Chemoproteomic profiling to identify activity changes and functional inhibitors of DNA-binding proteins

ABSTRACT: DNA-binding proteins are promising therapeutic targets but notoriously difficult to drug. Here, we evaluate a chemoproteomic DNA interaction platform as a complementary strategy for parallelized compound profiling. To enable this approach, we determined the proteomic binding landscape of 92 immobilized DNA sequences. Perturbation-induced activity changes of captured transcription factors in disease-relevant settings demonstrated functional relevance of the enriched sub-proteome. Chemoproteomic profiling of >300 cysteine-directed compounds against a coverage optimized bead mixture, which specifically captures >150 DNA binders, revealed competition of several DNA-binding proteins, including the transcription factors ELF1 and ELF2. We also discovered the first compound which displaces the DNA-repair complex MSH2-MSH3 from DNA. Compound binding to cysteine 252 on MSH3 was confirmed using chemoproteomic reactive cysteine profiling. Overall, these results suggested that chemoproteomic DNA bead pull-downs enable the specific read-out of transcription factor activity and can identify functional “hot-spots” on DNA binders towards expanding the druggable proteome.

INSTRUMENT(S): Orbitrap Fusion Lumos, Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: benjamin ruprecht  

LAB HEAD: An Chi

PROVIDER: PXD037297 | Pride | 2023-02-03

REPOSITORIES: Pride