Computer-Aided Techniques in the Engineering of Enzyme Binding Pockets: New Perspectives and Frontiers

Enzymes, recognized for their remarkable catalytic efficiency, play a crucial role in a myriad of biochemical reactions. However, the catalytic performance of natural enzymes frequently does not meet the demands of specific applications. To address this limitation, the integration of computer-aided technologies has emerged as a pivotal strategy in enzyme engineering, allowing for significant enhancements in enzyme properties. The binding pocket is one of the key factors for these enhancements, whose structural and conformational dynamics profoundly influence the enzyme's activity, selectivity, and stability. This review underscores the importance of employing advanced computer-aided techniques in the analysis and engineering of binding pockets, highlighting successful cases that demonstrate the modification of these pockets to achieve desired catalytic properties. By leveraging machine learning and artificial intelligence, it is now possible to design enzymes with customized binding pockets from the ground up. Furthermore, various software tools that facilitate the analysis of binding pocket, focusing on geometric dimensions, functional attributes, and dynamic conformations, which are essential for engineering of binding pockets are systematically reviewed. Finally, the challenges and future directions for the application of these technologies in the design of binding pockets are also discussed in-depth, emphasizing their transformative potential in biocatalysis.