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Fragment-based approaches to targeting EthR from mycobacterium tuberculosis 10.17863/CAM.37485 McConnell, Brendan Neil 0000000190029808 Abell, Christopher Tuberculosis affects millions of people worldwide every year. The current treatment for TB is divided into a regimen of both first- and second-line drugs, where first-line treatments are more tolerated and require shorter treatment lengths. With rising levels of resistance, alternative treatment regimes are urgently needed to fight this disease. Ethionamide, a second-line drug is administered as a prodrug which is activated in vivo by the enzyme EthA, which is in turn regulated by EthR. The disruption of the action of EthR could lead to novel therapeutics which could enhance the efficacy of ethionamide, and raise it to a first-line treatment. The work reported in this thesis examines the elaboration of three chemical scaffolds using fragment-based approaches to develop novel inhibitors capable of disrupting the EthR-DNA interaction. The first scaffold, 5-(furan-2-yl)isoxazole was investigated by fragment-merging approaches and produced compounds with the best of these having a KD of 7.4 uM. The second scaffold, an aryl sulfone was elaborated using fragment-merging strategies. This led to several modifications of the fragment, leading to several variants with KDs around 20 uM. With both of these series the affinity could not be improved below 10 uM and due to the synthetic complexity a further scaffold was prioritised. The third scaffold was explored was a 4-(4-(trifluoromethyl)phenyl)piperazine using fragmentgrowing from the NH of the piperazine to probe deeper into the EthR binding pocket. In addition to this, SAR around the 4-(trifluoromethyl)phenyl group was assessed to explore the interactions with EthR. These modifications led to compounds with nanomolar IC50s. A range of compounds were then screened by REMAssay to determine the boosting effect on ethionamide, and this identified compounds with up to 30 times boosting in the ethionamide MIC. The final chapter examines a concept where compounds were designed to exploit the dimeric nature of EthR by linking two chemical warheads with a flexible linker. These compounds are examined using mass spectrometry to investigate the stoichiometry of the interaction to provide insight into the binding of these extended compounds and exploring an alternative strategy to inhibit EthR. The work in this thesis demonstrated the successful use of fragment-based approaches for development of novel EthR inhibitors which showed significant ethionamide boosting effects. University of Cambridge 2019-05-18 Thesis Doctoral Doctor of Philosophy (PhD) en Cambridge Commonwealth, European and International Trust (Poynton Cambridge Australia Scholarship) Cambridge Philosophical Society Access to Learning Fund https://www.repository.cam.ac.uk/handle/1810/290255 https://www.repository.cam.ac.uk/bitstreams/40f1a5cd-8759-4b68-b28e-f1096cfd3dd8/download 37dde80c547c212532644e70d8d0d80d https://www.repository.cam.ac.uk/bitstreams/074254b5-c2cc-4bd8-8e3a-ae5ade7035e8/download 87eda9de84448d1f82354d60eee3eb5f https://www.rioxx.net/licenses/all-rights-reserved/ EthR tuberculosis ethionamide TB fragment-based drug design FBDD fragment-based ligand design FBLD isothermal titration calorimetry ITC thermal shift differential scanning fluorimetry DSF surface plasmon resonance SPR sulfone piperazine