Accurate PROTAC targeted degradation prediction with DegradeMaster

Motivation Proteolysis-targeting chimeras (PROTACs) are heterobifunctional molecules that can degrade ‘undruggable’ protein of interest (POI) by recruiting E3 ligases and hijacking the ubiquitin-proteasome system. Some efforts have been made to develop deep learning-based approaches to predict the degradation ability of a given PROTAC. However, existing deep learning methods either simplify proteins and PROTACs as 2D graphs by disregarding crucial 3D spatial information or exclusively rely on limited labels for supervised learning without considering the abundant information from unlabeled data. Nevertheless, considering the potential to accelerate drug discovery, it is critical to develop more accurate computational methods for PROTAC-targeted protein degradation prediction.

This study proposes DegradeMaster, a semi-supervised E(3)-equivariant graph neural network-based predictor for targeted degradation prediction of PROTACs. DegradeMaster leverages an E(3)-equivariant graph encoder to incorporate 3D geometric constraints into the molecular representations and utilises a memory-based pseudo-labeling strategy to enrich annotated data during training. A mutual attention pooling module is also designed for interpretable graph representation. Experiments on both supervised and semi-supervised PROTAC datasets demonstrate that DegradeMaster outperforms state-of-the-art baselines, with substantial improvement of AUROC by 10.5%. Case studies show DegradeMaster achieves 88.33% and 77.78% accuracy in predicting the degradability of VZ185 candidates on BRD9 and ACBI3 on KRAS mutants. Visualization of attention weights on 3D molecule graph demonstrates that DegradeMaster recognises linking and binding regions of warhead and E3 ligands and emphasizes the importance of structural information in these areas for degradation prediction. Together, this shows the potential for cutting-edge tools to highlight functional PROTAC components, thereby accelerating novel compound generation. Availability The source code and datasets are available at https://github.com/Jackson117/DegradeMaster and https://zenodo.org/records/14715718. Competing Interest Statement The authors have declared no competing interest.