Mechanism of PKR Activation by Small Molecules

Abstract

The innate immune pathway serves as the first line of defense against bacterial and viral infection and represents an attractive target for development of novel, broad-spectrum antiviral therapeutics. The RNA activated kinase, PKR, is the key antiviral effector in this pathway. PKR contains a dsRNA binding domain and a kinase domain. Co-localization of the kinase domains of PKR upon binding of two or more PKRs to a single dsRNA enhances dimerization and subsequent activation. Previously, we have demonstrated that short heparin-derived oligosaccharides activate PKR by binding to the kinase domain and enhancing dimerization. We have identified small, drug-like molecules that activate PKR kinase. Enzyme activation is characterized by AC50 (concentration yielding 50% activation) and the maximal extent of activation. The most active small molecules have AC50 lying in the low micromolar range and maximal activation approaching the most potent dsRNA activator of PKR, poly(rI:rC). The mechanism of activation is probed using analytical ultracentrifugation and other biophysical techniques to define the thermodynamic linkage between PKR dimerization and ligand binding.