Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
14 07 2023
14 07 2023
Historique:
received:
12
12
2022
accepted:
03
07
2023
medline:
17
7
2023
pubmed:
15
7
2023
entrez:
14
7
2023
Statut:
epublish
Résumé
SARS-CoV-2 Omicron subvariants have evolved to evade receptor-binding site (RBS) antibodies that exist in diverse individuals as public antibody clones. We rationally selected RBS antibodies resilient to mutations in emerging Omicron subvariants. Y489 was identified as a site of virus vulnerability and a common footprint of broadly neutralizing antibodies against the subvariants. Multiple Y489-binding antibodies were encoded by public clonotypes and additionally recognized F486, potentially accounting for the emergence of Omicron subvariants harboring the F486V mutation. However, a subclass of antibodies broadly neutralized BA.4/BA.5 variants via hydrophobic binding sites of rare clonotypes along with high mutation-resilience under escape mutation screening. A computationally designed antibody based on one of the Y489-binding antibodies, NIV-10/FD03, was able to bind XBB with any 486 mutation and neutralized XBB.1.5. The structural basis for the mutation-resilience of this Y489-binding antibody group may provide important insights into the design of therapeutics resistant to viral escape.
Identifiants
pubmed: 37452031
doi: 10.1038/s41467-023-39890-8
pii: 10.1038/s41467-023-39890-8
pmc: PMC10349087
doi:
Substances chimiques
Antibodies, Viral
0
Broadly Neutralizing Antibodies
0
Antibodies, Neutralizing
0
Spike Glycoprotein, Coronavirus
0
spike protein, SARS-CoV-2
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4198Informations de copyright
© 2023. The Author(s).
Références
Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):72-82
pubmed: 16369096
Lancet Infect Dis. 2023 Mar;23(3):280-281
pubmed: 36736338
Nat Methods. 2017 Mar;14(3):290-296
pubmed: 28165473
Science. 2021 Feb 19;371(6531):823-829
pubmed: 33495307
Patterns (N Y). 2021 Dec 09;3(2):100406
pubmed: 35199061
Science. 2020 Aug 21;369(6506):1014-1018
pubmed: 32540904
J Comput Chem. 2009 Jul 30;30(10):1545-614
pubmed: 19444816
Nat Commun. 2021 Jun 21;12(1):3802
pubmed: 34155214
Immunity. 2021 Aug 10;54(8):1841-1852.e4
pubmed: 34246326
Acta Crystallogr D Struct Biol. 2019 Oct 1;75(Pt 10):861-877
pubmed: 31588918
J Mol Biol. 2003 Aug 1;331(1):281-99
pubmed: 12875852
Nat Methods. 2017 Jan;14(1):71-73
pubmed: 27819658
Med. 2022 Apr 8;3(4):262-268.e4
pubmed: 35313451
Immunity. 2018 Jan 16;48(1):174-184.e9
pubmed: 29343437
Protein Sci. 2018 Jan;27(1):293-315
pubmed: 29067766
Bioinformatics. 2016 Aug 15;32(16):2451-6
pubmed: 27153634
Nat Rev Immunol. 2023 Mar;23(3):189-199
pubmed: 36168054
J Virol. 2004 Sep;78(17):9007-15
pubmed: 15308697
Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):235-42
pubmed: 21460441
Science. 2022 Jan 28;375(6579):449-454
pubmed: 34990214
Sci Transl Med. 2022 Jun 22;14(650):eabn7737
pubmed: 35471044
Cell. 2022 Jul 7;185(14):2422-2433.e13
pubmed: 35772405
Science. 2021 Aug 13;373(6556):
pubmed: 34210892
Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):264-9
pubmed: 23175789
Lancet Infect Dis. 2023 Mar;23(3):278-280
pubmed: 36746173
Nature. 2022 Feb;602(7898):664-670
pubmed: 35016195
J Comput Chem. 2004 Oct;25(13):1605-12
pubmed: 15264254
Sci Immunol. 2022 Apr 22;7(70):eabn8590
pubmed: 35113654
Cell. 2020 Apr 16;181(2):281-292.e6
pubmed: 32155444
Biophys Rev. 2020 Apr;12(2):371-375
pubmed: 32026396
Proc Natl Acad Sci U S A. 2009 Jul 21;106(29):11937-42
pubmed: 19571001
Nature. 2022 Aug;608(7923):593-602
pubmed: 35714668
PLoS Pathog. 2022 Nov 18;18(11):e1010951
pubmed: 36399443
Cell. 2021 Apr 15;184(8):2183-2200.e22
pubmed: 33756110
Nature. 2021 Aug;596(7873):583-589
pubmed: 34265844
Immunity. 2022 Jun 14;55(6):925-944
pubmed: 35623355
Biophys J. 2015 Oct 20;109(8):1528-32
pubmed: 26488642
J Immunol Methods. 2008 Jan 1;329(1-2):112-24
pubmed: 17996249
Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501
pubmed: 20383002
Science. 2020 Nov 20;370(6519):950-957
pubmed: 32972994
Cell. 2022 Jun 9;185(12):2116-2131.e18
pubmed: 35662412
Cell. 2020 Sep 3;182(5):1295-1310.e20
pubmed: 32841599
Bioinformatics. 2021 Oct 25;37(20):3657-3659
pubmed: 33822884
Elife. 2018 Nov 09;7:
pubmed: 30412051
Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):125-32
pubmed: 20124692
Nat Immunol. 2022 Jul;23(7):1008-1020
pubmed: 35761083
Nat Commun. 2022 Jun 13;13(1):3375
pubmed: 35697673
Nature. 2022 Aug;608(7923):603-608
pubmed: 35790190
Virol J. 2021 Jan 12;18(1):16
pubmed: 33435994
Nature. 2020 Dec;588(7839):682-687
pubmed: 33045718
Sci Adv. 2021 Feb 17;7(8):
pubmed: 33597251
MAbs. 2022 Jan-Dec;14(1):2072455
pubmed: 35543180
Lancet Infect Dis. 2022 Dec;22(12):1666-1668
pubmed: 36328002
PLoS One. 2013;8(4):e59004
pubmed: 23565140
PLoS One. 2020 Sep 18;15(9):e0239403
pubmed: 32946527
Nature. 2022 Feb;602(7898):676-681
pubmed: 35016198
Proteins. 2021 Apr;89(4):436-449
pubmed: 33249652
Nat Rev Microbiol. 2023 Mar;21(3):162-177
pubmed: 36653446
Nature. 2022 Jul;607(7917):119-127
pubmed: 35576972
Cell. 2020 Aug 20;182(4):828-842.e16
pubmed: 32645326
Nat Methods. 2020 Jul;17(7):665-680
pubmed: 32483333
Immunity. 2021 Oct 12;54(10):2385-2398.e10
pubmed: 34508662
Nature. 2020 May;581(7807):215-220
pubmed: 32225176
Protein Sci. 2018 Jan;27(1):14-25
pubmed: 28710774