| Autor: |
Lennon SR; Department of Biochemistry, University of Colorado, Boulder, Colorado 80309-0596, United States., Wierzba AJ; Department of Biochemistry, University of Colorado, Boulder, Colorado 80309-0596, United States.; BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303-0596, United States., Siwik SH; Department of Biochemistry, University of Colorado, Boulder, Colorado 80309-0596, United States., Gryko D; Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw 01-224, Poland., Palmer AE; Department of Biochemistry, University of Colorado, Boulder, Colorado 80309-0596, United States.; BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303-0596, United States., Batey RT; Department of Biochemistry, University of Colorado, Boulder, Colorado 80309-0596, United States. |
| Abstrakt: |
RNA-targeting small-molecule therapeutics is an emerging field hindered by an incomplete understanding of the basic principles governing RNA-ligand interactions. One way to advance our knowledge in this area is to study model systems where these interactions are better understood, such as riboswitches. Riboswitches bind a wide array of small molecules with high affinity and selectivity, providing a wealth of information on how RNA recognizes ligands through diverse structures. The cobalamin-sensing riboswitch is a particularly useful model system, as similar sequences show highly specialized binding preferences for different biological forms of cobalamin. This riboswitch is also widely dispersed across bacteria and therefore holds strong potential as an antibiotic target. Many synthetic cobalamin forms have been developed for various purposes including therapeutics, but their interaction with cobalamin riboswitches is yet to be explored. In this study, we characterize the interactions of 11 cobalamin derivatives with three representative cobalamin riboswitches using in vitro binding experiments (both chemical footprinting and a fluorescence-based assay) and a cell-based reporter assay. The derivatives show productive interactions with two of the three riboswitches, demonstrating simultaneous plasticity and selectivity within these RNAs. The observed plasticity is partially achieved through a novel structural rearrangement within the ligand binding pocket, providing insight into how similar RNA structures can be targeted. As the derivatives also show in vivo functionality, they serve as several potential lead compounds for further drug development. |
