Discovery and Optimization of Pyrimidone Indoline Amide PI3Kbeta Inhibitors for the Treatment of Phosphatase and TENsin homologue (PTEN)-Deficient Cancers

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.260 

Starting Model: experimental
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Discovery and Optimization of Pyrimidone Indoline Amide Pi3Kbeta Inhibitors for the Treatment of Phosphatase and Tensin Homologue (Pten)-Deficient Cancers.

Certal, V.Carry, J.B.Halley, F.Virone-Oddos, A.Thompson, F.Filoche-Romme, B.El-Ahmad, Y.Karlsson, A.Charrier, V.Delorme, C.Rak, A.Abecassis, P.Amara, C.Vincent, L.Bonnevaux, H.Nicolas, J.Mathieu, M.Bertrand, T.Marquette, J.Michot, N.Benard, T.Perrin, M.Lemaitre, O.Guerif, S.Perron, S.Monget, S.Gruss-Leleu, F.Doerflinger, G.Guizani, H.Brollo, M.Delbarre, L.Bertin, L.Richepin, P.Loyau, V.Garcia-Echeverria, C.Lengauer, C.Schio, L.

(2014) J Med Chem 57: 903

  • DOI: https://doi.org/10.1021/jm401642q
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Compelling molecular biology publications have reported the implication of phosphoinositide kinase PI3Kβ in PTEN-deficient cell line growth and proliferation. These findings supported a scientific rationale for the development of PI3Kβ-specific inhibitors for the treatment of PTEN-deficient cancers. This paper describes the discovery of 2-[2-(2,3-dihydro-indol-1-yl)-2-oxo-ethyl]-6-morpholin-4-yl-3H-pyrimidin-4-one (7) and the optimization of this new series of active and selective pyrimidone indoline amide PI3Kβ inhibitors. 2-[2-(2-Methyl-2,3-dihydro-indol-1-yl)-2-oxo-ethyl]-6-morpholin-4-yl-3H-pyrimidin-4-one (28), identified following a carefully designed methyl scan, displayed improved physicochemical and in vitro pharmacokinetic properties. Structural biology efforts enabled the acquisition of the first X-ray cocrystal structure of p110β with the selective inhibitor compound 28 bound to the ATP site. The nonplanar binding mode described herein is consistent with observed structure-activity relationship for the series. Compound 28 demonstrated significant in vivo activity in a UACC-62 xenograft model in mice, warranting further preclinical investigation. Following successful development, compound 28 entered phase I/Ib clinical trial in patients with advanced cancer.

  • Organizational Affiliation

    Oncology Drug Discovery, §Structure Design Informatics, and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi , 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
952Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8BTI9 (Mus musculus)
Explore Q8BTI9 
Go to UniProtKB:  Q8BTI9
IMPC:  MGI:1922019
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8BTI9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on J82

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C19 H22 N4 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
J82 BindingDB:  4BFR IC50: min: 4, max: 60 (nM) from 5 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.260 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.306α = 90
b = 129.034β = 90
c = 154.898γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-15
    Type: Initial release
  • Version 1.1: 2014-02-26
    Changes: Database references
  • Version 1.2: 2019-04-24
    Changes: Data collection, Other, Source and taxonomy
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description