Fig. 3: Results of structure-based de novo design with DRAGONFLY.
From: Prospective de novo drug design with deep interactome learning
a The scatter plot presented showcases the molecules designed de novo by utilizing the human peroxisome-proliferator-activated-receptor (PPAR)γ binding pocket as a template (PDB-ID 3G9E41). The plot displays the quantitative structure-activity relationship (QSAR) score representing the predicted binding affinity to PPARγ against the novelty score. The desired region for the generated molecules, which satisfies both, novelty and the predicted bioactivity requirements, is highlighted by a blue box located in the upper right corner of the plot. b Molecular structures of the top-ranking de novo designs. The predicted quality of the molecules decreases progressively from top to bottom. The ranking criteria were PPARγ + PPARδ dual-target affinity and structural novelty (left, 1 & 6–9), or PPARγ single-target affinity and structural novelty (right, 2 & 9–12). Molecule 9 ranks among the top five molecules on both lists. c Examples of non-carboxylic head groups and secondary amides from the top-100 molecules ranked for PPARγ, where the gray shaded R group represents an aromatic moiety connected to a linker. Source data are provided as a Source Data file.
