Discovery of Novel Molecular Frameworks of Farnesoid X Receptor Modulators by Ensemble Machine Learning

The bile acid activated transcription factor farnesoid X receptor (FXR) has revealed therapeutic potential as a molecular drug target for the treatment of hepatic and metabolic disorders. Despite strong efforts in FXR ligand development, the structural diversity among the known FXR modulators is limited. Only four molecular frameworks account for more than 50 % of the FXR modulators annotated in ChEMBL. Here, we leverage machine learning methods to expand the chemical space of FXR‐targeting small molecules by employing an ensemble of three complementary machine learning approaches. A counter‐propagation artificial neural network, a k‐nearest neighbor learner, and a three‐dimensional pharmacophore descriptor were combined to retrieve novel FXR ligands from a collection of more than 3 million compounds. The ensemble machine learning model identified six new FXR modulators among ten top‐ranked candidates. These active hits comprise both FXR activators and antagonists with micromolar potencies. With four novel FXR ligand scaffolds, these computationally identified bioactive compounds appreciably expand the chemical space of known FXR modulators and may serve as starting points for hit‐to‐lead expansion.