Fragment-Based Drug Discovery Targeting the T-Box Riboswitch

Due to the ever-growing health concern of antibiotic resistance, there is a need for novel drug development that can target bacteria in a way that is not resisted. In Gram positive bacteria, one of these potential targets is the T-box Riboswitch, which is a regulatory, non-coding region of RNA involved in amino acid regulation. Within the T-box Riboswitch is an antiterminator region, which dictates whether or not the downstream genes are transcribed. The genes that are regulated by the T-box riboswitch are directly involved in protein synthesis. The antiterminator is stabilized by the binding of uncharged tRNA, and when unbound forms the more stable terminator form, in which transcription is terminated. Drug design can be employed to target the antiterminator to prevent antitermination from occurring and cause the bacterial cell to die due to lack of protein synthesis. This thesis explores fragment-based computational docking studies to determine compounds that bind to the antiterminator with specificity and in regions that could potentially result in an inhibitory effect on antitermination. A compound library of 180 amino acid R groups were prepared and docked to the antiterminator as well as a control model without the tRNA-binding bulge region. Of the initial 180 amino acid R groups, 47 were determined to bind to the antiterminator in regions that may lead to inhibition with more specificity than in the control model. Additionally, 10 peptide links that were produced from these 47 compounds were further docked and each showed some level of binding to the regions of interest in the antiterminator. The results of this project indicated 47 amino acids that could potentially be used as building blocks for drug synthesis, in addition to 10 peptides that may produce an inhibitory effect on the antiterminator. Further studies can be performed on these compounds, such as fluorescence assays and transcriptional assays, to further test binding specificity and to determine if the compounds have the desired physiological outcome on the T-box riboswitch.