Design, Synthesis, and Experimental Validation of Peptide Ligands Targeting Mycobacterium tuberculosis σ Factors

Transcription in prokaryotes is a multistep process and is primarily regulated at the initiation stage. σ factors are involved in promoter recognition and thus govern prokaryotic gene expression. Mycobacterium tuberculosis (Mtb) σ factors have been previously suggested as important drug targets through large-scale genome analyses. Here we demonstrate the feasibility of specific targeting of Mtb σ factors using designed peptides. A peptide library was generated using three-dimensional structural features corresponding to the interface regions of σ factors and the RNA polymerase. In silico optimization of the peptides, employing structural as well as sequence features, aided specific targeting of σ^A and σ^B. We synthesized and characterized the best hit peptide from the peptide library along with other control peptides and studied the interaction of these peptides with σ^B using biolayer interferometry. The experimental data validate the design strategy. These studies suggest the feasibility of designing specific peptides via in silico methods that bind σ^B with nanomolar affinity. We note that this strategy can be broadly applied to modulate prokaryotic transcription by designed peptides, thereby providing a tool for studying bacterial adaptation as well as host-pathogen interactions in infectious bacteria.