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TitleStructural and functional characterization of nanobodies that neutralize Omicron variants of SARS-CoV-2.
Journal, issue, pagesOpen Biol, Vol. 14, Issue 6, Page 230252, Year 2024
Publish dateJun 4, 2024
AuthorsKaty Cornish / Jiandong Huo / Luke Jones / Parul Sharma / Joseph W Thrush / Sahar Abdelkarim / Anja Kipar / Siva Ramadurai / Miriam Weckener / Halina Mikolajek / Sai Liu / Imogen Buckle / Eleanor Bentley / Adam Kirby / Ximeng Han / Stephen M Laidlaw / Michelle Hill / Lauren Eyssen / Chelsea Norman / Audrey Le Bas / John Clarke / William James / James P Stewart / Miles Carroll / James H Naismith / Raymond J Owens /
PubMed AbstractThe Omicron strains of SARS-CoV-2 pose a significant challenge to the development of effective antibody-based treatments as immune evasion has compromised most available immune therapeutics. ...The Omicron strains of SARS-CoV-2 pose a significant challenge to the development of effective antibody-based treatments as immune evasion has compromised most available immune therapeutics. Therefore, in the 'arms race' with the virus, there is a continuing need to identify new biologics for the prevention or treatment of SARS-CoV-2 infections. Here, we report the isolation of nanobodies that bind to the Omicron BA.1 spike protein by screening nanobody phage display libraries previously generated from llamas immunized with either the Wuhan or Beta spike proteins. The structure and binding properties of three of these nanobodies (A8, H6 and B5-5) have been characterized in detail providing insight into their binding epitopes on the Omicron spike protein. Trimeric versions of H6 and B5-5 neutralized the SARS-CoV-2 variant of concern BA.5 both and in the hamster model of COVID-19 following nasal administration. Thus, either alone or in combination could serve as starting points for the development of new anti-viral immunotherapeutics.
External linksOpen Biol / PubMed:38835241
MethodsEM (single particle) / X-ray diffraction
Resolution1.73 - 4.0 Å
Structure data

17295

8oyt

EMDB-17295, PDB-8oyt:
Stabilised BA.1 SARS-CoV-2 spike with H6 nanobodies in '3 up' RBD conformation
Method: EM (single particle) / Resolution: 3.8 Å

17296

8oyu

EMDB-17296, PDB-8oyu:
Stabilised BA.1 SARS-CoV-2 spike with H6 nanobodies in '2 up 1 down' RBD conformation
Method: EM (single particle) / Resolution: 4.0 Å

PDB-8owt:
SARS-CoV-2 spike RBD with A8 and H3 nanobodies bound
Method: X-RAY DIFFRACTION / Resolution: 2.37 Å

PDB-8owv:
H6 and F2 nanobodies bound to SARS-CoV-2 spike RBD
Method: X-RAY DIFFRACTION / Resolution: 1.73 Å

PDB-8oww:
B5-5 nanobody bound to SARS-CoV-2 spike RBD (Wuhan)
Method: X-RAY DIFFRACTION / Resolution: 1.969 Å

Chemicals

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

ChemComp-MES:
2-(N-MORPHOLINO)-ETHANESULFONIC ACID / pH buffer*YM

ChemComp-HOH:
WATER

ChemComp-GOL:
GLYCEROL

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-NO3:
NITRATE ION

Source
  • lama glama (llama)
  • severe acute respiratory syndrome coronavirus 2
  • tequatrovirus t4
  • enterobacteria phage t4 (virus)
KeywordsVIRAL PROTEIN / Nanobody / Complex / Receptor binding domain / SARS-CoV-2 / spike

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