7WET

Crystal structure of Peroxiredoxin I in complex with the inhibitor Cela


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Celastrol suppresses colorectal cancer via covalent targeting peroxiredoxin 1.

Xu, H.Zhao, H.Ding, C.Jiang, D.Zhao, Z.Li, Y.Ding, X.Gao, J.Zhou, H.Luo, C.Chen, G.Zhang, A.Xu, Y.Zhang, H.

(2023) Signal Transduct Target Ther 8: 51-51

  • DOI: https://doi.org/10.1038/s41392-022-01231-4
  • Primary Citation of Related Structures:  
    7WET, 7WEU

  • PubMed Abstract: 

    As a terpenoids natural product isolated from the plant Thunder God Vine, Celastrol is widely studied for its pharmacological activities, including anti-tumor activities. The clinical application of Celastrol is strictly limited due to its severe side effects, whereas previously revealed targets and mechanism of Celastrol seldom reduce its in vivo toxicity via structural optimization. Target identification has a far-reaching influence on the development of innovative drugs, and omics data has been widely used for unbiased target prediction. However, it is difficult to enrich target of specific phenotype from thousands of genes or proteins, especially for natural products with broad promising activities. Here, we developed a text-mining-based web-server tool to enrich targets from omics data of inquired compounds. Then peroxiredoxin 1 (PRDX1) was identified as the ROS-manipulating target protein of Celastrol in colorectal cancer. Our solved high-resolution crystal structure revealed the unique covalent binding mode of Celastrol with PRDX1. New derivative compound 19-048 with improved potency against PRDX1 and selectivity towards PRDX2~PRDX6 were synthesized based on crystal structure analysis. Both Celastrol and 19-048 effectively suppressed the proliferation of colorectal cancer cells. The anti-tumor efficacy of Celastrol and 19-048 was significantly diminished on xenograft nude mice bearing PRDX1 knock-down colorectal cancer cells. Several downstream genes of p53 signaling pathway were dramatically up-regulated with Celastrol or 19-048 treatment. Our findings reveal that the side effects of Celastrol could be reduced via structural modification, and PRDX1 inhibition is promising for the treatment of colorectal cancer.


  • Organizational Affiliation

    School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxiredoxin-1
A, B
175Homo sapiensMutation(s): 0 
Gene Names: PRDX1PAGAPAGBTDPX2
EC: 1.11.1.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q06830 (Homo sapiens)
Explore Q06830 
Go to UniProtKB:  Q06830
PHAROS:  Q06830
GTEx:  ENSG00000117450 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06830
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AQR (Subject of Investigation/LOI)
Query on AQR

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(2R,4aS,6aS,12bR,14aS,14bR)-10-hydroxy-2,4a,6a,9,12b,14a-hexamethyl-11-oxo-1,2,3,4,4a,5,6,6a,11,12b,13,14,14a,14b-tetradecahydropicene-2-carboxylic acid
C29 H38 O4
KQJSQWZMSAGSHN-JJWQIEBTSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.625α = 90
b = 78.36β = 90
c = 81.202γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81903538

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-28
    Type: Initial release
  • Version 1.1: 2023-02-15
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description