The relentless rise of antibiotic-resistant strains of Neisseria gonorrhoeae threatens our ability to effectively treat gonorrhoea, posing a critical threat to public health. The rapid development of resistance underscores the urgent need for new antibiotics with novel mechanisms of action. RNase HI degrades the RNA strand of RNA:DNA hybrids to resolve transcription associated R loops and is genetically essential in N. gonorrhoeae, representing an unexploited vulnerability.
Our work validates RNase HI as a potential drug target in N. gonorrhoeae by identifying novel RNase HI inhibitors through enzyme activity and bacterial cell viability assays. A chemical scaffold library was synthesised, incorporating a canonical metal-chelating motif tailored to the enzyme's active site, as well as including FDA-approved antivirals originally designed against RNase H-like viral enzymes. A FRET enzymatic assay enabled screening of compound potency against purified N. gonorrhoeae RNase HI, allowing inhibitors to be identified. A bacterial viability assay was then used to determine the antibacterial efficacy of these compounds, with several emerging as dual-activity hits, inhibiting RNase HI catalysis and reducing N. gonorrhoeae viability at low micromolar concentrations. To confirm the specificity of these hits, compounds were then counter-screened against human RNase H1 to ensure limited off-target toxicity.
Structure-activity relationships from this biochemical and microbiological data guide iterative optimisation. We have determined the N. gonorrhoeae RNase HI structure at 1.4 Å resolution using X-ray crystallography, and crystal-soaking experiments have yielded inhibitor-bound complexes, providing a framework for improving compound affinity through structural-based drug design.
Our integrated biochemical, microbiological, and structural approach has validated RNase HI as a novel, druggable target. This work paves the way to advancing next generation N. gonorrhoeae therapeutics capable of overcoming existing resistance mechanisms.