Above-Filter Digestion Proteomics Reveals Drug Targets and Localizes Ligand Binding Site

Identifying how drugs interact with proteins is fundamental to understanding their therapeutic effects and side effects. While numerous chemical proteomics methods exist for determining protein targets of drugs, each exhibits "blind spots," necessitating complementary approaches. We introduce Above-Filter Digestion Proteomics (AFDIP), which monitors trypsin digestion rates that decrease at ligand-binding sites, while potentially increasing elsewhere. Molecular dynamics simulations showed that these changes relate to backbone flexibility. Using AFDIP, we identified targets of various drugs and metabolites, allowing two-dimensional analysis with the drug concentration as the second dimension. The method identifies binding sites within ≤10 Å of crystallography-determined locations with improved resolution (≤5 Å) for larger proteins. Compared with existing proteolysis approaches, AFDIP offers simpler sample preparation, deeper proteome analysis, and broader sequence coverage. AFDIP addresses the blind spots of current techniques and provides structural insights, enhancing the chemical proteomics toolkit.