Bi-paratopic and multivalent VH domains block ACE2 binding and neutralize SARS-CoV-2

Neutralizing agents against SARS-CoV-2 are urgently needed for the treatment and prophylaxis of COVID-19. Here, we present a strategy to rapidly identify and assemble synthetic human variable heavy (VH) domains toward neutralizing epitopes. We constructed a VH-phage library and targeted the angioten...

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Published inNature chemical biology Vol. 17; no. 1; pp. 113 - 121
Main Authors Bracken, Colton J., Lim, Shion A., Solomon, Paige, Rettko, Nicholas J., Nguyen, Duy P., Zha, Beth Shoshana, Schaefer, Kaitlin, Byrnes, James R., Zhou, Jie, Lui, Irene, Liu, Jia, Pance, Katarina, Zhou, Xin X., Leung, Kevin K., Wells, James A.
Format Journal Article
LanguageEnglish
Published New York Nature Publishing Group US 01.01.2021
Nature Publishing Group
Subjects
631/154/51
631/250/255
631/326/596/4130
631/45/535
631/92/469
ACE2
Affinity
Angiotensin
Angiotensin-converting enzyme 2
Angiotensin-Converting Enzyme 2 - antagonists & inhibitors
Angiotensin-Converting Enzyme 2 - chemistry
Angiotensin-Converting Enzyme 2 - genetics
Angiotensin-Converting Enzyme 2 - immunology
Animals
Antibodies
Antibodies, Neutralizing - chemistry
Antibodies, Neutralizing - genetics
Antibodies, Neutralizing - immunology
Antibodies, Viral - chemistry
Antibodies, Viral - genetics
Antibodies, Viral - immunology
Binders
Binding sites
Binding Sites, Antibody - genetics
Binding Sites, Antibody - immunology
Biochemical Engineering
Biochemistry
Bioorganic Chemistry
Cell Biology
Chemistry
Chemistry and Materials Science
Chemistry/Food Science
Chlorocebus aethiops
COVID-19
Cryoelectron Microscopy
Epitopes
HEK293 Cells
Humans
Models, Molecular
Neutralization
Neutralizing
Peptide Library
Peptidyl-dipeptidase A
Phages
Prophylaxis
Protein Binding
Protein Conformation, alpha-Helical
Protein Conformation, beta-Strand
Protein Interaction Domains and Motifs
Receptors
SARS-CoV-2
Severe acute respiratory syndrome coronavirus 2
Single-Chain Antibodies - chemistry
Single-Chain Antibodies - genetics
Single-Chain Antibodies - immunology
Spike Glycoprotein, Coronavirus - antagonists & inhibitors
Spike Glycoprotein, Coronavirus - chemistry
Spike Glycoprotein, Coronavirus - genetics
Spike Glycoprotein, Coronavirus - immunology
Spike protein
Vero Cells
Online AccessGet full text

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Abstract Neutralizing agents against SARS-CoV-2 are urgently needed for the treatment and prophylaxis of COVID-19. Here, we present a strategy to rapidly identify and assemble synthetic human variable heavy (VH) domains toward neutralizing epitopes. We constructed a VH-phage library and targeted the angiotensin-converting enzyme 2 (ACE2) binding interface of the SARS-CoV-2 Spike receptor-binding domain (Spike-RBD). Using a masked selection approach, we identified VH binders to two non-overlapping epitopes and further assembled these into multivalent and bi-paratopic formats. These VH constructs showed increased affinity to Spike (up to 600-fold) and neutralization potency (up to 1,400-fold) on pseudotyped SARS-CoV-2 virus when compared to standalone VH domains. The most potent binder, a trivalent VH, neutralized authentic SARS-CoV-2 with a half-maximal inhibitory concentration (IC 50 ) of 4.0 nM (180 ng ml −1 ). A cryo-EM structure of the trivalent VH bound to Spike shows each VH domain engaging an RBD at the ACE2 binding site, confirming our original design strategy. A screening approach finds VH-domain antibodies that bind the SARS-CoV-2 Spike protein receptor-binding domain at its interface with host ACE2. Bi-paratopic and multivalent binders have high affinity and potency.
AbstractList Neutralizing agents against SARS-CoV-2 are urgently needed for the treatment and prophylaxis of COVID-19. Here, we present a strategy to rapidly identify and assemble synthetic human variable heavy (VH) domains toward neutralizing epitopes. We constructed a VH-phage library and targeted the angiotensin-converting enzyme 2 (ACE2) binding interface of the SARS-CoV-2 Spike receptor-binding domain (Spike-RBD). Using a masked selection approach, we identified VH binders to two non-overlapping epitopes and further assembled these into multivalent and bi-paratopic formats. These VH constructs showed increased affinity to Spike (up to 600-fold) and neutralization potency (up to 1,400-fold) on pseudotyped SARS-CoV-2 virus when compared to standalone VH domains. The most potent binder, a trivalent VH, neutralized authentic SARS-CoV-2 with a half-maximal inhibitory concentration (IC 50 ) of 4.0 nM (180 ng ml −1 ). A cryo-EM structure of the trivalent VH bound to Spike shows each VH domain engaging an RBD at the ACE2 binding site, confirming our original design strategy. A screening approach finds VH-domain antibodies that bind the SARS-CoV-2 Spike protein receptor-binding domain at its interface with host ACE2. Bi-paratopic and multivalent binders have high affinity and potency.
Neutralizing agents against SARS-CoV-2 are urgently needed for the treatment and prophylaxis of COVID-19. Here, we present a strategy to rapidly identify and assemble synthetic human variable heavy (VH) domains toward neutralizing epitopes. We constructed a VH-phage library and targeted the angiotensin-converting enzyme 2 (ACE2) binding interface of the SARS-CoV-2 Spike receptor-binding domain (Spike-RBD). Using a masked selection approach, we identified VH binders to two non-overlapping epitopes and further assembled these into multivalent and bi-paratopic formats. These VH constructs showed increased affinity to Spike (up to 600-fold) and neutralization potency (up to 1,400-fold) on pseudotyped SARS-CoV-2 virus when compared to standalone VH domains. The most potent binder, a trivalent VH, neutralized authentic SARS-CoV-2 with a half-maximal inhibitory concentration (IC50) of 4.0 nM (180 ng ml-1). A cryo-EM structure of the trivalent VH bound to Spike shows each VH domain engaging an RBD at the ACE2 binding site, confirming our original design strategy.Neutralizing agents against SARS-CoV-2 are urgently needed for the treatment and prophylaxis of COVID-19. Here, we present a strategy to rapidly identify and assemble synthetic human variable heavy (VH) domains toward neutralizing epitopes. We constructed a VH-phage library and targeted the angiotensin-converting enzyme 2 (ACE2) binding interface of the SARS-CoV-2 Spike receptor-binding domain (Spike-RBD). Using a masked selection approach, we identified VH binders to two non-overlapping epitopes and further assembled these into multivalent and bi-paratopic formats. These VH constructs showed increased affinity to Spike (up to 600-fold) and neutralization potency (up to 1,400-fold) on pseudotyped SARS-CoV-2 virus when compared to standalone VH domains. The most potent binder, a trivalent VH, neutralized authentic SARS-CoV-2 with a half-maximal inhibitory concentration (IC50) of 4.0 nM (180 ng ml-1). A cryo-EM structure of the trivalent VH bound to Spike shows each VH domain engaging an RBD at the ACE2 binding site, confirming our original design strategy.
Neutralizing agents against SARS-CoV-2 are urgently needed for the treatment and prophylaxis of COVID-19. Here, we present a strategy to rapidly identify and assemble synthetic human variable heavy (VH) domains toward neutralizing epitopes. We constructed a VH-phage library and targeted the angiotensin-converting enzyme 2 (ACE2) binding interface of the SARS-CoV-2 Spike receptor-binding domain (Spike-RBD). Using a masked selection approach, we identified VH binders to two non-overlapping epitopes and further assembled these into multivalent and bi-paratopic formats. These VH constructs showed increased affinity to Spike (up to 600-fold) and neutralization potency (up to 1400-fold) on pseudotyped SARS-CoV-2 virus when compared to standalone VH domains. The most potent binder, a trivalent VH, neutralized authentic SARS-CoV-2 with half-maximal inhibitory concentration (IC 50 ) of 4.0 nM (180 ng/mL). A cryo-EM structure of the trivalent VH bound to Spike shows each VH domain engaging an RBD at the ACE2 binding site, confirming our original design strategy.
Neutralizing agents against SARS-CoV-2 are urgently needed for the treatment and prophylaxis of COVID-19. Here, we present a strategy to rapidly identify and assemble synthetic human variable heavy (VH) domains toward neutralizing epitopes. We constructed a VH-phage library and targeted the angiotensin-converting enzyme 2 (ACE2) binding interface of the SARS-CoV-2 Spike receptor-binding domain (Spike-RBD). Using a masked selection approach, we identified VH binders to two non-overlapping epitopes and further assembled these into multivalent and bi-paratopic formats. These VH constructs showed increased affinity to Spike (up to 600-fold) and neutralization potency (up to 1,400-fold) on pseudotyped SARS-CoV-2 virus when compared to standalone VH domains. The most potent binder, a trivalent VH, neutralized authentic SARS-CoV-2 with a half-maximal inhibitory concentration (IC ) of 4.0 nM (180 ng ml ). A cryo-EM structure of the trivalent VH bound to Spike shows each VH domain engaging an RBD at the ACE2 binding site, confirming our original design strategy.
Neutralizing agents against SARS-CoV-2 are urgently needed for the treatment and prophylaxis of COVID-19. Here, we present a strategy to rapidly identify and assemble synthetic human variable heavy (VH) domains toward neutralizing epitopes. We constructed a VH-phage library and targeted the angiotensin-converting enzyme 2 (ACE2) binding interface of the SARS-CoV-2 Spike receptor-binding domain (Spike-RBD). Using a masked selection approach, we identified VH binders to two non-overlapping epitopes and further assembled these into multivalent and bi-paratopic formats. These VH constructs showed increased affinity to Spike (up to 600-fold) and neutralization potency (up to 1,400-fold) on pseudotyped SARS-CoV-2 virus when compared to standalone VH domains. The most potent binder, a trivalent VH, neutralized authentic SARS-CoV-2 with a half-maximal inhibitory concentration (IC50) of 4.0 nM (180 ng ml−1). A cryo-EM structure of the trivalent VH bound to Spike shows each VH domain engaging an RBD at the ACE2 binding site, confirming our original design strategy.A screening approach finds VH-domain antibodies that bind the SARS-CoV-2 Spike protein receptor-binding domain at its interface with host ACE2. Bi-paratopic and multivalent binders have high affinity and potency.
Author Zhou, Jie
Leung, Kevin K.
Lui, Irene
Wells, James A.
Lim, Shion A.
Nguyen, Duy P.
Schaefer, Kaitlin
Byrnes, James R.
Pance, Katarina
Zhou, Xin X.
Rettko, Nicholas J.
Zha, Beth Shoshana
Liu, Jia
Solomon, Paige
Bracken, Colton J.
AuthorAffiliation 6 Present address: Lyell Immunopharama Inc., Seattle, WA 98109, USA
1 Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
4 Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, California, 94158, USA
5 Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
3 Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
7 Present address: Merck & Co., South San Francisco, CA 94080, USA
2 Department of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA 94158, USA
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  organization: Department of Pharmaceutical Chemistry, University of California, San Francisco
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/33082574$$D View this record in MEDLINE/PubMed
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ContentType Journal Article
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Copyright The Author(s), under exclusive licence to Springer Nature America, Inc. 2020
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QCRG Structural Biology Consortium.
C.J.B. and D.P.N. designed and constructed the VH-phage library. C.J.B., S.A.L., N.J.R., J.Z., I.L., J. L., K.P. cloned, expressed, and purified the VH binders and/or antigens. C.J.B., S.A.L., J.L. designed and/or conducted the in vitro characterization of the VH binders. J.R.B. designed and conducted the competition ELISA assay with convalescent patient sera. P.S., N.J.R., S.A.L. designed and conducted the pseudovirus neutralization assays. P.S., N.J.R., B.S.Z., S.A.L. designed and conducted the live virus neutralization assays. K.S. prepared samples for cryo-EM and the QCRG SBC performed cryo-EM data collection and analyses. S.A.L., X.X.Z., K.K.L., J.A.W. led the coordination of external collaborations and supervised the project. C.J.B., S.A.L., J.A.W. co-wrote the manuscript with input from all the authors.
In addition to those listed explicitly in the author contributions, the structural biology portion of this work was performed by the QCRG (Quantitative Biosciences Institute Coronavirus Research Group) Structural Biology Consortium. Listed below are the contributing members of the consortium listed by teams in order of team relevance to the published work. Within each team the team leads are italicized (responsible for organization of each team, and for the experimental design utilized within each team), then the rest of team members are listed alphabetically. CryoEM grid freezing/collection team: Caleigh M. Azumaya, Cristina Puchades, Ming Sun, Julian R. Braxton, Axel F. Brilot, Meghna Gupta, Fei Li, Kyle E. Lopez, Arthur Melo, Gregory E. Merz, Frank Moss, Joana Paulino, Thomas H. Pospiech, Jr., Sergei Pourmal, Alexandrea N. Rizo, Amber M. Smith, Paul V. Thomas, Feng Wang, Zanlin Yu. CryoEM data processing team: Miles Sasha Dickinson, Henry C. Nguyen, Daniel Asarnow, Julian R. Braxton, Melody G. Campbell, Cynthia M. Chio, Un Seng Chio, Devan Diwanji, Bryan Faust, Meghna Gupta, Nick Hoppe, Mingliang Jin, Fei Li, Junrui Li, Yanxin Liu, Gregory E. Merz, Joana Paulino, Thomas H. Pospiech, Jr., Sergei Pourmal, Smriti Sangwan, Raphael Trenker, Donovan Trinidad, Eric Tse, Kaihua Zhang, Fengbo Zhou. Mammalian cell expression team: Christian Billesboelle, Melody G. Campbell, Devan Diwanji, Carlos Nowotny, Amber M. Smith, Jianhua Zhao, Caleigh M. Azumaya, Alisa Bowen, Nick Hoppe, Yen-Li Li, Phuong Nguyen, Cristina Puchades, Mali Safari, Smriti Sangwan, Kaitlin Schaefer, Raphael Trenker, Tsz Kin Martin Tsui, Natalie Whitis. Protein purification team: Daniel Asarnow, Michelle Moritz, Tristan W. Owens, Sergei Pourmal, Caleigh M. Azumaya, Cynthia M. Chio, Bryan Faust, Meghna Gupta, Kate Kim, Joana Paulino, Jessica K. Peters, Kaitlin Schaefer, Tsz Kin Martin Tsui. Crystallography team: Nadia Herrera, Huong T. Kratochvil, Ursula Schulze-Gahmen, Iris D. Young, Justin Biel, Ishan Deshpande, Xi Liu. Bacterial expression team: Amy Diallo, Meghna Gupta, Erron W. Titus, Jen Chen, Loan Doan, Sebastian Flores, Mingliang Jin, Huong T. Kratochvil, Victor L. Lam, Yang Li, Megan Lo, Gregory E. Merz, Joana Paulino, Aye C. Thwin, Zanlin Yu, Fengbo Zhou, Yang Zhang. Infrastructure team: David Bulkley, Arceli Joves, Almarie Joves, Liam McKay, Mariano Tabios, Eric Tse. Leadership team: Oren S Rosenberg, Kliment A Verba, David A Agard, Yifan Cheng, James S Fraser, Adam Frost, Natalia Jura, Tanja Kortemme, Nevan J Krogan, Aashish Manglik, Daniel R. Southworth, Robert M Stroud. The QCRG Structural Biology Consortium has received support from: Quantitative Biosciences Institute, Defense Advanced Research Projects Agency HR0011-19-2-0020 (to D.A.A. and K.A.V.; B. Shoichet PI), FastGrants COVID19 grant (K.A.Verba PI), Laboratory For Genomics Research (O.S. Rosenberg PI) and Laboratory For Genomics Research (R.M. Stroud PI)
Author Contributions
ORCID 0000-0002-6171-5443
0000-0002-2087-4974
0000-0003-2136-2732
0000-0003-3499-7032
0000-0003-0297-1209
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– reference: 32817948 - bioRxiv. 2020 Aug 10;:
SSID ssj0036618
Score 2.5798662
Snippet Neutralizing agents against SARS-CoV-2 are urgently needed for the treatment and prophylaxis of COVID-19. Here, we present a strategy to rapidly identify and...
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pubmed
crossref
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SourceType Open Access Repository
Aggregation Database
Index Database
Enrichment Source
Publisher
StartPage 113
SubjectTerms 631/154/51
631/250/255
631/326/596/4130
631/45/535
631/92/469
ACE2
Affinity
Angiotensin
Angiotensin-converting enzyme 2
Angiotensin-Converting Enzyme 2 - antagonists & inhibitors
Angiotensin-Converting Enzyme 2 - chemistry
Angiotensin-Converting Enzyme 2 - genetics
Angiotensin-Converting Enzyme 2 - immunology
Animals
Antibodies
Antibodies, Neutralizing - chemistry
Antibodies, Neutralizing - genetics
Antibodies, Neutralizing - immunology
Antibodies, Viral - chemistry
Antibodies, Viral - genetics
Antibodies, Viral - immunology
Binders
Binding sites
Binding Sites, Antibody - genetics
Binding Sites, Antibody - immunology
Biochemical Engineering
Biochemistry
Bioorganic Chemistry
Cell Biology
Chemistry
Chemistry and Materials Science
Chemistry/Food Science
Chlorocebus aethiops
COVID-19
Cryoelectron Microscopy
Epitopes
HEK293 Cells
Humans
Models, Molecular
Neutralization
Neutralizing
Peptide Library
Peptidyl-dipeptidase A
Phages
Prophylaxis
Protein Binding
Protein Conformation, alpha-Helical
Protein Conformation, beta-Strand
Protein Interaction Domains and Motifs
Receptors
SARS-CoV-2
Severe acute respiratory syndrome coronavirus 2
Single-Chain Antibodies - chemistry
Single-Chain Antibodies - genetics
Single-Chain Antibodies - immunology
Spike Glycoprotein, Coronavirus - antagonists & inhibitors
Spike Glycoprotein, Coronavirus - chemistry
Spike Glycoprotein, Coronavirus - genetics
Spike Glycoprotein, Coronavirus - immunology
Spike protein
Vero Cells
Title Bi-paratopic and multivalent VH domains block ACE2 binding and neutralize SARS-CoV-2
URI https://link.springer.com/article/10.1038/s41589-020-00679-1
https://www.ncbi.nlm.nih.gov/pubmed/33082574
https://www.proquest.com/docview/2473304964
https://www.proquest.com/docview/2452982686
https://pubmed.ncbi.nlm.nih.gov/PMC8356808
Volume 17
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