Christopher R. Denz

Structure and Property Based Design of Pyrazolo[1,5-a]pyrimidine Inhibitors of CK2 Kinase with Activity in Vivo.

In this letter, we describe the design, synthesis, and structure-activity relationship of 5-anilinopyrazolo[1,5-a]pyrimidine inhibitors of CK2 kinase. Property-based optimization of early leads using the 7-oxetan-3-yl amino group led to a series of matched molecular pairs with lower lipophilicity, decreased affinity for human plasma proteins, and reduced binding to the hERG ion channel. Agents in this study were shown to modulate pAKT(S129), a direct substrate of CK2, in vitro and in vivo, and exhibited tumor growth inhibition when administered orally in a murine DLD-1 xenograft.

Potent and Selective Inhibitors of CK2 Kinase Identified through Structure-Guided Hybridization

In this paper we describe a series of 3-cyano-5-aryl-7-aminopyrazolo[1,5-a]pyrimidine hits identified by kinase-focused subset screening as starting points for the structure-based design of conformationally constrained 6-acetamido-indole inhibitors of CK2. The synthesis, SAR, and effects of this novel series on Akt signaling and cell proliferation in vitro are described.

Potent and Selective CK2 Kinase Inhibitors with Effects on Wnt Pathway Signaling in Vivo

The Wnt pathway is an evolutionarily conserved and tightly regulated signaling network with important roles in embryonic development and adult tissue regeneration. Impaired Wnt pathway regulation, arising from mutations in Wnt signaling components, such as Axin, APC, and β-catenin, results in uncontrolled cell growth and triggers oncogenesis. To explore the reported link between CK2 kinase activity and Wnt pathway signaling, we sought to identify a potent, selective inhibitor of CK2 suitable for proof of concept studies in vivo. Starting from a pyrazolo[1,5-a]pyrimidine lead (2), we identified compound 7h, a potent CK2 inhibitor with picomolar affinity that is highly selectivity against other kinase family enzymes and inhibits Wnt pathway signaling (IC50 = 50 nM) in DLD-1 cells. In addition, compound 7h has physicochemical properties that are suitable for formulation as an intravenous solution, has demonstrated good pharmacokinetics in preclinical species, and exhibits a high level of activity as a monotherapy in HCT-116 and SW-620 xenografts.

Structure-Based Design of Selective Noncovalent CDK12 Inhibitors

Cyclin‐dependent kinase (CDK) 12 knockdown via siRNA decreases the transcription of DNA‐damage‐response genes and sensitizes BRCA wild‐type cells to poly(ADP‐ribose) polymerase (PARP) inhibition. To recapitulate this effect with a small molecule, we sought a potent, selective CDK12 inhibitor. Crystal structures and modeling informed hybridization between dinaciclib and SR‐3029, resulting in lead compound 5 [(S)‐2‐(1‐(6‐(((6,7‐difluoro‐1H‐benzo[d]imidazol‐2‐yl)methyl)amino)‐9‐ethyl‐9H‐purin‐2‐yl)piperidin‐2‐yl)ethan‐1‐ol]. Further structure‐guided optimization delivered a series of selective CDK12 inhibitors, including compound 7 [(S)‐2‐(1‐(6‐(((6,7‐difluoro‐1H‐benzo[d]imidazol‐2‐yl)methyl)amino)‐9‐isopropyl‐9H‐purin‐2‐yl)piperidin‐2‐yl)ethan‐1‐ol]. Profiling of this compound across CDK9, 7, 2, and 1 at high ATP concentration, single‐point kinase panel screening against 352 targets at 0.1 μm, and proteomics via kinase affinity matrix technology demonstrated the selectivity. This series of compounds inhibits phosphorylation of Ser2 on the C‐terminal repeat domain of RNA polymerase II, consistent with CDK12 inhibition. These selective compounds were also acutely toxic to OV90 as well as THP1 cells.

Discovery of 2,6-disubstituted pyrazine derivatives as inhibitors of CK2 and PIM kinases

The design and synthesis of a novel series of 2,6-disubstituted pyrazine derivatives as CK2 kinase inhibitors is described. Structure-guided optimization of a 5-substituted-3-thiophene carboxylic acid screening hit (3a) led to the development of a lead compound (12b), which shows inhibition in both enzymatic and cellular assays. Subsequent design and hybridization efforts also led to the unexpected identification of analogs with potent PIM kinase activity (14f).

Target deconvolution efforts on Wnt pathway screen reveal dual modulation of oxidative phosphorylation and SERCA2

Wnt signaling is critical for development, cell proliferation and differentiation, and mutations in this pathway resulting in constitutive signaling have been implicated in various cancers. A pathway screen using a Wnt‐dependent reporter identified a chemical series based on a 1,2,3‐thiadiazole‐5‐carboxamide (TDZ) core with sub‐micromolar potency. Herein we report a comprehensive mechanism‐of‐action deconvolution study toward identifying the efficacy target(s) and biological implication of this chemical series involving bottom‐up quantitative chemoproteomics, cell biology, and biochemical methods. Through observing the effects of our probes on metabolism and performing confirmatory cellular and biochemical assays, we found that this chemical series inhibits ATP synthesis by uncoupling the mitochondrial potential. Affinity chemoproteomics experiments identified sarco(endo)plasmic reticulum Ca2+‐dependent ATPase (SERCA2) as a binding partner of the TDZ series, and subsequent validation studies suggest that the TDZ series can act as ionophores through SERCA2 toward Wnt pathway inhibition.

Abstract C274: FGF receptor mutations and fusions are therapeutic targets for inhibition by AZD4547.

Aberrant fibroblast growth factor (FGF) signaling has been implicated in tumorgenesis and chemoresistance in a number of cancer types including lung, breast, gastric, endometrial as well as others. The small molecule FGF receptor (FGFR) kinase inhibitor, AZD4547, is currently in Phase I/II clinical development (gastric, squamous lung and breast cancer) to test the FGFR amplified tumor-driven hypothesis. Our aim was to identify and characterize additional genetic subtypes based on reported FGFR aberrations and determine the sensitivity to AZD4547. Eight mutations in FGFR2: G614V, W290C, H544Q, D238N, N211I, T786K, K659N, and N550K and 3 mutations in FGFR3: S249C, R248C, Y373C, plus the FGFR fusions FGFR3-TACC3 and FGFR1-TACC1 found in ∼3% of glioblastoma [Singh et al., Science 337, 1231 (2012)] were assessed for in vitro transformation of normal breast epithelial cells (MCF10A) in a 3D soft agar colony formation assay. Several FGFR mutations/fusions were able to drive in vitro transformation as well as increase downstream signaling (pFGFR, pFRS2) in MCF10A engineered lines. For most FGFR mutations AZD4547 inhibited colony formation and downstream signaling at concentrations comparable to the WT isoforms (10- 100nM). Taken together, these findings characterized gain-of-function mutations in FGFR2, FGFR3, and FGFR-TACC fusions and demonstrated the antiproliferative activity of AZD4547 against key genetic sub-types of FGFR aberrant cancers. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C274. Citation Format: Christopher R. Denz, Nin Guan, Kelly Jacques, Elaine Kilgour, Emma Jenkins, Sylvie Guichard, Paul Smith. FGF receptor mutations and fusions are therapeutic targets for inhibition by AZD4547. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C274.

Abstract 3133: Identification and functional validation of novel genetically-linked breast cancer targets through pooled gain-of-function screening.

Breast cancer is one of the most common cancer types, with greater than 450,000 deaths reported per year worldwide. Through genome wide sequencing efforts, multiple genetic alterations have been identified, including mutations and amplifications in genes such as v-erb-b2 erythroblastic leukemia viral oncogene homolog 2 (ERBB2), GATA binding protein 3 (GATA3), phosphatidylinositol 3-kinase alpha catalytic subunit (PIK3CA) as well as novel genomic rearrangements such as the recently identified MAGI3-AKT3 fusion. Now that breast cancer can be characterized to an unprecedented level, one of the key challenges remaining is to identify and distinguish critical ‘driver’ events responsible for tumor progression, from neutral ‘passenger’ lesions. In order to achieve this, we utilized high resolution aCGH analysis of 50 purified breast cancer samples (made up of Her2+, estrogen receptor positive (ER+) and triple negative tumors with variable responses to SOC regimens), in combination with a Gain-of-Function transformation screen to identify and validate novel breast targets. 158 genomic regions were found to be recurrently amplified, consisting of 759 genes in total. The top 32 focally amplified genes, along with 12 cancer-relevant mutant alleles were prioritized and a library generated utilizing the pTRIPZ-tetracycline regulated inducible lentiviral vector system. These 44 genes were subsequently combined into 16 different target pools (5-13 targets per pool, co-expressing genes that were co-amplified in the same clinical specimen) and evaluated for their ability to transform immortalized breast epithelial MCF10A cells (both wild-type and p53 -/- cells). Through this screening approach, p21-activated kinase 1 (PAK1) was identified, whose kinase activity was required to robustly transform MCF10A cells through regulating multiple signalling pathways including MAPK. Several other putative oncogenes were also identified and will be presented here, including the glycosyltransferse asparagine-linked glycosylation 8 (ALG8). Interestingly, PAK1 and ALG8 are co-amplified in both breast (8%) and ovarian cancers (11%). Our target validation studies have suggested that ALG8 can support PAK1-induced transformation, as dramatic suppression of soft-agar colony growth was seen in co-amplified breast cancer cell lines upon combined siRNA treatment to both targets. Thus, this combined high resolution aCGH profiling and functional screening approach has enabled the successful identification of novel oncogenic targets in breast cancer. Citation Format: Krishna Vasudevan, Axel Hernandez, Zhongwu Lai, Yonghong Xiao, Nin Guan, Carolyn Hardy, Robert Godin, Christopher Denz, Minwei Ye, Elizabeth Lenkiewicz, Stephanie Savage, Michael T. Barrett, Donna Prunkard, Peter Rabinovitch, Mark Basik, Ewa Przybytkowski, Kevin Webster, Michael Zinda, Emma-Louise Jenkins. Identification and functional validation of novel genetically-linked breast cancer targets through pooled gain-of-function screening. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3133. doi:10.1158/1538-7445.AM2013-3133

Abstract 3770: PK/PD/Efficacy characterization of AZ285, a selective CK2 kinase inhibitor

Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL Casein Kinase 2 (CK2) is an abundant, highly conserved protein serine/threonine kinase with numerous physiological targets and participates in the maintenance of cell viability with a role in cell growth and proliferation. While the expression level of CK2 in normal cells is tightly regulated, there is an increasing body of evidence demonstrating its over expression in cancerous cells, thereby making inhibition a viable chemotherapeutic target. Here we will describe a mathematical tumor growth inhibition model describing the relationship between systemic exposure to a potent inhibitor of CK2 (AZ285) and efficacy in the HCT116 xenograft model. Furthermore, a PK/PD model describing the onset, intensity, and duration of the pAKT and cleaved caspase 3 response as function of concentration and time is described and linked to pre-clinical xenograft efficacy outcomes. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3770. doi:1538-7445.AM2012-3770

Abstract 3907: Discovery and characterization of AZ285 as a potent and selective inhibitor of CK2 kinase

Casein Kinase 2 (CK2) is a highly conserved and ubiquitously expressed serine/threonine kinase that regulates several key oncogenic signaling pathways, including PI3K/AKT, and NFkB and Wnt, and whose targeted overexpression in transgenic animal models results in neoplastic growth. Herein we describe the identification of AZ285, a potent pyrazolo[1,5-a]pyrimidine-derived inhibitor of CK2 with a high degree of kinase selectivity. AZ285 depletes levels of the CK2 substrates pAKT S129 and PTEN S370 and induces apoptosis in cells in a concentration-dependent manner. Optimization of early leads was aided in part by cell wash-out experiments and X-ray cocrystallography with huCK2a and resulted in an agent with physical properties and DMPK characteristics suitable for evaluation in disease model studies. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3907. doi:1538-7445.AM2012-3907