A synthetic nanobody targeting RBD protects hamsters from SARS-CoV-2 infection
SARS-CoV-2, the causative agent of COVID-19 1 , features a receptor-binding domain (RBD) for binding to the host cell ACE2 protein 1 – 6 . Neutralizing antibodies that block RBD-ACE2 interaction are candidates for the development of targeted therapeutics 7 – 17 . Llama-derived single-domain antibodi...
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| Published in | Nature communications Vol. 12; no. 1; pp. 4635 - 13 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
Nature Publishing Group UK
30.07.2021
Nature Publishing Group Nature Portfolio |
| Subjects | |
| Online Access | Get full text |
| ISSN | 2041-1723 2041-1723 |
| DOI | 10.1038/s41467-021-24905-z |
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| Abstract | SARS-CoV-2, the causative agent of COVID-19
1
, features a receptor-binding domain (RBD) for binding to the host cell ACE2 protein
1
–
6
. Neutralizing antibodies that block RBD-ACE2 interaction are candidates for the development of targeted therapeutics
7
–
17
. Llama-derived single-domain antibodies (nanobodies, ~15 kDa) offer advantages in bioavailability, amenability, and production and storage owing to their small sizes and high stability. Here, we report the rapid selection of 99 synthetic nanobodies (sybodies) against RBD by in vitro selection using three libraries. The best sybody, MR3 binds to RBD with high affinity (
K
D
= 1.0 nM) and displays high neutralization activity against SARS-CoV-2 pseudoviruses (IC
50
= 0.42 μg mL
−1
). Structural, biochemical, and biological characterization suggests a common neutralizing mechanism, in which the RBD-ACE2 interaction is competitively inhibited by sybodies. Various forms of sybodies with improved potency have been generated by structure-based design, biparatopic construction, and divalent engineering. Two divalent forms of MR3 protect hamsters from clinical signs after live virus challenge and a single dose of the Fc-fusion construct of MR3 reduces viral RNA load by 6 Log
10
. Our results pave the way for the development of therapeutic nanobodies against COVID-19 and present a strategy for rapid development of targeted medical interventions during an outbreak.
Here, the authors report the engineering, structural and biological characterization of synthetic nanobodies (sybodies) that display potent therapeutic activity against SARS-CoV-2 infection in animal models via targeting the virus receptor-binding domain. |
|---|---|
| AbstractList | SARS-CoV-2, the causative agent of COVID-19
1
, features a receptor-binding domain (RBD) for binding to the host cell ACE2 protein
1–6
. Neutralizing antibodies that block RBD-ACE2 interaction are candidates for the development of targeted therapeutics
7–17
. Llama-derived single-domain antibodies (nanobodies, ~15 kDa) offer advantages in bioavailability, amenability, and production and storage owing to their small sizes and high stability. Here, we report the rapid selection of 99 synthetic nanobodies (sybodies) against RBD by in vitro selection using three libraries. The best sybody, MR3 binds to RBD with high affinity (
K
D
= 1.0 nM) and displays high neutralization activity against SARS-CoV-2 pseudoviruses (IC
50
= 0.42 μg mL
−1
). Structural, biochemical, and biological characterization suggests a common neutralizing mechanism, in which the RBD-ACE2 interaction is competitively inhibited by sybodies. Various forms of sybodies with improved potency have been generated by structure-based design, biparatopic construction, and divalent engineering. Two divalent forms of MR3 protect hamsters from clinical signs after live virus challenge and a single dose of the Fc-fusion construct of MR3 reduces viral RNA load by 6 Log
10
. Our results pave the way for the development of therapeutic nanobodies against COVID-19 and present a strategy for rapid development of targeted medical interventions during an outbreak. SARS-CoV-2, the causative agent of COVID-19 , features a receptor-binding domain (RBD) for binding to the host cell ACE2 protein . Neutralizing antibodies that block RBD-ACE2 interaction are candidates for the development of targeted therapeutics . Llama-derived single-domain antibodies (nanobodies, ~15 kDa) offer advantages in bioavailability, amenability, and production and storage owing to their small sizes and high stability. Here, we report the rapid selection of 99 synthetic nanobodies (sybodies) against RBD by in vitro selection using three libraries. The best sybody, MR3 binds to RBD with high affinity (K = 1.0 nM) and displays high neutralization activity against SARS-CoV-2 pseudoviruses (IC = 0.42 μg mL ). Structural, biochemical, and biological characterization suggests a common neutralizing mechanism, in which the RBD-ACE2 interaction is competitively inhibited by sybodies. Various forms of sybodies with improved potency have been generated by structure-based design, biparatopic construction, and divalent engineering. Two divalent forms of MR3 protect hamsters from clinical signs after live virus challenge and a single dose of the Fc-fusion construct of MR3 reduces viral RNA load by 6 Log . Our results pave the way for the development of therapeutic nanobodies against COVID-19 and present a strategy for rapid development of targeted medical interventions during an outbreak. SARS-CoV-2, the causative agent of COVID-191, features a receptor-binding domain (RBD) for binding to the host cell ACE2 protein1–6. Neutralizing antibodies that block RBD-ACE2 interaction are candidates for the development of targeted therapeutics7–17. Llama-derived single-domain antibodies (nanobodies, ~15 kDa) offer advantages in bioavailability, amenability, and production and storage owing to their small sizes and high stability. Here, we report the rapid selection of 99 synthetic nanobodies (sybodies) against RBD by in vitro selection using three libraries. The best sybody, MR3 binds to RBD with high affinity (KD = 1.0 nM) and displays high neutralization activity against SARS-CoV-2 pseudoviruses (IC50 = 0.42 μg mL−1). Structural, biochemical, and biological characterization suggests a common neutralizing mechanism, in which the RBD-ACE2 interaction is competitively inhibited by sybodies. Various forms of sybodies with improved potency have been generated by structure-based design, biparatopic construction, and divalent engineering. Two divalent forms of MR3 protect hamsters from clinical signs after live virus challenge and a single dose of the Fc-fusion construct of MR3 reduces viral RNA load by 6 Log10. Our results pave the way for the development of therapeutic nanobodies against COVID-19 and present a strategy for rapid development of targeted medical interventions during an outbreak.Here, the authors report the engineering, structural and biological characterization of synthetic nanobodies (sybodies) that display potent therapeutic activity against SARS-CoV-2 infection in animal models via targeting the virus receptor-binding domain. SARS-CoV-2, the causative agent of COVID-191, features a receptor-binding domain (RBD) for binding to the host cell ACE2 protein1-6. Neutralizing antibodies that block RBD-ACE2 interaction are candidates for the development of targeted therapeutics7-17. Llama-derived single-domain antibodies (nanobodies, ~15 kDa) offer advantages in bioavailability, amenability, and production and storage owing to their small sizes and high stability. Here, we report the rapid selection of 99 synthetic nanobodies (sybodies) against RBD by in vitro selection using three libraries. The best sybody, MR3 binds to RBD with high affinity (KD = 1.0 nM) and displays high neutralization activity against SARS-CoV-2 pseudoviruses (IC50 = 0.42 μg mL-1). Structural, biochemical, and biological characterization suggests a common neutralizing mechanism, in which the RBD-ACE2 interaction is competitively inhibited by sybodies. Various forms of sybodies with improved potency have been generated by structure-based design, biparatopic construction, and divalent engineering. Two divalent forms of MR3 protect hamsters from clinical signs after live virus challenge and a single dose of the Fc-fusion construct of MR3 reduces viral RNA load by 6 Log10. Our results pave the way for the development of therapeutic nanobodies against COVID-19 and present a strategy for rapid development of targeted medical interventions during an outbreak.SARS-CoV-2, the causative agent of COVID-191, features a receptor-binding domain (RBD) for binding to the host cell ACE2 protein1-6. Neutralizing antibodies that block RBD-ACE2 interaction are candidates for the development of targeted therapeutics7-17. Llama-derived single-domain antibodies (nanobodies, ~15 kDa) offer advantages in bioavailability, amenability, and production and storage owing to their small sizes and high stability. Here, we report the rapid selection of 99 synthetic nanobodies (sybodies) against RBD by in vitro selection using three libraries. The best sybody, MR3 binds to RBD with high affinity (KD = 1.0 nM) and displays high neutralization activity against SARS-CoV-2 pseudoviruses (IC50 = 0.42 μg mL-1). Structural, biochemical, and biological characterization suggests a common neutralizing mechanism, in which the RBD-ACE2 interaction is competitively inhibited by sybodies. Various forms of sybodies with improved potency have been generated by structure-based design, biparatopic construction, and divalent engineering. Two divalent forms of MR3 protect hamsters from clinical signs after live virus challenge and a single dose of the Fc-fusion construct of MR3 reduces viral RNA load by 6 Log10. Our results pave the way for the development of therapeutic nanobodies against COVID-19 and present a strategy for rapid development of targeted medical interventions during an outbreak. SARS-CoV-2, the causative agent of COVID-19 1 , features a receptor-binding domain (RBD) for binding to the host cell ACE2 protein 1 – 6 . Neutralizing antibodies that block RBD-ACE2 interaction are candidates for the development of targeted therapeutics 7 – 17 . Llama-derived single-domain antibodies (nanobodies, ~15 kDa) offer advantages in bioavailability, amenability, and production and storage owing to their small sizes and high stability. Here, we report the rapid selection of 99 synthetic nanobodies (sybodies) against RBD by in vitro selection using three libraries. The best sybody, MR3 binds to RBD with high affinity ( K D = 1.0 nM) and displays high neutralization activity against SARS-CoV-2 pseudoviruses (IC 50 = 0.42 μg mL −1 ). Structural, biochemical, and biological characterization suggests a common neutralizing mechanism, in which the RBD-ACE2 interaction is competitively inhibited by sybodies. Various forms of sybodies with improved potency have been generated by structure-based design, biparatopic construction, and divalent engineering. Two divalent forms of MR3 protect hamsters from clinical signs after live virus challenge and a single dose of the Fc-fusion construct of MR3 reduces viral RNA load by 6 Log 10 . Our results pave the way for the development of therapeutic nanobodies against COVID-19 and present a strategy for rapid development of targeted medical interventions during an outbreak. Here, the authors report the engineering, structural and biological characterization of synthetic nanobodies (sybodies) that display potent therapeutic activity against SARS-CoV-2 infection in animal models via targeting the virus receptor-binding domain. Here, the authors report the engineering, structural and biological characterization of synthetic nanobodies (sybodies) that display potent therapeutic activity against SARS-CoV-2 infection in animal models via targeting the virus receptor-binding domain. SARS-CoV-2, the causative agent of COVID-19 1 , features a receptor-binding domain (RBD) for binding to the host cell ACE2 protein 1-6 . Neutralizing antibodies that block RBD-ACE2 interaction are candidates for the development of targeted therapeutics 7-17 . Llama-derived single-domain antibodies (nanobodies, ~15 kDa) offer advantages in bioavailability, amenability, and production and storage owing to their small sizes and high stability. Here, we report the rapid selection of 99 synthetic nanobodies (sybodies) against RBD by in vitro selection using three libraries. The best sybody, MR3 binds to RBD with high affinity (K D = 1.0 nM) and displays high neutralization activity against SARS-CoV-2 pseudoviruses (IC 50 = 0.42 μg mL -1 ). Structural, biochemical, and biological characterization suggests a common neutralizing mechanism, in which the RBD-ACE2 interaction is competitively inhibited by sybodies. Various forms of sybodies with improved potency have been generated by structure-based design, biparatopic construction, and divalent engineering. Two divalent forms of MR3 protect hamsters from clinical signs after live virus challenge and a single dose of the Fc-fusion construct of MR3 reduces viral RNA load by 6 Log 10 . Our results pave the way for the development of therapeutic nanobodies against COVID-19 and present a strategy for rapid development of targeted medical interventions during an outbreak. |
| ArticleNumber | 4635 |
| Author | Raoul, Hervé Yao, Hebang Rockx, Barry Lan, Jiaming Seeger, Markus A. Li, Tingting van Vlissingen, Martje Fentener Bi, Yuhai Cong, Yao Wong, Gary Zhou, Bingjie Shen, Quan Li, Dianfan Wang, Yanxing Zhang, Ning Tian, Xiao-Xu Kuo, Shu-Ming Liu, Caixuan Cai, Hongmin Kuiken, Thijs Richard, Audrey S. Gong, Yuhuan Lai, Yanling GeurtsvanKessel, Corine H. Hutter, Cedric A. J. Han, Wenyu Zhao, Yapei Qin, Wenming Bao, Juan Lavillette, Dimitri Peng, Chao Wang, Yifan |
| Author_xml | – sequence: 1 givenname: Tingting orcidid: 0000-0003-3146-2761 surname: Li fullname: Li, Tingting organization: State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS) – sequence: 2 givenname: Hongmin orcidid: 0000-0001-7221-8330 surname: Cai fullname: Cai, Hongmin organization: State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS) – sequence: 3 givenname: Hebang orcidid: 0000-0002-8588-5877 surname: Yao fullname: Yao, Hebang organization: State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS) – sequence: 4 givenname: Bingjie orcidid: 0000-0002-7753-4065 surname: Zhou fullname: Zhou, Bingjie organization: University of CAS, CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS – sequence: 5 givenname: Ning surname: Zhang fullname: Zhang, Ning organization: CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), CAS – sequence: 6 givenname: Martje Fentener orcidid: 0000-0003-2213-5910 surname: van Vlissingen fullname: van Vlissingen, Martje Fentener organization: Erasmus Laboratory Animal Science Center, Erasmus University Medical Center, European Research Infrastructure on Highly Pathogenic Agents (ERINHA-AISBL) – sequence: 7 givenname: Thijs orcidid: 0000-0001-5501-9049 surname: Kuiken fullname: Kuiken, Thijs organization: European Research Infrastructure on Highly Pathogenic Agents (ERINHA-AISBL), Department of Viroscience, Erasmus University Medical Center – sequence: 8 givenname: Wenyu surname: Han fullname: Han, Wenyu organization: State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), University of CAS – sequence: 9 givenname: Corine H. orcidid: 0000-0002-7678-314X surname: GeurtsvanKessel fullname: GeurtsvanKessel, Corine H. organization: European Research Infrastructure on Highly Pathogenic Agents (ERINHA-AISBL), Department of Viroscience, Erasmus University Medical Center – sequence: 10 givenname: Yuhuan surname: Gong fullname: Gong, Yuhuan organization: University of CAS, CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), CAS – sequence: 11 givenname: Yapei orcidid: 0000-0001-7738-6181 surname: Zhao fullname: Zhao, Yapei organization: University of CAS, CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS – sequence: 12 givenname: Quan surname: Shen fullname: Shen, Quan organization: CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), CAS – sequence: 13 givenname: Wenming surname: Qin fullname: Qin, Wenming organization: National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute (Zhangjiang Laboratory), CAS – sequence: 14 givenname: Xiao-Xu surname: Tian fullname: Tian, Xiao-Xu organization: National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute (Zhangjiang Laboratory), CAS – sequence: 15 givenname: Chao orcidid: 0000-0002-6814-2676 surname: Peng fullname: Peng, Chao organization: National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute (Zhangjiang Laboratory), CAS – sequence: 16 givenname: Yanling surname: Lai fullname: Lai, Yanling organization: State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), University of CAS – sequence: 17 givenname: Yanxing surname: Wang fullname: Wang, Yanxing organization: State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS) – sequence: 18 givenname: Cedric A. J. orcidid: 0000-0002-8920-3343 surname: Hutter fullname: Hutter, Cedric A. J. organization: Institute of Medical Microbiology, University of Zurich – sequence: 19 givenname: Shu-Ming orcidid: 0000-0002-4437-689X surname: Kuo fullname: Kuo, Shu-Ming organization: CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS – sequence: 20 givenname: Juan surname: Bao fullname: Bao, Juan organization: State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS) – sequence: 21 givenname: Caixuan surname: Liu fullname: Liu, Caixuan organization: State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), University of CAS – sequence: 22 givenname: Yifan surname: Wang fullname: Wang, Yifan organization: State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), University of CAS – sequence: 23 givenname: Audrey S. orcidid: 0000-0002-0207-0139 surname: Richard fullname: Richard, Audrey S. organization: European Research Infrastructure on Highly Pathogenic Agents (ERINHA-AISBL) – sequence: 24 givenname: Hervé orcidid: 0000-0002-4241-3255 surname: Raoul fullname: Raoul, Hervé organization: European Research Infrastructure on Highly Pathogenic Agents (ERINHA-AISBL) – sequence: 25 givenname: Jiaming surname: Lan fullname: Lan, Jiaming organization: CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS – sequence: 26 givenname: Markus A. orcidid: 0000-0003-1761-8571 surname: Seeger fullname: Seeger, Markus A. organization: Institute of Medical Microbiology, University of Zurich – sequence: 27 givenname: Yao orcidid: 0000-0002-7164-8694 surname: Cong fullname: Cong, Yao organization: State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS) – sequence: 28 givenname: Barry orcidid: 0000-0003-2463-027X surname: Rockx fullname: Rockx, Barry organization: European Research Infrastructure on Highly Pathogenic Agents (ERINHA-AISBL), Department of Viroscience, Erasmus University Medical Center – sequence: 29 givenname: Gary orcidid: 0000-0002-9044-8153 surname: Wong fullname: Wong, Gary email: garyckwong@ips.ac.cn organization: CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, Département de microbiologie-infectiologie et d’immunologie, Université Laval – sequence: 30 givenname: Yuhai orcidid: 0000-0002-5595-363X surname: Bi fullname: Bi, Yuhai email: beeyh@im.ac.cn organization: University of CAS, CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), CAS – sequence: 31 givenname: Dimitri orcidid: 0000-0002-4706-1519 surname: Lavillette fullname: Lavillette, Dimitri email: dlaville@ips.ac.cn organization: CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, Pasteurien College, Soochow University – sequence: 32 givenname: Dianfan orcidid: 0000-0003-4729-4678 surname: Li fullname: Li, Dianfan email: dianfan.li@sibcb.ac.cn organization: State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS) |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/34330908$$D View this record in MEDLINE/PubMed https://hal.science/hal-05023823$$DView record in HAL |
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| Snippet | SARS-CoV-2, the causative agent of COVID-19
1
, features a receptor-binding domain (RBD) for binding to the host cell ACE2 protein
1
–
6
. Neutralizing... SARS-CoV-2, the causative agent of COVID-19 1 , features a receptor-binding domain (RBD) for binding to the host cell ACE2 protein 1–6 . Neutralizing... SARS-CoV-2, the causative agent of COVID-19 , features a receptor-binding domain (RBD) for binding to the host cell ACE2 protein . Neutralizing antibodies that... SARS-CoV-2, the causative agent of COVID-191, features a receptor-binding domain (RBD) for binding to the host cell ACE2 protein1–6. Neutralizing antibodies... SARS-CoV-2, the causative agent of COVID-191, features a receptor-binding domain (RBD) for binding to the host cell ACE2 protein1-6. Neutralizing antibodies... SARS-CoV-2, the causative agent of COVID-19 1 , features a receptor-binding domain (RBD) for binding to the host cell ACE2 protein 1-6 . Neutralizing... Here, the authors report the engineering, structural and biological characterization of synthetic nanobodies (sybodies) that display potent therapeutic... |
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| Title | A synthetic nanobody targeting RBD protects hamsters from SARS-CoV-2 infection |
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