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R346K Mutation in the Mu Variant of SARS-CoV-2 Alters the Interactions with Monoclonal Antibodies from Class 2: A

Filip Fratev1,2

  • 1Micar Innovation (Micar21) Ltd., Persenk 34B, 1407 Sofia, Bulgaria.

Journal of Chemical Information and Modeling
|January 24, 2022
PubMed

Insights

The Mu variant's R346K mutation slightly reduces binding with class 2 neutralizing antibodies, offering limited resistance. This contrasts with the K417N mutation, which significantly impacts antibody binding.

Area of Science:

  • Virology
  • Immunology
  • Computational Biology

Background:

  • The SARS-CoV-2 Mu variant (B.1.621 lineage) is a variant of interest (VOI).
  • Limited data exists on the Mu variant's impact on neutralizing monoclonal antibodies (mAbs).
  • The R346K mutation in the receptor binding domain (RBD) is a key feature of the Mu variant.

Purpose of the Study:

  • To investigate the impact of the R346K mutation on the binding affinity of neutralizing monoclonal antibodies (mAbs).
  • To compare the effect of R346K with other mutations, such as K417N, found in SARS-CoV-2 variants.

Main Methods:

  • Free energy perturbation (FEP) calculations were employed.
  • Simulations focused on the interaction between the SARS-CoV-2 RBD and specific neutralizing mAbs.
  • Binding affinities were quantified in terms of changes in free energy (kcal/mol).

Main Results:

  • The R346K mutation showed a modest reduction in binding affinity (0.66 kcal/mol, ~3-fold) with class 2 antibodies.
  • Similar binding reductions were observed for antibody pairs BD-812/836 and BD-821/771.
  • In contrast, the K417N mutation significantly reduced binding (1.29 kcal/mol, ~10-fold) with class 1 antibodies.

Conclusions:

  • The R346K mutation in the Mu variant confers a degree of resistance to antibody neutralization, primarily by affecting class 2 antibodies.
  • The impact of R346K on antibody binding is less significant compared to mutations like K417N.
  • Further research is needed to fully understand the neutralization escape mechanisms of the Mu variant.

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