4B77

Aminoimidazoles as BACE-1 Inhibitors: From De Novo Design to Ab- lowering in Brain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Core Refinement Toward Permeable Beta-Secretase (Bace-1) Inhibitors with Low Herg Activity.

Ginman, T.Viklund, J.Malmstrom, J.Blid, J.Emond, R.Forsblom, R.Johansson, A.Kers, A.Lake, F.Sehgelmeble, F.Sterky, K.J.Bergh, M.Lindgren, A.Johansson, P.Jeppsson, F.Falting, J.Gravenfors, Y.Rahm, F.

(2013) J.Med.Chem. 56: 4181

  • DOI: 10.1021/jm3011349
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • By use of iterative design aided by predictive models for target affinity, brain permeability, and hERG activity, novel and diverse compounds based on cyclic amidine and guanidine cores were synthesized with the goal of finding BACE-1 inhibitors as a ...

    By use of iterative design aided by predictive models for target affinity, brain permeability, and hERG activity, novel and diverse compounds based on cyclic amidine and guanidine cores were synthesized with the goal of finding BACE-1 inhibitors as a treatment for Alzheimer's disease. Since synthesis feasibility had low priority in the design of the cores, an extensive synthesis effort was needed to make the relevant compounds. Syntheses of these compounds are reported, together with physicochemical properties and structure-activity relationships based on in vitro data. Four crystal structures of diverse amidines binding in the active site are deposited and discussed. Inhibitors of BACE-1 with 3 μM to 32 nM potencies in cells are shown, together with data on in vivo brain exposure levels for four compounds. The results presented show the importance of the core structure for the profile of the final compounds.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-SECRETASE 1
A
388Homo sapiensMutation(s): 0 
Gene 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
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
54M
Query on 54M

Download SDF File 
Download CCD File 
A
(5R)-5-(4-methoxyphenyl)-5-(3-pyrimidin-5-ylphenyl)-3,4-dihydropyrrol-2-amine
C21 H20 N4 O
MLDNPVIFXVSEGX-OAQYLSRUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
54MIC50: 7900 nM BINDINGMOAD
54MIC50: 7900 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.885α = 90.00
b = 75.636β = 90.00
c = 104.613γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2013-06-26
    Type: Initial release
  • Version 1.1: 2013-07-03
    Type: Database references