Biparatopic sybodies neutralize SARS-CoV-2 variants of concern and mitigate drug resistance

Justin 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

doi:10.15252/embr.202154199

Biparatopic sybodies neutralize SARS-CoV-2 variants of concern and mitigate drug resistance

Justin 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 SlotboomCristina Paulino^*, Philippe Plattet^*, Markus A Seeger^*

^*Corresponding author for this work

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

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Abstract

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.

Original language	English
Article number	e54199
Number of pages	19
Journal	Embo Reports
Volume	23
Issue number	4
Early online date	2022
DOIs	https://doi.org/10.15252/embr.202154199
Publication status	Published - 5-Apr-2022

Keywords

escape mutants
SARS-CoV-2
sybodies
synthetic nanobodies
variants of concern

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Biparatopic sybodies neutralize SARS-CoV-2 variants of concern and mitigate drug resistanceFinal publisher's version, 2.5 MBLicence: CC BY

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Walter, J. D., Scherer, M., Hutter, C. A. J., Garaeva, A. A., Zimmermann, I., Wyss, M., Rheinberger, J., Ruedin, Y., Earp, J. C., Egloff, P., Sorgenfrei, M., Hürlimann, L. M., Gonda, I., Meier, G., Remm, S., Thavarasah, S., van Geest, G., Bruggmann, R., Zimmer, G., ... Seeger, M. A. (2022). Biparatopic sybodies neutralize SARS-CoV-2 variants of concern and mitigate drug resistance. Embo Reports, 23(4), Article e54199. https://doi.org/10.15252/embr.202154199

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title = "Biparatopic sybodies neutralize SARS-CoV-2 variants of concern and mitigate drug resistance",

abstract = "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.",

keywords = "escape mutants, SARS-CoV-2, sybodies, synthetic nanobodies, variants of concern",

author = "Walter, {Justin D} and Melanie Scherer and Hutter, {Cedric A J} and Garaeva, {Alisa A} and Iwan Zimmermann and Marianne Wyss and Jan Rheinberger and Yelena Ruedin and Earp, {Jennifer C} and Pascal Egloff and Mich{\`e}le Sorgenfrei and H{\"u}rlimann, {Lea M} and Imre Gonda and Gianmarco Meier and Sille Remm and Sujani Thavarasah and {van Geest}, Geert and R{\'e}my Bruggmann and Gert Zimmer and Slotboom, {Dirk J} and Cristina Paulino and Philippe Plattet and Seeger, {Markus A}",

note = "{\textcopyright} 2022 The Authors. Published under the terms of the CC BY 4.0 license.",

year = "2022",

month = apr,

day = "5",

doi = "10.15252/embr.202154199",

language = "English",

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Walter, JD, Scherer, M, Hutter, CAJ, Garaeva, AA, Zimmermann, I, Wyss, M, Rheinberger, J, Ruedin, Y, Earp, JC, Egloff, P, Sorgenfrei, M, Hürlimann, LM, Gonda, I, Meier, G, Remm, S, Thavarasah, S, van Geest, G, Bruggmann, R, Zimmer, G, Slotboom, DJ , Paulino, C, Plattet, P & Seeger, MA 2022, 'Biparatopic sybodies neutralize SARS-CoV-2 variants of concern and mitigate drug resistance', Embo Reports, vol. 23, no. 4, e54199. https://doi.org/10.15252/embr.202154199

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T1 - Biparatopic sybodies neutralize SARS-CoV-2 variants of concern and mitigate drug resistance

AU - Walter, Justin D

AU - Scherer, Melanie

AU - Hutter, Cedric A J

AU - Garaeva, Alisa A

AU - Zimmermann, Iwan

AU - Wyss, Marianne

AU - Rheinberger, Jan

AU - Ruedin, Yelena

AU - Earp, Jennifer C

AU - Egloff, Pascal

AU - Sorgenfrei, Michèle

AU - Hürlimann, Lea M

AU - Gonda, Imre

AU - Meier, Gianmarco

AU - Remm, Sille

AU - Thavarasah, Sujani

AU - van Geest, Geert

AU - Bruggmann, Rémy

AU - Zimmer, Gert

AU - Slotboom, Dirk J

AU - Paulino, Cristina

AU - Plattet, Philippe

AU - Seeger, Markus A

PY - 2022/4/5

Y1 - 2022/4/5

N2 - 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.

AB - 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.

KW - escape mutants

KW - SARS-CoV-2

KW - sybodies

KW - synthetic nanobodies

KW - variants of concern

U2 - 10.15252/embr.202154199

DO - 10.15252/embr.202154199

M3 - Article

C2 - 35253970

SN - 1469-221X

VL - 23

JO - Embo Reports

JF - Embo Reports

IS - 4

M1 - e54199

ER -

Biparatopic sybodies neutralize SARS-CoV-2 variants of concern and mitigate drug resistance

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