Role of Halogen Bonds in Thyroid Hormone Receptor Selectivity: Pharmacophore-Based 3D-QSSR Studies

Most physiological effects of thyroid hormones are mediated by the two thyroid hormone receptor subtypes, TR alpha and TR beta. Several pharmacological effects mediated by TR beta might be beneficial in important medical conditions such as obesity, hypercholesterolemia and diabetes, and selective TR beta activation may elicit these effects while maintaining an acceptable safety profile, To understand the molecular determinants of affinity and subtype selectivity of TR ligands, we have successfully employed a ligand- and structure-guided pharmacophore-based approach to obtain the molecular alignment of a large series of thyromimetics. Statistically reliable three-dimensional quantitative structure-activity relationship (3D-QSAR) and three-dimensional quantitative structure-selectivity relationship (3D-QSSR) models were obtained using the comparative molecular field analysis (CoMFA) method, and the visual analyses of the contour maps drew attention to a number of possible opportunities for the development of analogs with improved affinity and selectivity. Furthermore, the 3D-QSSR analysis allowed the identification of a novel and previously unmentioned halogen bond, bringing new insights to the mechanism of activity and selectivity of thyromimetics.

Quantitative structure-activity relationships for a series of inhibitors of cruzain from Trypanosoma cruzi: Molecular modeling, CoMFA and CoMSIA studies

Human parasitic diseases are the foremost threat to human health and welfare around the world. Trypanosomiasis is a very serious infectious disease against which the currently available drugs are limited and not effective. Therefore, there is an urgent need for new chemotherapeutic agents. One attractive drug target is the major cysteine protease from Trypanosoma cruzi, cruzain. In the present work, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) studies were conducted on a series of thiosemicarbazone and semicarbazone derivatives as inhibitors of cruzain. Molecular modeling studies were performed in order to identify the preferred binding mode of the inhibitors into the enzyme active site, and to generate structural alignments for the three-dimensional quantitative structure-activity relationship (3D QSAR) investigations. Statistically significant models were obtained (CoMFA. r(2) = 0.96 and q(2) = 0.78; CoMSIA, r(2) = 0.91 and q(2) = 0.73), indicating their predictive ability for untested compounds. The models were externally validated employing a test set, and the predicted values were in good agreement with the experimental results. The final QSAR models and the information gathered from the 3D CoMFA and CoMSIA contour maps provided important insights into the chemical and structural basis involved in the molecular recognition process of this family of cruzain inhibitors, and should be useful for the design of new structurally related analogs with improved potency. (C) 2009 Elsevier Inc. All rights reserved.

CoMFA and CoMSIA 3D QSAR Models for a Series of Cyclic Imides with Analgesic Activity

Three-dimensional quantitative structure-activity relationships (3D-QSAR) were performed for a series of analgesic cyclic imides using the CoMFA and CoMSIA methods. Significant correlation coefficients ( CoMFA, r(2) = 0.95 and q(2) = 0.72; CoMSIA, r(2) = 0.96 and q(2) = 0.76) were obtained, and the generated models were externally validated using test sets. The final QSAR models as well as the information gathered from 3D contour maps should be useful for the design of novel cyclic imides having improved analgesic activity.

Structure-Based Approach for the Study of Estrogen Receptor Binding Affinity and Subtype Selectivity

Estrogens exert important physiological effects through the modulation of two human estrogen receptor (hER) subtypes, alpa (hER alpha) and beta (hER beta). Because the levels and relative proportion of hER alpha and hER beta differ significantly in different target cells, selective hER ligands could target specific tissues or pathways regulated by one receptor subtype without affecting the other. To understand the structural and chemical basis by which small molecule modulators are able to discriminate between the two subtypes, we have applied three-dimensional target-based approaches employing a series of potent hER-ligands. Comparative molecular field analysis (CoMFA) studies were applied to a data set of 81 hER modulators, for which binding affinity values were collected for both hER alpha and hER beta. Significant statistical coefficients were obtained (hER alpha, q(2) = 0.76; hER beta, q(2) = 0.70), indicating the internal consistency of the models. The generated models were validated using external test sets, and the predicted values were in good agreement with the experimental results. Five hER crystal structures were used in GRID/PCA investigations to generate molecular interaction fields (MIF) maps. hER alpha and hER beta were separated using one factor. The resulting 3D information was integrated with the aim of revealing the most relevant structural features involved in hER subtype selectivity. The final QSAR and GRID/PCA models and the information gathered from 3D contour maps should be useful for the design or novel hER modulators with improved selectivity.

Comparative molecular field analysis of a series of inhibitors of HIV-1 protease

Several protease inhibitors have reached the world market in the last fifteen years, dramatically improving the quality of life and life expectancy of millions of HIV-infected patients. In spite of the tremendous research efforts in this area, resistant HIV-1 variants are constantly decreasing the ability of the drugs to efficiently inhibit the enzyme. As a consequence, inhibitors with novel frameworks are necessary to circumvent resistance to chemotherapy. In the present work, we have created 3D QSAR models for a series of 82 HIV-1 protease inhibitors employing the comparative molecular field analysis (CoMFA) method. Significant correlation coefficients were obtained (q(2) = 0.82 and r(2) = 0.97), indicating the internal consistency of the best model, which was then used to evaluate an external test set containing 17 compounds. The predicted values were in good agreement with the experimental results, showing the robustness of the model and its substantial predictive power for untested compounds. The final QSAR model and the information gathered from the CoMFA contour maps should be useful for the design of novel anti-HIV agents with improved potency.

Fragment-guided approach to incorporating structural information into a CoMFA study: BACE-1 as an example

Alzheimer`s disease is an ultimately fatal neurodegenerative disease, and BACE-1 has become an attractive validated target for its therapy, with more than a hundred crystal structures deposited in the PDB. In the present study, we present a new methodology that integrates ligand-based methods with structural information derived from the receptor. 128 BACE-1 inhibitors recently disclosed by GlaxoSmithKline R&D were selected specifically because the crystal structures of 9 of these compounds complexed to BACE-1, as well as five closely related analogs, have been made available. A new fragment-guided approach was designed to incorporate this wealth of structural information into a CoMFA study, and the methodology was systematically compared to other popular approaches, such as docking, for generating a molecular alignment. The influence of the partial charges calculation method was also analyzed. Several consistent and predictive models are reported, including one with r (2) = 0.88, q (2) = 0.69 and r (pred) (2) = 0.72. The models obtained with the new methodology performed consistently better than those obtained by other methodologies, particularly in terms of external predictive power. The visual analyses of the contour maps in the context of the enzyme drew attention to a number of possible opportunities for the development of analogs with improved potency. These results suggest that 3D-QSAR studies may benefit from the additional structural information added by the presented methodology.

Improved voice activity detection algorithm using wavelet and support vector machine

This paper proposes an improved voice activity detection (VAD) algorithm using wavelet and support vector machine (SVM) for European Telecommunication Standards Institution (ETS1) adaptive multi-rate (AMR) narrow-band (NB) and wide-band (WB) speech codecs. First, based on the wavelet transform, the original IIR filter bank and pitch/tone detector are implemented, respectively, via the wavelet filter bank and the wavelet-based pitch/tone detection algorithm. The wavelet filter bank can divide input speech signal into several frequency bands so that the signal power level at each sub-band can be calculated. In addition, the background noise level can be estimated in each sub-band by using the wavelet de-noising method. The wavelet filter bank is also derived to detect correlated complex signals like music. Then the proposed algorithm can apply SVM to train an optimized non-linear VAD decision rule involving the sub-band power, noise level, pitch period, tone flag, and complex signals warning flag of input speech signals. By the use of the trained SVM, the proposed VAD algorithm can produce more accurate detection results. Various experimental results carried out from the Aurora speech database with different noise conditions show that the proposed algorithm gives considerable VAD performances superior to the AMR-NB VAD Options 1 and 2, and AMR-WB VAD. (C) 2009 Elsevier Ltd. All rights reserved.

Wavelet-based cepstrum calculation

In this paper we present a new wavelet-based algorithm for low-cost computation of the cepstrum. It can be used for real time precise pitch determination in automatic speech and speaker recognition systems. Many wavelet families are examined to determine the one that works best. The results confirm the efficacy and accuracy of the proposed technique for pitch extraction. (C) 2008 Elsevier B.V. All rights reserved.

Three-Dimensional Quantitative Structure-Activity Relationship Study of Antitumor 2-Formylpyridine Thiosemicarbazones Derivatives as Inhibitors of Ribonucleotide Reductase

In order to extend previous SAR and QSAR studies, 3D-QSAR analysis has been performed using CoMFA and CoMSIA approaches applied to a set of 39 alpha-(N)-heterocyclic carboxaldehydes thiosemicarbazones with their inhibitory activity values (IC(50)) evaluated against ribonucleotide reductase (RNR) of H.Ep.-2 cells (human epidermoid carcinoma), taken from selected literature. Both rigid and field alignment methods, taking the unsubstituted 2-formylpyridine thiosemicarbazone in its syn conformation as template, have been used to generate multiple predictive CoMFA and CoMSIA models derived from training sets and validated with the corresponding test sets. Acceptable predictive correlation coefficients (Q(cv)(2) from 0.360 to 0.609 for CoMFA and Q(cv)(2) from 0.394 to 0.580 for CoMSIA models) with high fitted correlation coefficients (r` from 0.881 to 0.981 for CoMFA and r(2) from 0.938 to 0.993 for CoMSIA models) and low standard errors (s from 0.135 to 0.383 for CoMFA and s from 0.098 to 0.240 for CoMSIA models) were obtained. More precise CoMFA and CoMSIA models have been derived considering the subset of thiosemicarbazones (TSC) substituted only at 5-position of the pyridine ring (n=22). Reasonable predictive correlation coefficients (Q(cv)(2) from 0.486 to 0.683 for CoMFA and Q(cv)(2) from 0.565 to 0.791 for CoMSIA models) with high fitted correlation coefficients (r(2) from 0.896 to 0.997 for CoMFA and r(2) from 0.991 to 0.998 for CoMSIA models) and very low standard errors (s from 0.040 to 0.179 for CoMFA and s from 0.029 to 0.068 for CoMSIA models) were obtained. The stability of each CoMFA and CoMSIA models was further assessed by performing bootstrapping analysis. For the two sets the generated CoMSIA models showed, in general, better statistics than the corresponding CoMFA models. The analysis of CoMFA and CoMSIA contour maps suggest that a hydrogen bond acceptor near the nitrogen of the pyridine ring can enhance inhibitory activity values. This observation agrees with literature data, which suggests that the nitrogen pyridine lone pairs can complex with the iron ion leading to species that inhibits RNR. The derived CoMFA and CoMSIA models contribute to understand the structural features of this class of TSC as antitumor agents in terms of steric, electrostatic, hydrophobic and hydrogen bond donor and hydrogen bond acceptor fields as well as to the rational design of this key enzyme inhibitors.

Expression, purification and kinetic characterization of His-tagged glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma cruzi

Trypanosomes are flagellated protozoa responsible for serious parasitic diseases that have been classified by the World Health Organization as tropical sicknesses of major importance. One important drug target receiving considerable attention is the enzyme glyceraldehyde-3-phosphate dehydrogenase from the protozoan parasite Trypanosoma cruzi, the causative agent of Chagas disease (T. cruzi Glyceraldehyde-3-phosphate dehydrogenase (TcGAPDH); EC 1.2.1.12). TcGAPDH is a key enzyme in the glycolytic pathway of T. cruzi and catalyzes the oxidative phosphorylation of D-glyceraldehyde-3-phosphate (G3P) to 1,3-bisphosphoglycerate (1,3-BPG) coupled to the reduction of oxidized nicotinamide adenine dinucleotide, (NAD(+)) to NADH, the reduced form. Herein, we describe the cloning of the T. cruzi gene for TcGAPDH into the pET-28a(+) vector, its expression as a tagged protein in Escherichia coli, purification and kinetic characterization. The His(6)-tagged TcGAPDH was purified by affinity chromatography. Enzyme activity assays for the recombinant His(6)-TcGAPDH were carried out spectrophotometrically to determine the kinetic parameters. The apparent Michaelis-Menten constant (K(M)(app)) determined for D-glyceraldehyde-3-phosphate and NAD(+) were 352 +/- 21 and 272 +/- 25 mu M, respectively, which were consistent with the values for the untagged enzyme reported in the literature. We have demonstrated by the use of Isothermal Titration Calorimetry (ITC) that this vector modification resulted in activity preserved for a higher period. We also report here the use of response surface methodology (RSM) to determine the region of optimal conditions for enzyme activity. A quadratic model was developed by RSM to describe the enzyme activity in terms of pH and temperature as independent variables. According to the RMS contour plots and variance analysis, the maximum enzyme activity was at 29.1 degrees C and pH 8.6. Above 37 degrees C, the enzyme activity starts to fall, which may be related to previous reports that the quaternary structure begins a process of disassembly. (C) 2010 Elsevier Inc. All rights reserved.

Insights into the Molecular Requirements for the Anti-obesity Activity of a Series of CB1 Ligands

Two-dimensional and 3D quantitative structure-activity relationships studies were performed on a series of diarylpyridines that acts as cannabinoid receptor ligands by means of hologram quantitative structure-activity relationships and comparative molecular field analysis methods. The quantitative structure-activity relationships models were built using a data set of 52 CB1 ligands that can be used as anti-obesity agents. Significant correlation coefficients (hologram quantitative structure-activity relationships: r 2 = 0.91, q 2 = 0.78; comparative molecular field analysis: r 2 = 0.98, q 2 = 0.77) were obtained, indicating the potential of these 2D and 3D models for untested compounds. The models were then used to predict the potency of an external test set, and the predicted (calculated) values are in good agreement with the experimental results. The final quantitative structure-activity relationships models, along with the information obtained from 2D contribution maps and 3D contour maps, obtained in this study are useful tools for the design of novel CB1 ligands with improved anti-obesity potency.

English Vowels: A World English Perspective

In spite of having a fixed standard of pronunciation, English is being used in various ways in parts of the world, particularly in its way of utterance. English vowel is playing one of the significant roles in making different varieties of English language. This essay tries to see into detail how some phonetic features (formant movement, frequency, pitch) of English vowels vary in relation to Bengali, Catalan, Italian, Spanish and Swedish speakers. It has been found that all these speakers vary a lot from each other in the utterance of English vowels.

Investigando a experiência da fruição do futebol : estádio versus televisão

A pesquisa procura estudar a forma como o espetáculo futebol é percebido e valorizado por espectadores no estádio e na televisão. O modelo proposto por Holbrook (1999) sustenta a análise de narrativas que relatam comportamentos dos consumidores nos dois ambientes: arquibancada e sofá. Com base na abordagem sugerida por McCracken (1988), os dados foram coletados por entrevistas pessoais, em profundidade, que possibilitaram explorar as experiências dos entrevistados como espectadores regulares de futebol na televisão e no estádio. Foram analisados os tipos de valor do modelo de Holbrook (1999) mais representativos encontrados nos relatos. As narrativas indicaram substantivas diferenças entre os valores percebidos ao longo das experiências na arquibancada e no sofá. Esta dualidade serviu de fio condutor para a emergência de outros duplos conceituais extraídos das entrevistas - que se revelam subsídios para o desenvolvimento de estratégias de marketing. Concluiu-se que a valorização da partida de futebol é influenciada pela forma com a qual o espectador constrói os significados na experiência de consumo. Percebeu-se, desta forma, uma associação entre a abordagem semiológica (Eco, 2001), para a qual o valor (da informação) decorre das possibilidades de significados possíveis; e a proposição de Holbrook, para o qual o valor de consumo se sustenta numa vivência interativa. Impõe-se ao gestor, portanto, a missão de executar a tabelinha sofá-arquibancada. De maneira a potencializar seus respectivos atributos para o consumo - como a riqueza simbólica e a riqueza referencial - e a reforçar os traços complementares apontados nas entrevistas.

A inscrição psicológica do sintoma: uma aproximação psicoanalítica a psicossomática

Os discursos familiares encerram, no seu bojo, mitos sociais, sentimentos e fantasias inconscientes a eles conectados, que permaneceram secretos e poderosos através de sua historicidade e que vão se inscrever na matéria-prima pura: o recém-nascido, que deve ser moldado mediante o processo de identificação, investimentos libidinais e registro do discurso das pulsões e seus representantes. A partir de uma abordagem psicanalítica dos sintomas psicossomáticos, estudamos os primórdios da constituição do sujeito do inconsciente, recorrendo à estruturação do narcisismo e do inconsciente, construindo-se como uma linguagem ao encadear os significantes por contiguidade ou semelhança, respectivamente, por deslocamentos e condensações, isto é, construindo-se numa cadeia como metonímias e metáforas que se organizam num discurso. O narcisismo seria a causa do corpo. Este último, suporte biológico, que se torna erógeno a partir do discurso materno cujo desejo antecipa uma gestalt à imagem, organizando e delimitando o corpo despedaçado e anárquico do bebê. Como estrutura narcísica relacionamos a articulação das pulsões, das zonas erógenas, do desejo, do recalcamento fixando os representantes que irão constituir um Ego corporal. O sintoma no real do corpo apareceria como efeito de uma desorganização na articulação dos significantes do desejo materno como legalidade de um discurso, dificultando a inscrição simbólica da significação dos limites e fronteiras do corpo erógeno do bebê, cujo representante da pulsão evidencia-se como demanda de significação.

Interesse público, interesse particular e acesso à justiça: reflexões a partir das prerrogativas da Fazenda Pública

Este trabalho acadêmico é fruto da observação profissional cotidiana acerca da relação do Estado e de suas entidades de Direito Público com o particular. De modo algum propende a deslustrar teorias, opiniões e suporte jurídico favoráveis ao modelo diferenciado e casuisticamente pró-estatal vigente. Assim, na linha do eixo acadêmico-científico deste Mestrado, de caráter marcadamente profissional, buscou-se no campo do pluralismo de idéias descrever, num diapasão dialético, o contexto factual e jurídico-legal consoante os dois primeiros capítulos, para assim ensejar discussão e reflexão sobre matéria que se oferece relevante para a efetiva melhoria dos serviços jurisdicionais, submetendo-os, a seguir, a diretivas teóricas e, em particular, à compreensão contextual de nossa ordem constitucional. Partiu-se assim, de situações concretas vivenciadas no ambiente forense de uma unidade da Justiça Federal (2ª Vara da Justiça Federal de Petrópolis, da Seção Judiciária do Estado do Rio de Janeiro), sabidamente competente para as causas em que a União, entidades autárquicas ou empresa pública federal forem interessadas na condição de autoras, rés, assistentes ou opoentes1. O tema central do estudo são as prerrogativas processuais da Fazenda Pública. Vem de longe um conjunto de protetivo processual em seu favor. Para ficarmos no século XX, por exemplo, o art. 32 do Decreto-Lei nº 1.608, de 18 de setembro de 1939 (Código de Processo Civil) já explicitava: “Art. 32. Aos representantes da Fazenda Pública contar-se-ão em quádruplo os prazos para a contestação e em dobro para a interposição de recurso.” O Código de Processo Civil atual conforme destacado na parte descritiva do texto, cuidou de aperfeiçoar e ampliar esse suporte pró-fazendário, como exemplo, o dispositivo mais conhecido é, seguramente, o art. 188 do Código de Processo Civil. No entanto, a multiplicidade de avanços no seio da sociedade brasileira – basicamente nos planos político, constitucional, legal, social, econômico, cultural, global e tecnológico – trouxe como corolário o imperativo da otimização dos mecanismos voltados para o que denominamos no trabalho de acesso qualificado à Justiça. Esse conjunto de fatores, em realidade, acha-se forrado pelos princípios da igualdade e da isonomia que permeiam todo o arcabouço de conquistas asseguradas no corpo político-jurídico constitucional. Nas palavras do professor e atual Ministro do Supremo Tribunal Federal Luiz Fux2, a neutralidade, sobretudo do juiz, constitui fator impediente para o magistrado manter a igualdade das partes na relação jurídica processual. Claro, frise-se, tanto quanto possível, isto é, observando a lei que, ao eventualmente promover, pontualmente, certo grau distintivo, o faça comprometida com a efetiva correção de discrímen para assim encontrar e assegurar a igualdade. Deve fazêlo, na linha desse pensamento, de modo a impedir que o resultado da aplicação da norma não seja expressão da deficiência e do desmerecimento de uma das partes em juízo. Tudo considerado importa que o entendimento ora realçado não se destine apenas ao juiz, mas no caso, também ao legislador, fonte criadora da normatividade posta em evidência.