The design and synthesis of targeted BET inhibitors

  • Craig Michael Robertson

Student thesis: Doctoral Thesis

Abstract

The field of epigenetics is an exciting new area for drug discovery. In particular, modulating proteins at the level of gene expression has already been verified as a valuable tool in treating disease. Within this area, bromodomain containing proteins recognise the epigenetic code on histone proteins, modulating gene expression. The bromodomains contained within the BET family have been implicated in multiple disease indications, including cancer, inflammation and viral infections. Furthermore, the BET family of bromodomains have been widely disclosed as amenable to inhibition by small molecules. However, of the four bromodomain containing proteins within the BET family, three (Brd2, Brd3 and Brd4) are expressed ubiquitously. Therefore inhibition of BET bromodomain function has the potential to affect all cell types, not just those associated with disease. In this regard, a targeted drug delivery system could minimise the broader systemic effects of BET inhibition and potentially improve the therapeutic index associated with this pharmacology. To this end, this thesis will focus on the use of an esterase sensitive motif (ESM) pro-drug targeting strategy. The ESM, developed by Chroma Therapeutics, consists of an amino acid ester which is selectively hydrolysed by the tissue-specific esterase human carboxyesterase 1 (hCE-1), mainly localised in the immune cells, monocytes and macrophages. However, the incorporation of this targeting motif contributes around 200 molecular weight to a small molecule inhibitor. Therefore, a small, ligand efficient BET bromodomain inhibitor was identified to initiate the work described within this thesis. The first section of results within this thesis describes attempts made to further improve the ligand efficient fragment. While modifying the electronics of a phenyl ring contained within this fragment did not give an improved profile, replacement of this ring with a pyridyl group showed promise for the future physicochemical properties of this series. Subsequently, the ESM was successfully incorporated onto this template, with the hydrolysis of the ESM, within target cells, being demonstrated. However, the resulting acid, produced in large quantities within the target cell, was less potent in biochemical assays of BET inhibition than the parent ester. Additional investigation of the linker between the aryl and amino acid ester demonstrated, for the first time, the importance of linker length in the observed potency of the acid and in modulating hydrolysis rate of the ester at the site of action. In the second results section, the aim was to introduce selectivity over the wider bromodomains. To achieve this, while maintaining desirable physicochemical properties, the aim was to utilise saturated groups to interact with the WPF shelf region of the BET bromodomains. Optimisation was conducted through a number of iterations, making use of modern medicinal chemistry techniques including: structure-based design, small molecule X-ray data and computational modelling. Overall, work towards this thesis has taken a fragment molecule and optimised it towards a well-rounded lead molecule with excellent potency and physicochemical properties. The lead molecule has provided a platform to progress this series into lead optimisation within our laboratory with the aim of discovering a clinical candidate molecule to be evaluated in the treatment of rheumatoid arthritis. The human biological samples used within this thesis were sourced ethically and their research use was in accord with the terms of the informed consents. All animal studies discussed within this thesis were ethically reviewed and carried out in accordance with Animals (Scientific Procedures) Act 1986 and the GSK Policy on the Care, Welfare and Treatment of Animals.
Date of Award2 Jun 2016
Original languageEnglish
Awarding Institution
  • University Of Strathclyde
SponsorsUniversity of Strathclyde & Glaxo Smithkline (UK)

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