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Optimizing variant-specific therapeutic SARS-CoV-2 decoys using deep-learning-guided molecular dynamics simulations.

Katharina Köchl1,2, Tobias Schopper1, Vedat Durmaz1

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|January 14, 2023
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Summary

Researchers optimized soluble human ACE2 (hACE2) to bind SARS-CoV-2, developing high-affinity variants like hACE2-Fc K31W. These variants show improved virus neutralization, offering a promising COVID-19 treatment strategy against emerging variants.

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Area of Science:

  • Virology
  • Computational Biology
  • Biochemistry

Background:

  • Soluble human angiotensin-converting enzyme 2 (hACE2) is a potential therapeutic for COVID-19 by blocking SARS-CoV-2 entry.
  • Optimization is needed to enhance binding affinity and effectiveness against evolving viral variants.

Purpose of the Study:

  • To computationally identify and experimentally validate optimized hACE2 variants with high binding affinity to SARS-CoV-2 spike receptor-binding domains (RBDs).
  • To assess the efficacy of these variants against Omicron sublineages and evaluate large-scale production methods.

Main Methods:

  • Molecular dynamics simulations and a novel convolutional neural network architecture were used for binding affinity assessments.
  • In vitro virus neutralization assays validated candidate variants.
  • Binding affinities were evaluated against Omicron BA.3, BA.4/BA.5, and BA.2.75 RBDs.
  • Expression in Nicotiana benthamiana was compared to CHO cells for production efficiency.

Main Results:

  • hACE2-Fc K31W and multi-mutation variants demonstrated high binding affinity to SARS-CoV-2 RBDs.
  • These variants showed significant virus neutralization capabilities in vitro.
  • Variants produced in Nicotiana benthamiana exhibited a 4.6-fold reduction in half-maximal inhibitory concentration (IC50) compared to CHO-produced variants.

Conclusions:

  • Optimized hACE2 variants, particularly hACE2-Fc K31W, are effective against SARS-CoV-2 and emerging Omicron variants.
  • Nicotiana benthamiana offers a more efficient production system for these therapeutic candidates, reducing IC50 values significantly compared to wild-type hACE2-Fc.