EPSRC-Royal Society fellowship engagement (2012): Development of Chemical Tools for Probing Histone Demethylases

Lead Research Organisation: University of Oxford
Department Name: Oxford Chemistry

Abstract

Please refer to attached Royal Society application

Planned Impact

Please refer to attached Royal Society application

Publications

10 25 50

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Belle R (2017) Investigating d-lysine stereochemistry for epigenetic methylation, demethylation and recognition. in Chemical communications (Cambridge, England)

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Bonnici J (2018) Inhibitors of both the N-methyl lysyl- and arginyl-demethylase activities of the JmjC oxygenases. in Philosophical transactions of the Royal Society of London. Series B, Biological sciences

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Dobrynin G (2017) KDM4A regulates HIF-1 levels through H3K9me3. in Scientific reports

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Gerken PA (2017) Discovery of a Highly Selective Cell-Active Inhibitor of the Histone Lysine Demethylases KDM2/7. in Angewandte Chemie (International ed. in English)

 
Description In this project, we have developed highly selective cyclic peptide inhibitors against histone demethylases, a biomedically important enzyme family involved regulation of transcription.
We have established a state-of-the-art peptide synthesis facility within the Department of Chemistry - this includes the introduction of EPSRC funded microwave assisted peptide synthesiser. This microwave peptide synthesizer has dramatically increased our throughput and the quality of the synthesis of complex peptides (including cyclic peptides). The cyclic peptides are then tested in vitro and in cells against the enzyme targets. We have established cellular assays to assess stability, permeability and target engagement of cyclic peptides. This data was crucial in taking our work on KDM4 cyclic peptides to publication (Nature Communication 2017). In addition, this facility has enabled the synthesis of a wide variety of other peptides, including that of histone substrates for the enzymes. We currently have a number of follow-up project on KDM4 cyclic peptides, first of which has been published in BioorgMedChem 2017. We have also been contacted by a number of international research groups to use our tool compounds in their biological assays / studies. Our work in this area has led to a number of collaborative projects with Pharmaceutical companies.
We have also established in vitro platform for cyclic peptide selection against novel targets. This will allow for identification of binding sequences against new targets.
In parallel to our inhibitor development work, we have been working on functional studies on histone demethylases. We have conducted histone substrate profiling work on this family of enzymes and have found novel substrates for certain KDMs. This work was published in Epigenetics (2015) and Nature Communications (2016). We believe that our work on biochemical functional studies of KDMs will be of interest to a wide range of scientists, including both academic and pharmaceutical scientists pursuing demethylases as therapeutic targets (particularly in oncology).
Exploitation Route Our findings can have wide-ranging use - firstly and most importantly in healthcare as the research outcome will most likely be useful for development of new drugs against histone demethylases (currently being actively pursued by multiple pharmaceutical / biotechnology companies, as well as academics).
Sectors Healthcare,Pharmaceuticals and Medical Biotechnology

 
Description The findings of this project have led to several collaborative projects with pharmaceutical companies (>5 companies) - e.g. studentships, pump-priming projects, postdoctoral projects. Our work has generated a number of important output, including several publications on the development of chemical tools and mechanistic understanding of histone demethylases/related enzymes, which has opened up further new research in this area.
Sector Pharmaceuticals and Medical Biotechnology
Impact Types Economic

 
Description ARC Fellowship to Alexandre Erdmann
Amount € 30,000 (EUR)
Organisation The ARC Foundation for Cancer Research 
Sector Charity/Non Profit
Country France
Start 10/2015 
End 09/2016
 
Description BHF CRE Pump Priming Fund
Amount £50,000 (GBP)
Funding ID RE/08/004 
Organisation University of Oxford 
Department BHF Centre of Research Excellence
Sector Academic/University
Country United Kingdom
Start 08/2013 
End 03/2014
 
Description Biomedical Vacation Studentship
Amount £1,440 (GBP)
Funding ID N/A 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 08/2013 
End 09/2014
 
Description British Heart Foundation CRE Oxford - Pump Priming Award
Amount £28,000 (GBP)
Organisation University of Oxford 
Sector Academic/University
Country United Kingdom
Start 10/2018 
End 03/2019
 
Description CRUK Programme Grant
Amount £763,416 (GBP)
Funding ID C8717/A18245 
Organisation Cancer Research UK 
Sector Charity/Non Profit
Country United Kingdom
Start 10/2014 
End 09/2019
 
Description ERC Consolidator Grant
Amount € 2,241,271 (EUR)
Funding ID 101003111 
Organisation European Research Council (ERC) 
Sector Public
Country Belgium
Start 10/2021 
End 09/2026
 
Description ERC Starter Grant
Amount € 1,758,846 (EUR)
Funding ID 679479 
Organisation European Research Council (ERC) 
Sector Public
Country Belgium
Start 04/2016 
End 03/2021
 
Description John Fell Fund
Amount £100,000 (GBP)
Organisation University of Oxford 
Sector Academic/University
Country United Kingdom
Start 08/2015 
End 07/2016
 
Description NovoNordisk PhD studentship (MoSMed CDT, University of Newcastle)
Amount £75,000 (GBP)
Organisation Novo Nordisk 
Sector Private
Country Denmark
Start 09/2021 
End 09/2025
 
Description NovoNordisk STAR Postdoctoral Fellowship
Amount £100,000 (GBP)
Organisation Novo Nordisk 
Sector Private
Country Denmark
Start 10/2018 
End 09/2020
 
Description Oxford Cancer Centre Development Fund
Amount £12,000 (GBP)
Funding ID CRUKDF 0318-AK 
Organisation University of Oxford 
Sector Academic/University
Country United Kingdom
Start 04/2018 
End 03/2019
 
Description Royal Society Newton Advance Fellowship with Dr Nathan Lack, Koc University
Amount £111,000 (GBP)
Funding ID NA150165 
Organisation The Royal Society 
Sector Charity/Non Profit
Country United Kingdom
Start 10/2015 
End 03/2019
 
Title Cellular assays for histone demethylase 
Description Target engagement assays in cells 
Type Of Material Technology assay or reagent 
Provided To Others? No  
Impact Publication just accepted, impact to be confirmed. 
 
Title Chemical tools for histone demethylase 
Description Potent and selective cyclic peptide inhibitors for the KDM4A-C family 
Type Of Material Technology assay or reagent 
Provided To Others? No  
Impact To be determined (publication just accepted and in press) 
 
Description COST EpiChemBio CM1406 
Organisation European Commission H2020
Country Belgium 
Sector Public 
PI Contribution I am a Management Committee Member representing UK for this EU COST action; I have helped organised events, contributed towards training programmes and collaborative grant writing
Collaborator Contribution European wide network of epigenetic researchers
Impact >200 PIs across has joined this action 5 publications arising from this action (contributions from my group) 1 Marie Curie ITN grant application (H2020-MSCA-ITN-2017) - although not funded, it provided a foundation for new collaborations / grant applications Multiple training schools, workshops and conferences across Europe
Start Year 2016
 
Description Emily Flashman 
Organisation University of Oxford
Country United Kingdom 
Sector Academic/University 
PI Contribution Expertise, intellectual input, training of students; use of facilities and equipment
Collaborator Contribution Expertise, intellectual input, training of students; use of facilities and equipment
Impact Currently preparing a review for submission to Epigenomics.
Start Year 2013
 
Description Hiro Suga 
Organisation University of Tokyo
Country Japan 
Sector Academic/University 
PI Contribution In collaboration with Hiro Suga's group in University of Tokyo, we are generating a series of cyclic peptide inhibitors against various epigenetic targets. My lab has been characterising the peptides, in vitro and in cells, using biophysical and kinetic assays, crystallography and in cell activity assays.
Collaborator Contribution My collaborators have been screening the cyclic peptide library against our targets and they have supplied the synthesised peptide hits.
Impact Currently preparing a manuscript to submit to Nature Chemical Biology
Start Year 2010
 
Description Professor Christopher Schofield 
Organisation University College Oxford
Country United Kingdom 
Sector Academic/University 
PI Contribution Expertise, intellectual input and training of staff. We also provide the use of the EPSRC funded peptide synthesiser to the Schofield lab also.
Collaborator Contribution Expertise, intellectual input and training of staff, as well as access to facility/ equipment use.
Impact Currently working closely together on a number of different projects - we have numerous published together (23 publications to date). We have a number of joint grants together, including two with BBSRC (BB/L009846/1; BB/L000121/1) and one with CRUK (C8717/A18245).
Start Year 2009
 
Description Target Discovery Institute 
Organisation University of Oxford
Country United Kingdom 
Sector Academic/University 
PI Contribution Expertise and intellectual input
Collaborator Contribution Equipment and use of facility; generation of data
Impact Multiple publications; development and distribution of chemical probes to academic and industrial researchers
Start Year 2009
 
Description UAE Ganesan 
Organisation University of East Anglia
Department School of Pharmacy
Country United Kingdom 
Sector Academic/University 
PI Contribution Biochemical analysis of the inhibitors provided by the collaborators
Collaborator Contribution Synthesis of inhibitors
Impact Manuscripts currently in preparation
Start Year 2013
 
Description "Protein-Protein Interactions: the next frontier" POPPI Event, Leeds University 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Invited speaker to talk about my research on cyclic peptides targeting protein protein interactions.
Year(s) Of Engagement Activity 2020
URL https://poppi.website/protein-protein-interactions-the-next-frontier-webinar/
 
Description BHF Blenheim 10K 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact BHF charity run with my research group. As researchers, we also discussed our research to the general public on the work we do.
Year(s) Of Engagement Activity 2015
URL https://www.bhf.org.uk/get-involved/events/runs/blenheim-palace-half-marathon-10k-and-family-fun-run
 
Description Biosense 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact This was a exhibition held at the University Museum of Natural History, Oxford, targeting the general audience. The general theme of the exhibition was how living organisms sense changes in their environment. The section I was involved in was on Oxygen sensing.
Year(s) Of Engagement Activity 2015
URL http://www.museums.ox.ac.uk/content/biosense
 
Description Bradford University, Institute of Cancer Therapeutics 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Weekly seminar organised at the Institute of Cancer Therapeutics; Research talk about my group's research, followed by 30min Q&A with PG students discussing about science / career
Year(s) Of Engagement Activity 2020
 
Description CRUK Open Doors 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Joanna Bonnici, a Research Assistant in the lab, was involved in showing people around the Chemistry Department and discussing our group's research on cancer during this CRUK run event
Year(s) Of Engagement Activity 2015
URL http://www.oxfordopendoors.org.uk/events/chemistry-research-laboratory-5/
 
Description CRUK Race for Life 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact CRUK Race for Life charity run with my research group. As researchers, we also discussed our research to the general public on the work we do.
Year(s) Of Engagement Activity 2015
URL http://raceforlife.cancerresearchuk.org/index.html
 
Description Cancer Research UK World Cancer Day event Oxford 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact 40 general public attended this event in the Chemistry Research Laboratory, University of Oxford. This involved presentations by the CRUK organiser and Prof. Chris Schofield FRS, followed by lab tours and poster session.
Year(s) Of Engagement Activity 2017
 
Description ChemBiOX 2019 Chemical Biology Conference 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact ChemBiOX 2019 Chemical Biology Conference - a 2-day postgraduate conference led and organised by the Chemical Biology CDT students.
Year(s) Of Engagement Activity 2019
URL https://chembiox.web.ox.ac.uk
 
Description ChemBioChem/ChemMedChem Joint Virtual Symposium: Chemical Epigenetics 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Invited to talk to speak about my research on cyclic peptides targeting epigenetic proteins
Year(s) Of Engagement Activity 2020
URL https://www.workcast.com/register?cpak=2043663598051070&referrer=ChemViews
 
Description Discovery on Target 2014 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact I was an invited speaker at an international conference on Epigenetics Drug Discovery. The talk led to good discussions and potential collaborative opportunities.
Year(s) Of Engagement Activity 2014
URL http://www.discoveryontarget.com/Discoveryontarget_content.aspx?id=143166
 
Description Epigenetics Discovery Congress 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Invited speaker at the Epigenetics Discovery Congress. New collaborations (academic / industry) were made as a result of my presentation.
Year(s) Of Engagement Activity 2015
URL http://www.globaleventslist.elsevier.com/events/2015/09/the-epigenetics-discovery-congress/
 
Description Epigenetics in Drug Discovery, SelectBio, Cambridge, UK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Conference focused on drug discovery in Epigenetics; audience included academic and industrial researchers; dissemination of data, networking and strengthened existing collaborations (and potential ones); Invited to become an editor for a volume on the chemical biology book series from the Royal Society of Chemistry
Year(s) Of Engagement Activity 2010,2017
URL https://selectbiosciences.com/conferences/agenda.aspx?pid=4770&conf=EDD2017
 
Description GlaxoSmithKline Emerging Academics Symposium Stevenage, Oct 2019 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Invited speaker at GlaxoSmithKline Emerging Academics Symposium Stevenage, Oct 2019
Year(s) Of Engagement Activity 2019
 
Description Gordon Research Conference in High Throughput Chemistry & Chemical Biology 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact 2019 Gordon Research Conference in High Throughput Chemistry & Chemical Biology - invited speaker
Year(s) Of Engagement Activity 2019
URL https://www.grc.org/high-throughput-chemistry-and-chemical-biology-conference/2019/
 
Description Institute of Chemical Biology MRes Conference, Sept 2019, Imperial College 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Keynote speaker at Institute of Chemical Biology MRes Conference, Sept 2019, Imperial College
Year(s) Of Engagement Activity 2019
 
Description International Innovation 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact My research has attracted public interest and an article featuring my research was published in International Innovation (special Women in Science, 3rd Edition). This has prompted a number of contacts from the media requesting my input into the research field.
Year(s) Of Engagement Activity 2014,2015
URL http://www.internationalinnovation.com/build/wp-content/uploads/2015/02/p58-59_Akane_Kawamura_Intl_I...
 
Description International Women's Day 2020 - Newcastle University 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact International Women's day talk, about my career to date
Year(s) Of Engagement Activity 2020
 
Description Invited lecture - 11th ABPP Meeting, Target Discovery Using Chemical Probes 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Dissemination of research via giving a lecture; collaboration arising from this conference talk
Year(s) Of Engagement Activity 2018
URL http://www.ox.ac.uk/event/11th-annual-abpp-meeting-target-discovery-using-chemical-probes
 
Description Invited lecture - 4th International Conference on Circular Proteins and Peptides, Kawasaki, Japan 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Dissemination of research
Year(s) Of Engagement Activity 2018
URL https://www.iccpp2018.com
 
Description Invited lecture - AstraZeneca / Oxford Cancer Symposium 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Industry/Business
Results and Impact Dissemination of research, identifying collaborations
Year(s) Of Engagement Activity 2018
 
Description Invited lecture - Hong Kong University Chemical Biology Symposium 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Dissemination of research; collaborations and networking
Year(s) Of Engagement Activity 2018
 
Description Invited lecture - Institute Pasteur, Paris 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Dissemination of research to academics; networking and collaborations
Year(s) Of Engagement Activity 2018
 
Description Invited lecture - RSC Chemistry and Biology of Peptides, Southampton 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Dissemination of research
Year(s) Of Engagement Activity 2018
URL https://www.sigmaaldrich.com/chemistry/chemical-synthesis/chemical-biology/novabiochem-chemistry-and...
 
Description Invited lecture - University of Leeds, School of Molecular and Cellular Biology 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Dissemination of research
Year(s) Of Engagement Activity 2018
 
Description Invited lecture - Vancouver Prostate Centre, Canada 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact Dissemination of research
Year(s) Of Engagement Activity 2018
 
Description Invited talk at Imperial College 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Invited talk at Imperial College, Molecular Medicine Lunchtime seminar. Following on the talk, there were good discussions and potential collaborative opportunities were identified.
Year(s) Of Engagement Activity 2016
 
Description Invited talk at UEA 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Invited speaker at School of Pharmacy at University of East Anglia, to discuss my research on Epigenetics.
Year(s) Of Engagement Activity 2015
 
Description Oxford Science Festival (IF), "Epigenetics: How do Identical twins differ?" 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Kawamura group (7 group members) set up a stand on Epigenetics ("Epigenetics: How do Identical twins differ?") at the Oxford Science Festival (IF) in Oxford City Town Hall for a full day. It was very well attended, and we had several activities at the stand targeting all ages / backgrounds. We had several interactive activities for primary aged children which included a histone post-translational modification game, a yo-yo (for explaining how DNA is wrapped and condensed), a tablet with interactive 'cell', as well as posters and further reading for adults. It was very well received and we had many positive feedback.
Year(s) Of Engagement Activity 2019
URL https://if-oxford.com/event/explorazone/
 
Description Periodic 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact My research was highlighted in the Oxford Chemistry Alumni magazine, Periodic.
Year(s) Of Engagement Activity 2015
URL http://www.chem.ox.ac.uk/Periodic2015/files/basic-html/index.html
 
Description Phenotype 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Postdoc in my team wrote an article about the group's research, which has led to a number of researchers contacting the group for further discussions on our work
Year(s) Of Engagement Activity 2016
URL http://oxphenotype.wix.com/oxphenotype15
 
Description RSC CSJ Symposium on Chemistry for Complex Biological Systems 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact RSC CSJ Symposium on Chemistry for Complex Biological Systems, Tohoku University, Japan Sept 2019 (UK representative); Collaborative symposium between Japanese and UK chemical biologists.
Year(s) Of Engagement Activity 2019
URL http://www.bunshi-kyouzatsu.jp/en/event/10th-rsc-csj-joint-symposium-chemistry-for-complex-biologica...
 
Description The Many Faces of Epigenetics: "Multidisciplinary Perspectives "over" genetics" 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Multi-disciplinary workshop / discussions / lectures on epigenetics from social and scientific perspectives. CJS - invited speaker, AK - session chair
Year(s) Of Engagement Activity 2017
URL http://www.mfo.cnrs.fr/calendar/2017-12-06/
 
Description UNIQ School 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact A lecture give on the theme of epigenetics to A-level students, as part of a summer school program in Oxford.
Year(s) Of Engagement Activity 2017
URL http://www.uniq.ox.ac.uk/chemistry