Chemical Proteomics with Novel Fully Functionalized Fragments and Stringent Target Prioritization Identifies the Glutathione-Dependent Isomerase GSTZ1 as a Lung Cancer Target

Photoreactive fragment-like probes have been applied
to discover
target proteins that constitute novel cellular vulnerabilities and
to identify viable chemical hits for drug discovery. Through forming
covalent bonds, functionalized probes can achieve stronger target
engagement and require less effort for on-target mechanism validation.
However, the design of probe libraries, which directly affects the
biological target space that is interrogated, and effective target
prioritization remain critical challenges of such a chemical proteomic
platform. In this study, we designed and synthesized a diverse panel
of 20 fragment-based probes containing natural product-based privileged
structural motifs for small-molecule lead discovery. These probes
were fully functionalized with orthogonal diazirine and alkyne moieties
and used for protein crosslinking in live lung cancer cells, target
enrichment via “click chemistry,” and
subsequent target identification through label-free quantitative liquid
chromatography–tandem mass spectrometry analysis. Pair-wise
comparison with a blunted negative control probe and stringent prioritization via individual cross-comparisons against the entire panel
identified glutathione S-transferase zeta 1 (GSTZ1)
as a specific and unique target candidate. DepMap database query,
RNA interference-based gene silencing, and proteome-wide tyrosine
reactivity profiling suggested that GSTZ1 cooperated
with different oncogenic alterations by supporting survival signaling
in refractory non-small cell lung cancer cells. This finding may form
the basis for developing novel GSTZ1 inhibitors to improve the therapeutic
efficacy of oncogene-directed targeted drugs. In summary, we designed
a novel fragment-based probe panel and developed a target prioritization
scheme with improved stringency, which allows for the identification
of unique target candidates, such as GSTZ1 in refractory lung cancer.