Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike

Huo, Jiandong; Zhao, Yuguang; Ren, Jingshan; Zhou, Daming; Duyvesteyn, H.M.E.; Ginn, H.; Carrique, L.; Malinauskas, Tomas; Ruza, R.R.; Shah, Pranav N.M.; Tan, Tiong Kit; Rijal, Pramila; Coombes, Naomi; Bewley, Kevin R.; Tree, Julia A.; Radecke, Julika; Paterson, Neil G.; Supasa, Piyasa; Mongkolsapaya, Juthathip; Screaton, Gavin; Carroll, Miles W.; Townsend, Alain; Fry, Elizabeth E.; Owens, Raymond J.; Stuart, David I.

doi:10.2139/ssrn.3613273

Cited by 90 publications

(143 citation statements)

References 0 publications

Supporting

Mentioning

132

Contrasting

Unclassified

Order By: Relevance

“…The locked conformation was observed alongside Spike trimers with "all-down" and "one-up" conformations in our single particle cryoEM data set. Inspection of the RBD density for the 'down' and 'up' conformations in our analyses and those reported previously (Huo et al, 2020;Walls et al, 2020;Wrapp et al, 2020) showed no evidence of pocket binder. However, since the density for RBDs in the 'up' conformation was of poor quality, we performed focused refinement of our data, isolating 'up' RBDs and their associated adjacent NTDs.…”

Section: The 'Locked' Conformation Is Stabilized By a Pocket Factor Wsupporting

confidence: 63%

“…Knowledge of the mechanism of stabilization of the prefusion form of Spike is also important for understanding the context of epitopes presented in vivo and hence optimisation of presentation in non-classical vaccines. It is remarkable that the locked state of Spike serves to hide three key neutralizing epitopes, namely those of (i) ACE2 competing antibodies, for instance (Wu et al, 2020), (ii) antibodies that bind the S2 'capping' epitope (exemplified by CR3022 (Huo et al, 2020)), and (iii) the extremely potent S309 antibody epitope (Pinto et al, 2020) (the major change in the conformation of the N343 glycan would be expected to disrupt antibody binding as the sugar contributes part of the epitope, Figure 2D, 3C). This suggests that a vaccine which presents these epitopes effectively, such as one using polyvalent displayed RBD domains might be more effective than a genuinely stable ('locked') prefusion Spike trimer.…”

Section: Discussionmentioning

confidence: 99%

“…A detailed analysis was performed of cryo-EM data collected during a study of the binding of the neutralizing antibody CR3022 (Huo et al, 2020) to engineered Spike ectodomain, which has residues K986 and V987 replaced with prolines (2P), an abrogated furin cleavage motif and a C-terminal foldon domain to maintain trimeric association (Wrapp et al, 2020) Table S1). This revealed an further Spike conformation (referred to here as 'locked') in addition to the 'up' or 'down' configurations previously observed (predominantly two, one with all three RBDs down ('all down') and the other with one RBD rotated up and two down ('one up') (Walls et al, 2020;Wrapp et al, 2020) (Methods, Figure S2).…”

Section: Locked Prefusion Sars-cov-2 Spike Dis-favours Conversion To mentioning

confidence: 99%

“…Efforts to meet the need for COVID-19 small molecule therapeutics have been primarily directed against essential viral proteases and polymerases (Khan et al, 2020;, with much interest, and some success, centred on opportunities for drug repurposing (Yin et al, 2020). An alternative approach is antibody therapy, either through the use of convalescent serum or monoclonal antibodies (Duan et al, 2020;Huo et al, 2020). By analogy with the search for AIDS therapeutics we would expect that, if there is sufficient will and resource, effective antivirals will be found that target a range of proteins, including non-enzyme targets, as exemplified by, for HIV, several clinically approved entry inhibitors (Esté and Telenti, 2007).…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

The SARS-CoV-2 Spike harbours a lipid binding pocket which modulates stability of the prefusion trimer

Carrique

Hme.

Malinauskas

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

Large trimeric Spikes decorate SARS-CoV-2 and bind host cells via receptor binding domains (RBDs). We report a conformation in which the trimer is locked into a compact well-ordered form. This differs from previous structures where the RBD can flip up to recognise the receptor. In the locked form regions associated with fusion transitions are stabilised and the RBD harbours curved lipids. The acyl chains bind a hydrophobic pocket in one RBD whilst the polar headgroups attach to an adjacent RBD of the trimer. By functional analogy with enteroviral pocket factors loss of the lipid would destabilise the locked form facilitating receptor attachment, conversion to the postfusion state and virus infection. The nature of lipids available at the site of infection might affect the antigenicity/pathogenicity of released virus. These results reveal a potentially druggable pocket and suggest that the natural prefusion state occludes neutralising RBD epitopes, achieving conformational shielding from antibodies.

show abstract

Section: The 'Locked' Conformation Is Stabilized By a Pocket Factor Wsupporting

confidence: 63%

Section: Discussionmentioning

confidence: 99%

Section: Locked Prefusion Sars-cov-2 Spike Dis-favours Conversion To mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

The SARS-CoV-2 Spike harbours a lipid binding pocket which modulates stability of the prefusion trimer

Carrique

Hme.

Malinauskas

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…The optimum method for detecting neutralisation of SARS-CoV-2 has not been established. For example, different laboratories have obtained varying results for the well-defined monoclonal antibody CR3022 (14,15,18). We have therefore compared results from neutralisation assays performed in four independent laboratories: a systematic survey of the thirty two anti-Spike MAbs at the Francis Crick Institute Figure 7).…”

Section: Neutralisation By Anti-spike Glycoprotein Antibodiesmentioning

confidence: 99%

Breadth and function of antibody response to acute SARS-CoV-2 infection in humans

Huang

Tan

Chen

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

Plasmablast responses and derived IgG monoclonal antibodies (MAbs) have been analysed in three COVID-19 patients. An average of 13.7% and 13.0% of plasmablast-derived IgG MAbs were reactive with virus spike glycoprotein or nucleocapsid, respectively. Of thirty-two antibodies specific for the spike glycoprotein, ten recognised the receptor-binding domain (RBD), thirteen were specific for non-RBD epitopes on the S1 subunit, and nine recognised the S2 subunit. A subset of anti-spike antibodies (10 of 32) cross-reacted with other betacoronaviruses tested, five targeted the non-RBD S1, and five targeted the S2 subunit. Of the plasmablast-derived MAbs reacting with nucleocapsid, over half of them (19 of 35) cross-reacted with other betacoronaviruses tested. The cross-reactive plasmablast-derived antibodies harboured extensive somatic mutations, indicative of an expansion of memory B cells upon SARS-CoV-2 infection. We identified 14 of 32 anti-spike MAbs that neutralised SARS-CoV-2 in independent assays at ≤ 133 nM (20 μg/ml) (five of 10 anti-RBD, three of 13 anti-non-RBD S1 subunit, six of nine anti-S2 subunit). Six of 10 anti-RBD MAbs showed evidence of blockade of ACE2 binding to RBD, and five of six of these were neutralising. Non-competing pairs of neutralising antibodies were identified, which offer potential templates for the development of prophylactic and therapeutic agents against SARS-CoV-2.

show abstract

The spike glycoprotein of highly pathogenic human coronaviruses: structural insights for understanding infection, evolution and inhibition

Qiao

Zhang

et al. 2022

FEBS Open Bio

View full text Add to dashboard Cite

Highly pathogenic human coronaviruses (CoV) including SARS‐CoV, MERS‐CoV and SARS‐CoV‐2 have emerged over the past two decades, resulting in infectious disease outbreaks that have greatly affected public health. The CoV surface spike (S) glycoprotein mediates receptor binding and membrane fusion for cell entry, playing critical roles in CoV infection and evolution. The S glycoprotein is also the major target molecule for prophylactic and therapeutic interventions, including neutralizing antibodies and vaccines. In this review, we summarize key studies that have revealed the structural basis of S‐mediated cell entry of SARS‐CoV, MERS‐CoV and SARS‐CoV‐2. Additionally, we discuss the evolution of the S glycoprotein to realize cross‐species transmission from the viewpoint of structural biology. Lastly, we describe the recent progress in developing antibodies, nanobodies and peptide inhibitors that target the SARS‐CoV‐2 S glycoprotein for therapeutic purposes.

show abstract

Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike

Cited by 90 publications

References 0 publications

The SARS-CoV-2 Spike harbours a lipid binding pocket which modulates stability of the prefusion trimer

The SARS-CoV-2 Spike harbours a lipid binding pocket which modulates stability of the prefusion trimer

Breadth and function of antibody response to acute SARS-CoV-2 infection in humans

The spike glycoprotein of highly pathogenic human coronaviruses: structural insights for understanding infection, evolution and inhibition

Contact Info

Product

Resources

About