Browsing by Author "Brown, Jodian A."
Now showing 1 - 2 of 2
Results Per Page
Sort Options
Item ALLOSTERIC INHIBITION IN VIRAL POLYMERASES: UNDERSTANDING THE IMPACT OF MULTIPLE INHIBITORS AND PREDICTING NOVEL BINDING SITES USING COMPUTATIONAL CHEMISTRY APPROACHES(2016-01-01) Brown, Jodian A.; Thorpe, Ian F; Chemistry & Biochemistry; BiochemistryViral pathogens are responsible for a large number of human infections. For example, the Hepatitis C virus (HCV) affects close to 3% of the world'spopulation. There has been significant progress in the therapeutic options available for the treatment of HCV and most of the highly effective existing therapies are a combination of small molecule inhibitors targeting key viral enzymes. One such target is the polymerase, which is a critical component of the viral life cycle. Our work focuses on understanding inhibition of the polymerase by small molecules that bind to pockets outside the active site (i.e. allosteric inhibitors). The first objective of this study is to determine how allosteric inhibitors alter the structural, dynamic and thermodynamic properties of the HCV polymerase so that these small molecules can synergistically inhibit the enzyme. Our second goal is to identify putative allosteric sites in the polymerases of the Dengue (DENV), West Nile (WNV) and Foot-and-mouth Disease (FMDV) viruses. One of the existing challenges in current HCV treatment is that low fidelity of NS5B increases the rate of mutations in the virus. This results in the generation of multiple enzyme variants and makes it difficult to target the enzyme with single inhibitors. In contrast, for DENV, WNV and FMDV one of the major hurdles is lack of biochemical and structural data that can help steer more structure-based drug discovery efforts. Results from our studies of the HCV polymerase suggest that allosteric inhibitors from nonoverlapping sites can bind simultaneously and synergistically modulate the enzyme conformation and free energy landscape. This work provides the first molecular descriptions of mechanisms underlying enhanced inhibition of the HCV polymerase. We used validated HCV allosteric sites as targets to evaluate several ligand binding site predictor tools and used the best tool to identify novel putative allosteric pockets in the DENV, WNV and FMDV polymerases. The identified sites displayed structural and/or chemical similarities with two of the NS5B validated allosteric pockets. Our approach provides an economic and faster means to facilitate an essential step of drug discovery (i.e. binding site identification), which is critical for infections with limited therapeutic options.Item Allosteric Inhibitors Have Distinct Effects, but Also Common Modes of Action, in the HCV Polymerase(2016-11-15) Davis, Brittny C.; Brown, Jodian A.; Thorpe, Ian F.The RNA-dependent RNA polymerase from the Hepatitis C Virus (gene product NS5B) is a validated drug target because of its critical role in genome replication. There are at least four distinct allosteric sites on the polymerase to which several small molecule inhibitors bind. In addition, numerous crystal structures have been solved with different allosteric inhibitors bound to the polymerase. However, the molecular mechanisms by which these small molecules inhibit the enzyme have not been fully elucidated. There is evidence that allosteric inhibitors alter the intrinsic motions and distribution of conformations sampled by the enzyme. In this study we use molecular dynamics simulations to understand the structural and dynamic changes that result when inhibitors are bound at three different allosteric binding sites on the enzyme. We observe that ligand binding at each site alters the structure and dynamics of NS5B in a distinct manner. Nonetheless, our studies also highlight commonalities in the mechanisms of action of the different inhibitors. Each inhibitor alters the conformational states sampled by the enzyme, either by rigidifying the enzyme and preventing transitions between functional conformational states or by destabilizing the enzyme and preventing functionally relevant conformations from being adequately sampled. By illuminating the molecular mechanisms of allosteric inhibition, these studies delineate the intrinsic functional properties of the enzyme and pave the way for designing novel and more effective polymerase inhibitors. This information may also be important to understand how allosteric regulation occurs in related viral polymerases and other enzymes.