Controlling Reactive Intermediates in Biocatalysis through Computational Design Tools

Objective

Enzymes are nature’s most efficient catalysts, enabling complex reactions with remarkable speed and selectivity. However, their scope is limited by evolutionary pressures, restricting their utility in synthetic and industrial applications. While enzyme engineering has achieved significant advancements, major challenges remain. Directed evolution has been transformative, but it is labor-intensive and relies on suitable starting scaffolds. Computational enzyme design is promising complementary strategy, however, its potential remains largely unrealized as designed enzymes often require extensive laboratory evolution, underscoring critical gaps in our understanding of enzyme catalysis. This project addresses these limitations by developing an integrative computational framework for designing enzymes capable of catalyzing new-to-nature reactions involving highly reactive intermediates. It proposes a transformative approach by combining a holistic understanding of enzymatic catalysis with cutting-edge computational tools inspired by nature’s evolutionary principles. The innovation lies in leveraging enzyme electrostatic preorganization and active site confinement to control and enhance catalysis in complex reactions involving high reactive intermediates. By harnessing conformational dynamics and introducing targeted sets of mutations, the project aims to create confined, polarized environments that stabilize reactive species and guide them along desired pathways. Integrating mechanistic insights with electrostatic preorganization and advanced AI-tools for protein structure prediction, this approach enables precise identification of protein sequences optimized for modern biocatalysis, including radical and photocatalytic processes. Beyond advancing fundamental understanding, the project will provide accessible AI tools to support researchers in best practices for computational enzyme modeling, driving innovation in green chemistry, pharmaceuticals, and biotechnology.