8AAA

Crystal structure of SARS-CoV-2 S RBD in complex with a stapled peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Multivalent bicyclic peptides are an effective antiviral modality that can potently inhibit SARS-CoV-2.

Gaynor, K.U.Vaysburd, M.Harman, M.A.J.Albecka, A.Jeffrey, P.Beswick, P.Papa, G.Chen, L.Mallery, D.McGuinness, B.Van Rietschoten, K.Stanway, S.Brear, P.Lulla, A.Ciazynska, K.Chang, V.T.Sharp, J.Neary, M.Box, H.Herriott, J.Kijak, E.Tatham, L.Bentley, E.G.Sharma, P.Kirby, A.Han, X.Stewart, J.P.Owen, A.Briggs, J.A.G.Hyvonen, M.Skynner, M.J.James, L.C.

(2023) Nat Commun 14: 3583-3583

  • DOI: https://doi.org/10.1038/s41467-023-39158-1
  • Primary Citation of Related Structures:  
    7Z8O, 8AAA

  • PubMed Abstract: 

    COVID-19 has stimulated the rapid development of new antibody and small molecule therapeutics to inhibit SARS-CoV-2 infection. Here we describe a third antiviral modality that combines the drug-like advantages of both. Bicycles are entropically constrained peptides stabilized by a central chemical scaffold into a bi-cyclic structure. Rapid screening of diverse bacteriophage libraries against SARS-CoV-2 Spike yielded unique Bicycle binders across the entire protein. Exploiting Bicycles' inherent chemical combinability, we converted early micromolar hits into nanomolar viral inhibitors through simple multimerization. We also show how combining Bicycles against different epitopes into a single biparatopic agent allows Spike from diverse variants of concern (VoC) to be targeted (Alpha, Beta, Delta and Omicron). Finally, we demonstrate in both male hACE2-transgenic mice and Syrian golden hamsters that both multimerized and biparatopic Bicycles reduce viraemia and prevent host inflammation. These results introduce Bicycles as a potential antiviral modality to tackle new and rapidly evolving viruses.


  • Organizational Affiliation

    Bicycle Therapeutics, Portway Building, Granta Park, Cambridge, CB21 6GS, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S1198Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Stapled peptide18synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
29N (Subject of Investigation/LOI)
Query on 29N

Download Ideal Coordinates CCD File 
C [auth B]1,1',1''-(1,3,5-triazinane-1,3,5-triyl)tripropan-1-one
C12 H21 N3 O3
AEPJNZPJFYDQLM-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.2α = 90
b = 112.2β = 90
c = 35.534γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-28
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary