Crystal structure of a potent and reversible dual binding site Acetylcholinesterase chiral inhibitor

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

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This is version 1.4 of the entry. See complete history


Chiral Separation, X-ray Structure, and Biological Evaluation of a Potent and Reversible Dual Binding Site AChE Inhibitor.

Catto, M.Pisani, L.de la Mora, E.Belviso, B.D.Mangiatordi, G.F.Pinto, A.Palma, A.Denora, N.Caliandro, R.Colletier, J.P.Silman, I.Nicolotti, O.Altomare, C.D.

(2020) ACS Med Chem Lett 11: 869-876

  • DOI: https://doi.org/10.1021/acsmedchemlett.9b00656
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Acetylcholinesterase (AChE) inhibitors (AChEIs) still remain the leading therapeutic options for the symptomatic treatment of cognitive deficits associated with mild-to-moderate Alzheimer's disease. The search for new AChEIs benefits from well-established knowledge of the molecular interactions of selective AChEIs, such as donepezil and related dual binding site inhibitors. Starting from a previously disclosed coumarin-based inhibitor (±)- cis - 1 , active as racemate in the nanomolar range toward AChE, we proceeded on a double track by (i) achieving chiral resolution of the enantiomers of 1 by HPLC and (ii) preparing two close achiral analogues of 1 , i.e., compounds 4 and 6 . An eudismic ratio as high as 20 was observed for the (-) enantiomer of cis - 1 . The X-ray crystal structure of the complex between the (-)- cis - 1 eutomer (coded as MC1420 ) and T. californica AChE was determined at 2.8 Å, and docking calculation results suggested that the eutomer in (1 R ,3 S ) absolute configuration should be energetically more favored in binding the enzyme than the eutomer in (1 S ,3 R ) configuration. The achiral analogues 4 and 6 were less effective in inhibiting AChE compared to (±)- cis - 1 , but interestingly butylamide 4 emerged as a potent inhibitor of butyrylcholinesterase (BChE).

  • Organizational Affiliation

    Department of Pharmacy-Drug Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acetylcholinesterase572Tetronarce californicaMutation(s): 0 
Gene Names: ache
Find proteins for P04058 (Tetronarce californica)
Explore P04058 
Go to UniProtKB:  P04058
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04058
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
N9T (Subject of Investigation/LOI)
Query on N9T

Download Ideal Coordinates CCD File 
B [auth A](1~{R},3~{S})-~{N}-(6,7-dimethoxy-2-oxidanylidene-chromen-3-yl)-3-[(phenylmethyl)amino]cyclohexane-1-carboxamide
C25 H28 N2 O5
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
C8 H15 N O6
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.42α = 90
b = 111.42β = 90
c = 137.37γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-10
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2021-05-12
    Changes: Derived calculations, Structure summary
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references
  • Version 1.4: 2024-01-24
    Changes: Refinement description