4B00

Design and Synthesis of BACE1 Inhibitors with In Vivo Brain Reduction of beta-Amyloid Peptides (COMPOUND (R)-41)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Design and synthesis of beta-site amyloid precursor protein cleaving enzyme (BACE1) inhibitors with in vivo brain reduction of beta-amyloid peptides.

Swahn, B.M.Kolmodin, K.Karlstrom, S.von Berg, S.Soderman, P.Holenz, J.Berg, S.Lindstrom, J.Sundstrom, M.Turek, D.Kihlstrom, J.Slivo, C.Andersson, L.Pyring, D.Rotticci, D.Ohberg, L.Kers, A.Bogar, K.von Kieseritzky, F.Bergh, M.Olsson, L.L.Janson, J.Eketjall, S.Georgievska, B.Jeppsson, F.Falting, J.

(2012) J Med Chem 55: 9346-9361

  • DOI: 10.1021/jm3009025
  • Primary Citation of Related Structures:  
    4B00, 4AZY

  • PubMed Abstract: 
  • The evaluation of a series of aminoisoindoles as β-site amyloid precursor protein cleaving enzyme 1 (BACE1) inhibitors and the discovery of a clinical candidate drug for Alzheimer's disease, (S)-32 (AZD3839), are described. The improvement in permeab ...

    The evaluation of a series of aminoisoindoles as β-site amyloid precursor protein cleaving enzyme 1 (BACE1) inhibitors and the discovery of a clinical candidate drug for Alzheimer's disease, (S)-32 (AZD3839), are described. The improvement in permeability properties by the introduction of fluorine adjacent to the amidine moiety, resulting in in vivo brain reduction of Aβ40, is discussed. Due to the basic nature of these compounds, they displayed affinity for the human ether-a-go-go related gene (hERG) ion channel. Different ways to reduce hERG inhibition and increase hERG margins for this series are described, culminating in (S)-16 and (R)-41 showing large in vitro margins with BACE1 cell IC(50) values of 8.6 and 0.16 nM, respectively, and hERG IC(50) values of 16 and 2.8 μM, respectively. Several compounds were advanced into pharmacodynamic studies and demonstrated significant reduction of β-amyloid peptides in mouse brain following oral dosing.


    Organizational Affiliation

    Department of Medicinal Chemistry, AstraZeneca R&D Södertälje, SE-151 85, Södertälje, Sweden. brittmarieswahn@gmail.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-SECRETASE 1A411Homo sapiensMutation(s): 2 
Gene Names: BACE1BACEKIAA1149
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
NIH Common Fund Data Resources
PHAROS  P56817
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I6X
Query on I6X

Download CCD File 
A
5-{(1R)-3-amino-4-fluoro-1-[3-(5-prop-1-yn-1-ylpyridin-3-yl)phenyl]-1H-isoindol-1-yl}-1-ethyl-3-methylpyridin-2(1H)-one
C30 H25 F N4 O
TUGLMYZSOPKJOA-PMERELPUSA-N
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
I6XIC50:  2.440000057220459   nM  Binding MOAD
I6XIC50 :  2.440000057220459   nM  PDBBind
I6XIC50:  2.5999999046325684   nM  BindingDB
I6XIC50:  2.4000000953674316   nM  BindingDB
I6XIC50:  0.1599999964237213   nM  BindingDB
I6XIC50:  0.20000000298023224   nM  BindingDB
I6XIC50:  2   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.956α = 90
b = 75.91β = 90
c = 104.646γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2012-11-21
    Changes: Database references
  • Version 1.2: 2018-02-14
    Changes: Database references
  • Version 1.3: 2018-04-04
    Changes: Data collection