Collaborative Research: RAPID: Computationally designed probes to experimentally characterize mechanisms of Ebola virus membrane fusion

Lay Abstract The 2014 Ebola epidemic is the largest outbreak in history (http://www.cdc.gov) and according to the World Health Organization (WHO), "There have been 9936 Ebola virus disease cases, and 4877 deaths, up to the end of 19 October." Just as alarming are the recent reports of Ebola transmission to hospital caregivers despite official warning to the contrary that spread would likely not be an issue in more developed countries such as the United States. Together, these unprecedented events highlight the severity of the potential of Ebola virus to become pandemic and the urgent need to more fully characterize how the virus replicates so that steps can be made to stop the current and likely future outbreaks. This project employs atomic-level computer modeling (docking, virtual screening) to predict and characterize how small molecule compound probes bind to and interact with specific viral proteins located on the surface of the Ebola virus. Top-scoring compounds will be experimentally tested to determine which molecules can stop viral entry. Characterization of how small molecules interact with Ebola proteins will ultimately enable a better understanding of how viral entry can be stopped and Ebola infection controlled. This will also be important for the study of other enveloped viruses such as influenza, HIV, SARS, MERS, among others. Broader impacts of the work include increased knowledge as to what types of molecules are most effective at stopping Ebola infection which will benefit study of related enveloped viruses and targeting of similar viral entry events mediated by analogous viral proteins. An important component of the project is educational training in use of cutting-edge computational and experimental tools for viral research at the undergraduate, graduate, and postdoctoral levels that includes the planned participation of women and underrepresented minorities. Technical Abstract The PI will conduct computational and experimental studies to identify and design small molecular probes that will arrest early membrane fusion events necessary for the life cycle of the virus. The project will employ a powerful new computational docking strategy that allows putative binding interfaces, such as those on Ebola viral entry proteins GP2 and GP1, to be mapped and exploited at the atomic level. Specifically, computational footprinting methods employing per-residue interaction energies will be used to identify targetable events in the Ebola pre-hairpin and pre-fusion models followed by docking to identify the most promising top-scoring compounds for additional in-depth characterization and experimental testing. The goal is to identify compounds that target favorable positions for disruption of N-helical coil formation and C-helix association, using large-scale high-throughput-virtual screening of commercially available compounds and experimental testing. An experimental pseudotyped virus system that uses a quantitative reporter gene in a non-replicating virus-like particle containing Ebola virus envelope proteins GP2 and GP1 will be used to confirm that compounds from the virtual screen arrest viral entry/fusion. Such compounds will be prioritized for additional study and development. Broader impacts of the work include increased knowledge as to what types of compounds are most effective at stopping Ebola infection which may both lead to development of Ebola virus-targeted therapeutics and also benefit study of related enveloped viruses and targeting of similar viral entry events mediated by analogous viral proteins. The project will also educate undergraduate, graduate, and postdoctoral students in the use and analysis of innovative computational docking and experimental biophysical methods to help prepare the next generation of scientists to attack important research problems in the future.