Pharmacophore-based 3D QSAR studies on a series of high affinity 5-HT(1A) receptor ligands

5-HT(1A) receptor antagonists have been employed to treat depression, but the lack of structural information on this receptor hampers the design of specific and selective ligands. In this study, we have performed CoMFA studies on a training set of arylpiperazines (high affinity 5-HT(1A) receptor ligands) and to produce an effective alignment of the data set, a pharmacophore model was produced using Galahad. A statistically significant model was obtained, indicating a good internal consistency and predictive ability for untested compounds. The information gathered from our receptor-independent pharmacophore hypothesis is in good agreement with results from independent studies using different approaches. Therefore, this work provides important insights on the chemical and structural basis involved in the molecular recognition of these compounds. (C) 2010 Elsevier Masson SAS. All rights reserved.

CDK9 a potential target for drug development

The family of Cyclin-Dependent Kinases (CDKs) can be subdivided into two major functional groups based on their roles in cell cycle and/or transcriptional control. CDK9 is the catalytic subunit of positive transcription elongation factor b (P-TEFb). CDK9 is the kinase of the TAK complex (Tat-associated kinase complex), and binds to Tat protein of HIV, suggesting a possible role for CDK9 in AIDS progression. CDK9 complexed with its regulatory partner cyclin T1, serves as a cellular mediator of the transactivation function of the HIV Tat protein. P-TEFb is responsible for the phosphorylation of the carboxyl-terminal domain of RNA Pol II, resulting in stimulation of transcription. Furthermore, the complexes containing CDK9 induce the differentiation in distinct tissue. The CDK9/cyclin T1 complex is expressed at higher level in more differentiated primary neuroectodermal and neuroblastoma tumors, showing a correlation between the kinase expression and tumor differentiation grade. This may have clinical and therapeutical implications for these tumor types. Among the CDK inhibitors two have shown to be effective against CDK9: Roscovitine and Flavopiridol. These two inhibitors prevented the replication of human immunodeficiency virus (HIV) type 1 by blocking Tat transactivation of the HIV type 1 promoter. These compounds inhibit CDKs by binding to the catalytic domain in place of ATP, preventing transfer of a phosphate group to the substrate. More sensitive therapeutic agents of CDK9 can be designed, and structural studies can add information in the understanding of this kinase. The major features related to CDK9 inhibition will be reviewed in this article.

Aplicação da parafina e do óleo de linhaça como hidrofobizantes da vermiculita, para remoção de derivados de óleo diesel resentes em água produzida sintética

Produced water has lately aroused interest due to their high degree of salinity, suspended oil particles, chemicals added in various manufacturing processes, heavy metals and radioactivity sometimes. Along with oil and due to its high volume production, water production is one of the pollutants of most concern in the process of oil extraction. PAHs due to their ubiquity and their characteristics carcinogenic or mutagenic and teratogenic even have attracted the attention of every scientific society. Formed from the incomplete combustion of organic matter may be natural or anthropogenic. Some materials have been researched with the goal of cleaning up environmental matrices that may be contaminated by hydrocarbons. Among these materials researched various clays have been employed, of which highlights the vermiculite. The family of phyllosilicates, vermiculite for its potential and its high hydrophobic surface area has been a tool widely used in the decontamination of water in processes of oil spills. However, when it loses its capacity expanded hydrophobic having the necessity of using a hidrofobizante to make it organophilic. Among the numerous hidrofobizantes researched and used the linseed oil was the pioneer. In this study sought to evaluate the capacity of removal of PAHs using the vermiculite hydrofobized with linseed oil and wax also, for it was made use of the 24 full factorial design as the main tool for the experiments. We also evaluated the clay grain size (-20 +48 and -48 +80 #), the percentage of hidrofobizante applied (5 and 10%) and salinity of the water produced synthesized in our laboratory (35,000 and 55,000 ppm). The molecular fluorescence spectroscopy due to its sensitivity and speed was used to verify the adsorption capacity of clay, as well as gas chromatography served as an auxiliary technique to identify and quantify the PAHs in solution. In order to characterize the vermiculite was made use of X-ray fluorescence and X-ray diffraction. The infrared and thermogravimetry were essential to note hydrophobization and the amount of coating of clay. According to the fluorescence analysis showed that the test 12 was the best result in about 98% adsorption of fluorescent compounds, however the high salinity, the smallest particle size, the highest percentage of hidrofobizante and the use of linseed oil showed greater efficiency in the removal capacity of these hydrocarbons, in accordance with the trend followed by the analysis of the major factors of the factorial design. To verify the adsorption capacity of clay using a fixed volume of water produced synthetically, used as the test base 12, at their respective levels and factors. Thus, it was observed that after adding about 1 ½ liters of water solution produced synthetically, about 300 times its volume in mass, the vermiculite was able to adsorb 80% of fluorescent species present in solution

COMPORTAMENTO do ÓLEO DE GIRASSOL COM ALTO TEOR DE ÁCIDO OLÉICO em TERMOXIDAÇÃO E FRITURA

Óleos de sementes de girassol com diferentes níveis de ácido oléico foram utilizados sob condições de termoxidação e fritura para avaliar o comportamento do óleo de girassol com alto teor de ácido oléico quanto ao seu grau de insaturação quando comparado com o óleo de girassol convencional. Os métodos analíticos aplicados incluíram a determinação de compostos polares totais, quantificação de compostos glicerídicos menores, quantificação da composição triglicerídica, período de indução a 100oC e níveis de a -tocoferol. Os resultados para compostos polares totais apresentaram menores valores em óleo de girassol com alto teor de ácido oléico quando comparados com óleo de girassol convencional. Quanto à distribuição dos compostos glicerídicos menores, verificou-se, de modo geral, que o aumento dos compostos polares totais estava relacionado essencialmente aos compostos de maior peso molecular, isto é, polímeros, dímeros e triglicerídios oxidados, os quais são representantes das alterações térmica e oxidativa. Já os diglicerídios e ácidos graxos, indicativos da alteração hidrolítica, permaneceram praticamente nos níveis originais; uma vez que a umidade não se encontrava presente no meio. A perda quantitativa da composição triglicerídica dependeu do grau de insaturação do triglicerídio, sendo mais elevada em triglicerídios que contêm duas ou três moléculas de ácido linoléico. em todos os casos, o óleo de girassol convencional teve uma maior tendência à polimerização, um maior grau de alteração total e uma maior perda de triglicerídios majoritários que o óleo de girassol com alto teor de ácido oléico. Assim, dentre os óleos utilizados neste estudo, os resultados mostraram um excelente comportamento do óleo de girassol com alto teor de ácido oléico em relação à termoxidação, independente do tipo de aquecimento e à fritura descontínua. Tais resultados demonstraram que sua resistência à alteração termoxidativa estava relacionada com seu baixo teor em ácidos graxos polinsaturados e alto teor em ácido oléico e trioleína.

Two short peptides including segments of subunit A of Escherichia coli DNA gyrase as potential probes to evaluate the antibacterial activity of quinolones

Quinolones constitute a family of compounds with a potent antibiotic activity. The enzyme DNA gyrase, responsible for the replication and transcription processes in DNA of bacteria, is involved in the mechanism of action of these drugs. In this sense, it is believed that quinolones stabilize the so-called 'cleavable complex' formed by DNA and gyrase, but the whole process is still far from being understood at the molecular level. This information is crucial in order to design new biological active products. As an approach to the problem, we have designed and synthesized low molecular weight peptide mimics of DNA gyrase. These peptides correspond to sequences of the subunit A of the enzyme from Escherichia coli, that include the quinolone resistance-determining region (positions 75-92) and a segment containing the catalytic Tyr-122 (positions 116-130). The peptide mimic of the non-mutated enzyme binds to ciprofloxin (CFX) only when DNA and Mg2+ were present (Kd = 1.6 × 10 -6 m), a result previously found with DNA gyrase. On the other hand, binding was reduced when mutations of Ser-83 to Leu-83 and Asp-87 to Asn-87 were introduced, a double change previously found in the subunit A of DNA gyrase from several CFX-resistant clinical isolates of E. coli. These results suggest that synthetic peptides designed in a similar way to that described here can be used as mimics of gyrases (topoisomerases) in order to study the binding of the quinolone to the enzyme-DNA complex as well as the mechanism of action of these antibiotics. Copyright © 2001 European Peptide Society and John Wiley & Sons, Ltd.

Caracterização estrutural e propriedades óticas e mecânicas do diglime polimerizado a plasma

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Characterization and optimization of levan production by Bacillus subtilis NATTO

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Novel aryl beta-aminocarbonyl derivatives as inhibitors of Trypanosoma cruzi trypanothione reductase: binding mode revised by docking and GRIND2-based 3D-QSAR procedures

Trypanothione reductase has long been investigated as a promising target for chemotherapeutic intervention in Chagas disease, since it is an enzyme of a unique metabolic pathway that is exclusively present in the pathogen but not in the human host, which has the analog Glutathione reductase. In spite of the present data-set includes a small number of compounds, a combined use of flexible docking, pharmacophore perception, ligand binding site prediction, and Grid-Independent Descriptors GRIND2-based 3D-Quantitative Structure-Activity Relationships (QSAR) procedures allowed us to rationalize the different biological activities of a series of 11 aryl beta-aminocarbonyl derivatives, which are inhibitors of Trypanosoma cruzi trypanothione reductase (TcTR). Three QSAR models were built and validated using different alignments, which are based on docking with the TcTR crystal structure, pharmacophore, and molecular interaction fields. The high statistical significance of the models thus obtained assures the robustness of this second generation of GRIND descriptors here used, which were able to detect the most important residues of such enzyme for binding the aryl beta-aminocarbonyl derivatives, besides to rationalize distances among them. Finally, a revised binding mode has been proposed for our inhibitors and independently supported by the different methodologies here used, allowing further optimization of the lead compounds with such combined structure- and ligand-based approaches in the fight against the Chagas disease.

Countering cooperative effects in protease inhibitors using constrained b-strand-mimicking templates in focused combinatorial libraries

A major problem in de novo design of enzyme inhibitors is the unpredictability of the induced fit, with the shape of both ligand and enzyme changing cooperatively and unpredictably in response to subtle structural changes within a ligand. We have investigated the possibility of dampening the induced fit by using a constrained template as a replacement for adjoining segments of a ligand. The template preorganizes the ligand structure, thereby organizing the local enzyme environment. To test this approach, we used templates consisting of constrained cyclic tripeptides, formed through side chain to main chain linkages, as structural mimics of the protease-bound extended beta-strand conformation of three adjoining amino acid residues at the N- or C-terminal sides of the scissile bond of substrates. The macrocyclic templates were derivatized to a range of 30 structurally diverse molecules via focused combinatorial variation of nonpeptidic appendages incorporating a hydroxyethylamine transition-state isostere. Most compounds in the library were potent inhibitors of the test protease (HIV-1 protease). Comparison of crystal structures for five protease-inhibitor complexes containing an N-terminal macrocycle and three protease-inhibitor complexes containing a C-terminal macrocycle establishes that the macrocycles fix their surrounding enzyme environment, thereby permitting independent variation of acyclic inhibitor components with only local disturbances to the protease. In this way, the location in the protease of various acyclic fragments on either side of the macrocyclic template can be accurately predicted. This type of templating strategy minimizes the problem of induced fit, reducing unpredictable cooperative effects in one inhibitor region caused by changes to adjacent enzyme-inhibitor interactions. This idea might be exploited in template-based approaches to inhibitors of other proteases, where a beta-strand mimetic is also required for recognition, and also other protein-binding ligands where different templates may be more appropriate.

Design, synthesis, antimicrobial activity and molecular modeling studies of novel benzofuroxan derivatives against Staphylococcus aureus

Molecular modi. cation is a quite promising strategy in the design and development of drug analogs with better bioavailability, higher intrinsic activity and less toxicity. In the search of new leads with potential antimicrobial activity, a new series of 14 4-substituted [N`-(benzofuroxan-5-yl) methylene] benzohydrazides, nifuroxazide derivatives, were synthesized and tested against standard and multidrug-resistant Staphylococcus aureus strains. The selection of the substituent groups was based on physicochemical properties, such as hydrophobicity and electronic effect. These properties were also evaluated through the lipophilic and electrostatic potential maps, respectively, considering the compounds with better biological pro. le. Twelve compounds exhibited similar bacteriostatic activity against standard and multidrug-resistant strains. The most active compound was the 4-CF(3) substituted derivative, which presented a minimum inhibitory concentration (MIC) value of 14.6-13.1 mu g/mL, and a ClogP value of 1.87. The results highlight the benzofuroxan derivatives as potential leads for designing new future antimicrobial drug candidates. (C) 2009 Elsevier Ltd. All rights reserved.

Use of virtual screening, flexible docking, and molecular interaction fields to design novel HMG-CoA reductase inhibitors for the treatment of hypercholesterolemia

Dietary changes associated with drug therapy can reduce high serum cholesterol levels and dramatically decrease the risk of coronary artery disease, stroke, and overall mortality. Statins are hypolipemic drugs that are effective in the reduction of cholesterol serum levels, attenuating cholesterol synthesis in liver by competitive inhibition regarding the substrate or molecular target HMG-CoA reductase. We have herewith used computer-aided molecular design tools, i.e., flexible docking, virtual screening in large data bases, molecular interaction fields to propose novel potential HMG-CoA reductase inhibitors that are promising for the treatment of hypercholesterolemia.

Molecular dynamics, flexible docking, virtual screening, ADMET predictions, and molecular interaction field studies to design novel potential MAO-B inhibitors

Monoamine oxidase is a flavoenzyme bound to the mitochondrial outer membranes of the cells, which is responsible for the oxidative deamination of neurotransmitter and dietary amines. It has two distinct isozymic forms, designated MAO-A and MAO-B, each displaying different substrate and inhibitor specificities. They are the well-known targets for antidepressant, Parkinson`s disease, and neuroprotective drugs. Elucidation of the x-ray crystallographic structure of MAO-B has opened the way for the molecular modeling studies. In this work we have used molecular modeling, density functional theory with correlation, virtual screening, flexible docking, molecular dynamics, ADMET predictions, and molecular interaction field studies in order to design new molecules with potential higher selectivity and enzymatic inhibitory activity over MAO-B.

Molecular characterization of the toxic cyanobacterium Cylindrospermopsis raciborskii and design of a species-specific PCR

Cylindrospermopsis raciborskii is a toxic-bloom-forming cyanobacterium that is commonly found in tropical to subtropical climatic regions worldwide, but it is also recognized as a common component of cyanobacterial communities in temperate climates. Genetic profiles of C. raciborskii were examined in 19 cultured isolates originating from geographically diverse regions of Australia and represented by two distinct morphotypes. A 609-bp region of rpoC1, a DNA-dependent RNA polymerase gene, was amplified by PCR from these isolates with cyanobacterium-specific primers. Sequence analysis revealed that all isolates belonged to the same species, including morphotypes with straight or coiled trichomes. Additional rpoC1 gene sequences obtained for a range of cyanobacteria highlighted clustering of C. raciborskii with other heterocyst-producing cyanobacteria (orders Nostocales and Stigonematales). In contrast, randomly amplified polymorphic DNA and short tandemly repeated repetitive sequence profiles revealed a greater level of genetic heterogeneity among C. raciborskii isolates than did rpoC1 gene analysis, and unique band profiles were also found among each of the cyanobacterial genera examined. A PCR test targeting a region of the rpoC1 gene unique to C. raciborskii was developed for the specific identification of C. raciborskii from both purified genomic DNA and environmental samples. The PCR was evaluated with a number of cyanobacterial isolates, but a PCR-positive result was only achieved with C, raciborskii. This method provides an accurate alternative to traditional morphological identification of C. raciborskii.

Bioprocess-centered molecular design (BMD) for the efficient production of an interfacially active peptide

The efficient expression and purification of an interfacially active peptide (mLac21) was achieved by using bioprocess-centered molecular design (BMD), wherein key bioprocess considerations are addressed during the initial molecular biology work. The 21 amino acid mLac21 peptide sequence is derived from the lac repressor protein and is shown to have high affinity for the oil-water interface, causing a substantial reduction in interfacial tension following adsorption. The DNA coding for the peptide sequence was cloned into a modified pET-31(b) vector to permit the expression of mLac21 as a fusion to ketosteroid isomerase (KSI). Rational iterative molecular design, taking into account the need for a scaleable bioprocess flowsheet, led to a simple and efficient bioprocess yielding mLac21 at 86% purity following ion exchange chromatography (and >98% following chromatographic polishing). This case study demonstrates that it is possible to produce acceptably pure peptide for potential commodity applications using common scaleable bioprocess unit operations. Moreover, it is shown that BMD is a powerful strategy that can be deployed to reduce bioseparation complexity. (C) 2004 Wiley Periodicals, Inc.

Polímeros conjugados baseados em calix[4]arenos: síntese e aplicações em electrónica molecular

Neste trabalho são descritas as sínteses de novos copolímeros do tipo p-fenileno-etinileno (PPE’s) contendo unidades de calix[4]areno com potencial aplicação em electrónica molecular. A preparação destes copolímeros envolveu a síntese e caracterização de duas unidades monoméricas distintas. O 1,4-bis-25-(oximetil) - 26,26,28-tripropoxi-2,5-di-iodo-benzeno-p-terc-butilcalix[4]areno e diferentes 1,4-di-etinil-2,5-bis(alcoxi)benzenos. Os materiais sintesidados foram analisados e caracterizados por espectroscopia de infravermelho por transformada de Fourier (FTIR), ressonância magnética nuclear de protão e de carbono (1H e 13C RMN), análise elementar (AE) e cromatografia de permeação em gel (GPC). Com o objectivo de estudar as suas propriedades espectroscópicas recorreu-se a técnicas de absorção de estado fundamental e luminescência de estado estacionário. O estudo das propriedades quirópticas do CALIX-p-PPE-C5q demonstrou que a homoquiralidade presente nas cadeias laterais de um dos componentes do copolímero é transferida para a cadeia principal do polímero conjugado, originando um polímero quiral. A realização de estudos electroquímicos por voltametria cíclica permitiu identificar nos diferentes polímeros processos oxidativos a potenciais semelhantes; o processo redutivo apenas foi observado no CALIX-p-PPE-C6. Os polímeros sintetizados foram posteriormente testados em duas aplicações de electrónica molecular. Num dos casos, a sua capacidade de funcionar com sensores químicos na detecção de explosivos nitroaromáticos foi avaliada usando técnicas de fotoluminescência enquanto a sua utilização como filmes emissivos em diodos emissores de luz foi avaliada por estudos de electroluminescência.