Publications

Abstract Potent and selective ligands with a nucleoside skeleton are generally thought as agonists of the human A(3) adenosine receptor (AR), however, some of them can also act as full antagonists. This work reports a Quantitative Structure-Activity Relationship (QSAR) study for predicting the binding affinity of such type of compounds towards the A(3) AR. Several different theoretical molecular descriptors, calculated only on the basis of knowledge of the molecular structure and an efficient variable selection procedure, such as forward stepwise regression, led to models with satisfactory accuracy and predictive ability. But the best-final QSAR model is based on the Molecule Representation of Structures based on Electron diffraction (3D-MoRSE) descriptors capturing a reasonable interpretation. This QSAR model is able to explain more than 85% of the variance in the experimental affinity and manifests good predictive ability as indicated by the higher Q(2)s of cross-and external-validations. The model obtained in this study may provide guidance for future design of new potent and selective human A(3) AR full antagonists with a nucleoside skeleton.

Abstract This paper presents the main results of RP-HPLC-MS and microscale NMR analysis performed on Accompanying similar to Luciferin (AsLn(x)), compounds present in extracts of the bioluminescent earthworm Fridericia heliota that display similarities with Fridericia's luciferin, the substrate of the bioluminescent reaction. Three isomers of AsLn were discovered, AsLn(1), AsLn(2) and AsLn(3), all of which present a molecular weight of 529 Da. Their UV-Vis absorption spectra show maxima at 235 nm for AsLn(1), 238 and 295 nm for AsLn(2) and 241 and 295 nm for AsLn(3). MSn fragmentation patterns suggest the existence of carboxylic acid and hydroxyl moieties, and possibly chemical groups found in other luciferins like pterin or benzothiazole. The major isomer, AsLn(2), presents an aromatic ring and alkene and alkyl moieties. These luciferin-like compounds can be used as models that could give further insights into the structure of this newly discovered luciferin.

Abstract Methamphetamine (METH) is a powerful stimulant drug of abuse that has steadily gained popularity worldwide. It is known that METH is highly neurotoxic and causes irreversible damage of brain cells leading to neurological and psychiatric abnormalities. Recent studies suggested that METH-induced neurotoxicity might also result from its ability to compromise blood-brain barrier (BBB) function. Due to the crucial role of BBB in the maintenance of brain homeostasis and protection against toxic molecules and pathogenic organisms, its dysfunction could have severe consequences. In this study, we investigated the effect of an acute high dose of METH (30 mg/kg) on BBB permeability after different time points and in different brain regions. For that, young adult mice were sacrificed 1 h, 24 h or 72 h post-METH administration. METH increased BBB permeability, but this effect was detected only at 24 h after administration, being therefore a transitory effect. Interestingly, we also found that the hippocampus was the most susceptible brain region to METH, comparing to frontal cortex and striatum. Moreover, in an attempt to identify the key players in METH-induced BBB dysfunction we further investigated potential alterations in tight junction (TJ) proteins and matrix metalloproteinase-9 (MMP-9). METH was able to decrease the protein levels of zonula occludens (ZO)-1, claudin-5 and occludin in the hippocampus 24 h post-injection, and increased the activity and immunoreactivity of MMP-9. The pre-treatment with BB-94 (30 mg/kg), a matrix metalloproteinase inhibitor, prevented the METH-induced increase in MMP-9 immunoreactivity in the hippocampus. Overall, the present data demonstrate that METH transiently increases the BBB permeability in the hippocampus, which can be explained by alterations on TJ proteins and MMP-9.

Abstract A convenient, new, and effective protocol for a rapid synthesis of different substituted 3-arylcoumarins is reported. The developed synthetic route involves Pd-catalyzed cross-coupling reaction, using a catalytic complex Pd-salen. Under these conditions, a series of different substituted boronic acids have been successfully reacted with a coumarin halide to afford the coupling products in good yields.

Abstract A fluorescent hybrid cadmium sulfide quantum dots (QDs) nanocomposites assembled in a porous phosphate heterostructures (PPH) functionalized with mercaptopropyl (PPH-SH) and propionitrile (PPH-CN) where synthesised in water and show high stability. Both materials, show fluorescence in the 450700 nm wavelength range but the PPH-SH-CdS is about five times more fluorescent than PPH-CN-CdS. The maximum emission wavelengths of the resulting materials are 576 nm (PPH-SH-CdS) and 616 nm (PPH-CN-CdS) and show Stokes shifts higher than 300 nm. The nanocomposites were characterized by TEM. EDS, FT-IR, XRD and fluorescence. These materials are suitable for fingerprint analysis.

Abstract There are several indices that provide an indication of different types on the performance of QSAR classification models, being the area under a Receiver Operating Characteristic (ROC) curve still the most powerful test to overall assess such performance. All ROC related parameters can be calculated for both the training and test sets, but, nevertheless, neither of them constitutes an absolute indicator of the classification performance by themselves. Moreover, one of the biggest drawbacks is the computing time needed to obtain the area under the ROC curve, which naturally slows down any calculation algorithm. The present study proposes two new parameters based on distances in a ROC curve for the selection of classification models with an appropriate balance in both training and test sets, namely the following: the ROC graph Euclidean distance (ROCED) and the ROC graph Euclidean distance corrected with Fitness Function (FIT(lambda)) (ROCFIT). The behavior of these indices was observed through the study on the mutagenicity for four genotoxicity end points of a number of nonaromatic halogenated derivatives. It was found that the ROCED parameter gets a better balance between sensitivity and specificity for both the training and prediction sets than other indices such as the Matthews correlation coefficient, the Wilk's lambda, or parameters like the area under the ROC curve. However, when the ROCED parameter was used, the follow-on linear discriminant models showed the lower statistical significance. But the other parameter, ROCFIT, maintains the ROCED capabilities while improving the significance of the models due to the inclusion of FIT(lambda)).

Abstract Cationic liposomes have been proposed as biocompatible gene delivery vectors, able to overcome the barriers imposed by cell membranes. Besides lipids, other surfactant molecules have been successfully used in the composition of gene carriers. In the present work, we used a Gemini surfactant, represented by the general structure [C(14)H(29)(CH(3))(2)N(+)(CH(2))(2)N(+)(CH(3))(2)C(14)H(29)]2Br(-) and herein designated 14-2-14, to prepare cationic gene carriers, both as the sole component and in combination with neutral helper lipids, cholesterol and DOPE. The effectiveness of three Gemini-based formulations, namely neat 14-2-14, 14-2-14:Chol (1:1 molar ratio) and 14-2-14:Chol:DOPE (2:1:1 molar ratio), to mediate gene delivery was evaluated in DNA mixtures of +/- charge ratios ranging from 1/1 to 12/1. After ruling out cytotoxicity as responsible for the differences observed in the transfection competence, structural and physical properties of the vector were investigated, using several techniques. The size and surface charge density (zeta potential) of surfactant-based structures were determined by conventional techniques and the thermotropic behaviour of aqueous dispersions of surfactant/lipid/DNA formulations was monitored by fluorescence polarization of DPH and DPH-PA probes. The capacity of lipoplexes to interact with membrane-mimicking lipid bilayers was evaluated, using the PicoGreen assay and a FRET technique. Our data indicate inefficiency of the neat 14-2-14 formulation for gene delivery, which could result from the large dimensions of the particles and/or from its relative incompetence to release DNA upon interaction with anionic lipids. The addition of cholesterol or cholesterol and DOPE conferred to Gemini-based gene carrier transfection activity at specific ranges of +/- charge ratios. Fluorescence polarization data suggest that an order parameter within a specific range was apparently needed for complexes to display maximal transfection efficiency. The transfection-competent formulations showed to be efficiently destabilized by interaction with different anionic and zwitterionic bilayers, including those containing PS and cardiolipin. These data are discussed in terms of the potential of these formulations to address different intracellular targets.

Abstract The detection of nitroaromatic compounds, best known as raw materials in explosives preparations, is important in many fields including environmental science, public security and forensics. CdSe quantum dots capped with PAMAM-G(4) dendrimer were synthetized in water and used for the detection of trace amounts of three nitroaromatic compounds: 4-methoxy-2-nitrophenol (MNP), 2-amine-5chloro-1,3-dinitrobenzene (ACNB) and 3-methoxy-4-nitrobenzoic acid (MNB). To increase the apparent water solubility of these compounds alpha-cyclodextrin (alpha-CD) was used to promote the formation of inclusion complexes. The studied nitroaromatic compounds (plus alpha-CD) significantly quenched the fluorescence intensity of the nanocomposite with linear Stern-Volmer plots. The Stern-Volmer constants (standard deviation in parenthesis) were: MNB, K(SV) = 65(5) x 10(4) M(-1); ACNB, K(SV) = 19(2) x 10(4) M(-1); and, MNP, K(SV) =33(1) x 10(2) M(-1). These constants suggest the formation of a ground state complex between the nitroaromatric compounds and the sensor which confers a relatively high analytical sensitivity. The detection sensibilities are about 0.01 mg L(-1) for MNB and ACNB and about 0.1 mg L(-1) for MNP. No interferences or small interferences are observed for trinitrotoluene [K(SV) =10(2) x 10(2) x M(-1)], 2,4-dinitrotoluene [K(SV) = 20(3) x 10 M(-1)], 2,6-dinitrotoluene [K(SV) = 11(4) x 10 M(-1)] and nitrobenzene [K(SV) = 2(1) x 10(3) x M(-1)].

Abstract Today, emerging and increasing resistance to antibiotics has become a threat to public health worldwide. Antimicrobial peptides have unique action mechanisms making them an attractive therapeutic prospect to be applied against resistant bacteria. However, the major drawback is related with their high hemolytic activity which cancels out the safety requirements for a human antibiotic. Therefore, additional efforts are needed to develop new antimicrobial peptides that possess a greater potency for bacterial cells and less or no toxicity over erythrocytes. In this paper, we introduce a practical approach to simultaneously deal with these two conflicting properties. The convergence of machine learning techniques and desirability theory allowed us to derive a simple, predictive, and interpretable multicriteria classification rule for simultaneously handling the antibacterial and hemolytic properties of a set of cyclic beta-hairpin cationic peptidomimetics (C beta-HCPs). The multicriteria classification rule exhibited a prediction accuracy of about 80% on training and external validation sets. Results from an additional concordance test have shown an excellent agreement between the multicriteria classification rule predictions and the predictions from independent classifiers for complementary antibacterial and hemolytic activities, respectively, evidencing the reliability of the multicriteria classification rule. The rule was also consistent with the general mode of action of cationic peptides pointing out its biophysical relevance. We also propose a multicriteria virtual screening strategy based on the joint use of the multicriteria classification rule, desirability, similarity, and chemometrics concepts. The ability of such a virtual screening strategy to prioritize selective (nonhemolytic) antibacterial C beta-HCPs was assessed and challenged for their predictivity regarding the training, validation, and overall data. In doing so, we were able to rank a selective antibacterial C beta-HCP earlier than a biologically inactive or nonselective antibacterial C beta-HCP with a probability of ca. 0.9. Our results thus indicate that promising chemoinformatics tools were obtained by considering both the multicriteria classification rule and the virtual screening strategy, which could, for instance, be used to aid the discovery and development of potent and nontoxic antimicrobial peptides.

Abstract We present molecular dynamics simulations of solvated cocaine and its metabolites in water, using both the Optimized Potentials for Liquid Simulations (OPLS) force field and the same force field but with Quantum Theory of Atoms In Molecules (QTAIM) atomic charges. We focus on the microscopic aspects of solvation, e.g. hydrogen bonds, and investigate influence of partial charges applied. Hydrophobicity or hydrophicility of these molecules were analyzed in terms of solute-solvent radial distribution functions and, for their most hydrophilic atoms, by spatial density functions. These hydration studies allowed us to classify these molecules according to their total coordination numbers, from the most hydrated metabolite to least hydrated, and this trend matches the degree of each metabolite is excreted in urine of patients with a high consumption of cocaine. Finally, we observed that QTAIM charges provide a more physically reasonable description of electrostatic environment of these solvated molecules than those of OPLS charges.