Predicting the macromolecular targets of drug-like molecules has become everyday practice in medicinal chemistry. We present an overview of our recent research activities in the area of polypharmacology-guided drug design. A focus is put on the self-organizing map (SOM) as a tool for compound clustering and visualization. We show how the SOM can be efficiently used for target-panel prediction, drug re-purposing, and the design of focused compound libraries. We also present the concept of virtual organic synthesis in combination with quantitative estimates of ligand-receptor binding, which we used for de novo designing target-selective ligands. We expect these and related approaches to enable the future discovery of personalized medicines.