A Chemoproteomic
Strategy for Direct and Proteome-Wide
Covalent Inhibitor Target-Site Identification
Christopher
M. Browne
Baishan Jiang
Scott B. Ficarro
Zainab M. Doctor
Jared L. Johnson
Joseph D. Card
Sindhu Carmen Sivakumaren
William M. Alexander
Tomer M. Yaron
Charles J. Murphy
Nicholas P. Kwiatkowski
Tinghu Zhang
Lewis C. Cantley
Nathanael S. Gray
Jarrod A. Marto
10.1021/jacs.8b07911.s008
https://acs.figshare.com/articles/journal_contribution/A_Chemoproteomic_Strategy_for_Direct_and_Proteome-Wide_Covalent_Inhibitor_Target-Site_Identification/7495799
Despite recent clinical
successes for irreversible drugs, potential
toxicities mediated by unpredictable modification of off-target cysteines
represents a major hurdle for expansion of covalent drug programs.
Understanding the proteome-wide binding profile of covalent inhibitors
can significantly accelerate their development; however, current mass
spectrometry strategies typically do not provide a direct, amino acid
level readout of covalent activity for complex, selective inhibitors.
Here we report the development of CITe-Id, a novel chemoproteomic
approach that employs covalent pharmacologic inhibitors as enrichment
reagents in combination with an optimized proteomic platform to directly
quantify dose-dependent binding at cysteine-thiols across the proteome.
CITe-Id analysis of our irreversible CDK inhibitor THZ1 identified
dose-dependent covalent modification of several unexpected kinases,
including a previously unannotated cysteine (C840) on the understudied
kinase PKN3. These data streamlined our development of JZ128 as a
new selective covalent inhibitor of PKN3. Using JZ128 as a probe compound,
we identified novel potential PKN3 substrates, thus offering an initial
molecular view of PKN3 cellular activity. CITe-Id provides a powerful
complement to current chemoproteomic platforms to characterize the
selectivity of covalent inhibitors, identify new, pharmacologically
addressable cysteine-thiols, and inform structure-based drug design
programs.
2018-12-06 00:00:00
PKN 3 substrates
covalent pharmacologic inhibitors
mass spectrometry strategies
covalent inhibitors
optimized proteomic platform
covalent drug programs
pharmacologically addressable cysteine-thiols
CDK inhibitor THZ 1
acid level readout
structure-based drug design programs
dose-dependent covalent modification
proteome-wide binding profile
kinase PKN 3.
novel chemoproteomic approach
CITe-Id
Proteome-Wide Covalent Inhibitor Target-Site Identification
JZ 128