Discovery of Small‐Molecule Antibiotics against a Unique tRNA‐Mediated Regulation of Transcription in Gram‐Positive Bacteria

Abstract

The emergence of multidrug‐resistant bacteria necessitates the identification of unique targets of intervention and compounds that inhibit their function. Gram‐positive bacteria use a well‐conserved tRNA‐responsive transcriptional regulatory element in mRNAs, known as the T‐box, to regulate the transcription of multiple operons that control amino acid metabolism. T‐box regulatory elements are found only in the 5′‐untranslated region (UTR) of mRNAs of Gram‐positive bacteria, not Gram‐negative bacteria or the human host. Using the structure of the 5′UTR sequence of the Bacillus subtilis tyrosyl‐tRNA synthetase mRNA T‐box as a model, in\u2005silico docking of 305\u2009000 small compounds initially yielded 700 as potential binders that could inhibit the binding of the tRNA ligand. A single family of compounds inhibited the growth of Gram‐positive bacteria, but not Gram‐negative bacteria, including drug‐resistant clinical isolates at minimum inhibitory concentrations (MIC 16–64\u2005μg\u2009mL−1). Resistance developed at an extremely low mutational frequency (1.21×10−10). At 4\u2005μg\u2009mL−1, the parent compound PKZ18 significantly inhibited in\u2005vivo transcription of glycyl‐tRNA synthetase mRNA. PKZ18 also inhibited in\u2005vivo translation of the S.\u2005aureus threonyl‐tRNA synthetase protein. PKZ18 bound to the Specifier Loop in\u2005vitro (Kd≈24\u2005μm). Its core chemistry necessary for antibacterial activity has been identified. These findings support the T‐box regulatory mechanism as a new target for antibiotic discovery that may impede the emergence of resistance.