No description available.

No description available.

No description available.

No description available.

No description available.

No description available.

No description available.

As a result of the high cost of drug discovery, it is imperative that promising targets with strong disease association are identified and validated before embarking on costly molecule discovery and development phases. Chemical inhibitors provide an excellent tool for target validation. This project was initiated with the aim of designing and characterising tool inhibitors of proteins involved in the DNA damage response, to enable detailed mechanistic biological investigation, disease validation and initiation of translational drug discovery projects. The SMC complexes are critically important in coordinating chromosome condensation, sister chromatid cohesion, DNA repair, homologous recombination and transcriptional regulation. They represent interesting oncology targets and are compelling targets for tool inhibitor development. The core SMC proteins and NSE subunits of SMC5/6 and cohesin SMC1 and SMC3 were modelled and their druggabilities assessed, with an aim to advance to inhibitor development for any of the proteins that proved druggable. Unfortunately, the SMC5/6 and cohesin complexes were established as not druggable. BAF180 represents a major clear cell renal cell carcinoma (ccRCC) cancer gene, exhibiting truncating mutations in 41% of samples in a series of primary ccRCCs.1 It has therefore been highlighted as a promising opportunity to target ccRCC using a synthetic lethal therapeutic approach.2 Hopkins et al. utilised a novel screening technique to identify several genes that are synthetic lethal with BAF180.3 In this work, the druggabilities of three of these genes were assessed, and KAT2A was identified as a promising target for tool inhibitor development. Druggable pockets were identified at the KAT2A histone acetyltransferase (HAT) domain and bromodomain. The catalytically active HAT domain was prioritised as the preferred target. Potential KAT2A HAT domain inhibitors were available from a high-throughput screen (HTS), which utilised a fluorescence based activity assay.4,5 Unfortunately, this assay format proved prohibitively unreliable, and moreover, after discounting the hits from the HTS as likely false positives, the inventory of KAT2A inhibitors was quickly exhausted and the target abandoned. Focus turned to the KAT2A bromodomain. Available X-ray crystal structures were utilised in a computational drug design effort, and Tm shift, TR-FRET, ITC and X-ray crystallography techniques were optimised and established in-house to enable characterisation of prospective KAT2A tool inhibitors. Over 3000 small molecules and fragments were screened, and an assortment of novel KAT2A bromodomain binders were identified. The optimised assays, novel chemical matter and ligand-bound crystal structures afford an exciting opportunity to develop potent and selective KAT2A bromodomain tool inhibitors.

The work described in this thesis involves developing synthetic methods to produce a range of drug-like small molecules that can be used as chemical tools to understand and modulate disease pathophysiology. There are two types of such tools investigated in this thesis: diagnostic tools for imaging experiments, and inhibitory tools for modulating biochemical pathways. The imaging tools are designed to target apoptosis, accumulating in cells undergoing early-stage apoptotic events, and contain a fluorescent tag, thus providing a realtime technique for observing and monitoring these events and even to modulate them from inside the cell. The imaging agent would then be used to guide the design of a radiolabelled small molecule that can be used alongside traditional cancer therapies, to preferentially enter cells going through apoptosis, ensuring that these cells commit to cell death and do not recover. The inhibitory tools are designed to study the molecular mechanisms of MK2, a protein that has been implicated in disease progression and cellular ageing events. This worked used the premature ageing syndrome, Werner's Syndrome as a model for normal human ageing. In Chapter 2, several fluorescent markers are considered for the development of a real-time imaging tool to target apoptosis. The structures of the fluorescent agents are based on two structures known to preferentially enter cells going through the early stages of apoptosis; didansyl cystine and ML10. The conclusion of this investigation led to ML10 being used as the basis for further development of fluorescent agents. The formation of several novel BODIPY compounds is described, with one compound tested in a cell line for its ability to preferentially enter cells going through the early stages of apoptosis. The results of this test led to an investigation into the lipophilicity of BODIPY compounds versus ML10. This investigation involved the use of software to generate cLogP values as a guide for potential designs of further BODIPY structures. The development of a drug-like structure that can mimic the action of the BODIPY compound is also explored, with the inclusion of a step to insert iodine-131 at a later stage in the development. In Chapter 3, microwave-assisted organic synthesis was used to develop novel routes toward benzothiophene derivatives, which formed part of a new route towards the Pfizer developed MK2 inhibitor PF-3644022. This work was published in Organic and Biomolecular Chemistry. The full route was proposed in the doctoral thesis of Dr. Jessica Dwyer, and the latter part of this thesis set out to improve the yield of the final step. A collaboration with the Kostakis group led to an investigation into the use of the catalyst Zn2Y2(C21H25NO3)4 for its applicability to the Doebnertype multi-component reaction that would lead to the formation of PF-3644022. Although no conclusive results were obtained from the reactions trialled, the work opened up new channels of collaboration for the Bagley group and potential for further exploration of the use of isoskeletal coordination cluster catalysts in organic multi-component reactions. Overall, the aim of this work was to deliver rapid routes to these chemical tools so that, through in vivo and in vitro biological studies, we can better understand the role of kinase targets during disease progression and therapy in healthy and diseased cells. In this context, this work establishes novel routes to new chemical tools, validates their identity and action, and explores their application in providing new insights into biochemical processes and new opportunities for chemical intervention in pathophysiological events.

No description available.