4FCQ

Targeting conserved water molecules: Design of 4-aryl-5-cyanopyrrolo[2,3-d]pyrimidine Hsp90 inhibitors using fragment-based screening and structure-based optimization


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.151 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Targeting conserved water molecules: Design of 4-aryl-5-cyanopyrrolo[2,3-d]pyrimidine Hsp90 inhibitors using fragment-based screening and structure-based optimization.

Davies, N.G.Browne, H.Davis, B.Drysdale, M.J.Foloppe, N.Geoffrey, S.Gibbons, B.Hart, T.Hubbard, R.Jensen, M.R.Mansell, H.Massey, A.Matassova, N.Moore, J.D.Murray, J.Pratt, R.Ray, S.Robertson, A.Roughley, S.D.Schoepfer, J.Scriven, K.Simmonite, H.Stokes, S.Surgenor, A.Webb, P.Wood, M.Wright, L.Brough, P.

(2012) Bioorg.Med.Chem. 20: 6770-6789

  • DOI: 10.1016/j.bmc.2012.08.050
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Inhibitors of the Hsp90 molecular chaperone are showing promise as anti-cancer agents. Here we describe a series of 4-aryl-5-cyanopyrrolo[2,3-d]pyrimidine ATP competitive Hsp90 inhibitors that were identified following structure-driven optimization o ...

    Inhibitors of the Hsp90 molecular chaperone are showing promise as anti-cancer agents. Here we describe a series of 4-aryl-5-cyanopyrrolo[2,3-d]pyrimidine ATP competitive Hsp90 inhibitors that were identified following structure-driven optimization of purine hits revealed by NMR based screening of a proprietary fragment library. Ligand-Hsp90 X-ray structures combined with molecular modeling led to the rational displacement of a conserved water molecule leading to enhanced affinity for Hsp90 as measured by fluorescence polarization, isothermal titration calorimetry and surface plasmon resonance assays. This displacement was achieved with a nitrile group, presenting an example of efficient gain in binding affinity with minimal increase in molecular weight. Some compounds in this chemical series inhibit the proliferation of human cancer cell lines in vitro and cause depletion of oncogenic Hsp90 client proteins and concomitant elevation of the co-chaperone Hsp70. In addition, one compound was demonstrated to be orally bioavailable in the mouse. This work demonstrates the power of structure-based design for the rapid evolution of potent Hsp90 inhibitors and the importance of considering conserved water molecules in drug design.


    Organizational Affiliation

    Vernalis Ltd., Granta Park, Great Abington, Cambridge, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heat shock protein HSP 90-alpha
A
236Homo sapiensMutation(s): 0 
Gene Names: HSP90AA1 (HSP90A, HSPC1, HSPCA)
Find proteins for P07900 (Homo sapiens)
Go to Gene View: HSP90AA1
Go to UniProtKB:  P07900
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2N6
Query on 2N6

Download SDF File 
Download CCD File 
A
4-(2,4-dimethylphenyl)-2-(methylsulfanyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile
C16 H14 N4 S
LXUVFEGNZXPXCA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2N6Ki: 195 nM (92) BINDINGDB
2N6Kd: 156 nM BINDINGMOAD
2N6Kd: 101 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.151 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.188 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 64.976α = 90.00
b = 87.957β = 90.00
c = 99.205γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2012-10-24
    Type: Initial release
  • Version 1.1: 2012-11-07
    Type: Database references