Novel small molecule inhibitors for the treatment of CCNE1-amplified cancers.

Lead Research Organisation: Newcastle University
Department Name: Translational and Clinical Res Institute

Abstract

This project aims to take important steps towards developing a drug that will target the Achilles' heel of the cancerous cells found in 1 in 5 patients diagnosed with high grade serous ovarian cancer. Patients with this form of cancer currently have a very poor prognosis, and undergo harsh chemotherapy that provides limited benefits in terms of quality or duration of life.

The vulnerability of the ovarian cancer in these patients arises from the fact that these particular cancer cells have multiple copies of the gene that encodes cyclin E. This results in cyclin E protein being produced at abnormally high levels and as a consequence the cells become addicted to cyclin E for their ability to further divide and survive.

Our structural studies have provided novel insights into how aberrant cyclin E signaling may be prevented with a small molecule inhibitor, which would be selectively toxic to ovarian cancers that are dependent upon this pathway for survival. The project team has extensive expertise in drug discovery and has established the experimental systems needed to develop such inhibitors, with chemical start points being identified. The team has also formed collaborations with clinical experts who specialise in the treatment of aggressive ovarian cancers. Clinicians would be able to easily identify the patients with elevated cyclin E who would benefit from a drug developed for these tumour cells; an example of a personalised medicine.

By the end of the project, the team aims to have developed the inhibitors to a point where they can demonstrate selective effects on ovarian cancer cells with elevated cyclin E levels. This would position the project for further development involving the final optimisation of inhibitors towards a drug that could be developed for clinical use.

Technical Summary

CCNE1 encodes for the cell cycle regulator cyclin E which binds to cyclin-dependent kinase-2 (CDK2) to drive cells through a G1/S cell cycle transition. Genetic perturbation of CDK2 indicates that its function is not essential for mitosis to complete in normal tissue development and homeostasis. In contrast, tumour cells in which CCNE1 is amplified are critically-dependent on CDK2 and cyclin E for survival. Such "oncogene-addiction" to CCNE1 occurs in a significant cohort of high-grade serous ovarian cancer (HGSOC) and confers a particularly poor patient outcome to current therapy. Although there have been many attempts to pharmacologically-inhibit CDK2 kinase activity, these have resulted in the development of ATP-competitive inhibitors that do not have sufficient selectivity against other CDKs (involved in essential cellular processes) to exert amplicon-dependent activity.

The current application aims to produce novel small molecule inhibitors that are selectively toxic to CCNE1-amplified tumour cells as a stratified medicine for the treatment of HGSOC. The strategy has been approached using crystallographic fragment screening and two series of molecules identified. In this hit-to-lead phase of the project we will utilise structure-based drug design to increase the potency of the hit molecules and aim to demonstrate proof-of-principle through the identification of a cell-penetrant tool compound.

Planned Impact

The primary impact will be through progress towards a new, more effective, treatment for high-grade serous ovarian cancer (HGSOC) with CCNE1-amplification. CCNE1-amplification is an independent-prognostic factor for overall survival in HGSOC and associated with a poor clinical response to current treatment, with progressive disease being evident within one year. There are currently no molecularly-targeted agents being developed specifically for this patient population.
Additional benefit may be derived from patients in other groups, including breast cancer sufferers where aberrant cyclin E activity is suggested by the accumulation of short forms of cyclin E.
As well as these direct impacts, the project will yield greater insight into CDK-activity and dysregulation in cancer in general, and further benefit will derive from subsequent translational research informed by increased understanding.
In addition, we expect to generate impact by ways that include:
i) Training a cohort of skilled researchers in interdisciplinary structure guided drug discovery. The biotechnology / life sciences industry is a leading contributor to the UK economy and the UK is a global leader in the area. This is envisaged to become even more important in the future. A report by PwC in March 2017 (The Economic contribution of the UK Life Sciences industry) commissioned by the Association of the British Pharmaceutical Industry and supported by the Association of the British Healthcare Industry showed that UK Life Sciences contributed £30.7bn to the economy in 2015 and an estimated tax contribution of £8.6bn to the exchequer. Moreover, each Life Sciences job supported 2.5 jobs elsewhere in the UK economy, meaning the sector supported a total of 482,000 jobs. For this vital component of the economy to thrive, it is critical that the training of highly skilled researchers is maintained.
ii) Identifying important interactions to be targeted in the development of personalized medicine by commercial and/or academic drug discoverers
CDKs are the end effectors of pathways that function aberrantly in diseases ranging from HIV-AIDS (CDK9), through cardiac hypertrophy (CDK9) to cancer (CDK9, CDK4/6, CDK2), with CDK inhibitors in preclinical development and/or clinical trials in each of these indications. These inhibitors all target the ATP-binding site. While this strategy has demonstrated utility, it does have drawbacks relating to selectivity and the potential for resistant mutations. This proposal will characterize a protein:protein interaction that is essential to CDK function. Such interactions are increasingly being targeted for drug discovery, being often more amenable to selective inhibition.
iii) Generating assays and reagents to enable the study of CDKs in diverse biological contexts
While study of the CDKs to identify novel routes to clinical inhibition is the focus of this programme, the protocols we have developed to prepare CDK1/2-cyclin A/B generate reagents that are widely applicable to mechanistic studies. The phospho-CDK2-cyclin A generating reagents and protocols that we developed have been widely distributed by JE to academic and commercial groups and commercialized by New England Biolabs.
iv) Participating in national and international networks
Networks provide a vehicle for disseminating results, know-how and practice that contribute broadly to the community. SW, CC, MN and JE will share outputs of the proposed programme through key networks that promote anticancer drug discovery, and structural biology software development.
v) Inspiring and educating chemistry and biomedical undergraduates in basic and applied research
The research will be conducted in the NICR, which contributes to Newcastle's undergraduate lecture courses, and hosts undergraduate and Masters students through 2-3 month projects. In both of these undertakings, the students will be exposed to the cutting-edge research supported by this grant.

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