A systematic study on the binding affinity of SARS-CoV-2 spike protein to antibodies

Ke An; Xiaohong Zhu; Junfang Yan; Peiyi Xu; Linfeng Hu; Chen Bai; Ke An; Xiaohong Zhu; Junfang Yan; Peiyi Xu; Linfeng Hu; Chen Bai

doi:10.3934/microbiol.2022038

AIMS Microbiology

2022, Volume 8, Issue 4: 595-611. doi: 10.3934/microbiol.2022038

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A systematic study on the binding affinity of SARS-CoV-2 spike protein to antibodies

1.
Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, 518172, Guangdong, People's Republic of China
2.
School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
3.
Chenzhu (MoMeD) Biotechnology Co., Ltd, Hangzhou, Zhejiang, 310005, P.R. China

Received: 29 September 2022 Revised: 18 December 2022 Accepted: 21 December 2022 Published: 26 December 2022

The COVID-19 pandemic has caused a worldwide health crisis and economic recession. Effective prevention and treatment methods are urgently required to control the pandemic. However, the emergence of novel SARS-CoV-2 variants challenges the effectiveness of currently available vaccines and therapeutic antibodies. In this study, through the assessment of binding free energies, we analyzed the mutational effects on the binding affinity of the coronavirus spike protein to neutralizing antibodies, patient-derived antibodies, and artificially designed antibody mimics. We designed a scoring method to assess the immune evasion ability of viral variants. We also evaluated the differences between several targeting sites on the spike protein of antibodies. The results presented herein might prove helpful in the development of more effective therapies in the future.
- SARS-CoV-2,
- variant,
- antibody,
- binding affinity,
- immune evasion
Citation: Ke An, Xiaohong Zhu, Junfang Yan, Peiyi Xu, Linfeng Hu, Chen Bai. A systematic study on the binding affinity of SARS-CoV-2 spike protein to antibodies[J]. AIMS Microbiology, 2022, 8(4): 595-611. doi: 10.3934/microbiol.2022038

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Abstract

The COVID-19 pandemic has caused a worldwide health crisis and economic recession. Effective prevention and treatment methods are urgently required to control the pandemic. However, the emergence of novel SARS-CoV-2 variants challenges the effectiveness of currently available vaccines and therapeutic antibodies. In this study, through the assessment of binding free energies, we analyzed the mutational effects on the binding affinity of the coronavirus spike protein to neutralizing antibodies, patient-derived antibodies, and artificially designed antibody mimics. We designed a scoring method to assess the immune evasion ability of viral variants. We also evaluated the differences between several targeting sites on the spike protein of antibodies. The results presented herein might prove helpful in the development of more effective therapies in the future.

Acknowledgments

This research was funded by the Warshel Institute for Computational Biology at the Chinese University of Hong Kong, Shenzhen (grant no. C10120180043).

Conflict of interest

The authors declare no conflict of interest.

Author contributions

CB supervised the project. XZ and KA designed the research study. XZ, KA, JY, PX, and LH, performed the research. XZ and KA analyzed the data and drafted the manuscript. All authors contributed to editorial changes in the manuscript. All authors read and approved the final manuscript.

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