Molecular profiling and combinatorial activity of CCT068127: a potent CDK2 and CDK9 inhibitor

Abstract

Deregulation of the cyclin‐dependent kinases (CDKs) has been implicated in the pathogenesis of multiple cancer types. Consequently, CDKs have garnered intense interest as therapeutic targets for the treatment of cancer. We describe herein the molecular and cellular effects of CCT068127, a novel inhibitor of CDK2 and CDK9. Optimized from the purine template of seliciclib, CCT068127 exhibits greater potency and selectivity against purified CDK2 and CDK9 and superior antiproliferative activity against human colon cancer and melanoma cell lines. X‐ray crystallography studies reveal that hydrogen bonding with the DFG motif of CDK2 is the likely mechanism of greater enzymatic potency. Commensurate with inhibition of CDK activity, CCT068127 treatment results in decreased retinoblastoma protein (RB) phosphorylation, reduced phosphorylation of RNA polymerase II, and induction of cell cycle arrest and apoptosis. The transcriptional signature of CCT068127 shows greatest similarity to other small‐molecule CDK and also HDAC inhibitors. CCT068127 caused a dramatic loss in expression of DUSP6 phosphatase, alongside elevated ERK phosphorylation and activation of MAPK pathway target genes. MCL1 protein levels are rapidly decreased by CCT068127 treatment and this associates with synergistic antiproliferative activity after combined treatment with CCT068127 and ABT263, a BCL2 family inhibitor. These findings support the rational combination of this series of CDK2/9 inhibitors and BCL2 family inhibitors for the treatment of human cancer.

P-TEFb as A Promising Therapeutic Target

“…Including Alvocidib, there are several CDK9 inhibitors including Dinaciclib, Seliciclib, Atuveciclib, Voruciclib, and SNS-032, which are being examined in clinical trials for treatments of these diseases [250][251][252][253] (Table 3). Moreover, many new and potent CDK9 inhibitors such as P276-00, CDKI-73, i-CDK9, Wogonin, CCT068127, MC180295, ABC1183, FIT-039, PC585, NVP-2, etc., have been reported and tested [220,234,[254][255][256][257][258][259][260][261] (summarized in Table 2). Increasing evidence indicates that inhibiting CDK9 kinase activity is a promising approach for chemotherapy in many types of cancer [74].…”

Comparative Modeling of CDK9 Inhibitors to Explore Selectivity and Structure-Activity Relationships

“…From the outset, we were quite surprised that optimization in this phenotypic assay yielded compounds that were not only potent against CDK9, but selective as well. This selectivity was most notable with respect to CDK2, given that most CDK9 inhibitors also inhibit CDK2 [29,30]. Given that simply optimizing for potency against CDK9 would not necessarily be expected to yield selective inhibitors, we therefore hypothesized that our phenotypic screen was indirectly yielding information on selectivity to guide our optimization.…”

“…With the emergence of CDK9 as a promising target for therapeutic intervention in cancer, we anticipate that comparative modeling can provide a valuable tool to guide optimization of potency and selectivity of new inhibitors targeting this kinase.anti-tumoral activity coupled with immunosensitization [28]. With respect to selectivity, the preference of 14e for CDK9 over CDK2 and CDK7 was especially notable: due to their structural and functional similarities, most CDK9 inhibitors also inhibit CDK2 and CDK7 [29,30]. In our first study, we explored selectivity of 14e by developing a comparative modeling approach to build a model of the 14e/CDK9 complex, and then using this model to propose a structural basis for the observed selectivity [28].In the present study we expand our understanding of the structure-activity relationship (SAR) of the series and use these data to critically evaluate our comparative modeling approach.…”

“…anti-tumoral activity coupled with immunosensitization [28]. With respect to selectivity, the preference of 14e for CDK9 over CDK2 and CDK7 was especially notable: due to their structural and functional similarities, most CDK9 inhibitors also inhibit CDK2 and CDK7 [29,30]. In our first study, we explored selectivity of 14e by developing a comparative modeling approach to build a model of the 14e/CDK9 complex, and then using this model to propose a structural basis for the observed selectivity [28].…”

Computational analysis for residue-specific CDK2-inhibitor bindings

“…In the past few decades, CDK2 has become an important therapeutic target for cancer, and many inhibitors with diverse scaffolds have surfaced out [16,17]. For example, a recently discovered inhibitor CCT068127 significantly reduces cell proliferation, effectively inhibits the phosphorylation of RB in human cancer cells, and thus induces cell cycle arrest and cell apoptosis [18]. However, no CDK2 inhibitor has been approved for therapeutic use so far.…”