Identifying New Tool Compounds Targeting Dengue Rdrp Using Open Science And Virtual Screening

• By: ISAKSSON, Rebecka (Ucl School Of Pharmacy, United Kingdom)
• Co-author(s): Dr Rebecka Isaksson (University College London School of Pharmacy, London, United Kingdom / Oregon Health & Science University, Portland, USA)
  Dr Konstantin Popov (University of North Carolina Eshelman School of Pharmacy, Chapel Hill, USA)
  Professor Ralph Baric (University of North Carolina Gillings School of Global Public Health, Chapel Hill, USA)
  Dr Tina Leisner (University of North Carolina Eshelman School of Pharmacy, Chapel Hill, USA)
  Dr Jessica Smith (Oregon Health & Science University, Portland, USA)
  Professor Matthew Todd (University College London School of Pharmacy, London, United Kingdom / The Structural Genomics Consortium)
  Professor Tim Willson (University of North Carolina Eshelman School of Pharmacy, Chapel Hill, USA / Oregon Health & Science University, Portland, USA)
  
• Abstract:

  Introduction
  Dengue infections are rising fast around the world with the WHO estimating as many as 400 million infections yearly, a 10-fold increase over the past two decades that is not stopping; this year saw a big surge in infections South America, with Brazil reporting over 600.000 cases in a few weeks. This is primarily driven by climate change that broadens the habitat for the virus-carrying mosquitoes. While most cases result in flu-like symptoms that require minimal healthcare interventions, severe cases can result in hemorrhagic fever that require hospitalization. The societal cost of Dengue is growing, as is the strain the increasing number of infections place on healthcare systems. Battling Dengue is complex and will require multiple tools, both impacting the vector itself and treatments such as the vaccines and drugs. To date there are no drugs on market and with an ever-increasing need for new therapies, efforts to identify new starting points for drug development are highly relevant. In this project, we are taking an open-science approach to identify new possible drug candidates and tool compounds to assist with continued research around Dengue infections. The aim of these efforts is to identify a new hit compound for the RNA-dependent RNA polymerase (RdRp), a key protein in the viral replication machinery.
  
  Method
  Using mutational studies, new sites for drug binding were explored on the Dengue RdRp. These results were used to guide a virtual screen of the Enamine REAL space to identify hits that could bind to this new site. For these hits, small libraries of chemical entities were generated to explore the structure-activity relationship (SAR) of these early hits and further explore their binding mode and stability. In this open science project, input from the scientific community has been sourced to support development.
  
  Results
  Mutational studies identified a new pocket on the protein that has previously not been reported in literature. Using this site in the virtual screening cascade generated 1000 candidates, and 65 of these were selected as representative compounds sent for assay testing. This resulted in three top compounds that showed antiviral activity in the low micro-molar range, and further studies showed binding to Rdrp in a surface plasmon resonance assay. We identified that solubility was moderate and thus our continued chemical exploration is aimed at improving potency, solubility, and metabolic stability. These efforts involve both identifying commercially available compounds to go into our SAR libraries, as well as synthetic chemistry. Further biological studies are focused at confirming the binding pocket by applying our hit compound, and other iterations, on the mutated strains used to identify the site, in addition to crystal structure generation.
  
  Conclusion
  In this project we have used mutational studies and combined that with a virtual screening campaign to generate new starting points for developing a chemical probe that binds to Dengue RdRp in a site previously not reported.