4BFR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.260 

wwPDB Validation 3D Report Full Report


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Literature

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: 10.1021/jm401642q

  • 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 inhib ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE 3-KINASE CATALYTIC S SUBUNIT BETA ISOFORM
A, B
952Mus musculusMutation(s): 0 
Gene Names: Pik3cb
EC: 2.7.1.153
Find proteins for Q8BTI9 (Mus musculus)
Go to UniProtKB:  Q8BTI9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J82
Query on J82

Download SDF File 
Download CCD File 
A, B
2-[2-(2-METHYL-2,3-DIHYDRO-INDOL-1-YL)-2-OXO-ETHYL]-6-MORPHOLIN-4-YL-3H-PYRIMIDIN-4-ONE
C19 H22 N4 O3
UAXHPOBBKRWJGA-ZDUSSCGKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
J82IC50: 4 - 60 nM (95) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 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 = 90.00
b = 129.034β = 90.00
c = 154.898γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
MOLREPphasing
BUSTERrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History