Epigenetic Chemical Probes in Drug Discovery

The major cause of failure in discovery of new medicines is due to a fundamental lack of understanding of the biology of disease.  The likelihood of a new medicine having a positive effect when tested in patients for the first time is less than 30%.  In order to find new medicines for diseases, like Alzheimer’s disease, cancer and chronic inflammation, we first need to discover a new

novel disease-associated protein target.   Following on from the discovery of a target, drug discovery is aimed at finding safe, effective means of modifying the target’s detrimental effects in disease.

Target Discovery currently uses a number of tools to associate a protein target with a disease: genetic comparisons of diseased versus healthy individuals (figure 1A); inhibition of every possible expressed gene in a cellular model of a disease (a process known as RNA interference - RNAi, figure 1B); or the use of chemical probes in cellular or animal disease models (figure 1C).  None of these approaches is perfect. Genetic comparisons are confounded by functional redundancy of genes, multiplicity of genetic effects and environmental factors. RNA interference removes an entire protein target when only a small piece of it may be important in the disease and the rest is necessary for normal, healthy functions.

Figure 1.  Target discovery is the first step in drug discovery

A. Comparison of the genes of diseased versus healthy cells can uncover new drug targets.  B.  RNA interference (RNAi) can show that a potential drug target (red) is responsible for the disease.  C. A chemical probe can show that a single region of the drug target (red crescent) is the culprit and the probe can be optimised to give a new medicine.

Chemical probes are available for only a small fraction of potential disease targets and are usually less specific than RNAi.  The scarcity of chemical probes is disappointing as they are especially useful; a probe that shows a positive effect can also serve as a chemical starting point for drug discovery.  If genetic or RNA interference methods identify an exciting disease target, it may still take many years to find a chemical starting point to move from target discovery to drug discovery, whereas using a chemical probe in target discovery jump-starts the process.

Epigenetics is an exciting new arena for target discovery.  Classically epigenetics is defined as the transfer of heritable traits from parent to off-spring other than by genetic means.  Understanding of the molecular processes of the epigenetic phenomena has led to an expanded definition.  Epigenetics can now be thought of as the control of gene expression via chemical marks which are written, read and erased by regulating proteins.  The largest variety of epigenetic marks is written on histones (figure 2).  Histones are proteins necessary to accomplish one of nature’s greatest feats: packaging two metres of DNA into a single cell which is 0.00001% as long.  Like a spool, the long threads of DNA (blue in figure 2) are wrapped around a histone core (green in figure 2).  Histones not only package the DNA, but they also control it.  In our thread and spool analogy, the spool can be programmed with epigenetic enzymes to decide when the thread should be unwound and used in gene transcription. 

Figure 2.  Epigenetic marks on histones

A lysine demethylases (KDM, red hexagon) removes an epigenetic mark (red) from histone (green).  A plant-homeodomain (PHD, red crescent) reads the epigenetic mark. A bromodomain (BRD, purple crescent) reads another epigenetic mark (purple).  The epigenetic marks regulate the gene encoded in the DNA (blue).

Epigenetic control of genes is a complex system of regulation by hundreds of enzymes that have multiple functions.  There are multiple epigenetic chemical marks and the combination of marks creates an epigenetic code, similar in concept but even more complex than the genetic code of DNA.  Since problems with control of gene expression are fundamental to many diseases, for example cancer, inflammation and neurological conditions, and enzymes control is the most common action of medicines, epigenetics offers a fortuitous meeting of disease biology with drug discovery capabilities and is generating unprecedented excitement in the global medical research community.  But target discovery in epigenetics is more difficult than other areas.  There is limited evidence from genetic comparisons of important epigenetic targets.  It is hard to interpret the results of RNAi experiments as the entire enzyme is removed and epigenetic enzymes have multiple regions with multiple purposes.  The few successful epigenetic drugs which are known affect only a single enzyme region.  What the field of epigenetic drug discovery desperately needs is the chemical probes to use in target discovery.

Research in our group is focussed on discovery of chemical probes for three classes of epigenetic enzymes, lysine demethylases (KDM, red hexagon in figure 2), plant-homeodomains (PHD, red crescent in figure 2) and bromodomains (BRD​ , purple crescent in figure 2).  There are over twenty KDMs and they collectively erase chemical marks important in gene regulation.  One of the KDMs, KDM4B is potentially import in breast cancer and the chemical probe my research group is developing will provide a chemical starting point for drug discovery if it proves the link between KDM4B and breast cancer.  PHDs read the same chemical mark that is erased by KDMs.  Reading of the epigenetic mark by PHDs is involved in gene transcription but there are hundreds of PHDs and the biology of most is a mystery.  There are more than sixty BRDs and they recognize a different epigenetic mark to the KDM/PHD system.  At least some of the BRDs are involved in many cancers.

Our Medicinal Chemistry group utilises high-throughput and fragment-basedscreening to discover chemical leads.  The leads are optimised for potency, selectivity and cellular activity via iterative cycles of structure based drug design, parallel organic synthesis, biophysical testing and compound structure-activity relationship (SAR) analysis.

The chemical probes developed in the group will decipher the function of epigenetic proteins in disease and provide starting points for drug discovery.  By using epigenetic chemical probes in target discovery, we will dramatically accelerate drug discovery in one of the most promising new areas of biomedical research.



Group Members

Andrea Nuzzi

Andrea Nuzzi got his MSc in Chemistry at the University of Calabria (Italy) in July 2003. One year later, he was admitted to the Graduate School of Chemistry at the University of Ferrara, supervised by Prof. Alessandro Dondoni and Prof. Alessandro Massi, and focussing his research interests in the synthesis of iminosugars, non-natural glycosyl aminoacids and structural modifications of internucleosidic linkage via “click-chemistry”. In this period, he produced five original papers published on international peer-reviewed journals.

He got his PhD in March 2008 and in April he started working as Junior Scientist at SienaBiotech, Siena. In this period, he was introduced to the Medicinal Chemistry world, being involved in several research projects (Huntington Disease, SMO Antagonist, Wnt Antagonist).

Between February 2010-2012, and then February 2012-2014 he was hired as Senior PostDoc at the Italian Institute of Technology, Genoa, with the aim to set up brand-new chemical labs, design novel N-Acyl-ethanolamide Acid Amidase (NAAA) inhibitors as anti-inflammatory agents and develop their synthetic routes. He was co-inventor of two patents and author of three original papers, two of them ready for submission.

Since February 2014 he has been working in Prof. Paul Brennan Group at the Target Discovery Institute, developing new lysine demethylase (KDM) inhibitors as epigenetic chemical probes.

Gian Filippo Ruda

Gian Filippo Ruda graduated in Organic Chemistry at the University of Sassari in 2002. During his thesis project he worked on the synthesis of peptides supported on polyethylene glycol under the supervision of Prof. Maurizio Taddei (University of Siena).

In February 2002 he joined the group of Prof. Ian Gilbert at the Welsh School of Pharmacy in Cardiff (UK) where he worked on the synthesis of inhibitors of the enzyme dUTPase for the treatment of infectious diseases. During his PhD study he spent few months at the Pharmacy Department of the Brighton University under the supervision of Prof. Jean-Yves Maillard. In July 2005 he received his PhD in Medicinal Chemistry.

In August 2005 Dr. Ruda moved with Prof. Gilbert to the Division of Chemical Biology and Drug Discovery of the University of Dundee (UK) where he worked as postdoctoral medicinal chemist collaborating to several projects on the field of neglected diseases in particular Human African Trypanosomiasis, Malaria and Aspergillosis. He also collaborated with Prof. Andrew Hopkins (University of Dundee) to test the proof-of -concept of new computational methods for rationally design of multi-target drugs with polypharmacology.

Gian Filippo Ruda joined the Department of Drug Discovery and Development D3 at the IIT in June 2010 as Senior Postdoc, until June 2013.

Then, he joined Prof. Paul Brennan Group at the Target Discovery Institute, focussing his research interests in lysine demethylase (KDM) inhibitors as novel epigenetic chemical probes.

Katherine England

Katherine graduated with an MChem in Chemistry from the University of Oxford in 2002, spending the fourth year as a member of the Jeremy Robertson group working on radical cyclisation reactions. Over the next 9 years she worked in Pfizer’s medicinal chemistry department in Sandwich, UK on a variety of drug discovery programmes in the allergy and respiratory, cardiovascular and genitourinary therapeutic areas.

She joined the group in 2011, working on the discovery of chemical probes for the JumonjiC domain containing histone lysine demethylases.

Melissa D'Ascenzio
Tamas Szommer

Tamas Szommer earned his MSc in Medicinal Chemistry at the Budapest University of Technology and Economics (under the supervision of Prof. Gyorgy Kalaus) in 2003. He started his industrial career at ComGenex Inc. in Hungary as medicinal chemist and he led numerous custom library and combinatorial library synthesis projects. He also actively participated in the development and introduction of ComGenex’s proprietary central ELN database system. In the meantime he was actively involved into the development of a database for structural evolution (EMIL - `Example-Mediated Innovation for Lead-Evolution` leading by  Prof. Toshio Fujita, CompuDrug Inc.). In 2006 ComGenex was acquired by Albany Molecular Research Inc. and Tamas was promoted to Head of Microwave and Parallel Chemistry and he was responsible for the operation and continuous development of the Parallel Chemistry Group in Hungary. He participated in the design and synthesis of small molecular libraries, custom library projects, fragment-based drug discovery projects and numerous natural product-like libraries. In 2012 Tamas successfully managed a technology transfer project at AMRI Hyderabad in India then he joined to ComInnex Inc. (Hungary) for a couple of months to `set up` a medicinal chemistry laboratory.

Stephen Wren

Stephen Wren was educated at the Universities of Cambridge (PhD in Organic Chemistry, under the supervision of Prof. Ian Paterson) and Manchester (BSc in Chemistry). He then conducted postdoctoral research in the synthesis of anti-cancer compounds with Prof. Phil Magnus at the University of Texas at Austin (1996-7).

He is highly experienced in medicinal chemistry and has worked on a diverse set of biological targets over many disease areas in several organisations (Xenova, Argenta Discovery, Summit). He has an extensive track record in project and team management, intellectual property and helped lead  the chemistry effort directed towards the identification of C1100 (Summit’s Duchenne Muscular Dystrophy drug, currently undergoing clinical evaluation).

Stephen Wren joined Prof. Paul Brennan’s Group at the Target Discovery Institute in June 2015 to work on Alzheimer’s drug discovery.

Saleta Vazquez Rodriguez
Miranda Wright
DPhil Student

I completed my MChem degree at the University of Warwick in June 2014. My placement year was spent at Novartis Pharmaceuticals in which I was involved in a medicinal chemistry project for the treatment of asthma. Under the supervision of Professor Mike Shipman, my master’s project was focused on an asymmetric synthetic step towards a natural product. My research interests are in the field of organic synthesis, in particular the development of new synthetic methodology and the total synthesis of natural products. In my spare time, I enjoy playing the flute as part of a wind orchestra.

Moses Moustakim
DPhil Student
Oakley Cox
DPhil Student

DPhil Project: "Design & Utilisation of a Poised Fragment Library in the search for Bromodomain Inhibitors", Medicinal Chemistry and Chemical Biology GroupSGC & in collaboration with Diamond Light Source, Didcot.

SABS-IDC - System Approaches to Biomedical Science: Industrial Doctoral Centre, Sept 2012 - present.

MChem, Masters of Chemistry, University of Oxford, Oct 2008 - June 2012.

4th Year Project: "Synthetic Investigations into tagged PIM1 Kinase Inhibitors", Angela Russell research group, Department of Chemistry, University of Oxford.

Additional Modules: Quantum Mechanics for Chemists (Distinction), March 2010. Chemical Pharmacology (Pass), March 2012.

Awards: Prize for First Year Practical Organic Chemistry, June 2009. AstraZeneca Organic Chemistry Bursary, Dec 2009 - June 2012.


Keywords: Fragment based drug discovery, Diamond Light Source, epigenetics, bromodomains, chemical probes, medicinal chemistry, x-ray crystallography, poised chemistry, structure activity relationship, hit-to-lead, structural biology.

Finn Wolfreys
DPhil Student


- B.Sc. Physics (Victoria University of Wellington)

- M.S. Bioengineering (KAIST)



- I am a member of the Chemical Biology and Medicinal Chemistry Group at the Structural Genomics Consortium, Nuffield Department of Medicine

Philip Gerken
DPhil Student


- 2006-2008: International Baccalaureate at the International School of Duesseldorf in Germany

- 2008-2012: Studied for MChem in Chemistry at the University in Oxford

- 2011-2012: Part II research project in medicinal chemistry


Work Experience & Research

- Summer 2010: Completed a 4-week industrial placement with Bayer-Sumika Inc. in Amagasaki, Japan investigating the properties of polyurethane coatings for the automotive industry.

- 2011-2012: Completed a 36-week research project, supervised by Dr. Angela Russell, in the University of Oxford chemistry research laboratory. The work involved synthesizing and testing small molecule inhibitors of the enzyme lactate dehydrogenase as part of an approach to target cancer cell metabolism.

- 2012-2013: Completed two ten-week research projects as part of the first year at the DTC. The first research project was supervised by Dr Martin Smith and involved using phase-transfer catalysis to generate a library of 3-dimensional fragments for drug discovery. The second project was supervised by Prof Christopher Schofield and focused on the biocatalytic scope of the enzyme FIH.

- Current work: DPhil supervised by Dr Martin Smith (Dep. of Chemistry) and Prof. Paul Brennan (SGC). The aim of my work is to use interesting chemical methodology to synthesize chemical probes for lysine demethylases.

Pavel Guzanov
DPhil Student


- 2013-now: DPhil on SABS-IDC doctoral training programme, University of Oxford

- 2008-2012: MChem, The University of York



Alternative synthesis research in asthma drug project, research chemist (6 months), Novartis Ltd., Basel, Switzerland. My work was supervised by Dr. Christian Mathes and Dr. Philipp Lustenberger. The goal of my research was to explore more efficient alternatives for established synthetic routes, which could be applied to kilogram production scale synthesis. The scope of the reserched reactions mainly comprised reductive aminations of nitrogen-containing heterocycles using different borohydride reagents.


Design and synthesis of protein inhibitors as a strating point for a perspective CNS drug, MChem. thesis project in industry, Hoffmann-La Roche Ltd., Basel, Switzerland, supervised by Dr Christian Lerner, Dr. Andrew Thomas and Dr. Paul Clarke. In 2011 I joined Dr. Christian Lerner's laboratory, which designed and synthesised protein inhibitors for a perspective CNS desease drug. This project involved organic synthesis using parallel synthesis, medicinal chemistry, X-ray crystallography and biology. Here not only did I significantly improve my synthetic skills, but also developed my theoretical knowledge in such areas as ligand-protein interactions and brain signalling pathways. I had an opportunity to improve my practical skills in crystallography by constructing several crystal structures of ligand-protein co-crystals for my project. Thanks to monthly organised meetings, where we had to report on development in our project, I was able to significantly improve my ability to give scientific presentations.


Crystallisation of Lin28 protein, Summer internship, York Structural Biology Laboratory (YSBL), The University of York, York, UK, supervised by Prof. Fred Antson. I was working in thos research group during summer 2009. The goal of the project I joined was determination of RNA-binding protein Lin28 structure. The goal was to crystallize this protein, so that its structure could be elucidated by X-ray crystallography, and optimize condition for its crystallization. I did all the steps of the research process starting from E.coli transformation with corresponding vector, protein extraction from bacteria, protein purification using a broad variety of techniques and research on the best crystallization conditions. I have got experience at different analytical and purification techniques like different kinds of chromatography, various kinds of electrophoresis. Moreover, I was using basic biochemical protocols like DNA and plasmid purification, PCR and etc. In addition, I really advanced my understanding of protein chemistry, gene expression mechanisms and biology associated with protein-RNA interactions.

Milan Fowkes
Research Assistant

I am currently working on the synthesis of peptide-based CT contrast agents for the in vivo imaging of cartilage degradation in Osteoarthritis under the supervision of Dr. Han Lim (Kennedy Institute) and Prof. Paul Brennan (Target Discovery Institute).




2007-2011: Master of Chemistry, MChem (University of Warwick, UK).


-Final year project: "Bond rotation and Radical Cyclisation Studies of N-alkenyl-N-2-bromobenzyl Acetamides" (Dr. Andrew Clark).


2012-2014: Master of Science, M.Sc Chemistry (Molecular Imaging)-(Western University, Canada). 


-Thesis: "Peptidomimetic GHS-R1a agonists as PET imaging agents for Prostate Cancer." (Dr. Leonard Luyt).


Conference Presentations: 


Fowkes, M.M., Dhanvantari, S., Kovacs, M., Luyt, L.G. Peptidomimetic GHS-R1a Agonists as

PET Imaging Agents for Prostate Cancer, 97th Canadian Chemistry Conference and Exhibition

(CSC), Vancouver, B.C., Canada, June 1-5th 2014 [oral presentation].

Group Publications


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