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

Li, Tingting; Xue, Wenhui; Zheng, Qingbing; Song, Shuo; Yang, Changqing; Xiong, Hualong; Zhang, Sibo; Hong, Minqing; Zhang, Yali; Yu, Hai; Zhang, Yuyun; Sun, Hui; Huang, Yang; Deng, Tingting; Chi, Xiaosa; Li, Jinjin; Wang, Shaojuan; Zhou, Lizhi; Chen, Tingting; Wang, Yingbin; Cheng, Tong; Zhang, Tianying; Yuan, Quan; Zhao, Qinjian; Zhang, Jun; McLellan, Jason S.; Zh, Zhou; Zhang, Zheng; Gu, Ying; Xia, Ningshao

doi:10.21203/rs.3.rs-582977/v1

Cited by 8 publications

(14 citation statements)

References 58 publications

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“…The structural model of SARS-CoV-2 spike PDB entry 6VYB (Walls et al, 2020) was used as initial template for model building of the trimer. PDB entries 7EAM (Li et al, 2021) and 7L2C (Cerutti et al, 2021b) were used as initial templates to build the RBD and the NTD respectively. Automated and manual model building were iteratively performed using real space refinement in Phenix (Adams et al, 2010) and Coot (Emsley and Cowtan, 2004) respectively.…”

Section: Cryo-em Sample Preparationmentioning

confidence: 99%

Cryo-EM structure of the SARS-CoV-2 Omicron spike

et al. 2022

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The recently reported B.1.1.529 omicron variant of SARS-CoV-2 includes 34 mutations in the spike protein relative to the Wuhan strain, including 15 mutations in the receptor binding domain (RBD). Functional studies have shown omicron to substantially escape the activity of many SARS-CoV-2-neutralizing antibodies. Here we report a 3.1 Å resolution cryo-electron microscopy (cryo-EM) structure of the omicron spike protein ectodomain. The structure depicts a spike that is exclusively in the 1-RBD-up conformation with high mobility of RBD. Many mutations cause steric clashes and/or altered interactions at antibody binding surfaces, whereas others mediate changes of the spike structure in local regions to interfere with antibody recognition. Overall, the structure of the omicron spike reveals how mutations alter its conformation and explains its extraordinary ability to evade neutralizing antibodies.

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Section: Cryo-em Sample Preparationmentioning

confidence: 99%

Cryo-EM structure of the SARS-CoV-2 Omicron spike

et al. 2022

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“…Transient domain movements that allow B9-scFv binding would break this glycan contact, potentially destabilising the Spike complex. Likewise, two previous neutralising antibodies that target this site cause destabilisation of the prefusion Spike complex [30] and shedding of the SARS-CoV-2 S1 domain.…”

Section: Resultsmentioning

confidence: 99%

“…6a). This site has, however, previously been proposed to be transiently exposed by interdomain movements [30]. Notably, a glycan from the NTD of the adjacent protomer (N165) is thought to block access to this region by inserting itself in the volume left by the RBD when it is in the “up” conformation [36].…”

Section: Resultsmentioning

confidence: 99%

“…Consistent with this, the epitope localises to a cryptic cleft on the inner face of the RBD that becomes available only transiently by inter-domain movements. This epitope has been identified only once previously as the target for two other pan-sarbecovirus antibodies [30] when multiple, repeated immunisations were required. Remarkably, here we isolate a bovine broadly reactive CDRH3 from a library of <1 × 10 4 sequences.…”

Section: Introductionmentioning

confidence: 99%

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An Ultralong Bovine CDRH3 that Targets a Conserved, Cryptic Epitope on SARS-CoV and SARS-CoV-2

Burke

Scott

Minshull

et al. 2022

Preprint

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The ability of broadly neutralising antibodies to target conserved epitopes gives them huge potential as antibody-based therapeutics, particularly in the face of constant viral antigen evolution. Certain bovine antibodies are highly adept at binding conserved, glycosylated epitopes, courtesy of their ultralong complementarity determining region (CDR)H3. Here, we used a SARS-naïve, bovine ultralong CDRH3 library and mammalian cell display, to isolate a bovine paratope that engages the SARS-CoV and SARS-CoV-2 receptor-binding domain (RBD). This neutralises viruses pseudo-typed with SARS-CoV Spike protein but not by competition with RBD binding to ACE2. Instead, using differential hydrogen-deuterium exchange mass spectrometry and site-directed mutagenesis, we demonstrate that this ultralong CDRH3 recognises a rarely identified, conserved, cryptic epitope that overlaps the target of pan-sarbecovirus antibodies (7D6/6D6). The epitope is glycan-shielded and becomes accessible only transiently via inter-domain movements. This represents the first bovine anti-sarbecovirus paratope and highlights the power of this approach in identifying novel tools to combat emerging pathogens.

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“…By contrast, the nanobodies in the G3 bound to the epitopes that are readily accessible regardless of up or down conformations of RBD. Interestingly, by screening and characterizing hundreds of monoclonal antibodies from convalescent or vaccinated individuals, a small but convincing number of cross-neutralizing antibodies with similar epitope specificity have also been found 39,[49][50][51][52][53][54][55][56][57][58][59][60] . The epitopes recognized by the G1, G2, and G3 nanobodies are therefore not only the viable targets in alpaca but also in humans.…”

Section: Discussionmentioning

confidence: 99%

Broadly neutralizing and protective nanobodies against diverse sarbecoviruses

Ren

et al. 2022

Preprint

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As SARS-CoV-2 Omicron and other variants of concern continue spreading around the world, development of antibodies and vaccines to confer broad and protective activity is a global priority. Here, we report on the identification of a special group of nanobodies from immunized alpaca with exceptional breadth and potency against diverse sarbecoviruses including SARS-CoV-1, Omicron BA.1, and BA.2. Crystal structure analysis of one representative nanobody, 3-2A2-4, revealed a highly conserved epitope between the cryptic and the outer face of the receptor binding domain (RBD). The epitope is readily accessible regardless of RBD in up or down conformation and distinctive from the receptor ACE2 binding site. Passive delivery of 3-2A2-4 protected K18-hACE2 mice from infection of authentic SARS-CoV-2 Delta and Omicron. This group of nanobodies and the epitope identified should provide invaluable reference for the development of next generation antibody therapies and vaccines against wide varieties of SARS-CoV-2 infection and beyond.

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

Cited by 8 publications

References 58 publications

Cryo-EM structure of the SARS-CoV-2 Omicron spike

Cryo-EM structure of the SARS-CoV-2 Omicron spike

An Ultralong Bovine CDRH3 that Targets a Conserved, Cryptic Epitope on SARS-CoV and SARS-CoV-2

Broadly neutralizing and protective nanobodies against diverse sarbecoviruses

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