Structural dynamics and inhibition of Hepatitis C RNA-dependent RNA polymerase

Combination therapy with direct-acting antivirals including nucleotide analogs (NAs) and non-nucleoside inhibitors (NNIs) targeting the RNA-dependent RNA polymerase NS5B have seen recent advancements and have dramatically improved the potency of Hepatitis C Virus (HCV) treatment. However, other than the identification of their site of action, very little is known about the inhibition mechanisms of these clinically relevant drugs. Lately, our lab has developed robust kinetic assays to characterize de novo RNA synthesis catalyzed by HCV NS5B, and then applied the assays to examine the mechanistic basis of action and to establish kinetic parameters governing the efficacy of various clinically relevant NAs and NNIs provided by three pharmaceutical companies (Gilead Sciences, Inc., Alios Biopharma and AbbVie Inc.). In addition, to probe the enzyme conformational dynamics of NS5B from de no initiation to elongation in the presence and absence of allosteric inhibitors, we collaborated with Dr. Patrick Wintrode on Hydrogen Deuterium exchange kinetics and Dr. Serdal Kirmizialtin on Molecular Dynamics simulations. Together, our collaborative efforts have provided a fundamental understanding of RNA-dependent RNA replication catalyzed by the HCV viral polymerase NS5B, and have established the inhibition mechanisms of anti-HCV agents. This work offers significant insights to aid the development of more effective drugs against HCV.