Allosteric Inhibitors of Erythromycin Resistance Methyltransferase Reverse Antibiotic Resistance

Methylation of a critical adenine residue of the 23S rRNA residing in the nascent exit tunnel of the bacterial ribosome, by Erythromycin resistant methyltransferases (Erms), reduces binding of macrolide, lincosamide, and streptogramin B (MLSB) class of antibiotics and confers high-level resistance. Using an allosteric site-directed focused virtual screening approach, nucleoside analogues were identified as the initial scaffold. 6-thioinosine, recognized as a significant initial hit molecule, was confirmed through in vitro screening to be a potent scaffold. Further, structure-based inhibitor evolution approach yielded improved analogues that demonstrated an MIC of 8 μg/mL via a combination therapy approach where Erm inhibitors were administered along with standard antibiotics in MLSB resistant clinical isolates. Our findings demonstrate that a strategy where allosteric inhibitors are developed to impede the ability of pathogenic ribosomal methyltransferases to recognize target RNA can serve as a generic approach for reversal of antibiotic resistance in a combination therapy mode.