Epimaps of the SARS-CoV-2 Receptor-Binding Domain Mutational Landscape: Insights into Protein Stability, Epitope Prediction, and Antibody Binding
Abstract
1. Introduction
2. Materials and Methods
2.1. Homology Modelling
2.2. Crystal Structures of WT RBD–Antibody Complexes
2.3. Protein Preparation
2.4. Protein–Antibody Modelling
2.5. Predicting the Effect of Single-Point Mutations on Protein Stability
2.6. Epitope Mapping
3. Results and Discussion
3.1. Modelling the RBD of SARS-CoV-2 Variants
3.2. Characterisation of Amino Acid Substitutions Affecting the Stability of the RBD
3.3. Epitope Mapping of the SARS-CoV-2 RBD
3.4. Predicting the Effects of RBD Mutations on the Binding of Monoclonal Antibodies
3.4.1. Class 1 and 2 Antibodies
Energy Contributions of Key Residues: F456, E484, F486, Q493
3.4.2. Class 3 and 6 Antibodies
Energy Contributions of Key Residues: R346, N440, L452, E484, F490, Q498
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Fehr, A.R.; Perlman, S. Coronaviruses: An overview of their replication and pathogenesis. Methods Mol. Biol. 2015, 1282, 1–23. [Google Scholar] [CrossRef] [PubMed]
- Chen, B.; Tian, E.-K.; He, B.; Tian, L.; Han, R.; Wang, S.; Xiang, Q.; Zhang, S.; El Arnaout, T.; Cheng, W. Overview of lethal human coronaviruses. Signal Transduct. Target. Ther. 2020, 5, 89. [Google Scholar] [CrossRef] [PubMed]
- Pustake, M.; Tambolkar, I.; Giri, P.; Gandhi, C. SARS, MERS and CoVID-19: An overview and comparison of clinical, laboratory and radiological features. J. Fam. Med. Prim. Care 2022, 11, 10–17. [Google Scholar] [CrossRef] [PubMed]
- Petrosillo, N.; Viceconte, G.; Ergonul, O.; Ippolito, G.; Petersen, E. COVID-19, SARS and MERS: Are they closely related? Clin. Microbiol. Infect. 2020, 26, 729–734. [Google Scholar] [CrossRef]
- Bai, C.; Zhong, Q.; Gao, G.F. Overview of SARS-CoV-2 genome-encoded proteins. Sci. China Life Sci. 2022, 65, 280–294. [Google Scholar] [CrossRef]
- Wu, C.-r.; Yin, W.-c.; Jiang, Y.; Xu, H.E. Structure genomics of SARS-CoV-2 and its Omicron variant: Drug design templates for COVID-19. Acta Pharmacol. Sin. 2022, 43, 3021–3033. [Google Scholar] [CrossRef]
- Jackson, C.B.; Farzan, M.; Chen, B.; Choe, H. Mechanisms of SARS-CoV-2 entry into cells. Nat. Rev. Mol. Cell Biol. 2022, 23, 3–20. [Google Scholar] [CrossRef]
- Huang, Y.; Yang, C.; Xu, X.-f.; Xu, W.; Liu, S.-w. Structural and functional properties of SARS-CoV-2 spike protein: Potential antivirus drug development for COVID-19. Acta Pharmacol. Sin. 2020, 41, 1141–1149. [Google Scholar] [CrossRef]
- Shang, J.; Ye, G.; Shi, K.; Wan, Y.; Luo, C.; Aihara, H.; Geng, Q.; Auerbach, A.; Li, F. Structural basis of receptor recognition by SARS-CoV-2. Nature 2020, 581, 221–224. [Google Scholar] [CrossRef]
- Lan, J.; Ge, J.; Yu, J.; Shan, S.; Zhou, H.; Fan, S.; Zhang, Q.; Shi, X.; Wang, Q.; Zhang, L.; et al. Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature 2020, 581, 215–220. [Google Scholar] [CrossRef]
- Hodcroft, E.B. CoVariants: SARS-CoV-2 Mutations and Variants of Interest. 2021. Available online: https://covariants.org/ (accessed on 2 January 2025).
- Gangavarapu, K.; Latif, A.A.; Mullen, J.L.; Alkuzweny, M.; Hufbauer, E.; Tsueng, G.; Haag, E.; Zeller, M.; Aceves, C.M.; Zaiets, K.; et al. Outbreak.info genomic reports: Scalable and dynamic surveillance of SARS-CoV-2 variants and mutations. Nat. Methods 2023, 20, 512–522. [Google Scholar] [CrossRef] [PubMed]
- Shah, M.; Woo, H.G. Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies. Front. Immunol. 2021, 12, 830527. [Google Scholar] [CrossRef] [PubMed]
- Andre, M.; Lau, L.S.; Pokharel, M.D.; Ramelow, J.; Owens, F.; Souchak, J.; Akkaoui, J.; Ales, E.; Brown, H.; Shil, R.; et al. From Alpha to Omicron: How Different Variants of Concern of the SARS-Coronavirus-2 Impacted the World. Biology 2023, 12, 1267. [Google Scholar] [CrossRef] [PubMed]
- World Health Organization. Historical Working Definitions and Primary Actions for SARS-CoV-2 Variants. 2023. Available online: https://www.who.int/publications/m/item/historical-working-definitions-and-primary-actions-for-sars-cov-2-variants (accessed on 30 December 2024).
- Meng, B.; Abdullahi, A.; Ferreira, I.A.T.M.; Goonawardane, N.; Saito, A.; Kimura, I.; Yamasoba, D.; Gerber, P.P.; Fatihi, S.; Rathore, S.; et al. Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity. Nature 2022, 603, 706–714. [Google Scholar] [CrossRef]
- Suzuki, R.; Yamasoba, D.; Kimura, I.; Wang, L.; Kishimoto, M.; Ito, J.; Morioka, Y.; Nao, N.; Nasser, H.; Uriu, K.; et al. Attenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variant. Nature 2022, 603, 700–705. [Google Scholar] [CrossRef] [PubMed]
- Reuschl, A.-K.; Thorne, L.G.; Whelan, M.V.X.; Ragazzini, R.; Furnon, W.; Cowton, V.M.; De Lorenzo, G.; Mesner, D.; Turner, J.L.E.; Dowgier, G.; et al. Evolution of enhanced innate immune suppression by SARS-CoV-2 Omicron subvariants. Nat. Microbiol. 2024, 9, 451–463. [Google Scholar] [CrossRef]
- Cui, L.; Li, T.; Xue, W.; Zhang, S.; Wang, H.; Liu, H.; Gu, Y.; Xia, N.; Li, S. Comprehensive Overview of Broadly Neutralizing Antibodies against SARS-CoV-2 Variants. Viruses 2024, 16, 900. [Google Scholar] [CrossRef]
- Barnes, C.O.; Jette, C.A.; Abernathy, M.E.; Dam, K.A.; Esswein, S.R.; Gristick, H.B.; Malyutin, A.G.; Sharaf, N.G.; Huey-Tubman, K.E.; Lee, Y.E.; et al. SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies. Nature 2020, 588, 682–687. [Google Scholar] [CrossRef]
- Singh, D.D.; Parveen, A.; Yadav, D.K. SARS-CoV-2: Emergence of New Variants and Effectiveness of Vaccines. Front. Cell Infect. Microbiol. 2021, 11, 777212. [Google Scholar] [CrossRef]
- Berman, H.M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.N.; Weissig, H.; Shindyalov, I.N.; Bourne, P.E. The Protein Data Bank. Nucleic Acids Res. 2000, 28, 235–242. [Google Scholar] [CrossRef]
- Schrödinger LLC. The PyMOL Molecular Graphics System. Schrödinger LLC: New York, NY, USA, 2015; Version 1.8. [Google Scholar]
- Schrödinger LLC. Schrödinger Release 2022-2: Maestro; Schrödinger LLC: New York, NY, USA, 2022. [Google Scholar]
- Pettersen, E.F.; Goddard, T.D.; Huang, C.C.; Couch, G.S.; Greenblatt, D.M.; Meng, E.C.; Ferrin, T.E. UCSF Chimera—A visualization system for exploratory research and analysis. J. Comput. Chem. 2004, 25, 1605–1612. [Google Scholar] [CrossRef] [PubMed]
- Sali, A.; Blundell, T.L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 1993, 234, 779–815. [Google Scholar] [CrossRef] [PubMed]
- Ovchynnykova, O.; Kapusta, K.; Sizochenko, N.; Sukhyy, K.M.; Kolodziejczyk, W.; Hill, G.A.; Saloni, J. Homology Modeling and Molecular Dynamics-Driven Search for Natural Inhibitors That Universally Target Receptor-Binding Domain of Spike Glycoprotein in SARS-CoV-2 Variants. Molecules 2022, 27, 7336. [Google Scholar] [CrossRef] [PubMed]
- Li, L.; Gao, M.; Li, J.; Xie, X.; Zhao, H.; Wang, Y.; Xu, X.; Zu, S.; Chen, C.; Wan, D.; et al. Identification of an immunogenic epitope and protective antibody against the furin cleavage site of SARS-CoV-2. EBioMedicine 2023, 87, 104401. [Google Scholar] [CrossRef]
- Samanta, A.; Alam, S.S.M.; Ali, S.; Hoque, M. Analyzing the interaction of human ACE2 and RBD of spike protein of SARS-CoV-2 in perspective of Omicron variant. Excli J. 2022, 21, 610–620. [Google Scholar] [CrossRef]
- Shen, M.Y.; Sali, A. Statistical potential for assessment and prediction of protein structures. Protein Sci. 2006, 15, 2507–2524. [Google Scholar] [CrossRef]
- Hansen, J.; Baum, A.; Pascal, K.E.; Russo, V.; Giordano, S.; Wloga, E.; Fulton, B.O.; Yan, Y.; Koon, K.; Patel, K.; et al. Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail. Science 2020, 369, 1010–1014. [Google Scholar] [CrossRef]
- Dong, J.; Zost, S.J.; Greaney, A.J.; Starr, T.N.; Dingens, A.S.; Chen, E.C.; Chen, R.E.; Case, J.B.; Sutton, R.E.; Gilchuk, P.; et al. Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail. Nat. Microbiol. 2021, 6, 1233–1244. [Google Scholar] [CrossRef]
- Jones, B.E.; Brown-Augsburger, P.L.; Corbett, K.S.; Westendorf, K.; Davies, J.; Cujec, T.P.; Wiethoff, C.M.; Blackbourne, J.L.; Heinz, B.A.; Foster, D.; et al. The neutralizing antibody, LY-CoV555, protects against SARS-CoV-2 infection in nonhuman primates. Sci. Transl. Med. 2021, 13. [Google Scholar] [CrossRef]
- Shi, R.; Shan, C.; Duan, X.; Chen, Z.; Liu, P.; Song, J.; Song, T.; Bi, X.; Han, C.; Wu, L.; et al. A human neutralizing antibody targets the receptor-binding site of SARS-CoV-2. Nature 2020, 584, 120–124. [Google Scholar] [CrossRef]
- Westendorf, K.; Žentelis, S.; Wang, L.; Foster, D.; Vaillancourt, P.; Wiggin, M.; Lovett, E.; van der Lee, R.; Hendle, J.; Pustilnik, A.; et al. LY-CoV1404 (bebtelovimab) potently neutralizes SARS-CoV-2 variants. Cell Rep. 2022, 39, 110812. [Google Scholar] [CrossRef] [PubMed]
- Starr, T.N.; Czudnochowski, N.; Liu, Z.; Zatta, F.; Park, Y.J.; Addetia, A.; Pinto, D.; Beltramello, M.; Hernandez, P.; Greaney, A.J.; et al. SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape. Nature 2021, 597, 97–102. [Google Scholar] [CrossRef] [PubMed]
- Kim, C.; Ryu, D.-K.; Lee, J.; Kim, Y.-I.; Seo, J.-M.; Kim, Y.-G.; Jeong, J.-H.; Kim, M.; Kim, J.-I.; Kim, P.; et al. A therapeutic neutralizing antibody targeting receptor binding domain of SARS-CoV-2 spike protein. Nat. Commun. 2021, 12, 288. [Google Scholar] [CrossRef] [PubMed]
- Rouet, R.; Henry, J.Y.; Johansen, M.D.; Sobti, M.; Balachandran, H.; Langley, D.B.; Walker, G.J.; Lenthall, H.; Jackson, J.; Ubiparipovic, S.; et al. Broadly neutralizing SARS-CoV-2 antibodies through epitope-based selection from convalescent patients. Nat. Commun. 2023, 14, 687. [Google Scholar] [CrossRef]
- Krissinel, E.; Henrick, K. Inference of Macromolecular Assemblies from Crystalline State. J. Mol. Biol. 2007, 372, 774–797. [Google Scholar] [CrossRef]
- Guex, N.; Peitsch, M.C. SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis 1997, 18, 2714–2723. [Google Scholar] [CrossRef]
- Ambrosetti, F.; Olsen, T.H.; Olimpieri, P.P.; Jiménez-García, B.; Milanetti, E.; Marcatilli, P.; Bonvin, A.M.J.J. proABC-2: PRediction of AntiBody contacts v2 and its application to information-driven docking. Bioinformatics 2020, 36, 5107–5108. [Google Scholar] [CrossRef]
- Meng, E.C.; Goddard, T.D.; Pettersen, E.F.; Couch, G.S.; Pearson, Z.J.; Morris, J.H.; Ferrin, T.E. UCSF ChimeraX: Tools for structure building and analysis. Protein Sci. 2023, 32, e4792. [Google Scholar] [CrossRef]
- Abraham, M.J.; Murtola, T.; Schulz, R.; Páll, S.; Smith, J.C.; Hess, B.; Lindahl, E. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 2015, 1–2, 19–25. [Google Scholar] [CrossRef]
- Berendsen, H.J.; van der Spoel, D.; van Drunen, R. GROMACS: A message-passing parallel molecular dynamics implementation. Comput. Phys. Commun. 1995, 91, 43–56. [Google Scholar] [CrossRef]
- Bjelkmar, P.; Larsson, P.; Cuendet, M.A.; Hess, B.; Lindahl, E. Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models. J. Chem. Theory Comput. 2010, 6, 459–466. [Google Scholar] [CrossRef] [PubMed]
- Price, D.J.; Brooks, C.L., III. A modified TIP3P water potential for simulation with Ewald summation. J. Chem. Phys. 2004, 121, 10096–10103. [Google Scholar] [CrossRef]
- Pitsillou, E.; Liang, J.J.; Kino, N.; Lockwood, J.L.; Hung, A.; El-Osta, A.; AbuMaziad, A.S.; Karagiannis, T.C. An In Silico Investigation of the Pathogenic G151R G Protein-Gated Inwardly Rectifying K+ Channel 4 Variant to Identify Small Molecule Modulators. Biology 2024, 13, 992. [Google Scholar] [CrossRef] [PubMed]
- Pitsillou, E.; Liang, J.J.; Beh, R.C.; Hung, A.; Karagiannis, T.C. Molecular dynamics simulations highlight the altered binding landscape at the spike-ACE2 interface between the Delta and Omicron variants compared to the SARS-CoV-2 original strain. Comput. Biol. Med. 2022, 149, 106035. [Google Scholar] [CrossRef] [PubMed]
- Liang, J.; Pitsillou, E.; Karagiannis, C.; Darmawan, K.K.; Ng, K.; Hung, A.; Karagiannis, T.C. Interaction of the prototypical α-ketoamide inhibitor with the SARS-CoV-2 main protease active site in silico: Molecular dynamic simulations highlight the stability of the ligand-protein complex. Comput. Biol. Chem. 2020, 87, 107292. [Google Scholar] [CrossRef] [PubMed]
- Laskowski, R.A.; MacArthur, M.W.; Thornton, J.M. PROCHECK: Validation of protein-structure coordinates. In International Tables for Crystallography; Wiley: Hoboken, NJ, USA, 2012; pp. 684–687. [Google Scholar] [CrossRef]
- Studer, G.; Rempfer, C.; Waterhouse, A.M.; Gumienny, R.; Haas, J.; Schwede, T. QMEANDisCo—Distance constraints applied on model quality estimation. Bioinformatics 2020, 36, 1765–1771. [Google Scholar] [CrossRef]
- Honorato, R.V.; Trellet, M.E.; Jiménez-García, B.; Schaarschmidt, J.J.; Giulini, M.; Reys, V.; Koukos, P.I.; Rodrigues, J.P.G.L.M.; Karaca, E.; van Zundert, G.C.P.; et al. The HADDOCK2.4 web server for integrative modeling of biomolecular complexes. Nat. Protoc. 2024, 19, 3219–3241. [Google Scholar] [CrossRef]
- Bonvin Lab. HADDOCK2.4 Antibody—Antigen Tutorial Using PDB-Tools Webserver. 2024. Available online: https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-antibody-antigen/#scenario-2-a-loose-definition-of-the-epitope-is-known (accessed on 5 October 2024).
- Méndez, R.; Leplae, R.; De Maria, L.; Wodak, S.J. Assessment of blind predictions of protein–protein interactions: Current status of docking methods. Proteins Struct. Funct. Bioinform. 2003, 52, 51–67. [Google Scholar] [CrossRef]
- Romero-Durana, M.; Jiménez-García, B.; Fernández-Recio, J. pyDockEneRes: Per-residue decomposition of protein–protein docking energy. Bioinformatics 2020, 36, 2284–2285. [Google Scholar] [CrossRef]
- Zhou, Y.; Pan, Q.; Pires, D.E.V.; Rodrigues, C.H.M.; Ascher, D.B. DDMut: Predicting effects of mutations on protein stability using deep learning. Nucleic Acids Res. 2023, 51, W122–W128. [Google Scholar] [CrossRef]
- Rodrigues, C.H.M.; Pires, D.E.V.; Ascher, D.B. DynaMut2: Assessing changes in stability and flexibility upon single and multiple point missense mutations. Protein Sci. 2021, 30, 60–69. [Google Scholar] [CrossRef] [PubMed]
- Ivanisenko, N.V.; Shashkova, T.I.; Shevtsov, A.; Sindeeva, M.; Umerenkov, D.; Kardymon, O. SEMA 2.0: Web-platform for B-cell conformational epitopes prediction using artificial intelligence. Nucleic Acids Res. 2024, 52, W533–W539. [Google Scholar] [CrossRef] [PubMed]
- Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual molecular dynamics. J. Mol. Graph. 1996, 14, 33–38. [Google Scholar] [CrossRef]
- World Health Organization. Tracking SARS-CoV-2 Variants. 2025. Available online: https://www.who.int/activities/tracking-SARS-CoV-2-variants (accessed on 2 January 2025).
- Han, P.; Li, L.; Liu, S.; Wang, Q.; Zhang, D.; Xu, Z.; Han, P.; Li, X.; Peng, Q.; Su, C.; et al. Receptor binding and complex structures of human ACE2 to spike RBD from omicron and delta SARS-CoV-2. Cell 2022, 185, 630–640.e610. [Google Scholar] [CrossRef]
- Li, L.; Liao, H.; Meng, Y.; Li, W.; Han, P.; Liu, K.; Wang, Q.; Li, D.; Zhang, Y.; Wang, L.; et al. Structural basis of human ACE2 higher binding affinity to currently circulating Omicron SARS-CoV-2 sub-variants BA.2 and BA.1.1. Cell 2022, 185, 2952–2960.e10. [Google Scholar] [CrossRef]
- Cao, Y.; Song, W.; Wang, L.; Liu, P.; Yue, C.; Jian, F.; Yu, Y.; Yisimayi, A.; Wang, P.; Wang, Y.; et al. Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.75. Cell Host Microbe 2022, 30, 1527–1539.e5. [Google Scholar] [CrossRef]
- Yue, C.; Song, W.; Wang, L.; Jian, F.; Chen, X.; Gao, F.; Shen, Z.; Wang, Y.; Wang, X.; Cao, Y. ACE2 binding and antibody evasion in enhanced transmissibility of XBB.1.5. Lancet Infect. Dis. 2023, 23, 278–280. [Google Scholar] [CrossRef]
- Yang, S.; Yu, Y.; Jian, F.; Song, W.; Yisimayi, A.; Chen, X.; Xu, Y.; Wang, P.; Wang, J.; Yu, L.; et al. Antigenicity and infectivity characterisation of SARS-CoV-2 BA.2.86. Lancet Infect. Dis. 2023, 23, e457–e459. [Google Scholar] [CrossRef]
- Yamasoba, D.; Uriu, K.; Plianchaisuk, A.; Kosugi, Y.; Pan, L.; Zahradnik, J.; Ito, J.; Sato, K. Virological characteristics of the SARS-CoV-2 omicron XBB.1.16 variant. Lancet Infect. Dis. 2023, 23, 655–656. [Google Scholar] [CrossRef]
- Yang, S.; Yu, Y.; Xu, Y.; Jian, F.; Song, W.; Yisimayi, A.; Wang, P.; Wang, J.; Liu, J.; Yu, L.; et al. Fast evolution of SARS-CoV-2 BA.2.86 to JN.1 under heavy immune pressure. Lancet Infect. Dis. 2024, 24, e70–e72. [Google Scholar] [CrossRef]
- Wang, Q.; Mellis, I.A.; Ho, J.; Bowen, A.; Kowalski-Dobson, T.; Valdez, R.; Katsamba, P.S.; Wu, M.; Lee, C.; Shapiro, L.; et al. Recurrent SARS-CoV-2 spike mutations confer growth advantages to select JN.1 sublineages. Emerg. Microbes Infect. 2024, 13, 2402880. [Google Scholar] [CrossRef] [PubMed]
- Rodrigues, C.H.M.; Portelli, S.; Ascher, D.B. Exploring the effects of missense mutations on protein thermodynamics through structure-based approaches: Findings from the CAGI6 challenges. Hum. Genet. 2024. [Google Scholar] [CrossRef] [PubMed]
- Jacob, J.J.; Vasudevan, K.; Pragasam, A.K.; Gunasekaran, K.; Veeraraghavan, B.; Mutreja, A. Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. mBio 2021, 12, e0118821. [Google Scholar] [CrossRef] [PubMed]
- Chakraborty, C.; Bhattacharya, M.; Sharma, A.R.; Mallik, B. Omicron (B.1.1.529)—A new heavily mutated variant: Mapped location and probable properties of its mutations with an emphasis on S-glycoprotein. Int. J. Biol. Macromol. 2022, 219, 980–997. [Google Scholar] [CrossRef]
- Zhao, Z.; Zhou, J.; Tian, M.; Huang, M.; Liu, S.; Xie, Y.; Han, P.; Bai, C.; Han, P.; Zheng, A.; et al. Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape. Nat. Commun. 2022, 13, 4958. [Google Scholar] [CrossRef]
- U.S. Food and Drug Administration. Emergency Use Authorization—Archived Information. 2024. Available online: https://www.fda.gov/emergency-preparedness-and-response/mcm-legal-regulatory-and-policy-framework/emergency-use-authorization-archived-information#covid19 (accessed on 23 December 2024).
- Therapeutic Goods Administration. Update on Effectiveness of Monoclonal Antibodies Against COVID Variants. 2023. Available online: https://www.tga.gov.au/news/news/update-effectiveness-monoclonal-antibodies-against-covid-variants#:~:text=Monoclonal%20antibodies%20targeting%20the%20SARS,spike%20protein%20on%20its%20surface (accessed on 23 December 2024).
- Greaney, A.J.; Starr, T.N.; Barnes, C.O.; Weisblum, Y.; Schmidt, F.; Caskey, M.; Gaebler, C.; Cho, A.; Agudelo, M.; Finkin, S.; et al. Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies. Nat. Commun. 2021, 12, 4196. [Google Scholar] [CrossRef]
- Nguyen, H.; Lan, P.D.; Nissley, D.A.; O’Brien, E.P.; Li, M.S. Cocktail of REGN Antibodies Binds More Strongly to SARS-CoV-2 Than Its Components, but the Omicron Variant Reduces Its Neutralizing Ability. J. Phys. Chem. B 2022, 126, 2812–2823. [Google Scholar] [CrossRef]
- Fung, K.M.; Lai, S.J.; Lin, T.L.; Tseng, T.S. Antigen-Antibody Complex-Guided Exploration of the Hotspots Conferring the Immune-Escaping Ability of the SARS-CoV-2 RBD. Front. Mol. Biosci. 2022, 9, 797132. [Google Scholar] [CrossRef]
- Li, W.; Xu, Z.; Niu, T.; Xie, Y.; Zhao, Z.; Li, D.; He, Q.; Sun, W.; Shi, K.; Guo, W.; et al. Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins. EMBO J. 2024, 43, 1484–1498. [Google Scholar] [CrossRef]
- Pinto, D.; Park, Y.-J.; Beltramello, M.; Walls, A.C.; Tortorici, M.A.; Bianchi, S.; Jaconi, S.; Culap, K.; Zatta, F.; De Marco, A.; et al. Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody. Nature 2020, 583, 290–295. [Google Scholar] [CrossRef]
- Focosi, D.; Casadevall, A.; Franchini, M.; Maggi, F. Sotrovimab: A Review of Its Efficacy against SARS-CoV-2 Variants. Viruses 2024, 16, 217. [Google Scholar] [CrossRef] [PubMed]
- He, Q.; Wu, L.; Xu, Z.; Wang, X.; Xie, Y.; Chai, Y.; Zheng, A.; Zhou, J.; Qiao, S.; Huang, M.; et al. An updated atlas of antibody evasion by SARS-CoV-2 Omicron sub-variants including BQ.1.1 and XBB. Cell Rep. Med. 2023, 4, 100991. [Google Scholar] [CrossRef] [PubMed]
- Li, L.; Shi, K.; Gu, Y.; Xu, Z.; Shu, C.; Li, D.; Sun, J.; Cong, M.; Li, X.; Zhao, X.; et al. Spike structures, receptor binding, and immune escape of recently circulating SARS-CoV-2 Omicron BA.2.86, JN.1, EG.5, EG.5.1, and HV.1 sub-variants. Structure 2024, 32, 1055–1067.e1056. [Google Scholar] [CrossRef] [PubMed]
- Wang, Q.; Iketani, S.; Li, Z.; Liu, L.; Guo, Y.; Huang, Y.; Bowen, A.D.; Liu, M.; Wang, M.; Yu, J.; et al. Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants. Cell 2023, 186, 279–286.e278. [Google Scholar] [CrossRef]
- Deng, X.; Garcia-Knight, M.A.; Khalid, M.M.; Servellita, V.; Wang, C.; Morris, M.K.; Sotomayor-González, A.; Glasner, D.R.; Reyes, K.R.; Gliwa, A.S.; et al. Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant. Cell 2021, 184, 3426–3437.e8. [Google Scholar] [CrossRef]
- Wilhelm, A.; Toptan, T.; Pallas, C.; Wolf, T.; Goetsch, U.; Gottschalk, R.; Vehreschild, M.; Ciesek, S.; Widera, M. Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. Viruses 2021, 13, 1693. [Google Scholar] [CrossRef]
Conserved | Non-Conserved | |
---|---|---|
SEMA-1D | 333–339, 341–347, 356–357, 359–362, 375, 377–389, 405, 409–417, 424, 426–431, 440–449, 456–458, 460, 471–499, 501–503, 505, 526 | 340, 355, 358, 369, 370, 371–374, 376, 403–404, 406, 408, 425, 432, 450–455, 459, 462, 500, 504, and 523 |
SEMA-3D | 333–347, 355–360, 370, 373, 383, 385–386, 405, 414, 436–451, 472–494, 496, 516–521 | 348, 349, 354, 361, 367, 369, 371, 374–378, 380–382, 389, 393, 396, 408–409, 413, 415–420, 427–428, 430, 452, 454, 456–458, 470–471, 495, 497–498, 500–505, 509, 522–523 |
Antibody | Heavy Chain | Light Chain |
---|---|---|
Casirivimab | R403, E406, K417, Y449, F456, Y473, A475, E484, G485, F486, N487, C488, Y489, F490, L492, Q493, S494, Y495, G496, Q498, N501 | A475, G476, S477, T478, F486, N487 |
Imdevimab | R346, N439, N440, L441, S443, K444, V445, G446, G447, N448, Y449, N450, Q498, P499 | N439, V445, P499, T500, N501 |
Tixagevimab | K417, F456, K458, Y473, A475, G476, S477, T478, E484, G485, F486, N487, Y489, Q493 | T478, P479, C480, V483, E484, G485, F486, C488 |
Bebtelovimab | T345, R346, N439, N440, L441, S443, K444, V445, N450, P499 | V445, G446, G447, Y449, N450, L452, E484, F490, L492, Q493, S494 |
Regdanvimab | R403, K417, G446, Y449, N450, L452, F456, E484, G485, F486, Y489, F490, L492, Q493, S494, Y495, G496, Q498, N501, Y505 | T478, V483, E484, G485, F486 |
Bamlanivimab | Y449, L452, F456, I472, N481, G482, V483, E484, G485, Y489, F490, L492, Q493, S494 | N481, V483, E484, G485, F486, Y489 |
Etesevimab | R408, T415, G416, K417, F456, R457, K458, S459, N460, Y473, Q474, A475, G476, S477, F486, N487, Y489, F490, Q493 | R403, D405, E406, R408, Q409, K417, Y449, S494, Y495, Q498, T500, N501, G502, G504, Y505 |
Bebtelovimab | T345, R346, N439, N440, L441, D442, S443, K444, V445, G446, G447, N448, Y449, N450, P499, R509 | N439, N440, V445, G446, Q498, P499, T500, N501, G502, V503, Q506 |
S309 | T333, N334, L335, P337, G339, E340, V341, F342, N343, A344, T345, R346, N354, K356, R357, I358, S359, N360, C361, L441, R509 | T345, N440, L441, K444, V445, R509 |
GAR12 | R346, F347, A348, K444, G446, G447, N448, Y449, N450, L452, T470, I472, N481, G482, V483, E484 F490, L492, S494 | T345, R346, N440, L441, D442, S443, K444, V445, G446, N448, Y451, R509 |
Class 1 | Class 2 | ||||
---|---|---|---|---|---|
Casirivimab | Tixagevimab | Regdanvimab | Etesevimab | Bamlanivimab | |
WT | −32.2 | −50.9 | −40.5 | −28.0 | −44.2 |
Alpha | −31.9 | −52.4 | −36.2 | −40.5 | −41.6 |
Beta | −30.5 | −39.9 | −29.9 | −45.7 | −19.7 |
Gamma | −31.1 | −51.6 | −33.1 | −44.4 | −29.5 |
Delta | −41.1 | −30.9 | −30.1 | −32.7 | −35.5 |
BA.1 | −33.1 | −42.3 | −31.7 | −26.1 | −26.0 |
BA.2 | −35.8 | −36.0 | −32.7 | −25.7 | −23.2 |
BA.4/5 | −24.0 | −27.4 | −24.1 | −24.1 | −31.4 |
XBB.1.5 | −20.2 | −29.4 | −23.4 | −26.9 | −7.4 |
XBB.1.16 | −33.6 | −16.8 | −21.1 | −33.8 | −20.0 |
EG.5 | −20.9 | −17.5 | −19.0 | −26.1 | −26.6 |
BA.2.86 | −28.8 | −10.1 | −29.8 | −30.9 | −19.0 |
JN.1 | −23.9 | −22.5 | −36.8 | −34.3 | −12.0 |
KP.2 | −23.2 | −15.8 | −17.6 | −16.9 | −27.5 |
KP.3 | −12.7 | −24.7 | −35.7 | −20.8 | −23.4 |
Class 3 | Class 6 | ||||
---|---|---|---|---|---|
Imdevimab | Cilgavimab | Bebtelovimab | S309 | GAR12 | |
WT | −10.9 | −19.7 | −27.6 | −20.0 | −23.6 |
Alpha | −20.8 | −16.6 | −28.8 | −24.0 | −35.4 |
Beta | −22.3 | −23.1 | −25.9 | −16.0 | −21.9 |
Gamma | −20.3 | −21.7 | −28.2 | −16.7 | −28.4 |
Delta | −9.4 | −10.6 | −22.6 | −18.7 | −11.0 |
BA.1 | −16.2 | −20.4 | −20.1 | −22.5 | −24.0 |
BA.2 | −20.1 | −18.1 | −17.3 | −6.1 | −19.1 |
BA.4/5 | −27.5 | −14.1 | −19.1 | −31.4 | −25.2 |
XBB.1.5 | −17.1 | −22.4 | −14.1 | −17.0 | −21.9 |
XBB.1.16 | −21.3 | −16.1 | −10.6 | −38.2 | −17.7 |
EG.5 | −9.3 | −11.9 | −18.0 | −14.7 | −17.0 |
BA.2.86 | −21.5 | −25.8 | −22.6 | −24.3 | −21.0 |
JN.1 | −9.7 | −23.2 | −20.9 | −34.2 | −21.6 |
KP.2 | −22.2 | −26.7 | −16.9 | −21.5 | −29.6 |
KP.3 | −7.4 | −10.3 | −13.3 | −20.0 | −20.4 |
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2025 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Pitsillou, E.; El-Osta, A.; Hung, A.; Karagiannis, T.C. Epimaps of the SARS-CoV-2 Receptor-Binding Domain Mutational Landscape: Insights into Protein Stability, Epitope Prediction, and Antibody Binding. Biomolecules 2025, 15, 301. https://doi.org/10.3390/biom15020301
Pitsillou E, El-Osta A, Hung A, Karagiannis TC. Epimaps of the SARS-CoV-2 Receptor-Binding Domain Mutational Landscape: Insights into Protein Stability, Epitope Prediction, and Antibody Binding. Biomolecules. 2025; 15(2):301. https://doi.org/10.3390/biom15020301
Chicago/Turabian StylePitsillou, Eleni, Assam El-Osta, Andrew Hung, and Tom C. Karagiannis. 2025. "Epimaps of the SARS-CoV-2 Receptor-Binding Domain Mutational Landscape: Insights into Protein Stability, Epitope Prediction, and Antibody Binding" Biomolecules 15, no. 2: 301. https://doi.org/10.3390/biom15020301
APA StylePitsillou, E., El-Osta, A., Hung, A., & Karagiannis, T. C. (2025). Epimaps of the SARS-CoV-2 Receptor-Binding Domain Mutational Landscape: Insights into Protein Stability, Epitope Prediction, and Antibody Binding. Biomolecules, 15(2), 301. https://doi.org/10.3390/biom15020301