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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-SECRETASE 1
A
411Homo sapiensGene Names: BACE1 (BACE, KIAA1149)
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Go to Gene View: BACE1
Go to UniProtKB:  P56817
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
I6X
Query on I6X

Download SDF File 
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
I6XIC50: 0.2 - 2.6 nM (99) BINDINGDB
I6XIC50: 2.44 nM BINDINGMOAD
I6XIC50: 2.44 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.956α = 90.00
b = 75.910β = 90.00
c = 104.646γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
SCALAdata scaling
XDSdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

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