Cross-neutralizing antibodies bind a SARS-CoV-2 cryptic site and resist circulating variants

被引:58
作者
Li, Tingting [1 ,2 ]
Xue, Wenhui [1 ,2 ]
Zheng, Qingbing [1 ,2 ]
Song, Shuo [3 ,4 ]
Yang, Chuanlai [1 ,2 ]
Xiong, Hualong [1 ,2 ]
Zhang, Sibo [1 ,2 ]
Hong, Minqing [1 ,2 ]
Zhang, Yali [1 ,2 ]
Yu, Hai [1 ,2 ]
Zhang, Yuyun [1 ,2 ]
Sun, Hui [1 ,2 ]
Huang, Yang [1 ,2 ]
Deng, Tingting [1 ,2 ]
Chi, Xin [1 ,2 ]
Li, Jinjin [1 ,2 ]
Wang, Shaojuan [1 ,2 ]
Zhou, Lizhi [1 ,2 ]
Chen, Tingting [1 ,2 ]
Wang, Yingbin [1 ,2 ]
Cheng, Tong [1 ,2 ]
Zhang, Tianying [1 ,2 ]
Yuan, Quan [1 ,2 ]
Zhao, Qinjian [1 ,2 ]
Zhang, Jun [1 ,2 ]
McLellan, Jason S. [5 ]
Zhou, Z. Hong [6 ,7 ]
Zhang, Zheng [3 ,4 ]
Li, Shaowei [1 ,2 ]
Gu, Ying [1 ,2 ]
Xia, Ningshao [1 ,2 ,8 ]
机构
[1] Xiamen Univ, Sch Life Sci, Sch Publ Hlth, State Key Lab Mol Vaccinol & Mol Diagnost, Xiamen 361102, Fujian, Peoples R China
[2] Xiamen Univ, Natl Inst Diagnost & Vaccine Dev Infect Dis, Xiamen 361102, Fujian, Peoples R China
[3] Shenzhen Third Peoples Hosp, Natl Clin Res Ctr Infect Dis, Inst Hepatol, Shenzhen 518112, Guangdong, Peoples R China
[4] Southern Univ Sci & Technol, Sch Med, Affiliated Hosp 2, Shenzhen 518112, Guangdong, Peoples R China
[5] Univ Texas Austin, Dept Mol Biosci, Austin, TX 78712 USA
[6] Univ Calif Los Angeles, Calif NanoSyst Inst CNSI, Los Angeles, CA 90095 USA
[7] Univ Calif Los Angeles, Dept Microbiol Immunol & Mol Genet, Los Angeles, CA 90095 USA
[8] Chinese Acad Med Sci, Res Unit Frontier Technol Struct Vaccinol, Xiamen 518112, Fujian, Peoples R China
基金
中国国家自然科学基金;
关键词
CRYO-EM STRUCTURE; INFLUENZA; INFECTION; PROTECT; DOMAIN; VIRUS; SPIKE; IGG;
D O I
10.1038/s41467-021-25997-3
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
The emergence of numerous variants of SARS-CoV-2, the causative agent of COVID-19, has presented new challenges to the global efforts to control the COVID-19 pandemic. Here, we obtain two cross-neutralizing antibodies (7D6 and 6D6) that target Sarbecoviruses' receptor-binding domain (RBD) with sub-picomolar affinities and potently neutralize authentic SARS-CoV-2. Crystal structures show that both antibodies bind a cryptic site different from that recognized by existing antibodies and highly conserved across Sarbecovirus isolates. Binding of these two antibodies to the RBD clashes with the adjacent N-terminal domain and disrupts the viral spike. Both antibodies confer good resistance to mutations in the currently circulating SARS-CoV-2 variants. Thus, our results have direct relevance to public health as options for passive antibody therapeutics and even active prophylactics. They can also inform the design of pan-sarbecovirus vaccines. Antibodies (Abs) targeting highly conserved epitopes are important tools against emerging virus variants. Here, the authors characterize Abs that recognize a cryptic epitope in the receptor-binding domain of SARS-CoV-2 spike that is well conserved and show that these Abs can neutralize several variants of concerns.
引用
收藏
页数:12
相关论文
共 69 条
[1]   PHENIX: a comprehensive Python']Python-based system for macromolecular structure solution [J].
Adams, Paul D. ;
Afonine, Pavel V. ;
Bunkoczi, Gabor ;
Chen, Vincent B. ;
Davis, Ian W. ;
Echols, Nathaniel ;
Headd, Jeffrey J. ;
Hung, Li-Wei ;
Kapral, Gary J. ;
Grosse-Kunstleve, Ralf W. ;
McCoy, Airlie J. ;
Moriarty, Nigel W. ;
Oeffner, Robert ;
Read, Randy J. ;
Richardson, David C. ;
Richardson, Jane S. ;
Terwilliger, Thomas C. ;
Zwart, Peter H. .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2010, 66 :213-221
[2]   A Site of Vulnerability on the Influenza Virus Hemagglutinin Head Domain Trimer Interface [J].
Bangaru, Sandhya ;
Lang, Shanshan ;
Schotsaert, Michael ;
Vanderven, Hillary A. ;
Zhu, Xueyong ;
Kose, Nurgun ;
Bombardi, Robin ;
Finn, Jessica A. ;
Kent, Stephen J. ;
Gilchuk, Pavlo ;
Gilchuk, Iuliia ;
Turner, Hannah L. ;
Garcia-Sastre, Adolfo ;
Li, Sheng ;
Ward, Andrew B. ;
Wilson, Ian A. ;
Crowe, James E., Jr. .
CELL, 2019, 177 (05) :1136-+
[3]   SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies [J].
Barnes, Christopher O. ;
Jette, Claudia A. ;
Abernathy, Morgan E. ;
Dam, Kim-Marie A. ;
Esswein, Shannon R. ;
Gristick, Harry B. ;
Malyutin, Andrey G. ;
Sharaf, Naima G. ;
Huey-Tubman, Kathryn E. ;
Lee, Yu E. ;
Robbiani, Davide F. ;
Nussenzweig, Michel C. ;
West, Anthony P., Jr. ;
Bjorkman, Pamela J. .
NATURE, 2020, 588 (7839) :682-+
[4]  
Barnes CO, 2020, CELL, V182, P828, DOI [10.1016/j.cell.2020.06.025, 10.1101/2020.05.28.121533]
[5]   A SARS-CoV-2 neutralizing antibody selected from COVID-19 patients binds to the ACE2-RBD interface and is tolerant to most known RBD mutations [J].
Bertoglio, Federico ;
Fuehner, Viola ;
Ruschig, Maximilian ;
Heine, Philip Alexander ;
Abassi, Leila ;
Kluenemann, Thomas ;
Rand, Ulfert ;
Meier, Doris ;
Langreder, Nora ;
Steinke, Stephan ;
Ballmann, Rico ;
Schneider, Kai-Thomas ;
Roth, Kristian Daniel Ralph ;
Kuhn, Philipp ;
Riese, Peggy ;
Schaeckermann, Dorina ;
Korn, Janin ;
Koch, Allan ;
Chaudhry, M. Zeeshan ;
Eschke, Kathrin ;
Kim, Yeonsu ;
Zock-Emmenthal, Susanne ;
Becker, Marlies ;
Scholz, Margitta ;
Moreira, Gustavo Marcal Schmidt Garcia ;
Wenzel, Esther Veronika ;
Russo, Giulio ;
Garritsen, Hendrikus S. P. ;
Casu, Sebastian ;
Gerstner, Andreas ;
Roth, Guenter ;
Adler, Julia ;
Trimpert, Jakob ;
Hermann, Andreas ;
Schirrmann, Thomas ;
Duebel, Stefan ;
Frenzel, Andre ;
Van den Heuvel, Joop ;
Cicin-Sain, Luka ;
Schubert, Maren ;
Hust, Michael .
CELL REPORTS, 2021, 36 (04)
[6]   Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability [J].
Brouwer, Philip J. M. ;
Caniels, Tom G. ;
van der Straten, Karlijn ;
Snitselaar, Jonne L. ;
Aldon, Yoann ;
Bangaru, Sandhya ;
Torres, Jonathan L. ;
Okba, Nisreen M. A. ;
Claireaux, Mathieu ;
Kerster, Gius ;
Bentlage, Arthur E. H. ;
van Haaren, Marlies M. ;
Guerra, Denise ;
Burger, Judith A. ;
Schermer, Edith E. ;
Verheul, Kirsten D. ;
van der Velde, Niels ;
van der Kooi, Alex ;
van Schooten, Jelle ;
van Breemen, Marielle J. ;
Bijl, Tom P. L. ;
Sliepen, Kwinten ;
Aartse, Aafke ;
Derking, Ronald ;
Bontjer, Ilja ;
Kootstra, Neeltje A. ;
Wiersinga, W. Joost ;
Vidarsson, Gestur ;
Haagmans, Bart L. ;
Ward, Andrew B. ;
de Bree, Godelieve J. ;
Sanders, Rogier W. ;
van Gils, Marit J. .
SCIENCE, 2020, 369 (6504) :643-+
[7]   MHC class II transactivator CIITA induces cell resistance to Ebola virus and SARS-like coronaviruses [J].
Bruchez, Anna ;
Sha, Ky ;
Johnson, Joshua ;
Chen, Li ;
Stefani, Caroline ;
McConnell, Hannah ;
Gaucherand, Lea ;
Prins, Rachel ;
Matreyek, Kenneth A. ;
Hume, Adam J. ;
Muhlberger, Elke ;
Schmidt, Emmett V. ;
Olinger, Gene G. ;
Stuart, Lynda M. ;
Lacy-Hulbert, Adam .
SCIENCE, 2020, 370 (6513) :241-+
[8]  
Burki T, 2021, LANCET, V397, P462, DOI 10.1016/S0140-6736(21)00298-1
[9]   The prevalence of antibodies to SARS-CoV-2 among blood donors in China [J].
Chang, Le ;
Hou, Wangheng ;
Zhao, Lei ;
Zhang, Yali ;
Wang, Yanbin ;
Wu, Linfeng ;
Xu, Tingting ;
Wang, Lilin ;
Wang, Juan ;
Ma, Jian ;
Wang, Lan ;
Zhao, Junpeng ;
Xu, Jing ;
Dong, Juan ;
Yan, Ying ;
Yang, Ru ;
Li, Yu ;
Guo, Fei ;
Cheng, Wenjuan ;
Su, Yingying ;
Zeng, Jinfeng ;
Han, Wei ;
Cheng, Tong ;
Zhang, Jun ;
Yuan, Quan ;
Xia, Ningshao ;
Wang, Lunan .
NATURE COMMUNICATIONS, 2021, 12 (01)
[10]   MolProbity: all-atom structure validation for macromolecular crystallography [J].
Chen, Vincent B. ;
Arendall, W. Bryan, III ;
Headd, Jeffrey J. ;
Keedy, Daniel A. ;
Immormino, Robert M. ;
Kapral, Gary J. ;
Murray, Laura W. ;
Richardson, Jane S. ;
Richardson, David C. .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2010, 66 :12-21