Expedited mapping of the ligandable proteome using fully functionalized enantiomeric probe pairs

• Published in: Nature chemistry 2019-12, Vol.11 (12), p.1113-1123
• Main Authors: Wang, Yujia, Dix, Melissa M., Bianco, Giulia, Remsberg, Jarrett R., Lee, Hsin-Yu, Kalocsay, Marian, Gygi, Steven P., Forli, Stefano, Vite, Gregory, Lawrence, R. Michael, Parker, Christopher G., Cravatt, Benjamin F.
• Format: Article
• Language: English
• Subjects: 631/92; 631/92/475; 631/92/613; 639/638/309/507; Analytical Chemistry; Biochemistry; Chemistry; Chemistry and Materials Science; Chemistry/Food Science; Chirality; Fragments; Humans; Inorganic Chemistry; Ligands; Mapping; Molecular Probes - chemistry; Molecular Structure; Organic Chemistry; Peptide mapping; Physical Chemistry; Physicochemical properties; Protein interaction; Protein structure; Proteins; Proteins - chemistry; Proteome - chemistry; Proteomes; Proteomics; Robustness (mathematics); Small Molecule Libraries - chemistry; Stereochemistry; Stereoisomerism; Stereoselectivity
• ISSN: 1755-4330; 1755-4349; 1755-4349
• DOI: 10.1038/s41557-019-0351-5

A fundamental challenge in chemical biology and medicine is to understand and expand the fraction of the human proteome that can be targeted by small molecules. We recently described a strategy that integrates fragment-based ligand discovery with chemical proteomics to furnish global portraits of reversible small-molecule/protein interactions in human cells. Excavating clear structure–activity relationships from these ‘ligandability’ maps, however, was confounded by the distinct physicochemical properties and corresponding overall protein-binding potential of individual fragments. Here, we describe a compelling solution to this problem by introducing a next-generation set of fully functionalized fragments differing only in absolute stereochemistry. Using these enantiomeric probe pairs, or ‘enantioprobes’, we identify numerous stereoselective protein–fragment interactions in cells and show that these interactions occur at functional sites on proteins from diverse classes. Our findings thus indicate that incorporating chirality into fully functionalized fragment libraries provides a robust and streamlined method to discover ligandable proteins in cells. A set of enantioprobes—photoreactive, clickable fragment pairs differing only in absolute stereochemistry—have been used to provide a robust and streamlined chemical proteomic map of small-molecule/protein interactions in human cells. More than 170 stereoselective fragment–protein interactions were discovered and shown to occur at functional sites on proteins from diverse classes.