[Show abstract][Hide abstract] ABSTRACT: Time-averaged conformations of (+/-)-1-[3,4-(methylenedioxy)phenyl]-2-methylaminopropane hydrochloride (MDMA, "ecstasy") in D(2)O, and of its free base and trifluoroacetate in CDCl(3), were deduced from their (1)H NMR spectra and used to calculate their conformer distribution. Their rotational potential energy surface (PES) was calculated at the RHF/6-31G(d,p), B3LYP/6-31G(d,p), B3LYP/cc-pVDZ and AM1 levels. Solvent effects were evaluated using the polarizable continuum model. The NMR and theoretical studies showed that, in the free base, the N-methyl group and the ring are preferentially trans. This preference is stronger in the salts and corresponds to the X-ray structure of the hydrochloride. However, the energy barriers separating these forms are very low. The X-ray diffraction crystal structures of the anhydrous salt and its monohydrate differed mainly in the trans or cis relationship of the N-methyl group to the alpha-methyl, although these two forms interconvert freely in solution.
Journal of Molecular Graphics and Modelling 07/2008; 26(8):1296-305. DOI:10.1016/j.jmgm.2007.12.004 · 1.72 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Conformational analysis of famotidine (FAMO) and some analogues have been performed using AM1 calculations. In addition, Conformational analysis were done on the 2-guanidinylthiazole moiety in order to see the effect of the N-sulfamoyl fragment and the methylthioethyl chain of FAMO on the thiazole ring. The results revealed that the N6H form (the guanidinium cation) was the most stable and might therefore be the best candidate for interacting with the histamine H2-receptor. The calculations for the N6H forms of FAMO and analogues showed a strong hydrogen bond anchoring the guanidine chain in the same plane as the thiazole ring, in agreement with X-ray diffraction and 1H NMR studies.
[Show abstract][Hide abstract] ABSTRACT: The interactions between the H2 antagonists cimetidine, ranitidine and famotidine with a basic molecular model for the histamine H2 receptor have been analyzed. The calculated potential energies of the antagonist-H2 receptor complexes follow an order consistent with the published binding data, indicating that famotidine is the best H2 receptor ligand. Comparison with the interactions found for histamine and this H2 receptor model suggests that the protonated imiddazole moiety of cimetidine, the dimethylammonio moiety of protonated ranitidine and the protonated guanidinyl moiety of famotidine are bioisosteric with the protonated aliphatic amine group of histamine. Asp 98 in helix 3 appears to be the main residue for antagonist recognition, but some residues in helix 5 may be involved, apparently by serving to guide the antagonist into the binding pocket.
[Show abstract][Hide abstract] ABSTRACT: A 3D model of the canine H2 receptor was built and analysed. This model was constructed using primary sequence comparisons and three-dimensional homology building with bacteriorhodopsin serving as a template. The energy analysis of the interaction between the N3H+ form and the N1H+ form of histamine with the receptor shows that both have the same binding affinity for the H2 receptor, but only the N3H+ form provokes structural changes. The calculated potential energies are consistent with the published binding data and suggest that Asp 98 is the principal residue for ligand recognition. On the basis of sequence alignment studies we postulate that Glu 270 in helix 7 may be important for activation of the H2 receptor. Docking studies of the N3H+ folded conformation in our model show that an intramolecular hydrogen bond between N3 and the amino group of the histamine molecule is broken, and the histamine then adopts a conformation similar to the N3H+ extended form to interact optimally with the H2 receptor. Mutations were made in the H2 receptor model to mimic published experimental point mutations. The interactions of the mutated receptor models with histamine are consistent with the experimental data.