EZPro-Multi: Contrastive Learning-Enhanced Multi-property Prediction for Enzyme Engineering

Accurately predicting the functional attributes of enzyme mutants is crucial for accelerating enzyme engineering and optimizing biocatalytic systems. Most existing methods focus on enzyme information or a limited set of properties while overlooking key interactions between enzyme mutants and their substrates. To address this limitation, we propose EZPro-Multi, a unified deep learning framework for predicting multiple biochemical properties, including catalytic efficiency (kcat), stability (ΔΔG), and solubility (ΔSol). EZPro-Multi integrates ProtT5-based protein representations with Molformer-based substrate representations through a cross-attention module to capture mutant–substrate interactions. The framework further incorporates supervised contrastive learning to improve feature discriminability by contrasting mutant–substrate pairs with similar or distinct catalytic changes measured on the same substrate. In addition, an auxiliary classification head is introduced to provide extra supervision and enhance the performance of the primary regression task. We evaluate EZPro-Multi using a curated kcat data set comprising diverse enzyme-substrate pairs, achieving state-of-the-art results. Comparative experiments show that EZPro-Multi outperforms existing methods in both regression accuracy and classification consistency. The framework also demonstrates promising performance in predicting ΔΔG and ΔSol across multiple benchmark data sets. Notably, on the deep mutational scanning (DMS) data set, integrating kcat, ΔΔG, and ΔSol significantly improves the hit rate for the top 10% high-activity mutants compared with single-property prediction, further highlighting the value of multi-property integration. Overall, EZPro-Multi provides a unified computational framework for multi-property assessment of enzyme variants and offers practical value for candidate prioritization in enzyme engineering.