Chemical tools to expand the ligandable proteome: Diversity-oriented synthesis-based photoreactive stereoprobes

Daisuke Ogasawara; David B Konrad; Zher Yin Tan; Kimberly L Carey; Jessica Luo; Sang Joon Won; Haoxin Li; Trever R Carter; Kristen E DeMeester; Evert Njomen; Stuart L Schreiber; Ramnik J Xavier; Bruno Melillo; Benjamin F Cravatt

doi:10.1016/j.chembiol.2024.10.005

Chemical tools to expand the ligandable proteome: Diversity-oriented synthesis-based photoreactive stereoprobes

Cell Chem Biol. 2024 Dec 19;31(12):2138-2155.e32. doi: 10.1016/j.chembiol.2024.10.005. Epub 2024 Nov 14.

Authors

Affiliations

¹ Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: [email protected].
² Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA.
³ Immunology Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
⁴ Immunology Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
⁵ Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
⁶ Immunology Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
⁷ Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: [email protected].
⁸ Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: [email protected].

PMID: 39547236
DOI: 10.1016/j.chembiol.2024.10.005

Abstract

Chemical proteomics enables the global analysis of small molecule-protein interactions in native biological systems and has emerged as a versatile approach for ligand discovery. The range of small molecules explored by chemical proteomics has, however, remained limited. Here, we describe a diversity-oriented synthesis (DOS)-inspired library of stereochemically defined compounds bearing diazirine and alkyne units for UV light-induced covalent modification and click chemistry enrichment of interacting proteins, respectively. We find that these "photo-stereoprobes" interact in a stereoselective manner with hundreds of proteins from various structural and functional classes in human cells and demonstrate that these interactions can form the basis for high-throughput screening-compatible NanoBRET assays. Integrated phenotypic screening and chemical proteomics identified photo-stereoprobes that modulate autophagy by engaging the mitochondrial serine protease CLPP. Our findings show the utility of DOS-inspired photo-stereoprobes for expanding the ligandable proteome, furnishing target engagement assays, and facilitating the discovery and characterization of bioactive compounds in phenotypic screens.

Keywords: NanoBRET; autophagy; chemical proteomics; diazirine; diversity-oriented synthesis; ligands; phenotypic screening; photoreactive; probes; proteomics; stereochemistry.

MeSH terms

Alkynes / chemistry
Click Chemistry
Diazomethane / chemistry
High-Throughput Screening Assays
Humans
Ligands
Molecular Structure
Proteome* / analysis
Proteome* / metabolism
Proteomics
Small Molecule Libraries / chemical synthesis
Small Molecule Libraries / chemistry
Small Molecule Libraries / pharmacology
Stereoisomerism
Ultraviolet Rays*

Substances

Proteome
Ligands
Alkynes
Small Molecule Libraries
Diazomethane