| Sumario: | <p>Development of ligands for bromodomains has expanded our understanding of gene regulation and epigenetic links to disease. These acetylated lysine ‘reader’ domains are found within larger macromolecules that are involved in gene transcription and degradation. This thesis looks to employ a range of computational tools to compliment the development of inhibitors to a selection bromodomain targets. The first target was TRIM33b, an E3 ubiquitin ligase that also contains a methylated lysine reader, known as a plant homeodomain. After identifying putative binding locations for ligands identified in a previously performed high-throughput screen through docking and molecular dynamics studies, one ligand was taken forward for further optimisation. Subsequent free energy calculations on both the ligand and water molecules were used to justify a proposed binding model, in the absence of a co-crystal structure. This model identified a stable water molecule in the ZA channel and was used to design the highest affinity ligands known for the TRIM33b bromodomain. The model was also scrutinised to understand why vector elaborations above the binding site did not yield a higher affinity probe molecule.</p> <p>The second set of targets were bromodomains within parasites responsible for a range of tropical diseases. In the absence of co-crystal structures, homology models and molecular dynamics studies were used to design binding models for a set of existing bromodomain ligands. These models were used to aid development of tool compounds, based on the BRD4(1)/PLK1 inhibitor BI-2536, and propose future modifications to increase affinity for parasite bromodomains. Two of the homology models were later confirmed by a subsequent co-crystal structure. Finally, several computational methods are employed to understand the trends in binding affinity for a range of ligands against the CREBBP bromodomain and BRD4(1). These studies highlighted the importance of an intramolecular hydrogen bond in analogues of OXFBD02, the role of a ZA channel water molecule on imposing selectivity for CREBBP ligands, and supported the role of a proposed cation-p interaction.</p>
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