Locating an antagonist in the 5-HT3 receptor binding site using modeling and radioligand binding

Structure-based 3D-QSAR studies on thiazoles as 5-HT3 receptor antagonists

Structure-based 3D-QSAR studies were performed on 20 thiazoles against their binding affinities to the 5-HT(3) receptor with comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). The thiazoles were initially docked into the binding pocket of a human 5-HT(3A) receptor homology model, constructed on the basis of the crystal structure of the snail acetylcholine binding protein (AChBP), using the GOLD program. The docked conformations were then extracted and used to build the 3D-QSAR models, with cross-validated r2omega values 0.785 and 0.744 for CoMFA and CoMSIA, respectively. An additional five molecules were used to validate the models further, giving satisfactory predictive r2 values of 0.582 and 0.804 for CoMFA and CoMSIA, respectively. The results would be helpful for the discovery of new potent and selective 5-HT(3) receptor antagonists.

Locating the carboxylate group of GABA in the homomeric rho GABA(A) receptor ligand-binding pocket

gamma-Aminobutyric acid, type A (GABA(A)) receptors, of which the GABA(C) receptor family is a subgroup, are members of the Cys loop family of neurotransmitter receptors. Homology modeling of the extracellular domain of these proteins has revealed many molecular details, but it is not yet clear how GABA is orientated in the binding pocket. Here we have examined the role of arginine residues that the homology model locates in or close to the binding site of the GABA(C) receptor (Arg-104, Arg-170, Arg-158, and Arg-249) using mutagenesis and functional studies. The data suggest that Arg-158 is critical for GABA binding and/or function; substitution with Lys, Ala, or Glu resulted in nonfunctional receptors, and modeling placed the carboxylate of GABA within 3A of this residue. Substitution of Arg-104 with Ala or Glu resulted in >10,000-fold increases in EC(50) values compared with wild type receptors, and modeling indicated a role of this residue both in binding GABA and in the structure of the binding pocket. Substitution of Arg-170 with Asp or Ala yielded nonfunctional receptors, whereas Lys caused an approximately 10-fold increase in EC(50). Arg-249 was substituted with Ala, Glu, or Asp with relatively small ( approximately 4-30-fold) changes in EC(50). These and data from other residues that the model suggested could interact with GABA (His-105, Ser-168, and Ser-243) support a location for GABA in the binding site with its carboxylate pincered between Arg-158 and Arg-104, with Arg-104, Arg-170, and Arg-249 contributing to the structure of the binding pocket through salt bridges and/or hydrogen bonds.

Mapping residues in the ligand-binding domain of the 5-HT(3) receptor onto d-tubocurarine structure

The serotonin 5-HT(3) receptor (5-HT(3)R) is a member of the cys-loop ligand-gated ion channel family. We have used the combination of site-directed mutagenesis, homology modeling of the 5-HT(3)R extracellular domain, and ligand docking simulations as a way to map the architecture of the 5-HT(3)R ligand binding domain. Mutation of Phe226 in loop C of the binding site to tyrosine (F226Y) has no effect on the apparent affinity of the competitive antagonist d-tubocurarine (dTC) for the receptor. On the other hand, replacement of Asn128 in loop A of the binding site with alanine (N128A) increases the apparent affinity of dTC by approximately 10-fold. Double-mutant cycle analysis employing a panel of dTC analogs with substitutions at various positions to identify specific points of interactions between the dTC analogs and Asn128 suggests that Asn128 makes a direct interaction with the 2'N of dTC. Molecular modeling of the 5-HT(3)R extracellular domain using the antagonist-bound conformation of the Aplysia californica acetylcholine binding protein as a template followed by ligand docking simulations produces two classes of structures of the 5-HT(3)R/dTC complex; only one of these has the 2'N of dTC positioned at Asn128 and thus is consistent with the data from this study and previously published data. The use of the rigid dTC analogs as "molecular rulers" in conjunction with double-mutant cycle analysis of mutant receptors can allow the spatial mapping of the position of various residues in the ligand-binding site.

Mutagenesis and molecular modeling reveal the importance of the 5-HT3 receptor F-loop

The 5-HT(3) receptor is a member of the Cys-loop family of ligand-gated ion channels. The extracellular domains of these proteins contain six amino acid loops (A-F) that converge to form the ligand binding site. In this study we have mutated 21 residues in or close to the 5-HT(3) receptor F-loop (Ile(192) to Gly(212)) to Ala or to a residue with similar chemical properties. Mutant receptors were expressed in HEK293 cells, and binding affinity was measured using [(3)H]granisetron. Two regions displayed decreases in binding affinity when mutated to Ala (Ile(192)-Arg(196) and Asp(204)-Ser(206)), but only one region was sensitive when mutated to chemically similar residues (Ile(192)-Val(201)). Homology modeling using acetylcholine-binding protein crystal structures with a variety of different bound ligands suggests there may be distinct movements of Trp(195) and Asp(204) upon ligand binding, indicating that these residues and their immediate neighbors have the ability to interact differently with different ligands. The models suggest predominantly lateral movement around Asp(204) and rotational movement around Trp(195), indicating the former is in a more flexible region. Overall our results are consistent with a flexible 5-HT(3) receptor F-loop with two regions that have specific but distinct roles in ligand binding.

Molecular cloning and pharmacological characterization of serotonin 5-HT(3A) receptor subtype in dog

In order to establish if the canine 5-hydroxytryptamine type 3A (5-HT(3A)) receptors share the pharmacological profile with human 5-HT(3A) receptors, we cloned and performed a molecular pharmacological characterization of the canine 5-HT(3A) receptor. The 5-HT(3A) cDNA was cloned from canine brain by polymerase chain reaction amplification. It encodes a 483 amino acid peptide that exhibits from 80% (mice) to 90% (ferrets) identity to other sequenced mammalian 5-HT(3A) receptors. The receptor agonists 5-hydroxytryptamine (5-HT) and meta-chlorophenylbiguanide (mCPBG) showed little differences between the two species, whereas 2-methyl-5-hydroxytryptamine (2-Me-5-HT) was ten times weaker at canine receptors than at human receptors. The potencies at the canine 5-HT(3) receptors were 9.9 microM (5-HT), 79 microM (2-Me-5-HT) and 0.8 microM (mCPBG). The selective, competitive receptor antagonist ondansetron was ten times more potent at human receptors compared to canine receptors (K(b)=0.9 nM), while (+)-tubocurarine was 1000-fold more potent at canine receptors (K(b)=3.0 nM) than at human receptors. Examination of the presumed ligand binding extracellular domain revealed one residue, where the canine receptor differs from all previously characterized 5-HT(3A) receptors, i.e. other species contain a conserved Trp(195), whereas the canine orthologue contains a Leu(195). To address the differences in potencies at the human and canine 5-HT(3A) receptors seen in this study, we introduced a L195W point mutation in the canine orthologue. Data showed that the 195 residue can affect receptor agonist potency and efficacy as well as antagonist potency, but did produce a pharmacological profile identical to the human orthologue. We therefore conclude that position 195 is strongly involved in the receptor-ligand interaction, but additional residues must contribute to the overall pharmacological profile.

N-terminal domains in mouse and human 5-hydroxytryptamine3A receptors confer partial agonist and antagonist properties to benzylidene analogs of anabaseine

The present study tested the hypothesis that mouse and human 5-hydroxytryptamine3A (5-HT3A) receptors may be differentially modulated by benzylidene analogs of anabaseine (BA) and that these analogs may be useful in assessing residues involved in receptor gating. Mouse and human wild-type and mouse and human chimeric 5-HT3A receptors expressed in Xenopus oocytes were evaluated with the two-electrode voltage clamp technique. Our previous studies demonstrated that 3-(2,4-dimethoxybenzylidene)-anabaseine (DMXBA) is an antagonist at the mouse wild-type 5-HT3A receptor, but that its metabolites 3-(2-hydroxy, 4-methoxybenzylidene)-anabaseine (2-OHMBA), 3-(2-methoxy, 4-hydroxybenzylidene)-anabaseine (4-OHMBA), and 3-(2,4-dihydroxybenzylidene)-anabaseine (2,4-DiOHBA) are partial agonists (J Pharmacol Exp Ther, 299: 1112-1117, 2001). In the human wild-type (HWT) 5-HT3A receptor, none of the BA compounds possessed partial agonist activity. BA compounds antagonized 1.5 microM 5-HT-mediated (EC50) responses in the HWT 5-HT3A receptor with a rank order of potency (IC50 in muM) of 2-OHMBA (1.5 +/- 0.1) > DMXBA (3.1 +/- 0.2) > 4-OHMBA (7.4 +/- 0.5) > 2,4-DiOHBA (12.8 +/- 0.7). In mouse receptor chimeras containing N-terminal human receptor orthologs, 2-OHMBA inhibited 5-HT-mediated (EC50) currents with IC50 values of 2.0 +/- 0.08 and 3.0 +/- 0.13 microM, respectively. In human receptor chimeras containing N-terminal mouse receptor orthologs, 2-OHMBA displayed partial agonist activities with EC50 values of 1.3 +/- 0.15 and 5.0 +/- 0.4 microM; efficacies were 43 and 57%, respectively. Thus, amino acids present in the distal one-third of the N terminus of mouse and human 5-HT3A receptors are necessary and sufficient to confer partial agonist or antagonist properties of 2-OHMBA.

Unbinding pathways of an agonist and an antagonist from the 5-HT3 receptor

The binding sites of 5-HT3 and other Cys-loop receptors have been extensively studied, but there are no data on the entry and exit routes of ligands for these sites. Here we have used molecular dynamics simulations to predict the pathway for agonists and antagonists exiting from the 5-HT3 receptor binding site. The data suggest that the unbinding pathway follows a tunnel at the interface of two subunits, which is approximately 8 A long and terminates approximately 20 A above the membrane. The exit routes for an agonist (5-HT) and an antagonist (granisetron) were similar, with trajectories toward the membrane and outward from the ligand binding site. 5-HT appears to form many hydrogen bonds with residues in the unbinding pathway, and experiments show that mutating these residues significantly affects function. The location of the pathway is also supported by docking studies of granisetron, which show a potential binding site for granisetron on the unbinding route. We propose that leaving the binding pocket along this tunnel places the ligands close to the membrane and prevents their immediate reentry into the binding pocket. We anticipate similar exit pathways for other members of the Cys-loop receptor family.

Interactions of anesthetics with their targets: non-specific, specific or both?

What makes a general anesthetic a general anesthetic? We shall review first what general anesthesia is all about and which drugs are being used as anesthetics. There is neither a unique definition of general anesthesia nor any consensus on how to measure it. Diverse drugs and combinations of drugs generate general anesthetic states of sometimes very different clinical quality. Yet the principal drugs are still considered to belong to the same class of 'general anesthetics'. Effective concentrations of inhalation anesthetics are in the high micromolar range and above, and even for intravenous anesthetics they do not go below the micromolar range. At these concentrations, many molecular and higher level targets are affected by inhalation anesthetics, fewer probably by intravenous anesthetics. The only physicochemical characteristic shared by anesthetics is the correlation of their anesthetic potencies with hydrophobicity. These correlations depend on the group of general anesthetics considered. In this review, anesthetic potencies for many different targets are plotted against octanol/water partition coefficients as measure of hydrophobicity. Qualitatively, similar correlations result, suggesting several but weak interactions with proteins as being characteristic of anesthetic actions. The polar interactions involved are weak, being roughly equal in magnitude to hydrophobic interactions. Generally, intravenous anesthetics are noticeably more potent than inhalation anesthetics. They differ considerably more between each other in their interactions with various targets than inhalation anesthetics do, making it difficult to come to a decision which of these should be used in future studies as representative 'prototypical general anesthetics'.