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μMap Photoproximity Labeling Enables Small Molecule Binding Site Mapping.

Sean W Huth^1,2, James V Oakley^1,2, Ciaran P Seath^1,2

¹Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States.

Journal of the American Chemical Society

|July 20, 2023

Summary

We developed a new photocatalytic method, μMap, for mapping protein binding sites. This approach identifies amino acids near the ligand binding pocket, offering a powerful tool for drug discovery and target engagement analysis in vitro and in live cells.

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Area of Science:

Chemical Biology
Drug Discovery
Proteomics

Background:

Ligand binding site characterization is vital in drug discovery, especially for phenotypic screening where targets are initially unknown.
Existing methods like X-ray crystallography and photoaffinity labeling (PAL) have limitations, including technical challenges, poor signal, and complex data analysis.

Purpose of the Study:

To establish a robust and general photocatalytic approach for mapping protein binding sites, identifying residues proximal to the ligand binding pocket.
To demonstrate the utility of this method for analyzing various protein targets and drug candidates, including those without existing structural data.

Main Methods:

Development of a catalytic photocatalytic method (μMap) for protein binding site mapping.
Utilizing catalytic activation to label amino acids in proximity to the ligand binding site.
Application of the method in vitro to six protein targets and in live cells.

Main Results:

Successfully mapped binding sites of six diverse protein targets, including kinases and molecular glues.
Investigated the binding site of the STAT3 inhibitor MM-206, a ligand lacking crystal structure data.
Demonstrated successful mapping of drug binding sites within live cells.

Conclusions:

μMap provides a powerful and generalizable method for identifying amino acids near ligand binding pockets.
The technique generates valuable amino-acid- and peptide-level target engagement data.
μMap enables binding site characterization in vitro and in live cells, advancing drug discovery efforts.