(325f) Biosynth Pipeline: An Integrated Software to Merge the Computational Design of Chimeric Type I Polyketide Synthases with Enzymatic Pathways for Chemical Biosynthesis

With recent advances in metabolic engineering and synthetic biology, the ability to harness various biological machinery for sustainable biomanufacturing is on the horizon for a wide range of key commodity chemicals. Regular, mono-functional enzymes within biology are often employed for the synthesis of such molecules via the construction and optimization of metabolic pathways either in native or heterologous bacterial hosts. Although extremely valuable for the precise and regioselective modification of certain functional groups, such mono-functional enzymes represent only one of the many engineering tools available in nature. Another crucial but often under-utilized set of biological resources that can be integrated into our biomanufacturing capabilities are polyketide synthases (PKSs). Type I PKSs, in particular, are versatile, tunable, and modular multifunctional enzymes capable of producing a large diversity of natural products. While sometimes difficult to engineer, they are invaluable in catalyzing carbon-carbon bond formation reactions and consequently, creating elongated carbon backbones. As such, their chemistries are complementary to those conferred by multifunctional enzymes and by integrating the two approaches, a larger chemical space of platform molecules can be tapped into than would be possible by either route alone. While some computationally-aided synthesis planning (CASP) tools exist to help navigate the large, complex design space of PKSs, and even more for de novo metabolic pathway design, no tool yet exists that hybridizes both biological systems. In order to tackle this larger combined pathway design space, we built Biosynth Pipeline, an open-source and freely-available CASP tool. Our software seamlessly integrates an existing software for PKS design - ClusterCAD and another for pathway design - Pickaxe - along with the incorporation of additional tools for predicting reaction feasibility, calculating reaction thermodynamics, and performing molecular docking. Users can therefore use Biosynth Pipeline to not only elucidate potential combined pathways to their desired molecules but also to perform in-depth pathway feasibility and structural biology analyses. By leveraging complementary strengths of both enzyme types, Biosynth Pipeline enables users to find alternative pathways to commodity chemicals that have previously been produced only using mono-functional enzymes as well as to find pathways to chemicals for which no known pathway exists.