Publications

Abstract This paper is concerned with experimental and computational thermochemical studies of epsilon-caprolactam and epsilon-caprothiolactam, molecules whose flexible ring structure provides several conformational forms. The gas-phase standard enthalpy of formation at the reference temperature of 298.15 K of the two title compounds have been determined from the enthalpy of formation in the crystalline phase, derived from bomb combustion calorimetry, and from the enthalpy of sublimation, derived from Calvet microcalorimetry and Knudsen effusion techniques. The equilibrium geometries and the thermodynamic properties of three minimum energy conformers obtained with the composite G3(MP2)//B3LYP approach were used to determine the conformational composition of the two lactam derivatives, by means of Boltzmann's distribution. The computed gas-phase standard molar enthalpies of formation of epsilon-caprolactam and epsilon-caprothiolactam have been determined using hypothetical gas-phase reactions, taking into account the conformational compositions of each one of the species. This parameter together with the corresponding experimental one are compared. (C) 2019 Elsevier Ltd.

Abstract <jats:title>Abstract</jats:title><jats:p>Consensus scoring has become a commonly used strategy within structure-based virtual screening (VS) workflows with improved performance compared to those based in a single scoring function. However, no research has been devoted to analyze the worth of docking scoring functions components in consensus scoring. We implemented and tested a method that incorporates docking scoring functions components into the setting of high performance VS workflows. This method uses genetic algorithms for finding the combination of scoring components that maximizes the VS enrichment for any target. Our methodology was validated using a dataset that contains ligands and decoys for 102 targets that has been widely used in VS validation studies. Results show that our approach outperforms other methods for all targets. It also boosts the initial enrichment performance of the traditional use of whole scoring functions in consensus scoring by an average of 45%. CompScore is freely available at: <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://bioquimio.udla.edu.ec/compscore/">http://bioquimio.udla.edu.ec/compscore/</jats:ext-link></jats:p>

Abstract Molecular dynamics simulations of the electrical double layer at electrode-ionic liquid interfaces allow for molecular level interpretation of the interfacial phenomena and properties, such as differential capacitance (C). In this work, we have simulated an ionic liquid - 1-butyl-3-methylimidazolium hexafluorophosphate - at three gold surfaces, namely: Au(100), Au(110), and Au(111) surfaces. Atomic corrugation of the gold surface leads to higher C values due to the rapprochement of the surface and electrolyte charge planes. Likewise, by accounting for the shift of surface charge plane position towards the electrolyte also results in higher C values. The presented insight shows that a simple correction to the simulation data improves the agreement with the experimental data.

Abstract Background: Malaria or Paludism is a tropical disease caused by parasites of the Plasmodium genre and transmitted to humans through the bite of infected mosquitos of the Anopheles genre. This pathology is considered one of the first causes of death in tropical countries and, despite several existing therapies, they have a high toxicity. Computational methods based on Quantitative Structure-Activity Relationship studies have been widely used in drug design work flows. Objective: The main goal of the current research is to develop computational models for the identification of antimalarial hit compounds. Materials and Methods: For this, a data set suitable for the modeling of the antimalarial activity of chemical compounds was compiled from the literature and subjected to a thorough curation process. In addition, the performance of a diverse set of ensemble-based classification methodologies was evaluated and one of these ensembles was selected as the most suitable for the identification of antimalarial hits based on its virtual screening performance. Data curation was conducted to minimize noise. Among the explored ensemble-based methods, the one combining Genetic Algorithms for the selection of the base classifiers and Majority Vote for their aggregation showed the best performance. Results: Our results also show that ensemble modeling is an effective strategy for the QSAR modeling of highly heterogeneous datasets in the discovery of potential antimalarial compounds. Conclusion: It was determined that the best performing ensembles were those that use Genetic Algorithms as a method of selection of base models and Majority Vote as the aggregation method

Abstract N-(3′-Chlorophenyl)-4-oxo-4H-chromene-3-carboxamide, compound 20 (IC 50 = 403 pM), acts as noncompetitive reversible inhibitor, and N-(3′,4′-dimethylphenyl)-4-oxo-4Hchromene- 3-carboxamide, compound 27 (IC 50 = 669 pM), acts as competitive reversible inhibitor. Therefore, the following corrections to the above article are as follows. Page 5879. In the abstract, line 9, "N-(3′-chlorophenyl)-4- oxo-4H-chromene-3-carboxamide (20)" should be "N-(3′- chlorophenyl)-4-oxo-4H-chromene-3-carboxamide (27)". Page 5884. In Figure 3 "mechanism of hMAO-B inhibition by chromones 20 (A) and 27 (B)" should be "mechanism of hMAO-B inhibition by chromones 27 (A) and 20 (B)". Page 5885. Line 4, "Concerning compound 20" should be "Concerning compound 27". Page 5885. Line 6, "different concentrations of 20" should be "different concentrations of 27". Page 5885. Line 8, "As for compound 27" should be "As for compound 20". Page 5885. Line 11, "for different concentrations of compound 27" should be "for different concentrations of compound 20". Page 5885. Line 19, should be "Chromones 27 (Figure 3A) and 20 (Figure 3B)" instead of "Chromones 20 (Figure 3A) and 27 (Figure 3B)". Page 5885. Lines 23-26, should be "27 (IC 50 = 0.67 nM) displayed IC 50 and Ki values within the picomolar range, and compound 20 (IC 50 = 0.40 nM), as a noncompetitive inhibitor, also showed a Ki extremely close to its IC 50 " instead of "20 (IC 50 = 0.40 nM) displayed IC 50 and Ki values slightly different but within the picomolar range, and compound 27 (IC 50 = 0.67 nM), as a noncompetitive inhibitor, showed a Ki equal to its IC 50 ." Page 5887. In the Conclusion, line 12, "competitive IMAOB" should be "noncompetitive IMAO-B". Page 5887. In the Conclusion, line 14, "a noncompetitive IMAO-B" should be "a competitive IMAO-B". © 2018 American Chemical Society.

Abstract This work was designed to assess the potential role of silicon dioxide nanomaterial (nano-SiO2) in enhancing barley's tolerance to nickel oxide nanomaterial (nano-NiO). For this purpose, plants were grown for 14 days under nano-NiO (120 mg kg(-1)) single and co-exposure with nano-SiO2 (3 mg kg(-1)). The exposure of barley to nano-NiO caused a significant decrease in growth-related parameters and induced a negative response on the photosynthetic apparatus. However, upon nano-SiO2 co-exposure, the inhibitory effects of nano-NiO were partially reduced, with lower reductions in fresh and dry biomass, and with the recovery of the photosynthesis-related parameters. Plants growing under nano-NiO stress showed an overproduction of superoxide anion (O-2(-)), which favored the occurrence of oxidative stress and the enhancement of lipid peroxidation (LP), but the co-treatment with nano-SiO2 reverted this tendency, generally lowering or maintaining the levels of LP and stimulating the redox pathway of thiols. The evaluation of the antioxidant (AOX) system revealed that nano-NiO induced the accumulation of proline, along with a decrease in ascorbate in leaves. Furthermore, superoxide dismutase (SOD) activity was significantly enhanced and catalase (CAT) and ascorbate peroxidase (APX) seemed to have a pivotal role in H2O2 detoxification in leaves and roots, respectively. The response of the AOX system was even more prominent upon nano-SiO2 co-exposure, reinforcing the ameliorating functions of this nanomaterial. Overall, the present study highlighted the protective role of nano-SiO2 in barley plants under nano-NiO stress, possibly due to the Si-mediated protection against oxidative stress, by a more proactive performance of the plant AOX system.

Abstract The wide ranges of uses for acetophenone make it more available and expected to accumulate in the biosphere, where consequently it can threat ecosystems. To remediate this problem, the use of Solanum nigrum L. plants for the clean-up of acetophenone-contaminated sites was explored. Also, plant root and shoot biometry and metabolism where assayed to better understand the effects of this organic compound and to pinpoint possible metabolic pathways to be targeted for future manipulations for increasing this plant species' remediation efficiency. Although undergoing through some stress, detected by increases in ROS and lipid peroxidation in both organs, plants were able to rapidly eliminate all acetophenone from the nutrient solution after 7 days of exposure, being this compound mainly detoxified at the root level. Additionally, acetophenone lead to a differential metabolic response in roots and shoots, where antioxidant mechanisms where differentially activated, while nitrogen assimilation was repressed in shoots and activated in roots. These results confirm that S. nigrum is a good phytoremediation tool for acetophenone and suggest that enhancing shoot GS activity may provide more nitrogen precursors for the synthesis of thiolated proteins and glutathione to increase tolerance to acetophenone in roots and shoots, respectively.

Abstract The discovery of new chemical entities endowed with potent, selective, and reversible monoamine oxidase B inhibitory activity is a clinically relevant subject. Therefore, a small library of chromone derivatives was synthesized and screened toward human monoamine oxidase isoforms (hMAO-A and hMAO-B). The structure-activity relationships studies strengthen the importance of the amide spacer and the direct linkage of carbonyl group to the γ-pyrone ring, along with the presence of meta and para substituents in the exocyclic ring. The most potent MAO-B inhibitors were N-(3′-chlorophenyl)-4-oxo-4H-chromene-3-carboxamide (20) (IC50 = 403 pM) and N-(3′,4′-dimethylphenyl)-4-oxo-4H-chromene-3-carboxamide (27) (IC50 = 669 pM), acting as competitive and noncompetitive reversible inhibitors, respectively. Computational docking studies provided insights into enzyme-inhibitor interactions and a rationale for the observed selectivity and potency. Compound 27 stands out due to its favorable toxicological profile and physicochemical properties, which pointed toward blood-brain barrier permeability, thus being a valid candidate for subsequent animal studies. © 2016 American Chemical Society.

Abstract An alternative route is proposed for direct electrodeposition of TiO2 films. The electrochemical behaviour of Ti (IV) species in the deep eutectic solvent formed between choline chloride (ChCl) and ethylene glycol (EG) was studied by chronoamperometry and cyclic voltammetry. It was discussed that during the cathodic scan soluble subvalent TiCl chi species were formed using the eutectic system 1ChCl:2EG. Using ethylenediamine or LiF as additives it was possible to obtain a titanium dioxide thin film in the orthorhombic variant named brookite. Chronoamperometric investigations revealed a nucleation mechanism involving the simultaneous presence of 2D instantaneous nucleation process including lattice incorporation and a 3D diffusion-limited nucleation and growth process.