Molecular dynamics-powered hierarchical geometric deep learning framework for protein-ligand interaction

Accurate prediction of the drug binding between proteins and ligands can significantly advance the development of structure-based drug design. Recent advances have shown great potential in applying equivariant graph neural network (EGNN) -based methods to learn representations of protein-ligand (PL) complexes. However, most of them typically focus on atom-level graph representations and omit the residue-level information in PL complexes, which are considered essential for understanding the binding mechanism. In this article, we develop a SO(3)-equivariant hierarchical graph neural network (EHGNN) that effectively captures the intrinsic hierarchy of biomolecular structures to enhance the predictive performance of PL interactions. Based on the SO(3)-EHGNN, we further propose a molecular dynamics-powered and energy-guided deep learning framework, called Dynamics-PLI, to capture the spatial structures and energetic information inside molecular dynamic (MD) trajectories. Extensive experimental results show significant improvements over current state-of-the-art methods, with a decrease of 4.03% in RMSE for the binding affinity problem and an average increase of 3.95% in AUROC and AUPRC for the ligand efficacy problem, demonstrating the superiority of Dynamics-PLI for PL interaction prediction. Our findings indicate that the SO(3)-EHGNN exhibits enhanced performance without the necessity of pre-training, emphasizing the inherent analytical strength of SO(3)-EHGNN.