Accelerating ligand discovery by combining Bayesian optimization with MMGBSA-based binding affinity calculations

Abstract

Predicting protein-ligand binding affinity with high accuracy is critical in structure-based drug discovery. While docking methods offer computational efficiency, they often lack the precision required for reliable affinity ranking. In contrast, molecular dynamics (MD)-based approaches such as MMGBSA provide more accurate binding free energy estimates but are computationally intensive, limiting their scalability. To address this trade-off, we introduce an active learning framework that automates molecule selection for docking and MD simulations, replacing manual expert-driven decisions with a data-efficient, model-guided strategy. Our approach integrates fixed -- partly pre-trained deep learning -- molecular embeddings (MolFormer, ChemBERTa-2, and Morgan fingerprints) with adaptive regression models (e.g. Bayesian Ridge and Random Forest) to iteratively improve binding affinity predictions. We evaluate this approach retro-spectively on a new dataset of 59,356 chemically diverse compounds from ZINC-22 targeting the MCL1 protein using both AutoDock Vina and MMGBSA binding free energy scores. Our results show that incorporating MMGBSA scores into the active learning loop significantly enhances performance, recovering 79.9% of the top 1% binders in the whole dataset, compared to only 6.7% when using docking scores alone. Notably, MMGBSA exhibits a stronger correlation with experimental binding affinities than AutoDock Vina on our dataset and enables more accurate ranking of candidate compounds in a runtime efficient way. Furthermore, we demonstrate that a one-at-a-time acquisition active learning strategy consistently outperforms traditional batched acquisition, the latter achieving just 78.4% recovery with MolFormer and Bayesian Ridge. These findings underscore the potential of integrating deep learning-based molecular representations with MD-level accuracy in an active learning framework, offering a scalable and efficient path to accelerate virtual screening and improve hit identification in drug discovery.