Mechanisms of SARS-CoV-2 neutralization by shark variable new antigen receptors elucidated through X-ray crystallography

Ubah, Obinna C.; Lake, Eric W.; Gunaratne, Gihan S.; Gallant, Joseph P.; Fernie, Marie; Robertson, Austin J.; Marchant, Jonathan S.; Bold, Tyler D.; Langlois, Ryan A.; Matchett, William E.; Thiede, Joshua M.; Shi, Ke; Yin, Lulu; Moeller, Nicholas H.; Banerjee, Surajit; Ferguson, Laura; Kovaleva, Marina; Porter, Andrew J.; Aihara, Hideki; LeBeau, Aaron M.; Barelle, Caroline J.

doi:10.1038/s41467-021-27611-y

Title: Mechanisms of SARS-CoV-2 neutralization by shark variable new antigen receptors elucidated through X-ray crystallography

Journal Article · 15 December 2021 · Nature Communications

DOI: https://doi.org/10.1038/s41467-021-27611-y · OSTI ID:1841247

^[1]; Lake, Eric W. ^[2]; Gunaratne, Gihan S. ^[3]; Gallant, Joseph P. ^[2]; Fernie, Marie ^[1]; Robertson, Austin J. ^[2];

^[4]; Bold, Tyler D. ^[5]; Langlois, Ryan A. ^[6];

^[6];

^[7]; Shi, Ke ^[6]; Yin, Lulu ^[6]; Moeller, Nicholas H. ^[6]; Banerjee, Surajit ^[8]; Ferguson, Laura ^[1]; Kovaleva, Marina ^[1]; Porter, Andrew J. ^[9];

^[6];

^[2] more »

Elasmogen Ltd., Aberdeen (United Kingdom)
Univ. of Wisconsin, Madison, WI (United States). School of Medicine and Public Health
Univ. of Wisconsin, Madison, WI (United States). School of Medicine and Public Health; Medical School of Wisconsin, Milwaukee, WI (United States)
Medical School of Wisconsin, Milwaukee, WI (United States)
Univ. of Minnesota Medical School, Minneapolis, MN (United States); Univ. of Minnesota, Minneapolis, MN (United States)
Univ. of Minnesota, Minneapolis, MN (United States)
Univ. of Minnesota Medical School, Minneapolis, MN (United States)
Cornell Univ., Lemont, IL (United States). Advanced Photon Source (APS)
Elasmogen Ltd., Aberdeen (United Kingdom); Univ. of Aberdeen (United Kingdom)

Single-domain Variable New Antigen Receptors (VNARs) from the immune system of sharks are the smallest naturally occurring binding domains found in nature. Possessing flexible paratopes that can recognize protein motifs inaccessible to classical antibodies, VNARs have yet to be exploited for the development of SARS-CoV-2 therapeutics. Here, we detail the identification of a series of VNARs from a VNAR phage display library screened against the SARS-CoV-2 receptor binding domain (RBD). The ability of the VNARs to neutralize pseudotype and authentic live SARS-CoV-2 virus rivalled or exceeded that of full-length immunoglobulins and other single-domain antibodies. Crystallographic analysis of two VNARs found that they recognized separate epitopes on the RBD and had distinctly different mechanisms of virus neutralization unique to VNARs. Structural and biochemical data suggest that VNARs would be effective therapeutic agents against emerging SARS-CoV-2 mutants, including the Delta variant, and coronaviruses across multiple phylogenetic lineages. This study highlights the utility of VNARs as effective therapeutics against coronaviruses and may serve as a critical milestone for nearing a paradigm shift of the greater biologic landscape.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: NIH; USDOE Office of Science (SC)

OSTI ID:: 1841247

Journal Information:: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 12; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

References (35)

Immunogenicity of a Single Dose of SARS-CoV-2 Messenger RNA Vaccine in Solid Organ Transplant Recipients Boyarsky, Brian J.; Werbel, William A.; Avery, Robin K. JAMA, Vol. 325, Issue 17 https://doi.org/10.1001/jama.2021.4385	journal	May 2021
Vpr Is Required for Efficient Replication of Human Immunodeficiency Virus Type-1 in Mononuclear Phagocytes Connor, Ruth I.; Chen, Benjamin Kuan; Choe, Sunny Virology, Vol. 206, Issue 2 https://doi.org/10.1006/viro.1995.1016	journal	February 1995
Potent Neutralizing Antibodies against SARS-CoV-2 Identified by High-Throughput Single-Cell Sequencing of Convalescent Patients’ B Cells Cao, Yunlong; Su, Bin; Guo, Xianghua Cell, Vol. 182, Issue 1 https://doi.org/10.1016/j.cell.2020.05.025	journal	July 2020
Structural Basis for Potent Neutralization of Betacoronaviruses by Single-Domain Camelid Antibodies Wrapp, Daniel; De Vlieger, Dorien; Corbett, Kizzmekia S. Cell, Vol. 181, Issue 6 https://doi.org/10.1016/j.cell.2020.05.047	journal	June 2020
COVID-19-neutralizing antibodies predict disease severity and survival Garcia-Beltran, Wilfredo F.; Lam, Evan C.; Astudillo, Michael G. Cell, Vol. 184, Issue 2 https://doi.org/10.1016/j.cell.2020.12.015	journal	January 2021
An Infectious cDNA Clone of SARS-CoV-2 Xie, Xuping; Muruato, Antonio; Lokugamage, Kumari G. Cell Host & Microbe, Vol. 27, Issue 5 https://doi.org/10.1016/j.chom.2020.04.004	journal	May 2020
Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies Greaney, Allison J.; Loes, Andrea N.; Crawford, Katharine H. D. Cell Host & Microbe, Vol. 29, Issue 3 https://doi.org/10.1016/j.chom.2021.02.003	journal	March 2021
Maturation of Shark Single-domain (IgNAR) Antibodies: Evidence for Induced-fit Binding Stanfield, Robyn L.; Dooley, Helen; Verdino, Petra Journal of Molecular Biology, Vol. 367, Issue 2 https://doi.org/10.1016/j.jmb.2006.12.045	journal	March 2007
Rapid human metapneumovirus microneutralization assay based on green fluorescent protein expression Biacchesi, Stéphane; Skiadopoulos, Mario H.; Yang, Lijuan Journal of Virological Methods, Vol. 128, Issue 1-2 https://doi.org/10.1016/j.jviromet.2005.05.005	journal	September 2005
A new antigen receptor gene family that undergoes rearrangement and extensive somatic diversification in sharks Greenberg, Andrew S.; Avila, David; Hughes, Marianne Nature, Vol. 374, Issue 6518 https://doi.org/10.1038/374168a0	journal	March 1995
Structure of MERS-CoV spike receptor-binding domain complexed with human receptor DPP4 Wang, Nianshuang; Shi, Xuanling; Jiang, Liwei Cell Research, Vol. 23, Issue 8 https://doi.org/10.1038/cr.2013.92	journal	July 2013
Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor Ge, Xing-Yi; Li, Jia-Lu; Yang, Xing-Lou Nature, Vol. 503, Issue 7477 https://doi.org/10.1038/nature12711	journal	October 2013
Origin and evolution of pathogenic coronaviruses Cui, Jie; Li, Fang; Shi, Zheng-Li Nature Reviews Microbiology, Vol. 17, Issue 3 https://doi.org/10.1038/s41579-018-0118-9	journal	December 2018
Structural basis of receptor recognition by SARS-CoV-2 Shang, Jian; Ye, Gang; Shi, Ke Nature, Vol. 581, Issue 7807 https://doi.org/10.1038/s41586-020-2179-y	journal	March 2020
Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike Liu, Lihong; Wang, Pengfei; Nair, Manoj S. Nature, Vol. 584, Issue 7821 https://doi.org/10.1038/s41586-020-2571-7	journal	July 2020
SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies Barnes, Christopher O.; Jette, Claudia A.; Abernathy, Morgan E. Nature, Vol. 588, Issue 7839 https://doi.org/10.1038/s41586-020-2852-1	journal	October 2020
Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7 Wang, Pengfei; Nair, Manoj S.; Liu, Lihong Nature, Vol. 593, Issue 7857 https://doi.org/10.1038/s41586-021-03398-2	journal	March 2021
Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient Zhou, Daming; Duyvesteyn, Helen M. E.; Chen, Cheng-Pin Nature Structural & Molecular Biology, Vol. 27, Issue 10 https://doi.org/10.1038/s41594-020-0480-y	journal	July 2020
Next-generation flexible formats of VNAR domains expand the drug platform's utility and developability Ubah, Obinna C.; Buschhaus, Magdalena J.; Ferguson, Laura Biochemical Society Transactions, Vol. 46, Issue 6 https://doi.org/10.1042/BST20180177	journal	October 2018
Neutralizing Activity of BNT162b2-Elicited Serum Liu, Yang; Liu, Jianying; Xia, Hongjie New England Journal of Medicine, Vol. 384, Issue 15 https://doi.org/10.1056/NEJMc2102017	journal	April 2021
Neutralization of Variant Under Investigation B.1.617.1 With Sera of BBV152 Vaccinees Yadav, Pragya D.; Sapkal, Gajanan N.; Abraham, Priya Clinical Infectious Diseases https://doi.org/10.1093/cid/ciab411	journal	May 2021
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
SARS‐CoV‐2 neutralization and serology testing of COVID‐19 convalescent plasma from donors with nonsevere disease Gniadek, Thomas J.; Thiede, Joshua M.; Matchett, William E. Transfusion, Vol. 61, Issue 1 https://doi.org/10.1111/trf.16101	journal	October 2020
Crystal Structure of a Shark Single-Domain Antibody V Region in Complex with Lysozyme Stanfield, R. L. Science, Vol. 305, Issue 5691 https://doi.org/10.1126/science.1101148	journal	September 2004
Relief and worry for immune-suppressed people Couzin-Frankel, Jennifer Science, Vol. 372, Issue 6541 https://doi.org/10.1126/science.372.6541.443	journal	April 2021
A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV Yuan, Meng; Wu, Nicholas C.; Zhu, Xueyong Science, Vol. 368, Issue 6491 https://doi.org/10.1126/science.abb7269	journal	April 2020
Impaired humoral immunity to SARS-CoV-2 BNT162b2 vaccine in kidney transplant recipients and dialysis patients Rincon-Arevalo, Hector; Choi, Mira; Stefanski, Ana-Luisa Science Immunology, Vol. 6, Issue 60 https://doi.org/10.1126/sciimmunol.abj1031	journal	June 2021
Essential requirement for JPT2 in NAADP-evoked Ca ²⁺ signaling Gunaratne, Gihan S.; Brailoiu, Eugen; He, Shijun Science Signaling, Vol. 14, Issue 675 https://doi.org/10.1126/scisignal.abd5605	journal	March 2021
Human immunodeficiency virus type 1 viral protein R (Vpr) arrests cells in the G2 phase of the cell cycle by inhibiting p34cdc2 activity He, J.; Choe, S.; Walker, R. Journal of Virology, Vol. 69, Issue 11 https://doi.org/10.1128/jvi.69.11.6705-6711.1995	journal	November 1995
Novel, Anti-hTNF-α Variable New Antigen Receptor Formats with Enhanced Neutralizing Potency and Multifunctionality, Generated for Therapeutic Development Ubah, Obinna C.; Steven, John; Kovaleva, Marina Frontiers in Immunology, Vol. 8 https://doi.org/10.3389/fimmu.2017.01780	journal	December 2017
An Anti-hTNF-α Variable New Antigen Receptor Format Demonstrates Superior in vivo Preclinical Efficacy to Humira® in a Transgenic Mouse Autoimmune Polyarthritis Disease Model Ubah, Obinna C.; Steven, John; Porter, Andrew J. Frontiers in Immunology, Vol. 10 https://doi.org/10.3389/fimmu.2019.00526	journal	March 2019
The development of Nanosota-1 as anti-SARS-CoV-2 nanobody drug candidates Ye, Gang; Gallant, Joseph; Zheng, Jian eLife, Vol. 10 https://doi.org/10.7554/eLife.64815	journal	August 2021

Similar Records

Shark nanobodies with potent SARS-CoV-2 neutralizing activity and broad sarbecovirus reactivity

Journal Article · 2023 · Nature Communications · OSTI ID:2423606

Chen, Wei-Hung; Hajduczki, Agnes; Martinez, Elizabeth J.; +42 more

A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody

Journal Article · 2020 · PLoS Pathogens · OSTI ID:1777660

Wu, Nicholas C.; Yuan, Meng; Bangaru, Sandhya; +11 more

Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies

Journal Article · 2020 · Cell · OSTI ID:1816377

Barnes, Christopher O.; West, Anthony P.; Huey-Tubman, Kathryn E.; +20 more

Related Subjects

60 APPLIED LIFE SCIENCES

Title: Mechanisms of SARS-CoV-2 neutralization by shark variable new antigen receptors elucidated through X-ray crystallography

Citation Formats

References (35)

Similar Records

Related Subjects