Chemoproteomics-Enabled Covalent Ligand Screening Reveals ALDH3A1 as a Lung Cancer Therapy Target

Chemical
genetics is a powerful approach for identifying therapeutically
active small molecules, but identifying the mechanisms of action underlying
hit compounds remains challenging. Chemoproteomic platforms have arisen
to tackle this challenge and enable rapid mechanistic deconvolution
of small-molecule screening hits. Here, we have screened a cysteine-reactive
covalent ligand library to identify hit compounds that impair cell
survival and proliferation in nonsmall cell lung carcinoma cells,
but not in primary human bronchial epithelial cells. Through this
screen, we identified a covalent ligand hit, DKM 3-42, which impaired
both in situ and in vivo lung cancer
pathogenicity. We used activity-based protein profiling to discover
that the primary target of DKM 3-42 was the catalytic cysteine in
aldehyde dehydrogenase 3A1 (ALDH3A1). We performed further chemoproteomics-enabled
covalent ligand screening directly against ALDH3A1, and identified
a more potent and selective lead covalent ligand, EN40, which inhibits
ALDH3A1 activity and impairs lung cancer pathogenicity. We show here
that ALDH3A1 represents a potentially novel therapeutic target for
lung cancers that express ALDH3A1 and put forth two selective ALDH3A1
inhibitors. Overall, we show the utility of combining chemical genetics
screening of covalent ligand libraries with chemoproteomic approaches
to rapidly identify anticancer leads and targets.