Design, Synthesis and SAR of the First Inhibitors of Methicillin-Resistant S. Aureus RnpA as Novel Antimicrobial Agents

Abstract

RNase P is a bacterial ribozyme that catalyzes the maturation of tRNA and is conserved across Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA). RNase P consists of a RNA component and a protein component, RnpA. In Gram-positive bacteria, RnpA itself possesses ribonuclease activity. The Dunman group demonstrated that inhibition of RnpA activity alone or as part of the RNase P complex was sufficient to inhibit RNA degradation and exert antimicrobial activity in MRSA. Because of its low amino acid homology to mammalian homologs, RnpA may represent a novel, selective antimicrobial target for MRSA. A high throughput screen by the Dunman group identified a number of compounds which inhibit RnpA activity, including RNPA1000. However, RNPA1000 demonstrated cytotoxic effects at higher concentrations and required a high dose to achieve efficacy in a murine model of MRSA infection. We therefore selected another “hit” from the screen (RNPA2000), which contains metabotoxic hydrazide, thiourea and furan moieties, as the starting point for hit to lead activities. We sought to replace these groups, as well as the isopropylphenoxy group, to provide enhanced inhibitory potency against RNase P and RnpA, as well as lowered MIC values against MRSA1000. We designed and synthesized analogs posessing bioisosteres for these moieties and evaluated their effects in an RNase P assay as well as a RNA degradation assay. Compounds with acceptable results in both assays were tested for their antimicrobial effects in MRSA cultures. As a result of this work, several compounds with improved potency for RnpA inhibition were identified, although improved MIC was not seen. Two compounds demonstrated synergy with mupirocin, an isoleucyl-tRNA synthase inhibitor, which may represent a potential way to re-sensitize resistant bacteria to mupirocin.