Discovery of Inhibitors Targeting Protein–Protein Interaction between Bacterial RNA Polymerase and NusG as Novel Antimicrobials

Bacterial
RNA polymerase (RNAP), the core enzyme responsible for
bacterial transcription, requires the NusG factor for efficient transcription
elongation and termination. As the primary binding site for NusG,
the RNAP clamp-helix (CH) domain represents a potential protein–protein
interaction (PPI) target for novel antimicrobial agent design and
discovery. In this study, we designed a pharmacophore model based
on the essential amino acids of the CH for binding to NusG, such as
R270, R278, and R281 (Escherichia coli numbering), and identified a hit compound with mild antimicrobial
activity. Subsequent rational design and synthesis of this hit compound
led to improved antimicrobial activity against Streptococcus
pneumoniae, with the minimum inhibitory concentration
(MIC) reduced from 128 to 1 μg/mL. Additional characterization
of the antimicrobial activity, inhibitory activity against RNAP-NusG
interaction, and cell-based transcription and fluorescent assays of
the optimized compounds demonstrated their potential for further lead
optimization.