FT-MIR-ATR Associated with Chemometrics Methods: A Preliminary Analysis of Deterioration State of Brazil Nut Oil.

Brazil nut oil is highly valued in the food, cosmetic, chemical, and pharmaceutical industries, as well as other sectors of the economy. This work aims to use the Fourier transform infrared (FTIR) technique associated with partial least squares regression (PLSR) and principal component analysis (PCA) to demonstrate that these methods can be used in a prior and rapid analysis in quality control. Natural oils were extracted and stored for chemical analysis. PCA presented two groups regarding the state of degradation, subdivided into super-degraded and partially degraded groups in 99.88% of the explained variance. The applied PLS reported an acidity index (AI) prediction model with root mean square error of calibration (RMSEC) = 1.8564, root mean square error of cross-validation (REMSECV) = 4.2641, root mean square error of prediction (RMSEP) = 2.1491, R2cal (calibration correlation coefficient) equal to 0.9679, R2val (validation correlation coefficient) equal to 0.8474, and R2pred (prediction correlation coefficient) equal to 0, 8468. The peroxide index (PI) prediction model showed RMSEC = 0.0005, REMSECV = 0.0016, RMSEP = 0.00079, calibration R2 equal to 0.9670, cross-validation R2 equal to 0.7149, and R2 of prediction equal to 0.9099. The physical-chemical analyses identified that five samples fit in the food sector and the others fit in other sectors of the economy. In this way, the preliminary monitoring of the state of degradation was reported, and the prediction models of the peroxide and acidity indexes in Brazil nut oil for quality control were determined.

Caffeic Acid-Zinc Basic Salt/Chitosan Nanohybrid Possesses Controlled Release Properties and Exhibits In Vivo Anti-Inflammatory Activities.

Caffeic acid (CA) exhibits a myriad of biological activities including cardioprotective action, antioxidant, antitumor, anti-inflammatory, and antimicrobial properties. On the other hand, CA presents low water solubility and poor bioavailability, which have limited its use for therapeutic applications. The objective of this study was to develop a nanohybrid of zinc basic salts (ZBS) and chitosan (Ch) containing CA (ZBS-CA/Ch) and evaluate its anti-edematogenic and antioxidant activity in dextran and carrageenan-induced paw edema model. The samples were obtained by coprecipitation method and characterized by X-ray diffraction, Fourier transform infrared (FT-IR), scanning electron microscope (SEM) and UV-visible spectroscopy. The release of caffeate anions from ZBS-CA and ZBS-CA/Ch is pH-dependent and is explained by a pseudo-second order kinetics model, with a linear correlation coefficient of R2 ≥ 0.99 at pH 4.8 and 7.4. The in vivo pharmacological assays showed excellent anti-edematogenic and antioxidant action of the ZBS-CA/Ch nanoparticle with slowly releases of caffeate anions in the tissue, leading to a prolongation of CA-induced anti-edematogenic and anti-inflammatory activities, as well as improving its inhibition or sequestration antioxidant action toward reactive species. Overall, this study highlighted the importance of ZBS-CA/Ch as an optimal drug carrier.

Assessment of the PETase conformational changes induced by poly(ethylene terephthalate) binding.

Recently, a bacterium strain of Ideonella sakaiensis was identified with the uncommon ability to degrade the poly(ethylene terephthalate) (PET). The PETase from I. sakaiensis strain 201-F6 (IsPETase) catalyzes the hydrolysis of PET converting it to mono(2-hydroxyethyl) terephthalic acid (MHET), bis(2-hydroxyethyl)-TPA (BHET), and terephthalic acid (TPA). Despite the potential of this enzyme for mitigation or elimination of environmental contaminants, one of the limitations of the use of IsPETase for PET degradation is the fact that it acts only at moderate temperature due to its low thermal stability. Besides, molecular details of the main interactions of PET in the active site of IsPETase remain unclear. Herein, molecular docking and molecular dynamics (MD) simulations were applied to analyze structural changes of IsPETase induced by PET binding. Results from the essential dynamics revealed that the ß1-ß2 connecting loop is very flexible. This loop is located far from the active site of IsPETase and we suggest that it can be considered for mutagenesis to increase the thermal stability of IsPETase. The free energy landscape (FEL) demonstrates that the main change in the transition between the unbound to the bound state is associated with the ß7-α5 connecting loop, where the catalytic residue Asp206 is located. Overall, the present study provides insights into the molecular binding mechanism of PET into the IsPETase structure and a computational strategy for mapping flexible regions of this enzyme, which can be useful for the engineering of more efficient enzymes for recycling plastic polymers using biological systems.

QM/MM Study of the Fosfomycin Resistance Mechanism Involving FosB Enzyme.

Multidrug-resistant organisms contain antibiotic-modifying enzymes that facilitate resistance to a variety of antimicrobial compounds. Particularly, the fosfomycin (FOF) drug can be structurally modified by several FOF-modifying enzymes before it reaches the biological target. Among them, FosB is an enzyme that utilizes l-cysteine or bacillithiol in the presence of a divalent metal to open the epoxide ring of FOF and, consequently, inactivate the drug. Here, we have used hybrid quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulations to explore the mechanism of the reaction involving FosB and FOF. The calculated free-energy profiles show that the cost to open the epoxide ring of FOF at the C2 atom is ∼3.0 kcal/mol higher than that at the C1 atom. Besides, our QM/MM MD results revealed the critical role of conformation change of Cys9 and Asn50 to release the drug from the active site. Overall, the present study provides insights into the mechanism of FOF-resistant proteins.

Molecular description of α-keto-based inhibitors of cruzain with activity against Chagas disease combining 3D-QSAR studies and molecular dynamics.

In this work, a group of α-keto-based inhibitors of the cruzain enzyme with anti-chagas activity was selected for a three-dimensional quantitative structure-activity relationship study (3D-QSAR) combined with molecular dynamics (MD). Firstly, statistical models based on Partial Least Square (PLS) regression were developed employing comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) descriptors. Validation parameters (q2 and r2 )for the models were, respectively, 0.910 and 0.997 (CoMFA) and 0.913 and 0.992 (CoMSIA). In addition, external validation for the models using a test group revealed r2pred  = 0.728 (CoMFA) and 0.971 (CoMSIA). The most relevant aspect in this study was the generation of molecular fields in both favorable and unfavorable regions based on the models developed. These fields are important to interpret modifications necessary to enhance the biological activities of the inhibitors. This analysis was restricted considering the inhibitors in a fixed conformation, not interacting with their target, the cruzain enzyme. Then, MD was employed taking into account important variables such as time and temperature. MD helped describe the behavior of the inhibitors and their properties showed similar results as those generated by QSAR-3D study.

Synthesis, antimalarial activity in vitro, and docking studies of novel neolignan derivatives.

The absence of effective vaccines against malaria and the difficulties associated with controlling mosquito vectors have left chemotherapy as the primary control measure against malaria. However, the emergence and spread of parasite resistance to conventional antimalarial drugs result in a worrisome scenario making the search for new drugs a priority. In the present study, the activities of nine neolignan derivatives were evaluated as follows: (i) against blood forms of chloroquine-resistant Plasmodium falciparum (clone W2), using the tritiated hypoxanthine incorporation and anti-HRPII assays; (ii) for cytotoxic activity against cultured human hepatoma cells (HepG2); and (iii) for intermolecular interaction with the P. falciparum cysteine protease of falcipain-2 (F2) by molecular docking. The neolignan derivatives 9 and 10 showed activity against the blood form of the chloroquine-resistant P. falciparum clone W2 and were not cytotoxic against cultured human hepatoma cells. A molecular docking study of these two neolignans with FP2 revealed several intermolecular interactions that should guide the design of future analogs.

A Computational Analysis of Indomethacin Derivative as Tubulin Inhibitor: Insights into Development of Chemotherapeutic Agents.

Tubulin is a potent molecular target for development of anticancer agents. In this report, the binding of non-steroidal anti-inflammatory drugs as tubulin inhibitors potential are investigated by extensive computational techniques, such as, molecular docking, molecular dynamics simulations and binding free energy calculations. The results suggest that a potent indomethacin derivative inhibits the tubulin polymerization by interacting on the colchicine-site binding. This potential chemotherapeutic agent showed high stability in the molecular dynamics simulations, when complexed on the same binding site of colchicine, a potent and toxic, tubulin inhibitor. Then, our results can be useful designing new compounds for cancer treatments.

Pentacycloundecane lactam vs lactone norstatine type protease HIV inhibitors: binding energy calculations and DFT study.

BACKGROUND: Novel pentacycloundecane (PCU)-lactone-CO-EAIS peptide inhibitors were designed, synthesized, and evaluated against wild-type C-South African (C-SA) HIV-1 protease. Three compounds are reported herein, two of which displayed IC50 values of less than 1.00 µM. A comparative MM-PB(GB)SA binding free energy of solvation values of PCU-lactam and lactone models and their enantiomers as well as the PCU-lactam-NH-EAIS and lactone-CO-EAIS peptide inhibitors and their corresponding diastereomers complexed with South African HIV protease (C-SA) was performed. This will enable us to rationalize the considerable difference between inhibitory concentration (IC50) of PCU-lactam-NH-EAIS and PCU-lactone-CO-EAIS peptides. RESULTS: The PCU-lactam model exhibited more negative calculated binding free energies of solvation than the PCU-lactone model. The same trend was observed for the PCU-peptide inhibitors, which correspond to the experimental activities for the PCU-lactam-NH-EAIS peptide (IC50 = 0.076 µM) and the PCU-lactone-CO-EAIS peptide inhibitors (IC50 = 0.850 µM). Furthermore, a density functional theory (DFT) study on the natural atomic charges of the nitrogen and oxygen atoms of the three PCU-lactam, PCU-lactim and PCU-lactone models were performed using natural bond orbital (NBO) analysis. Electrostatic potential maps were also used to visualize the electron density around electron-rich regions. The asymmetry parameter (η) and quadrupole coupling constant (χ) values of the nitrogen and oxygen nuclei of the model compounds were calculated at the same level of theory. Electronic molecular properties including polarizability and electric dipole moments were also calculated and compared. The Gibbs theoretical free solvation energies of solvation (∆Gsolv) were also considered. CONCLUSIONS: A general trend is observed that the lactam species appears to have a larger negative charge distribution around the heteroatoms, larger quadrupole constant, dipole moment and better solvation energy, in comparison to the PCU-lactone model. It can be argued that these characteristics will ensure better eletronic interaction between the lactam and the receptor, corresponding to the observed HIV protease activities in terms of experimental IC50 data.

Analysis of the structure of calpain-10 and its interaction with the protease inhibitor SNJ-1715.

Calpain-10 (CAPN10) is a cysteine protease that is activated by intracellular calcium (Ca(2+)) and known to be involved in diseases such as cancer, heart attack, and stroke. A role for the CAPN10 gene in diabetes mellitus type II was recently identified. Hyper activation of the enzyme initiates a series of destructive cycles that can cause irreversible damage to cells. The development of inhibitors may be useful as therapeutic agents for a number of calpainopathies. In this paper, we have used the homology modelling technique to determine the 3D structure of calpain-10 from Homo sapiens. The model of calpain-10 obtained by homology modelling suggests that its active site is conserved among family members and the main interactions are similar to those observed for µ-calpain. Structural analysis revealed that there are small differences in the charge distribution and molecular surface of the enzyme. These differences are probably less dependent on calcium for calpain-10 than they are for µ-calpain. In addition, the ion pair Cys(-)/His(+) formation was observed using of Molecular Dynamics (MD) simulations that were based upon hybrid quantum mechanical/molecular mechanical (QM/MM) approaches. Finally, the binding of the SNJ-1715 inhibitor to calpain-10 was investigated in order to further understand the mechanism of inhibition of calpain-10 by this inhibitor at the molecular level.

The catalytic mechanism of glyceraldehyde 3-phosphate dehydrogenase from Trypanosoma cruzi elucidated via the QM/MM approach.

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has been identified as a key enzyme involved in glycolysis processes for energy production in the Trypanosoma cruzi parasite. This enzyme catalyses the oxidative phosphorylation of glyceraldehyde 3-phosphate (G3P) in the presence of inorganic phosphate (Pi) and nicotinamide adenosine dinucleotide (NAD+). The catalytic mechanism used by GAPDH has been intensively investigated. However, the individual roles of Pi and the C3 phosphate of G3P (Ps) sites, as well as some residues such as His194 in the catalytic mechanism, remain unclear. In this study, we have employed Molecular Dynamics (MD) simulations within hybrid quantum mechanical/molecular mechanical (QM/MM) potentials to obtain the Potential of Mean Force of the catalytic oxidative phosphorylation mechanism of the G3P substrate used by GAPDH. According to our results, the first stage of the reaction (oxidoreduction) takes place in the Pi site (energetically more favourable), with the formation of oxyanion thiohemiacetal and thioacylenzyme intermediates without acid-base assistance of His194. Analysis of the interaction energy by residues shows that Arg249 has an important role in the ability of the enzyme to bind the G3P substrate, which interacts with NAD+ and other important residues, such as Cys166, Glu109, Thr167, Ser247 and Thr226, in the GAPDH active site. Finally, the inhibition mechanism of the GAPDH enzyme by the 3-(p-nitrophenoxycarboxyl)-3-ethylene propyl dihydroxyphosphonate inhibitor was investigated in order to contribute to the design of new inhibitors of GAPDH from Trypanosoma cruzi.

Synthesis, 2D-NMR and molecular modelling studies of pentacycloundecane lactam-peptides and peptoids as potential HIV-1 wild type C-SA protease inhibitors.

In this study, eight non-natural peptides and peptoids incorporating the pentacycloundecane (PCU) lactam were designed and synthesized as potential inhibitors of the wild type C-SA HIV-protease. Five of these inhibitors gave IC(50) values ranging from 0.5 up to 0.75 µM against the resistance-prone wild type C-South African HIV-protease. NMR EASY-ROESY studies enabled us to describe the secondary structure of three of these compounds in solution. The 3D structures of the selected cage peptides were also modelled in solution using QM/MM/MD simulations. Satisfactory agreement between the NMR observations and the low energy calculated structures exists. Only one of these inhibitors (11 peptoid), which showed the best IC(50)(0.5 µM), exhibited a definable 3-D structure in solution. Autodock4 and AutodockVina were used to model the potential interaction between these inhibitors and the HIV-PR. It appears that the docking results are too crude to be correlated with the relative narrow range of experimental IC(50) values (0.5-10 µM). The PCU-peptides and peptoides were several orders less toxic (145 µM for 11 and 102 µM for 11 peptoid) to human MT-4 cells than lopinavir (0.025 µM). This is the first example of a polycyclic cage framework to be employed as an HIV-PR transition state analogue inhibitor and can potentially be utilized for other diseases related proteases. [Figure: see text].

Computational analysis of human OGA structure in complex with PUGNAc and NAG-thiazoline derivatives.

The substitution of serine and threonine residues in nucleocytoplasmic proteins with 2-acetamido-2-deoxy-ß-D-glucopyranose (O-GlcNAc) residues is an essential post-translational modification found in many multicellular eukaryotes. O-glycoprotein 2-acetamino-2-deoxy-ß-D-glucopyranosidase (O-GlcNAcase) hydrolyzes O-GlcNAc residues from post-translationally modified serine/threonine residues of nucleocytoplasmic protein. O-GlcNAc has been implicated in several disease states such as cancer, Alzheimer's disease, and type II diabetes. For this paper, a model of the human O-GlcNAcase (hOGA) enzyme based on the X-ray structures of bacterial Clostridium perfringens (CpNagJ) and Bacteroides thetaiotaomicrometer (BtOGA) homologues has been generated through molecular homology modeling. In addition, molecular docking, molecular dynamics (MD) simulations, and Linear Interaction Energy (LIE) were employed to determine the bind for derivatives of two potent inhibitors: O-(2-acetamido-2-deoxy-D-glucopyranosylidene)amino-N-phenylcarbamate (PUGNAc) and 1,2-dideoxy-2'-methyl-R-D-glucopyranoso-[2,1-d]-Δ2'-thiazoline (NAG-thiazoline), with hOGA. The results show that the binding free energy calculations using the Linear Interaction Energy (LIE) are correlated with inhibition constant values. Therefore, the model of the human O-GlcNAcase (hOGA) obtained here may be used as a target for rational design of new inhibitors.

Diversity and three-dimensional structures of the alpha Mcr of the methanogenic Archaea from the anoxic region of Tucuruí Lake, in Eastern Brazilian Amazonia

Methanogenic archaeans are organisms of considerable ecological and biotechnological interest that produce methane through a restricted metabolic pathway, which culminates in the reaction catalyzed by the Methyl-coenzyme M reductase (Mcr) enzyme, and results in the release of methane. Using a metagenomic approach, the gene of the a subunit of mcr (mcrα) was isolated from sediment sample from an anoxic zone, rich in decomposing organic material, obtained from the Tucuruí hydroelectric dam reservoir in eastern Brazilian Amazonia. The partial nucleotide sequences obtained were 83 to 95 percent similar to those available in databases, indicating a low diversity of archaeans in the reservoir. Two orders were identified -the Methanomicrobiales, and a unique Operational Taxonomic Unit (OTU) forming a clade with the Methanosarcinales according to low bootstrap values. Homology modeling was used to determine the three-dimensional (3D) structures, for this the partial nucleotide sequence of the mcrα were isolated and translated on their partial amino acid sequences. The 3D structures of the archaean mcrα observed in the present study varied little, and presented approximately 70 percent identity in comparison with the mcrα of Methanopyrus klanderi. The results demonstrated that the community of methanogenic archaeans of the anoxic C1 region of the Tucurui reservoir is relatively homogeneous.

Composição química e valor nutricional para grandes herbívoros das folhas e frutos de aninga (Montrichardia linifera, Araceae) / Chemical composition and nutritional value of leaves and fruits of aninga (Montrichardia linifera, Araceae) for large herbivores

Montrichardia linifera (Araceae), conhecida popularmente como 'aninga', faz parte dos ecossistemas de várzea da Amazônia e da dieta natural de animais como peixe-boi, tartarugas, peixes, búfalo e gado. Com o objetivo de contribuir para o conhecimento químico e valor nutricional da mesma, folhas e frutos de M. linifera foram coletados às margens dos rios Guamá e Maratauíra, no Estado do Pará, Brasil. Em folhas e frutos foram realizadas análises de umidade, resíduo mineral fixo (cinzas), lipídios, proteínas, fibra bruta, concentração de carboidratos e valor calórico. A composição mineral (Ca, Mg, Cu, Fe, Zn e Mn) foi obtida por espectrometria de absorção atômica de chama. Observou-se que tanto as folhas quanto os frutos da aninga, apesar de calóricos (289,75 kcal e 355,12 kcal, respectivamente), possuem baixo valor protéico (0,44% e 0,24 %, respectivamente). As concentrações de manganês obtidas (folha = 3279,46 mg kg-1e fruto = 18151,53 mg kg-1) foram consideradas tóxicas, extrapolando o limite máximo tolerável para ruminantes (1000 mg kg-1). A M. linifera, tem capacidade de absorver e bioacumular grandes quantidades de Ca, Mg e Mn presentes no solo, o que torna inadequada a sua utilização exclusiva na alimentação de quelônios, bovinos e bubalinos, havendo necessidade de mais estudos para sua aplicação como parte da ração.

The aninga (Montrichardia linifera, Araceae) is often found in the floodplain ecosystems of the Amazon and is the natural diet of animals such as manatees, turtles, fish, buffalo and cattle. Aiming to contribute to the chemical knowledge and nutritional value of this plant, leaves and fruits of M. linifera were collected on the banks of the Guama and Maratauira rivers, Para State, Brazil. We determined the moisture content, ash mineral composition, lipids, protein, fiber, carbohydrate and caloric value of the fruits and leaves. The mineral composition (Ca, Mg, Cu, Fe, Zn and Mn) was obtained by flame atomic absorption spectrometry. The leaves and the fruits of M. linifera had caloric values of 289.75 kcal and 355.12 kcal, respectively; and a low protein concentration, 0.44% for leaves and 0.24% for fruits. Manganese concentrations were 3279.46 mg kg-1 for leaves and 18151.53 mg kg-1 for fruits. These Mn concentrations are considered toxic, as they exceed the maximum tolerable for the ruminants (1000 mg kg-1). The M. linifera has the capacity to absorb and bioaccumulate large amounts of Ca, Mg and Mn in the soil, which makes it inappropriate for exclusive use as food for turtles, cattle and buffaloes, requiring more studies for its application as part of the diet.

Avaliação de minerais em plantas medicinais amazônicas / Minerals evaluation in Amazonian medicinal plants

Amazônia brasileira oferece um apreciável potencial de plantas com propriedades terapêuticas, embora a maioria seja pouco conhecida. Dessa forma, com o objetivo de verificar a potencialidade nutricional de ervas medicinais, determinou-se a concentração de Ca, Mg, Fe, Cu e Zn nas folhas e nos chás das espécies: Piper callosum Ruiz & Pav., Piperaceae, Mikania lindleyana DC., Asteraceae e Arrabidaea chica (Humb. & Bonpl.) B. Verl., Bignoniaceae. As amostras de plantas depois de terem sido processadas, foram submetidas a digestão e em seguida realizada as leituras dos metais em um espectrofotômetro de absorção atômica. Para o chá de Arrabidaea chica foram detectados teores de Ca (6955 a 20058 mg/L), Mg (2390 a 3094 mg/L) e Fe (40 a 61 mg/L). Para o chá de Mikania lindleyana além da presença de altos valores de Ca (17722 a 22336 mg/L), Mg (4531 a 9370 mg/L) e Fe (20 a 87 mg/L) foram encontrados de 7 a 16 mg/L de Cu e 9 a 41 mg/L de Zn. O chá do Piper callosum apresentou em média 2036 a 4344 mg/L de Ca, 618 a 4023 mg/L de Mg e 39 a 60 mg/L de Fe. Comparando-se os resultados dos minerais com os valores recomendados pela Organização Mundial da Saúde, conclui-se que os metais presentes nos chás das plantas poderiam contribuir na complementação das dietas alimentares das pessoas que as utilizam.

The Amazonian Brazilian offers an appreciable potential of plants with therapeutic properties, although most are little known. In this way, with the objective of verifying the potentiality nutritional of medicinal herbs, a work was developed to determine the concentration of Ca, Mg, Fe, Cu and Zn in the leaves and in the teas of these species: Piper callosum Ruiz & Pav., Piperaceae, Mikania lindleyana DC., Asteraceae e Arrabidaea chica (Humb. & Bonpl.) B. Verl., Bignoniaceae. After the plants samples have been processed, they were submitted to digestion and soon afterwards the metals were analyzed in an spectrophotometer of Atomic Absorption. The results showed the follow yields: for the tea of Arrabidaea chica Ca were detected (6955 to 20058 mg/L), Mg (2390 to 3094 mg/L) and Fe (40 to 61 mg/L). For the tea of Mikania lindleyana besides the presence of high values of Ca (17722 to 22336 mg/L), Mg (4531 to 9370 mg/L) and Fe (20 to 87 mg/L) they were found from 7 to 16 mg/L of Cu and 9 to 41 mg/L of Zn. The tea of the Piper callosum presented 2036 to 4344 mg/L of Ca, 618 to 4023 mg/L of Mg and 39 to 60 mg/L of Fe. Being compared the results of the minerals with the values recommended by the Health World Organization, is possible that the present metals in the teas of the plants could contribute in the complementation of the people's alimentary diets that use these medicinal plants.

A quantum mechanics/molecular mechanics study of the protein-ligand interaction of two potent inhibitors of human O-GlcNAcase: PUGNAc and NAG-thiazoline.

O-glycoprotein 2-acetamino-2-deoxy-beta- d-glucopyranosidase ( O-GlcNAcase) hydrolyzes 2-acetamido-2-deoxy-beta- d-glucopyranose ( O-GlcNAc) residues of serine/threonine residues of modified proteins. O-GlcNAc is present in many intracellular proteins and appears to have a role in the etiology of several diseases including cancer, Alzheimer's disease, and type II diabetes. In this work, we have carried out molecular dynamics simulations using a hybrid quantum mechanics/molecular mechanics approach to determine the binding of two potent inhibitors, PUGNAc and NAG, with a bacterial O-GlcNAcase. The results of these simulations show that Asp-401, Asp-298, and Asp-297 residues play an important role in the protein-inhibitor interactions. These results might be useful to design compounds with more interesting inhibitory activity on the basis of its three-dimensional structure.