Conformational analysis and pharmacophore design for selected 1-(2-pyrimidinyl)piperazine derivatives with sedative-hypnotic activity.

The conformational of selected 1-(2-pyrimidinyl)piperazine derivatives with high sedative-hypnotic activity was analysed and the model bioactive conformations were suggested. Subsequently, the pharmacophores of analysed compounds were designed. It was suggested that the pharmacophore of bioactive derivatives should be composed of 11 features that characterise the binding model of pyrimidinylpiperazine ligands to the binding site at the hypothetic receptor. This 11 feature pharmacophore was compared to three other pharmacophores designed for the selected anxiolytics (benzodiazepines and buspirone analogues) and the sedative-hypnotic agents (benzodiazepines and barbiturates). Several substantial differences between the pharmacophores were found: the number of pharmacophoric features and their distribution in 3-D space were unique for selected groups of compounds that exhibit sedative-hypnotic or anxiolytic activity.

Molecular dynamics of buspirone analogues interacting with the 5-HT1A and 5-HT2A serotonin receptors.

Three-dimensional (3-D) models of the human serotonin 5-HT1A and 5-HT2A receptors were constructed, energy refined, and used to study the interactions with a series of buspirone analogues. For both receptors, the calculations showed that the main interactions of the ligand imide moieties were with amino acids in transmembrane helix (TMH) 2 and 7, while the main interactions of the ligand aromatic moieties were with amino acids in TMH5, 6 and 7. Differences in binding site architecture in the region of highly conserved serine and tyrosine residues in TMH7 gave slightly different binding modes of the buspirone analogues at the 5-HT1A and 5-HT2A receptors. Molecular dynamics simulations of receptor-ligand interactions indicated that the buspirone analogues did not alter the interhelical hydrogen bonding patterns upon binding to the 5-HT2A receptor, while interhelical hydrogen bonds were broken and others were formed upon ligand binding to the 5-HT1A receptor. The ligand-induced changes in interhelical hydrogen bonding patterns of the 5-HT1A receptor were followed by rigid body movements of TMH2, 4 and 6 relative to each other and to the other TMHs, which may reflect the structural conversion into an active receptor structure.

Ligand induced conformational states of the 5-HT(1A) receptor.

It has been shown that G-protein coupled receptors have seven transmembrane alpha-helices, but the structural changes occurring in a G-protein coupled receptor as a response on agonist stimulus and the molecular events leading to blockade of the signal transduction by antagonists are not well understood. In the present study, the AMBER 5.0 force field was used for comparative molecular dynamics simulations of a 5-HT(1A) receptor model in the absence of ligand, in complex with a 5-HT(1A) receptor agonist (R)-8-hydroxy-2-(di-n-propylamino)tetralin [(R)-8-OH-DPAT], in complex with a selective 5-HT(1A) receptor antagonist (S)-N-tert-butyl-3-[4-(2-methoxyphenyl)piperazin-1-yl ]-2-phenylpropanamide [(S)-WAY100135], and in complex with the partial agonist, buspirone. In the simulations, the agonist induced larger conformational changes into transmembrane helix 3 and 6 than into the other helices, while the main conformational differences between the agonist bound receptor and the antagonist bound receptor were in transmembrane helix 5 and 6. During the simulations, all the three ligands constrained the helical movements compared to those observed in the receptor without any ligand.

Molecular dynamics of 5-HT1A and 5-HT2A serotonin receptors with methylated buspirone analogues.

In the present study experimentally determined ligand selectivity of three methylated buspirone analogues (denoted as MM2, MM5 and P55) towards 5-HT1A and 5-HT2A serotonin receptors was theoretically investigated on a molecular level. The relationships between the ligand structure and 5-HT1A and 5-HT2A receptor affinities were studied and the results were found to be in agreement with the available site-directed mutagenesis and binding affinity data. Molecular dynamics (MD) simulations of ligand-receptor complexes were performed for each investigated analogue, docked twice into the central cavity of 5-HT1A/5-HT2A, each time in a different orientation. Present results were compared with our previous theoretical results, obtained for buspirone and its non-methylated analogues. It was found that due to the presence of the methyl group in the piperazine ring the ligand position alters and the structure of the ligand-receptor complex is modified. Further, the positions of derivatives with pyrimidinyl aromatic moiety and quinolinyl moiety are significantly different at the 5-HT2A receptor. Thus, methylation of such derivatives alters the 3D structures of ligand-receptor complexes in different ways. The ligand-induced changes of the receptor structures were also analysed. The obtained results suggest, that helical domains of both receptors have different dynamical behaviour. Moreover, both location and topography of putative binding sites for buspirone analogues are different at 5-HT1A and 5-HT2A receptors.

Molecular modeling of buspirone-serotonin receptor interactions.

Modern concepts of buspirone activity as an anxiolytic drug are reviewed. Particular attention is focused on the molecular aspects of buspirone interactions in the phases that simulate cellular environment. Three-dimensional models of buspirone-serotonin receptor complexes are discussed as well.

Theoretical models of interactions between buspirone analogues and 5-HT1A and 5-HT2A serotonin receptor subtypes.

In present study the structure-selectivity relationship of buspirone and six of its analogues towards 5-HT1A and 5-HT2A serotonin receptors was investigated on molecular level. Molecular mechanics energy minimisation and advanced molecular dynamics (MD) simulations allowed us to perform a dynamic structural analysis of transmembrane helical domains of the human 5-HT1A and 5-HT2A receptors and investigate the ligand-induced changes of the entire structure of the ligand-receptor complex. The obtained results suggest, that helical and extracellular domains of both receptors have different topography of the putative binding sites and also different dynamical behaviour. The results of this study are consistent with experimental site-directed mutagenesis data and binding affinities of examined ligands towards both serotonin receptors.