title: The potent Cdc7-Dbf4 (DDK) kinase inhibitor XL413 has limited activity in many cancer cell lines and discovery of potential new DDK inhibitor scaffolds.
abstract: Cdc7-Dbf4 kinase or DDK (Dbf4-dependent kinase) is required to initiate DNA replication by phosphorylating and activating the replicative Mcm2-7 DNA helicase. DDK is overexpressed in many tumor cells and is an emerging chemotherapeutic target since DDK inhibition causes apoptosis of diverse cancer cell types but not of normal cells. PHA-767491 and XL413 are among a number of potent DDK inhibitors with low nanomolar IC50 values against the purified kinase. Although XL413 is highly selective for DDK, its activity has not been extensively characterized on cell lines. We measured anti-proliferative and apoptotic effects of XL413 on a panel of tumor cell lines compared to PHA-767491, whose activity is well characterized. Both compounds were effective biochemical DDK inhibitors but surprisingly, their activities in cell lines were highly divergent. Unlike PHA-767491, XL413 had significant anti-proliferative activity against only one of the ten cell lines tested. Since XL413 did not effectively inhibit DDK in multiple cell lines, this compound likely has limited bioavailability. To identify potential leads for additional DDK inhibitors, we also tested the cross-reactivity of ∼400 known kinase inhibitors against DDK using a DDK thermal stability shift assay (TSA). We identified 11 compounds that significantly stabilized DDK. Several inhibited DDK with comparable potency to PHA-767491, including Chk1 and PKR kinase inhibitors, but had divergent chemical scaffolds from known DDK inhibitors. Taken together, these data show that several well-known kinase inhibitors cross-react with DDK and also highlight the opportunity to design additional specific, biologically active DDK inhibitors for use as chemotherapeutic agents.
authors.affiliation: Laboratory of Genome Integrity and Tumorigenesis, Van Andel Research Institute (VARI), Grand Rapids, MI, United States of America; Graduate Program in Genetics, Michigan State University, East Lansing, MI, United States of America.
authors.forename: Nanda Kumar
authors.initials: NK
authors.lastname: Sasi
authors.affiliation: Laboratory of Genome Integrity and Tumorigenesis, Van Andel Research Institute (VARI), Grand Rapids, MI, United States of America.
authors.forename: Kanchan
authors.initials: K
authors.lastname: Tiwari
authors.affiliation: Laboratory of Structural Sciences, VARI, Grand Rapids, MI, United States of America.
authors.forename: Fen-Fen
authors.initials: FF
authors.lastname: Soon
authors.affiliation: Laboratory of Genome Integrity and Tumorigenesis, Van Andel Research Institute (VARI), Grand Rapids, MI, United States of America.
authors.forename: Dorine
authors.initials: D
authors.lastname: Bonte
authors.affiliation: Translational Drug Development, Inc. (TD2), Scottsdale, AZ, United States of America.
authors.forename: Tong
authors.initials: T
authors.lastname: Wang
authors.affiliation: Laboratory of Structural Biology and Biochemistry, VARI, Grand Rapids, MI, United States of America.
authors.forename: Karsten
authors.initials: K
authors.lastname: Melcher
authors.affiliation: Laboratory of Structural Sciences, VARI, Grand Rapids, MI, United States of America.
authors.forename: H Eric
authors.initials: HE
authors.lastname: Xu
authors.affiliation: Laboratory of Genome Integrity and Tumorigenesis, Van Andel Research Institute (VARI), Grand Rapids, MI, United States of America.
authors.forename: Michael
authors.initials: M
authors.lastname: Weinreich
mesh_terms: D017209:Apoptosis / Q000187:drug effects; D001682:Biological Availability; D018797:Cell Cycle Proteins / Q000037:antagonists & inhibitors*; D045744:Cell Line, Tumor / Q000187:drug effects*; D049109:Cell Proliferation / Q000187:drug effects; D058492:Drug Repositioning; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D045325:HCT116 Cells / Q000187:drug effects; D006367:HeLa Cells / Q000187:drug effects; D006801:Humans; D010881:Piperidones / Q000494:pharmacology*; D047428:Protein Kinase Inhibitors / Q000494:pharmacology*; D017346:Protein Serine-Threonine Kinases / Q000037:antagonists & inhibitors*; D011744:Pyrimidinones / Q000493:pharmacokinetics / Q000494:pharmacology*; D011758:Pyrroles / Q000494:pharmacology*
chemical_list: D018797:Cell Cycle Proteins; C531237:PHA 767491; D010881:Piperidones; D047428:Protein Kinase Inhibitors; D011744:Pyrimidinones; D011758:Pyrroles; C574818:XL413 compound; C068619:CDC7 protein, human; D017346:Protein Serine-Threonine Kinases