Investigation of G4(MP2)-XK theory for antimony compounds' thermochemistry.

The heats of formation of thirty-five molecules containing antimony atoms have been calculated using G4(MP2)-XK, B3LYP, M06, M06-HF, M06-2X, BMK, wB97XD, and TPSSh atomization. The discrepancies between the predicted and the reported heats of formation vary in the range of 0.0-83 kcal mol-1 when compared with experimental and literature. The best agreement with experimental and literature data was achieved by using G4(MP2)-XK. The functionals used did not show results as good as G4(MP2)-XK. In its development, G4 (MP2)-XK showed itself comparable in accuracy to the G4(MP2)-6X. Importantly, the precision of G4(MP2)-XK for heavier elements such as antimony is similar to that of the first- and second-row species, although it contains parameters that are only adjusted to the systems of the first two rows. In this study, we can observe that G4(MP2)-XK has excellent requirements for elements such as antimony and leads us to believe that its scope will be further expanded in future studies with formation enthalpy such as iodine and xenonium.

Cecropia pachystachya Trécul: identification, isolation of secondary metabolites, in silico study of toxicological evaluation and interaction with the enzymes 5-LOX and α-1-antitrypsin.

Cecropia pachystachya Tréc., popularly known as embaúba, belongs to the Cecropiaceae family and is used by the native population in the treatment of bronchitis, asthma, high blood pressure, fever, and as a diuretic. The pharmacological actions including anti-inflammatory, antioxidant, cardiotonic and sedative were previously reported. The objective of this study was to (1) isolate and identify bioactive compounds extracted from the ethanolic extract of C. pachystachya roots (ERCP), as well as (2) verify the affinity of these metabolites with the enzymes 5-lipoxygenase (5-LOX) and α-1-antitrypsin through in silico tests. Isolation and/or identification were performed using GC-MS, HPLC, Infrared (IR), and nuclear magnetic resonance (NMR) techniques. After isolation and identification of the active compounds, these substances were subjected to the in silico investigation that proceeded by performing PreADMET simulations and molecular docking calculations. The bioactive compounds identified were 1-(+)-ascorbic acid 2,6-dihexadecanoate, ethyl hexadecanoate, ethyl (9E,12E)-octadec-9,12-dienoate, ethyl (Z)-octadec-9-enoate and ethyl octadecanoate by GC-MS; chlorogenic acid, catechin, epicatechin, syringaldehyde by HPLC; ß-sitosterol, sitostenone, beccaridiol, tormentic acid, lupeol, α- and ß-amyrin by classical chromatography, IR, 1H and 13C NMR techniques. The ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties were determined for each bioactive compound. Tormentic acid demonstrated a greater affinity for 5-LOX enzyme while sitostenone demonstrated a higher affinity for the α-1-antitrypsin enzyme. Our findings demonstrated a diverse range of secondary metabolites isolated from C. pachystachya that showed relevant interactions with the enzymes 5-LOX and α-1-antitrypsin. Thus, "embaúba" may be employed in in vivo experimental studies as a form of alternative treatment for chronic lung diseases.Abbreviations: ADT: Autodock Tools; BBB: Blood-brain barrier; CaCo2: Human colonic adenocarcinoma cells; CC: Classic/open Column; TLC: Thin Layer Chromatography; CD40: Differentiation Cluster 40; CENAUREMN: Centro Nordestino de Aplicação e Uso da Ressonância Magnética Nuclear; GC-MS: Gas Chromatography coupled to mass spectrometry; HPLC: High-Perfomance Liquid Chromatography; CYP2C9, CYP2C19, CYP2D6 and CYP3A4: Cytochrome P450 isoenzymes; COPD: Chronic Obstructive Pulmonary Disease; DRX-500: X-Ray Diffraction - 500; ERCP: Ethanolic extract of the roots of C. pachystachya; FAPEPI: Fundação de Amparo à Pesquisa do Piauí; HIA: Human Intestinal Absorption; IR: Infrared; Ki: Inhibition constant; 5-LOX: 5-Lipoxygenase; mM: miliMolar; nM: nanoMolar; OECD423: acute toxic class method; PDB: Protein Data Bank; P-gP: P-glycoprotein; PM2,5: Small inhalable particles 2,5; PPB: Plasm Protein Binding; PreADMET: Prediction Absorption, Distribution, Metabolization, Excretion and Toxicity; NMR: Nuclear Magnetic Resonance; +S9: with metabolic activation; -S9: no metabolic activation; SisGen: Sistema Nacional de Gestão de Patrimônio Genético e do Conhecimento Tradicional Associado; RT: Retention time; TA100: Ames test with TA100 cells line; TA1535: Ames test with cells of the TA1535 cell line; UESPI: State University of Piauí; V79: lung fibroblast cells; ΔG: Gibbs free energy (Kcal/mol); µM: microMolar.

pHLA3D: Updating the database of predicted three-dimensional structures of HLA with HLA-DR, HLA-DQ and HLA-DP molecules.

To improve the availability of three-dimensional (3D) structures of HLA molecules, we created the pHLA3D database. In its first version, we modeled and published 106 3D structures of HLA class I molecules from the HLA-A, HLA-B, and HLA-C loci. This paper presents an update of this database, providing more 127 3D structures of HLA class II molecules (41 DR, 42 DQ, and 44 DP), predicted via homology modeling with MODELLER and SWISS-MODEL. These new 3D structures of HLA class II molecules are now freely available at pHLA3D (www.phla3d.com.br) for immunologists and other researchers working with HLA molecules.

On polarization functions for Gaussian basis sets.

In this work, we introduce a technique to choose polarization functions directly from the primitive set of Gaussian exponent without the necessity to optimize or even reoptimized them. For this purpose, initially, we employed Gaussian basis sets generated by using the Polynomial Generator Coordinate Hartree-Fock (PGCHF) method, and later we extended our technique to the cc-pVQZ and pc-3 Gaussian basis sets in order to show how our technique works and how good it is. Using the new polarized basis sets, from our technique, total electronic energies, equilibrium geometries, and vibrational frequencies were calculated for a set of molecules containing atoms from H(Z = 1) to Ba(Z = 56). The technique presented here can be used with any Gaussian basis set flexible (large) enough and also can be used to choose Gaussian basis set exponents from one basis set to another as polarization functions.

Ruthenium (II) complexes with N, O-chelating proline and threonine ligands cause selective cytotoxicity by the induction of genomic instability, cell cycle arrest and apoptosis in breast and prostate tumor cells.

Ruthenium complexes are being considered as novel chemotherapeutic alternatives for cancer treatment. In our study, we assessed the antitumoral activities of novel ruthenium complexes coupled to the amino acids proline (RuPro) and threonine (RuThr) in prostate tumor cell lines (DU145) and breast (MCF7), and normal cell lines of the lung fibroblast (GM07492A). Our results revealed that the EC50 of the complexes for DU145 and MCF7 was two times lower than that GM07492A. Moreover, RuPro and RuThr were not able to induce significant genomic instability, cell cycle arrest or cell death in GM07492A, but could induce DNA damage, arrest in G2/M and apoptosis in DU145 and MCF7. Furthermore, BAX, TP53 and ATM were found to be upregulated in DU145 and MCF7 treated with RuPro and RuThr, in which, a higher ASCT2 gene expression was also observed. Using molecular docking, RuPro and RuThr interact with ASCT2, suggesting that this transporter might have a pivotal role in the execution of their activities. Hence, our results with RuPro and RuThr are capable of selectively inducing genetic damage, cell cycle arrest and apoptosis in DU145 and MCF7. We suggest that the selective action of the RuPro and RuThr complexes is related to the higher expression of ASCT2 in the tumor cells.

pHLA3D: An online database of predicted three-dimensional structures of HLA molecules.

HLA epitope analysis emerged as a strategy to determine alloimmune risk in solid organ transplantation. However, it requires not only knowledge on HLA amino acids sequences, but also on HLA three-dimensional structures. Unfortunately, the number of structures available is still unsatisfactory. This work reports the modelling of 106 heterotrimeric (alpha chain + ß2M + peptide) HLA class I molecules. The models were generated by homology modelling using Modeller, refined using GalaxyRefine server, heterodimerized with Swiss-PDB Viewer and, finally, assessed as to their structural quality through Dali server. The final structures were made available through a free online database, pHLA3D (www.phla3d.com.br), developed in Ruby language using the Ruby on Rails web framework. Structural parameters were similar between refined molecules and their templates. The new database may improve HLA epitope analysis and better guide risk assessment in solid organ transplantation setting.

Cry1A(b)16 toxin from Bacillus thuringiensis: Theoretical refinement of three-dimensional structure and prediction of peptides as molecular markers for detection of genetically modified organisms.

Transgenic maize produced by the insertion of the Cry transgene into its genome became the second most cultivated crop worldwide. Cry gene from Bacillus thuringiensis kurstaki expresses protein derivatives of crystalline endotoxins which confer insect resistance onto the maize crop. Mandatory labeling of processed food containing or made by genetically modified organisms is in force in many countries, so, it is very urgent to develop fast and practical methods for GMO identification, for example, biosensors. In the absence of an available empirical structure of Cry1A(b)16 protein, a theoretical model was effectively generated, in this work, by homology modeling and molecular dynamics simulations based on two available homologous protein structures. Molecular dynamics simulations were carried out to refine the selected model, and an analysis of its global structure was performed. The refined models of Cry1A(b)16 showed a standard fold and structural characteristics similar to those seen in Bacillus thuringiensis Cry1A(a) insecticidal toxin and Bacillus thuringiensis serovar kurstaki Cry1A(c) toxin. After in silico analysis of Cry1A(b)16, two immunoreactive candidate peptides were selected and specific polyclonal antibodies were produced resulting in antibody-peptide interaction. Biosensing devices are expected to be developed for detection of the Cry1A(b) protein as a marker of transgenic maize in food. Proteins 2017; 85:1248-1257. © 2017 Wiley Periodicals, Inc.