Docking studies of benzylidene anabaseine interactions with α7 nicotinic acetylcholine receptor (nAChR) and acetylcholine binding proteins (AChBPs): application to the design of related α7 selective ligands

Eur J Med Chem. 2011 Nov;46(11):5625-35. doi: 10.1016/j.ejmech.2011.09.033. Epub 2011 Sep 29.


AChBPs isolated from Lymnaea stagnalis (Ls), Aplysia californica (Ac) and Bulinus truncatus (Bt) have been extensively used as structural prototypes to understand the molecular mechanisms that underlie ligand-interactions with nAChRs [1]. Here, we describe docking studies on interactions of benzylidene anabaseine analogs with AChBPs and α7 nAChR. Results reveal that docking of these compounds using Glide software accurately reproduces experimentally-observed binding modes of DMXBA and of its active metabolite, in the binding pocket of Ac. In addition to the well-known nicotinic pharmacophore (positive charge, hydrogen-bond acceptor, and hydrophobic aromatic groups), a hydrogen-bond donor feature contributes to binding of these compounds to Ac, Bt, and the α7 nAChR. This is consistent with benzylidene anabaseine analogs with OH and NH(2) functional groups showing the highest binding affinity of these congeners, and the position of the ligand shown in previous X-ray crystallographic studies of ligand-Ac complexes. In the predicted ligand-Ls complex, by contrast, the ligand OH group acts as hydrogen-bond acceptor. We have applied our structural findings to optimizing the design of novel spirodiazepine and spiroimidazoline quinuclidine series. Binding and functional studies revealed that these hydrogen-bond donor containing compounds exhibit improved affinity and selectivity for the α7 nAChR subtype and demonstrate partial agonism. The gain in affinity is also due to conformational restriction, tighter hydrophobic enclosures, and stronger cation-π interactions. The use of AChBPs structure as a surrogate to predict binding affinity to α7 nAChR has also been investigated. On the whole, we found that molecular docking into Ls binding site generally scores better than when a α7 homology model, Bt or Ac crystal structure is used.

MeSH terms

  • Anabasine / analogs & derivatives*
  • Anabasine / chemistry
  • Anabasine / metabolism
  • Animals
  • Benzylidene Compounds / chemistry*
  • Carrier Proteins / chemistry
  • Carrier Proteins / metabolism*
  • Drug Design*
  • Hydrogen Bonding
  • Ligands
  • Models, Molecular*
  • Protein Conformation
  • Rats
  • Receptors, Nicotinic / chemistry
  • Receptors, Nicotinic / metabolism*
  • Substrate Specificity
  • alpha7 Nicotinic Acetylcholine Receptor


  • AChBP protein, Lymnaea
  • Benzylidene Compounds
  • Carrier Proteins
  • Chrna7 protein, rat
  • Ligands
  • Receptors, Nicotinic
  • alpha7 Nicotinic Acetylcholine Receptor
  • anabaseine
  • Anabasine