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Developing Proteolysis Targeted Chimeras (PROTACs) to individual class-I Histone Deacetylase complexes

Principal supervisor: Professor Shaun Cowley, Department of Molecular and Cell Biology

Industry partner: LifeArc

Project Title: Developing Proteolysis Targeted Chimeras (PROTACs) to individual class-I Histone Deacetylase complexes

University of registration: University of Leicester

Project outline:

The highly related histone deacetylases (HDAC) 1, 2 and 3 regulate global levels of lysine acetylation as the catalytic components of five distinct multi-protein complexes: Sin3, NuRD, CoREST, MiDAC and NCoR [1, 2]. These complexes have been implicated in numerous cellular processes, including: cell cycle, DNA synthesis, DNA repair and gene expression. In the clinic, pan- HDAC inhibitors (e.g. SAHA) are used to treat cancer and depression, although their use is associated with a number of debilitating side-effects. However, even specific HDACi, such as Entinostat (which targets HDAC1/2), still have the issue that HDAC1/2 are common to at least four different complexes, all of which have unique functions in the cell. Given the positive therapeutic value of HDAC inhibition in numerous disease states, and the detrimental side-effects of generic HDAC inhibition, the logical way forward is to perturb individual HDAC complexes.

Proteolysis Targeting Chimaeras (PROTAC) are hetero-bifunctional molecules which incorporate a known binding moiety to the protein of interest (POI, e.g. an inhibitor), coupled to a ligand for an E3 ubiquitin ligase complex (Fig 1). Direct recruitment of the E3 ligase to the POI via the PROTAC, targets it for ubiquitination and ultimately degradation, thus down-regulating its activity [3, 4]. There is enormous interest in the industrial sector for PROTAC technology because it allows targeted degradation of proteins thought previously to be undruggable (transcription factors, chromatin associated proteins, etc). Already PROTAC have been generated to the orphan nuclear receptor ERR, and the bromodomain containing protein, Brd4 [4], that are currently being tested as potential therapeutics. The aim of this studentship is to develop novel PROTAC-based tools to interrogate the roles of class-I HDAC complexes in cells and thus identify lead compounds for the development of a new class of HDAC inhibitors.


Specific Aim 1: Develop novel PROTAC to the LSD1/CoREST/HDAC1 complex

Lysine specific demethylase 1 (LSD1) is an amine oxidase which removes the methyl moiety from histone H3 Lys4 (H3K4me/me2 an active transcriptional mark) as part of the CoREST complex, along with CoREST1 and HDAC1. There are a large and increasing number of LSD1 inhibitors, derivatives of tranylcypromine (TCP), which can be functionalized for the attachment of an E3 ligand (Fig 1). An LSD1-PROTAC should reduce LSD1 protein levels, which in turn will cause increased degradation of its binding partner, CoREST [5], thus disrupting the entire complex.

Specific Aim 2: Targeted degradation of the NCoR/HDAC3 complex using PROTACs

HDAC3 specific inhibitors have been developed (e.g. RGFP966, T247) with enhanced specificity over other HDAC isotypes. HDAC3 is found solely in the NCoR1/2 complex which mediates transcriptional repression of unliganded nuclear receptors. We predict that targeted degradation of HDAC3, using an E3-ligand conjugated to an HDAC3 inhibitor, will also cause increased proteolysis of NCoR1/2 complex, whose function has been linked to the development of acute myeloid leukaemia [6].

Contact: Professor Shaun Cowley, University of Leicester