To demonstrate how the developed model could be practically applied to drug design problems, we formulate a hypothetical lead optimization scenario where we aim to improve a Phosphoinositide-dependent kinase-1 (PDK1) inhibitor based on the original structure-based design work of Angiolini et al. , using the 2XCH crystal structure from the PDB and the associated dihydro-pyrazoloquinazoline ligand as the starting structure. The objective of our case study is to identify small chemical modifications to the native ligand that could plausibly improve binding affinity without compromising the drug-likeness of the crystallized molecule.