Inhibitory mechanism of reveromycin A at the tRNA binding site of a class I synthetase

The polyketide natural product reveromycin A (RM-A) exhibits antifungal, anticancer, anti-bone metastasis, anti-periodontitis and anti-osteoporosis activities by selectively inhibiting eukaryotic cytoplasmic isoleucyl-tRNA synthetase (IleRS). Herein, a co-crystal structure suggests that the RM-A molecule occupies the substrate tRNA Ile binding site of Saccharomyces cerevisiae IleRS ( Sc IleRS), by partially mimicking the binding of tRNA Ile . RM-A binding is facilitated by the copurified intermediate product isoleucyl-adenylate (Ile-AMP). The binding assays confirm that RM-A competes with tRNA Ile while binding synergistically with l -isoleucine or intermediate analogue Ile-AMS to the aminoacylation pocket of Sc IleRS. This study highlights that the vast tRNA binding site of the Rossmann-fold catalytic domain of class I aminoacyl-tRNA synthetases could be targeted by a small molecule. This finding will inform future rational drug design.