Degradation of Cyclin-Dependent Kinase: A New Weapon for Cancer Therapy

The family of human Cyclin dependent kinases (CDKs) comprises 20 different CDKs that play critical roles in the regulation of cell cycle progression, gene transcription and neuronal function. Deregulation of different CDKs is frequently observed in human cancer. Enzymatic kinase activity of CDKs is dependent on the binding of a member of the Cyclin protein family. So far more than 15 Cyclins have been described most of them can bind and activate different CDKs. Current data suggest the physiological relevance of at least 50 different CDK/Cyclin complexes. Since the 20 CDKs share significant structural homology and regulate different function in cell growth and development, selectivity of compounds within the CDK family is of critical importance. Approval of a first CDK inhibitor (Palbociclib) targeting CDK4/6 for the treatment of ER+/HER+- breast cancer served as a clinical proof that targeting specific members of the CDK protein kinase family is a versatile approach to treat cancer. The approval of the first CDK inhibitor sparked the research and development of other inhibitors targeting different members of the CDK-family. Currently, four additional CDK4/6 inhibitors have been approved and more than 15 CDK inhibitors with limited selectivity are in different preclinical or clinical development phases. However, the critical importance of selectivity within the CDK family is underlined by the fact that the clinical development of four CDK9 inhibitors has been stopped due to the lack of selectivity and high toxicity. Different approaches (including inhibition by covalent binding) have resulted in more selective inhibitors, especially against CDKs like CDK7, CDK9 and CDK12. Although several biochemical activity assays for different CDKs have been set up and used for selectivity testing, so far no panel covering all 20 human CDKs using one assay technology has been described. We report here the setup of a biochemical in-vitro activity assay panel of 32 CDK/Cyclins complexes generated recombinantly in insect cells covering the complete set of all 20 human CDKs. For all 32 complexes a radiometric biochemical activity assay has successfully been established allowing to characterize inhibitors with respect to their biochemical selectivity applying the same assay technology. Using the comprehensive CDK panel we determined the IC50 values of more than 15 CDK inhibitors that have been either approved or are in different preclinical and clinical development phases. Results will be presented showing the selectivity of these inhibitors not only for all 20 CDKs but also for specific CDKs forming active complexes with two or more different cyclins. This CDK screening panel allows the generation of comparative data on compound selectivity early in development, thereby helping to reduce the risk of designing compounds with suboptimal target selectivity. Citation Format: Daniel Müller, Frank Totzke, Thomas Weber, Andreas Gericke, Diane Krämer, Carolin Heidemann-Dinger, Constance Ketterer, Michael H. Kubbutat. Comprehensive characterization of CDK inhibitors using a complete panel of all 20 human cyclin-dependent kinases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2304.

Members of the family of cyclin dependent kinases (CDKs) have been recognized as pivotal regulators of cell cycle progression for more than 20 years. Concordant to their central role in the control of cell division they have been in the focus of research of proliferation associated diseases ever since, most prominently amongst these cancer. Although initial results obtained from first and second generation, low specificity CDK inhibitors (e.g. Flavopyridol, Roscovitine, Dinaciclib, AT7519, R547) have been sobering the recent approval of the first CDK-inhibitor Palbociclib for the treatment of certain forms of breast cancer clearly demonstrates the suitability of cell cycle CDKs as targets in oncology. Furthermore, in addition to cell cycle CDKs a second group of CDKs have been shown to have important roles in the regulation of gene transcription, and several of the “transcriptional” CDKs have become interesting targets in oncology. Recent results underline the notion that for being effective in the treatment of cancer, CDK inhibition requires very high specificity towards the respective target CDK(s). For example CDK1 knockdown or CDK9 inhibition have been shown to be synthetically lethal in combination with MYC overexpression. Selectivity of compounds within the family of CDKs could so far only be tested using a quite limited number of CDK-Cyclin complexes expressed in human cells. To date there are 20 CDK genes and at least 17 different Cyclin genes described, many of which give rise to different variants, e.g. there are 3 D-type cyclins, two A- and E-type cyclins etc.. Experimental data indicates that at least 50-60 different, biologically relevant CDK-Cyclin complexes may exist, but only a limited number of these are available for biochemical testing of drug candidates so far. We have recombinantly expressed and purified 28 different CDK-Cyclin complexes, covering a significant part of the CDK family, and established in-vitro kinase-activity assays for these recombinant enzymes. The resulting CDK panel represents the most comprehensive array for biochemical testing of this enzyme group currently available. We characterized the specificity of several CDK inhibitors that have been or are currently in preclinical or clinical development with this CDK collection. Results will be presented showing the specificity of these inhibitors not only for CDKs but also for CDKs complexed to different Cyclins. In several cases we could detect signifcant differences in the inhibition of the same CDK complexed to different Cyclins, e.g. a 10fold difference was seen for CDK6 complexes with Cyclin D1-3. A >100 fold difference was detected for CDK3 complexed to either Cyclin E1 or Cyclin C. This screening panel allows generating data on compound selectivity early in development, diminishing the risk of designing a compound with suboptimal target specificity. Citation Format: Daniel Mueller, Frank Totzke, Thomas Weber, Christian Beisenherz-Huss, Diane Kraemer, Carolin Heidemann-Dinger, Constance Ketterer, Chris Eckert, Michael H.G. Kubbutat. Characterization of CDK inhibitors in a biochemical assay using a comprehensive panel of human CDK-cyclin complexes. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2821.

Simple SummaryCyclin-dependent kinases (CDKs) are rich and viable therapeutic targets for various cancers. The emergence of event-driven pharmacology as an alternative to occupancy-driven pharmacology has begun to address the challenges associated with selectively targeting CDKs. In this review article, we summarize the CDK inhibitors that are currently in clinical trials. In addition, we provide an overview of PROTAC- and molecular glue-based strategies to modulate CDK function.The cyclin-dependent kinase (CDK) family of proteins play prominent roles in transcription, mRNA processing, and cell cycle regulation, making them attractive cancer targets. Palbociclib was the first FDA-approved CDK inhibitor that non-selectively targets the ATP binding sites of CDK4 and CDK6. In this review, we will briefly inventory CDK inhibitors that are either part of over 30 active clinical trials or recruiting patients. The lack of selectivity among CDKs and dose-limiting toxicities are major challenges associated with the development of CDK inhibitors. Proteolysis Targeting Chimeras (PROTACs) and Molecular Glues have emerged as alternative therapeutic modalities to target proteins. PROTACs and Molecular glues utilize the cellular protein degradation machinery to destroy the target protein. PROTACs are heterobifunctional molecules that form a ternary complex with the target protein and E3-ligase by making two distinct small molecule–protein interactions. On the other hand, Molecular glues function by converting the target protein into a “neo-substrate” for an E3 ligase. Unlike small molecule inhibitors, preclinical studies with CDK targeted PROTACs have exhibited improved CDK selectivity. Moreover, the efficacy of PROTACs and molecular glues are not tied to the dose of these molecular entities but to the formation of the ternary complex. Here, we provide an overview of PROTACs and molecular glues that modulate CDK function as emerging therapeutic modalities.

Cyclin‐dependent kinase 12‐mediated super‐enhancers as promising targets in cancer therapy

We describe a method to create ligands specific for a given protein family. The method is applied to generate ligand candidates for the cyclin-dependent kinase (CDK) family. The CDK family of proteins is involved in regulating the cell cycle by alternately activating and deactivating the cell's progression through the cycle. CDKs are activated by association with cyclin and are inhibited by complexation with small molecules. X-ray crystal structures are available for three of the thirteen known CDK family members: CDK2, CDK5 and CDK 6. In this work, we use novel computational approaches to design ligand candidates that are potentially inhibitory across the three CDK family members as well as more specific molecules which can potentially inhibit one or any combination of two of the three CDK family members. We define a new scoring term, SpecScore, to quantify the potential inhibitory power of the generated structures. According to a search of the World Drug Alerts, the highest scoring SpecScore molecule that is specific for the three CDK family members shows very similar chemical characteristics and functional groups to numerous molecules known to deactivate several members of the CDK family.

Cyclin-dependent kinase 12 (CDK12) belongs to the cyclin-dependent kinase (CDK) family of serine/threonine protein kinases. In contrast to CDKs which promote cell cycle progression, CDK12 is a transcriptional regulator of various cellular functions, most importantly cellular response to DNA damage and stress. Genomic alterations in CDK12 have been detected in up to 7% of patients with metastatic castration-resistant prostate cancer (CRPC). Phosphoproteomic studies have revealed that Protein Kinase D1 (PrKD1), another member of the serine/threonine kinase family, is the only kinase known to phosphorylate CDK12 at serine 681 (s681) and serine 685 (s685). While there is an increasing body of literature on CDK12 downstream signaling, there is almost no published data on upstream effectors or regulation of CDK12. Using site-directed mutagenesis, we generated CDK12 s681a and s681a+s685 mutants and transfected them into stable C4-2 and C4-2-PrKD1 cell lines to evaluate the interaction between CDK12 and PrKD1. Immunoprecipitation and immunoblotting revealed that endogenous CDK12 is stable in C4-2 cells with known levels of PrKD1 expression. However, stable transfection of C4-2-PrKD1 cells with wild-type CDK12 resulted in the degradation of nascent CDK12, whereas the non-phosphorylated mutants (s681 and s681+s685) remained stable. Our results suggest that PrKD1-mediated phosphorylation of s681and/or s685 residues affect CDK12 stability in C4-2-PrKD1 cells. We confirmed this finding by treating C4-2-PrKD1 cells with MG-132, a 26 S proteasome inhibitor, and repeating the experiment. Proteasomal inhibition rescued nascent transfected CDK12 levels even after PrKD1 phosphorylation. Our study demonstrates that CDK12 degradation might be mediated by PrKD1 phosphorylation at s681 and/or s685. Because PrKD1 and CKD12 are dysregulated across cancers, the results herein presented have potential implications for the treatment of not only prostate cancer but also other human malignancies. Citation Format: Victor Chalfant, Carlos Riveros, Sanjeev Shukla, Teruko Osumi, K Balaji. Signaling of cyclin-dependent kinase 12 (CDK12) in prostate cancer cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1622.

The family of cyclin-dependent kinases (CDKs) has critical functions in cell cycle regulation and controlling of transcriptional elongation. Moreover, dysregulated CDKs have been linked to cancer initiation and progression. Pharmacological CDK inhibition has recently emerged as a novel and promising approach in cancer therapy. This idea is of particular interest to combat pancreatic ductal adenocarcinoma (PDAC), a cancer entity with a dismal prognosis which is owed mainly to PDAC’s resistance to conventional therapies. Here, we review the current knowledge of CDK biology, its role in cancer and the therapeutic potential to target CDKs as a novel treatment strategy for PDAC.

The eukaryotic cell cycle is a tightly regulated series of events coordinated by the periodic activation of members of the cyclin dependent kinases (CDK) family. In addition, a subset of CDK family members play critical roles in transcriptional regulation. Dysregulation of CDK activity by a variety of genetic and epigenetic mechanisms is universally observed in cancer and is thought to be a primary driving force in carcinogenesis, such that there has been longstanding interest in targeting CDKs for cancer therapy.Along with orchestrating the cell cycle and transcriptional events, CDKs have also been directly implicated in the DNA damage response. CDK activity governs cell cycle phase and thus indirectly affects double strand break (DSB) repair pathway choice. Recent evidence also directly implicates CDKs 1 and 2 in homologous recombination DNA repair (HRR) since their activities are crucial at early stages of the repair pathway. These findings suggest that CDK inhibition may not only address aberrant cell proliferation, but may also sensitize cells to a variety of DNA damaging agents as well as PARP inhibition.KeywordsCyclin dependent kinaseCDKCyclinCell cycleHomologous recombinationPARPBRCADNA repairDSB

This study aimed to explore critical genes as potential biomarkers for the diagnosis and prognosis of colorectal cancer (CRC) for clinical utility. To identify and screen candidate genes involved in CRC carcinogenesis and disease progression, we downloaded microarray datasets GSE89076, GSE73360, and GSE32323 from the GEO database identified differentially expressed genes (DEGs), and performed a functional enrichment analysis. A protein-protein interaction network was constructed, and correlated module analysis was performed using STRING and Cytoscape. The Kaplan-Meier survival curve shows the survival of the hub genes. The expression of cyclin-dependent kinase (CDK1), cyclin B1 (CCNB1), and PCNA in tissues and changes in tumor grade were analyzed. A total of 329 DEGs were identified, including 264 upregulated and 65 downregulated genes. The functions and pathways of DEGs include the mitotic cell cycle, poly(A) RNA binding replication, ATP binding, DNA replication, ribosome biogenesis in eukaryotes, and RNA transport. Forty-seven Hub genes were identified, and biological process analysis showed that these genes were mainly enriched in cell cycle and DNA replication. Patients with mutations in CDK1, PCNA, and CCNB1 had poorer survival rates. CDK1, PCNA, and CCNB1 were significantly overexpressed in the tumor tissues. The expression of CDK1 and CCNB1 gradually decreased with increasing tumor grade. CDK1, CCNB1, and PCNA can be used as potential markers for the diagnosis and prognosis of CRC. These genes are overexpressed in colon cancer tissues and are associated with low survival rates in CRC patients.

Simple SummaryInhibition of cyclin-dependent kinase 9 (CDK9) can impact multiple survival pathways in cancers and may be a promising therapeutic approach for glioblastoma, which is known to be highly resistant to treatments and thus challenging to treat. This review assesses the mechanisms by which CDK9 inhibition impacts cancer cell survival pathways in glioblastoma and other cancer types and presents results from clinical trials involving CDK9 inhibitors. A more thorough understanding of these mechanisms may lead to novel combination treatment strategies involving CDK9 inhibitors that can ultimately improve clinical outcomes for glioblastoma patients.Glioblastoma is the most common and aggressive primary malignant brain tumor, and more than two-thirds of patients with glioblastoma die within two years of diagnosis. The challenges of treating this disease mainly include genetic and microenvironmental features that often render the tumor resistant to treatments. Despite extensive research efforts, only a small number of drugs tested in clinical trials have become therapies for patients. Targeting cyclin-dependent kinase 9 (CDK9) is an emerging therapeutic approach that has the potential to overcome the challenges in glioblastoma management. Here, we discuss how CDK9 inhibition can impact transcription, metabolism, DNA damage repair, epigenetics, and the immune response to facilitate an anti-tumor response. Moreover, we discuss small-molecule inhibitors of CDK9 in clinical trials and future perspectives on the use of CDK9 inhibitors in treating patients with glioblastoma.

Recent research highlights that RNA processing is systematically altered in cancer, demonstrating the pivotal influence of RNA deregulation on tumorigenesis, growth and progression. Based on our expanding knowledge of RNA biology, RNA deregulation has drawn much attention from the perspective of cancer therapy. Indeed, small molecules that attack the RNA maturation processes and produce aberrant RNA are currently under development. The first step in gene expression is transcription, which involves copying a DNA sequence to make an RNA. Transcription is performed by enzymes called RNA polymerase (Pol II) that links nucleotides to form RNA strand. The C-terminal domain (CTD) of Pol II comprises heptapeptide Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 repeats and is dynamically post-translationally phosphorylated to regulate the distinct stages of transcription initiation, elongation and termination steps. Particularly, Ser2 and Ser5 phosphorylation have the closest association with the regulation of transcription. Therefore, we focus on the kinases that carry out this modification. Cyclin-dependent kinase 12 (CDK12) belongs to the cyclin-dependent kinase (CDK) family of serine/threonine protein kinases. CDK12 regulates the elongation step of RNA transcription by phosphorylation of Ser2 on the CTD. CDK12 complexes with cyclin K to promote the elongation of transcripts, such as BRCA1 and BRCA2, involved in DNA damage responses. It is expected that the inhibition of CDK12 have a synergistic effect with PARP inhibitors and chemotherapeutic reagents. Here we present data on CRD-1835439, orally available, selective, and first in class CDK12 inhibitor with optimized drug-properties. Biochemically, CRD-1835439 is more than 300-fold selective over other CDK isoforms such as CDK7 and CDK9. Importantly, cell based assays showed CRD-1835439 has selective inhibitory activity for phosphorylation of Ser2 on the CTD but not for other Ser5 and Ser7 phosphorylation. Comprehensive analysis by PolyA-seq, Chip-seq and RNA-seq revealed that CRD-1835439 inhibits transcriptional elongation on DNA damage response genes including BRCA1 and BRCA2. The effects on DNA damage and repair were assessed by immunofluorescence staining for γH2AX and RAD51 proteins. In vivo, oral treatment with CRD-1835439 in cell line derived xenograft models, resulted in increase of DNA damage biomarkers, induction of apoptosis and tumor regressions in a dose-dependent fashion. Besides the efficacy as a single reagent, the efficacy was augmented when CRD-1835439 was combined with PARP inhibitors in in vitro and in vivo. In summary, the novel small-molecule CDK12 inhibitor CRD-1835439 demonstrated preclinical efficacy along with target engagement. Our results underscore the preclinical therapeutic potential of CRD-1835439 as a single-agent or in combination with PARP inhibitors for the treatment of intractable cancers. Citation Format: Hiroko Yamakawa, Akio Mizutani, Yasuyoshi Arikawa, Shunsuke Ebara, Yoshihiko Satoh, Daisuke Morishita. Discovery and preclinical evaluation of a novel highly selective and potent CDK12 inhibitor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5485.

The regulation of the cancer cell cycle heavily relies on cyclin-dependent kinases (CDKs). Targeting CDKs has been identified as a promising approach for effective cancer therapy. In recent years, there has been significant attention paid towards developing small-molecule CDK inhibitors in the field of drug discovery. Notably, five such inhibitors have already received regulatory approval for the treatment of different cancers, including breast tumors, lung malignancies, and hematological malignancies. This review provides an overview of the synthetic routes used to produce 17 representative small-molecule CDK inhibitors that have obtained regulatory approval or are currently being evaluated through clinical trials. It also discusses their clinical applications for treating CDK-related diseases and explores the challenges and limitations associated with their use in a clinical setting, which will stimulate the further development of novel CDK inhibitors. By integrating therapeutic applications, synthetic methodologies, and mechanisms of action observed in various clinical trials involving these CDK inhibitors, this review facilitates a comprehensive understanding of the versatile roles and therapeutic potential offered by interventions targeting CDKs.

We describe a method to create ligands specific for a given protein family. The method is applied to generate ligand candidates for the cyclin-dependent kinase (CDK) family. The CDK family of proteins is involved in regulating the cell cycle by alternately activating and deactivating the cell's progression through the cycle. CDKs are activated by association with cyclin and are inhibited by complexation with small molecules. X-ray crystal structures are available for three of the thirteen known CDK family members: CDK2, CDK5 and CDK 6. In this work, we use novel computational approaches to design ligand candidates that are potentially inhibitory across the three CDK family members as well as more specific molecules which can potentially inhibit one or any combination of two of the three CDK family members. We define a new scoring term, SpecScore, to quantify the potential inhibitory power of the generated structures. According to a search of the World Drug Alerts, the highest scoring SpecScore molecule that is specific for the three CDK family members shows very similar chemical characteristics and functional groups to numerous molecules known to deactivate several members of the CDK family.

CDK12 and CDK13 belong to the cyclin-dependent kinase (CDK) family, which includes at least 20 different human CDKs and CDK-like enzymes. One subclass of CDKs (e.g. CDK7, CDK8, CDK9, CDK12 and CDK13) preferentially regulates transcription by phosphorylation of the C-terminal domain of RNA polymerase II (RNAPII), whereas another subgroup of CDKs plays a pivotal role in controlling cell cycle progression (e.g. CDK1, CDK2, CDK4, CDK6 and CDK7). Both groups - cell cycle as well as transcriptional CDKs - have been reported to be involved in cancer development and progression. Recent reports indicated CDK12 to be involved in DNA damage repair mechanisms and linked its mutation to high-grade serous ovarian carcinoma rendering CDK12 a promising target for drug development. However, the pivotal role of individual CDKs and their complex regulation requests for highly selective inhibitors to avoid unwanted adverse effects. Non-specific first-generation CDK-inhibitors cause toxicity in vivo issues. They showed little to no therapeutic window in clinical trials and thus shifted the focus to the optimization of selective small molecule CDK inhibitors. To identify selective small molecular weight inhibitors of CDK12 and CDK13 we employed a rationale drug discovery approach based on a focused kinase library screen. Screening of slightly over 16.000 compounds identified several hit compound classes. Medicinal chemistry based optimization yielded nanomolar CDK12 inhibitors. The selectivity of these improved CDK12 inhibitors is excellent, when tested against 12 CDK family members. Such selective CDK12 inhibitors have also shown promising physicochemical properties, indicating lead- and drug-likeness. Although, potency on the target still needs to be improved, the frontrunners from our selective CDK12 inhibitor family have shown cellular inhibition of CDK12 substrate phosphorylation such as those of RNA polymerase II. Currently, potency of these CDK12 inhibitors is being improved by using structure-guided medicinal chemistry-based optimization. The resulting lead candidates will then be tested in in vivo cancer models. Citation Format: Axel Choidas, Carsten Schultz-Fademrecht, Carsten Degeenhardt, Peter Habenberger, Uwe Koch, Jan E. Eickhoff, Ann Kathrin Greifenberg, Peter Nussbaumer, Matthias Geyer, Bert M. Klebl. Identification of highly selective inhibitors of cyclin-dependent kinase 12. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2823.

Polycystic Kidneys Diseases (PKDs) represent a group of disorders characterized by the growth of fluid filled cysts in kidneys and other organs. No effective treatment is currently available for PKDs. A link between dysfunctional cilia and cell cycle regulation has been recently discovered as the most proximal trigger of cystogenesis. We examined the benefit of therapeutic correction of the cell cycle dysregulation in PKD with the cyclin dependent kinase (CDK) inhibitor roscovitine. Our data show that CDK inhibition results in the robust, long lasting arrest of cystogenesis in both slowly progressive and in aggressive mouse models of PKD. Dissection of the molecular mechanism of CDK inhibitor action shows effective cell cycle arrest, transcriptional inhibition and attenuation of apoptosis. Roscovitine treatment has proven highly effective in preserving the renal function in treated animals. We also detected significant downregulation of cAMP and aquaporin 2 in treated kidneys, suggesting the effect of CDK inhibition on preservation of epithelial differentiation. CDK inhibition was shown to be efficacious in multiple other types of renal diseases with abnormal cell cycle and proliferation. Thus, therapies directly targeting coordinate regulation of proliferation and apoptosis are emerging as effective approaches to treat multiple renal diseases.