Biomedical subjects

E Gálvez-Ruano

Publications and source records attributed to E Gálvez-Ruano.

4 recordsLinked to original sources

PubMed2001

Superimposition-based protocol as a tool for determining bioactive conformations. I. Application to ligands of the glycinergic receptor (GlyR).

The natural templates (NT) approach, which is a superimposition-based protocol that has been successfully employed in several studies, is here applied to ligands of the glycine ligand-gated ion channel receptor. Bioactive conformations for glycine and its analogs were obtained using strychnine (a natural and specific competitive antagonist) as template. Experimental evidence was used to guide the superimposition protocol. Three essential regions have been defined in strychnine's structure that serve as a pharmacophore for agonist and antagonist activities. Reasonable alignments of known ligands were found in the majority of the cases. Molecular mechanics (i.e., conformational searches for the relatively flexible ligands) and molecular dynamics (for relatively rigid ligands such as strychnine and 5,6,7,8-tetrahydro-4H-isoxazolo[3,4-d]azepin-3-ol) were used to assess the energetic accessibility of the proposed bioactive conformations.

Amino Acids↗

PubMed2001

Superimposition-based protocol as a tool for determining bioactive conformations. II. Application to the GABA(A) receptor.

The natural templates (NT) superimposition method is used to determine the pharmacophoric requirements of the A subtype of the gamma-aminobutyric acid (GABA) receptor. Bioactive conformations for antagonists and agonists are found by superimposing them on a relatively rigid alkaloid bicuculline, which itself is a competitive antagonist at this ligand-gated ion channel receptor. As has been usual in the application of this modeling method, consideration of available experimental data is the cornerstone for obtaining realistic models. The identification of two substructural fragments of bicuculline permitted classification of the ligands. Analysis of the antagonists and agonists with respect to the two substructural fragments revealed two bioactive conformations of the highly flexible GABA molecule, one of which is extended with the nonhydrogenic atoms roughly coplanar torsional angles of -37 and -179 degrees at N-C-C-C and C-C-C-C (carboxyl), respectively. The second bioactive compound is clearly non planar (torsional angles of -81 and -109 degrees at N-C-C-C and C-C-C-C (carboxyl), respectively).

Bicuculline↗

PubMed1999

A computational model of the nicotinic acetylcholine binding site.

We have derived a model of the nicotinic acetylcholine binding site. This was accomplished by using three known agonists (acetylcholine, nicotine and epibatidine) as templates around which polypeptide side chains, found to be part of the receptor cavity from published molecular biology studies, are allowed to flow freely in molecular dynamics simulations and mold themselves around these templates. The resulting supramolecular complex should thus be a complement, both in terms of steric effects as well as electronic effects, to the agonists and it should be a good estimation of the true receptor cavity structure. The shapes of those minireceptor cavities equilibrated rapidly on the simulation time scale and their structural congruence is very high, implying that a satisfactory model of the nicotinic acetylcholine binding site has been achieved. The computational methodology was internally tested against two rigid and specific antagonists (dihydro-beta-erytroidine and erysoidine), that are expected to give rise to a somewhat differently shaped binding site compared to that derived from the agonists. Using these antagonists as templates there were structural reorganizations of the initial receptor cavities leading to distinctly different cavities compared to agonists. This indicates that adequate times and temperatures were used in our computational protocols to achieve equilibrium structures for the agonists. Overall, both minireceptor geometries for agonists and antagonists are similar with the exception of one amino acid (ARG209).

Acetylcholine↗

PubMed1998

Arylpiperazines with serotonin-3 antagonist activity: a comparative molecular field analysis.

Comparative molecular field analysis (CoMFA) is applied to antagonists of the 5-HT3 receptor. Analysis is done separately on three published sets of arylpiperazines and on a combination of the three sets. d-Tubocurarine, a conformationally restricted 5-HT3 ligand, is used as a template to assist in selecting the conformation of the antagonists for CoMFA alignment. Two forms of the arylpiperazines (neutral and protonated) and three different kinds of calculated charges (Gasteiger-Hückel, AM1, and AM1 with solvation effect included) are compared. Protonated structures give better statistical results than the neutral species. The way in which charges are calculated does not greatly affect the results. In terms of molecular fields, the behavior in each separate set of compounds cannot be extrapolated to the combined set of 47 compounds. The average value of r2cv from PLS cross-validation on the combined set is 0.70 and varies between 0.56 and 0.80 depending on the orientation of the molecules in the coordinate system. The CoMFA model is tested on four compounds not in the training set: quipazine, N-methylquipazine, 4-phenyl-N-methylquipazine, and KB-6933. Mean agreement of experimental and predicted pKi values of the antagonists is 0.7 log unit. Novel structural modifications are interpreted by the CoMFA model.

Ligands↗