The in silico investigation of pharmacological targets of the zika virus : insights into the structural characteristics of the NS5 and NS3 proteins from atomistic molecular simulations.

Abstract

The re-emerging Zika virus has evolved into a catastrophic epidemic during the past year, with an estimated 1.5 million reported cases of Zika infections worldwide, since the 2015 outbreak in Brazil. The virus has received considerable attention during 2016 with a flood of new discoveries, from evolving modes of viral transmission to viral-linked neurological disorders, unique specificity to host cells and increasing mutation rates. However, prior to the devastating 2015 outbreak in Brazil, the virus was classified as a neglected pathogen similar to Dengue and the West Nile virus. Despite the wide-scale research initiative, there is still no cure for the virus. There are currently vaccine clinical trials that are on-going but there has not been a breakthrough with regard to small molecule inhibitors. A lot of experimental resources have been allocated to repuposing FDA-approved drugs as possible inhibitors, however, even some of the most potent flavivirus inhibitors have adverse toxic effects. The first crystal structure of the zika virus was released in May 2016 and since then, six viral protein structures have been made available. Due to this lack in structural information, there is little known regarding the structural dynamics, active binding sites and the mechanism of inhibition of ZIKV enzymes. This study delves into the structural characteristics of three of the most crucial enzymatic targets of the zika virus, the NS5 RNA-dependent RNA polymerase and Methyltransferase as well as the NS3 Helicase. With emerging diseases, such as ZIKV, computational techniques including molecular modeling and docking, virtual screening and molecular dynamic simulations have allowed chemists to screen millions of compounds and thus funnel out possible lead drugs. These in silico approaches have warranted Computer-Aided Drug Design as a cost-effective strategy to fast track the drug discovery process. The The above techniques, amongst numerous other computational tools were employed in this study to provide insights into conformational changes that elucidate potential inhibitory mechanisms, active site identification and characterization and pharmacophoric features leading to promising small molecule inhibitor cadidates. The first study (Chapter 4), provided a comprehensive review on potential host/viral targets as well as provided a concise route map depicting the steps taken toward identifying potential inhibitors of drug targets when no crystal structure is available. A homology model case study, of the NS5 viral protein, was also demonstrated. The second study (Chapter 5) used the validated NS5 homology model to investigate the active sites at both the RNA-dependent RNA polymerase and Methyltransferase domains and subsequently employ a generated pharmacophore model to screen for potential inhibitors. Chapter 6 reports the third study, which investigates the structural dynamics and in turn, the possible mechanism of inhibition of the ZIKV NS3 Helicase enzyme when bound to ATP-competitive inhibitor, NITD008. The study also provides insight on the binding mode at the ATPase active site, thus assisting in the design of effective inhibitors against this detrimental viral target. Chapter 7 maps out the binding landscape of the ATPase and ssRNA site by demonstrating the chemical characteristics of potent flavivirus lead compounds, Lapachol, HMC-HO1α and Ivermectin at the respective NS3 Helicase binding sites. This study offers a comprehensive in silico perspective to fill the gap in drug design research against the Zika virus, thus giving insights toward the structural characteristics of pivotal targets and describing promising drug candidates. To this end, the work presented in this study is considered to be a fundamental platform in the advancements of research toward targeted drug design/delivery against ZIKV.