Binding of Helix-Threading Peptides to E. coli 16S Ribosomal RNA and Inhibition of the S15-16S Complex

Helix‐threading peptides (HTPs) constitute a new class of small molecules that bind selectively to duplex RNA structures adjacent to helix defects and project peptide functionality into the dissimilar duplex grooves. To further explore and develop the capabilities of the HTP design for binding RNA selectively, we identified helix 22 of the prokaryotic ribosomal RNA 16S as a target. This helix is a component of the binding site for the ribosomal protein S15. In addition, the S15–16S RNA interaction is important for the ordered assembly of the bacterial ribosome. Here we present the synthesis and characterization of helix‐threading peptides that bind selectively to helix 22 of E. coli 16S RNA. These compounds bind helix 22 by threading intercalation placing the N termini in the minor groove and the C termini in the major groove. Binding is dependent on the presence of a highly conserved purine‐rich internal loop in the RNA, whereas removal of the loop minimally affects binding of the classical intercalators ethidium bromide and methidiumpropyl–EDTA⋅Fe (MPE⋅Fe). Moreover, binding selectivity translates into selective inhibition of formation of the S15–16S complex. Catch 22. Helix‐threading peptides (HTPs) that bind helix 22 of E. coli 16S RNA and block interaction with the ribosomal protein S15 are described. HTP binding is dependent on the presence of a highly conserved, purine‐rich internal loop that influences conformational flexibility at the binding site.