4FM8

Crystal Structure of BACE with Compound 12a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Spirocyclic sulfamides as beta-secretase 1 (BACE-1) inhibitors for the treatment of Alzheimer's disease: utilization of structure based drug design, WaterMap, and CNS penetration studies to identify centrally efficacious inhibitors.

Brodney, M.A.Barreiro, G.Ogilvie, K.Hajos-Korcsok, E.Murray, J.Vajdos, F.Ambroise, C.Christoffersen, C.Fisher, K.Lanyon, L.Liu, J.Nolan, C.E.Withka, J.M.Borzilleri, K.A.Efremov, I.Oborski, C.E.Varghese, A.O'Neill, B.T.

(2012) J Med Chem 55: 9224-9239

  • DOI: 10.1021/jm3009426
  • Primary Citation of Related Structures:  
    4FM7, 4FM8

  • PubMed Abstract: 
  • β-Secretase 1 (BACE-1) is an attractive therapeutic target for the treatment and prevention of Alzheimer's disease (AD). Herein, we describe the discovery of a novel class of BACE-1 inhibitors represented by sulfamide 14g, using a medicinal chemistry strategy to optimize central nervous system (CNS) penetration by minimizing hydrogen bond donors (HBDs) and reducing P-glycoprotein (P-gp) mediated efflux ...

    β-Secretase 1 (BACE-1) is an attractive therapeutic target for the treatment and prevention of Alzheimer's disease (AD). Herein, we describe the discovery of a novel class of BACE-1 inhibitors represented by sulfamide 14g, using a medicinal chemistry strategy to optimize central nervous system (CNS) penetration by minimizing hydrogen bond donors (HBDs) and reducing P-glycoprotein (P-gp) mediated efflux. We have also taken advantage of the combination of structure based drug design (SBDD) to guide the optimization of the sulfamide analogues and the in silico tool WaterMap to explain the observed SAR. Compound 14g is a potent inhibitor of BACE-1 with excellent permeability and a moderate P-gp liability. Administration of 14g to mice produced a significant, dose-dependent reduction in central Aβ(X-40) levels at a free drug exposure equivalent to the whole cell IC(50) (100 nM). Furthermore, studies of the P-gp knockout mouse provided evidence that efflux transporters affected the amount of Aβ lowering versus that observed in wild-type (WT) mouse at an equivalent dose.


    Related Citations: 
    • High yield expression of human BACE constructs in Eschericia coli for refolding, purification, and high resolution diffracting crystal forms.
      Tomasselli, A.G., Paddock, D.J., Emmons, T.L., Mildner, A.M., Leone, J.W., Lull, J.M., Cialdella, J.I., Prince, D.B., Fischer, H.D., Heinrikson, R.L., Benson, T.E.
      (2008) Protein Pept Lett 15: 131

    Organizational Affiliation

    Department of Neuroscience, Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States. michael.a.brodney@pfizer.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A404Homo sapiensMutation(s): 0 
Gene Names: BACE1BACEKIAA1149
EC: 3.4.23.46
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
PHAROS:  P56817
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0UQ (Subject of Investigation/LOI)
Query on 0UQ

Download Ideal Coordinates CCD File 
B [auth A](5R,7S)-1-(3-fluorophenyl)-3,7-dimethyl-8-[3-(propan-2-yloxy)benzyl]-2-thia-1,3,8-triazaspiro[4.5]decane 2,2-dioxide
C24 H32 F N3 O3 S
CVPXZTQJPHYLAQ-YADARESESA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
0UQ BindingDB:  4FM8 IC50: min: 1800, max: 2400 (nM) from 2 assay(s)
PDBBind:  4FM8 IC50: 2400 (nM) from 1 assay(s)
Binding MOAD:  4FM8 IC50: 2400 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.719α = 90
b = 103.262β = 90
c = 98.619γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2013-06-19
    Changes: Database references