Computer-Aided Engineering of Trans-Anethole Oxygenase for Enhanced Catalytic Synthesis of Vanillin from Isoeugenol

Trans-anethole oxygenase (TAO) exhibits broad arylpropene substrate specificity but has low activity in converting isoeugenol to high-value vanillin. Herein, we employed computer-aided rational design to engineer TAO from Pseudomonas putida (PpTAO) for enhanced catalytic efficiency toward isoeugenol. Structural modeling and AlphaFold 3 docking identified two key catalytic residues, Arg86 and His118. Through substrate channel engineering and computation-guided mutagenesis, a series of targeted variants were constructed. Three variants, H93A, Q207R/G249C, and I59T/F62T, showed significant improvements in whole-cell performance, with activity increases of 1.8-, 2.13-, and 4.83-fold over the wild type (WT), respectively. Purified enzyme kinetics corroborated these findings, as reflected in kcat/Km values that reached 1.6, 2.1, and 4.7 times that of the WT. Mechanistic molecular dynamics simulations revealed that H93A enhances activity by widening the access tunnel, whereas Q207R/G249C exerts beneficial distal effects. Notably, the I59T/F62T variant significantly increases substrate affinity by optimizing hydrophobic interactions within the binding pocket. These results validate the efficacy of computational modeling in enzyme redesign and provide a robust biocatalyst for the sustainable biosynthesis of vanillin.