Cheminformatics and Materials

Research Publications

Total publications: 603

153. Computer-aided drug design approaches to study key therapeutic targets in alzheimer’s disease
Lemos, A; Melo, R; Moreira, IS; Cordeiro, MNDS
in Neuromethods, 2018, ISSN: 0893-2336,  Volume: 132, 
Book Chapter,  Indexed in: crossref, scopus 
Alzheimer’s Disease (AD) is one of the most common and complex age-related neurodegenerative disorders in elderly people. Currently there is no cure for AD, and available therapeutic alternatives only improve both cognitive and behavioral functions. For that reason, the search for anti-AD therapeutic agents with neuroprotective properties is highly demanding. Several research studies have implicated the involvement of G-Protein-Coupled Receptors (GPCRs) in diverse neurotransmitter systems that are dysregulated in AD, mainly in modulation of amyloidogenic processing of Amyloid Precursor Protein (APP) and of microtubule-associated protein tau phosphorylation and in learning and memory activities in in vivo AD models subjected to numerous behavioral procedures. In this chapter, a special focus will be given to the structure- and ligand-based in silico approaches and their applicability on the development of small molecules that target various GPCRs potentially involved in AD such as 5-hydroxytryptamine receptors, adenosine receptors, adrenergic receptors, chemokine receptors, histamine receptors, metabotropic glutamate receptors, muscarinic acetylcholine receptors, and opioid receptors. © Springer Science+Business Media LLC 2018.
154. Cytoprotection of lipoic acid against toxicity induced by saxitoxin in hippocampal cell line HT-22 through in silico modeling and in vitro assays
Ramos, P; Schmitz, M; Gama, S; Portantiolo, A; Durruthy, MG; de Souza Votto, AP; Cornetet, LR; dos Santos Machado, K; Werhli, A; Tonel, MZ; Fagan, SB; Yunes, JS; Monserrat, JM
in Toxicology, 2018, ISSN: 0300-483X,  Volume: 393, 
Article,  Indexed in: crossref 
155. Detection of simple inorganic and organic molecules over Cu-decorated circumcoronene: a combined DFT and QTAIM study
Malcek, M; Bucinsky, L; Teixeira, F; Cordeiro, MNDS
in PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2018, ISSN: 1463-9076,  Volume: 20, 
Article,  Indexed in: crossref, scopus, wos 
Nowadays graphene materials have attracted a considerable attention because of their potential utilization as gas sensors, biosensors, or adsorbents. Doping or decorating the graphene surface with transition metals can significantly tune its electronic properties and chemical reactivity. Circumcoronene, being a polyaromatic hydrocarbon composed of 19 benzene rings, can be used as a model system of a tiny graphene quantum dot. The adsorption of a set of small molecules (water, hydrogen peroxide, methanol, ethanol, and oxygen) over the copper-decorated circumcoronene was theoretically investigated using density functional theory (DFT) and Bader's quantum theory of atoms in molecules (QTAIM). Following the obtained B3LYP energies, the adsorption of O-2 and the chemisorption of H2O2 were found to be energetically the most favorable, with energetic outcomes of -3.6 eV and -3.7 eV, respectively. Moreover, an H2O2 molecule was decomposed during the chemisorption on the Cu atom to form a neutral Cu(OH)(2) molecule. Changes in the electronic structure of the studied systems, in particular the oxidation of copper, after the adsorption were investigated within the framework of QTAIM (e.g., charges, bond critical points, and delocalization indices) and partial density of states (PDOS) analysis. The results of this study suggest the suitability of the Cu-decorated graphene materials as adsorbents and/or gas sensors in practical applications.
156. Different crystalline forms of titanium dioxide nanomaterial (rutile and anatase) can influence the toxicity of copper in golden mussel Limnoperna fortunei?
Manske Nunes, S; Josende, ME; González Durruthy, M; Pires Ruas, C; Gelesky, MA; Romano, LA; Fattorini, D; Regoli, F; Monserrat, JM; Ventura Lima, J
in Aquatic Toxicology, 2018, ISSN: 0166-445X,  Volume: 205, 
Article,  Indexed in: crossref, scopus 
Although some studies have showed the effects of different crystalline structures of nTiO2 (anatase and rutile) and their applicability in several fields, few studies has analyzed the effect of coexposure with other environmental contaminants such as copper. Thus, the objective of this study was to evaluate if the coexposure to nTiO2 (nominal concentration of 1 mg/L; anatase or rutile) can increase the incorporation and toxic effect induced by Cu (nominal concentration of 56 μg/L) in different tissues of Linmoperna fortunei after 120 h of exposure. Our results showed that the coexposure increased the accumulation of Cu in the gills and adductor muscle independently of the crystalline form and can positively or negatively modulate the antioxidant system, depending on the tissue analyzed. However, exposure only to rutile nTiO2 induced damage in the adductor muscle evidenced by the infiltration of hemocytes in this tissue. Additionally, histomorphometric changes based on fractal dimension analysis showed that coexposure to both forms of nTiO2 induced damage in the same tissue. These results suggest that both crystalline forms exhibited toxicity depending on the analyzed tissue and that coexposure of nTiO2 with Cu may be harmful in L. fortunei, indicating that increased attention to the use and release of nTiO2 in the environment is needed to avoid deleterious effects in aquatic biota. © 2018 Elsevier B.V.
157. Enhancement of differential double layer capacitance and charge accumulation by tuning the composition of ionic liquids mixtures
Costa, R; Voroshylova, IV; Cordeiro, MNDS; Pereira, CM; Fernando Silva, AF
in ELECTROCHIMICA ACTA, 2018, ISSN: 0013-4686,  Volume: 261, 
Article,  Indexed in: crossref, scopus, wos 
Evolution from fossil fuel energy to renewable energy sources and technologies is in the spotlight towards an accelerated energy transition process. One of the challenges of the intermittent renewable energy production is related to the existence of an appropriate energy storage technology in order to effectively use the renewable energy generated. Electrochemical energy storage devices rely on the key property of the electrical double layer integral capacitance. The use of mixed ionic liquids can be an effective strategy to increase the performance of electric double layer capacitors. Here, the studies on the interfacial behaviour of ionic liquids mixtures containing a common ion for a model mercury/ionic liquid interface are reported. Enhancement of the differential capacitance, nearly 3 times higher compared to ILs in the pure state, was achieved by an appropriate combination of ion size both in cation and the anion and asymmetry. The results are interpreted as a consequence of surface voids occupation and by the accumulation of more counter ions and displacement larger anion by the smaller anion in the mixture.
158. Estimation of the Toxicity of Different Substituted Aromatic Compounds to the Aquatic Ciliate Tetrahymena pyriformis by QSAR Approach
Luan, F; Wang, T; Tang, LL; Zhang, S; Cordeiro, MNDS
in MOLECULES, 2018, ISSN: 1420-3049,  Volume: 23, 
Article,  Indexed in: crossref, scopus, wos 
Nowadays, quantitative structure-activity relationship (QSAR) methods have been widely performed to predict the toxicity of compounds to organisms due to their simplicity, ease of implementation, and low hazards. In this study, to estimate the toxicities of substituted aromatic compounds to Tetrahymena pyriformis, the QSAR models were established by the multiple linear regression (MLR) and radial basis function neural network (RBFNN). Unlike other QSAR studies, according to the difference of functional groups (-NO2, -X), the whole dataset was divided into three groups and further modeled separately. The statistical characteristics for the models are obtained as the following: MLR: n = 36, R-2 = 0.829, RMS (root mean square) = 0.192, RBFNN: n = 36, R-2 = 0.843, RMS = 0.167 for Group 1; MLR: n = 60, R-2 = 0.803, RMS = 0.222, RBFNN: n = 60, R-2 = 0.821, RMS = 0.193 for Group 2; MLR: n = 31 R-2 = 0.852, RMS = 0.192; RBFNN: n = 31, R-2 = 0.885, RMS = 0.163 for Group 3, respectively. The results were within the acceptable range, and the models were found to be statistically robust with high external predictivity. Moreover, the models also gave some insight on those characteristics of the structures that most affect the toxicity.
159. Exploring rare chemical phenomena using fractional nuclear charges: The cis-effect in N2F2
Teixeira, F; Melo, A; Cordeiro, MNDS
in INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 2018, ISSN: 0020-7608,  Volume: 118, 
Article,  Indexed in: crossref, scopus, wos 
The so called cis-effect, in which the cis form of an ethylenic compound is more stable than its trans-isomer. is a good example of a rare phenomenon described only for a few isomeric pairs. In this work, a novel approach to the study of this rare effect is attempted by changing the nuclear charges of the fluoride and nitrogen in cis- and trans-N2F2. This allowed the survey of a large number of isomeric pairs composed sharing the same molecular topology, while varying the electronegativity of selected atoms. The results show an increasing stabilization of the cis-isomers when increasing the electronegativity of the fluoride atoms. in line with the accepted zeitgeist linking this effect to the electronegativity of the peripheral groups. However, a similar behavior was also found when varying the nuclear charge of the nitrogen atoms. This prompted a more in-depth look at the electronic structure of these compounds, gathering descriptors from Bader's Quantum Theory of Atoms in Molecules. A descriptive linear model was derived from these descriptors using a two-stage step-wise linear regression. Further inspection of the model linked the destabilization of the trans-isomers with a deviation from the idealized trigonal planar geometry predicted by the Valence Shell Electron Pair Repulsion model. This tendency was explained by an increase in the ionic character of the N-F bonds. Furthermore, the current model suggests that the Coulombic repulsion between the two peripheral atoms in the cis-isomers prevents such large deviations from the idealized geometry, thus, contributing to their relative stabilization. The qualitative rules governing the cis-effect in N2F2 were further tested on other compounds with a similar bond topology.
160. Exploring the flap dynamics of the South African HIV subtype C protease in presence of FDA-approved inhibitors: MD study
Maphumulo, SI; Halder, AK; Govender, T; Maseko, S; Maguire, GEM; Honarparvar, B; Kruger, HG
in Chemical Biology & Drug Design, 2018, ISSN: 1747-0277,  Volume: 92, 
Article,  Indexed in: crossref