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

## TL;DR

A new proteomics method called AFDIP helps identify drug targets and locate where drugs bind to proteins, improving drug research and understanding.

## Contribution

AFDIP introduces a novel proteomics approach that identifies drug targets and binding sites with higher resolution and broader coverage.

## Key findings

- AFDIP identifies drug targets and binding sites within 10 Å of known locations with resolution ≤5 Å for larger proteins.
- AFDIP offers simpler sample preparation and deeper proteome analysis compared to existing proteolysis methods.
- AFDIP complements current techniques by addressing their blind spots and providing structural insights.

## Abstract

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.