Phylogenetic analysis, computer modeling and catalytic prediction of an Amazonian soil ß-glucosidase against a soybean saponin.

Saponins are amphipathic glycosides with detergent properties present in vegetables. These compounds, when ingested, can cause difficulties in absorbing nutrients from food and even induce inflammatory processes in the intestine. There is already some evidence that saponins can be degraded by ß-glucosidases of the GH3 family. In the present study, we evaluated, through computational tools, the possibility of a ß-glucosidase (AMBGL17) obtained from a metagenomic analysis of the Amazonian soil, to catalytically interact with a saponin present in soybean. For this, the amino acid sequence of AMBGL17 was used in a phylogenetic analysis to estimate its origin and to determine its three-dimensional structure. The 3D structure of the enzyme was used in a molecular docking analysis to evaluate its interaction with soy saponin as a ligand. The results of the phylogenetic analysis showed that AMBGL17 comes from a microorganism of the phylum Chloroflexi, probably related to species of the order Aggregatinales. Molecular docking showed that soybean saponin can interact with the catalytic site of AMBGL17, with the amino acid GLY345 being important in this catalytic interaction, especially with a ß-1,2 glycosidic bond present in the carbohydrate portion of saponin. In conclusion, AMBGL17 is an enzyme with interesting biotechnological potential in terms of mitigating the anti-nutritional and pro-inflammatory effects of saponins present in vegetables used for human and animal food.

Mefloquine synergism with anti-tuberculosis drugs and correlation to membrane effects: Biologic, spectroscopic and molecular dynamics simulations studies.

Studies displaying the combination of mefloquine (MFL) with anti-tuberculosis (TB) substances are limited in the literature. In this work, the effect of MFL-association with two first-line anti-TB drugs and six fluoroquinolones was evaluated against Mycobacterium tuberculosis drug resistant strains. MFL showed synergistic interaction with isoniazid, pyrazinamide, and several fluoroquinolones, reaching fractional inhibitory concentration indexes (FICIs) ranging from 0.03 to 0.5. In order to better understand the observed results, two approaches have been explored: (i) spectroscopic responses attributed to the effect of MFL on physicochemical properties related to a liposomal membrane model composed by soybean asolectin; (ii) molecular dynamics (MD) simulation data regarding MFL interaction with a membrane model based on PIM2, a lipid constituent of the mycobacterial cell wall. FTIR and NMR data showed that MFL affects expressively the region between the phosphate and the first methylene groups of soybean asolectin membranes, disordering these regions. MD simulations results detected high MFL density in the glycolipid interface and showed that the drug increases the membrane lateral diffusion, enhancing its permeability. The obtained results suggest that synergistic activities related to MFL are attributed to its effect of lipid disorder and membrane permeability enhancement.

Use of Text Messaging (SMS) for the Management of Side Effects in Cancer Patients Undergoing Chemotherapy Treatment: a Randomized Controlled Trial.

Cancer patients are often not sufficiently oriented to manage side effects at home. Sending text messages with self-care guidelines aimed managing side effects is the main objective of this randomized controlled trial. Patients who started outpatient chemotherapy treatment between March and December 2017 at a hospital in southern Brazil were invited to participate in this study and were allocated to the intervention or control group (ratio 1: 1). Each patient in the intervention group received a daily SMS (short message service) with some guidance on management or prevention of side effects. All text messages were sent to the intervention group patients in an automated and tailored way by our app called cHEmotHErApp. Side effects experienced by patients were verified using the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire Core-30 (EORTC QLQ-C30). Results showed intervention group patients experienced fewer side effects compared to the control group in cycle 1 (p < 0.05), in general. In addition, intervention group experienced less nausea in relation to the control group, in the cycle 1 and cycle 2 (p < 0.05). This study indicate text messaging may be a tool for supporting side effect management in patients receiving chemotherapy. This study was enrolled in ClinicalTrials.gov with the identification number NCT03087422. This research was performed in accordance with the Declaration of Helsinki.

A comparison of classifiers for predicting the class color of fluorescent proteins.

Fluorescent proteins have been applied in a wide variety of fields ranging from basic science to industrial applications. Apart from the naturally occurring fluorescent proteins, there is a growing interest in genetically modified variants that emit light in a specific wavelength. Genetically modifying a protein is not an easy task, especially because the exchange of one residue by other has to achieve the desired property while maintaining protein stability. To help in the choice of residue exchange, computational methods are applied to predict function and stability of proteins. In this work we have prepared a dataset composed by 109 fluorescent proteins and tested four classical supervised classification algorithms: artificial neural networks (ANNs), decision trees (DTs), support vector machines (SVMs) and random forests (RFs). This is the first time that algorithms are compared in this task. Results of comparing the algorithm's performance shows that DT, SVM and RF were significantly better than ANNs, and RF was the best method in all the scenarios. However, the interpretability of DTs is highly relevant and can provide important clues about the mechanisms involved in protein color emission. The results are promising and indicate that the use of in silico methods can greatly reduce the time and cost of the in vitro experiments.

Silencing the OCT4-PG1 pseudogene reduces OCT-4 protein levels and changes characteristics of the multidrug resistance phenotype in chronic myeloid leukemia.

Cancer stem cells show epigenetic plasticity and intrinsic resistance to anti-cancer therapy, rendering capable of initiating cancer relapse and progression. Transcription factor OCT-4 regulates various pathways in stem cells, but its expression can be regulated by pseudogenes. This work evaluated how OCT4-PG1 pseudogene can affect OCT-4 expression and mechanisms related to the multidrug resistance (MDR) phenotype in FEPS cells. Considering that OCT-4 protein is a transcription factor that regulates expression of ABC transporters, level of gene expression, activity of ABC proteins and cell sensitivity to chemotherapy were evaluated after OCT4-PG1 silencing. Besides we set up a STRING network. Results showed that after OCT4-PG1 silencing, cells expressed OCT-4 gene and protein to a lesser extent than mock cells. The gene and protein expression of ABCB1, as well as its activity were reduced. On the other hand, ALOX5 and ABCC1 genes was increased even as the activity of this transporter. Moreover, the silencing cells become sensitive to two chemotherapics tested. The network structure demonstrated that OCT4-PG1 protein interacts directly with OCT-4, SOX2, and NANOG and indirectly with ABC transporters. We conclude that OCT4-PG1 pseudogene plays a key role in the regulation OCT-4 transcription factor, which alters MDR phenotype in the FEPS cell line.

Cytoprotection of lipoic acid against toxicity induced by saxitoxin in hippocampal cell line HT-22 through in silico modeling and in vitro assays.

Saxitoxins (STXs) are potent neurotoxins that block voltage-gated channels in neurons and induce cytotoxicity. These toxins not only can generate reactive oxygen species but also can alter antioxidant levels, promoting oxidative stress. Under this pro-oxidant situation, the use of the antioxidant lipoic acid (LA) can represent a chemoprotective alternative to minimize the deleterious effects induced by neurotoxins as STXs. P-glycoprotein (P-gp) is a well-known ATP-binding cassette (ABC) transporter that plays a crucial role in the extrusion of toxic substances, decreasing their accumulation and potential intracellular effects in virtue of its broad substrate specificity, its expression in many excretory tissues and its large efflux capacity. The interaction of STXs with LA was evaluated by ab initio simulation, molecular docking and bioassays using the cell line HT-22. The interaction of STXs with LA occurs by physisorption. Molecular docking indicated that STXs can be a substrate of P-gp and, estimating the Free Energy of Binding (FEB), LA has lower amino acids residues binding sites, similar to verapamil, while STX and STX+LA_1 have similar amino acids residues and binding sites with similar FEB between this ligands.Cells were exposed to STXs and LA for 30min and 24h. LA treatment minimizes STX cytotoxicity, evaluated by trypan blue and MTT assay and both STX and STX-LA treatments were efficient to induce P-gp activity measured by rhodamine 123 dye extrusion. LA and STX+LA treatments induced low reactive oxygen species levels and low oxygen consumption. Based on our results, it can be concluded that LA was able to induce cytoprotection, including induction of cellular glutathione levels, and that STX+LA interaction reduced toxicity effects induced by STX. Overall, the in vitro results corroborated the semi-empirical evidences found using density functional theory ab initio simulation and molecular docking.

Text Messaging (SMS) Helping Cancer Care in Patients Undergoing Chemotherapy Treatment: a Pilot Study.

Cancer treatment is an extremely stressful life experience that is accompanied by a range of psychological, social, physical, and practical difficulties. Cancer patients need to receive information that helps them to better understand the disease, assists them in decision-making, and helps them deal with treatment. Patients are interested in receiving such information. The degree of satisfaction with the information received has been associated with positive health outcomes, specifically regarding quality of life, severity of side effects, and psychological well-being. This study investigates a method of guiding cancer patients, in relation to outpatient chemotherapy treatment, using SMS (short message service) text messaging. A smartphone application called cHEmotHErApp was developed, and its primary function is to send out SMS text messages with guidance for self-care and emotional support for oncology patients undergoing chemotherapy. Thus, the main objective of this study is to evaluate the acceptance and perception of patients of the receipt of these SMS messages, as well as to evaluate the possible benefits reported by the participants. Adult patients diagnosed with cancer, who started the first outpatient chemotherapy treatment scheme between August and November 2016 at the School Hospital (HE) of the Federal University of Pelotas (UFPel), were invited to participate in this pilot study. In total, 14 cancer patients were adherent to this study. Each of these patients received a daily text message on their cell phone with some guidance on encouraging self-care and emotional support. Patients reported that, because of the SMS text messages they received, they felt more confident in their treatment, felt more supported and encouraged, and that the text messages facilitated self-care. In addition, patients reported that the SMS text messages they received helped them to take better care of themselves and to continue further treatment.