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TitleBiparatopic sybodies neutralize SARS-CoV-2 variants of concern and mitigate drug resistance.
Journal, issue, pagesEMBO Rep, Vol. 23, Issue 4, Page e54199, Year 2022
Publish dateApr 5, 2022
AuthorsJustin D Walter / Melanie Scherer / Cedric A J Hutter / Alisa A Garaeva / Iwan Zimmermann / Marianne Wyss / Jan Rheinberger / Yelena Ruedin / Jennifer C Earp / Pascal Egloff / Michèle Sorgenfrei / Lea M Hürlimann / Imre Gonda / Gianmarco Meier / Sille Remm / Sujani Thavarasah / Geert van Geest / Rémy Bruggmann / Gert Zimmer / Dirk J Slotboom / Cristina Paulino / Philippe Plattet / Markus A Seeger /
PubMed AbstractThe ongoing COVID-19 pandemic represents an unprecedented global health crisis. Here, we report the identification of a synthetic nanobody (sybody) pair, Sb#15 and Sb#68, that can bind simultaneously ...The ongoing COVID-19 pandemic represents an unprecedented global health crisis. Here, we report the identification of a synthetic nanobody (sybody) pair, Sb#15 and Sb#68, that can bind simultaneously to the SARS-CoV-2 spike RBD and efficiently neutralize pseudotyped and live viruses by interfering with ACE2 interaction. Cryo-EM confirms that Sb#15 and Sb#68 engage two spatially discrete epitopes, influencing rational design of bispecific and tri-bispecific fusion constructs that exhibit up to 100- and 1,000-fold increase in neutralization potency, respectively. Cryo-EM of the sybody-spike complex additionally reveals a novel up-out RBD conformation. While resistant viruses emerge rapidly in the presence of single binders, no escape variants are observed in the presence of the bispecific sybody. The multivalent bispecific constructs further increase the neutralization potency against globally circulating SARS-CoV-2 variants of concern. Our study illustrates the power of multivalency and biparatopic nanobody fusions for the potential development of therapeutic strategies that mitigate the emergence of new SARS-CoV-2 escape mutants.
External linksEMBO Rep / PubMed:35253970 / PubMed Central
MethodsEM (single particle)
Resolution2.98 - 4.76 Å
Structure data

PDB-7p77:
SARS-CoV-2 spike protein in complex with sybody#15 and sybody#68 in a 3up conformation
Method: ELECTRON MICROSCOPY / Resolution: 2.98 Å

PDB-7p78:
SARS-CoV-2 spike protein in complex with sybody#15 and sybody#68 in a 1up/1up-out/1down conformation
Method: ELECTRON MICROSCOPY / Resolution: 3.32 Å

PDB-7p79:
SARS-CoV-2 spike protein in complex with sybodyb#15 in a 1up/1up-out/1down conformation.
Method: ELECTRON MICROSCOPY / Resolution: 4.0 Å

PDB-7p7a:
SARS-CoV-2 spike protein in complex with sybody#68 in a 2up/1flexible conformation
Method: ELECTRON MICROSCOPY / Resolution: 4.76 Å

PDB-7p7b:
SARS-CoV-2 spike protein in complex with sybody no68 in a 1up/2down conformation
Method: ELECTRON MICROSCOPY / Resolution: 3.13 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

Source
  • severe acute respiratory syndrome coronavirus 2
  • synthetic construct (others)
KeywordsVIRAL PROTEIN / SARS-CoV-2 spike protein sybody

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