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Could Digital Visualizations Speed Up the Development of Drugs to Treat Ebola?
An interactive Web app generates 3-D views of Ebola proteins to assist with treatment and prevention.
In the midst of current clinical challenges facing patients at risk of Ebola virus disease and the hospital staff caring for them, researchers are tasked with predicting how the virus may evolve in an attempt to create effective treatment options for the future. During the initial decades of monitoring, the virus and outbreaks of its related disease were not seen to be mutating in any significant way. But during the most recent outbreak, the virus has been seen to be changing, breaking into multiple strains.
Thanks to the Mutation Position Imaging Toolkit, or MuPIT for short, researchers could create drugs for the treatment or prevention of the disease sooner rather than later. MuPIT is a free online tool developed by Johns Hopkins biomedical engineers that allows scientific investigators to better visualize the changes taking place within the virus on a molecular level.
An Up-Close View of Ebola, Online
Originally developed in 2012 to visualize gene mutations in human proteins, the new Ebola version of MuPIT enables a researcher to visualize Ebola gene mutations in the context of three-dimensional protein structures. It also offers views of antibody binding sites called epitopes that are situated on protein surfaces. These sites may give researchers new targets for preventive vaccines and serums to treat those who are already infected.
“Learning more about the mutations and binding sites can be valuable in developing new and better ways to treat Ebola patients and to keep the virus from infecting people in the first place,” says Rachel Karchin, a Johns Hopkins biomedical engineer who supervised the project.
Partnering for a Closer Look
The Karchin Lab developed the software in response to a request from University of California, Santa Cruz bioinformatics researcher David Haussler. He wanted a digital display tool to connect with the new Ebola Genome Browser recently released by the university.
The Ebola Genome Browser offers detailed genetic information about the virus and allows researchers and health care experts around the world to track the mutational adaptations of the virus during the outbreak. The Johns Hopkins add-on provides 3-D views of Ebola’s proteins, making it easier to interpret the functional implications of mutations, their relationship to Ebola virus evolution and the virus’ potential vulnerabilities.
An Evolving Scene
This initial version of MuPIT Ebola provides visualization of user-specified mutations and mutations from 101 viral genome sequences, derived from blood samples taken from Ebola patients in West Africa. It includes functional annotations from the Universal Protein Resource database and epitope sequences from the Immune Epitope Database Analysis Resource.
“We hope to continually update and improve the tool through interaction with Ebola researchers,” Karchin says.
The MuPIT Ebola edition represents a collaboration involving the Karchin Lab at the Johns Hopkins Institute for Computational Medicine, the bioinformatics software company In Silico Solutions and the University of California, Santa Cruz Ebola Genome Portal. The Institute for Computational Medicine includes researchers from Johns Hopkins’ Whiting School of Engineering and its school of medicine.