Broadening a SARS-CoV-1-neutralizing Antibody for Potent SARS-CoV-2 Neutralization Through Directed Evolution

Overview

Journal Sci Signal

Specialties Cell Biology
Physiology
Science

Date 2023 Aug 15

PMID 37582161

Authors

Fangzhu Zhao

Meng Yuan

Celina Keating

Namir Shaabani

Oliver Limbo

Collin Joyce

Jordan Woehl

Shawn Barman

Alison Burns

Quoc Tran

Xueyong Zhu

Michael Ricciardi

Linghang Peng

Jessica Smith

Deli Huang

Bryan Briney

Devin Sok

David Nemazee

John R Teijaro

Ian A Wilson

Dennis R Burton

Joseph G Jardine

Affiliations

Soon will be listed here.

Abstract

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underscores the need for strategies to rapidly develop neutralizing monoclonal antibodies that can function as prophylactic and therapeutic agents and to help guide vaccine design. Here, we demonstrate that engineering approaches can be used to refocus an existing antibody that neutralizes one virus but not a related virus. Through a rapid affinity maturation strategy, we engineered CR3022, a SARS-CoV-1-neutralizing antibody, to bind to the receptor binding domain of SARS-CoV-2 with >1000-fold increased affinity. The engineered CR3022 neutralized SARS-CoV-2 and provided prophylactic protection from viral challenge in a small animal model of SARS-CoV-2 infection. Deep sequencing throughout the engineering process paired with crystallographic analysis of engineered CR3022 elucidated the molecular mechanisms by which the antibody can accommodate sequence differences in the epitopes between SARS-CoV-1 and SARS-CoV-2. This workflow provides a blueprint for the rapid broadening of neutralization of an antibody from one virus to closely related but resistant viruses.

Citing Articles

Structural Immunology of SARS-CoV-2.

Yuan M, Wilson I Immunol Rev. 2024; 329(1):e13431.

PMID: 39731211 PMC: 11727448. DOI: 10.1111/imr.13431.

Targeting peptide antigens using a multiallelic MHC I-binding system.

Du H, Mallik L, Hwang D, Sun Y, Kaku C, Hoces D Nat Biotechnol. 2024; .

PMID: 39672954 DOI: 10.1038/s41587-024-02505-8.

Fully synthetic platform to rapidly generate tetravalent bispecific nanobody-based immunoglobulins.

Misson Mindrebo L, Liu H, Ozorowski G, Tran Q, Woehl J, Khalek I Proc Natl Acad Sci U S A. 2023; 120(24):e2216612120.

PMID: 37276407 PMC: 10268213. DOI: 10.1073/pnas.2216612120.

Broadly neutralizing and protective nanobodies against SARS-CoV-2 Omicron subvariants BA.1, BA.2, and BA.4/5 and diverse sarbecoviruses.

Li M, Ren Y, Aw Z, Chen B, Yang Z, Lei Y Nat Commun. 2022; 13(1):7957.

PMID: 36575191 PMC: 9792944. DOI: 10.1038/s41467-022-35642-2.

Engineering SARS-CoV-2 neutralizing antibodies for increased potency and reduced viral escape pathways.

Zhao F, Keating C, Ozorowski G, Shaabani N, Francino-Urdaniz I, Barman S iScience. 2022; 25(9):104914.

PMID: 35971553 PMC: 9367177. DOI: 10.1016/j.isci.2022.104914.

References

Bushnell B, Rood J, Singer E . BBMerge - Accurate paired shotgun read merging via overlap. PLoS One. 2017; 12(10):e0185056. PMC: 5657622. DOI: 10.1371/journal.pone.0185056. View

Huang J, Kang B, Pancera M, Lee J, Tong T, Feng Y . Broad and potent HIV-1 neutralization by a human antibody that binds the gp41-gp120 interface. Nature. 2014; 515(7525):138-42. PMC: 4224615. DOI: 10.1038/nature13601. View

Wu N, Yuan M, Bangaru S, Huang D, Zhu X, Lee C . A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. PLoS Pathog. 2020; 16(12):e1009089. PMC: 7744049. DOI: 10.1371/journal.ppat.1009089. View

Huang J, Doria-Rose N, Longo N, Laub L, Lin C, Turk E . Isolation of human monoclonal antibodies from peripheral blood B cells. Nat Protoc. 2013; 8(10):1907-15. PMC: 4844175. DOI: 10.1038/nprot.2013.117. View

Otwinowski Z, Minor W . Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 1997; 276:307-26. DOI: 10.1016/S0076-6879(97)76066-X. View

Julian M, Li L, Garde S, Wilen R, Tessier P . Efficient affinity maturation of antibody variable domains requires co-selection of compensatory mutations to maintain thermodynamic stability. Sci Rep. 2017; 7:45259. PMC: 5368667. DOI: 10.1038/srep45259. View

Yuan M, Wu N, Zhu X, Lee C, So R, Lv H . A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV. Science. 2020; 368(6491):630-633. PMC: 7164391. DOI: 10.1126/science.abb7269. View

Ju B, Zhang Q, Ge J, Wang R, Sun J, Ge X . Human neutralizing antibodies elicited by SARS-CoV-2 infection. Nature. 2020; 584(7819):115-119. DOI: 10.1038/s41586-020-2380-z. View

Sok D, van Gils M, Pauthner M, Julien J, Saye-Francisco K, Hsueh J . Recombinant HIV envelope trimer selects for quaternary-dependent antibodies targeting the trimer apex. Proc Natl Acad Sci U S A. 2014; 111(49):17624-9. PMC: 4267403. DOI: 10.1073/pnas.1415789111. View

10.

Emsley P, Lohkamp B, Scott W, Cowtan K . Features and development of Coot. Acta Crystallogr D Biol Crystallogr. 2010; 66(Pt 4):486-501. PMC: 2852313. DOI: 10.1107/S0907444910007493. View

11.

Crooks G, Hon G, Chandonia J, Brenner S . WebLogo: a sequence logo generator. Genome Res. 2004; 14(6):1188-90. PMC: 419797. DOI: 10.1101/gr.849004. View

12.

Huo J, Zhao Y, Ren J, Zhou D, Duyvesteyn H, Ginn H . Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike. Cell Host Microbe. 2020; 28(3):497. PMC: 7480219. DOI: 10.1016/j.chom.2020.07.002. View

13.

Manenti A, Maggetti M, Casa E, Martinuzzi D, Torelli A, Trombetta C . Evaluation of SARS-CoV-2 neutralizing antibodies using a CPE-based colorimetric live virus micro-neutralization assay in human serum samples. J Med Virol. 2020; 92(10):2096-2104. PMC: 7267461. DOI: 10.1002/jmv.25986. View

14.

Li A, Acevedo-Rocha C, Sun Z, Cox T, Xu J, Reetz M . Beating Bias in the Directed Evolution of Proteins: Combining High-Fidelity on-Chip Solid-Phase Gene Synthesis with Efficient Gene Assembly for Combinatorial Library Construction. Chembiochem. 2017; 19(3):221-228. DOI: 10.1002/cbic.201700540. View

15.

Wu Y, Li C, Xia S, Tian X, Kong Y, Wang Z . Identification of Human Single-Domain Antibodies against SARS-CoV-2. Cell Host Microbe. 2020; 27(6):891-898.e5. PMC: 7224157. DOI: 10.1016/j.chom.2020.04.023. View

16.

McCoy A, Grosse-Kunstleve R, Adams P, Winn M, Storoni L, Read R . Phaser crystallographic software. J Appl Crystallogr. 2009; 40(Pt 4):658-674. PMC: 2483472. DOI: 10.1107/S0021889807021206. View

17.

Zhou T, Tsybovsky Y, Gorman J, Rapp M, Cerutti G, Chuang G . Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains. Cell Host Microbe. 2020; 28(6):867-879.e5. PMC: 7670890. DOI: 10.1016/j.chom.2020.11.004. View

18.

Lan J, Ge J, Yu J, Shan S, Zhou H, Fan S . Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature. 2020; 581(7807):215-220. DOI: 10.1038/s41586-020-2180-5. View

19.

Wrapp D, De Vlieger D, Corbett K, Torres G, Wang N, Van Breedam W . Structural Basis for Potent Neutralization of Betacoronaviruses by Single-Domain Camelid Antibodies. Cell. 2020; 181(6):1436-1441. PMC: 7289117. DOI: 10.1016/j.cell.2020.05.047. View

20.

Anand S, Chen Y, Prevost J, Gasser R, Beaudoin-Bussieres G, Abrams C . Interaction of Human ACE2 to Membrane-Bound SARS-CoV-1 and SARS-CoV-2 S Glycoproteins. Viruses. 2020; 12(10). PMC: 7601831. DOI: 10.3390/v12101104. View