Computational planning and experimental implementation of enzyme catalyzed routes towards small molecules

Biocatalysis uses enzymes to catalyze chemical transformations to yield a desired small molecule or natural product, e.g., agrochemicals, commodity chemicals and pharmaceutical agents. Enzymes catalyze stereo-, regio-, and enatio- specific reactions; as a result, biocatalysis catalysis enables more efficient, shorter, synthetic routes with less need for protection and deprotection reactions. Because of the many advantages of employing enzymes, biocatalysis has been synergistically used with organic chemistry- the workhorse of the modern chemical manufacturing industry- to produce small molecules. However, organic chemists’ educational experience has only a small overlap with that of enzymologists, making it challenging for some synthetic chemists to tap into benefits at the interface between organic- and enzyme chemistry. To support these chemists, Computer-Aided Synthesis Planning (CASP) tools employ retrosynthesis techniques to propose feasible synthetic routes to a target from available starting materials by starting with the target and choosing appropriate disconnections recursively. The methods predict enzymatic and chemo-enzymatic routes to a desired target using rule-based methods and machine learning to generalize known reactions. Notwithstanding these impressive advances, there remains a strong need for a suite of user-friendly enzymatic synthesis planning tools to produce realistic synthetic routes towards a target molecule. Further, these tools need to be tested experimentally to plan routes to medicinally relevant targets. Some relevant publications on this topic include:

• Sankaranarayanan, K. & Jensen, K. F. Computer-assisted multistep chemoenzymatic retrosynthesis using a chemical synthesis planner. Chemical Science 14, 6467–6475 (2023).

• Sankaranarayanan K., Heid E., Coley C.W., Verma D., Green W.H., Jensen K.F. Similarity based enzymatic retrosynthesis. Chemical Science 13, 6039–6053 (2022).

• Sankaranarayanan K.*, Antaris X.X.*, Palanski B.A., Gamal A.E., Kao C.M., Fitch W.L., Fischer C.R., Khosla C. Tunable enzymatic synthesis of the immunomodulator Lipid IVA to enable structure-activity analysis. J. Am. Chem. Soc. 141, 9474–9478 (2019)