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 used chemoproteomic profiling and structure-based design to develop...

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Published inNature chemical biology Vol. 16; no. 6; pp. 635 - 643
Main Authors Ferguson, Fleur M., Nabet, Behnam, Raghavan, Srivatsan, Liu, Yan, Leggett, Alan L., Kuljanin, Miljan, Kalekar, Radha L., Yang, Annan, He, Shuning, Wang, Jinhua, Ng, Raymond W. S., Sulahian, Rita, Li, Lianbo, Poulin, Emily J., Huang, Ling, Koren, Jost, Dieguez-Martinez, Nora, Espinosa, Sergio, Zeng, Zhiyang, Corona, Cesear R., Vasta, James D., Ohi, Ryoma, Sim, Taebo, Kim, Nam Doo, Harshbarger, Wayne, Lizcano, Jose M., Robers, Matthew B., Muthaswamy, Senthil, Lin, Charles Y., Look, A. Thomas, Haigis, Kevin M., Mancias, Joseph D., Wolpin, Brian M., Aguirre, Andrew J., Hahn, William C., Westover, Kenneth D., Gray, Nathanael S.
Format Journal Article
LanguageEnglish
Published New York Nature Publishing Group US 01.06.2020
Nature Publishing Group
Subjects
631/67/1059
631/92/96
Adenocarcinoma
Animals
Biochemical Engineering
Biochemistry
Bioorganic Chemistry
Cancer
Carcinoma, Pancreatic Ductal - drug therapy
Cell Biology
Cell Line, Tumor
Cell Movement
Chemistry
Chemistry and Materials Science
Chemistry/Food Science
Doublecortin Protein
Doublecortin-Like Kinases
Drug Screening Assays, Antitumor
Enzyme inhibitors
Gene expression
Gene Expression Regulation
Gene sequencing
Humans
Intracellular Signaling Peptides and Proteins - antagonists & inhibitors
Intracellular Signaling Peptides and Proteins - metabolism
Kinases
Male
Mice
Molecular Docking Simulation
Molecular Structure
Organoids
Pancreas
Pancreatic cancer
Pancreatic Neoplasms
Pancreatic Neoplasms - drug therapy
Protein Kinase Inhibitors - chemistry
Protein Kinase Inhibitors - pharmacokinetics
Protein Serine-Threonine Kinases - antagonists & inhibitors
Proteomics
Rats
Ribonucleic acid
RNA
Structure-Activity Relationship
Therapeutic applications
Therapeutic targets
Transcriptomes
Zebrafish
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Summary: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 used chemoproteomic profiling and structure-based design to develop a 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. A highly selective inhibitor of the DCLK1/2 kinases is used to uncover the consequences of DCLK1 inhibition on viability, phosphosignaling and the transcriptome in patient-derived organoid models of pancreatic ductal adenocarcinoma.
Bibliography:F.M.F., B.N., and N.S.G. conceived and led the study. F.M.F. performed medicinal chemistry optimization, with input from J.W, supervised by N.S.G. B.N. developed and characterized dTAG model systems, performed cellular PDAC studies and performed DCLK1 nanoBRET assays, supervised by N.S.G. B.N., S.R., R.L.K., R.W.S.N. and R.S. performed patient-derived organoid culture assays and prepared organoid samples for RNA-sequencing, proteomics and phosphoproteomics, supervised by B.M.W., A.J.A. and W.C.H. B.N. and A.L.L. performed pulldown experiments and prepared cellular samples for KiNativ, RNA-sequencing, proteomics and phosphoproteomics, supervised by N.S.G. Y.L., W.H. and L.L. performed DCLK1 protein purification, isothermal titration calorimetry and molecular shift assay, supervised by K.W. M.K. performed proteomics and phosphoproteomics experiments, supervised by J.D.M. A.Y. performed the maximum tolerated dose studies, supervised by A.J.A. S.H. performed zebrafish toxicity assays, supervised by A.T.L. E.J.P. performed western blot and immunohistochemistry analysis of mouse model tissues, supervised by K.M.H. L.H. performed validation of organoid sensitivity, supervised by S.M.
AUTHOR CONTRIBUTIONS
J.K. performed RNA-sequencing data analysis, supervised by C.Y.L. N.D.-M. and S.E performed ERK5 biochemical and cellular assays, supervised by J.M.L. Z.Z., C.R.C., J.D.V. and M.B.R. developed the DCLK1 nanoBRET assay reagents. R.O. performed viability and morphology testing on rat cortical neurons. T.S. and N.D.K. performed molecular modeling. F.M.F., B.N., and S.R. wrote the manuscript, with edits from N.S.G. All authors read and approved the manuscript.
ISSN:1552-4450
1552-4469
DOI:10.1038/s41589-020-0506-0