Small molecule based targeting of the CssA RNA thermometer: insights from computational and biophysical approaches

Abstract

The exploration of RNA as a therapeutic target is relatively recent. The field of RNA targeting with small molecules remains elusive despite significant advances via approaches such as the development of bioinformatics tools and strategies facilitating improved modes of action. Non-coding RNAs like RNA thermometers reported in many bacterial pathogens are exciting targets due to the translational control exerted by these RNA elements. The current work involves virtual screening of an in house library of small molecules against CssA RNA thermometer from Neisseria meningitidis via docking and molecular dynamics (MD) simulations followed by in vitro experiments to affirm the binding of small molecules to the target RNA. Fluorescence binding assay and NMR provide evidence for RNA thermometer-small molecule binding. The present study would open new avenues in the domain of small molecule-based targeting of RNA. Interestingly, an RNA thermometer has never been exploited as a drug target. Targeting such RNA elements with small molecules would facilitate structure-based small molecule design with better affinity for the target RNA. From among spiro-pyrrolidine based heterocycles that showed the best binding affinity with the RNAs, a small molecule was identified as the top lead with the potential for targeting the CssA RNA thermometer.