SepPCNET: Deeping Learning on a 3D Surface Electrostatic Potential Point Cloud for Enhanced Toxicity Classification and Its Application to Suspected Environmental Estrogens

Deep learning (DL) offers an unprecedented opportunity to revolutionize the landscape of toxicity prediction based on quantitative structure–activity relationship (QSAR) studies in the big data era. However, the structural description in the reported DL-QSAR models is still restricted to the two-dimensional level. Inspired by point clouds, a type of geometric data structure, a novel three-dimensional (3D) molecular surface point cloud with electrostatic potential (SepPC) was proposed to describe chemical structures. Each surface point of a chemical is assigned its 3D coordinate and molecular electrostatic potential. A novel DL architecture SepPCNET was then introduced to directly consume unordered SepPC data for toxicity classification. The SepPCNET model was trained on 1317 chemicals tested in a battery of 18 estrogen receptor-related assays of the ToxCast program. The obtained model recognized the active and inactive chemicals at accuracies of 82.8 and 88.9%, respectively, with a total accuracy of 88.3% on the internal test set and 92.5% on the external test set, which outperformed other up-to-date machine learning models and succeeded in recognizing the difference in the activity of isomers. Additional insights into the toxicity mechanism were also gained by visualizing critical points and extracting data-driven point features of active chemicals.