(197bd) Expanding Chemical Synthesis Planning to Explore Chemo-Enzymatic Pathways Using Minimal Transitions

Chemo-enzymatic pathway design involves chemical synthesis planning utilizing both enzymatic and non-enzymatic chemical reactions. Combining enzymatic and chemical steps can expand the chemical space accessible for synthesis beyond the capabilities of either set of reactions working independently. However, while molecules like tetrahydrofuran are straightforward to synthesize through chemical means, they can be challenging to produce using biological methods due to issues such as toxicity or a dearth of enzymes capable of catalyzing the necessary reactions. On the other hand, chemistry faces obstacles regarding regioselectivity and the ability to make alterations to complex and heavily functionalized molecules. Therefore, the chemo-enzymatic pathway design approach leveraging both chemical and biochemical reactions for synthesis planning enables the usage of enzymes to catalyze specific reactions and reduce the number of synthetic steps required to produce the target chemical. Recently, numerous studies have shown the advantages of leveraging enzymatic steps into industrial-scale chemical processes such as for the blood sugar regulator Sitagliptin (Merck) and anti-malarial drug Artemisinin (Amyris).

However, designing optimal chemo-enzymatic pathways is a complex task that involves encoding and understanding of chemical and biochemical reactions, as well as the knowledge of enzyme substrate activity and specificity. Furthermore, the task is complicated by the high-dimensional search space of potential reactions that combines both chemical/biochemical reactions and the need to optimize for factors such as maximizing yield, minimizing waste, and reducing the use of costly chemicals. Herein, we present a pathway design framework for exploring chemo-enzymatic pathways for chemical synthesis, connecting a starting chemical to the target molecule using both chemical and enzymatic reaction steps. Our approach minimizes the transitions between enzymatic and chemical reactions while designing pathways. The notion behind this concept is that executing these hybrid synthesis routes in experiments necessitates multiple stages of purification and separation of chemicals when there is a transition between enzymatic and chemical reactions. For instance, if a pathway involves a chemical reaction followed by an enzymatic reaction, it entails isolating and purifying the product of the enzymatic reaction to utilize it as the reactant for the subsequent chemical steps. Conversely, if the pathway involves a transition from a chemical to an enzymatic reaction, the purified product of the chemical reaction serves as the reactant for the subsequent enzymatic steps. Therefore, our goal is to reduce these transitions by identifying steps from both chemical and biochemical reactions to create pathways for chemical synthesis. To accomplish this, we use a mixed-integer linear programming algorithm to identify hybrid chemo-enzymatic pathways with the least possible number of such transitions. This approach enables us to investigate chemo-enzymatic routes that require minimal transitions, streamlining the planning of chemical synthesis using hybrid reactions and potentially leading to the development of more effective synthesis strategies. Additionally, our method provides the advantage of exploring an expanded chemical space for chemical synthesis, which could aid researchers in designing more efficient, sustainable, and eco-friendly synthetic routes.