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TitleIntegrating artificial intelligence-based epitope prediction in a SARS-CoV-2 antibody discovery pipeline: caution is warranted.
Journal, issue, pagesEBioMedicine, Vol. 100, Page 104960, Year 2024
Publish dateJan 16, 2024
AuthorsDelphine Diana Acar / Wojciech Witkowski / Magdalena Wejda / Ruifang Wei / Tim Desmet / Bert Schepens / Sieglinde De Cae / Koen Sedeyn / Hannah Eeckhaut / Daria Fijalkowska / Kenny Roose / Sandrine Vanmarcke / Anne Poupon / Dirk Jochmans / Xin Zhang / Rana Abdelnabi / Caroline S Foo / Birgit Weynand / Dirk Reiter / Nico Callewaert / Han Remaut / Johan Neyts / Xavier Saelens / Sarah Gerlo / Linos Vandekerckhove /
PubMed AbstractBACKGROUND: SARS-CoV-2-neutralizing antibodies (nABs) showed great promise in the early phases of the COVID-19 pandemic. The emergence of resistant strains, however, quickly rendered the majority of ...BACKGROUND: SARS-CoV-2-neutralizing antibodies (nABs) showed great promise in the early phases of the COVID-19 pandemic. The emergence of resistant strains, however, quickly rendered the majority of clinically approved nABs ineffective. This underscored the imperative to develop nAB cocktails targeting non-overlapping epitopes.
METHODS: Undertaking a nAB discovery program, we employed a classical workflow, while integrating artificial intelligence (AI)-based prediction to select non-competing nABs very early in the pipeline. We identified and in vivo validated (in female Syrian hamsters) two highly potent nABs.
FINDINGS: Despite the promising results, in depth cryo-EM structural analysis demonstrated that the AI-based prediction employed with the intention to ensure non-overlapping epitopes was inaccurate. The two nABs in fact bound to the same receptor-binding epitope in a remarkably similar manner.
INTERPRETATION: Our findings indicate that, even in the Alphafold era, AI-based predictions of paratope-epitope interactions are rough and experimental validation of epitopes remains an essential cornerstone of a successful nAB lead selection.
FUNDING: Full list of funders is provided at the end of the manuscript.
External linksEBioMedicine / PubMed:38232633 / PubMed Central
MethodsEM (single particle)
Resolution3.5 - 3.8 Å
Structure data

18560

8qpr

EMDB-18560, PDB-8qpr:
SARS-CoV-2 S protein bound to human neutralising antibody UZGENT_G5
Method: EM (single particle) / Resolution: 3.8 Å

18571

8qq0

EMDB-18571, PDB-8qq0:
SARS-CoV-2 S protein bound to neutralising antibody UZGENT_A3
Method: EM (single particle) / Resolution: 3.5 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

Source
  • severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
  • tequatrovirus t4
  • enterobacteria phage t4 (virus)
KeywordsVIRAL PROTEIN / neutralizing antibody / Spike protein

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