Poised Fragment Libraries for Atypical Bromodomain Inhibition

Melanoma is an increasingly devastating cancer of the skin, whose occurrence is on the rise. It can be treated surgically but long term survival tends to be poor. Often, once detected, it has already metastasised (spread to other parts of the body) and surgical intervention merely removes the original cancer, with the more aggressive form inoperable or intractable (unresponsive) to chemo- or radio- therapies). Thereafter, fatality is inevitable.
Fortunately, there are a number of new therapies available for melanoma including "vemurafenib", which is a synthetic molecule acting on a specific mutation (change in a key protein vital for cancer progression, called BRAFV600E (amino acid residue number 600 of the BRAF protein has changed from a valine to a glutamic acid, drastically altering the cancerous nature of the protein)). However, around 50% of melanomas do not carry this particular mutation and therapy is ineffective in these cases.
Ipilimumab or pembrolizumab (Keytruda) are newly introduced immunotherapy-based antibody drugs, which cause cells to attack the melanoma by activating the immune system. Many of these drugs are dramatically more effective in combination with others since they can attack the cancer in complementary ways, preventing problematic resistance to the treatments. Indeed, recent clinical trials on the immunotherapy approach have shown very encouraging results with > 2 years survival noted for a number of patients, although side effects in over half of the patients halted their treatment (http://www.bbc.co.uk/news/health-36043882).
Hence, despite huge strides in melanoma treatments, the search for new therapies is still vital particularly for melanomas that are not harbouring BRAF-mutations. We have recently discovered a range of molecules that target parts of proteins called bromodomains (BRDs) that are crucial in gene transcription in cancer. One particular BRD, called PHIP, is highly expressed in many melanomas, particularly aggressive types and it has been shown (by De Semir et al., who is a collaborator on this application) that stopping PHIP production biologically, slows down melanoma progression in cells (in vitro), as well as in mice (in vivo).
Our recent study has shown, for the first time, how small molecules can inhibit and bind to PHIP(2), one of the forms of PHIP, at the atomic level, by x-ray crystallography.
The next stage is to take our original PHIP(2) acting molecules and improve their biological activity and selectivity over other BRDs (there are over 60 of these) in order to be able to use smaller doses, to lower toxicity, side effects and cost. This will act as a proof of principle to show that PHIP(2) inhibition by drug-like molecules is a vital new armoury in our fight against skin cancer.
Although a study of this magnitude is unlikely to yield a drug, since this tends to cost a billion or so pounds and take over 12 years, it is expected to contribute to a better understanding of the role of PHIP(2) in melanoma and to a new line of chemical reactions towards biologically active molecules, which may act on either PHIP(2) or on other BRDs. PHIP(2) is an example of an atypical BRD (there are 13 of these vs 48 typical BRDs). Little is known about their inhibition so this study will also have ramifications in atypical BRD inhibition and lead to others studying other atypical BRDs.
It will also add to the very important area of epigenetics, a study of inheritable changes of the genome not related to DNA sequence changes, which is an area of science that is en vogue, spanning different branches of science such as environmental factors including diet-related disease and addiction (Brazil, R. Chemistry World, 2016, 34-39).

This study will improve our understanding of atypical bromodomain inhibitors, which represents untrodden terrain compared with the much greater studied typical bromodomains such as BRD4, BRD9 and CREBBP. By optimising a library of PHIP(2) inhibitors we will gain a better understanding of SAR (structure activity relationships), binding modes, selectivity profiles and bioavailability in the development of a selective, low nM active, cell penetrant PHIP(2) inhibitor probe. We will establish proof of principle and target validation for PHIP(2) inhibition in metastatic melanoma leading to improved future therapeutic interventions in unmet areas of growing clinical concern in oncology.


This collaborative venture will have clear long term future societal and economic impact allied to healthcare innovation. Future beneficiaries will be cancer patients whose lifespan and quality of life will be improved and healthcare providers, who will have access to safer and more effective anticancer agents.

By employing state-of-the-art palladium catalysis and other atom economical routes we will produce a number of valuable probes for the oncology and academic community, stimulating further research in complementary or related themes. These will be distributed via the SGC or via Tocris Biosciences, our industrial partners. Dissemination of (i) novel synthetic routes, (ii) novel structural biology and (iii) new chemical probe generation will be in open access high quality, high impact publications, at national and international conferences and via media, including press releases, podcasts and on personal and institutional websites as well as via ORCID, ResearchFish and institutional repositories.

The PI and co-Is have very good track records in postgraduate and postdoctoral fellow training. The project will provide a postdoctoral fellow with a range of interdisciplinary skills in catalysis and chemical biology as well as invaluable experience in helping manage a dynamic research laboratory. Following the completion of the project the postdoctoral fellow will be have mastered a number of competencies and be in a strong position to enter industry or academia.

Industry
This multifactorial ambitious study is of both fundamental and applied importance. It will potentially lead to future intellectual property, benefitting the UK economy, leading to long-term future income streams via licensing and outsourcing of the technology. Likely beneficiaries include industrial stakeholders and academic groups, both nationally and internationally, interested in palladium catalysis, structural biology and chemical probe generation as well as high value organic chemical intermediates, catalysts and drug-like substrates.

The Public
On a local level, schools and teachers will learn of state-of-the-art in catalysis, oncology research and chemical probe design through open days, class visits and the annual Sussex Chemistry Teacher's Conference, where we often attract over 50 teachers from associated colleges.