8QFZ

TSLP-Bicycle complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery and Characterization of a Bicyclic Peptide (Bicycle) Binder to Thymic Stromal Lymphopoietin.

Narjes, F.Edfeldt, F.Petersen, J.Oster, L.Hamblet, C.Bird, J.Bold, P.Rae, R.Back, E.Stomilovic, S.Zlatoidsky, P.Svensson, T.Hidestal, L.Kunalingam, L.Shamovsky, I.De Maria, L.Gordon, E.Lewis, R.J.Watcham, S.van Rietschoten, K.Mudd, G.E.Harrison, H.Chen, L.Skynner, M.J.

(2024) J Med Chem 67: 2220-2235

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c02163
  • Primary Citation of Related Structures:  
    8QFZ

  • PubMed Abstract: 

    Thymic stromal lymphopoietin (TSLP) is an epithelial-derived pro-inflammatory cytokine involved in the development of asthma and other atopic diseases. We used Bicycle Therapeutics' proprietary phage display platform to identify bicyclic peptides (Bicycles) with high affinity for TSLP, a target that is difficult to drug with conventional small molecules due to the extended protein-protein interactions it forms with both receptors. The hit series was shown to bind to TSLP in a hotspot, that is also used by IL-7Rα. Guided by the first X-ray crystal structure of a small peptide binding to TSLP and the identification of key metabolites, we were able to improve the proteolytic stability of this series in lung S9 fractions without sacrificing binding affinity. This resulted in the potent Bicycle 46 with nanomolar affinity to TSLP ( K D = 13 nM), low plasma clearance of 6.4 mL/min/kg, and an effective half-life of 46 min after intravenous dosing to rats.


  • Organizational Affiliation

    BicycleTx Limited, Portway Building, Granta Park, Cambridge CB21 6GS, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thymic stromal lymphopoietin128Homo sapiensMutation(s): 0 
Gene Names: TSLP
UniProt & NIH Common Fund Data Resources
Find proteins for Q969D9 (Homo sapiens)
Explore Q969D9 
Go to UniProtKB:  Q969D9
PHAROS:  Q969D9
GTEx:  ENSG00000145777 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ969D9
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CYS-HIS-TRP-LEU-GLU-ASN-CYS-TRP-ARG-GLY-PHE-CYS12synthetic 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
LFI (Subject of Investigation/LOI)
Query on LFI

Download Ideal Coordinates CCD File 
C [auth B]1-[3,5-bis(3-bromanylpropanoyl)-1,3,5-triazinan-1-yl]-3-bromanyl-propan-1-one
C12 H18 Br3 N3 O3
UYNTZRFVDTZUQI-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.92α = 90
b = 52.349β = 90
c = 65.829γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
MOLREPphasing
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2024-02-07 
  • Deposition Author(s): Petersen, J.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Database references