Cheminformatics and Materials

Research Publications

Total publications: 603

145. The Action of Polyphenols in Diabetes Mellitus and Alzheimer's Disease: A Common Agent for Overlapping Pathologies
Silveira, AC; Dias, JP; Santos, VM; Oliveira, PF; Alves, MG; Rato, L; Silva, BM
in CURRENT NEUROPHARMACOLOGY, 2019, ISSN: 1570-159X,  Volume: 17, 
Review,  Indexed in: crossref, scopus, wos 
Diabetes Mellitus (DM) and Alzheimer's disease (AD) are two prevalent diseases in modern societies, which arc caused mainly by current lifestyle, aging and genetic alterations. It has already been demonstrated that these two diseases are associated, since individuals suffering from DM are prone to develop AD. Conversely, it is also known that individuals with AD are more susceptible to DM, namely type 2 diabetes (T2DM). Therefore, these two pathologies, although completely different in terms of symptomatology, end up sharing several mechanisms at the molecular level, with the most obvious being the increase of oxidative stress and inflammation. Polyphenols are natural compounds widely spread in fruits and vegetables whose dietary intake has been considered inversely proportional to the incidence of DM and AD. So, it is believed that this group of phytochemicals may have preventive and therapeutic potential, not only by reducing the risk and delaying the development of these pathologies, but also by improving brain's metabolic profile and cognitive function. The aim of this review is to understand the extent to which DM and AD are related pathologies, the degree of similarity and the relationship between them, to detail the molecular mechanisms by which polyphenols may exert a protective effect, such as antioxidant and anti-inflammatory effects, and highlight possible advantages of their use as common preventive and therapeutic alternatives.
146. A desirability-based multi objective approach for the virtual screening discovery of broad-spectrum anti-gastric cancer agents
Perez Castillo, Y; Sanchez Rodriguez, A; Tejera, E; Cruz Monteagudo, M; Borges, F; Cordeiro, MNDS; Huong, LTT; Hai, PT
in PLOS ONE, 2018, ISSN: 1932-6203,  Volume: 13, 
Article,  Indexed in: crossref, scopus, wos 
Gastric cancer is the third leading cause of cancer-related mortality worldwide and despite advances in prevention, diagnosis and therapy, it is still regarded as a global health concern. The efficacy of the therapies for gastric cancer is limited by a poor response to currently available therapeutic regimens. One of the reasons that may explain these poor clinical outcomes is the highly heterogeneous nature of this disease. In this sense, it is essential to discover new molecular agents capable of targeting various gastric cancer subtypes simultaneously. Here, we present a multi-objective approach for the ligand-based virtual screening discovery of chemical compounds simultaneously active against the gastric cancer cell lines AGS, NCI-N87 and SNU-1. The proposed approach relays in a novel methodology based on the development of ensemble models for the bioactivity prediction against each individual gastric cancer cell line. The methodology includes the aggregation of one ensemble per cell line using a desirability-based algorithm into virtual screening protocols. Our research leads to the proposal of a multi-targeted virtual screening protocol able to achieve high enrichment of known chemicals with anti-gastric cancer activity. Specifically, our results indicate that, using the proposed protocol, it is possible to retrieve almost 20 more times multi-targeted compounds in the first 1% of the ranked list than what is expected from a uniform distribution of the active ones in the virtual screening database. More importantly, the proposed protocol attains an outstanding initial enrichment of known multi-targeted anti-gastric cancer agents.
147. A DFT and QTAIM study of the adsorption of organic molecules over the copper-doped coronene and circumcoronene
Malcek, M; Cordeiro, MNDS
in PHYSICA E-LOW-DIMENSIONAL SYSTEMS & NANOSTRUCTURES, 2018, ISSN: 1386-9477,  Volume: 95, 
Article,  Indexed in: crossref, scopus, wos 
Graphene based materials are nowadays extensively studied because of their potential applications as gas sensors, biosensors or adsorbents. Doping the graphene surface with heteroatoms or transition metals can improve its electronic properties and chemical reactivity. Polyaromatic hydrocarbons coronene and circumcoronene can be used as models of tiny graphene quantum dots. The adsorption of a set of organic molecules (water, hydrogen peroxide, hydrogen sulfide, methanol, ethanol and oxygen molecule) over the copper-doped coronene and circumcoronene was theoretically studied using density functional theory (DFT) and quantum theory of atoms in molecules (QTAIM). In the case of coronene, only one site was considered for the Cu-doping, whereas in the case of circumcoronene being a polyaromatic hydrocarbon composed of 54 carbon atoms, three different sites for Cu-doping were considered. For the systems under study, the adsorption of O-2 was found energetically the most favorable, with energetic outcome ranging from -3.1 to -3.7 eV related to the position of dopant Cu atom. Changes in the topology of charge densities at Cu and in its vicinity after the adsorption of studied molecules were investigated in the framework of QTAIM. In addition, QTAIM analysis of bond critical points (BCP) was employed to study the character of the newly formed chemical bonds. The results of this study point out the suitability of Cu-doped graphene materials as sensors and/or adsorbents in practical applications.
148. A further development of the QNAR model to predict the cellular uptake of nanoparticles by pancreatic cancer cells
Luan, F; Tang, LL; Zhang, LH; Zhang, S; Monteagudo, MC; Cordeiro, MNDS
in FOOD AND CHEMICAL TOXICOLOGY, 2018, ISSN: 0278-6915,  Volume: 112, 
Article,  Indexed in: crossref, scopus, wos 
Nanotechnology has led to the development of new nanomaterials with unique properties and a wide variety of applications. In the present study, we focused on the cellular uptake of a group of nanoparticles with a single metal core by pancreatic cancer cells, which has been studied by Yap et al. (Rsc Advances, 2012, 2 (2):8489-8496) using classification models. In this work, the development of a further Quantitative Nanostructure Activity Relationship (QNAR) model was performed by linear multiple linear regression (MLR) and nonlinear artificial neural network (ANN) techniques to accurately predict the cellular uptake values of these compounds by dividing them into three groups. Judging from the attained statistical results, our derived QNAR models have an acceptable overall accuracy and robustness, as well as good predictivity on the external data sets. Moreover, the results of this study provide some insights on how engineered nanomaterial features influence cellular responses and thereby outline possible approaches for developing and applying predictive computational models for biological responses caused by exposure to nanomaterials.
149. A novel QSAR model to predict epidermial growth factor inhibitors
Concu, R; Dias Soeiro Cordeiro, MN
in Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition, 2018,
Proceedings Paper,  Indexed in: crossref 
150. Assessment of electronic transitions involving intermolecular charge transfer in complexes formed by fullerenes and donor–acceptor nanohoops
González-Veloso, I; Rodríguez-Otero, J; Cabaleiro-Lago, EM
in Physical Chemistry Chemical Physics, 2018, ISSN: 1463-9076,  Volume: 20, 
Article,  Indexed in: crossref 
<p>Inserting an anthraquinone or tetracyanoanthraquinone unit in cycloparaphenylene nanohoops facilitates intermolecular electron transfer to a fullerene guest.</p>
151. Benzamide porphyrins with directly conjugated and distal pyridyl or pyridinium groups substituted to the porphyrin macrocycles: Study of the photosensitising abilities as inducers of apoptosis in cancer cells under photodynamic conditions
Sengupta, D; Mazumdar, ZH; Mukherjee, A; Sharma, D; Halder, AK; Basu, S; Jha, T
in Journal of Photochemistry and Photobiology B: Biology, 2018, ISSN: 1011-1344,  Volume: 178, 
Article,  Indexed in: crossref, scopus 
Amphiphilic porphyrin photosensitisers (PSs) having combinations of directly substituted pyridyl group(s) at the meso-position of a porphyrin macrocycle, and/or indirectly linked pyridyl groups as benzamide derivatives are reported. The compounds 5,10,15,20-tetrakis-(4-pyridylbenzamide)porphyrin (A.2), 5,10,15,20-tetra[N-(pyridine-4-yl)benzamidium] porphyrin (A.3), 5-mono-(4-pyridyl)-10,15,20-tris-(4-pyridylbenzamide)porphyrin (B.2) and 5-mono-(4-methylpyridinium)-10,15,20-tris-(4-pyridiniumbenzamide)porphyrin (B.3) were synthesised. The compounds were successfully characterised through UV–Vis, Emission, 1H NMR, and ESI-HRMS techniques. To evaluate the effect of this combination of directly conjugated and non-conjugated pyridyl/cationic pyridinium groups on the porphyrin macrocycle, the efficacy of the synthesised compounds was compared to a known standard 5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin (TMPyP). These compounds show better efficacy (IC50’s ranging between 0.66 ± 0.04 μM to 3.71 ± 1.01 μM) against A549 (human epithelial adenocarcinoma lung cancer) cell line under in vitro photodynamic conditions in comparison to MDA-MB-231 (breast cancer) (IC50’s ranging between 3.7 ± 0.087 μM to 12.1 ± 0.12 μM) and Pa-1 (ovarian cancer) (IC50’s ranging between 17.9 ± 0.01 μM to 42.45 ± 0.02 μM) cell lines. It was found that B.3, having a pyridinium group attached to the meso-position of the macrocycle along with three distal cationic pyridinium groups, independent of the porphyrinic electron delocalisation cycle, showed better photocytotoxic efficacy (IC50 = 0.66 ± 0.04 μM, A549 lung cancer cell line) and higher potential to promote apoptosis and hence better efficacy as PS towards cancer photodynamic therapy (PDT). The PDT activity of B.3 was further verified and established by various biological assays, viz. Annexin V assay, cell cycle assay, and reactive oxygen species (ROS) activity assay. © 2017 Elsevier B.V.
152. Cetuximab and the Head and Neck Squamous Cell Cancer
Concu, R; Cordeiro, MNDS
in CURRENT TOPICS IN MEDICINAL CHEMISTRY, 2018, ISSN: 1568-0266,  Volume: 18, 
Review,  Indexed in: crossref, scopus, wos 
The Head and Neck Squamous Cell Cancer (HNSCC) is the most common type of head and neck cancer (more than 90%), and all over the world more than a half million people have been developing this cancer in the last years. This type of cancer is usually marked by a poor prognosis with a really significant morbidity and mortality. Cetuximab received early favor as an exciting and promising new therapy with relatively mild side effect, and due to this, received authorization in 2004 from the European Medicines Agency (EMA) and in 2006 from the Food and Drug Association (FDA) for the treatment of patients with squamous cell cancer of the head and neck in combination with radiation therapy for locally advanced disease. In this work we will review the application and the efficacy of the Cetuximab in the treatment of the HNSCC.