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Nature. 2016 Jun 23;534(7608):570-4. doi: 10.1038/nature18002. Epub 2016 Jun 15.

Proteome-wide covalent ligand discovery in native biological systems.

Author information

1
Department of Chemical Physiology, The Scripps Research Institute. La Jolla, California 92307, USA.
2
Department of Integrative Structural and Computational Biology, The Scripps Research Institute. La Jolla, California 92307, USA.
3
Department of Molecular and Experimental Medicine, The Scripps Research Institute. La Jolla, California 92307, USA.
4
Department of Immunology and Microbial Science, The Scripps Research Institute. La Jolla, California 92307, USA.

Abstract

Small molecules are powerful tools for investigating protein function and can serve as leads for new therapeutics. Most human proteins, however, lack small-molecule ligands, and entire protein classes are considered 'undruggable'. Fragment-based ligand discovery can identify small-molecule probes for proteins that have proven difficult to target using high-throughput screening of complex compound libraries. Although reversibly binding ligands are commonly pursued, covalent fragments provide an alternative route to small-molecule probes, including those that can access regions of proteins that are difficult to target through binding affinity alone. Here we report a quantitative analysis of cysteine-reactive small-molecule fragments screened against thousands of proteins in human proteomes and cells. Covalent ligands were identified for >700 cysteines found in both druggable proteins and proteins deficient in chemical probes, including transcription factors, adaptor/scaffolding proteins, and uncharacterized proteins. Among the atypical ligand-protein interactions discovered were compounds that react preferentially with pro- (inactive) caspases. We used these ligands to distinguish extrinsic apoptosis pathways in human cell lines versus primary human T cells, showing that the former is largely mediated by caspase-8 while the latter depends on both caspase-8 and -10. Fragment-based covalent ligand discovery provides a greatly expanded portrait of the ligandable proteome and furnishes compounds that can illuminate protein functions in native biological systems.

PMID:
27309814
PMCID:
PMC4919207
DOI:
10.1038/nature18002
[Indexed for MEDLINE]
Free PMC Article

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