4YBI

Crystal structure of BACE with amino thiazine inhibitor LY2811376


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Robust central reduction of amyloid-beta in humans with an orally available, non-peptidic beta-secretase inhibitor.

May, P.C.Dean, R.A.Lowe, S.L.Martenyi, F.Sheehan, S.M.Boggs, L.N.Monk, S.A.Mathes, B.M.Mergott, D.J.Watson, B.M.Stout, S.L.Timm, D.E.Smith Labell, E.Gonzales, C.R.Nakano, M.Jhee, S.S.Yen, M.Ereshefsky, L.Lindstrom, T.D.Calligaro, D.O.Cocke, P.J.Greg Hall, D.Friedrich, S.Citron, M.Audia, J.E.

(2011) J.Neurosci. 31: 16507-16516

  • DOI: 10.1523/JNEUROSCI.3647-11.2011

  • PubMed Abstract: 
  • According to the amyloid cascade hypothesis, cerebral deposition of amyloid-β peptide (Aβ) is critical for Alzheimer's disease (AD) pathogenesis. Aβ generation is initiated when β-secretase (BACE1) cleaves the amyloid precursor protein. For more than ...

    According to the amyloid cascade hypothesis, cerebral deposition of amyloid-β peptide (Aβ) is critical for Alzheimer's disease (AD) pathogenesis. Aβ generation is initiated when β-secretase (BACE1) cleaves the amyloid precursor protein. For more than a decade, BACE1 has been a prime target for designing drugs to prevent or treat AD. However, development of such agents has turned out to be extremely challenging, with major hurdles in cell penetration, oral bioavailability/metabolic clearance, and brain access. Using a fragment-based chemistry strategy, we have generated LY2811376 [(S)-4-(2,4-difluoro-5-pyrimidin-5-yl-phenyl)-4-methyl-5,6-dihydro-4H-[1,3]thiazin-2-ylamine], the first orally available non-peptidic BACE1 inhibitor that produces profound Aβ-lowering effects in animals. The biomarker changes obtained in preclinical animal models translate into man at doses of LY2811376 that were safe and well tolerated in healthy volunteers. Prominent and long-lasting Aβ reductions in lumbar CSF were measured after oral dosing of 30 or 90 mg of LY2811376. This represents the first translation of BACE1-driven biomarker changes in CNS from preclinical animal models to man. Because of toxicology findings identified in longer-term preclinical studies, this compound is no longer progressing in clinical development. However, BACE1 remains a viable target because the adverse effects reported here were recapitulated in LY2811376-treated BACE1 KO mice and thus are unrelated to BACE1 inhibition. The magnitude and duration of central Aβ reduction obtainable with BACE1 inhibition positions this protease as a tractable small-molecule target through which to test the amyloid hypothesis in man.


    Organizational Affiliation

    Lilly Research Laboratories, Eli Lilly & Co., Indianapolis, Indiana 46285, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A, B
442Homo 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
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
4B2
Query on 4B2

Download SDF File 
Download CCD File 
A, B
(4S)-4-[2,4-difluoro-5-(pyrimidin-5-yl)phenyl]-4-methyl-5,6-dihydro-4H-1,3-thiazin-2-amine
LY2811376; BACE inhibitor
C15 H14 F2 N4 S
MJQMRGWYPNIERM-HNNXBMFYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4B2EC50: 300 nM (100) BINDINGDB
4B2IC50: 240 - 270 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.768α = 90.00
b = 90.786β = 90.00
c = 131.753γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
REFMACphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-02-18 
  • Released Date: 2015-04-01 
  • Deposition Author(s): Timm, D.E.

Revision History 

  • Version 1.0: 2015-04-01
    Type: Initial release