Polycationic Peptides That Bind T-Box Riboswitch Antiterminator RNA and Inhibit Riboswitch Function

Resistance to antibiotic treatments continues to be a significant health challenge and necessitates investigating novel antibacterial targets including noncoding regulatory RNA. The antiterminator RNA element of the T-box riboswitch is one such novel target. In this report, we investigated a spatially dispersed polycationic pharmacophore model for targeting the T-box antiterminator RNA. Decapeptides were designed based on a known alkyl polyamine agonist of the T-box riboswitch. Antiterminator model RNA binding was assessed using native mass spectrometry and modulation of T-box riboswitch function determined using a previously validated fluorescence-based assay. One peptide was identified that formed a complex with antiterminator model RNA and selectively inhibited T-box riboswitch transcription readthrough (both with and without tRNA induction). The inhibitory activity of this polycationic peptide, which was designed to mimic biogenic polyamines, has implications for future drug discovery efforts targeting the T-box riboswitch and other medicinally important noncoding regulatory RNA.