4N00

Discovery of 7-THP chromans: BACE1 inhibitors that reduce A-beta in the CNS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of 7-tetrahydropyran-2-yl chromans: beta-site amyloid precursor protein cleaving enzyme 1 (BACE1) inhibitors that reduce amyloid beta-protein (A beta ) in the central nervous system.

Thomas, A.A.Hunt, K.W.Volgraf, M.Watts, R.J.Liu, X.Vigers, G.Smith, D.Sammond, D.Tang, T.P.Rhodes, S.P.Metcalf, A.T.Brown, K.D.Otten, J.N.Burkard, M.Cox, A.A.Do, M.K.Dutcher, D.Rana, S.DeLisle, R.K.Regal, K.Wright, A.D.Groneberg, R.Scearce-Levie, K.Siu, M.Purkey, H.E.Lyssikatos, J.P.Gunawardana, I.W.

(2014) J.Med.Chem. 57: 878-902

  • DOI: 10.1021/jm401635n

  • PubMed Abstract: 
  • In an attempt to increase selectivity vs Cathepsin D (CatD) in our BACE1 program, a series of 1,3,4,4a,10,10a-hexahydropyrano[4,3-b]chromene analogues was developed. Three different Asp-binding moieties were examined: spirocyclic acyl guanidines, ami ...

    In an attempt to increase selectivity vs Cathepsin D (CatD) in our BACE1 program, a series of 1,3,4,4a,10,10a-hexahydropyrano[4,3-b]chromene analogues was developed. Three different Asp-binding moieties were examined: spirocyclic acyl guanidines, aminooxazolines, and aminothiazolines in order to modulate potency, selectivity, efflux, and permeability. Using structure-based design, substitutions to improve binding to both the S3 and S2' sites of BACE1 were explored. An acyl guanidine moiety provided the most potent analogues. These compounds demonstrated 10-420 fold selectivity for BACE1 vs CatD, and were highly potent in a cell assay measuring Aβ1-40 production (5-99 nM). They also suffered from high efflux. Despite this undesirable property, two of the acyl guanidines achieved free brain concentrations (Cfree,brain) in a guinea pig PD model sufficient to cover their cell IC50s. Moreover, a significant reduction of Aβ1-40 in guinea pig, rat, and cyno CSF (58%, 53%, and 63%, respectively) was observed for compound 62.


    Organizational Affiliation

    Array BioPharma , 3200 Walnut Street, Boulder, Colorado 80301, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A
406Homo 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
2EX
Query on 2EX

Download SDF File 
Download CCD File 
A
(4R,4a'S,10a'S)-2-amino-8'-(2-fluoropyridin-3-yl)-1-methyl-3',4',4a',10a'-tetrahydro-1'H-spiro[imidazole-4,10'-pyrano[4,3-b]chromen]-5(1H)-one
C20 H19 F N4 O3
DWEUDIDNAOSEBW-UVFQYZLESA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2EXIC50: 9.9 nM (100) BINDINGDB
2EXIC50: 9.5 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.196 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 74.990α = 90.00
b = 103.910β = 90.00
c = 100.420γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
MOLREPphasing
REFMACrefinement
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Structure summary