Biopolym. Cell. 2024; 40(3):212-212.
http://dx.doi.org/10.7124/bc.000AEB
Chronicle and Information
Antibodies targeting the spike protein of SARS-CoV-2 can be modified to increase their affinity for new virus variants
1, 2Peka M. Yu., 2Balatsky V. M.
  1. V. N. Karazin Kharkiv National University
    4, Svobody Sq., Kharkiv, Ukraine, 61022
  2. Institute of Pig Breeding and Agroindustrial Production, NAAS of Ukraine
    1, Shvedska Mohyla Str., Poltava, Ukraine, 36013

Abstract

Aim. The accumulation of numerous mutations in emerging SARS-CoV-2 variants contributes to viral escape from immune response, necessitating an assessment of the effectiveness of known antibodies and consideration of their modification. Conclusions. The accumulation of mutations in the S-protein of emerging SARS-CoV-2 variants can potentially reduce the affinity of neutralizing antibodies. However, modifying amino acid sequences of antibody chains offers a promising strategy to re-establish efficient binding to the S-protein, thereby enabling the adaptation of antibodies in response to the virus’s evolutionary changes.
Keywords: SARS–CoV–2, COVID–19, antibody, mutation, molecular dynamics, binding free energy
Full text: (PDF, in English)

References

[1] Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, Heer FT, de Beer TAP, Rempfer C, Bordoli L, Lepore R, Schwede T. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 2018; 46(W1):W296-W303.
[2] Bertoglio F, Fühner V, Ruschig M, Heine PA, Abassi L, Klünemann T, Rand U, Meier D, Langreder N, Steinke S, Ballmann R, Schneider KT, Roth KDR, Kuhn P, Riese P, Schäckermann D, Korn J, Koch A, Chaudhry MZ, Eschke K, Kim Y, Zock-Emmenthal S, Becker M, Scholz M, Moreira GMSG, Wenzel EV, Russo G, Garritsen HSP, Casu S, Gerstner A, Roth G, Adler J, Trimpert J, Hermann A, Schirrmann T, Dübel S, Frenzel A, Van den Heuvel J, Čičin-Šain L, Schubert M, Hust M. A SARS-CoV-2 neutralizing antibody selected from COVID-19 patients binds to the ACE2-RBD interface and is tolerant to most known RBD mutations. Cell Rep. 2021; 36(4):109433.
[3] Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol. 1993; 234(3):779-815.
[4] Abraham MJ, Murtola T, Schulz R, Páll S, Smith JC, Hess B, Lindahl E. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX. 2015; 1-2:19-25.
[5] Valdés-Tresanco MS, Valdés-Tresanco ME, Valiente PA, Moreno E. gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS. J Chem Theory Comput. 2021; 17(10):6281-91.