Discovery of a selective inhibitor of Doublecortin Like Kinase 1

Doublecortin like kinase 1 (DCLK1) is an understudied kinase that is upregulated in a wide range of cancers, including pancreatic ductal adenocarcinoma (PDAC). However, little is known about its potential as a therapeutic target. We leveraged chemoproteomic profiling and structure-based design to develop the first selective, in vivo-compatible chemical probe of the DCLK1 kinase domain, DCLK1-IN-1. We demonstrate activity of DCLK1-IN-1 against clinically relevant patient-derived PDAC organoid models and use a combination of RNA sequencing, proteomics and phosphoproteomics analysis to reveal that DCLK1 inhibition modulates proteins and pathways associated with cell motility in this context. DCLK1-IN-1 will serve as a versatile tool to investigate DCLK1 biology and establish its role in cancer. We performed an ERCC spike-in normalized RNA-sequencing experiment to quantify transcriptional changes upon DMSO or DCLK1-IN-1 treatment of PDAC cell lines. We profiled PATU-8988T and PATU-8902 cells treated with DMSO or DCLK1-IN-1 for 6 or 24 h. All samples were prepared in biological triplicate.