Probing ligand-induced local stability shifts: A sensitive approach to identify target proteins and binding sites at the proteomic scale

Abstract

Deciphering ligand-induced structural alterations represents a critical frontier in functional proteomics, offering transformative potential for both target identification and mechanistic understanding of ligand actions. Therefore, it is of great interest to develop robust proteomic approaches to uncover the binding relationship between ligands and the targeting proteins. The ligand modification-free approaches have the advantages of bypassing chemical modification and thus are broadly applicable to diverse ligands. Herein, in this review, we will introduce some recent methodology advancements for modification-free approaches in the identification of interactions between ligands and proteins. Especially, we will focus on a newly developed method, peptide-centric local stability assay (PELSA), which was designed to probe the ligand-induced local stability shifts and was demonstrated to have high sensitivity in revealing the binding regions at proteome level. The continued refinement and wider implementation of such technologies are expected to revolutionize fundamental research related with ligand–protein interactions.