Molecular Modeling Approaches for Determining Gene Function: application to a Putative Poly-A Binding Protein from Leishmania amazonensis (LaPABP)

The great expansion in the number of genome sequencing projects has revealed the importance of computational methods to speed up the characterization of unknown genes. These studies have been improved by the use of three dimensional information from the predicted proteins generated by molecular modeling techniques. In this work, we disclose the structure-function relationship of a gene product from Leishmania amazonensis by applying molecular modeling and bioinformatics techniques. The analyzed sequence encodes a 159 aminoacids polypeptide (estimated 18 kDa) and was denoted LaPABP for its high homology with poly-A binding proteins from trypanosomatids. The domain structure, clustering analysis and a three dimensional model of LaPABP, basically obtained by homology modeling on the structure of the human poly-A binding protein, are described. Based on the analysis of the electrostatic potential mapped on the model's surface and conservation of intramolecular contacts responsible for folding stabilization we hypothesize that this protein may have less avidity to RNA than it's L. major counterpart but still account for a significant functional activity in the parasite. The model obtained will help in the design of mutagenesis experiments aimed to elucidate the mechanism of gene expression in trypanosomatids and serve as a starting point for its exploration as a potential source of targets for a rational chemotherapy.

Schistosoma mansoni major egg antigen Smp40: molecular modeling and potential immunoreactivity for anti-pathology vaccine development

The pathogenesis of Schistosoma mansoni infection is largely determined by host T-cell mediated immune responses such as the granulomatous response to tissue deposited eggs and subsequent fibrosis. The major egg antigens have a valuable role in desensitizing the CD4+ Th cells that mediate granuloma formation, which may prevent or ameliorate clinical signs of schistosomiasis.S. mansoni major egg antigen Smp40 was expressed and completely purified. It was found that the expressed Smp40 reacts specifically with anti-Smp40 monoclonal antibody in Western blotting. Three-dimensional structure was elucidated based on the similarity of Smp40 with the small heat shock protein coded in the protein database as 1SHS as a template in the molecular modeling. It was figured out that the C-terminal of the Smp40 protein (residues 130 onward) contains two alpha crystallin domains. The fold consists of eight beta strands sandwiched in two sheets forming Greek key. The purified Smp40 was used for in vitro stimulation of peripheral blood mononuclear cells from patients infected with S. mansoni using phytohemagglutinin mitogen as a positive control. The obtained results showed that there is no statistical difference in interferon-g, interleukin (IL)-4 and IL-13 levels obtained with Smp40 stimulation compared with the control group (P > 0.05 for each). On the other hand, there were significant differences after Smp40 stimulation in IL-5 (P = 0.006) and IL-10 levels (P < 0.001) compared with the control group. Gaining the knowledge by reviewing the literature, it was found that the overall pattern of cytokine profile obtained with Smp40 stimulation is reported to be associated with reduced collagen deposition, decreased fibrosis, and granuloma formation inhibition. This may reflect its future prospect as a leading anti-pathology schistosomal vaccine candidate.

Cloning and Molecular Characterization of the Schistosoma mansoni Genes RbAp48 and Histone H4

The human nuclear protein RbAp48 is a member of the tryptophan/aspartate (WD) repeat family, which binds to the retinoblastoma (Rb) protein. It also corresponds to the smallest subunit of the chromatin assembly factor and is able to bind to the helix 1 of histone H4, taking it to the DNA in replication. A cDNA homologous to the human gene RbAp48 was isolated from a Schistosoma mansoni adult worm library and named SmRbAp48. The full length sequence of SmRbAp48 cDNA is 1036 bp long, encoding a protein of 308 amino acids. The transcript of SmRbAp48 was detected in egg, cercariae and schistosomulum stages. The protein shows 84% similarity with the human RbAp48, possessing four WD repeats on its C-terminus. A hypothetical tridimensional structure for the SmRbAp48 C-terminal domain was constructed by computational molecular modeling using the b-subunit of the G protein as a model. To further verify a possible interaction between SmRbAp48 and S. mansoni histone H4, the histone H4 gene was amplified from adult worm genomic DNA using degenerated primers. The gene fragment of SmH4 is 294 bp long, encoding a protein of 98 amino acids which is 100% identical to histone H4 from Drosophila melanogaster.

Modelagem Molecular: Uma Ferramenta para o Planejamento Racional de Fármacos em Química Medicinal

The molecular basis of modern therapeutics consist in the modulation of cell function by the interaction of microbioactive molecules as drug cells macromolecules structures. Molecular modeling is a computational technique developed to access the chemical structure. This methodology, by means of the molecular similarity and complementary paradigm, is the basis for the computer-assisted drug design universally employed in pharmaceutical research laboratories to obtain more efficient, more selective, and safer drugs. In this work, we discuss some methods for molecular modeling and some approaches to evaluate new bioactive structures in development by our research group.

Molecular mechanics application in inorganic Chemistry

The present paper is a review about basic principles of the molecular mechanics that is the most important tool used in molecular modeling area, and their applications to the calculation of the relative stability and chemical reactivity of organometalic and coordination compounds. We show how molecular mechanics can be successfully applied to a wide variety of inorganic systems.

Introdução a modelagem molecular de fármacos no curso experimental de química farmacêutica

Molecular Modeling is an important tool in drug design and it is very useful to predict biological activity from a library of compounds. A wide variety of computer programs and methods have been developed to visualize the tridimensional geometry and calculate physical properties of drugs. In this work, we describe a practical approach of molecular modeling as a powerful tool to study structure-activity relationships of drugs, including some antibacterials, hormones, cholinergic and adrenergic agents. At first, the students learn how to draw 3D structures and use them to perform conformational and molecular analysis. Thus, they compare drugs with similar pharmacological activity by superimposing one structure on the top of another and evaluate the geometry and physical properties.

Síntese, avaliação biológica e modelagem molecular de arilfuranos como inibidores da enzima tripanotiona redutase

Trypanosoma cruzi is a protozoan parasite that causes a severe disease (Chagas'disease) in Central and South America. The currently available chemotherapeutic agents against this disease are still inadequate. The enzyme trypanothione reductase (TR) is considered a validated molecular target for the development of new drugs against this parasite. In this regard, a series of arylfurans based on 2,5-bis-(4-acetamidophenyl)furan was synthesized and tested for their in vitro inhibitory activity against TR. Molecular modeling studies of putative enzyme-inhibitor complexes revealed a possible mechanism of interaction. From synthesized compounds, a benzylaminofuran derivative was found to be more active than the lead compound.

Termocromismo em soluções de alcóxidos de Vanádio(IV): uma abordagem pela modelagem molecular

The thermochromic behavior exhibited by vanadium(IV) alkoxides, [V2(μ-OPr i)2(OPr i) 6] and [V2(μ-ONep)2(ONep)6 ], OPr i = isopropoxide and ONep = neopentoxide, was studied by molecular modeling using DFT, TDDFT and INDO/S methods. The vibrational and electronic spectra calculated for [V2(μ-OPr i)2(OPr i) 6] were very similar to the experimental data registered for crystalline samples of the complex and for its solutions at low temperature (< 210 K), while spectra recorded at high temperature (> 315 K) were compatible with those calculated for the monomeric form, [V(OPr i)4]. These results consistently point to a monomer/dimer equilibrium as an explanation for the solution thermochromism of {V(OPr i)4}n. In spite of the structural similarity between [V2(μ-ONep)2(ONep)6 ] and [V2(μ-OPr i)2(OPr i) 6] in the solid state, the thermochromic behavior of the former could not be explained by the same model, and the possibility of tetranuclear aggregation at low temperatures was also investigated.

Uso de modelagem molecular no estudo dos conceitos de nucleofilicidade e basicidade

Molecular modeling enables the students to visualize the abstract relationships underlying theoretical concepts that explain experimental data on the molecular and atomic levels. With this aim we used the free software "Arguslab 4.0.1" (semi-empirical method) to study the reaction of 1-chloropropane with ethoxide in solution, known to lead to methyl propyl ether, through the S N2 mechanism, and propene, through the E2 mechanism. This tool allows users to calculate some properties (i. e. heat formation or electric charges) and to produce 3D images (molecular geometry, electrostatic potential surface, etc.) that render the comprehension of the factors underlying the reaction's progress, which are related to the structure of the reagents, and the process kinetic clearer and easier to understand by the students

Febrifugine derivative antimalarial activity: quantum mechanical predictors

Plasmodium falciparum resistant strain development has encouraged the search for new antimalarial drugs. Febrifugine is a natural substance with high activity against P. falciparum presenting strong emetic property and liver toxicity, which prevent it from being used as a clinical drug. The search for analogues that could have a better clinical performance is a current topic. We aim to investigate the theoretical electronic structure by means of febrifugine derivative family semi-empirical molecular orbital calculations, seeking the electronic indexes that could help the design of new efficient derivatives. The theoretical results show there is a clustering in well-defined ranges of several electronic indexes of the most selective molecules. The model proposed for achieving high selectivity was tested with success.

Estudio estructural del MoO3 y sus planos cristalinos

In the present work we present geometric models of the most studied MoO3 surfaces, which were obtained using the DTMM 2.0 Molecular Modeller software. MoO3 has an orthorhombic layered structure, with each layer comprised of two interleaved planes of MoO6 octahedral. These layers are parallel to the (010) crystal plane and only oxygen ions are exposed on their surfaces. This situation results in weak van der Waals bonding between layers and in a relatively inert surface. In our approach to surface geometric structure we consider "ideal" crystal surface, in which the bulk atomic arrangement is maintained. These surfaces were generated by imaginary cleavage along appropriate planes in the bulk crystal structure.

Estudo experimental e teórico da redução de bases de Schiff derivadas da 3,3-difenilpropilamina

A series of seven Schiff bases have been synthesized from 3,3-diphenylpropilamine and substituted benzaldehydes. These imines were treated with NaBH4 in ethanol affording the corresponding amines in 98-55% yields. A molecular modeling study was performed with the Schiff bases in order to compare the theoretical parameters with the experimental results. The theoretical parameters were obtained by AM1 and PM3 semi-empirical methods. The analysis of charge, electron densities and LUMO coefficients suggested that the most favorable interactions should occur with Schiff bases containing electron-donating groups, in accordance with experimental yields, showing that the higher reactivity is due to higher electrophilic character of imine carbons.

Um paradigma da química medicinal: a flexibilidade dos ligantes e receptores

In general, molecular modeling techniques applied in medicinal chemistry have been static and drug based. However the active site geometry and the intrinsic flexibility of both receptor and ligand are fundamental properties for molecular recognition and drug action. As a consequence, the use of dynamic models to describe the ligand-receptor complex is becoming a more common procedure. In this work we discuss the relevance of considering the receptor structure in medicinal chemistry studies as well as the flexibility of the ligand-receptor complex.

Estrutura e propriedades da difenil-4-amina sulfonato de sódio: um dopante de filmes condutores

This work contains the theoretical simulation of the conformation of diphenyl-4-amine sodium sulphonate (DASNa) and correlates its geometry with conductivity, showing that the conductivity increases as the molecule becomes more planar. The solvent effect was also evaluated, using water and dimethylsulfoxide. Some properties, such as bond distance, vibration al frequency and effective charge were calculated. The utilization of diphenyl-4-amine sodium sulphonate (DASNa) as dopant of aniline was investigated in view of the HOMO-LUMO energy gap.

Improvement of genistein content in solid genistein/-cyclodextrin complexes β

Genistein:β-cyclodextrin complexes with high drug loading (19.22%) were prepared by freeze-drying and characterized by differential scanning calorimetry and hydrogen nuclear magnetic resonance spectroscopy. The spatial configuration of the complex was proposed by means of 2D-NOESY experiment combined with molecular modeling. According to the results obtained, the interaction of genistein with β -cyclodextrin in a 1:1 complex is supposed to occur mainly through the insertion of the guest A-ring in cyclodextrin cavity, without rule out the possibility of inclusion through the B-ring, as previously reported in the literature.