Computational Modeling of β-Secretase 1 (BACE-1) Inhibitors Using Ligand Based Approaches

The binding affinities (IC50) reported for diverse structural and chemical classes of human beta-secretase 1 (BACE-1) inhibitors in literature were modeled using multiple in silico ligand based modeling approaches and statistical techniques. The descriptor space encompasses simple binary molecular fingerprint, one- and two-dimensional constitutional, physicochemical, and topological descriptors, and sophisticated three-dimensional molecular fields that require appropriate structural alignments of varied chemical scaffolds in one universal chemical space. The affinities were modeled using qualitative classification or quantitative regression schemes involving linear, nonlinear, and deep neural network (DNN) machine-learning methods used in the scientific literature for quantitative-structure activity relationships (QSAR). In a departure from tradition, similar to 20% of the chemically diverse data set (205 compounds) was used to train the model with the remaining similar to 80% of the structural and chemical analogs used as part of an external validation (1273 compounds) and prospective test (69 compounds) sets respectively to ascertain the model performance. The machine -learning methods investigated herein performed well in both the qualitative classification (similar to 70% accuracy) and quantitative IC50 predictions (RMSE similar to 1 log). The success of the 2D descriptor based machine learning approach when compared against the 3D field based technique pursued for hBACE-1 inhibitors provides a strong impetus for systematically applying such methods during the lead identification and optimization efforts for other protein families as well.