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.

Predição computacional de alvos moleculares de um complexo metálico de rutênio com epiisopiloturina e óxido nítrico

A Leishmaniose é uma doença infecciosa que ocasiona a morte de 26.000 a 65.000 pessoas anualmente, estima-se que no ano de 2019 houve 700.000 a 1 milhão de novos casos. Estes dados são preocupantes e está relacionado à falta de saneamento básico que favorece a proliferação dos vetores, além da ausência de medicamentos eficientes com mecanismos de ação alternativos e com menos efeitos colaterais. Em meio a essa necessidade de novos agentes inibitórios, este estudo teve como objetivo realizar uma predição computacional de alvos moleculares de Leishmania para um complexo metálico de rutênio com epiisopiloturina e óxido nítrico (Epiruno2). O processo de docking molecular foi realizado empregando-se o software Autodock Tools (ADT) versão 1.5.6. As proteínas alvos foram consideradas rígidas, enquanto que o Epiruno2 foi considerado flexível. A glicoproteína GP63 (1lml) representa mais de 1% da proteína total do parasito tendo em vista que a 1lml é uma metaloprotease que predomina grupos funcionais em seu sítio ativo, torna-se um alvo atrativo em estudos de atividade inibitória. O docking molecular entre o Epiruno2 e a 1lml resultou na melhor conformação de encaixe deste estudo, com energia de Gbinda de -8,05 Kcal.mol-1 e uma constante de inibição de 1,26 µM. Também foi observada a formação de quatro pontes de hidrogênio, demonstrando ser um forte candidato a fármaco antileishmania. Concluindo-se que o composto epiruno2 é clinicamente atrativo para estudos experimentais futuros ex vivo, in vitro e in vivo, pois seus resultados in sílico apresentaram boas interações moleculares para todas as proteínas alvo deste estudo.

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.

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.

Behavioral effects induced by antitumor cleronade diterpenes from Casearia sylvestris and in silico interactions with neuron receptors

ETHNOPHARMACOLOGICAL RELEVANCE

Casearia sylvestris is a medicinal plant traditionally used to treat snakebites, wounds, inflammation and gastric ulcers and scientific supports for have demonstrated its antitumor, antihyperlipidemic and antiparasitic properties.

AIM OF THE STUDY

To assess the effects of a fraction with casearins (FC) on adult mice using classical experimental models of animal behavior and theoretical calculations to verify the interaction of Casearin X (Cas X) with neuron receptors.

MATERIALS AND METHODS

Animals divided in 6 groups (n=9/group) were intraperitoneally treated with vehicle (DMSO 4%), FC (2.5, 5, 10 and 25mg/kg/day) and diazepam (2mg/kg) for 7 days. Thirty minutes after the last dose of treatment, acute toxicity and behavioral experiments were performed.

RESULTS

The highest dose of FC (25mg/kg/day) caused diarrhea, weight loss and death of one animal. Elevated plus maze test showed that lower doses [2.5mg/kg/day (36.4±5.1s) and 5mg/kg/day (43.9±6.2s)] increased the time spent in open arms (TSOA). Open field test revealed reduction in the number of crossings (54.9%, 51.1%, 48% and 67.7% for 2.5, 5, 10 and 25mg/kg/day, respectively) in all doses of FC studied and decrease of rearings at 25mg/kg/day (p<0.05). Computational calculations showed that the inhibition constant (Ki) for the Cas X-D₁ complex is up to 1000-fold more favourable than the Cas X-GABA_A complex. All ∆G° values obtained for Cas X-D₁ complexes were more negative than those seen with Cas X-GABA_A complexes.

CONCLUSIONS

Findings indicate a probable anxiolytic action of the FC since it reduces the number of crossings and rearings and prolonged the time spent in open arms, without sedative and myorelaxant effects, probably due to the interaction of Cas X with dopaminergic system.