Apr 5, 2020

Computational Recipe for Designing Antibodies against the Ebola Virus

BioRxiv : the Preprint Server for Biology
Amir Barati FarimaniE. Jakobsson

Abstract

A conceptual basis for antiviral therapy is to deliver a synthetic antibody that binds to a viral surface protein, and thus prevents the virus from deploying its cell-entry mechanism. The fast and untraceable virus mutations take lives of thousands of people before the immune system can produce the inhibitory antibody. In this paper, we devised a computational recipe to predict both the viral escape mutations and the possible inhibitory synthetic antibodies. We combined bioinformatics, structural biology, and molecular dynamics (MD) simulations to explore the most likely viral mutations and the candidate antibodies that can inhibit those escape mutations. Specifically, using the crystal structures of the Sudan and Zaire Ebola viral GPs in complex to their respective antibodies (ABs), we have performed an extensive set of MD simulations, both on the wild-type structures and on a large array of additional complexes designed and generated through combinatorial mutations. We discovered that our methods enabled the successful redesign of antibody sequences to essentially all likely glycoprotein mutations. Our findings and the computational methodology developed here for general antibody design can facilitate therapy of current and p...Continue Reading

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Mentioned in this Paper

Cross Validation
Proteomics
Genomics
Hypersensitivity
Fisher's Exact Test
Validation
Fuzzy Logic
Statistical Analysis

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