Molecular modeling of the interactions of glutamate carboxypeptidase II with its potent NAAG-based inhibitors.
Glutamate carboxypeptidase II (GCPII, NAALADase, or NAAG peptidase) is a catalytic zinc metallopeptidase. Its extracellular domain hydrolyzes the abundant neuropeptide, N-acetyl-L-aspartyl-L-glutamate (NAAG), to produce N-acetylaspartate and glutamate following the synaptic release of this transmitter. Thus, GCPII influences the extracellular concentrations of both glutamate and NAAG. NAAG activates group II metabotropic glutamate receptors, and activation of this receptor has been found to protect against anoxia-induced excitotoxic nerve cell death. In contrast, high levels of glutamate can be neurotoxic. Thus, GCPII is a potential therapeutic target for the reduction of excitotoxic levels of glutamate and enhancement of extracellular NAAG. To explore the structural basis of the interaction between GCPII and its inhibitors, we modeled the three-dimensional structure of the GCPII extracellular domain using a homology modeling approach. On the basis of the GCPII model, the structures of GCPII in complex with its potent inhibitors 2-(phosphonomethyl)pentanedioic acid (PMPA) and 4,4'-phosphinicobis(butane-1,3-dicarboxylic acid) (PBDA) were built by a computational docking method. The model of GCPII mainly consists of two alpha/beta/alpha sandwiches, between which two zinc ions are quadrivalently coordinated by the His379-Asp389-Asp455-H(2)O and the Asp389-Glu427-His555-H(2)O clusters, respectively. The ligand binding pocket is situated between these two sandwiches and is comprised of two subpockets: one is a surface-exposed highly positively charged subpocket; the other is a buried hydrophobic subpocket. The positively charged subpocket can accommodate the pharmacophore groups of inhibitor molecules (PMPA and PBDA) through the coordination of Zn(2+) with their phosphorus functionality and hydrogen-bonding interactions with Arg536, Arg538, and Ser456 (or Asn521), while the hydrophobic subpocket is engaged in hydrophobic and hydrogen-bonding interactions with the nonpharmacophore groups of PBDA. The predicted binding mode is consistent with the experimental data obtained from site-directed mutagenesis. On the basis of the predicted interaction mode, our structure-based design has led to a series of highly potent GCPII inhibitors.
Rong
Suo-Bao
SB
Department of Neurology, Department of Pharmacology, Georgetown University Medical Center, 3970 Reservoir Road, Washington, DC 20007, USA.
Zhang
Jiazhong
J
Neale
Joseph H
JH
Wroblewski
Jarda T
JT
Wang
Shaomeng
S
Kozikowski
Alan P
AP
D000595:Amino Acid Sequence; D002268:Carboxypeptidases / Q000037:antagonists & inhibitors* / Q000737:chemistry; D004151:Dipeptides / Q000737:chemistry*; D004791:Enzyme Inhibitors / Q000737:chemistry*; D043425:Glutamate Carboxypeptidase II; D005977:Glutarates / Q000737:chemistry*; D006860:Hydrogen Bonding; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009943:Organophosphorus Compounds / Q000737:chemistry*; D010721:Phosphinic Acids / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid; D055672:Static Electricity; D013329:Structure-Activity Relationship
C402107:2-(phosphonomethyl)pentanedioic acid; C465768:4,4'-phosphinicobis(butane-1,3-dicarboxylic acid); D004151:Dipeptides; D004791:Enzyme Inhibitors; D005977:Glutarates; D008024:Ligands; D009943:Organophosphorus Compounds; D010721:Phosphinic Acids; C027172:isospaglumic acid; D002268:Carboxypeptidases; D043425:Glutamate Carboxypeptidase II