Poised Fragment Libraries for Atypical Bromodomain Inhibition
Lead Research Organisation:
University of Sussex
Department Name: Sch of Life Sciences
Abstract
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).
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).
Planned Impact
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.
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.
Publications
Sansook S
(2018)
Probing the Anticancer Action of Novel Ferrocene Analogues of MNK Inhibitors
in Molecules
Hassell-Hart S
(2019)
Synthesis and Biological Investigation of (+)-JD1, an Organometallic BET Bromodomain Inhibitor
in Organometallics
Luparello, C.
(2019)
Cytotoxic Activity of the Histone Deacetylase 3-Selective Inhibitor Pojamide on MDA-MB-231 Triple-Negative Breast Cancer Cells
in International Journal of Molecular Sciences
Luparello C
(2019)
Cytotoxic Activity of the Histone Deacetylase 3-Selective Inhibitor Pojamide on MDA-MB-231 Triple-Negative Breast Cancer Cells.
in International journal of molecular sciences
Khan Tareque R
(2020)
Deliberately Losing Control of C-H Activation Processes in the Design of Small-Molecule-Fragment Arrays Targeting Peroxisomal Metabolism.
in ChemMedChem
Ditsiou A
(2020)
The structure-function relationship of oncogenic LMTK3.
in Science advances
Sansook S
(2020)
Ferrocenes in medicinal chemistry; a personal perspective
in Journal of Organometallic Chemistry
Devonport J
(2021)
Room-Temperature Cu(II) Radical-Triggered Alkyne C-H Activation.
in JACS Au
Gil-Moles M
(2021)
Metallodrug Profiling against SARS-CoV-2 Target Proteins Identifies Highly Potent Inhibitors of the S/ACE2 interaction and the Papain-like Protease PLpro.
in Chemistry (Weinheim an der Bergstrasse, Germany)
Hassell-Hart S
(2021)
Probing BRD Inhibition Substituent Effects in Bulky Analogues of (+)-JQ1
in Helvetica Chimica Acta
Description | We have been able to show that molecules can be synthesized quickly and tested, without purification against a key melanoma target. If we compare "normal" chemistry, we could possibly make 6 molecules a week, purify them and test them. This is one of the most expensive parts of drug discovery (molecule synthesis).. Our new approach looks at array synthesis, e.g. 10 x 50, making 500 new molecules in a simil;ar timeframe using robotic, liquid handling techniques. These are not purified and are tested on protein immediately. We save time, gain in efficiency. We hope that this will pave the way to merging rapid chemical synthesis with high throughput protein xray cocrystal structure. A paper is in preparation, delayed due to covid pandemic. |
Exploitation Route | Once the anticipated paper is submitted/accepted. |
Sectors | Chemicals Healthcare Pharmaceuticals and Medical Biotechnology |
Title | Data for 'The development of DUAL BRD4 and CBP/p300 degraders from ISOX-DUAL' thesis by Anthony Edmonds (2022) |
Description | ESI related to AE Edmonds' thesis entitled 'The Development of DUAL BRD4 and CBP/p300 Degraders From ISOX-DUAL' (published 21.03.2022)Contains 1H, 13C and other NMR spectra, HRMS, HPLC data and also scans of the original data.AbstractThe development of Heterobifunctional molecules in the field of targeted degradation is a hot topic, with various modalities appearing over the past 20 years, with examples such as; PROTACs, SNIPERs, dTAGs, HaloTags, AUTACS, ATTECs and LYTACs. In 2019 alone there were 107 PROTAC publications, an increase of 55 from the previous year. ISOX-DUAL is an inhibitor of both BRD4 (IC50 = 1.5 µM) and CBP/p300 (IC50 = 0.65 µM) bromodomains and, as such, is a useful chemical probe for research into epigenetics.2 The published and our in-house protocols toward this target molecule were poor yielding and not amenable to scale-up. Here, synthetic routes towards the title compound were re- investigated, and now achieves an overall yield of 42%, compared to the literature published 1%. Using literature co-crystal structures in the bromodomains of BRD4 and CBP/p300 of the, structurally similar, inhibitor BDOIA383, two solvent exposed exit vectors were discovered for potential linkage to E3 recruiters. ISOX-DUAL was then re-designed with the optimised synthetic route to afford two degrader precursors (3.07) and (3.27) which were designed through replacement of the N,N-dimethylpropylamine to a propyl carboxylic acid (3.07) and the replacement of the morpholine moiety to a piperazine (3.27). Degrader mimics (3.09, 3.29) were synthesised from these compounds and showed no loss in binding affinities to the bromodomains of BRD4 or CBP/p300. A small library of 20 ISOX-DUAL based degraders were synthesised, guided by predicted physiochemical properties. Select degraders (4.69-4.72) were subjected to cell-free ubiquitination assays, to which, confirmed induction of ubiquitination of the target. The 20 synthesised degraders were initially treated in HeLa cells and 4.68 caused a reduction in BRD4 (75%) and CBP (73%), the most potent degrader in this assay. The investigation goes on to highlight the importance of cell lines when assessing these compounds and describes a series of future experiments, which, should be performed. |
Type Of Material | Database/Collection of data |
Year Produced | 2023 |
Provided To Others? | Yes |
Impact | new methods for making important CBP/BRD4 inhibitors and protacs |
URL | https://sussex.figshare.com/articles/dataset/Data_for_The_development_of_DUAL_BRD4_and_CBP_p300_degr... |
Company Name | Stingray Bio |
Description | Stingray Bio develops cancer-treatment drugs that aims to suppress the LMTK3 molecule caused by breast cancer. |
Year Established | 2020 |
Impact | Just started, covid impact has slowed down growth so far. |
Website | https://stingraybio.com/ |
Description | Conference presentation |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | I gave an invited talk at : ISBOMC'19 The 9th International Symposium on Bioorganometallic Chemistry at the University of York. 28-30th July 2019. |
Year(s) Of Engagement Activity | 2020 |
URL | https://twitter.com/isbomc19?lang=en |
Description | Invited Lecture/Workshop |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | SCI Epigenetics (7 Sept, 2017) Talk on Cancer |
Year(s) Of Engagement Activity | 2017 |
Description | Radio Interview |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | I was asked about the possible role of metals to reduce resistance in drugs after a Nigerian student had published findings showing the inclusion of metals can increase the effectveness of certain drug treatments. |
Year(s) Of Engagement Activity | 2020 |
URL | https://radio.org.ng/nigeria/ |
Description | School visit |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | Gave a workshop on organic chemistry to a local sixth form (Lewes Old Grammar). |
Year(s) Of Engagement Activity | 2020 |
Description | School visit (Godalming College) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Schools |
Results and Impact | 30 people came to this meeting. I would estimate that 28 were female, which is very exciting in terms of STEM engagement and possible future applications.This was an informal lecture and many students asked questions as we went along. We hope to host the college over the summer for a lab event or for them to participate in Spectroscopy in a Suitcase. |
Year(s) Of Engagement Activity | 2019 |
Description | School visit (London) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Schools |
Results and Impact | Approx 40 students attended my talk on cancer at a Greenwich School. There was feedback, feedforward. As a result of the talk, 40 students wish to visit Sussex Chemistry in July to see the department. |
Year(s) Of Engagement Activity | 2018 |
Description | School visit (Worthing College) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Schools |
Results and Impact | I talked about cancer treatments, modern and old. They will be interested in further visits, possibly coming to our department for an experimental day. |
Year(s) Of Engagement Activity | 2019 |
Description | Video Interview |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Not known, only a few weeks ago |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.worldwidecancerresearch.org/stories/2019/december/fixing-broken-cancer-cells/ |
Description | invited seminar |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Visit to Muenster, Germany. I gave a talk on palladium chemistry. This sparked interest with colleagues, who wish to collaborate on various projects. |
Year(s) Of Engagement Activity | 2018 |
Description | presentation at Institute of Cancer Research |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Invited seminar at ICR |
Year(s) Of Engagement Activity | 2018 |
Description | school visit (Uckfield) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | Presentation on our work and a general presentation on cancer, some related to bromodomains and p53. School has requested a visit day to come to Sussex and to do some experimental chemistry, also involvement in "Spectroscopy in a Suitcase." We've had 2 student applicant visits from this school following my talk. |
Year(s) Of Engagement Activity | 2018 |
Description | seminar/conference participation Liverpool University |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Postgraduate students |
Results and Impact | Invited speaker at Romark Medicinal Chemistry Symposium. |
Year(s) Of Engagement Activity | 2018 |
Description | visit (Lisbon) |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | I gave a seminar on our chemistry projects. We were in Lisbon for a related EU (RISE) project debate but I had the opportunity to show some of our cancer and palladium studies. As a result of this, I should be soon welcoming a Chilean PhD student for 6 months in my lab from one of the EU-funded partner groups (outside of EU-Santiago, Chile). I've also been invited as a visiting professor in Santiago. |
Year(s) Of Engagement Activity | 2018 |