Characterization of a ligand-receptor binding event using receptor-dependent four-dimensional quantitative structure-activity relationship analysis.
Receptor-dependent four-dimensional quantitative structure-activity relationship (RD-4D-QSAR) analysis is used to map the ligand-receptor binding event characteristic of a set of 47 glucose analogue inhibitors of glycogen phosphorylase (GPb). Specifically, the geometric and energetic binding profiles are constructed, conformational changes are determined, and conformational couplings among structural units are identified for the composite set of ligand-receptor complexes. A pruned ligand-receptor model is used to estimate ligand-receptor thermodynamics. Rather than explicitly handling the large amount of structural data generated from each of the pruned ligand-receptor models, these complexes were divided into three subregions. The subregions consist of a "functional" region, the smallest region providing definitive information about inhibitor binding, and two "allosteric" regions that surround the "functional" region and are based on distances from the center of the catalytic site. Maximum information on inhibitor binding and/or inhibitor-receptor conformational changes is extracted from each of these subregions. The key sites for inhibitor binding and conformational changes in GPb are presented as grid cell occupancy descriptors (GCODs), which can be both numerically and graphically represented. An induced conformational change in both the inhibitor and the binding site of GPb occurs in a distinct manner for each complex. The inter-relationships (correlations) between GCODs from different regions are identified and probed. Such correlations validate the ligand-receptor interactions identified from the "functional" region. A long-range network of conformational associations involving ligands and the receptor is also found by exploring correlations among the GCODs for the set of inhibitors.
Pan
Dahua
D
Laboratory of Molecular Modeling and Design (M/C 781), College of Pharmacy, The University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612-7231, USA.
Liu
Jianzhong
J
Senese
Craig
C
Hopfinger
Anton J
AJ
Tseng
Yufeng
Y
D000495:Allosteric Site; D001665:Binding Sites; D004791:Enzyme Inhibitors / Q000737:chemistry; D008024:Ligands; D008958:Models, Molecular; D008968:Molecular Conformation; D010763:Phosphorylase b / Q000037:antagonists & inhibitors / Q000737:chemistry; D011485:Protein Binding; D021281:Quantitative Structure-Activity Relationship
D004791:Enzyme Inhibitors; D008024:Ligands; D010763:Phosphorylase b