Abstract 129: Assessing the mechanism and therapeutic potential of modulators of the human mediator complex-associated protein kinases CDK8 and CDK19

Mediator-associated protein kinases CDK8 and CDK19 are context-dependent drivers or suppressors of tumorigenesis. Their inhibition is predicted to have pleiotropic effects, but it is unclear whether this will impact on the clinical utility of CDK8/19 inhibitors. We identified two structurally differentiated chemical series, suitable for exploring their function. In addition to tools that fulfil the criteria set out for chemical probes, the lead compounds from each series, CCT251921 and MSC2530818, had optimal pharmacological and pharmaceutical properties making them suitable for preclinical studies. Having potent, highly selective, orally bioavailable exemplar compounds from these series in hand, we were well positioned to investigate the therapeutic potential of dual CDK8/19 inhibition. The compounds exhibited modest anti-tumor activity in colorectal cancer cell line xenograft models with modulation of p-STAT1SER727, a target engagement biomarker, and altered gene expression profiles, including super-enhancer regulated gene expression, consistent with the inhibition of CDK8/19. In PDX-derived cell cultures we observed inhibition of soft-agar growth in cells derived from different tumor types. However, we only detected significant antitumour activity in 1 of 6 colorectal PDX models tested in vivo, and one example of sensitization to standard of care chemotherapy, despite showing inhibition of p-STAT1SER727. Acute myeloid leukemia cells were the most sensitive cancer type in the PDX panel with therapeutic potency seen in systemic and sub-cutaneous models. Significantly, the compounds impacted on stem cell biology. In a bone progenitor model we saw dose-responsive activation and inhibition of markers of bone matrix and bone deposition that was distinct from WNT blockade. Treatment of a diverse collection of normal cell co-culture models detected a unique response profile consistent with stimulation of an immune/inflammatory response. In vivo treatment of a genetically engineered mouse model expressing oncogenic beta-catenin shifted cells within hyperplastic intestinal crypts from a stem cell to a transit amplifying phenotype. Finally, in pre-clinical tolerability studies we observed a similar, widespread adverse safety profile at therapeutically relevant exposures for both CCT251921 and MSC2530818. At the concentrations tested we detected >80% inhibition of p-STAT1SER727 and increased IL-12 plasma levels. Since the observed pathological effects were generated with two potent, highly selective, but structurally distinct compounds, we conclude that the adverse consequences of treatment are the direct result of inhibition of CDK8 and/or CDK19. The serious and complex nature of the toxicity observed indicates that the clinical development of either series of CDK8/19 modulators, or other chemotypes with similar profiles, will be extremely challenging.

Citation Format: Paul A. Clarke, Maria-Jesus Ortiz-Ruiz, Robert Te Poele, Olajumoke Adeniji-Popoola, Gary Box, Christina Esdar, Kenneth Ewan, Sharon Gowan, Alexis De Haven Brandon, Phllip Hewitt, Wolfgang Kaufmann, Aurelie Mallinger, Florence Raynaud, Felix Rohdich, Kai Schiemann, Stephanie Simon, Richard Schneider, Melanie Valenti, Julian Blagg, Trevor Dale, Suzanne Eccles, Paul Workman, Dirk Wienke Dirk Wienke. Assessing the mechanism and therapeutic potential of modulators of the human mediator complex-associated protein kinases CDK8 and CDK19 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 129. doi:10.1158/1538-7445.AM2017-129

Assessing the mechanism and therapeutic potential of modulators of the human Mediator complex-associated protein kinases

Mediator-associated kinases CDK8/19 are context-dependent drivers or suppressors of tumorigenesis. Their inhibition is predicted to have pleiotropic effects, but it is unclear whether this will impact on the clinical utility of CDK8/19 inhibitors. We discovered two series of potent chemical probes with high selectivity for CDK8/19. Despite pharmacodynamic evidence for robust on-target activity, the compounds exhibited modest, though significant, efficacy against human tumor lines and patient-derived xenografts. Altered gene expression was consistent with CDK8/19 inhibition, including profiles associated with super-enhancers, immune and inflammatory responses and stem cell function. In a mouse model expressing oncogenic beta-catenin, treatment shifted cells within hyperplastic intestinal crypts from a stem cell to a transit amplifying phenotype. In two species, neither probe was tolerated at therapeutically-relevant exposures. The complex nature of the toxicity observed with two structurally-differentiated chemical series is consistent with on-target effects posing significant challenges to the clinical development of CDK8/19 inhibitors.

Structure-Based Optimization of Potent, Selective, and Orally Bioavailable CDK8 Inhibitors Discovered by High-Throughput Screening

The mediator complex-associated cyclin dependent kinase CDK8 regulates β-catenin-dependent transcription following activation of WNT signaling. Multiple lines of evidence suggest CDK8 may act as an oncogene in the development of colorectal cancer. Here we describe the successful optimization of an imidazo-thiadiazole series of CDK8 inhibitors that was identified in a high-throughput screening campaign and further progressed by structure-based design. In several optimization cycles, we improved the microsomal stability, potency, and kinase selectivity. The initial imidazo-thiadiazole scaffold was replaced by a 3-methyl-1H-pyrazolo[3,4-b]-pyridine which resulted in compound 25 (MSC2530818) that displayed excellent kinase selectivity, biochemical and cellular potency, microsomal stability, and is orally bioavailable. Furthermore, we demonstrated modulation of phospho-STAT1, a pharmacodynamic biomarker of CDK8 activity, and tumor growth inhibition in an APC mutant SW620 human colorectal carcinoma xenograft model after oral administration. Compound 25 demonstrated suitable potency and selectivity to progress into preclinical in vivo efficacy and safety studies.

Abstract 3869: Phosphoproteomic-based identification of CDK8/CDK19 substrates in colorectal cancer

Introduction

CDK8 is an oncogenic cyclin-dependent kinase that exists as part of the kinase module within the Mediator complex. This complex interacts with the transcription machinery to regulate transcription; signal transduction pathways, including the WNT pathway; and biological processes, such as cell cycle progression. Recently, we identified a series of 3,4,5-trisubstituted pyridines as inhibitors of CDK8 and, its paralogue, CDK19 in colorectal cancer (CRC). Until now, there have been few validated substrates of CDK8/19. Here, we describe a motif-based phospho-proteomic approach, utilizing our 3,4,5-trisubstituted pyridine inhibitors that we have used to identify substrates of CDK8/19. These substrates could represent useful biomarkers for future drug discovery research.

Experimental Outline

We used a COLO205 cell line (COLO205 C4) carrying a TCF/LEF reporter construct responsive to CDK8/19 inhibition and CCT251545, a compound we have previously shown to be a potent and selective inhibitor of CDK8/19. Cells were treated with 350 nM CCT251545 (10 x EC50) for 2 or 6 hours. Proteins were then extracted from treated and control cells, trypsin-digested and immunoprecipitated for phospho-peptide enrichment using proline-directed motifs: PXS*P, S*PXR/K, PXS*PXR/K + T*PE + ST*P + K/HS*P. Potential substrates were identified by LC-MS/MS and validated by immunoprecipitation and western blotting. Substrates were validated in another CRC cell line, SW620, which harbors CRISPR knockouts for CDK8/19.

Summary of Results

LC-MS/MS analyses of COLO205 C4 cell extracts revealed a number of potential CDK8/19 substrates, including some Mediator complex subunits such as MED13, transcriptional coactivators such as HCFC1, and transcription factors such as STAT1. Phosphorylation of STAT1SER727 was the top ranked hit and follow-up studies, in COLO205 C4 cells and xenografts, confirmed repression of STAT1SER727 phosphorylation in the presence of CCT251545. An inactive analogue, CCT251099, and other kinase inhibitors (flavopiridol, KN-93, PD 0325901 and SB 202190) did not block STAT1SER727 phosphorylation. Repression of STAT1SER727 phosphorylation upon treatment with CCT251545 was also observed in SW620 and LS174T CRC cells and xenografts.

Conclusion

A motif-driven, mass spectroscopy-based phospho-proteomic study identified candidate substrates of CDK8/19. Phosphorylation of STAT1SER727 was validated as a useful marker of target engagement in CRC cell lines both in vitro and in vivo.

Citation Format: Olajumoke O. Popoola, Rahul Samant, Maria-Jesus Ortiz-Ruiz, Aurelie Mallinger, Will Court, Steve Hobbs, Robert Te-Poele, Mark Stubbs, Rosemary Burke, Christina Esdar, Kai Schiemann, Dirk Wienke, Sue Eccles, Julian Blagg, Paul Workman, Paul Clarke. Phosphoproteomic-based identification of CDK8/CDK19 substrates in colorectal cancer. [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 3869.

Discovery of Potent, Selective, and Orally Bioavailable Small-Molecule Modulators of the Mediator Complex-Associated Kinases CDK8 and CDK19

The Mediator complex-associated cyclin-dependent kinase CDK8 has been implicated in human disease, particularly in colorectal cancer where it has been reported as a putative oncogene. Here we report the discovery of 109 (CCT251921), a potent, selective, and orally bioavailable inhibitor of CDK8 with equipotent affinity for CDK19. We describe a structure-based design approach leading to the discovery of a 3,4,5-trisubstituted-2-aminopyridine series and present the application of physicochemical property analyses to successfully reduce in vivo metabolic clearance, minimize transporter-mediated biliary elimination while maintaining acceptable aqueous solubility. Compound 109 affords the optimal compromise of in vitro biochemical, pharmacokinetic, and physicochemical properties and is suitable for progression to animal models of cancer.

Abstract PR02: Identification of a potent and selective chemical probe for exploring the role of CDK8/19 in cancer biology

The discovery of chemical probes by testing libraries of small molecules against cellular pathway screens has re-emerged as a hit discovery strategy. We previously reported a series of 3,4,5-trisubstituted pyridines identified from a high-throughput cell-based reporter assay of WNT pathway signalling. We were able to optimise this series and identified CCT251545 as a chemical tool that potently inhibits readouts of WNT signalling pathway activity with evidence for in vivo activity. A series of cell-based assays activating WNT signalling at distinct loci identified the TCF locale as the likely target. CCT251545 was not a general inhibitor of the transcription machinery and did not affect expression of TCFs. Regulation of beta-catenin/TCF transcription involves recruitment or loss of DNA binding proteins, histone modification and also interaction with additional protein networks. Given the potential complexity of these multiple networked interactions, we employed an unbiased chemical proteomics strategy to identify molecular targets of CCT251545. Knowledge of the structure-activity-relationships of the series allowed us to identify derivatives that retained cellular potency and were suitable for linker coupling to generate an affinity matrix. SILAC-based quantitative mass spectrometry identified target proteins captured by incubation of the immobilised compound with lysates from cells grown in media with different forms of isotopically-labeled amino acids. Competition experiments with unconjugated analogues allowed us to identify affinities of proteins bound to the immobilised probe. These experiments identified Mediator complex-associated protein kinases CDK8 and CDK19 as targets of the 3,4,5-trisubstituted pyridine series. We show that CCT251545, is a selective and potent ATP competitive chemical probe for these two kinases, with >100-fold selectivity over 291 other kinases. X-ray crystallography demonstrates a Type 1 binding mode involving insertion of the CDK8 C-terminus into the ligand-binding site. In contrast to Type II-like CDK8/19 ligands, CCT251545 displays potent cell-based activity. We demonstrate that CCT251545 not only alters WNT-pathway regulated gene expression, but also other CDK8/19 targets including genes regulated by STAT1. Consistent with this we find that phosphorylation of STAT1SER727 is a biomarker of CDK8 kinase activity in vitro and in vivo. Finally, we show in vivo activity of CCT251545 in WNT-dependent tumours. The potential role for CDK8, and by implication CDK19, as an oncoprotein further highlights the need for an active and specific probe compound that can be used as a complementary reagent to RNAi tools. Here we demonstrate that the small molecule CCT251545 fulfils this requirement as a potent, selective, cell-active chemical probe that can be used with confidence to explore the consequences of CDK8/19 kinase function in cellular and in vivo animal models.

Citation Format: Paul A. Clarke, Trevor Dale, Christina Esdar, Dennis Waalboer, Olajumoke Adeniji-Popoola, Maria-Jesus Ortiz-Ruiz, Aurelie Mallinger, Ken Ewan, Robert te Poele, Sharon Gowan, Paul Workman, Kai Schiemann, Suzanne A. Eccles, Dirk Wienke, Julian Blagg. Identification of a potent and selective chemical probe for exploring the role of CDK8/19 in cancer biology. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr PR02.

A selective chemical probe for exploring the role of CDK8 and CDK19 in human disease

There is unmet need for chemical tools to explore the role of the Mediator complex in human pathologies ranging from cancer to cardiovascular disease. Here we determine that CCT251545, a small-molecule inhibitor of the WNT pathway discovered through cell-based screening, is a potent and selective chemical probe for the human Mediator complex-associated protein kinases CDK8 and CDK19 with >100-fold selectivity over 291 other kinases. X-ray crystallography demonstrates a type 1 binding mode involving insertion of the CDK8 C terminus into the ligand binding site. In contrast to type II inhibitors of CDK8 and CDK19, CCT251545 displays potent cell-based activity. We show that CCT251545 and close analogs alter WNT pathway-regulated gene expression and other on-target effects of modulating CDK8 and CDK19, including expression of genes regulated by STAT1. Consistent with this, we find that phosphorylation of STAT1(SER727) is a biomarker of CDK8 kinase activity in vitro and in vivo. Finally, we demonstrate in vivo activity of CCT251545 in WNT-dependent tumors.

Discovery of potent, orally bioavailable, small-molecule inhibitors of WNT signaling from a cell-based pathway screen

WNT signaling is frequently deregulated in malignancy, particularly in colon cancer, and plays a key role in the generation and maintenance of cancer stem cells. We report the discovery and optimization of a 3,4,5-trisubstituted pyridine 9 using a high-throughput cell-based reporter assay of WNT pathway activity. We demonstrate a twisted conformation about the pyridine-piperidine bond of 9 by small-molecule X-ray crystallography. Medicinal chemistry optimization to maintain this twisted conformation, cognisant of physicochemical properties likely to maintain good cell permeability, led to 74 (CCT251545), a potent small-molecule inhibitor of WNT signaling with good oral pharmacokinetics. We demonstrate inhibition of WNT pathway activity in a solid human tumor xenograft model with evidence for tumor growth inhibition following oral dosing. This work provides a successful example of hypothesis-driven medicinal chemistry optimization from a singleton hit against a cell-based pathway assay without knowledge of the biochemical target.

P3-16-14: Effect of TG02, a Multikinase Inhibitor, on Triple Negative Breast Cancer Cells

Background

Breast cancer is the most common neoplasia in women. Formerly, we reported that the MAPK Erk5 participates in the proliferation of breast cancer cells in vitro, it is overexpressed in the tumours of a number of breast cancer patients, and its overexpression is an independent prognostic marker for disease-free survival. In addition, inhibition of Erk5 sensitized cells to treatments commonly used in the breast cancer clinic. Therefore, Erk5 may represent a novel therapeutic target in breast cancer. Here we describe the preclinical activity of TG02, a novel multi-kinase inhibitor being developed by Tragara Pharmaceuticals, in triple negative breast cancer (TNBC). TG02 presents a unique kinase inhibitory spectrum, combining Erk5 inhibitory properties with inhibition of CDKs and certain receptor tyrosine kinases.

Material and methods: The action of TG02 on cell proliferation of TNBC cell lines was carried out by the MTT-based assay, and its action on cell death and cell cycle progression was analyzed by flow cytometry. The expression of different kinases and other proteins implicated in cell cycle, apoptosis and DNA damage responses were analyzed by western blotting. Studies on the action of TG02 in combination with chemotherapy were performed in MDAMB231 and HBL100 cells, and the potency of the combination was quantitated with the Calcusyn software. In vivo studies on the action of TG02 were performed in mice xenografted with the TNBC cell line MDA-MB231.

Results: The TNBC cell lines analyzed showed high levels of Erk5 expression, and Erk5 was active under resting conditions in some of them. TG02 inhibited the kinase activity of Erk5 even though TG02 did not affect the Erk5 upstream activating kinase Mek5. TG02 showed an inhibitory effect of phosphorylation of residue Thr732 in the C-terminal tail of Erk5 without affecting the phosphorylation of the activation loop TEY motif. Cell proliferation studies indicated that one group of TNBC cells were very sensitive to the action of this compound (IC50 ≤100 nM) and another group were more resistant. TG02 induced cell cycle arrest at the early G1 and G2 phases of cell cycle, and triggered cell death in MDAMB231 (representative cell line of the most resistant group), and induced a strong effect of apoptosis and a DNA damage response in HCC1187(representative of the most sensitive group). In vitro studies indicated that TG02 sensitizes TNBC cells to chemotherapy, showing additive or synergistic effects depending of the doses. In vivo studies indicated that TG02 exerted a strong antitumoral action in mice bearing MDA-MB231-derived tumours.

Conclusions: TNBC cells are very sensitive to TG02, both in vitro and in vivo. The inhibits the kinase activity of Erk5, which, together with the targeting of other kinases, may contribute to the induction of cell cycle arrest or apoptosis in response to the compound in TNBC cells. TG02 synergized with chemotherapy, supporting the possibility of using this drug in combination therapy. Taken together, these preclinical studies establish the bases for the clinical development of this compound for the treatment of TNBC.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P3-16-14.