Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants
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...
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| Published in | Nature communications Vol. 14; no. 1; pp. 4198 - 17 |
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| Main Authors | , , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
Nature Publishing Group UK
14.07.2023
Nature Publishing Group Nature Portfolio |
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| Online Access | Get full text |
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| Abstract | 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.
In this study, the authors isolated SARS-CoV-2 receptor binding site monoclonal antibodies resistant to Omicron mutations. An amino acid in the receptor binding domain, tyrosine-489, is a virus-vulnerable site and a common footprint of broadly neutralizing antibodies. |
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| AbstractList | 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.
In this study, the authors isolated SARS-CoV-2 receptor binding site monoclonal antibodies resistant to Omicron mutations. An amino acid in the receptor binding domain, tyrosine-489, is a virus-vulnerable site and a common footprint of broadly neutralizing antibodies. 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. Abstract 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. 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.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. 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.In this study, the authors isolated SARS-CoV-2 receptor binding site monoclonal antibodies resistant to Omicron mutations. An amino acid in the receptor binding domain, tyrosine-489, is a virus-vulnerable site and a common footprint of broadly neutralizing antibodies. |
| ArticleNumber | 4198 |
| Author | Hashiguchi, Takao Kuroda, Yudai Onodera, Taishi Adachi, Yu Someya, Taiyou Yumoto, Kohei Hoshino, Atsushi Kita, Shunsuke Yamamoto, Tsukasa Maenaka, Katsumi Higuchi, Yusuke Anraku, Yuki Kirita, Yuhei Moriyama, Saya Kuroda, Daisuke Tonouchi, Keisuke Nakamura-Uchiyama, Fukumi Takahashi, Yoshimasa Kotaki, Ryutaro Fukuhara, Hideo Suzuki, Tateki Fukushi, Shuetsu Taminishi, Shunta Maeda, Ken |
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Shinjuku-ku – sequence: 6 givenname: Shunsuke orcidid: 0000-0003-3969-302X surname: Kita fullname: Kita, Shunsuke organization: Laboratory of Biomolecular Science, and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University; Sapporo – sequence: 7 givenname: Yusuke surname: Higuchi fullname: Higuchi, Yusuke organization: Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine; Kyoto – sequence: 8 givenname: Yuhei orcidid: 0000-0002-5240-5531 surname: Kirita fullname: Kirita, Yuhei organization: Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine; Kyoto – sequence: 9 givenname: Ryutaro orcidid: 0000-0001-7965-1671 surname: Kotaki fullname: Kotaki, Ryutaro organization: Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases; Shinjuku-ku – sequence: 10 givenname: Keisuke surname: Tonouchi fullname: Tonouchi, Keisuke organization: Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases; 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Shinjuku-ku – sequence: 16 givenname: Tsukasa surname: Yamamoto fullname: Yamamoto, Tsukasa organization: Department of Veterinary Science, National Institute of Infectious Diseases; Shinjuku-ku – sequence: 17 givenname: Taishi surname: Onodera fullname: Onodera, Taishi organization: Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases; Shinjuku-ku – sequence: 18 givenname: Shuetsu surname: Fukushi fullname: Fukushi, Shuetsu organization: Department of Virology I, National Institute of Infectious Diseases; Shinjuku-ku – sequence: 19 givenname: Ken orcidid: 0000-0002-3488-5439 surname: Maeda fullname: Maeda, Ken organization: Department of Veterinary Science, National Institute of Infectious Diseases; Shinjuku-ku – sequence: 20 givenname: Fukumi surname: Nakamura-Uchiyama fullname: Nakamura-Uchiyama, Fukumi organization: Department of Infectious Diseases, Tokyo Metropolitan Bokutoh Hospital; Sumida-ku – sequence: 21 givenname: Takao orcidid: 0000-0001-7578-7571 surname: Hashiguchi fullname: Hashiguchi, Takao organization: Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University; Kyoto – sequence: 22 givenname: Atsushi orcidid: 0000-0002-4015-1319 surname: Hoshino fullname: Hoshino, Atsushi organization: Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine; Kyoto – sequence: 23 givenname: Katsumi orcidid: 0000-0002-5459-521X surname: Maenaka fullname: Maenaka, Katsumi organization: Laboratory of Biomolecular Science, and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University; Sapporo, Division of Pathogen Structure, International Institute for Zoonosis Control, Hokkaido University, Global Station for Biosurfaces and Drug Discovery, Hokkaido University; Sapporo, Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University; Sapporo – sequence: 24 givenname: Yoshimasa orcidid: 0000-0001-6342-4087 surname: Takahashi fullname: Takahashi, Yoshimasa email: ytakahas@niid.go.jp organization: Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases; Shinjuku-ku |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/37452031$$D View this record in MEDLINE/PubMed |
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| DOI | 10.1038/s41467-023-39890-8 |
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| Snippet | SARS-CoV-2 Omicron subvariants have evolved to evade receptor-binding site (RBS) antibodies that exist in diverse individuals as public antibody clones. We... Abstract SARS-CoV-2 Omicron subvariants have evolved to evade receptor-binding site (RBS) antibodies that exist in diverse individuals as public antibody... |
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| SubjectTerms | 13/1 13/31 38 38/39 38/47 38/77 38/88 49 59 631/250/2152/2153/1291 631/250/255/2514 631/61/24 64 Amino acids Antibodies Antibodies, Neutralizing Antibodies, Viral Binding Sites Broadly Neutralizing Antibodies COVID-19 Footprints Humanities and Social Sciences Humans Hydrophobicity Monoclonal antibodies multidisciplinary Mutation Neutralizing Receptors Resilience SARS-CoV-2 - genetics Science Science (multidisciplinary) Severe acute respiratory syndrome coronavirus 2 Spike Glycoprotein, Coronavirus - genetics Tyrosine Viral diseases Viruses |
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| Title | Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants |
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