6GE0

Fragment-based discovery of a highly potent, orally bioavailable inhibitor which modulates the phosphorylation and catalytic activity of ERK1/2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Fragment-Based Discovery of a Potent, Orally Bioavailable Inhibitor That Modulates the Phosphorylation and Catalytic Activity of ERK1/2.

Heightman, T.D.Berdini, V.Braithwaite, H.Buck, I.M.Cassidy, M.Castro, J.Courtin, A.Day, J.E.H.East, C.Fazal, L.Graham, B.Griffiths-Jones, C.M.Lyons, J.F.Martins, V.Muench, S.Munck, J.M.Norton, D.O'Reilly, M.Palmer, N.Pathuri, P.Reader, M.Rees, D.C.Rich, S.J.Richardson, C.Saini, H.Thompson, N.T.Wallis, N.G.Walton, H.Wilsher, N.E.Woolford, A.J.Cooke, M.Cousin, D.Onions, S.Shannon, J.Watts, J.Murray, C.W.

(2018) J. Med. Chem. 61: 4978-4992

  • DOI: 10.1021/acs.jmedchem.8b00421
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Aberrant activation of the MAPK pathway drives cell proliferation in multiple cancers. Inhibitors of BRAF and MEK kinases are approved for the treatment of BRAF mutant melanoma, but resistance frequently emerges, often mediated by increased signaling ...

    Aberrant activation of the MAPK pathway drives cell proliferation in multiple cancers. Inhibitors of BRAF and MEK kinases are approved for the treatment of BRAF mutant melanoma, but resistance frequently emerges, often mediated by increased signaling through ERK1/2. Here, we describe the fragment-based generation of ERK1/2 inhibitors that block catalytic phosphorylation of downstream substrates such as RSK but also modulate phosphorylation of ERK1/2 by MEK without directly inhibiting MEK. X-ray crystallographic and biophysical fragment screening followed by structure-guided optimization and growth from the hinge into a pocket proximal to the C-α helix afforded highly potent ERK1/2 inhibitors with excellent kinome selectivity. In BRAF mutant cells, the lead compound suppresses pRSK and pERK levels and inhibits proliferation at low nanomolar concentrations. The lead exhibits tumor regression upon oral dosing in BRAF mutant xenograft models, providing a promising basis for further optimization toward clinical pERK1/2 modulating ERK1/2 inhibitors.


    Organizational Affiliation

    Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge , CB4 0QA , U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 1
A
368Homo sapiensMutation(s): 0 
Gene Names: MAPK1 (ERK2, PRKM1, PRKM2)
EC: 2.7.11.24
Find proteins for P28482 (Homo sapiens)
Go to Gene View: MAPK1
Go to UniProtKB:  P28482
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EVQ
Query on EVQ

Download SDF File 
Download CCD File 
A
2-[5-[5-chloranyl-2-(oxan-4-ylamino)pyrimidin-4-yl]-3-oxidanylidene-1~{H}-isoindol-2-yl]-~{N}-[(1~{R})-1-(3-methoxyphenyl)ethyl]ethanamide
C28 H30 Cl N5 O4
OWNMUXCNXXWVMJ-QGZVFWFLSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
A
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.880α = 90.00
b = 70.637β = 109.96
c = 60.801γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
BUSTERphasing
Aimlessdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-04-25 
  • Released Date: 2018-05-30 
  • Deposition Author(s): O'Reilly, M.

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-06-13
    Type: Data collection, Database references
  • Version 1.2: 2018-06-27
    Type: Data collection, Database references