Polyketides are a large group of plant and microbial secondary metabolites from which many blockbuster drugs and agricultural/animal health products are derived. They are biosynthesized by huge enzymatic assemblies whereby enzyme activities are organized into modules. Each module is responsible for the selection and condensation of small molecule building blocks into the growing product chain. Thus, the structure of the natural product is determined by the number, specificity, and order of modules within the assembly line, raising the exciting prospect of designing new hybrid biosynthetic systems for the synthesis of designer molecules.

Chemo-enzymatic generation of extender and starter units

The chemical diversity of polyketide natural products is largely determined by the small-molecule building blocks — extender and starter units — used during their assembly. Nature’s repertoire of these units is limited, constraining the structural space accessible through biosynthesis alone. We are developing chemo-enzymatic strategies that combine engineered acyl-CoA synthetases and related enzymes with non-natural substrates to expand this building block toolkit, enabling the production of polyketides bearing fluorinated, alkylated, and other non-natural moieties that would be inaccessible through fermentation or traditional synthesis alone.

Engineering the extender unit specificity of polyketide synthases

Polyketide synthases are modular enzymatic assembly lines in which each module selects and incorporates a specific extender unit into the growing product chain. Reprogramming this selectivity — swapping one extender unit for another — is a powerful strategy for generating structural analogues, but has historically been limited by poor compatibility between re-engineered modules and the surrounding biosynthetic machinery. We are using computational tools and structure-guided engineering to rationally redesign the acyltransferase domains responsible for extender unit selection, creating hybrid polyketide synthases that incorporate non-natural extender units with high efficiency and fidelity.

Directed evolution of polyketide biosynthesis

Rational engineering of polyketide synthases is often hampered by our incomplete understanding of the complex protein-protein interactions and conformational dynamics that govern their function. Directed evolution offers a complementary approach, allowing us to improve or reprogram enzyme activity without requiring detailed mechanistic knowledge. By pairing our genetically encoded biosensor platform with high-throughput screening, we can survey large libraries of polyketide synthase variants and rapidly identify mutants with altered substrate specificity, improved activity, or entirely new catalytic capabilities — accelerating the discovery of enzymes suited for the production of designer natural products.