From reactants to products: computational methods for biosynthetic pathway design

One of the main goals in synthetic biology is to produce value-added compounds from available precursors using enzymatic approaches. The construction of biosynthetic pathways for synthesizing target molecules plays a crucial role in this process. However, it is challenging and time-consuming for researchers to design efficient pathways manually. In recent decades, pathway design has advanced through data- and algorithm-driven approaches. In this article, we review key computational tools involved in biosynthetic pathway design, covering: 1) Biological Big-Data including compounds, reactions/pathways and enzymes. 2) Retrosynthesis methods leveraging multi-dimensional biosynthesis data to predict potential pathways for target compounds synthesis. 3) Enzyme engineering relying on data mining to identify/de novo design enzymes with desired functions. Integrating these three key components can significantly enhance the efficiency and accuracy of biosynthetic pathway design in synthetic biology.