Antibiotic resistance is a global problem, with very few new compounds in development. Transcription is an underutilised target for antibiotic discovery, and only two antimicrobial agents (Rifampicin, Lipiarmycin) targeting bacterial transcription have been approved for clinical use. However, resistance to these drugs can easily develop through point mutation at multiple sites within the active site formed by the major β and β' subunits of RNA polymerase (RNAP). Rather than focus on this active site, we have taken the approach of targeting essential protein-protein interactions in the transcription complex. We quantified the role of individual amino acids in the region of RNAP required for binding to the unique bacterial initiation factor σ. We then screened a unique in-house indole-based peptidomimetic library to identify compounds that could inhibit the RNAP-σ interaction. One compound, GKL003, was chosen for further characterisation and was shown to be able to prevent σ factor binding to RNAP with an inhibition constant in the low nM range. Furthermore, this compound has activity against both Gram positive and negative organisms, including a community acquired methicillin resistant strain of the major pathogen Staphylococcus aureus, providing the basis for development of a new class of antimicrobial compound.