PK/DB: database for pharmacokinetic properties and predictive in silico ADME models

The study of pharmacokinetic properties (PK) is of great importance in drug discovery and development. In the present work, PK/DB (a new freely available database for PK) was designed with the aim of creating robust databases for pharmacokinetic studies and in silico absorption, distribution, metabolism and excretion (ADME) prediction. Comprehensive, web-based and easy to access, PK/DB manages 1203 compounds which represent 2973 pharmacokinetic measurements, including five models for in silico ADME prediction (human intestinal absorption, human oral bioavailability, plasma protein binding, bloodbrain barrier and water solubility).

In silico screening of HIV-1 non-nucleoside reverse transcriptase and protease inhibitors

Two targets, reverse transcriptase (RT) and protease from HIV-1, were used during the past two decades to the discovery of non-nucleoside reverse transcriptase inhibitors (NNRTI) and protease inhibitors (PI) that belong to the arsenal of the antiretroviral therapy. Herein these enzymes were chosen as templates for conducting a computer-aided ligand design. Ligand and structure-based drug designs were the starting points to select compounds from a database bearing more than five million compounds by means of cheminformatic tools. New promising lead structures are retrieved from the database, which are open to acquisition and test. Classes of molecules already described as NNRTI or PI in the literature also came out and were useful to prove the reliability of the workflow, and thus validating the work carried out so far. (c) 2007 Elsevier Masson SAS. All rights reserved.

Viabilidade tecnica da producao de blocos silico-calcarios na regiao de Santa Maria, no Rio Grande do Sul

Este trabalho é camposto por dois estudos basicamente: um estudo teórico sobre os blocos sílico-calcários de areia-cal e um estudo prático sobre a viabilidade técnica de produção destes blocos em uma região determinada. A pesquisa teórica procurou elucidar o que vem a ser um bloco síilico-calcário, buscando a viabilidade da pesquisa prática e os pontos principais a serem abordados. Foram estudados, nesta parte, as matérias-primas e o processo produtivo empregado na confecção destes elementos, mostrando a importância de cada item para as características do produto final. Foi dada atenção ainda às características técnicas, aos fatores que determinam a produção e emprego e aos aspectos positivos e negativos dos elementos deste tipo produzido em outros locais. A pesquisa prática buscou a disponibilidade de matéria-prima conveniente para a produção de blocos sílicos-calcários, e o efeito das variações do processo produtivo sobre os produtos confeccionados com os materiais estudados. A matéria-prima empregada foi uma areia quartzosa da região de Santa Maria-RS, cal calcítica virgem de São Sepé-RS, e cinza volante da termoelétrica Presidente Médici, em Bagé-RS, fazendo-se variações nas percentagens destes componentes. As variações do processo produtivo foram efetuadas no tipo de moldagem dos corpos de prova, em que foi usada pressão, vibração e vibro-compressão, e na pressão de autoclavagem. Para todas as variações efetuadas foram obtidas as seguintes características: variações por autoclavagem, massa específica aparente, absorção d´água, resistência à compressão, resistência à tração e módulo de elasticidade à compressão, as quais foram relacionadas através de quadros e figuras às diversas variações.

Qualidade de vida em gestantes no terceiro trimestre com pirose e/ou regurgitação : contribuição da cafeína, acido ascórbico e ácidos graxos

Introdução: Pirose e regurgitação são manifestações da Doença do Refluxo Gastresofágico (DRGE) que ocorrem freqüentemente no terceiro trimestre da gravidez, porém seu impacto na qualidade de vida de gestantes é pouco conhecido. Objetivos: 1. Mensurar a qualidade de vida em gestantes no terceiro trimestre da gravidez com Pirose e Regurgitação; 2. Avaliar a relação entre Pirose e Regurgitação e a dieta. Pacientes e Métodos: Gestantes no terceiro trimestre acompanhadas ambulatorialmente foram entrevistadas para colher dados referentes à história obstétrica, freqüência, intensidade e passado de P e R, qualidade de vida (mensurada a partir do questionário genérico SF-36), ingestão alimentar (avaliada por recordatório de 24h) e medidas antropométricas; Resultados: Foram estudadas consecutivamente 82 gestantes: 62 com pirose e/ou regurgitação e 20 assintomáticas. Pirose foi relatada por 62 (76%) gestantes e regurgitação por 58 (71%). A idade gestacional média foi 33,8±3,7 semanas, 35 (43%) apresentavam história familiar positiva de pirose e/ou regurgitação e 57 (70%) não apresentavam tais sintomas fora da gravidez. Houve redução estatisticamente significativa na qualidade de vida das gestantes sintomáticas nos seguintes domínios: Para pirose, em Limitação Física e Aspectos Sociais; para regurgitação, em Limitação Física, Aspectos Sociais, Aspectos Emocionais e Dor. Houve concordância entre presença de pirose em gestações passadas e a atual. Gestantes com pirose apresentaram-se significativamente com maior peso corporal. Ácidos graxos poli e monoinsaturados, cafeína, ácido ascórbico e sulfato ferroso foram significativamente associados com pirose e/ou regurgitação. Conclusões: 1.Pirose e / ou regurgitação diminuíram a qualidade de vida em gestantes no terceiro trimestre; 2. ácidos graxos, cafeína, ácido ascórbico e sulfato ferroso estiveram associados com pirose e/ou regurgitação.

Enzymatic inhibitory activity of hydroxycinnamates (HCs): in silico studies

Diabetes is a worldwide health issue that has been expanding mainly in developed countries. It is characterized by abnormal levels of blood sugar due to several factors. The most common are resistance to insulin and the production of defective insulin which exerts little or no effect. Its most common symptoms include tissue damage to several systems due to elevated levels of blood sugar. One of the key enzymes in hydrocarbon metabolism is α-glucosidase (EC 3.2.1.20). It catalyzes the breakdown of complex carbohydrates into their respective monomers (glucose) which allows them to be absorbed. In this work, caffeoyl quinic acids and their metabolites were analyzed as potential inhibitors for α-glucosidase. The search for the best inhibitor was conducted using molecular docking. The affinity of each compound was compared to the inhibitor present in the crystal structure of the protein. As no inhibitor with a similar affinity was´found, a new approach was used, in situ drug design. It was not possible to achieve an inhibitor capable of competing with the one present in the crystal structure of the enzyme, which is also its current commercial inhibitor. It is possible to draw some conclusions as to which functional groups interact best with certain residues of the active site. This work was divided into three main sections. The first section, Diabetes, serves as an introduction to what is Diabetes, its symptoms and/or side effects and how caffeoyl quinic acids could be used as a treatment. The second section, Caffeoylquinic acids and their metabolites as inhibitors for Alfa-glucosidase, corresponds to the search through molecular docking of caffeoyl quinic acids as inhibitors for α-glucosidase and what was possible to draw from this search. The last section, In situ design of an inhibitor for α-glucosidase (EC 3.2.1.20), corresponds to the in situ drug design study and what it achieved. The representation of each of the molecules used as a ligand can be found in the Annexes.

Construção de modelos de interação in silico e in vitro do inibidor do tipo Kunitz de Adenanthera pavonina L. para as enzimas cisteínicas e serínicas

Serines proteinases inhibitors (PIs) are widely distributed in nature and are able to inhibit both in vitro and in vivo enzymatic activites. Seed PIs in than leguminous are classified in seven families, Bowman-Birk and Kunitz type families that most studied representing an important role in the first line of defense toward insects pests. Some Kunitz type inhibitors possess activities serine and cysteine for proteinases named bifunctional inhibitor, as ApTKI the inhibitor isolate from seed of Adenanthera pavonina. The A. pavonina inhibitor presenting the uncommon property and was used for interaction studies between proteinases serine (trypsin) and cysteine (papain). In order to determinate the in vitro interaction of ApTKI against enzymes inhibitor purification was carried cut by using chromatographic techniques and inhibition assays. The 3D model of the bifunctional inhibitor ApTKI was constructed SWISS-MODEL program by homology modeling using soybean trypsin inhibitor (STI, pdb:1ba7), as template which presented 40% of identity to A. pavonina inhibitor. Model quality was evaluated by PROCHECK program. Moreover in silico analyzes of formed complex between the enzymes and ApTKI was evaluated by HEX 4.5 program. In vitro results confirmed the inhibitory assays, where the inhibitor presented the ability to simultaneously inhibit trypsin and papain. The residues encountered in the inhibitor model of folder structural three-dimensional that make contact to enzymes target coud explain the specificity pattern against serine and cysteine proteinases

Determinação de motivos de ligação à quitina em vicilinas de Canavalia ensiformis e Vigna unguiculata através de métodos in silico e relação com suas toxicidades para o bruquídeo Callosobruchus maculatus (Coleoptera:Bruchidae)

Chitin is an important structural component of the cellular wall of fungi and exoskeleton of many invertebrate plagues, such as insects and nematodes. In digestory systems of insects it forms a named matrix of peritrophic membrane. One of the most studied interaction models protein-carbohydrate is the model that involves chitin-binding proteins. Among the involved characterized domains already in this interaction if they detach the hevein domain (HD), from of Hevea brasiliensis (Rubber tree), the R&R consensus domain (R&R), found in cuticular proteins of insects, and the motif called in this study as conglicinin motif (CD), found in the cristallography structure of the β-conglicinin bounded with GlcNac. These three chitin-binding domains had been used to determine which of them could be involved in silico in the interaction of Canavalia ensiformis and Vigna unguiculata vicilins with chitin, as well as associate these results with the WD50 of these vicilins for Callosobruchus maculatus larvae. The technique of comparative modeling was used for construction of the model 3D of the vicilin of V. unguiculata, that was not found in the data bases. Using the ClustalW program it was gotten localization of these domains in the vicilins primary structure. The domains R&R and CD had been found with bigger homology in the vicilins primary sequences and had been target of interaction studies. Through program GRAMM models of interaction ( dockings ) of the vicilins with GlcNac had been gotten. The results had shown that, through analysis in silico, HD is not part of the vicilins structures, proving the result gotten with the alignment of the primary sequences; the R&R domain, although not to have structural similarity in the vicilins, probably it has a participation in the activity of interaction of these with GlcNac; whereas the CD domain participates directly in the interaction of the vicilins with GlcNac. These results in silico show that the amino acid number, the types and the amount of binding made for the CD motif with GlcNac seem to be directly associates to the deleterious power that these vicilins show for C. maculatus larvae. This can give an initial step in the briefing of as the vicilins interact with alive chitin in and exert its toxic power for insects that possess peritrophic membrane

Estudo in silico da interação da albumina de soro humano com o ibuprofeno

Currently, computational methods have been increasingly used to aid in the characterization of molecular biological systems, especially when they relevant to human health. Ibuprofen is a nonsteroidal antiinflammatory or broadband use in the clinic. Once in the bloodstream, most of ibuprofen is linked to human serum albumin, the major protein of blood plasma, decreasing its bioavailability and requiring larger doses to produce its antiinflamatory action. This study aimes to characterize, through the interaction energy, how is the binding of ibuprofen to albumin and to establish what are the main amino acids and molecular interactions involved in the process. For this purpouse, it was conducted an in silico study, by using quantum mechanical calculations based on Density Functional Theory (DFT), with Generalized Gradient approximation (GGA) to describe the effects of exchange and correlation. The interaction energy of each amino acid belonging to the binding site to the ligand was calculated the using the method of molecular fragmentation with conjugated caps (MFCC). Besides energy, we calculated the distances, types of molecular interactions and atomic groups involved. The theoretical models used were satisfactory and show a more accurate description when the dielectric constant ε = 40 was used. The findings corroborate the literature in which the Sudlow site I (I-FA3) is the primary binding site and the site I-FA6 as secondary site. However, it differs in identifying the most important amino acids, which by interaction energy, in order of decreasing energy, are: Arg410, Lys414, Ser 489, Leu453 and Tyr411 to the I-Site FA3 and Leu481, Ser480, Lys351, Val482 and Arg209 to the site I-FA6. The quantification of interaction energy and description of the most important amino acids opens new avenues for studies aiming at manipulating the structure of ibuprofen, in order to decrease its interaction with albumin, and consequently increase its distribution

Floração precoce em cana-de-açúcar - um estudo utilizando ferramentas de análise in silico e proteômica

Sugarcane is one of the most important products of the world and Brazil is responsible for 25 % of the world production. One problem of this culture at northeast of Brazil is the early flowering. In our laboratory, it has been made before four subtractive libraries using early and late flowering genotypes in order to identify messages related to the flowering process. In this work, two cDNAs were chosen to make in silico analysis and overexpression constructs. Another approach to understand the flowering process in sugarcane was to use proteomic tools. First, the protocol for protein extraction using apical meristem was set up. After that, these proteins were separated on two bidimensional gels. It was possible to observe some difference for some regions of these gels as well as some proteins that can be found in all conditions. The next step, spots will be isolated and sequence on MS spectrometry in order to understand this physiological process in sugarcane

Estudos in silico da proteína AlkB e prospecção de bactérias alcanotróficas em solos da bacia petrolífera potiguar

Some microorganisms from virgin ecosystems are able to use petroleum it as source of carbon and energy. The knowledge of microbial biodiversity can help to reveal new metabolic systems for utilization alkanes with biotechnological importance. The aim of this study is: i) Accomplish an in silico study of the AlkB protein aimed to understand the probable mechanism involved on selectivity of alkanes in Gram positive and Gram negative bactéria. ii) prospect and analyze the response of the microbial alkanotrophics communities in soil and mangrove sediments of BPP RN and soil of Atlantic forest in the Horto Dois Irmãos Reserve area/PE using the molecular biomarker, gene alkB; with the PCR and PCR-DGGE approach

A contextualização e a interdisplinaridade no ensino de Química: uma analise de livros didáticos ACIDO-BASE e das propostas pedagógicas realizadas pelos docentes diante da temática

Nowadays, chemistry contents taught in high school continue to be presented in a fragmented and decontextualized manner by the teachers and the textbooks. Even though it is known that contextualization and interdisciplinary exchange play an important role in the process of Chemistry teaching/learning. Therefore, the present study aims at enlightening the importance of these methodological foundations in the learning of chemistry. The data acquisition about the subject Contextualization and Interdisciplinary Exchange involved in Chemistry Teaching was developed through bibliographical researches on chemistry textbooks, which focused on the analysis of the topics acid and base , since it is a theme studied throughout all three years of high school. The present study also developed questionnaires which were applied to analyze to what extent chemistry teachers are working in a contextualized and interdisciplinary manner throughout the process of Chemistry teaching/learning. The results obtained in the researches show that a contextualized and interdisciplinary teaching contributes to a more meaningful acquisition of chemistry knowledge, in a dynamic and interactive way, but there are still many roadblocks towards the achievement of this kind of Chemistry teaching/learning process

Highly polymorphic in silico-derived microsatellite loci in the potato-infecting fungal pathogen Rhizoctonia solani anastomosis group 3 from the Colombian Andes

Fourteen polymorphic microsatellite DNA markers derived from the draft genome sequence of Rhizoctonia solani anastomosis group 3 (AG-3), strain Rhs 1AP, were designed and characterized from the potato-infecting soil fungus R. solani AG-3. All loci were polymorphic in two field populations collected from Solanum tuberosum and S. phureja in the Colombian Andes. The total number of alleles per locus ranged from two to seven, while gene diversity (expected heterozygosity) varied from 0.11 to 0.81. Considering the variable levels of genetic diversity observed, these markers should be useful for population genetic analyses of this important dikaryotic fungal pathogen on a global scale.

In silico network topology-based prediction of gene essentiality

The identification of genes essential for survival is important for the understanding of the minimal requirements for cellular life and for drug design. As experimental studies with the purpose of building a catalog of essential genes for a given organism are time-consuming and laborious, a computational approach which could predict gene essentiality with high accuracy would be of great value. We present here a novel computational approach, called NTPGE (Network Topology-based Prediction of Gene Essentiality), that relies on the network topology features of a gene to estimate its essentiality. The first step of NTPGE is to construct the integrated molecular network for a given organism comprising protein physical, metabolic and transcriptional regulation interactions. The second step consists in training a decision-tree-based machine-learning algorithm on known essential and non-essential genes of the organism of interest, considering as learning attributes the network topology information for each of these genes. Finally, the decision-tree classifier generated is applied to the set of genes of this organism to estimate essentiality for each gene. We applied the NTPGE approach for discovering the essential genes in Escherichia coli and then assessed its performance. (C) 2007 Elsevier B.V. All rights reserved.

Boron transport in Eucalyptus. 2. Identification in silico of a putative boron transporter for xylem loading in eucalypt

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)