Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice

Phillip Pymm; Amy Adair; Li Jin Chan; James P. Cooney; Francesca L. Mordant; Cody C. Allison; Ester Lopez; Ebene R. Haycroft; Matthew T. O'Neill; Li Lynn Tan; Melanie H. Dietrich; Damien Drew; Marcel Doerflinger; Michael A. Dengler; Nichollas E. Scott; Adam K. Wheatley; Nicholas A. Gherardin; Hariprasad Venugopal; Deborah Cromer; Miles P. Davenport; Raelene Pickering; Dale I. Godfrey; Damian F.J. Purcell; Stephen J. Kent; Amy W. Chung; Kanta Subbarao; Marc Pellegrini; Alisa Glukhova; Wai Hong Tham

doi:10.1073/pnas.2101918118

Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice

Phillip Pymm, Amy Adair, Li Jin Chan, James P. Cooney, Francesca L. Mordant, Cody C. Allison, Ester Lopez, Ebene R. Haycroft, Matthew T. O'Neill, Li Lynn Tan, Melanie H. Dietrich, Damien Drew, Marcel Doerflinger, Michael A. Dengler, Nichollas E. Scott, Adam K. Wheatley, Nicholas A. Gherardin, Hariprasad Venugopal, Deborah Cromer, Miles P. DavenportRaelene Pickering, Dale I. Godfrey, Damian F.J. Purcell, Stephen J. Kent, Amy W. Chung, Kanta Subbarao, Marc Pellegrini, Alisa Glukhova, Wai Hong Tham^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

97 Citations (Scopus)

Abstract

Neutralizing antibodies are important for immunity against SARS-CoV-2 and as therapeutics for the prevention and treatment of COVID-19. Here, we identified high-affinity nanobodies from alpacas immunized with coronavirus spike and receptor-binding domains (RBD) that disrupted RBD engagement with the human receptor angiotensinconverting enzyme 2 (ACE2) and potently neutralized SARS-CoV-2. Epitope mapping, X-ray crystallography, and cryo-electron microscopy revealed two distinct antigenic sites and showed two neutralizing nanobodies from different epitope classes bound simultaneously to the spike trimer. Nanobody-Fc fusions of the four most potent nanobodies blocked ACE2 engagement with RBD variants present in human populations and potently neutralized both wild-type SARS-CoV-2 and the N501Y D614G variant at concentrations as low as 0.1 nM. Prophylactic administration of either single nanobody- Fc or as mixtures reduced viral loads by up to 104-fold in mice infected with the N501Y D614G SARS-CoV-2 virus. These results suggest a role for nanobody-Fc fusions as prophylactic agents against SARS-CoV-2.

Original language	English
Article number	e2101918118
Number of pages	12
Journal	Proceedings of the National Academy of Sciences of the United States of America
Volume	118
Issue number	19
DOIs	https://doi.org/10.1073/pnas.2101918118
Publication status	Published - 2021
Externally published	Yes

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Pymm, P., Adair, A., Chan, L. J., Cooney, J. P., Mordant, F. L., Allison, C. C., Lopez, E., Haycroft, E. R., O'Neill, M. T., Tan, L. L., Dietrich, M. H., Drew, D., Doerflinger, M., Dengler, M. A., Scott, N. E., Wheatley, A. K., Gherardin, N. A., Venugopal, H., Cromer, D., ... Tham, W. H. (2021). Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. Proceedings of the National Academy of Sciences of the United States of America, 118(19), Article e2101918118. https://doi.org/10.1073/pnas.2101918118

@article{34e875cf0de5469b992e9eaaeb7ad85d,

title = "Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice",

abstract = "Neutralizing antibodies are important for immunity against SARS-CoV-2 and as therapeutics for the prevention and treatment of COVID-19. Here, we identified high-affinity nanobodies from alpacas immunized with coronavirus spike and receptor-binding domains (RBD) that disrupted RBD engagement with the human receptor angiotensinconverting enzyme 2 (ACE2) and potently neutralized SARS-CoV-2. Epitope mapping, X-ray crystallography, and cryo-electron microscopy revealed two distinct antigenic sites and showed two neutralizing nanobodies from different epitope classes bound simultaneously to the spike trimer. Nanobody-Fc fusions of the four most potent nanobodies blocked ACE2 engagement with RBD variants present in human populations and potently neutralized both wild-type SARS-CoV-2 and the N501Y D614G variant at concentrations as low as 0.1 nM. Prophylactic administration of either single nanobody- Fc or as mixtures reduced viral loads by up to 104-fold in mice infected with the N501Y D614G SARS-CoV-2 virus. These results suggest a role for nanobody-Fc fusions as prophylactic agents against SARS-CoV-2.",

keywords = "Antiviral therapeutics, Cryo-EM, Crystallography, Nanobodies, SARS-CoV-2",

author = "Phillip Pymm and Amy Adair and Chan, {Li Jin} and Cooney, {James P.} and Mordant, {Francesca L.} and Allison, {Cody C.} and Ester Lopez and Haycroft, {Ebene R.} and O'Neill, {Matthew T.} and Tan, {Li Lynn} and Dietrich, {Melanie H.} and Damien Drew and Marcel Doerflinger and Dengler, {Michael A.} and Scott, {Nichollas E.} and Wheatley, {Adam K.} and Gherardin, {Nicholas A.} and Hariprasad Venugopal and Deborah Cromer and Davenport, {Miles P.} and Raelene Pickering and Godfrey, {Dale I.} and Purcell, {Damian F.J.} and Kent, {Stephen J.} and Chung, {Amy W.} and Kanta Subbarao and Marc Pellegrini and Alisa Glukhova and Tham, {Wai Hong}",

year = "2021",

doi = "10.1073/pnas.2101918118",

language = "English",

volume = "118",

journal = "Proceedings of the National Academy of Sciences of the United States of America",

issn = "0027-8424",

publisher = "National Academy of Sciences",

number = "19",

}

Pymm, P, Adair, A, Chan, LJ, Cooney, JP, Mordant, FL, Allison, CC, Lopez, E, Haycroft, ER, O'Neill, MT, Tan, LL, Dietrich, MH, Drew, D, Doerflinger, M, Dengler, MA, Scott, NE, Wheatley, AK, Gherardin, NA, Venugopal, H, Cromer, D, Davenport, MP, Pickering, R, Godfrey, DI, Purcell, DFJ, Kent, SJ, Chung, AW, Subbarao, K, Pellegrini, M, Glukhova, A & Tham, WH 2021, 'Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice', Proceedings of the National Academy of Sciences of the United States of America, vol. 118, no. 19, e2101918118. https://doi.org/10.1073/pnas.2101918118

TY - JOUR

T1 - Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice

AU - Pymm, Phillip

AU - Adair, Amy

AU - Chan, Li Jin

AU - Cooney, James P.

AU - Mordant, Francesca L.

AU - Allison, Cody C.

AU - Lopez, Ester

AU - Haycroft, Ebene R.

AU - O'Neill, Matthew T.

AU - Tan, Li Lynn

AU - Dietrich, Melanie H.

AU - Drew, Damien

AU - Doerflinger, Marcel

AU - Dengler, Michael A.

AU - Scott, Nichollas E.

AU - Wheatley, Adam K.

AU - Gherardin, Nicholas A.

AU - Venugopal, Hariprasad

AU - Cromer, Deborah

AU - Davenport, Miles P.

AU - Pickering, Raelene

AU - Godfrey, Dale I.

AU - Purcell, Damian F.J.

AU - Kent, Stephen J.

AU - Chung, Amy W.

AU - Subbarao, Kanta

AU - Pellegrini, Marc

AU - Glukhova, Alisa

AU - Tham, Wai Hong

PY - 2021

Y1 - 2021

N2 - Neutralizing antibodies are important for immunity against SARS-CoV-2 and as therapeutics for the prevention and treatment of COVID-19. Here, we identified high-affinity nanobodies from alpacas immunized with coronavirus spike and receptor-binding domains (RBD) that disrupted RBD engagement with the human receptor angiotensinconverting enzyme 2 (ACE2) and potently neutralized SARS-CoV-2. Epitope mapping, X-ray crystallography, and cryo-electron microscopy revealed two distinct antigenic sites and showed two neutralizing nanobodies from different epitope classes bound simultaneously to the spike trimer. Nanobody-Fc fusions of the four most potent nanobodies blocked ACE2 engagement with RBD variants present in human populations and potently neutralized both wild-type SARS-CoV-2 and the N501Y D614G variant at concentrations as low as 0.1 nM. Prophylactic administration of either single nanobody- Fc or as mixtures reduced viral loads by up to 104-fold in mice infected with the N501Y D614G SARS-CoV-2 virus. These results suggest a role for nanobody-Fc fusions as prophylactic agents against SARS-CoV-2.

AB - Neutralizing antibodies are important for immunity against SARS-CoV-2 and as therapeutics for the prevention and treatment of COVID-19. Here, we identified high-affinity nanobodies from alpacas immunized with coronavirus spike and receptor-binding domains (RBD) that disrupted RBD engagement with the human receptor angiotensinconverting enzyme 2 (ACE2) and potently neutralized SARS-CoV-2. Epitope mapping, X-ray crystallography, and cryo-electron microscopy revealed two distinct antigenic sites and showed two neutralizing nanobodies from different epitope classes bound simultaneously to the spike trimer. Nanobody-Fc fusions of the four most potent nanobodies blocked ACE2 engagement with RBD variants present in human populations and potently neutralized both wild-type SARS-CoV-2 and the N501Y D614G variant at concentrations as low as 0.1 nM. Prophylactic administration of either single nanobody- Fc or as mixtures reduced viral loads by up to 104-fold in mice infected with the N501Y D614G SARS-CoV-2 virus. These results suggest a role for nanobody-Fc fusions as prophylactic agents against SARS-CoV-2.

KW - Antiviral therapeutics

KW - Cryo-EM

KW - Crystallography

KW - Nanobodies

KW - SARS-CoV-2

UR - http://www.scopus.com/inward/record.url?scp=85105252430&partnerID=8YFLogxK

U2 - 10.1073/pnas.2101918118

DO - 10.1073/pnas.2101918118

M3 - Article

C2 - 33893175

AN - SCOPUS:85105252430

SN - 0027-8424

VL - 118

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

IS - 19

M1 - e2101918118

ER -

Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice

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