title: Design, Synthesis, and Experimental Validation of Peptide Ligands Targeting Mycobacterium tuberculosis σ Factors.
abstract: 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 σAand σB. 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 σBusing biolayer interferometry. The experimental data validate the design strategy. These studies suggest the feasibility of designing specific peptides via in silico methods that bind σBwith 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.
authors.affiliation: Molecular Biophysics Unit, Indian Institute of Science , Bangalore 560012, India.
authors.forename: Sneha
authors.initials: S
authors.lastname: Vishwanath
authors.affiliation: Molecular Biophysics Unit, Indian Institute of Science , Bangalore 560012, India.
authors.forename: Sunaina
authors.initials: S
authors.lastname: Banerjee
authors.affiliation: Molecular Biophysics Unit, Indian Institute of Science , Bangalore 560012, India.
authors.forename: Anil K
authors.initials: AK
authors.lastname: Jamithireddy
authors.affiliation: Molecular Biophysics Unit, Indian Institute of Science , Bangalore 560012, India.
authors.forename: Narayanaswamy
authors.identifier: http://orcid.org/0000-0002-6566-6239
authors.initials: N
authors.lastname: Srinivasan
authors.affiliation: Molecular Biophysics Unit, Indian Institute of Science , Bangalore 560012, India.
authors.forename: Balasubramanian
authors.initials: B
authors.lastname: Gopal
authors.affiliation: Molecular Biophysics Unit, Indian Institute of Science , Bangalore 560012, India.
authors.forename: Jayanta
authors.initials: J
authors.lastname: Chatterjee
mesh_terms: D000595:Amino Acid Sequence; D002942:Circular Dichroism; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry; D007700:Kinetics; D008024:Ligands; D008958:Models, Molecular; D009169:Mycobacterium tuberculosis / Q000378:metabolism*; D010446:Peptide Fragments / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D017386:Sequence Homology, Amino Acid; D012808:Sigma Factor / Q000378:metabolism*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
chemical_list: D008024:Ligands; D010446:Peptide Fragments; D012808:Sigma Factor; D012321:DNA-Directed RNA Polymerases