Complementary Backbone and Side-chain Analysis of Drug – Protein Interactions: Combining Hydrogen/Deuterium Exchange and Protein Oxidative Footprinting to Discriminate the Binding of Small Molecule Therapeutics

Characterizing and distinguishing protein-ligand interactions is crucial for understanding cellular metabolism and guiding drug discovery and development. We employ hydrogen/deuterium exchange mass spectrometry (HDX-MS) and a new Fenton chemistry-based approach to protein oxidative mass spectrometry (OX-MS) to provide complementary insight into the binding of the small molecule therapeutic Venetoclax (ABT-199, GDC-0199-Abbvie and Genentech) and a drug candidate S55746 (Servier) to the apoptotic regulatory protein Bcl-2. The combination of the orthogonal techniques HDX-MS and OX-MS clearly differentiate the binding profiles of the two drug molecules.