Assay-Based High Throughput Screening of Diverse Libraries Identifies Selective Inhibitors of Staphylococcus aureus...

Bacterial ribonuclease P (RNase P) is an essential ribonucleoprotein enzyme that contains a catalytic RNA (P RNA) and single protein subunit (RnpA) and is a potentially valuable antibiotic target. Although assay-based screens of libraries containing diverse or drug-like compounds have been reported, the discovery of potent and specific bacterial RNase P inhibitors has proved challenging. To survey chemical space better suited for targeting a ribonucleoprotein enzyme, we screened commercial (Enamine) libraries of RNA-targeted and protein mimetic compounds for inhibition of Staphylococcus aureus RNase P. Five distinct chemical scaffolds were discovered with micromolar IC₅₀ values. Two independent hits shared the same amide scaffold and a common tetrahydroisoquinoline group. These results motivated further SAR analyses that established the active pharmacophore. Importantly, two of the active compounds are selective inhibitors of S. aureus RNase P, with lower IC₅₀ compared to the RNase P enzymes from Escherichia coli and Enterococcus faecium. Thus, expanding assay-based screening into broader chemical space can reveal novel scaffolds as potential starting points for the development of selective inhibitors targeting an essential bacterial RNA processing enzyme.