Detecting Drug Promiscuity Using Gaussian Ensemble Screening

Polypharmacology describes the binding of a ligand to multiple protein targets (a promiscuous ligand) or multiple diverse ligands binding to a given target (a promiscuous target). Pharmaceutical companies are discovering increasing numbers of both promiscuous drugs and drug targets. Hence, polypharmacology is now recognized as an important aspect of drug design. Here, we describe a new and fast way to predict polypharmacological relationships between drug classes quantitatively, which we call Gaussian Ensemble Screening (GES). This approach represents a cluster of molecules with similar spherical harmonic surface shapes as a Gaussian distribution with respect to a selected center molecule. Calculating the Gaussian overlap between pairs of such clusters allows the similarity between drug classes to be calculated analytically without requiring thousands of bootstrap comparisons, as in current promiscuity prediction approaches. We find that such cluster similarity scores also follow a Gaussian distribution. Hence, a cluster similarity score may be transformed into a probability value, or “p-value”, in order to quantify the relationships between drug classes. We present results obtained when using the GES approach to predict relationships between drug classes in a subset of the MDL Drug Data Report (MDDR) database. Our results indicate that GES is a useful way to study polypharmacology relationships, and it could provide a novel way to propose new targets for drug repositioning.