Development of a 3D pharmacophore for nonspecific ligand recognition of alpha1, alpha2, alpha3, alpha5, and alpha6 containing GABA(A)/benzodiazepine receptors

Design, Synthesis, and Pharmacological Evaluation of Novel β2/3 Subunit-Selective γ-Aminobutyric Acid Type A (GABAA) Receptor Modulators

Subunit-selective modulation of γ-aminobutyric acid type A receptors (GABA_AR) is considered to exert fewer side effects compared to unselective clinically used drugs. Here, the β2/3 subunit-selective GABA_AR modulators valerenic acid (VA) and loreclezole (LOR) guided the synthesis of novel subunit-selective ligands with simplified structures. We studied their effects on GABA_ARs expressed in Xenopus laevis oocytes using two-microelectrode voltage clamp technique. Five compounds showed significantly more efficacious modulation of GABA-evoked currents than VA and LOR with retained potency and selectivity. Compound 18 [( E)-2-Cyano-3-(2,4-dichlorophenyl)but-2-enamide] induced the highest maximal modulation of GABA-induced chloride currents ( E_max: 3114 ± 242%), while 12 [( Z)-3-(2,4-dichlorophenyl)but-2-enenitrile] displayed the highest potency (EC₅₀: 13 ± 2 μM). Furthermore, in hippocampal neurons 12 facilitated phasic and tonic GABAergic inhibition, and in vivo studies revealed significantly more potent protection against pentylenetetrazole (PTZ)-induced seizures compared to VA and LOR. Collectively, compound 12 constitutes a novel, simplified, and subunit-selective GABA_AR modulator with low-dose anticonvulsant activity.

High affinity central benzodiazepine receptor ligands. Part 3: insights into the pharmacophore and pattern recognition study of intrinsic activities of pyrazolo[4,3-c]quinolin-3-ones

Novel 2-phenyl-2,5-dihydropyrazolo[4,3-c]quinolin-3-(3H)-ones (PQs) endowed with high affinity for central benzodiazepine receptor (BzR) were synthesized. In particular, 9-fluoro-2-(2-fluorophenyl)-2,5-dihydro-3H-pyrazolo[4,3-c]quinolin-3-one (2(2)) showed binding affinity in the subnanomolar concentration range and proved to be in vitro a potent antagonist. This finding allowed the nature of the hydrogen bonding receptor site H(2) to be established, as located between the N-1 nitrogen of the PQ nucleus and the ortho position of the N-2-aryl group. [35S]tert-Butylbicyclophosphorothionate ([35S]TBPS) binding assays and electrophysiological measurements of the effects on GABA-evoked Cl(-) currents at recombinant human alpha(1)beta(2)gamma(2)(L) GABA(A) receptors, expressed in Xenopus laevis oocytes, were used to assess the intrinsic activities of a large series of PQs. With the aim of extracting discriminant information and distinguishing BzR ligands with different profiles of efficacy, 51 PQ derivatives, including full and partial agonists, antagonists, and inverse agonists, were analyzed in a multidimensional chemical descriptor space, defined by the lipophilicity parameter CLOG P and 3-D molecular WHIM descriptors, by means of principal component analysis, k-nearest neighbors (k-NN) method, and linear discriminant analysis (LDA). The classification methods were applied to subsets of pairs of efficacy classes, and lipophilicity and 3-D size descriptors were detected as the discriminant variables by a stepwise linear discriminant analysis. LDA proved to be superior to k-NN, especially in classifying PQ ligands (60-84% of success in prediction ability) into categories of efficacies which were contiguous and quite overlapped in the hyperspace of variables.

Pseudoreceptor Models and 3D-QSAR for Imidazobenzodiazepines at GABAA/BzR Subtypes αxβ3γ2 [x = 1−3, 5, and 6] via Flexible Atom Receptor Model

Since benzodiazepines have been used widely in the treatment of anxiety, sleeplessness, and epilepsy, the receptor sites for the benzodiazepine are of prime importance. Quantitative structure-activity relationship (QSAR) studies and receptor modeling via Flexible Atom Receptor Model (FLARM) for the binding affinities of a series of imidazobenzodiazepines at five recombinant receptor subtypes were carried out successfully. The 3D-QSAR models for all five receptor subtypes were examined by a set of test set and demonstrated their high predictability for affinities of imidazobenzodiazepines at five receptor subtypes. The pseudoreceptors yielded by FLARM were compared to the united pharmacophore/receptor model. The result shows that two hydrogen bonds and other regions in the united pharmacophore/receptor model are presented in the pseudoreceptors, which demonstrates the receptor modeling capability of FLARM. The models and pseudoreceptors can help design high affinity ligands on the GABA(A)/BZ receptor and understand the GABA(A) receptor.

2D conformationally sampled pharmacophore: a ligand-based pharmacophore to differentiate delta opioid agonists from antagonists

Pharmacophores are widely used for rational drug design and include those based on receptor binding sites or on known ligands. To date, ligand-based pharmacophores have typically used one or a small number of conformers of known receptor ligands. However, this method does not take into account the inherent dynamic nature of molecules, which sample a wide range of conformations, any of which could be the bound form. In the present study, molecular dynamics (MD) simulations were used as a means to sample the conformational space of ligands to include all accessible conformers at room temperature in the development of a pharmacophore. On the basis of these conformers, probability distributions of selected distances and angles in a series of delta specific opioid ligands were obtained and correlated with agonist versus antagonist activities. Individually, the distributions did not allow for unique agonist and antagonist pharmacophores to be identified. However, by extending the conformational analysis to two dimensions, a 2D conformationally sampled pharmacophore (CSP) for distinguishing delta receptor agonists and antagonists was developed. Application of this model to the compound DPI2505 suggests that it may have agonist activity. It is anticipated that the CSP method, which does not require alignment of compounds during pharmacophore development, will be a useful tool for obtaining structure-function relationships of ligands particularly in systems where the receptor 3D structure is not known.