5T1U

Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging Gly230 without an Anilide Functionality

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

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Literature

Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging Gly230 without an Anilide Functionality.

Butler, C.R., Ogilvie, K., Martinez-Alsina, L., Barreiro, G., Beck, E.M., Nolan, C.E., Atchison, K., Benvenuti, E., Buzon, L., Doran, S., Gonzales, C., Helal, C.J., Hou, X., Hsu, M.H., Johnson, E.F., Lapham, K., Lanyon, L., Parris, K., O'Neill, B.T., Riddell, D., Robshaw, A., Vajdos, F., Brodney, M.A.

(2017) J Med Chem 60: 386-402

  • DOI: 10.1021/acs.jmedchem.6b01451
  • Primary Citation of Related Structures:  
    5T1U, 5T1W, 5TFT, 5TFU

  • PubMed Abstract: 

    • A growing subset of β-secretase (BACE1) inhibitors for the treatment of Alzheimer's disease (AD) utilizes an anilide chemotype that engages a key residue (Gly230) in the BACE1 binding site. Although the anilide moiety affords excellent potency, it simultaneously introduces a third hydrogen bond donor that limits brain availability and provides a potential metabolic site leading to the formation of an aniline, a structural motif of prospective safety concern ...

    A growing subset of β-secretase (BACE1) inhibitors for the treatment of Alzheimer's disease (AD) utilizes an anilide chemotype that engages a key residue (Gly230) in the BACE1 binding site. Although the anilide moiety affords excellent potency, it simultaneously introduces a third hydrogen bond donor that limits brain availability and provides a potential metabolic site leading to the formation of an aniline, a structural motif of prospective safety concern. We report herein an alternative aminomethyl linker that delivers similar potency and improved brain penetration relative to the amide moiety. Optimization of this series identified analogues with an excellent balance of ADME properties and potency; however, potential drug-drug interactions (DDI) were predicted based on CYP 2D6 affinities. Generation and analysis of key BACE1 and CYP 2D6 crystal structures identified strategies to obviate the DDI liability, leading to compound 16, which exhibits robust in vivo efficacy as a BACE1 inhibitor.

    Organizational Affiliation: 

    Molecular and Experimental Medicine, The Scripps Research Institute , 10550 Torrey Pines Road, La Jolla, California 92024, United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A415Homo sapiensMutation(s): 0 
Gene Names: BACE1, BACE, KIAA1149
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P6U
Query on P6U
Download Ideal Coordinates CCD File 
B [auth A](4S)-4-[2,4-difluoro-5-({[1-(trifluoromethyl)cyclopropyl]amino}methyl)phenyl]-4-methyl-5,6-dihydro-4H-1,3-thiazin-2-amine
C16 H18 F5 N3 S
XKONRMXLBXCJAM-AWEZNQCLSA-N		 Ligand Interaction
IOD
Query on IOD
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]		IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
P6U BindingDB:  5T1U IC50: min: 18, max: 69 (nM) from 2 assay(s)
Binding MOAD:  5T1U IC50: 69 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.497α = 90
b = 102.497β = 90
c = 171.693γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Database references