Development of an Antibody Targeting Variants of the SARS-CoV-2 Spike Protein

The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which enters human cells through its spike protein binding the human receptor (ACE2), has evolving variants of concern (VOCs). This in silico study aimed to enhance the binding efficacy of a fragment in the SARS-CoV-2 antibody, by designing single-chain variable fragments (scFv) to block ACE2 from binding various receptor binding domain (RBD) variants. Material and Methods: The modified scFv structures were derived from the regdanvimab (CT-P59) IgG antibody. The binding interactions between the scFv and RBD of VOC variants were characterized using molecular docking and molecular dynamic (MD) simulations. Additionally, computational mutagenesis was also performed to optimize the scFv binding efficacy against the RBD variants. Results: The unmodified CT-P59 scFv exhibited stronger binding affinities to VOC variants as compared to those of the Fab fragment; except for the Beta and Omicron XBB.1.5 variants. The docking results of the mutated antibody revealed that the R105W mutation in the scFv exhibited the most significant improvement in binding affinity across all VOCs. Additional MD simulation showed that the R105W mutation resulted in stronger binding affinity and stability than those of the wild-type CT-P59 Fab fragment; particularly against the Delta and Omicron variants. The R105W mutation induced binding by consistently interacting with virus-conserved residues Y452, F486, and Y489 on the RBD. Conclusion: This study successfully highlights the potential of the scFv with R105W mutation, targeting conserved RBD regions. This suggests that scFv_R105W is a promising therapeutic candidate against SARS-CoV-2. Additionally, it provides a framework for developing potent therapeutic antibodies against COVID-19 and potential future pandemics; emphasizing the importance of adaptive strategies in response to viral mutations. © 2025 JHSMR. Hosted by Prince of Songkla University. All rights reserved.