8A46

Crystal structure of the human Kelch domain of Keap1 in complex with compound S217879


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Selective disruption of NRF2-KEAP1 interaction leads to NASH resolution and reduction of liver fibrosis in mice.

Seedorf, K.Weber, C.Vinson, C.Berger, S.Vuillard, L.M.Kiss, A.Creusot, S.Broux, O.Geant, A.Ilic, C.Lemaitre, K.Richard, J.Hammoutene, A.Mahieux, J.Martiny, V.Durand, D.Melchiore, F.Nyerges, M.Paradis, V.Provost, N.Duvivier, V.Delerive, P.

(2023) JHEP Rep 5: 100651-100651

  • DOI: https://doi.org/10.1016/j.jhepr.2022.100651
  • Primary Citation of Related Structures:  
    8A46

  • PubMed Abstract: 

    Oxidative stress is recognized as a major driver of non-alcoholic steatohepatitis (NASH) progression. The transcription factor NRF2 and its negative regulator KEAP1 are master regulators of redox, metabolic and protein homeostasis, as well as detoxification, and thus appear to be attractive targets for the treatment of NASH. Molecular modeling and X-ray crystallography were used to design S217879 - a small molecule that could disrupt the KEAP1-NRF2 interaction. S217879 was highly characterized using various molecular and cellular assays. It was then evaluated in two different NASH-relevant preclinical models, namely the methionine and choline-deficient diet (MCDD) and diet-induced obesity NASH (DIO NASH) models. Molecular and cell-based assays confirmed that S217879 is a highly potent and selective NRF2 activator with marked anti-inflammatory properties, as shown in primary human peripheral blood mononuclear cells. In MCDD mice, S217879 treatment for 2 weeks led to a dose-dependent reduction in NAFLD activity score while significantly increasing liver Nqo1 mRNA levels, a specific NRF2 target engagement biomarker. In DIO NASH mice, S217879 treatment resulted in a significant improvement of established liver injury, with a clear reduction in both NAS and liver fibrosis. αSMA and Col1A1 staining, as well as quantification of liver hydroxyproline levels, confirmed the reduction in liver fibrosis in response to S217879. RNA-sequencing analyses revealed major alterations in the liver transcriptome in response to S217879, with activation of NRF2-dependent gene transcription and marked inhibition of key signaling pathways that drive disease progression. These results highlight the potential of selective disruption of the NRF2-KEAP1 interaction for the treatment of NASH and liver fibrosis. We report the discovery of S217879 - a potent and selective NRF2 activator with good pharmacokinetic properties. By disrupting the KEAP1-NRF2 interaction, S217879 triggers the upregulation of the antioxidant response and the coordinated regulation of a wide spectrum of genes involved in NASH disease progression, leading ultimately to the reduction of both NASH and liver fibrosis progression in mice.


  • Organizational Affiliation

    Cardiovascular and Metabolic Diseases Research, Institut de Recherches Servier, Suresnes, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kelch-like ECH-associated protein 1308Mus musculusMutation(s): 0 
Gene Names: Keap1Inrf2Kiaa0132
UniProt
Find proteins for Q9Z2X8 (Mus musculus)
Explore Q9Z2X8 
Go to UniProtKB:  Q9Z2X8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Z2X8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L5F (Subject of Investigation/LOI)
Query on L5F

Download Ideal Coordinates CCD File 
B [auth A]2-[(1S,2R,8S)-2,4,32-trimethyl-28,28-bis(oxidanylidene)-19,22,27-trioxa-28$l^{6}-thia-1,14,15,16-tetrazahexacyclo[21.5.3.1^{3,7}.1^{9,13}.0^{12,16}.0^{26,30}]tritriaconta-3(33),4,6,9(32),10,12,14,23,25,30-decaen-8-yl]ethanoic acid
C30 H32 N4 O7 S
CAHCZMVBPKUGCY-IBVKSMDESA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.373α = 90
b = 103.373β = 90
c = 55.712γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-01
    Changes: Refinement description