Crystal Structure of Torpedo Californica Acetylcholinesterase in Complex With an (R)-Tacrine-(10)-Hupyridone Inhibitor.
See also 1zgc and AChE bivalent inhibitors
Publication Abstract from PubMed
Recently, alkylene-linked heterodimers of tacrine (1) and 5-amino-5,6,7,8-tetrahydroquinolinone (2, hupyridone) were shown to exhibit higher acetylcholinesterase (AChE) inhibition than either monomeric 1 or 2. Such inhibitors are potential drug candidates for ameliorating the cognitive decrements in early Alzheimer patients. In an attempt to understand the inhibition mechanism of one such dimer, (RS)-(+/-)-N-9-(1,2,3,4-tetrahydroacridinyl)-N'-5-[5,6,7,8-tetrahydro-2'(1 'H)-quinolinonyl]-1,10-diaminodecane [(RS)-(+/-)-3] bisoxalate, the racemate was soaked in trigonal Torpedo californica AChE (TcAChE) crystals, and the X-ray structure of the resulting complex was solved to 2.30 A resolution. Its structure revealed the 1 unit bound to the "anionic" subsite of the active site, near the bottom of the active-site gorge, as seen for the 1/TcAChE complex. Interestingly, only the (R)-enantiomer of the 2 unit was seen in the peripheral "anionic" site (PAS) at the top of the gorge, and was hydrogen-bonded to the side chains of residues belonging to an adjacent, symmetry-related AChE molecule covering the gorge entrance. When the same racemate was soaked in orthorhombic crystals of TcAChE, in which the entrance to the gorge is more exposed, the crystal structure of the corresponding complex revealed no substantial enantiomeric selectivity. This observation suggests that the apparent enantiomeric selectivity of trigonal crystals of TcAChE for (R)-3 is mainly due to crystal packing, resulting in preferential binding of one enantiomeric inhibitor both to its "host" enzyme and to its neighbor in the asymmetric unit, rather than to steric constraints imposed by the geometry of the active-site gorge.
Crystal packing mediates enantioselective ligand recognition at the peripheral site of acetylcholinesterase., Haviv H, Wong DM, Greenblatt HM, Carlier PR, Pang YP, Silman I, Sussman JL, J Am Chem Soc. 2005 Aug 10;127(31):11029-36. PMID:16076210
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
The of Torpedo californica AChE (TcAChE, EC 3.1.1.7) is located at the bottom of a gorge which contains 14 conserved aromatic residues. This active site consists of two binding subsites. First is the "catalytic anionic site" (CAS), which
involves 3 catalytic residues (colored orange) which hydrolyze the ester bond in acetylcholine (ACh). This subsite also includes the conserved residues (colored magenta) and (colored orange) which participate in ligands' recognition. Another conserved residue (colored cyan) is situated at the second binding subsite, termed the "peripheral anionic site" (PAS), ~14 Å from CAS. Therefore, ligands which can interact with both these subsites simultaneously, are more potent AChE inhibitors in comparison to compounds interacting with CAS only. One of the ways to produce such ligands is to construct a compound with two reactive moieties. These moieties should be separated by an alkyl linker of suitable length. According to this strategy, the (RS)-(±)-tacrine-(10)-hupyridone ((R)-3 or (S)-3) was designed and synthesized. It consists of ([1]; colored magenta), 10-carbon (yellow), and (red). The tacrine moiety of this inhibitor binds at the CAS, the linker spans the gorge, and the hupyridone moiety binds at the PAS.
The comparison of the (R)-3/TcAChE and tacrine/TcAChE complexes at the . A of the trigonal (R)-3/TcAChE structure ((R)-3 colored cyan, TcAChE residues interacting with (R)-3 are colored sea-green) with the crystal structure of tacrine/TcAChE (1acj; tacrine colored magenta; residues interacting with tacrine are colored pink) reveals a similar binding mode for the tacrine moiety. In both structures the tacrine ring is situated at the CAS, between the aromatic residues Trp84 and Phe330. Steric clash with the 10-carbon linker could explain the tilt observed for the Phe330 (yellow and transparent in the tacrine/TcAChE). Water molecules are shown as red spheres.
The tacrine unit of (R)-3 N forms [2] with His440 O (3.0 Å) similar to that of tacrine alone. Similarly to the tacrine/TcAChE structure the system of three water molecules at the CAS ((R)-3/TcAChE) binds the tacrine-linker N via hydrogen bonds to Ser81 O, Ser122 Oγ, and Asn85 Oδ1 (2.6-3.5 Å) .
The comparison of the (R)-3/TcAChE and hupyridone/TcAChE complexes (1h22 and 1h23) at the . of the (R)-tacrine-(10)-hupyridone ((R)-3, cyan) and (S,S)-(-)-Bis(12)-hupyridone ((S,S)-(-)-4b, orange, i.e. 12-carbon-tether-linked hupyridone dimer) and (S,S)-(-)-Bis(10)-hupyridone ((S,S)-(-)-4a, plum) complexes demonstrates the binding mode of the hupyridone moiety. TcAChE residues of symmetry-related molecule are shown in magenta. X-ray structures of TcAChE complexed with these 10- and 12-carbon-tether-linked 2 (S,S)-(-)-4a and (S,S)-(-)-4b show one moiety bound at the , the linker spanning the gorge, and the other moiety bound at the .
There are two connecting the hupyridone O to Lys11 Nζ and hupyridone N to Gln185 Oε1 of a symmetry-related molecule in the (R)-3/TcAChE complex structure. Water molecules are shown as red spheres. Another hydrogen bond connects the hupyridone O to a water molecule, which is bound to Ser286 N. Similarly, the hupyridone-PAS unit of both (-)-4a and (-)-4b forms direct and an water-mediated hydrogen bonds with the protein backbone in the PAS region.
About this Structure
1ZGB is a Single protein structure of sequence from Torpedo californica. Full crystallographic information is available from OCA.
Additional Resources
For additional information, see: Alzheimer's Disease
