Ramón García-Domenech

Charge Indexes. New Topological Descriptors

New topological descriptors, namely “charge indexes”, are presented in this paper. Their ability for the description of the molecular charge distribution is established by correlating them with the dipole moment of a heterogeneous set of hydrocarbons, as well as with the boiling temperature of alkanes and alcohols and the vaporization enthalpy of alkanes. Moreover, it is clearly demonstrated that this ability is higher than that shown by the x connectivity and Wiener indexes.

Some New Trends in Chemical Graph Theory

Unidad de Investigación de Diseño de Farmacos y Conectividad Molecular, Departamento de Quı́mica Fisica, Facultad de Farmacı́a, Universitat de València, 46100 Burjassot, València, Spain, Instituto de Tecnologia Quimica, CSIC-Universidad Politecnica de Valencia, Av. de los Naranjos s/n, 46022 València, Spain, and Dipartimento di Chimica, Università della Calabria, via P. Bucci 14/C, 87036 Rende (CS), Italy

Designing sedative/hypnotic compounds from a novel substructural graph-theoretical approach

A novel approach to computer-aided molecular design is illustrated. This approach is based on the calculation of the spectral moments of the bond adjacency matrix of graphs representing molecular structures. Spectral moments are then expressed as linear combinations of the different sub-structures present in molecules. Two series of compounds, one containing sedative/hypnotic and the other containing different classes of drugs were used to find a discriminant function with the present approach. Several compounds from the Merck Index were identified by the model as sedative/hypnotic, five of them were found in the recent literature as possessing this activity. The critical fragments, actives and inactive ones, were detected.

Pharmacological distribution diagrams: A tool for de novo drug design

Discriminant analysis applied to SAR studies using topological descriptors allows us to plot frequency distribution diagrams: a function of the number of drugs within an interval of values of discriminant function vs. these values. We make use of these representations, pharmacological distribution diagrams (PDDs), in structurally heterogeneous groups where generally they adopt skewed Gaussian shapes or present several maxima. The maxima afford intervals of discriminant function in which exists a good expectancy to find new active drugs. A set of beta-blockers with contrasted activity has been selected to test the ability of PDDs as a visualizing technique, for the identification of new beta-blocker active compounds.

Prediction of properties of chiral compounds by molecular topology

A common assumption in chemistry is that chiral behavior is associated with 3-D geometry. However, chiral information is related to symmetry, which allows the topological handling of chiral atoms by weighted graphs and the calculation of new descriptors that give a weight to the corresponding entry in the main diagonal of the topological matrix. In this study, it is demonstrated that, operating in this way, chiral topological indices are obtained that can differentiate the pharmacological activity between pairs of enantiomers. The 50% inhibitory concentration (IC50) values of the D2 dopamine receptor and the sigma receptor for a group of 3-hydroxy phenyl piperidines are specifically predicted. Moreover, the sedative character of a group of chiral barbiturates can be identified.

Topological virtual screening: a way to find new anticonvulsant drugs from chemical diversity.

A topological virtual screening (tvs) test is presented, which is capable of identifying new drug leaders with anticonvulsant activity. Molecular structures of both anticonvulsant-active and non active compounds, extracted from the Merck Index database, were represented using topological indexes. By means of the application of a linear discriminant analysis to both sets of structures, a topological anticonvulsant model (tam) was obtained, which defines a connectivity function. On the basis of this model, 41 new structures with anticonvulsant activity have been identified by a topological virtual screening.

ANTIMICROBIAL ACTIVITY CHARACTERIZATION IN A HETEROGENEOUS GROUP OF COMPOUNDS

In this work we carry out a study of pattern recognition to detect the microbiological activity in a group of heterogeneous compounds. The structural descriptors utilized are the topological connectivity indexes. The methods followed are stepwise linear discriminant analysis (linear analysis) and artificial neural network (nonlinear analysis). Although both methods are appropriate to differentiate between active and inactive compounds, the artificial neural network is, in this case, more adequate, since it shows in a test set a prediction success of 98%, versus 92% obtained with linear discriminant analysis.

New Active Drugs against Liver Stages of Plasmodium Predicted by Molecular Topology

ABSTRACT We conducted a quantitative structure-activity relationship (QSAR) study based on a database of 127 compounds previously tested against the liver stage of Plasmodium yoelii in order to develop a model capable of predicting the in vitro antimalarial activities of new compounds. Topological indices were used as structural descriptors, and their relation to antimalarial activity was determined by using linear discriminant analysis. A topological model consisting of two discriminant functions was created. The first function discriminated between active and inactive compounds, and the second identified the most active among the active compounds. The model was then applied sequentially to a large database of compounds with unknown activity against liver stages of Plasmodium. Seventeen drugs that were predicted to be active or inactive were selected for testing against the hepatic stage of P. yoelii in vitro. Antiretroviral, antifungal, and cardiotonic drugs were found to be highly active (nanomolar 50% inhibitory concentration values), and two ionophores completely inhibited parasite development. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay was performed on hepatocyte cultures for all compounds, and none of these compounds were toxic in vitro. For both ionophores, the same in vitro assay as those for P. yoelii has confirmed their in vitro activities on Plasmodium falciparum. A similar topological model was used to estimate the octanol/water partition of each compound. These results demonstrate the utility of the QSAR and molecular topology approaches for identifying new drugs that are active against the hepatic stage of malaria parasites. We also show the remarkable efficacy of some drugs that were not previously reported to have antiparasitic activity.

Anti-toxoplasma activities of 24 quinolones and fluoroquinolones in vitro : Prediction of activity by molecular topology and virtual computational techniques

ABSTRACT The apicoplast, a plastid-like organelle of Toxoplasma gondii, is thought to be a unique drug target for quinolones. In this study, we assessed the in vitro activity of quinolones againstT. gondii and developed new quantitative structure-activity relationship models able to predict this activity. The anti-Toxoplasma activities of 24 quinolones were examined by means of linear discriminant analysis (LDA) using topological indices as structural descriptors. In parallel, in vitro 50% inhibitory concentrations (IC50s) were determined in tissue culture. A multilinear regression (MLR) analysis was then performed to establish a model capable of classifying quinolones by in vitro activity. LDA and MLR analysis were applied to virtual structures to identify the influence of each atom or substituent of the quinolone ring on anti-Toxoplasma activity. LDA predicted that 20 of the 24 quinolones would be active against T. gondii. This was confirmed in vitro for most of the quinolones. Trovafloxacin, grepafloxacin, gatifloxacin, and moxifloxacin were the quinolones most potent against T. gondii, with IC50s of 0.4, 2.4, 4.1, and 5.1 mg/liter, respectively. Using MLR analysis, a good correlation was found between measured and predicted IC50s (r2 = 0.87, cross-validationr2 = 0.74). MLR analysis showed that the carboxylic group at position C-3 of the quinolone ring was not essential for anti-Toxoplasma activity. In contrast, activity was totally dependent on the presence of a fluorine at position C-6 and was enhanced by the presence of a methyl group at C-5 or an azabicyclohexane at C-7. A nucleophilic substituent at C-8 was essential for the activity of gatifloxacin and moxifloxacin.

New bronchodilators selected by molecular topology.

Molecular topology has been applied to find new lead compounds with bronchodilator activity. Among the selected compounds stands out 3-(1H-tetrazol-5yl)-9H-thioxanthene-9 -one-10,10-dioxide, anthrarobin, 9-oxo-9H-thioxantene-3-carboxylic-10,10-dioxide acid, acenocoumarol and griseofulvin, with a percentage of relaxation, at 0.1 mM, of 91, 92, 85, 69, and 74%, respectively. Theophylline shows a correspondent value of 77% (Emax = 100% at 1 mM).