5M96

Synthesis and biological evaluation of new triazolo and imidazolopyridine RORgt inverse agonists


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 
    0.208 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted Q6YClick on this verticalbar to view details

This is version 2.1 of the entry. See complete history


Literature

Synthesis and Biological Evaluation of New Triazolo- and Imidazolopyridine ROR gamma t Inverse Agonists.

Hintermann, S.Guntermann, C.Mattes, H.Carcache, D.A.Wagner, J.Vulpetti, A.Billich, A.Dawson, J.Kaupmann, K.Kallen, J.Stringer, R.Orain, D.

(2016) ChemMedChem 11: 2640-2648

  • DOI: https://doi.org/10.1002/cmdc.201600500
  • Primary Citation of Related Structures:  
    5M96

  • PubMed Abstract: 

    Retinoic-acid-related orphan receptor γt (RORγt) is a key transcription factor implicated in the production of pro-inflammatory Th17 cytokines, which drive a number of autoimmune diseases. Despite diverse chemical series having been reported, combining high potency with a good physicochemical profile has been a very challenging task in the RORγt inhibitor field. Based on available chemical structures and incorporating in-house knowledge, a new series of triazolo- and imidazopyridine RORγt inverse agonists was designed. In addition, replacement of the terminal cyclopentylamide metabolic soft spot by five-membered heterocycles was investigated. From our efforts, we identified an optimal 6,7,8-substituted imidazo[1,2-a]pyridine core system and a 5-tert-butyl-1,2,4-oxadiazole as cyclopentylamide replacement leading to compounds 10 ((S)-N-(8-((4-(cyclopentanecarbonyl)-3-methylpiperazin-1-yl)methyl)-7-methylimidazo[1,2-a]pyridin-6-yl)-2-methylpyrimidine-5-carboxamide) and 33 ((S)-N-(8-((4-(5-(tert-butyl)-1,2,4-oxadiazol-3-yl)-3-methylpiperazin-1-yl)methyl)-7-methylimidazo[1,2-a]pyridin-6-yl)-2-methylpyrimidine-5-carboxamide). Both derivatives showed good pharmacological potencies in biochemical and cell-based assays combined with excellent physicochemical properties, including low to medium plasma protein binding across species. Finally, 10 and 33 were shown to be active in a rodent pharmacokinetic/pharmacodynamic (PK/PD) model after oral gavage at 15 mg kg -1 , lowering IL-17 cytokine production in ex vivo antigen recall assays.


  • Organizational Affiliation

    Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor ROR-gamma
A, B
230Homo sapiensMutation(s): 1 
Gene Names: RORCNR1F3RORGRZRG
UniProt & NIH Common Fund Data Resources
Find proteins for P51449 (Homo sapiens)
Explore P51449 
Go to UniProtKB:  P51449
PHAROS:  P51449
GTEx:  ENSG00000143365 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51449
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
Q6Y BindingDB:  5M96 IC50: 13 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free:  0.208 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.017α = 90
b = 100.017β = 90
c = 115.686γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
XSCALEdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted Q6YClick on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2016-12-14 
  • Deposition Author(s): Kallen, J.

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 1.1: 2016-12-28
    Changes: Database references
  • Version 2.0: 2018-12-19
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2024-05-08
    Changes: Data collection, Database references