State-dependent ligandability profilling in human cells

ABSTRACT: Post-translational modifications (PTMs) profoundly expand the diversity of the ~20,000 proteins encoded by the human genome and dynamically vary in response to changes in cellular environment, exposure to perturbagens, or the acquisition of disease. These changes can not only dramatically affect protein function, structure, and interactions but also the accessibility to small molecules (i.e. ligandability). Central to the development of "targeted therapies" are methods that not only identify proteins important for disease progression, but also enable the discovery of chemical probes that selectively engage these proteins under disease relevant conditions. In this study, we developed a chemoproteomic strategy to create global “fingerprints” that delineate alterations in protein ligandability in response to changes in PTM status. Employing fragment-based photoaffinity probes, we generated a comprehensive map of drug-like ligand-protein interactions that are sensitive to changes in N-glycosylation and phosphorylation in human cells. By integrating binding site information and structural analysis, we identified and orthogonally validated functionally diverse binding pockets whose ligandability is PTM-dependent. Among these targets, we discovered changes in the phosphorylation status of common oncogenic KRAS mutants affect accessibility to small molecules. Overall, our strategy unveils new insights into dynamic chemical tractability of the proteome mediated by PTMs and provides a blueprint for the development of chemical probes to selectively target proteins under specific states.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Weichao Li  

LAB HEAD: Christopher G. Parker

PROVIDER: PXD056976 | Pride | 2026-03-19

REPOSITORIES: Pride