Proteome-wide covalent ligand discovery in native biological systems.
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.
Department of Chemical Physiology, The Scripps Research Institute. La Jolla, California 92307, USA.
Keriann M
KM
Backus
Department of Chemical Physiology, The Scripps Research Institute. La Jolla, California 92307, USA.
Bruno E
BE
Correia
Department of Chemical Physiology, The Scripps Research Institute. La Jolla, California 92307, USA.
Kenneth M
KM
Lum
Department of Integrative Structural and Computational Biology, The Scripps Research Institute. La Jolla, California 92307, USA.
Stefano
S
Forli
Department of Chemical Physiology, The Scripps Research Institute. La Jolla, California 92307, USA.
Benjamin D
BD
Horning
Department of Molecular and Experimental Medicine, The Scripps Research Institute. La Jolla, California 92307, USA.
Gonzalo E
GE
González-Páez
Department of Molecular and Experimental Medicine, The Scripps Research Institute. La Jolla, California 92307, USA.
Sandip
S
Chatterjee
Department of Chemical Physiology, The Scripps Research Institute. La Jolla, California 92307, USA.
Bryan R
BR
Lanning
Department of Immunology and Microbial Science, The Scripps Research Institute. La Jolla, California 92307, USA.
John R
JR
Teijaro
Department of Integrative Structural and Computational Biology, The Scripps Research Institute. La Jolla, California 92307, USA.
Arthur J
AJ
Olson
Department of Molecular and Experimental Medicine, The Scripps Research Institute. La Jolla, California 92307, USA.
Dennis W
DW
Wolan
Department of Chemical Physiology, The Scripps Research Institute. La Jolla, California 92307, USA.
Benjamin F
BF
Cravatt
D017209:Apoptosis; D053455:Caspase 10 / Q000737:chemistry / Q000378:metabolism; D053181:Caspase 8 / Q000737:chemistry / Q000378:metabolism; D002478:Cells, Cultured; D003545:Cysteine / Q000378:metabolism*; D004353:Drug Evaluation, Preclinical / Q000379:methods*; D004792:Enzyme Precursors / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D008024:Ligands; D010446:Peptide Fragments / Q000737:chemistry / Q000378:metabolism; D020543:Proteome / Q000737:chemistry* / Q000378:metabolism*; D054852:Small Molecule Libraries / Q000378:metabolism* / Q000494:pharmacology*; D013601:T-Lymphocytes / Q000737:chemistry / Q000378:metabolism*; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism
D004792:Enzyme Precursors; D008024:Ligands; D010446:Peptide Fragments; D020543:Proteome; D054852:Small Molecule Libraries; D014157:Transcription Factors; C505530:CASP8 protein, human; D053455:Caspase 10; D053181:Caspase 8; C506438:CASP10 protein, human; D003545:Cysteine