EMoMiS: A Pipeline for Epitope-based Molecular Mimicry Search in Protein Structures with Applications to SARS-CoV-2

  1. Vitalii Stebliankin
  2. Prabin Baral
  3. Christian Balbin
  4. Janelle Nunez-Castilla
  5. Masrur Sobhan
  6. Trevor Cickovski
  7. Ananda Mohan Mondal
  8. Jessica Siltberg-Liberles
  9. Prem Chapagain
  10. Kalai Mathee
  11. Giri Narasimhan
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Abstract

Motivation

Epitope-based molecular mimicry occurs when an antibody cross-reacts with two different antigens due to structural and chemical similarities. Molecular mimicry between proteins from two viruses can lead to beneficial cross-protection when the antibodies produced by exposure to one also react with the other. On the other hand, mimicry between a protein from a pathogen and a human protein can lead to auto-immune disorders if the antibodies resulting from exposure to the virus end up interacting with host proteins. While cross-protection can suggest the possible reuse of vaccines developed for other pathogens, cross-reaction with host proteins may explain side effects. There are no computational tools available to date for a large-scale search of antibody cross-reactivity.

Results

We present a comprehensive Epitope-based Molecular Mimicry Search (EMoMiS) pipeline for computational molecular mimicry searches. EMoMiS, when applied to the SARS-CoV-2 Spike protein, identified eight examples of molecular mimicry with viral and human proteins. These findings provide possible explanations for (a) differential severity of COVID-19 caused by cross-protection due to prior vaccinations and/or exposure to other viruses, and (b) commonly seen COVID-19 side effects such as thrombocytopenia and thrombophilia. Our findings are supported by previously reported research but need validation with laboratory experiments. The developed pipeline is generic and can be applied to find mimicry for novel pathogens. It has applications in improving vaccine design.

Availability

The developed Epitope-based Molecular Mimicry Search Pipeline (EMoMiS) is available from <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://biorg.cs.fiu.edu/emomis/">https://biorg.cs.fiu.edu/emomis/</ext-link>.

Contact

<email>giri@cs.fiu.edu</email>

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