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Title: Selective targeting of riboswitches with small molecules
Author: Chen, L.
Awarding Body: University of Cambridge
Current Institution: University of Cambridge
Date of Award: 2011
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Riboswitches are folded structures within messenger RNA that can directly bind cell metabolites to trigger induction or suppression of essential metabolic pathways. Owing to their critical role in gene regulation, developing selective modulators of riboswitch function could lead to novel antimicrobial agents or multipurpose chemical biology tools. To find selective small molecule binders of thiamine pyrophosphate responsive riboswitches, we took a two-pronged approach. Firstly we tackled the more traditional route of screening analogues of the natural ligand in order to quickly furnish us with high-affinity ligands and structure-activity data. Secondly we applied the fragment-based approach as a fundamentally different but complementary way of achieving the same goal. By developing a suite of biophysical screening methods we were able to test a library of over one thousand low molecular weight fragments for selective binding to the E. coli thiM riboswitch. Our experiments demonstrate the validity of using fragment-based methods against RNA targets, thus extending the scope of this already valuable methodology. Our screening programme identified ligands with KD values as low as 9 nM (from the analogues) and ligand efficiencies as high as 0.69 (from the fragments). These compounds provide a solid basis for the further development of ligands that not only exhibit selective and potent binding to riboswitches but crucially also affect gene expression.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available