Rational design of femtomolar inhibitors of isoleucyl tRNA synthetase froma binding model for pseudomonic acid-A

This paper describes the design and characterization of novel inhibitors of IleRS, whose binding affinity approaches the tightest reported for noncova lent inhibition. Compounds were designed from a binding model for the natur al product pseudomonic acid-A (PS-A) together with a detailed understanding of the reaction cycle of IleRS and characterization of the mode of binding of the reaction intermediate IleAMP. The interactions of the compounds wit h IleRS were characterized by inhibition of aminoacylation of tRNA or PPi/A TP exchange at supersaturating substrate concentration and by transient kin etics and calorimetry methods. A detailed understanding of the interaction of a comprehensive series of compounds with IleRS allowed the identificatio n of key features and hence the design of exquisitely potent inhibitors. Pr edictions based on these results have been recently supported by a docking model based on the crystal structure of IleRS with PS-A [Silvian, L. F., Wa ng J. M., and Steitz T. A. (1999) Science 285 1074-1077].