9MGY

Cryo-EM structure of Human NLRP3 complex with compound 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Discovery of Potent and Brain-Penetrant Bicyclic NLRP3 Inhibitors with Peripheral and Central In Vivo Activity.

Mammoliti, O.Carbajo, R.Perez-Benito, L.Yu, X.Prieri, M.L.C.Bontempi, L.Embrechts, S.Paesmans, I.Bassi, M.Bhattacharya, A.Canellas, S.De Hoog, S.Demin, S.Gijsen, H.J.M.Hache, G.Jacobs, T.Jerhaoui, S.Leenaerts, J.Lutter, F.H.Mahieu, M.Matico, R.Miller, R.Oehlrich, D.Perrier, M.Ryabchuk, P.Schepens, W.Sharma, S.Somers, M.Suarez, J.Surkyn, M.Van Opdenbosch, N.Verhulst, T.Bottelbergs, A.

(2025) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c03108
  • Primary Citation of Related Structures:  
    9MGY, 9MIE, 9MIG

  • PubMed Abstract: 

    NLRP3 is a danger sensor protein responsible for inflammasome activation. This leads to pro-inflammatory cytokines release, like IL-1β, and pyroptosis, a regulated cell death. Mounting evidence associates excessive NLRP3 activation to neurodegenerative conditions, such as Alzheimer's and Parkinson's diseases. Thus, NLRP3 inhibitors could potentially provide therapeutic benefit for these disorders. We describe here the evolution of inhibitors relying on a pyridazine-based motif for their key interactions with NLRP3. A Cryo-EM structure helped optimizing protein-ligand complementarity. Subsequently, conformational NMR studies pointed the efforts toward 5,6-bicyclic cores that allowed a balance between brain penetration and undesirable properties, such as hERG inhibition. The effort culminated in compound 19 , which showed moderate (mouse) to good (rat) brain penetration and was active at low dose in an LPS challenge model. Importantly, an earlier compound was active in a central neuroinflammation model providing a valuable proof of concept for NLRP3 inhibition.


  • Organizational Affiliation

    Janssen Pharmaceutica NV, A Johnson & Johnson Company, Turnhoutseweg 30, Beerse 2340, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NACHT, LRR and PYD domains-containing protein 3A [auth C]1,036Homo sapiensMutation(s): 0 
Gene Names: NLRP3C1orf7CIAS1NALP3PYPAF1
EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q96P20 (Homo sapiens)
Explore Q96P20 
Go to UniProtKB:  Q96P20
PHAROS:  Q96P20
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96P20
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
B [auth C]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
A1BLR (Subject of Investigation/LOI)
Query on A1BLR

Download Ideal Coordinates CCD File 
C
(2M)-2-(6-{[(3R)-1-methylpiperidin-3-yl]amino}pyridazin-3-yl)-5-(trifluoromethyl)phenol
C17 H19 F3 N4 O
CDQFNDRUBJQABO-GFCCVEGCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information