Design and Synthesis of Substrate Peptidomimetic Inhibitors (SPIs): New Probes for Epigenetic Target Validation

Lead Research Organisation: University of Glasgow
Department Name: School of Chemistry


The aim of the proposed research is to develop a novel type of synthetic molecule that will allow validation of epigenetic enzymes as therapeutic targets in oncology and provide lead compounds to initiate anticancer drug discovery programmes. The target proteins include deubiquitinase (DUB) and histone deacetylase (HDAC) enzymes.

We will develop peptidomimetics based on the natural peptide substrates of the enzymes. Using advance, automated synthetic chemistry techniques we will produce a range of molecules that target Zn-dependent DUBs and class 1 HDACs with unprecedented selectivity. These molecules will have two main applications 1) as isozyme selective inhibitors to determine the mechanistic role of these enzymes in a cellular context (ex. their role in gene expression), 2) as tool molecules to facilitate advanced structural biology studies (ex. protein identification within complexes using cryo-EM).

The insights gained from these experiments will be used to validate these enzymes as therapeutic targets, and inform structure-based design of selective inhibitors.


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Studentship Projects

Project Reference Relationship Related To Start End Student Name
EP/N509668/1 01/10/2016 30/09/2021
1944289 Studentship EP/N509668/1 01/10/2017 31/03/2021 Lewis John Archibald
Description 1. A novel Fmoc-amino acid building block containing a zinc-binding hydroxamic acid side chain has been developed and synthesised for the purpose of being incorporated into peptidomimetic histone deacetylase inhibitors based on histone tails. This amino acid represents the first time such functionality has been introduced in a convenient Fmoc-building block form for its facile incorporation into peptides via Fmoc-SPPS.

2. This amino acid has been used to facilitate the synthesis of a small library of 17 peptidic histone deacetylase inhibitors based on the sequence fragments of the N-terminal tail regions of histones 3 and 4 by advanced, automated Fmoc-SPPS. The successful synthesis of these peptides demonstrates the potential of the amino acid to facilitate the relatively rapid synthesis of peptidic HDAC inhibitor libraries.

3. These peptidic inhibitors have been assessed for their inhibition of the HMR partial HDAC corepressor complex. The potency of inhibition of the HMR complex by an initial library of 9 peptides showed that potency was dependent on the peptide sequence. The binding affinity of the three most potent peptides and the least potent peptide of the original library was assessed by synthesising and testing fluorescently labelled analogues. The two most potent sequences were subjected to an 'alanine scan' in which analogues were synthesised replacing each functional residue with alanine in turn to assess which are important for inhibition of the enzyme. These studies have identified specific residues on the histone tail sequences themselves which appear to be important for substrate recognition by the HDAC corepressor complex.

4. Work is in an advanced stage toward the total synthesis of the entire histone 3 protein sequence containing the hydroxamic acid amino acid at a specified site by convergent Fmoc-SPPS and ligation with a view to assessing this construct's ability to inhibit HDAC corepressor complexes. This was initially attempted by a semi-synthetic strategy, the conclusion of which was that due to the relative difficulty of obtaining truncated histone proteins by bacterial expression a total synthetic strategy was preferable.
Exploitation Route The outcomes of this funding will be published in the scientific literature. This will allow others to synthesise the hydroxamic acid Fmoc-amino acid building block and variants thereof to facilitate its incorporation into peptides. The studies on the peptidic HDAC inhibitors synthesised with this funding will be used to inform the community on the mechanisms of HDAC corepressor complex substrate specificity and help direct the design of corepressor complex-selective inhibitors.
Sectors Pharmaceuticals and Medical Biotechnology

Description Collaboration with Schwabe Group at the University of Leicester 
Organisation University of Leicester
Department Department of Molecular and Cell Biology
Country United Kingdom 
Sector Academic/University 
PI Contribution I have provided novel synthetic peptides based on stretches of the histone 3 and histone 4 tails for testing against the HMR partial HDAC corepressor complex.
Collaborator Contribution The collaborators have tested my synthetic peptides for their potency of inhibition and binding affinity to the HMR partial HDAC complex in their in-house assays and provided the data from these experiments.
Impact 1. The differences in potency of a library of histone tail peptidomimetic HDAC inhibitors have demostrated that the strength of inhibition is governed by the peptide sequence. 2. Residues important for binding of a peptidomimetic inhibitor to an HDAC complex have been systematically identified and provide insight into the mechanisms by which HDAC corepressor complexes achieve substrate specificity.
Start Year 2017