QSAR as a random event: criteria of predictive potential for a chance model

The CORAL software (http://www.insilico.eu/coral) was suggested as a tool to build up quantitative structure–property/activity relationships (QSPRs/QSARs). This software is based on conception “a QSPR/QSAR model should be interpreted as a random event.” This is reflection of fact: different distributions into the training set (substances involved in modeling process) and the validation set (substances, which are not known at the moment of the modeling process) give models with significant dispersion in the statistical quality of the QSPR/QSAR. Results of experiments with the software and possible ways of further improvement of this software are discussed. The most attractive new ways to estimate predictive potential of the CORAL model seem to be the following ones: (i) index of ideality of correlation and (ii) correlation contradiction index. These can be also proposed as criteria of predictive potential for arbitrary QSPR/QSAR.

     

QSAR models for ACE-inhibitor activity of tri-peptides based on representation of the molecular structure by graph of atomic orbitals and SMILES

The CORAL software (http:/www.insilico.eu/CORAL) has been examined as a tool of modeling of the angiotensin-converting enzyme-inhibitor activity of 54 tri-peptides. Three versions of the models were examined: (i) models based on the graph of atomic orbitals (GAO); (ii) models based on the simplified molecular input-line entry systems (SMILES); and (iii) hybrid models based on both GAO and SMILES. The hybrid models have provided the best prediction. The robustness of the approach has been checked with four random splits into training set and test set.     

The definition of the molecular structure for potential anti-malaria agents by the Monte Carlo method

A series of 53 endochin analogs (4(1-H)-quinolone derivatives) with anti-malarial activity against the clinically relevant multidrug resistant malarial strain TM-90-C2B has been studied. The CORAL (http://www.insilico.eu/coral) software has been used as a tool to build up the quantitative structure–activity relationships (QSAR) for the anti-malaria activity. The QSAR models were calculated with the representation of the molecular structure by simplified molecular input-line entry system and by the molecular graph of atomic orbitals. The method for splitting data into the sub-training set, the calibration set, the test set, and the validation set is suggested. Three various splits were examined. Statistical quality of models for the validation sets (which are not involved in the building up models) is good. Structural indicators (alerts) for increase and decrease of the anti-malaria activity are defined.     

The index of ideality of correlation: improvement of models for toxicity to algae

Toxicity to algae is important characteristic of substances from ecologic point of view. The CORAL software (http://www.insilico.eu/coral) gives possibility to build up model of toxicity to algae using data on the molecular architecture and experimental toxicity, without additional data on physicochemical and/or biochemical parameters. Considerable improvement of the model is observed in the case of using the index of ideality of correlation (IIC) in the role of additional criterion of predictive potential. The IIC is calculated with using of the correlation coefficient between experimental and calculated values of endpoint for the calibration set, with taking into account the positive and negative dispersions between experimental and calculated values. The best model calculated with use the IIC is characterized (the validation set) by n?=?50, r²?=?0.947, RMSE?=?0.401 whereas, model calculated without use the IIC is characterized by n?=?50, r²?=?0.805, and RMSE?=?0.539. The suggested models are built up in accordance to five OECD principles.

     

Coral: QSAR models for acute toxicity in fathead minnow (Pimephales promelas)

CORrelation And Logic (CORAL) is a software that generates quantitative structure activity relationships (QSAR) for different endpoints. This study is dedicated to the QSAR analysis of acute toxicity in Fathead minnow (Pimephales promelas). Statistical quality for the external test set is a complex function of the split (into training and test subsets), the number of epochs of the Monte Carlo optimization, and the threshold that is a criterion for dividing the correlation weights into two classes rare (blocked) and not rare (active). Computational experiments with three random splits (data on 568 compounds) indicated that this approach can satisfactorily predict the desired endpoint (the negative decimal logarithm of the 50% lethal concentration, in mmol/L, pLC₅₀). The average correlation coefficients (r²) are 0.675 ± 0.0053, 0.824 ± 0.0242, 0.787 ± 0.0101 for subtraining, calibration, and test set, respectively. The average standard errors of estimation (s) are 0.837 ± 0.021, 0.555 ± 0.047, 0.606 ± 0.049 for subtraining, calibration, and test set, respectively. The CORAL software together with three random splits into subtraining, calibration, and test sets can be downloaded on the Internet ( http://www.insilico.eu/coral/ ). © 2012 Wiley Periodicals, Inc.     

Side chain flexibility and the pore dimensions in the GABA<Subscript>A</Subscript> receptor

Permeation of ions through open channels and their accessibility to pore-targeting drugs depend on the pore cross-sectional dimensions, which are known only for static X-ray and cryo-EM structures. Here, we have built homology models of the closed, open and desensitized α₁β₂γ₂ GABA_A receptor (GABA_AR). The models are based, respectively, on the X-ray structure of α₃ glycine receptor (α₃ GlyR), cryo-EM structure of α₁ GlyR and X-ray structure of β₃ GABA_AR. We employed Monte Carlo energy minimizations to explore how the pore lumen may increase due to repulsions of flexible side chains from a variable-diameter electroneutral atom (an expanding sphere) pulled through the pore. The expanding sphere computations predicted that the pore diameter averaged along the permeation pathway is larger by approximately 3 Å than that computed for the models with fixed sidechains. Our models predict three major pore constrictions located at the levels of ?2′, 9′ and 20′ residues. Residues around the ?2′ and 9′ rings are known to form the desensitization and activation gates of GABA_AR. Our computations predict that the 20′ ring may also serve as GABA_AR gate whose physiological role is unclear. The side chain flexibility of residues ?2′, 9′ and 20′ and hence the dimensions of the constrictions depend on the GABA_AR functional state.     

The GABAA-Benzodiazepine Receptor Antagonist Flumazenil Abolishes the Anxiolytic Effects of the Active Constituents of Crocus sativus L. Crocins in Rats

Anxiety is a chronic severe psychiatric disorder. Crocins are among the various bioactive components of the plant Crocus sativus L. (Iridaceae) and their implication in anxiety is well-documented. However, which is the mechanism of action underlying the anti-anxiety effects of crocins remains unknown. In this context, it has been suggested that these beneficial effects might be ascribed to the agonistic properties of these bioactive ingredients of saffron on the GABA type A receptor. The current experimentation was undertaken to clarify this issue in the rat. For this research project, the light/dark and the open field tests were used. A single injection of crocins (50 mg/kg, i.p., 60 min before testing) induces an anti-anxiety-like effect revealed either in the light-dark or open field tests. Acute administration of the GABA_A-benzodiazepine receptor antagonist flumazenil (10 mg/kg, i.p., 30 min before testing) abolished the above mentioned anxiolytic effects of crocins. The current findings suggest a functional interaction between crocins and the GABA_A receptor allosteric modulator flumazenil on anxiety.     

GABAA Receptor-Mediated Sleep-Promoting Effect of Saaz–Saphir Hops Mixture Containing Xanthohumol and Humulone

Hops contain flavonoids that have sedative and sleep-promoting activities such as α-acid, β-acid, and xanthohumol. In this study, the sleep-enhancing activity of a Saaz–Saphir hops mixture was measured. In the caffeine-induced insomnia model, the administration of a Saaz–Saphir mixture increased the sleep time compared to Saaz or Saphir administration alone, which was attributed to the increase in NREM sleep time by the δ-wave increase. Oral administration of the Saaz–Saphir mixture for 3 weeks increased the γ-amino butyric acid (GABA) content in the brain and increased the expression of the GABA_A receptor. As the GABA antagonists picrotoxin and bicuculline showed a decrease in sleep activity, it was confirmed that the GABA_A receptor was involved in the Saaz–Saphir mixture activity. In addition, the GABA_A receptor antagonist also reduced the sleep activity induced by xanthohumol and humulone contained in the Saaz–Saphir mixture. Therefore, xanthohumol and humulone contained in the Saaz–Saphir mixture showed sleep-promoting activity mediated by the GABA_A receptors. The mixture of the Saaz and Saphir hop varieties may thus help mitigate sleep disturbances compared to other hop varieties.     

QSAR models for biocides: The example of the prediction of Daphnia magna acute toxicity

ABSTRACT

Biocides are multi-component products used to control undesired and harmful organisms able to affect human or animal health or to damage natural and manufactured products. Because of their widespread use, aquatic and terrestrial ecosystems could be contaminated by biocides. The environmental impact of biocides is evaluated through eco-toxicological studies with model organisms of terrestrial and aquatic ecosystems. We focused on the development of in silico models for the evaluation of the acute toxicity (EC₅₀) of a set of biocides collected from different sources on the freshwater crustacean Daphnia magna, one of the most widely used model organisms in aquatic toxicology. Toxicological data specific for biocides are limited, so we developed three models for daphnid toxicity using different strategies (linear regression, random forest, Monte Carlo (CORAL)) to overcome this limitation. All models gave satisfactory results in our datasets: the random forest model showed the best results with a determination coefficient r² = 0.97 and 0.89, respectively, for the training (TS) and the validation sets (VS) while linear regression model and the CORAL model had similar but lower performance (r² = 0.83 and 0.75, respectively, for TS and VS in the linear regression model and r² = 0.74 and 0.75 for the CORAL model).     

A novel urea derivative anticonvulsant: In vivo biological evaluation,radioreceptor analysis of GABAA receptors and molecular docking studies of enantiomers

It has been experimentally established that the original new generation anticonvulsant Galodif, N-[(3-chlorophenyl)-(phenyl)methyl]urea, allosterically modulates GABA_A receptor (GABA_AR). Binding of [³H]flunitrazepam and [³H]Ro5-4864 to the benzodiazepine (BZD) site of GABA_AR in the brain of Galodif-treated rats showes an increase in receptor affinity in Scatchard Plot for Ligand Receptor binding analysis. The results of molecular docking (Schrödinger program Glide) reveal that the enantiomers of Galodif are complementary to the BZD binding site of GABA_AR; binding energy of R-Galodif is lower than that of S-Galodif (scoring GScore being –11.14 and –10.7 kcal mol^–1, respectively); R-Galodif interacts with key amino acids at the α1γ2 interface: Tyr159, Tyr209, H101 Phe77 with high model fit – dG of insert: 7.41.     

Synthesis of fluorinated analogues of the neurosteroid GABAA receptor antagonist, 17-PA

The steroid 17-PA is a GABA_A receptor antagonist which is finding use as a tool in evaluating agonistic/antagonistic activity at GABA_A receptors. Compounds with improved efficacy over 17-PA would be are advantageous for such studies. Accordingly a series of novel analogues of the neurosteroid 17-PA have been prepared and a convenient two-step route is presented which is amenable to the synthesis of analogues with electron-donating para-aromatic substituents including fluorine. However, for the meta-fluoro analogue then the original four-step route to 17-PA remains more efficient overall. The paper describes these syntheses and discusses the electronic factors which influence this synthetic chemistry.     

Theoretical approach to the pharmacophoric pattern of GABAB analogs

In order to determine the structural requirements that are important for GABA_B binding affinity, a quantum-chemical-based conformational study has been performed, followed by a similarity analysis which includes 12 GABA_B analogs. Due to the flexibility of the structures, a semigrid GABA_B analog [2RS-(5,5-dimethyl) morpholinyl-acetic acid] has been used as a template for the amonium moiety in order to help to identify the active conformation. Both in vacuo, and solvent-simulated calculations, for the physiological media modeled as water molecules, have been compared, for this analog, at ab initio (G94, 6-31+G(d,p)) and semiempirical (PM3) levels, respectively. On the basis of this comparison, the results of in vacuo PM3 calculations have been chosen for the similarity analysis. We have included, in the calculations, a group of molecules heterogeneous enough to become representative of the different families that can bind to the GABA_B receptor site. Following their comparison we report the leading characteristics that can be related to their binding capability and define a pharmacophoric pattern for GABA_B analogs. The latter is compared with the one previously found for the binding affinity at the GABA_A receptor site. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 1195–1208, 1998     

Methodological approaches for the study of GABA<Subscript>A</Subscript> receptor pharmacology and functional responses

Inhibitory GABA_A receptor ion channels are the target for a wide range of clinically-used therapeutic agents. The complex structural diversity of these ligand-gated channels, revealed by molecular cloning studies, together with increasing requirements for higher-throughput functional assays in drug discovery, has led to the development of a wide range of techniques to examine GABA_A receptor pharmacology and function. In the current article we review some of the methodologies which have contributed to the expansion of knowledge in this field. The techniques include: molecular approaches, immunoprecipitation, and immunopurification to study receptor assembly, structure, and functional expression; in situ hybridization, immunocytochemistry, and autoradiography to examine receptor distribution in native tissues; radioligand binding, site-directed mutagenesis, and electrophysiology to examine pharmacology and allosteric modulation; and patch clamp, ion flux, microphysiometry, and a variety of novel fluorescence-based technologies to examine ion-channel function. The use of gene targetting approaches in transgenic mice has also provided important insights into the role of specific GABA_A receptor subtypes in vivo. The continuing evolution of novel technologies and assay approaches with appropriate sensitivity and resolution to measure subtle modulation of GABA_A ion channels will facilitate ongoing investigation of the physiological functions of these important inhibitory receptors.