Deep Learning-Driven Insights into Enzyme–Substrate Interaction Discovery

Enzymes are ubiquitous catalysts with enormous application potential in biomedicine, green chemistry, and biotechnology. However, accurately predicting whether a molecule serves as a substrate for a specific enzyme, especially for novel entities, remains a significant challenge. Compared with traditional experimental methods, computational approaches are much more resource-efficient and time-saving, but they often compromise on accuracy. To address this, we introduce the molecule-enzyme interaction (MEI) model, a novel machine learning framework designed to predict the probability that a given molecule is a substrate for a specified enzyme with high accuracy. Utilizing a comprehensive data set that encapsulates extensive information on enzymatic reactions and enzyme sequences, the MEI model seamlessly combines atomic environmental data with amino acid sequence features through an advanced attention mechanism within a hierarchical neural network. Empirical evaluations have confirmed that the MEI model outperforms the current state-of-the-art model by at least 6.7% in prediction accuracy and 8.5% in AUROC, underscoring its enhanced predictive capabilities. Additionally, the MEI model demonstrates remarkable generalization across data sets of varying qualities and sizes. This adaptability is further evidenced by its successful application in diverse areas, such as predicting interactions within the CYP450 enzyme family and achieving an outstanding accuracy of 90.5% in predicting the enzymatic breakdown of complex plastics within environmental applications. These examples illustrate the model's ability to effectively transfer knowledge from coarsely annotated enzyme databases to smaller, high-precision data sets, robustly modeling both sparse and high-quality databases. We believe that this versatility firmly establishes the MEI model as a foundational tool in enzyme research with immense potential to extend beyond its original scope.