Spirocyclic Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1) Inhibitors

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Spirocyclic beta-site amyloid precursor protein cleaving enzyme 1 (BACE1) inhibitors: from hit to lowering of cerebrospinal fluid (CSF) amyloid beta in a higher species.

Hunt, K.W.Cook, A.W.Watts, R.J.Clark, C.T.Vigers, G.Smith, D.Metcalf, A.T.Gunawardana, I.W.Burkard, M.Cox, A.A.Geck Do, M.K.Dutcher, D.Thomas, A.A.Rana, S.Kallan, N.C.DeLisle, R.K.Rizzi, J.P.Regal, K.Sammond, D.Groneberg, R.Siu, M.Purkey, H.Lyssikatos, J.P.Marlow, A.Liu, X.Tang, T.P.

(2013) J Med Chem 56: 3379-3403

  • DOI: https://doi.org/10.1021/jm4002154
  • Primary Citation of Related Structures:  
    4JOO, 4JP9, 4JPC, 4JPE

  • PubMed Abstract: 

    A hallmark of Alzheimer's disease is the brain deposition of amyloid beta (Aβ), a peptide of 36-43 amino acids that is likely a primary driver of neurodegeneration. Aβ is produced by the sequential cleavage of APP by BACE1 and γ-secretase; therefore, inhibition of BACE1 represents an attractive therapeutic target to slow or prevent Alzheimer's disease. Herein we describe BACE1 inhibitors with limited molecular flexibility and molecular weight that decrease CSF Aβ in vivo, despite efflux. Starting with spirocycle 1a, we explore structure-activity relationships of core changes, P3 moieties, and Asp binding functional groups in order to optimize BACE1 affinity, cathepsin D selectivity, and blood-brain barrier (BBB) penetration. Using wild type guinea pig and rat, we demonstrate a PK/PD relationship between free drug concentrations in the brain and CSF Aβ lowering. Optimization of brain exposure led to the discovery of (R)-50 which reduced CSF Aβ in rodents and in monkey.

  • Organizational Affiliation

    Array BioPharma, 3200 Walnut Street, Boulder, CO 80301, USA. hunt@arraybiopharma.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1406Homo sapiensMutation(s): 0 
Gene Names: BACE1BACEKIAA1149
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
PHAROS:  P56817
GTEx:  ENSG00000186318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 1M7

Download Ideal Coordinates CCD File 
C [auth A](4R)-2-amino-1,3',3'-trimethyl-7'-(pyrimidin-5-yl)-3',4'-dihydro-2'H-spiro[imidazole-4,1'-naphthalen]-5(1H)-one
C19 H21 N5 O
Query on NI

Download Ideal Coordinates CCD File 
Binding Affinity Annotations 
IDSourceBinding Affinity
1M7 BindingDB:  4JPE IC50: min: 48, max: 138 (nM) from 2 assay(s)
EC50: min: 27, max: 53 (nM) from 2 assay(s)
PDBBind:  4JPE IC50: 48 (nM) from 1 assay(s)
Binding MOAD:  4JPE IC50: 48 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.16α = 90
b = 103.94β = 90
c = 100.56γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-10
    Type: Initial release
  • Version 1.1: 2013-10-23
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description