6TPE

Fragment-based discovery of pyrazolopyridones as JAK1 inhibitors with excellent subtype selectivity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.249 

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Literature

Fragment-Based Discovery of Pyrazolopyridones as JAK1 Inhibitors with Excellent Subtype Selectivity.

Hansen, B.B.Jepsen, T.H.Larsen, M.Sindet, R.Vifian, T.Burhardt, M.N.Larsen, J.Seitzberg, J.G.Carnerup, M.A.Jerre, A.Molck, C.Lovato, P.Rai, S.Nasipireddy, V.R.Ritzen, A.

(2020) J Med Chem 63: 7008-7032

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00359
  • Primary Citation of Related Structures:  
    6TPD, 6TPE, 6TPF

  • PubMed Abstract: 

    Herein, we report the discovery of a series of JAK1-selective kinase inhibitors with high potency and excellent JAK family subtype selectivity. A fragment screening hit 1 with a pyrazolopyridone core and a JAK1 bias was selected as the starting point for our fragment-based lead generation efforts. A two-stage strategy was chosen with the dual aims of improving potency and JAK1 selectivity: Optimization of the lipophilic ribose pocket-targeting substituent was followed by the introduction of a variety of P-loop-targeting functional groups. Combining the best moieties from both stages of the optimization afforded compound 40 , which showed excellent potency and selectivity. Metabolism studies in vitro and in vivo together with an in vitro safety evaluation suggest that 40 may be a viable lead compound for the development of highly subtype-selective JAK1 inhibitors.


  • Organizational Affiliation

    Medicinal Chemistry, GVK Biosciences Private Limited, 28 A, IDA Nacharam, Hyderabad 500076, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase JAK1
A, B
291Homo sapiensMutation(s): 0 
Gene Names: JAK1JAK1AJAK1B
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P23458 (Homo sapiens)
Explore P23458 
Go to UniProtKB:  P23458
PHAROS:  P23458
GTEx:  ENSG00000162434 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23458
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NTW (Subject of Investigation/LOI)
Query on NTW

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
2-[4-(3-methyl-6-oxidanylidene-1,7-dihydropyrazolo[3,4-b]pyridin-4-yl)cyclohexyl]ethanenitrile
C15 H18 N4 O
ZPCWQNHNXIMUEY-XYPYZODXSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A, B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.249 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.423α = 90
b = 169.558β = 90.54
c = 43.245γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-10
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references