N-Skatyltryptamines—Dual 5-HT6R/D2R Ligands with Antipsychotic and Procognitive Potential

A series of N-skatyltryptamines was synthesized and their affinities for serotonin and dopamine receptors were determined. Compounds exhibited activity toward 5-HT_1A, 5-HT_2A, 5-HT₆, and D₂ receptors. Substitution patterns resulting in affinity/activity switches were identified and studied using homology modeling. Chosen hits were screened to determine their metabolism, permeability, hepatotoxicity, and CYP inhibition. Several D₂ receptor antagonists with additional 5-HT₆R antagonist and agonist properties were identified. The former combination resembled known antipsychotic agents, while the latter was particularly interesting due to the fact that it has not been studied before. Selective 5-HT₆R antagonists have been shown previously to produce procognitive and promnesic effects in several rodent models. Administration of 5-HT₆R agonists was more ambiguous—in naive animals, it did not alter memory or produce slight amnesic effects, while in rodent models of memory impairment, they ameliorated the condition just like antagonists. Using the identified hit compounds 15 and 18, we tried to sort out the difference between ligands exhibiting the D₂R antagonist function combined with 5-HT₆R agonism, and mixed D₂/5-HT₆R antagonists in murine models of psychosis.     

Molecular docking,dynamics simulations and 3D-QSAR modeling of arylpiperazine derivatives of 3,5-dioxo-(2H,4H)-1,2,4-triazine as 5-HT1AR agonists

Serotonin receptor, 5-HT_1AR, agonists and partial agonists have established drug candidates for psychiatric and neurologic disorders. Recently, we reported the synthesis and evaluation of arylpiperazine derivatives of 3,5-dioxo-(2H,4H)-1,2,4-triazine as 5-HT_1AR ligands. Herein, we generated a homology model of the receptor and docked the ligands against it, predicted the stability of the receptor model and complexes by molecular dynamics and generated a 3D-QSAR model for the arylpiperazine derivatives of 3,5-dioxo-(2H,4H)-1,2,4-triazine. The model suggests the hydrophobic part that arises from the aromatic region and the electron withdrawing parts play a vital role in the agonist activity of the lead molecules.     

5-HT1A receptor pharmacophores to screen for off-target activity of α1-adrenoceptor antagonists

The α₁-adrenoceptors (α₁-ARs), in particular the α_1A-AR subtype, are current therapeutic targets of choice for the treatment of urogenital conditions, such as benign prostatic hyperplasia (BPH). Due to the similarity between the transmembrane domains of the α₁-AR subtypes, and the serotonin receptor subtype 1A (5-HT_1A-R), currently used α₁-AR subtype-selective drugs to treat BPH display considerable off-target affinity for the 5-HT_1A-R, leading to side effects. We describe the construction and validation of pharmacophores for 5-HT_1A-R agonists and antagonists. Through the structural diversity of the training sets used in their development, these pharmacophores define the properties of a compound needed to bind to 5-HT_1A receptors. Using these and previously published pharmacophores in virtual screening and profiling, we have identified unique chemical compounds (hits) that fit the requirements to bind to our target, the α_1A-AR, selectively over the off-target, the 5-HT_1A-R. Selected hits have been obtained and their affinities for α_1A-AR, α_1B-AR and 5-HT_1A-R determined in radioligand binding assays, using membrane preparations which contain human receptors expressed individually. Three of the tested hits demonstrate statistically significant selectivity for α_1A-AR over 5-HT_1A-R. All seven tested hits bind to α_1A-AR, with two compounds displaying K _i values below 1 μM, and a further two K _i values of around 10 μM. The insights and knowledge gained through the development of the new 5-HT_1A-R pharmacophores will greatly aid in the design and synthesis of derivatives of our lead compound, and allow the generation of more efficacious and selective ligands.     

Molecular Structure and Affinity to 5-HT1A Receptor of Chlorophenyl(Piperazinylalkyl)Phthalimides

Abstract

X-ray crystallography, quantum-chemical calculations and conformational analysis have been employed to study chlorophenyl(piperazinylalkyl)phthalimides, potential ligands of 5-HT_1A receptor. The molecular recognition of investigated compounds by 5-HT_1Aserotonin receptor has been estimated according to their ability to inhibit the [³H8]-DPAT binding. The model for 5-HT_1A pharmacophore has been proposed based on crystal structures of N-(aryl)piperazinyl — alkylphthalimides.     

Three-dimensional Quantitative Structure-Activity Relationship Analyses of a Series of Butenolide ETA Antagonists

Two kinds of Three-dimensional Quantitative Structure-activity Relationship(3D-QSAR) methods,comparative molecular filed analysis(CoMFA) and comparative molecular similarity indices analysis (CoMSIA) ,were applied to analyze the structure-activity relationship of a series of 63 butenolide ETA selective antagonists with respect to their inhibition against human ETA receptor,The CoMFA and CoMSIA models were developed for the conceivable alignment of the molecules based on a template structure from the crystallized data.The statistical results from the initial orientation of the aligned molecules show that the 3D-QSAR model from CoMFA(q^2=0.543) is obviously superior to that from the conventional CoMSIA(q^2=0.407).In order to refine the model,all-space search (ASS) was applied to minimize the field sampling process.By rotating and translating the molecular aggregate within the grid systematically,all the possible samplings of the molecular fields were tested and subsequently the one with the highest q^2 was picked out .The comparison of the sensitivity of CoMFA and CoMSIA to different space orientation shows that the CoMFA q^2 values are more sensitive to the translations and rotations of the aligned molecules with respect to the lattice than those of CoMSIA.The best CoMFA model from ASS was further refined by the region focused technique.The high quality of the best model is indicated by the high corss-validated correlation and the prediction on the external test set.The CoMFA coefficient contour plots identify several key features that explain the wide range of activities,which may help us to design new effective ETA selective antagonists.     

Multiconformational composite molecular potential fields in the analysis of drug action. I. Methodology and first evaluation using 5-HT and histamine action as examples

Summary The quality of molecular electrostatic maps generated by non-quantum mechanical methods has been improved using extended electron distributions. Further simplification has been achieved by distilling these maps down to their energy extrema. A new means of defining surface interaction has been added and the resulting composite map has been plotted for a limited number of low-lying conformers of a series of agonists and antagonists of the H₂ and H₃ receptors and 5-HT_1A and 5-HT_1D receptors. The results from the cross-comparison of these maps indicate their ability to distinguish the specific receptor. Interesting consequences of the method are that structural overlay is irrelevant, that several conformations may contribute to the overall binding pattern and that lesser pharmacological activities may be deduced from the results.     

Synthesis of GR 125487, a selective 5-HT4 receptor antagonist

The 5-HT₄ receptor (5-HT₄R) agonists are important in treating gastrointestinal motility disorders. Their role is currently being evaluated for the treatment of cognitive and mood disorders. A selective 5-HT₄R antagonist GR 125487 is used in many biological assays to cross confirm the 5-HT₄R agonist’s activity. A practical synthesis of GR 125487 is developed so as to have it in desired quantities. The synthesis consists of seven steps starting from commercially available methyl 5-fluoroindole 3-carboxylate. The GR 125487 thus synthesized was used in blocking the activity of 5-HT₄R agonist compound in animal models of cognition.     

Binding mode similarity measures for ranking of docking poses: a case study on the adenosine A<Subscript>2A</Subscript> receptor

We report an investigation designed to explore alternative approaches for ranking of docking poses in the search for antagonists of the adenosine A_2A receptor, an attractive target for structure-based virtual screening. Calculation of 3D similarity of docking poses to crystallographic ligand(s) as well as similarity of receptor–ligand interaction patterns was consistently superior to conventional scoring functions for prioritizing antagonists over decoys. Moreover, the use of crystallographic antagonists and agonists, a core fragment of an antagonist, and a model of an agonist placed into the binding site of an antagonist-bound form of the receptor resulted in a significant early enrichment of antagonists in compound rankings. Taken together, these findings showed that the use of binding modes of agonists and/or antagonists, even if they were only approximate, for similarity assessment of docking poses or comparison of interaction patterns increased the odds of identifying new active compounds over conventional scoring.     

Homology modelling of the human adenosine A2B receptor based on X-ray structures of bovine rhodopsin, the β2-adrenergic receptor and the human adenosine A2A receptor

A three-dimensional model of the human adenosine A_2B receptor was generated by means of homology modelling, using the crystal structures of bovine rhodopsin, the β₂-adrenergic receptor, and the human adenosine A_2A receptor as templates. In order to compare the three resulting models, the binding modes of the adenosine A_2B receptor antagonists theophylline, ZM241385, MRS1706, and PSB601 were investigated. The A_2A-based model was much better able to stabilize the ligands in the binding site than the other models reflecting the high degree of similarity between A_2A and A_2B receptors: while the A_2B receptor shares about 21% of the residues with rhodopsin, and 31% with the β₂-adrenergic receptor, it is 56% identical to the adenosine A_2A receptor. The A_2A-based model was used for further studies. The model included the transmembrane domains, the extracellular and the intracellular hydrophilic loops as well as the terminal domains. In order to validate the usefulness of this model, a docking analysis of several selective and nonselective agonists and antagonists was carried out including a study of binding affinities and selectivities of these ligands with respect to the adenosine A_2A and A_2B receptors. A common binding site is proposed for antagonists and agonists based on homology modelling combined with site-directed mutagenesis and a comparison between experimental and calculated affinity data. The new, validated A_2B receptor model may serve as a basis for developing more potent and selective drugs.     

Therapeutic Potential of Highly Selective A3 Adenosine Receptor Ligands in the Central and Peripheral Nervous System

Ligands of the G_i protein-coupled adenosine A₃ receptor (A₃R) are receiving increasing interest as attractive therapeutic tools for the treatment of a number of pathological conditions of the central and peripheral nervous systems (CNS and PNS, respectively). Their safe pharmacological profiles emerging from clinical trials on different pathologies (e.g., rheumatoid arthritis, psoriasis and fatty liver diseases) confer a realistic translational potential to these compounds, thus encouraging the investigation of highly selective agonists and antagonists of A₃R. The present review summarizes information on the effect of latest-generation A₃R ligands, not yet available in commerce, obtained by using different in vitro and in vivo models of various PNS- or CNS-related disorders. This review places particular focus on brain ischemia insults and colitis, where the prototypical A₃R agonist, Cl-IB-MECA, and antagonist, MRS1523, have been used in research studies as reference compounds to explore the effects of latest-generation ligands on this receptor. The advantages and weaknesses of these compounds in terms of therapeutic potential are discussed.     

Design,Sustainable Synthesis and Biological Evaluation of a Novel Dual α2A/5-HT7 Receptor Antagonist with Antidepressant-Like Properties

The complex pathophysiology of depression, together with the limits of currently available antidepressants, has resulted in the continuous quest for alternative therapeutic strategies. Numerous findings suggest that pharmacological blockade of α₂-adrenoceptor might be beneficial for the treatment of depressive symptoms by increasing both norepinephrine and serotonin levels in certain brain areas. Moreover, the antidepressant properties of 5-HT₇ receptor antagonists have been widely demonstrated in a large set of animal models. Considering the potential therapeutic advantages in targeting both α₂-adrenoceptors and 5-HT₇ receptors, we designed a small series of arylsulfonamide derivatives of (dihydrobenzofuranoxy)ethyl piperidines as dually active ligands. Following green chemistry principles, the designed compounds were synthesized entirely using a sustainable mechanochemical approach. The identified compound 8 behaved as a potent α_2A/5-HT₇ receptor antagonist and displayed moderate-to-high selectivity over α₁-adrenoceptor subtypes and selected serotonin and dopaminergic receptors. Finally, compound 8 improved performance of mice in the forced swim test, displaying similar potency to the reference drug mirtazapine.     

A homology-based model of the human 5-HT2A receptor derived from an in silico activated G-protein coupled receptor

A homology-based model of the 5-HT_2A receptor was produced utilizing an activated form of the bovine rhodopsin (Rh) crystal structure [1,2]. In silico activation of the Rh structure was accomplished by isomerization of the 11-cis-retinal (1) chromophore, followed by constrained molecular dynamics to relax the resultant high energy structure. The activated form of Rh was then used as a structural template for development of a human 5-HT_2A receptor model. Both the 5-HT_2A receptor and Rh are members of the G-protein coupled receptor (GPCR) super-family. The resulting homology model of the receptor was then used for docking studies of compounds representing a cross-section of structural classes that activate the 5-HT_2A receptor, including ergolines, tryptamines, and amphetamines. The ligand/receptor complexes that ensued were refined and the final binding orientations were observed to be compatible with much of the data acquired through both diversified ligand design and site directed mutagenesis.     

Comparative receptor mapping of serotoninergic 5-HT3 and 5-HT4 binding sites*

The clinical use of currently available drugs acting at the5-HT₄ receptor has been hampered by their lack of selectivityover 5-HT₃ binding sites. For this reason, there is considerableinterest in the medicinal chemistry of these serotonin receptor subtypes, andsignificant effort has been made towards the discovery of potent and selectiveligands. Computer-aided conformational analysis was used to characterizeserotoninergic 5-HT₃ and 5-HT₄ receptorrecognition. On the basis of the generally accepted model of the5-HT₃ antagonist pharmacophore, we have performed a receptormapping of this receptor binding site, following the active analog approach(AAA) defined by Marshall. The receptor excluded volume was calculated as theunion of the van der Waals density maps of nine active ligands(pK_i 8.9), superimposed in pharmacophoric conformations.Six inactive analogs (pK_i < 7.0) were subsequently used todefine the essential volume, which in its turn can be used to define theregions of steric intolerance of the 5-HT₃ receptor. Five activeligands (pK_i 9.3) at 5-HT₄ receptors wereused to construct an antagonist pharmacophore for this receptor, and todetermine its excluded volume by superimposition of pharmacophoricconformations. The volume defined by the superimposition of five inactive5-HT₄ receptor analogs that possess the pharmacophoric elements(pK_i 6.6) did not exceed the excluded volume calculated forthis receptor. In this case, the inactivity may be due to the lack of positiveinteraction of the amino moiety with a hypothetical hydrophobic pocket, whichwould interact with the voluminous substituents of the basic nitrogen ofactive ligands. The difference between the excluded volumes of both receptorshas confirmed that the main difference is indeed in the basic moiety. Thus,the 5-HT₃ receptor can only accommodate small substituents inthe position of the nitrogen atom, whereas the 5-HT₄ receptorrequires more voluminous groups. Also, the basic nitrogen is located at ca.8.0 Å from the aromatic moiety in the 5-HT₄ antagonistpharmacophore, whereas this distance is ca. 7.5 Å in the5-HT₃ antagonist model. The comparative mapping of bothserotoninergic receptors has allowed us to confirm the three-componentpharmacophore accepted for the 5-HT₃ receptor, as well as topropose a steric model for the 5-HT₄ receptor binding site. Thisstudy offers structural insights to aid the design of new selective ligands,and the resulting models have received some support from the synthesis of twonew active and selective ligands: 24 (K_i(5-HT₃)= 3.7 nM; K_i(5-HT₄) > 1000 nM) and 25(K_i(5-HT₄) = 13.7 nM;K_i(5-HT₃) > 10 000 nM).     

A computational model of the 5-HT3 receptor extracellular domain: search for ligand binding sites

A three-dimensional model of the 5-HT₃ receptor extarcellular domain has been derived on the basis of the nicotinic acetylcholine receptor model recently published by Tsigelny et al. Maximum complementarity between the position and characteristics of mutated residues putatively involved in ligand interaction and the pharmacophoric elements derived by the indirect approach applied on several series of 5-HT₃ ligands have been exploited to gain insights into the ligand binding modalities and to speculate on the mechanistic role of the structural components. The analysis of the three-dimensional model allows one to distinguish among amino acids that exert key roles in ligand interactions, subunit architecture, receptor assembly and receptor dynamics. For some of these, alternative roles with respect to the ones hypothesized by experimentalists are assigned. Different binding modalities for agonists and antagonists are highlighted, and residues which probably play a role in the transduction of binding into a change in conformational state of the receptor are suggested. Received: 27 July 2000 / Accepted: 15 September 2000 / Published online: 21 December 2000     

Functional group interactions of a 5-HT3R antagonist

Background  

Lerisetron, a competitive serotonin type 3 receptor (5-HT₃R) antagonist, contains five functional groups capable of interacting with amino acids in the 5-HT₃R binding site. Site directed mutagenesis studies of the 5-HT_3AR have revealed several amino acids that are thought to form part of the binding domain of this receptor. The specific functional groups on the ligand that interact with these amino acids are, however, unknown. Using synthetic analogs of lerisetron as molecular probes in combination with site directed mutagenesis, we have identified some of these interactions and have proposed a model of the lerisetron binding site.     

New,Eco-Friendly Method for Synthesis of 3-Chlorophenyl and 1,1′-Biphenyl Piperazinylhexyl Trazodone Analogues with Dual 5-HT1A/5-HT7 Affinity and Its Antidepressant-like Activity

Serotonin 5-HT_1A and 5-HT₇ receptors play an important role in the pathogenesis and pharmacotherapy of depression. Previously identified N-hexyl trazodone derivatives, 2-(6-(4-(3-chlorophenyl)piperazin-1-yl)hexyl)-[1,2,4]triazolo[4,3-a]pyridin-3(2H)-one hydrochloride (7a·HCl), with high affinity for 5-HT_1AR and 2-(6-(4-([1,1′-biphenyl]-2-yl)piperazin-1-yl)hexyl)-[1,2,4]triazolo[4,3-a]pyridin-3(2H)-one hydrochloride (7b·HCl), a dual-acting 5-HT_1A/5-HT₇ receptor ligand, were prepared with a new microwave-assisted method. The protocol for the synthesis of 7a and 7b involved reductive alkylation under a mild reducing agent. We produced the final compounds with yield of 56–63% using ethanol or 51–56% in solvent-free conditions in 4 min. We then determined the 5-HT₇R binding mode for compounds 7a and 7b using in silico methods and assessed the preliminary ADME and safety properties (hepatotoxicity and CYP3A4 inhibition) using in vitro methods for 7a·HCl and 7b·HCl. Furthermore, we evaluated antidepressant-like activity of the dual antagonist of 5-HT_1A/5-HT₇ receptors (7b·HCl) in the forced swim test (FST) in mice. The 5-HT_1AR ligand (7a·HCl) with a much lower affinity for 5-HT₇R compared to that of 7b·HCl was tested comparatively. Both compounds showed antidepressant activity, while 5-HT_1A/5-HT₇ double antagonist 7b·HCl showed a stronger and more specific response.     

Modelling of ORL1 receptor-ligand interactions

An opioid receptor like (ORL1) receptor is one of a family of G-protein-coupled receptors (GPCR); it represents a new pharmaceutical target with extensive therapeutic potential for the regulation of important biological functions such as nociception, mood disorders, drug abuse, learning or cardiovascular control. Although the crystal structure of the inactive form of the ORL1 receptor has been determined, little is known about its activation. By using X-ray structures of the β2-adrenegic receptor in its inactive (2RH1) and active (3P0G) states as templates, inactive and active homology models of the ORL1 receptor were constructed. Structurally diverse sets of strongly binding antagonists and agonists were docked with both ORL1 receptor forms. The major receptor-ligand interactions responsible for antagonist and agonist binding were identified. Although both sets of ligands, agonists and antagonists, bind to the same region of the receptor, they occupy partially different binding pockets. Agonists bind to the inactive receptor in a slightly different manner than antagonists. This difference is more pronounced in binding to the active ORL1 receptor model and points to the amino acids at the extracellular end of TM6, suggesting that this region is important for receptor-activation.     

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-HT_1A and 5-HT_2A serotonin receptors was theoretically investigated on a molecular level. The relationships between the ligand structure and 5-HT_1A and 5-HT_2A 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-HT_1A/5-HT_2A, 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-HT_2A 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-HT_1A and 5-HT_2A receptors.     

A genetic algorithm for flexible molecular overlay and pharmacophore elucidation

Summary A genetic algorithm (GA) has been developed for the superimposition of sets of flexible molecules. Molecules are represented by a chromosome that encodes angles of rotation about flexible bonds and mappings between hydrogen-bond donor proton, acceptor lone pair and ring centre features in pairs of molecules. The molecule with the smallest number of features in the data set is used as a template, onto which the remaining molecules are fitted with the objective of maximising structural equivalences. The fitness function of the GA is a weighted combination of: (i) the number and the similarity of the features that have been overlaid in this way; (ii) the volume integral of the overlay; and (iii) the van der Waals energy of the molecular conformations defined by the torsion angles encoded in the chromosomes. The algorithm has been applied to a number of pharmacophore elucidation problems, i.e., angiotensin II receptor antagonists, Leu-enkephalin and a hybrid morphine molecule, 5-HT_1D agonists, benzodiazepine receptor ligands, 5-HT₃ antagonists, dopamine D₂ antagonists, dopamine reuptake blockers and FKBP12 ligands. The resulting pharmacophores are generated rapidly and are in good agreement with those derived from alternative means.