8CGO | pdb_00008cgo

Structure of human butyrylcholinesterase in complex with N-{[2-(benzyloxy)-3-methoxyphenyl]methyl}-N-[3-(2-fluorophenyl)propyl]cyclobutanamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 
    0.215 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Highly selective butyrylcholinesterase inhibitors related to Amaryllidaceae alkaloids - Design, synthesis, and biological evaluation.

Pidany, F.Kroustkova, J.Al Mamun, A.Suchankova, D.Brazzolotto, X.Nachon, F.Chantegreil, F.Dolezal, R.Pulkrabkova, L.Muckova, L.Hrabinova, M.Finger, V.Kufa, M.Soukup, O.Jun, D.Jenco, J.Kunes, J.Novakova, L.Korabecny, J.Cahlikova, L.

(2023) Eur J Med Chem 252: 115301-115301

  • DOI: https://doi.org/10.1016/j.ejmech.2023.115301
  • Primary Citation Related Structures: 
    8CGO

  • PubMed Abstract: 

    Butyrylcholinesterase (BChE) is one of the most frequently implicated enzymes in the advanced stage of Alzheimer's disease (AD). As part of our endeavors to develop new drug candidates for AD, we have focused on natural template structures, namely the Amaryllidaceae alkaloids carltonine A and B endowed with high BChE selectivity. Herein, we report the design, synthesis, and in vitro evaluation of 57 novel highly selective human BChE (hBChE) inhibitors. Most synthesized compounds showed hBChE inhibition potency ranging from micromolar to low nanomolar scale. Compounds that revealed BChE inhibition below 100 nM were selected for detailed biological investigation. The CNS-targeted profile of the presented compounds was confirmed theoretically by calculating the BBB score algorithm, these data were corroborated by determining the permeability in vitro using PAMPA-assay for the most active derivatives. The study highlighted compounds 87 (hBChE IC 50  = 3.8 ± 0.2 nM) and 88 (hBChE IC 50  = 5.7 ± 1.5 nM) as the top-ranked BChE inhibitors. Compounds revealed negligible cytotoxicity for the human neuroblastoma (SH-SY5Y) and hepatocellular carcinoma (HepG2) cell lines compared to BChE inhibitory potential. A crystallographic study was performed to inspect the binding mode of compound 87, revealing essential interactions between 87 and hBChE active site. In addition, multidimensional QSAR analyses were applied to determine the relationship between chemical structures and biological activity in a dataset of designed agents. Compound 87 is a promising lead compound with potential implications for treating the late stages of AD.


  • Organizational Affiliation
    • Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, 500 05, Hradec Kralove, Czech Republic.

Macromolecule Content 

  • Total Structure Weight: 63.45 kDa 
  • Atom Count: 4,588 
  • Modeled Residue Count: 527 
  • Deposited Residue Count: 529 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cholinesterase529Homo sapiensMutation(s): 4 
Gene Names: BCHECHE1
EC: 3.1.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P06276 (Homo sapiens)
Explore P06276 
Go to UniProtKB:  P06276
PHAROS:  P06276
GTEx:  ENSG00000114200 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06276
Glycosylation
Glycosylation Sites: 6Go to GlyGen: P06276-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
B, C
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G86851RC
GlyCosmos: G86851RC
GlyGen: G86851RC
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
D, E
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB
GlyCosmos: G21290RB
GlyGen: G21290RB

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XB8
(Subject of Investigation/LOI)

Query on XB8



Download:Ideal Coordinates CCD File
I [auth A]~{N}-[3-(2-fluorophenyl)propyl]-~{N}-[(3-methoxy-2-phenylmethoxy-phenyl)methyl]cyclobutanamine
C28 H32 F N O2
KZOIYQAEEQKJSB-UHFFFAOYSA-N
SIA

Query on SIA



Download:Ideal Coordinates CCD File
J [auth A]N-acetyl-alpha-neuraminic acid
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MES

Query on MES



Download:Ideal Coordinates CCD File
H [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
L [auth A],
M [auth A],
N [auth A],
O [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
K [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
XB8 BindingDB:  8CGO Ki: 4 (nM) from 1 assay(s)
IC50: 4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free:  0.215 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.388α = 90
b = 153.388β = 90
c = 126.467γ = 90
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
PHASERphasing
MxCuBEdata collection
autoPROCdata processing
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French Ministry of Armed ForcesFranceNBC-5-C-4120

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Structure summary