2‑(3-Oxo-1,3-diphenylpropyl)malonic Acids as Potent Allosteric Ligands of the PIF Pocket of Phosphoinositide-Dependent Kinase-1: Development and Prodrug Concept

• Published in: Journal of medicinal chemistry 2012-11, Vol.55 (22), p.9817-9830
• Main Authors: Wilhelm, Adriana, Lopez-Garcia, Laura A, Busschots, Katrien, Fröhner, Wolfgang, Maurer, Frauke, Boettcher, Stefan, Zhang, Hua, Schulze, Jörg O, Biondi, Ricardo M, Engel, Matthias
• Format: Article
• Language: English
• Subjects: Allosteric Site; Binding Sites; DNA Helicases - antagonists & inhibitors; DNA Helicases - metabolism; Drug Design; Enzyme Activation; Humans; Immunoblotting; Malonates - chemical synthesis; Malonates - chemistry; Malonates - pharmacology; Models, Molecular; Molecular Structure; Muscle Cells - drug effects; Muscle Cells - metabolism; Prodrugs - chemical synthesis; Prodrugs - pharmacology; Protein Binding; Protein Kinase Inhibitors - chemical synthesis; Protein Kinase Inhibitors - pharmacology; Protein-Serine-Threonine Kinases - antagonists & inhibitors; Protein-Serine-Threonine Kinases - metabolism; Structure-Activity Relationship
• ISSN: 0022-2623; 1520-4804
• DOI: 10.1021/jm3010477

The protein kinase C-related kinase 2 (PRK2)-interacting fragment (PIF) pocket of phosphoinositide-dependent kinase-1 (PDK1) was proposed as a novel target site for allosteric modulators. In the present work, we describe the design, synthesis, and structure–activity relationship of a series of 2-(3-oxo-1,3-diphenylpropyl)malonic acids as potent allosteric activators binding to the PIF pocket. Some congeners displayed AC50 values for PDK1 activation in the submicromolar range. The potency of the best compounds to stabilize PDK1 in a thermal stability shift assay was in the same order of magnitude as that of the PIF pocket binding peptide PIFtide, suggesting comparable binding affinities to the PIF pocket. The crystal structure of PDK1 in complex with compound 4h revealed that additional ionic interactions are mainly responsible for the increased potency compared to the monocarboxylate analogues. Notably, several compounds displayed high selectivity for PDK1. Employing a prodrug strategy, we were able to corroborate the novel mechanism of action in cells.