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We describe here the identification and characterization of 2 novel inhibitors of the fibroblast growth factor receptor (FGFR) family of receptor tyrosine kinases. The compounds exhibit selective inhibition of FGFR over the closely related VEGFR2 receptor in cell lines and in vivo. The pharmacologic profile of these inhibitors was defined using a panel of human tumor cell lines characterized for specific mutations, amplifications, or translocations known to activate one of the four FGFR receptor isoforms. This pharmacology defines a profile for inhibitors that are likely to be of use in clinical settings in disease types where FGFR is shown to play an important role. Mol Cancer Ther; 10(9); 1542–52. ©2011 AACR.

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Purpose: Deregulated phosphatidylinositol 3-kinase pathway signaling through AGC kinases including AKT, p70S6 kinase, PKA, SGK and Rho kinase is a key driver of multiple cancers. The simultaneous inhibition of multiple AGC kinases may increase antitumor activity and minimize clinical resistance compared with a single pathway component. Experimental Design: We investigated the detailed pharmacology and antitumor activity of the novel clinical drug candidate AT13148, an oral ATP-competitive multi-AGC kinase inhibitor. Gene expression microarray studies were undertaken to characterize the molecular mechanisms of action of AT13148. Results: AT13148 caused substantial blockade of AKT, p70S6K, PKA, ROCK, and SGK substrate phosphorylation and induced apoptosis in a concentration and time-dependent manner in cancer cells with clinically relevant genetic defects in vitro and in vivo. Antitumor efficacy in HER2-positive, PIK3CA-mutant BT474 breast, PTEN-deficient PC3 human prostate cancer, and PTEN-deficient MES-SA uterine tumor xenografts was shown. We show for the first time that induction of AKT phosphorylation at serine 473 by AT13148, as reported for other ATP-competitive inhibitors of AKT, is not a therapeutically relevant reactivation step. Gene expression studies showed that AT13148 has a predominant effect on apoptosis genes, whereas the selective AKT inhibitor CCT128930 modulates cell-cycle genes. Induction of upstream regulators including IRS2 and PIK3IP1 as a result of compensatory feedback loops was observed. Conclusions: The clinical candidate AT13148 is a novel oral multi-AGC kinase inhibitor with potent pharmacodynamic and antitumor activity, which shows a distinct mechanism of action from other AKT inhibitors. AT13148 will now be assessed in a first-in-human phase I trial. Clin Cancer Res; 18(14); 3912–23. ©2012 AACR.

Herein, we describe the discovery of potent and highly selective inhibitors of both CDK4 and CDK6 via structure-guided optimization of a fragment-based screening hit. CDK6 X-ray crystallography and pharmacokinetic data steered efforts in identifying compound 6, which showed >1000-fold selectivity for CDK4 over CDKs 1 and 2 in an enzymatic assay. Furthermore, 6 demonstrated in vivo inhibition of pRb-phosphorylation and oral efficacy in a Jeko-1 mouse xenograft model.

A ubiquitously expressed chaperone, heat shock protein 90 (HSP90) is of considerable interest as an oncology target because tumor cells and oncogenic proteins are acutely dependent on its activity. AT13387 (2,4‐dihydroxy‐5‐isopropyl‐phenyl)‐[5‐(4‐methyl‐piperazin‐1‐ylmethyl)‐1,3‐dihydro‐isoindol‐2‐yl] methanone, l‐lactic acid salt) a novel, high‐affinity HSP90 inhibitor, which is currently being clinically tested, has shown activity against a wide array of tumor cell lines, including lung cancer cell lines. This inhibitor has induced the degradation of specific HSP90 client proteins for up to 7 days in tumor cell lines in vitro. The primary driver of cell growth (mutant epidermal growth factor receptors) was particularly sensitive to HSP90 inhibition. The long duration of client protein knockdown and suppression of phospho‐signaling seen in vitro after treatment with AT13387 was also apparent in vivo, with client proteins and phospho‐signaling suppressed for up to 72 h in xenograft tumors after treatment with a single dose of AT13387. Pharmacokinetic analyses indicated that while AT13387 was rapidly cleared from blood, its retention in tumor xenografts was markedly extended, and it was efficacious in a range of xenograft models. AT13387's long duration of action enabled, in particular, its efficacious once weekly administration in human lung carcinoma xenografts. The use of longer‐acting HSP90 inhibitors, such as AT13387, on less frequent dosing regimens has the potential to maintain antitumor efficacy as well as minimize systemic exposure and unwanted effects on normal tissues. (Cancer Sci, 2012; 103: 522–527)

We describe here the identification and characterization of 2 novel inhibitors of the fibroblast growth factor receptor (FGFR) family of receptor tyrosine kinases. The compounds exhibit selective inhibition of FGFR over the closely related VEGFR2 receptor in cell lines and in vivo. The pharmacologic profile of these inhibitors was defined using a panel of human tumor cell lines characterized for specific mutations, amplifications, or translocations known to activate one of the four FGFR receptor isoforms. This pharmacology defines a profile for inhibitors that are likely to be of use in clinical settings in disease types where FGFR is shown to play an important role. Mol Cancer Ther; 10(9); 1542–52. ©2011 AACR.

Cyclin-dependent kinases (CDK), and their regulatory cyclin partners, play a central role in eukaryotic cell growth, division, and death. This key role in cell cycle progression, as well as their deregulation in several human cancers, makes them attractive therapeutic targets in oncology. A series of CDK inhibitors was developed using Astex's fragment-based medicinal chemistry approach, linked to high-throughput X-ray crystallography. A compound from this series, designated AT7519, is currently in early-phase clinical development. We describe here the biological characterization of AT7519, a potent inhibitor of several CDK family members. AT7519 showed potent antiproliferative activity (40-940 nmol/L) in a panel of human tumor cell lines, and the mechanism of action was shown here to be consistent with the inhibition of CDK1 and CDK2 in solid tumor cell lines. AT7519 caused cell cycle arrest followed by apoptosis in human tumor cells and inhibited tumor growth in human tumor xenograft models. Tumor regression was observed following twice daily dosing of AT7519 in the HCT116 and HT29 colon cancer xenograft models. We show that these biological effects are linked to inhibition of CDKs in vivo and that AT7519 induces tumor cell apoptosis in these xenograft models. AT7519 has an attractive biological profile for development as a clinical candidate, and the tolerability and efficacy in animal models compare favorably with other CDK inhibitors in clinical development. Studies described here formed the biological rationale for investigating the potential therapeutic benefit of AT7519 in cancer patients. [Mol Cancer Ther 2009;8(2):324–32]

The application of fragment-based screening techniques to cyclin dependent kinase 2 (CDK2) identified multiple (>30) efficient, synthetically tractable small molecule hits for further optimization. Structure-based design approaches led to the identification of multiple lead series, which retained the key interactions of the initial binding fragments and additionally explored other areas of the ATP binding site. The majority of this paper details the structure-guided optimization of indazole (6) using information gained from multiple ligand−CDK2 cocrystal structures. Identification of key binding features for this class of compounds resulted in a series of molecules with low nM affinity for CDK2. Optimisation of cellular activity and characterization of pharmacokinetic properties led to the identification of 33 (AT7519), which is currently being evaluated in clinical trials for the treatment of human cancers.

Inhibitors of the molecular chaperone heat shock protein 90 (Hsp90) are currently generating significant interest in clinical development as potential treatments for cancer. In a preceding publication (DOI: 10.1021/jm100059d ) we describe Astex's approach to screening fragments against Hsp90 and the subsequent optimization of two hits into leads with inhibitory activities in the low nanomolar range. This paper describes the structure guided optimization of the 2,4-dihydroxybenzamide lead molecule 1 and details some of the drug discovery strategies employed in the identification of AT13387 (35), which has progressed through preclinical development and is currently being tested in man.

Successful drug development in oncology requires a deeper understanding of the functional consequences of the diverse genetic changes observed in human cancers. For example, responses to epidermal growth factor receptor (EGFR) inhibitors are observed in patients whose tumors express EGFR alleles with activating mutations, rather than in tumors overexpressing EGFR. Furthermore, antibodies against EGFR are ineffective in tumors bearing certain activating alleles of KRAS. Horizon Discovery has used its proprietary rAAV gene engineering technology to generate isogenic cell lines covering a range of mutations commonly found in cancer patients. Use of a non-tumorigenic ‘clean’ cell line background such as MCF10A allows specific evaluation of the mutations without any confounding factors due to the presence of other genetic alterations. Mutations introduced into cancer cell line backgrounds allow the contextual evaluation of a cancer related gene. Here we describe the use of isogenic cell line panels as powerful tools for investigating sensitivity and resistance markers to cancer therapeutics. Some 50% of human tumors exhibit p53 loss or inactivation. To investigate how p53 loss in combination with other common cancer-driving mutations may influence therapeutic responses, we have generated a suite of MCF10A isogenic cell lines covering some of the major cancer genotypes, either in isolation or on a TP53 (-/-) background. These genotypes include EGFR (delE746-A750/+), EGFR (L858R/+), KRAS (G12V/+), BRAF (V600E/+), BRAF (V600K/+) and PIK3CA (H1047R/+). Thus, we have been able to investigate the interaction effects of discrete mutations in molecularly defined, but more tumor-like cell models. One data highlight arose from the profiling of the EGFR mutant panel using small molecule EGFR inhibitors; in isolation, the introduction of common activating EGFR mutations L858R or deletion of E746-A750 led to increased sensitivity, recapitulating clinical findings. However, combining EGFR mutation with loss of p53 further enhanced the cell response. Through systematic profiling of this panel to targeted therapeutic agents such as gefinitib, selumetinib, vemurafenib, and pictilisib, we have identified interesting differential sensitivities, which can be directly attributable to introduction of a given mutation. Results such as these can enable better patient stratification for anticancer agents, and allow incorporation of molecular markers into clinical trial design for personalised therapeutic regimens. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):A148. Citation Format: Annette S. Little, Jessica Hunt, David Hughes, Ruth Feltell, Daniel Gitterman, Rachel Leah, Holly Astley, Ramu Mangena, Kyla Grimshaw, Christopher Torrance. Modeling patient responses to targeted therapy with rAAV mediated gene editing. [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 A148.

The AGC kinase AKT is a key component of the phosphatidylinositol 3-kinase (PI3K) pathway, which is frequently deregulated in cancer, making AKT a target of major therapeutic interest. However, PI3K signaling through both AKT-dependent and AKT-independent mechanisms involving other AGC kinases, such as p70S6K, PKA, SGK and ROCK, is important in a range of cancers. Hence, the pharmacological inhibition of these multiple AGC kinases may increase response rates and minimize clinical resistance compared with targeting AKT alone. The clinical drug candidate AT13148 is a multi-AGC kinase, ATP-competitive inhibitor, identified utilizing high-throughput X-ray crystallography and fragment-based lead discovery techniques. Screening of this oral small molecule against a panel of kinases at 10μM revealed >80% inhibition of the structurally related AGC kinases AKT, PKA, ROCK2, p70S6K, MSK, RSK1/2, and SGK. We demonstrate that AT13148 has antiproliferative activity in a range of in vitro models harboring relevant genetic abnormalities, including PTEN, KRAS, PIK3CA and HER2 aberrations. AT13148 caused substantial blockade of AKT, p70S6K, PKA, ROCK and SGK substrate phosphorylation and induction of apoptosis in both a concentration and time-dependent manner in cancer cells with clinically relevant genetic defects both in vitro and in vivo. Antitumor efficacy in HER2-positive, PIK3CA-mutant BT474 breast, PTEN-deficient PC3 human prostate cancer and PTEN-deficient MES-SA uterine tumor xenografts was demonstrated. We show for the first time that induction of AKT phosphorylation at serine 473 by AT13148, as reported for other ATP competitive inhibitors of AKT, is not a therapeutically relevant reactivation step for this compound. We used gene expression microarray studies to characterize the underlying molecular mechanisms of action of AT13148 and the selective AKT inhibitor CCT128930, and observed the induction of upstream regulators including insulin receptor substrate-2 and PIK3IP1 due to compensatory feedback loops, consistent with blockade of AKT signaling. These studies also showed that AT13148 and CCT128930 have distinct molecular effects in cancer cells: AT13148 had a predominant effect on apoptosis genes and caused a greater apoptotic phenotype, while CCT128930 modulated genes in the network regulating cell cycle. This finding emphasizes the functional differences of AT13148 as a multi-AGC kinase inhibitor in contrast to a more AKT-selective inhibitor. In view of the potential mechanistic advantages detailed above, and the potent antitumor activity observed at well tolerated doses against established human tumor xenografts with clinically relevant genetic drivers, the clinical utility of such an AGC kinase inhibitor strategy will now be assessed in a first-in-human Phase I trial of AT13148. 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 928. doi:1538-7445.AM2012-928

Targeting tumor metabolism is becoming a major new area of pharmaceutical endeavor. Consequently, a systematic search to define whether there are specific energy source dependencies in tumors, and how these might be dictated by upstream driving genetic mutations, is now required. This is particularly relevant given the potential ability of cancer cells to switch between metabolic pathways. The PI3K-Akt-mTOR signaling pathway has a seminal role in regulating diverse cellular processes including cell proliferation and survival. This pathway has also been associated with metabolic dysregulation, particularly gluconeogenesis, largely through effects on Akt and mTOR. We have used isogenic cell models, wherein homologous recombination is used to specifically delete endogenous mutant PI3KCA alleles or introduce PIK3CA activating mutations in human cell lines. By performing rtPCR on candidate metabolic genes, we have found gene expression signatures indicative of a consistent up-regulation of glycolysis in PIK3CA mutant cells. Interestingly, the genes up- and down-regulated varied between isogenic models suggesting that the primary node of regulation is not the same between models. In MCF10A breast epithelial ‘knock-in’ lines, hexokinase 2 (HK2) is the primary target of up-regulation. However, in HCT116 colon cancer cells that are heterozygous for the H1047R PIK3CA mutation, knocking-out mutant PIK3CA resulted in a marked reduction of Glut1. Altered expression of asparagine synthetase (ASNS) and glutaminase (GLS2) was also observed in both models, suggestive of a potential increased dependency on glutaminolysis, while up-regulation of the fatty acid transporter SLC27A2 was observed in HCT116 PIK3CA mutant cells. To determine whether any of these metabolic expression changes impart hard-wired nutrient dependencies, we next performed nutrient switching experiments. These demonstrated that growth of PIK3CA mutant cells is highly dependent on glucose, whereas glutamine dependency is independent of PIK3CA status. In addition, the glucose dependency exhibited by PIK3CA mutant cells could not be overridden by supplementation with other nutrients such as alternative monosaccharides, fatty acids or aspartic acid. The extent of glucose dependency of the PIK3CA mutant cells suggested that targeted disruption of the glycolytic pathway should inhibit growth, even in the presence of glucose. The use of hexokinase 2 siRNA to disrupt glycolysis did indeed result in anti-proliferative effects that were selective for the PIK3CA mutant cells. In conclusion, we have demonstrated that glycolysis-associated genes are up-regulated in PIK3CA mutant cells and that the shift to a glycolytic phenotype does not appear to be controlled by a single rate limiting molecule. Despite suggestions that cancer cells are adept at utilizing alternative nutrient sources, this study has demonstrated that PIK3CA mutant cell are not able to compensate for glucose withdrawal. This specific dependence on glucose for growth, identified using precise isogenic models, was also present across a wider panel of cancer cell lines harboring endogenous PIK3CA mutations. Understanding the metabolic dependencies of PIK3CA mutant cancers will provide critical information for the design of effective therapies. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr B140.

Recent data in a number of tumour types has implicated Fibroblast Growth Factor (FGF) and Fibroblast Growth Factor receptor (FGFR) signalling as being key to the molecular pathology of cancer. FGFR is a receptor tyrosine kinase which activates the extracellular signal-regulated kinase / mitogen-activated protein kinase and the protein kinase B / Akt pathways which promote cell growth and survival. Amplification, over-expression or activating mutations of fibroblast growth factor receptors have been associated with bladder tumours, multiple myeloma, hormone-refractory prostate cancer and breast cancer. Multiple lead series of FGFR inhibitors were developed using Astex's fragment based medicinal chemistry approach, Pyramid™, linked to high throughput X-ray Crystallography. We describe here the characterisation of some examples of these lead molecules. In particular we detail the pharmacological profile of a compound from one of these lead series that demonstrated activity against FGFR 1-4 with an IC50 10 fold lower in cell lines lacking FGFR expression. We demonstrate inhibition of FGFR 2 and 3 phosphorylation in gastric and multiple myeloma cell lines respectively with associated inhibition of downstream signalling pathways. This lead molecule has an excellent pharmacokinetic profile and high oral bioavailibility in mice and rats. In xenograft models in mice where aberrant FGF signalling underlies tumour pathology, tumour growth inhibition is observed at doses of 100mg/kg /day orally for 21 days. This xenograft efficacy was observed in several models, with significantly lower activity in models where aberrant FGF signalling is not involved in tumour pathology. This suggests that the mechanism of action is consistent with FGFR inhibition. The pharmacological profile in these models is also distinct from other broader spectrum receptor tyrosine kinase inhibitors. The pre-clinical data shown here suggests that such compounds warrant further investigation pre-clinically and may benefit patients whose disease is driven by FGFR activity. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3626.

Cyclin Dependent Kinases (CDKs) play a central role in the eukaryotic cell cycle. The activation of these kinases is modulated by the expression and binding of their regulatory cyclin partners. Their key role in cell cycle progression, coupled to evidence that pathways leading to their activation are deregulated in a number of human cancers makes them attractive therapeutic targets. More recently the role of CDKs 7, 8 and 9 in the regulation of transcription has been explored. CDK9 has been shown to play a role in the regulation of transcription via phosphorylation of RNA polymerase II. The outcome of transcriptional inhibition via CDK9 exhibits significant variation between cell lines. Many leukemic cell lines, which are dependent upon the expression of short half-life transcripts such as Mcl-1 for survival, undergo apoptosis following transcriptional inhibition and the cell cycle effects of such inhibitors are masked. AT7519 is a potent inhibitor of cyclin dependent kinases 1, 2 and 9 and is currently in early phase clinical development. These studies profile the mechanism of action of AT7519 in leukemia cell lines (HL60 and MOLT-4). AT7519 causes rapid induction of apoptosis (within 6 hours of initial exposure) in the absence of cell cycle arrest. This induction of apoptosis occurs in parallel with a reduction in the levels of anti-apoptotic proteins such as Mcl-1. In HL60 xenograft models anti-tumour efficacy is observed following 2 cycles of daily dosing of 15 or 10mg/kg for 5 days followed by 2 days off treatment. We observe a 50% cure rate (4/8 mice) at the 15mg/kg dose and a 30% cure rate at the 10mg/kg dose level 40 days following dosing. Pharmacodynamic biomarker studies demonstrate that a greater extent and duration of Mcl-1 knockdown and apoptosis induction are associated with efficacious doses. B-Cell lymphoproliferative disorders, including CLL, rely on the expression of transcripts with a short half-life such as Mcl-1, Bcl-2 and XIAP for survival. In vitro studies have demonstrated that compounds with transcriptional inhibitory effects are effective pro-apoptotic agents in models of this disease. Therefore, we also characterised the transcriptional effects of AT7519 on CLL cells isolated from patients. AT7519 was shown to induce apoptosis (by MTS, morphology and PARP cleavage) in these samples at concentrations of 100–300nM. These effects were correlated with the cytogenetic background of individual patients and the data supports further clinical investigation of AT7519 in B-Cell lymphoproliferative disorders where survival proteins play a pivotal role.