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TitleNeutralization of SARS-CoV-2 by highly potent, hyperthermostable, and mutation-tolerant nanobodies.
Journal, issue, pagesEMBO J, Vol. 40, Issue 19, Page e107985, Year 2021
Publish dateOct 1, 2021
AuthorsThomas Güttler / Metin Aksu / Antje Dickmanns / Kim M Stegmann / Kathrin Gregor / Renate Rees / Waltraud Taxer / Oleh Rymarenko / Jürgen Schünemann / Christian Dienemann / Philip Gunkel / Bianka Mussil / Jens Krull / Ulrike Teichmann / Uwe Groß / Volker C Cordes / Matthias Dobbelstein / Dirk Görlich /
PubMed AbstractMonoclonal anti-SARS-CoV-2 immunoglobulins represent a treatment option for COVID-19. However, their production in mammalian cells is not scalable to meet the global demand. Single-domain (VHH) ...Monoclonal anti-SARS-CoV-2 immunoglobulins represent a treatment option for COVID-19. However, their production in mammalian cells is not scalable to meet the global demand. Single-domain (VHH) antibodies (also called nanobodies) provide an alternative suitable for microbial production. Using alpaca immune libraries against the receptor-binding domain (RBD) of the SARS-CoV-2 Spike protein, we isolated 45 infection-blocking VHH antibodies. These include nanobodies that can withstand 95°C. The most effective VHH antibody neutralizes SARS-CoV-2 at 17-50 pM concentration (0.2-0.7 µg per liter), binds the open and closed states of the Spike, and shows a tight RBD interaction in the X-ray and cryo-EM structures. The best VHH trimers neutralize even at 40 ng per liter. We constructed nanobody tandems and identified nanobody monomers that tolerate the K417N/T, E484K, N501Y, and L452R immune-escape mutations found in the Alpha, Beta, Gamma, Epsilon, Iota, and Delta/Kappa lineages. We also demonstrate neutralization of the Beta strain at low-picomolar VHH concentrations. We further discovered VHH antibodies that enforce native folding of the RBD in the E. coli cytosol, where its folding normally fails. Such "fold-promoting" nanobodies may allow for simplified production of vaccines and their adaptation to viral escape-mutations.
External linksEMBO J / PubMed:34302370 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.25 - 3.5 Å
Structure data

EMDB-13105:
SARS-CoV-2 S (Spike) protein in complex with VHH Re5D06 (multi-body-refined RBD-Re5D06 body)
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-13106:
SARS-CoV-2 S (Spike) protein in complex with VHH Re5D06 (one RBD down)
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-13107:
SARS-CoV-2 S (Spike) protein in complex with VHH Re5D06 (all RBDs up)
Method: EM (single particle) / Resolution: 2.8 Å

PDB-7olz:
Crystal structure of the SARS-CoV-2 RBD with neutralizing-VHHs Re5D06 and Re9F06
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-7on5:
Crystal structure of the SARS-CoV-2 neutralizing nanobody Re5D06
Method: X-RAY DIFFRACTION / Resolution: 1.25 Å

Chemicals

ChemComp-DMX:
3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE

ChemComp-SO4:
SULFATE ION

ChemComp-HOH:
WATER

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-EOH:
ETHANOL

Source
  • severe acute respiratory syndrome coronavirus 2
  • vicugna pacos (alpaca)
KeywordsVIRAL PROTEIN / COVID19 / Neutralizing VHH / IMMUNE SYSTEM

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