analyze enzyme sequences and engineer them more effectively. Unlike traditional AI, generative AI learns from vast datasets, allowing it to model complex biochemical processes. Xie compares this approach to ChatGPT’s ability to understand human language, explaining that in this case, AI is learning the language of proteins, where semantics correspond to physical chemistry principles.  

Xie’s work in enzyme engineering has broad implications, from improving treatments for genetic disorders to advancing industrial biotechnology. However, generative AI alone has limitations in designing novel enzyme activity. To overcome these challenges, Xie is integrating AI with molecular simulations to enhance enzyme design, aiming to develop new catalytic functions beyond those found in nature. Understanding the principles of enzyme catalysis is crucial to achieving this goal, and generative AI provides a unique perspective to systematically explore these principles.  

Xie’s research benefits from the collaborative environment within the UF Department of Medicinal Chemistry, where computational scientists, chemists, and life scientists work together in AI-driven drug discovery, enzymology, bioinformatics, and biochemistry. As one of nine new AI-focused faculty members in the College of Pharmacy and part of a larger AI initiative at UF, Xie is contributing to the university’s leadership in AI research and education. His goal is to design highly efficient enzymes capable of catalyzing any given chemical reaction, a breakthrough that could transform biotechnology and redefine scientific approaches to enzyme engineering.

Source: https://pharmacy.ufl.edu/2025/03/24/using-generative-ai-to-engineer-enzymes-uf-researchers-help-transform-biotechnology/