The following example is shown in the text " Molecular Modeling: Basic Principles and Applications ", by Holtje & Folkers, VCH: New York, 1997.
28 different serotoninergic 5-HT2a receptor antagonists were modeled to define the pharmacophore. These antagonists can be divided into four structural subsets:
| Compound | Representative in Figure 1 | Color in Figure 1 |
|---|---|---|
| tricyclic compounds | clothiapine | red |
| 4-(phenylketo)-piperidines | altanserin | aqua |
| irindalone compounds | irindalone | green |
| butyrophenone derivatives | spiperone | purple |
FIGURE 1: Representative Serotoninergic 5-HT2a Receptor Antagonists
Confomational searches were performed for each ligand, and low-energy conformers that represent binding configurations were selected. This study utilized the "Active Analog Approach", in which conformationally constrained molecules were matched with diverse regions of highly flexible congeners Also, from comparisons of the structures of the 28 ligands, it was evident that the pharmacophore most likely included two planar or heterocyclic ring systems connected by an aliphatic or alicyclic chain with a protonable nitrogen. These structural elements of conformers were superimposed to aid in the selection of the consensus binding configurations.
FIGURE 2: Conformational Similarities of Structural Elements Derived from the Conformational Searches. Comparable structural elements of the four main groups of antagonists are color-coded and the stepwise superpositioning procedure followed is indicated. Clothiapine, irindalone, altanserin, and spiperone are shown from left to right.
Molecular Electrostatic Potentials using AM1-derived charges (AM1 is a semi-empirical quantum mechanical method) showed two slightly different electrostatic pharmacophores among the four representatives (Figure 3). In one of the two models, all of the protons at the pharmacophorically important cationic tertiary nitrogens are pointing in the same direction. In the other model, this is not the case. Assuming that this cationic protonated nitrogen involved ina hydrogen bond or electrostatic interaction with the receptor binding site, the first pharmacophore would clearly be favored.
FIGURE 3: Isopotential contours of clothiapine (upper left), altanserin (upper right), irindalone (lower left), and spiperone (lower right). blue = -1.0 kcal/mol, red = +1.0 kcal/mol, yellow = 0 kcal/mol
The hydrophilic and hydrophobic Molecular Interaction Fields (MIFs) of the antagonists show several common sites for hydrogen bonds and hydrophobic contacts.
FIGURE 4: Hydrophilic Molecular Interaction Field GRID contours fo the same molecules as shown in FIGURE 3 derived from an aliphatic hydroxyl probe. Energy contoured at -4.0 kcal/mol.
FIGURE 5: Hydrophobic Molecular Interaction Field GRID contours fo the same molecules as shown in FIGURE 3 derived from an aliphatic methyl probe. Energy contoured at -1.4 kcal/mol.
FIGURE 6: The Concensus Pharmacophore. purple = hydrophobic area, green = electron-deficient aromatic system, red = electronegative heteroatoms, pink = protonated nitrogen, blue = large planar ring system.
FIGURE 7: Receptor Map. Positions A, B, C, D, and F depict hydrophobic contacts. Position E is an ionic interaction.
FIGURE 8: Calculated Interaction Energies and Experimental Binding Affinitites
QSAR Studies of Glycogen Phosphorelase Inhibitors
EXAMPLE 3:
Modeling of the active conformation of Lobatamide A and Salicylihalamide A
EXAMPLE 4:
FGF Binding and FGF Receptor Activation by Synthetic Heparan-Derived Di- and Trisaccharides
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