Deep neural network affinity model for BACE inhibitors in D3R Grand Challenge 4

Drug Design Data Resource (D3R) Grand Challenge 4 (GC4) offered a unique opportunity for designing and testing novel methodology for accurate docking and affinity prediction of ligands in an open and blinded manner. We participated in the beta-secretase 1 (BACE) Subchallenge which is comprised of cross-docking and redocking of 20 macrocyclic ligands to BACE and predicting binding affinity for 154 macrocyclic ligands. For this challenge, we developed machine learning models trained specifically on BACE. We developed a deep neural network (DNN) model that used a combination of both structure and ligand-based features that outperformed simpler machine learning models. According to the results released by D3R, we achieved a Spearman's rank correlation coefficient of 0.43(7) for predicting the affinity of 154 ligands. We describe the formulation of our machine learning strategy in detail. We compared the performance of DNN with linear regression, random forest, and support vector machines using ligand-based, structure-based, and combining both ligand and structure-based features. We compared different structures for our DNN and found that performance was highly dependent on fine optimization of the L2 regularization hyperparameter, alpha. We also developed a novel metric of ligand three-dimensional similarity inspired by crystallographic difference density maps to match ligands without crystal structures to similar ligands with known crystal structures. This report demonstrates that detailed parameterization, careful data training and implementation, and extensive feature analysis are necessary to obtain strong performance with more complex machine learning methods. Post hoc analysis shows that scoring functions based only on ligand features are competitive with those also using structural features. Our DNN approach tied for fifth in predicting BACE-ligand binding affinities.