Ebola Scare: New Online 3D Tool Developed to Help Researchers Develop Vaccines

Johns Hopkins biomedical engineers have developed a free, Internet tool that could speed up the creation of new drugs to treat Ebola virus infections and take preventive steps as well.

The software, called MuPIT Ebola Edition, enables a researcher to visualize Ebola gene mutations with 3-D protein structures, offers views of anti-body binding sites or epitopes on protein surfaces. These online sites may give researchers new targets for preventive vaccines and serums to treat those already infected.

MuPIT or Mutation Position Imaging Toolkit, developed by Rachel Karchin and her team to understand the evolutionary and functional aspect of mutation in the Ebola genome to anticipate how the virus will change in the future and develop vaccines.

“Learning more about the mutations and binding sites can be enormously valuable in developing new and better ways to treat Ebola patients and, ideally, to keep the virus from infecting people in the first place,” said Karchin, who is a Johns Hopkins associate professor of biomedical engineering and a core faculty member of the university’s Institute for Computational Medicine.

Karchin pointed out that many existing vaccines are made by engineering specific antibodies, which are Y-shaped molecules that bind to viral surface proteins and help prevent the virus from replicating and spreading. Citing the drug ZMapp, which was recently used to treat several Ebola-infected health care workers, she said it is also a cocktail of three antibodies.

The new digital Ebola Genome Browser offers detailed genetic information about the virus, with an add-on that provides 3-D views of Ebola’s proteins, making it easier to interpret the functional implications of mutations and their relationship to Ebola virus evolution and its potential vulnerabilities.

UC Santa Cruz bioinformatics researcher David Haussler, who was one of Karchin’s graduate faculty advisers, said, “The Ebola Genome Browser allows researchers and health care experts around the world to track the mutational adaptations of the virus during the outbreak.”

This first edition of MuPIT Ebola provides visualization of user-specified mutations as well as 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 and Analysis Resource.

The MuPIT Ebola edition browser can be accessed at http://mupit-ebola.icm.jhu.edu/

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