8W0R

Human EBP complexed with compound 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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 and Optimization of Selective Brain-Penetrant EBP Inhibitors that Enhance Oligodendrocyte Formation.

Dorel, R.Sun, D.Carruthers, N.Castanedo, G.M.Ung, P.M.Factor, D.C.Li, T.Baumann, H.Janota, D.Pang, J.Salphati, L.Meklemburg, R.Korman, A.J.Harper, H.E.Stubblefield, S.Payandeh, J.McHugh, D.Lang, B.T.Tesar, P.J.Dere, E.Masureel, M.Adams, D.J.Volgraf, M.Braun, M.G.

(2024) J Med Chem 67: 4819-4832

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c02396
  • Primary Citation of Related Structures:  
    8W0R, 8W0S

  • PubMed Abstract: 

    The inhibition of emopamil binding protein (EBP), a sterol isomerase within the cholesterol biosynthesis pathway, promotes oligodendrocyte formation, which has been proposed as a potential therapeutic approach for treating multiple sclerosis. Herein, we describe the discovery and optimization of brain-penetrant, orally bioavailable inhibitors of EBP. A structure-based drug design approach from literature compound 1 led to the discovery of a hydantoin-based scaffold, which provided balanced physicochemical properties and potency and an improved in vitro safety profile. The long half-lives of early hydantoin-based EBP inhibitors in rodents prompted an unconventional optimization strategy, focused on increasing metabolic turnover while maintaining potency and a brain-penetrant profile. The resulting EBP inhibitor 11 demonstrated strong in vivo target engagement in the brain, as illustrated by the accumulation of EBP substrate zymostenol after repeated dosing. Furthermore, compound 11 enhanced the formation of oligodendrocytes in human cortical organoids, providing additional support for our therapeutic hypothesis.


  • Organizational Affiliation

    Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-beta-hydroxysteroid-Delta(8),Delta(7)-isomerase
A, B
238Homo sapiensMutation(s): 0 
Gene Names: EBP
EC: 5.3.3.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q15125 (Homo sapiens)
Explore Q15125 
Go to UniProtKB:  Q15125
PHAROS:  Q15125
GTEx:  ENSG00000147155 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15125
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AEU (Subject of Investigation/LOI)
Query on A1AEU

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
1-methyl-1'-[(oxan-4-yl)methyl]-5-(trifluoromethyl)spiro[indole-2,4'-piperidin]-3(1H)-one
C20 H25 F3 N2 O2
CEQWEVQYPPXCIW-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release