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

Transcription in prokaryotes is a multistep process and is :primarily regulated at the initiation stage. sigma factors are involved in promoter recognition and thus govern prokaryotic gene expression. Mycobacterium tuberculosis (MO) sigma factors have been previously suggested as important drug targets through large-scale genome analyses. Here we demonstrate the feasibility of specific targeting of Mtb sigma factors using designed peptides. A peptide library was generated using three-dimensional structural features corresponding to the interface regions of sigma factors and the RNA polymerase. In silico optimization of the peptides, employing structural as well as sequence features, aided specific targeting of sigma(A) and sigma(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;sigma(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 sigma(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

Determination of Redox Sensitivity in Structurally Similar Biological Redox Sensors

Redox stimuli govern a variety of biological processes. The relative sensitivity of redox sensors plays an important role in providing a calibrated response to environmental stimuli and cellular homeostasis. This cellular machinery plays a crucial role in the human pathoge<i>n Mycobacterium tuberculosis</i> as it encounters diverse microenvironments in the host. The redox sensory mechanism in <i>M. tuberculosis</i> is governed by two component and one-component systems, alongside a class of transcription factors called the extra cytoplasmic function (ECF) σ factors. ECF σ factors that govern the cellular response to redox stimuli are negatively regulated by forming a complex with proteins called zinc associated anti-σ factors (ZAS). ZAS proteins release their cognate σ factor in response to oxidative stress. The relative sensitivity of the ZAS sensors to redox processes dictate the concentration of free ECF σ factors in the cell. However, factors governing the redox threshold of these sensors remain unclear. We describe here, the molecular characterization of three σ factor/ZAS pairsσ^L/RslA, σ^E/RseA, and σ^H/RshAusing a combination of biophysical and electrochemical techniques. This study reveals, conclusively, the differences in redox sensitivity in these proteins despite apparent structural similarity and rationalizes the hierarchy in the activation of the cognate ECF σ factors. Put together, the study provides a basis for examining sequence and conformational features that modulate redox sensitivity within the confines of a conserved structural scaffold. The findings provide the guiding principles for the design of intracellular redox sensors with tailored sensitivity and predictable redox thresholds, providing a much needed biochemical tool for understanding host–pathogen interaction

Design, Synthesis, and Experimental Validation of Peptide Ligands Targeting <i>Mycobacterium tuberculosis</i> 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. <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) σ factors have been previously suggested as important drug targets through large-scale genome analyses. Here we demonstrate the feasibility of specific targeting of <i>Mtb</i> 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. <i>In silico</i> 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 <i>in silico</i> 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