Greenwood, SOR; (2016) Design and evaluation of novel histone deacetylase 8 inhibitors. Doctoral thesis , UCL (University College London).

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Abstract

Chapter One gives an introduction to the biological importance of HDACs and in particular of HDAC8. It discusses the structural features of the HDAC proteins, the different structural classes of inhibitors that have been reported and the isoform selectivity profiles of different inhibitors. The evaluation of a fluorogenic N -Bocprotected acetyl-lysine substrate in comparison to a commercially available acetyllysine containing tetrapeptide is also discussed and its suitability for inhibition assays is demonstrated. The synthesis and evaluation of eight 1st generation α-amino amide HDAC8 inhibitors is described in Chapter Two. These inhibitiors were inspired by a literature compound utilizing a novel zinc-binding α-amino amide group. The deversity in the inhibitors was envisaged to explore the chemical space around this novel zincbinding group into two of the major structural features of HDAC8, the substrate tunnel and the acetate release pocket. Nineteen 2nd generation α-amino amide HDAC8 inhibitors were designed as a result of the HDAC8 inhibition assays of the 1st generation compounds. Chapter Three discusses the design, synthesis and biological activity of these compounds. The results of HDAC8 inhibition assays are rationalised using manual docking of the inhibitors into an HDAC8 crystal structure. Through calculation of binding energies investigation is carried out into the contribution of each feature of the compound to the overall potency of the molecule. A potential beneficial HDAC8-inhibitor contact is revealed, though no 2nd generation inhibitors show potencies that are similar to that of the lead compound. Following the hypothesised interactions observed in manual docking of the most potent inhibitors from the 2nd generation of compounds, a 3rd and final round of α-amino amide inhibitors was designed and synthesised. These compounds extend the isoindoline scaffold of the lead compound in an attempt to form extra contacts with a specific and conserved asartate residue in a flexible loop at the mouth of substrate tunnel of the enzyme. In Chapter Four, two routes to obtain a substituted isoindoline ring system are evaluated and the synthesis of six substituted isoindolines is described, these isoindolines were coupled to generate α-amino amide HDAC8 inhibitors which were of comparable potency to the lead compound. Two of these novel compounds show improved potency compared to the lead compound, demonstrating the importance of the key hydrogen bonding interaction and validating the hypothesis that introduction of a hydrogen bond acceptor results in improved potency. An exploratory nuclear magnetic resonance spectroscopy inhibitor binding experiment is also described which demonstrates the potential for investigations using this technique in the future. Chapter Five describes all the experimental procedures which were followed in the biological evaluation of inhibitors and synthesis of inhibitors including physical and spectroscopic characterisation of all the synthesised compounds and intermediates.

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