Selecting a method to compute partial atomic charges is not trivial because different methods usually provide different charge values and there is no consensus on the most useful approach. In this work, Mulliken, MBS, Chelp, Chelpg, MK, Hirshfeld, NPA, DMA and AIM methods were selected to compute atomic charges and electric dipole moment vector of N-{N-(Pterin-7-yl)carbonylglycyl}-L-tyrosine molecule, a ricin inhibitor which has different types of bonds and chemical environments. While MBS and DMA methods provided the most chemically consistent charges according to atomic electronegativity and electron resonance effects criteria, Chelp, Chelpg and MK had the worst performances. Atomic charges and dipole moment calculated by the Hirshfeld method had the smallest magnitudes, a well-known behavior. Despite the differences among atomic charges predicted by all methods, the direction of the dipole moment vector was essentially the same. Further charge calculations using different basis sets and quantum methods indicated that the dependency on this aspect was the highest for Mulliken and Chelp and the lowest for MBS, Hirshfeld and DMA methods. Thus, results point to MBS and DMA as the most suitable methods for computing chemically consistent atomic charges and dipole moment vectors of similar systems for different applications; e.g., molecular dynamics.

Keggin heteropolyacids (HPW) supported on niobia have been considered for both homogeneous and heterogeneous catalysis due to its special features, like the strong Brönsted acidity, low volatility, high activity and high selectivity for various reactions in comparison with mineral acids. Literature reports many different preparation methods for these catalysts through the addition of HPW solutions, in either water or acid, over niobia under stirring. However not much is known about the way how HPW interacts with the support, neither how the temperature influences this interaction. In order to contribute to expand the knowledge on this field we report here a new way of preparing HPW supported catalysts over niobia calcined at 500 and 600 ºC, followed by a theoretical study meant to check the influence of the temperature increase on the adsorption behavior of the catalysts over the support. Our proposed method showed to be an efficient alternative for impregnation of HPW over niobia, while the theoretical results suggest that pseudohexagonal and orthorhombic are the most likely crystalline forms for these catalysts.

This work aims to establish a hierarchy of risks of the stabilizers used in nitrocellulose-based propellants concerning to toxicity, carcinogenicity and mutagenicity. Four stabilizers - diphenylamine, ethyl centralite, akardite-II and 2-nitrodiphenylamine - and their products of degradation were investigated. The prediction of the toxicity was based on the analysis of their structures with the software Lazar, using the OpenTox framework. Our results provide a quantitative reference of the risks involved in the manufacturing and disposal of propellants due to the use of such stabilizers.

Endosulfan is an organochlorine insecticide, widely used in insect control. Unfortunately, it is also an acute neurotoxic compound to both insects and mammals, including humans, and has been responsible for many severe poisonings and several fatal cases. Endosulfan also imitates or enhances the effect of the female hormone estrogen, having the capability of causing reproductive and developmental damage in both, animals and humans, and its exposure has been linked to liver tissue injury. This persistent lipophilic compound is one of the most abundant organochlorine pesticides in the environment, capable of undergoing long range transport to remote locations such as the Arctic. It is practically water-insoluble, but readily adheres to clay particles and persists in soil and water for several years. Its indiscriminate and injudicious use in the control of insects on a wide range of agricultural products and in the extermination of house-hold pests, has considerably increased the hazard risk for human health. Also, this compound has a high fatality rate in humans when ingested accidentally, from food or water contaminated, or in suicidal cases. The aim of this article is to review and summarize chemical, biochemical, environmental, and toxicological data of endosulfan and draw attention to its toxicological potential risk to human health.

Organophosphorus compounds (OPs) are a large and diverse class of chemicals that have been synthesized, since the XIX century for several purposes like chemical weapons, flame-retardants, ectoparasiticides and investigational new drugs, but mainly as agrochemicals in agriculture and indoor. Although the amount of OP pesticides being used is declining, especially in developed countries, OPs continue being one of the most important classes of insecticides and chemical warfare agents today due to its toxic effects on the enzyme acetylcholinesterase (AChE). Existing research on the toxicological effects of OPs is extensive, however, there is a lack of knowledge on the long-term effects of low levels of OPs and their exactly pathways of toxicity. Recent data prove that other molecular targets than AChE could be targeted by OPs, triggering these effects. Here these data are reviewed and it is highlighted that the current uses of OPs are producing several neurotoxic effects. It is also shown that, to protect people from possible uses and misuses of OPs, more regulations on OPs are needed. Moreover, more mechanistic studies are needed to completely understand their toxicological interactions and mechanisms of action and to identify the whole group of enzymes that interact with them.

Alzheimer's disease (AD) is a progressive degenerative brain disease which causes mental and physical decline, gradually resulting in death. Currently, this disease represents one of the uppermost human issues, both from the medical and economic point of view. Interest in the discovery of a drug for AD is enormous. However, despite the long-term and worldwide effort for a more effective therapy, the only available treatment is a symptomatic use of acetylcholinesterase inhibitors (AChEIs) and memantine. New therapeutic approaches as well as those based on cholinergic or amyloid theory have not brought the desired benefits yet. Thus, the question is whether an effective drug for this progressive disease will ever be developed or whether people will have to rely only on prevention and minimize risk factors of AD.

Mosquitos são responsáveis pela transmissão de várias doenças causadas por vírus, parasitas e helmintos. Considerando o custo e a complexidade do tratamento dessas doenças, o uso de repelentes para proteção contra mosquitos vetores se torna uma alternativa interessante. Nesse contexto, no presente trabalho foram feitos estudos por ancoramento e dinâmica molecular (DM) de potenciais ligantes da proteína odorante do mosquito Anopheles gambiae (AgOBP1), o principal vetor da malária. Os modos de ligação na AgOBP1 de moléculas com conhecida atividade atrativa e dos principais componentes do óleo do cravo da índia (Syzygium aromaticum), com potencial atividade repelente, foram comparados com o conhecido repelente N,N-dietil-3-metilbenzamida (DEET). Os resultados sugerem que o acetato de eugenila é um repelente melhor do que o DEET e também revelam as principais características do sítio de ligação da AgOBP1 importantes para o planejamento de novos e mais eficientes repelentes.

Mosquitoes are responsible for conveying various diseases caused by viruses, parasites and helminthes. Considering the cost and complexity of the treatment of these diseases, the use of repellents for protection from the mosquito vectors becomes an interesting alternative. In the present work, docking and molecular dynamics (MD) studies were performed on potential ligands to the odorant binding protein of the mosquito Anopheles gambiae (AgOBP1), the main vector of malaria. The binding modes on AgOBP1 of molecules with known attractive activities and the main components of the oil of indian clove (Syzygium aromaticum) with potential repellent activities were compared to the known repellent N,N-diethyl-3-methylbenzamide (DEET). Results suggest the eugenyl acetate as a better repellent than DEET and also reveal the main features of the binding site of AgOBP1 important to the design of new and more efficient repellents.

Uma combinação de técnicas analíticas foi utilizada para acompanhar a evolução da mesofase em pixes de petróleo em fase sólida. As amostras foram caracterizadas por dessorção a laser assistida por matriz, seguida de espectrometria de massas por tempo de vôo (MALDI-TOF-MS), ressonância magnética nuclear de 13C (13C NMR) de alto campo, ¹H NMR de baixo campo, ressonância eletrônica de spin (EPR), microscopia ótica polarizada e análise termogravimétrica (TGA). A análise por MALDI-TOF-MS revelou uma distribuição oligomérica de pesos moleculares no pixe: monomérica (m/z 200 a 400), dimérica (m/z 400 a 650), trimérica (m/z 650 a 950) e tetramérica (m/z 950 a 1600), fator essential para a produção de fibras de carbono, bem como outros compósitos de carbono. Estudos de tempo de relaxação (T1) permitiram a observação de duas grandes áreas: a dos aromáticos e a de mesofase. Estes resultados também mostraram que o tempo de aquecimento aumenta a área de mesofase. Através de medidas não destrutivas de 13C NMR, foram obtidos os conteúdos de carbonos aromáticos e alifáticos, e também o grau de protonação desses carbonos. A microscopia ótica com luz polarizada mostrou as interfaces entre as regiões anisotrópicas e isotrópicas, bem como o processo de coalescência da mesofase. Os resultados obtidos pelas outras técnicas corroboram com os resultados de MALDI-TOF-MS e NMR.

A combination of analytical techniques was used to follow the mesophase evolution of petroleum pitches in the solid phase. The samples were characterized by matrix assisted laser desorption and time of flight analysis by mass spectrometry (MALDI-TOF-MS), high field 13C nuclear magnetic resonance (13C NMR), low field ¹H NMR, electron spin resonance (EPR), polarized optical microscopy and thermogravimetric analysis (TGA). MALDI-TOF-MS revealed an oligomeric distribution of molecular weights in the pitch: monomeric (m/z 200 to 400), dimeric (m/z 400 to 650), trimeric (m/z 650 to 950) and tetrameric (m/z 950 to 1600), an essential factor for the production of carbon fibers, among other advanced composite of carbon. Relaxation time (T1) studies permitted to observe two large areas: the aromatics and the mesophases. These results also showed that the heating time increases the mesophasic area. Also through direct and non-destructive 13C NMR measurements, we obtained the content of aromatic and aliphatic carbons, as well as the degree of protonation of these carbons. Optical microscopy with polarized light showed the interfaces between the anisotropic and isotropic regions as well as the process of coalescence of mesophase. The results obtained by the other techniques corroborate the MALDI-TOF-MS and NMR results.

No presente trabalho foi aplicada uma metodologia teórica desenvolvida em um trabalho anterior que utiliza os programas Molegro® e Spartan® para avaliar as constantes cinéticas de associação e reativação de oximas, em relação a resultados in vitro previamente reportados na literatura. Como observado antes, os resultados mostraram boa correlação entre as energias livres teóricas de ligação das oximas e os dados experimentais, corroborando a metodologia como adequada para a predição de parâmetros cinéticos e termodinâmicos, os quais podem ser úteis para o planejamento e seleção de novas e mais efetivas oximas.

In this work we applied a theoretical methodology developed in a former work, using the Molegro® and Spartan® softwares, to evaluate the association and kinetic reactivation constants of oximes, facing in vitro data previously reported in the literature. As reported before, results showed a good agreement between the theoretical binding free energies of the oximes and experimental data, corroborating the methodology as suitable for the prediction of kinetic and thermodynamic parameters that might be helpful for the design and selection of new and more effective oximes.

A elucidação das rotas de reativação da acetilcolinesterase humana (HuAChE) inibida por organofosforados é de crucial importância para o desenvolvimento de antídotos eficientes contra a intoxicação causada por agentes de guerra química. Com o objetivo de contribuir para uma melhor compreensão do mecanismo de reativação, foram aplicadas neste trabalho simulações de dinâmica molecular (DM) clássica para estudar as interações entre a pralidoxima e aminoácidos do sítio ativo da HuAChE inibida pelo agente neurotóxico tabun. Além disso, métodos híbridos de mecânica quântica/mecânica molecular (QM/MM) foram usados para propor um mecanismo de reativação para a enzima inibida. Os resultados mostraram que a DM clássica manteve a pralidoxima no interior do sítio ativo da enzima, em uma região favorável à ocorrência de uma possível reação de desfosforilação, que foi confirmada por métodos de QM/MM, levando à proposta de um mecanismo de reativação, energeticamente favorável.

The elucidation of the reactivation routes of human acetylcholinesterase (HuAChE) inhibited by organophosphorous compounds is of crucial importance to the development of efficient antidotes against poisoning by chemical warfare agents. In order to contribute to a better understanding of the reactivation mechanism, we applied, in this work, classical molecular dynamics (MD) simulations to study the interactions between pralidoxime and the active site's amino acids of HuAChE inhibited by the neurotoxic agent tabun. Further, quantum mechanical/molecular mechanical (QM/MM) hybrid methods were used to propose a reactivation mechanism for the inhibited enzyme. The results showed that the classic MD kept pralidoxime inside the enzyme's active site, in a favorable region to the occurrence of possible reactions of dephosphorilation, which were confirmed by QM/MM methods, and lead to the proposition of an energetically favorable mechanism of reactivation.

Neste trabalho, após validação por comparação com resultados obtidos por DFT, os métodos semi-empíricos PM6 e RM1 foram utilizados para análise conformacional de três oximas usadas em defesa química. Os resultados sugerem conformações de menor energia destes compostos que poderão ser utilizadas em futuras parametrizações para estudos por modelagem molecular.

In this work, after validation by comparison with results obtained by DFT, the semi-empirical methods RM1 and PM6 were employed to perform conformational analysis of three oximes employed in chemical defense. The results suggested low energy conformations for those compounds that could be useful in further parameterizations for molecular modeling studies.

Malaria is still a very serious worldwide public health problem affecting between 300 and 500 million people and causing from 1.0 to 2.5 million deaths annually. The major problems with this disease are the lack of efficient vaccines and the rapid emergence of chemotherapy resistant P. falciparum strains. In this work we present a synopsis and discussion on malaria to provide the readers with some information on the historical aspects and relevance of this disease as well as the chemotherapy in use today.

Neste trabalho é proposto o primeiro modelo por homologia para a nucleosídeo hidrolase de Leishmania donovani construído a partir das estruturas das nucleosídeo hidrolases de Crithidia fasciculata e de Leishmania major. Usando as informações de interação entre o inibidor p-aminofeniliminoribitol e a nucleosídeo hidrolase de Crithidia fasciculata foram planejados dois novos potenciais inibidores, os quais apresentam novas interações com alguns resíduos da bolsa hidrofóbica do sítio ativo do modelo. Simulações por dinâmica molecular dos protótipos ancorados nos sítios ativos do modelo e das enzimas usadas como moldes, mostraram que, diferente do p-aminofeniliminoribitol, eles permaneceram ancorados nos sítios ativos das três enzimas ao longo de toda a dinâmica, interagindo fortemente com os aminoácidos da bolsa hidrofóbica.

In this work we propose the first homology model for nucleoside hydrolase from Leishmania donovani, built based on the crystallographic structures of Crithidia fasciculata and Leishmania major nucleoside hydrolases. We used the interaction information from the crystallographic model of the enzyme of C. fasciculata in complex with the inhibitor p-aminophenyliminoribitol, to design two new potential inhibitors, which present new interactions with some residues of the hydrophobic pocket of the model active site. Molecular dynamics simulations of the prototypes inside the active sites of the model and the template enzymes showed that, differently from p-aminophenyliminoribitol, they remained tightly bound inside the active sites, interacting strongly with the amino acids from the hydrophobic pocket.

A Serina Hidroximetiltransferase de Plasmodium falciparum nunca foi vista como alvo para a quimioterapia antimalarial, possivelmente devido a sua grande similaridade seqüencial com a enzima humana. Esta similaridade sugere que este parasita pode ser incapaz de mutar esta enzima para desenvolver resistência à quimioterapia. Neste trabalho, diferenças observadas no comportamento dinâmico dos sítios ativos da estrutura cristalográfica da enzima humana e um modelo, por homologia, da enzima do parasita, ambos complexados com glicina, como N-glicina-[3-hidróxi-2-metil-5-fosfonooximetil-piridin-4-il-metano], e ácido 5-formil-6-hidrofólico, foram utilizadas para o planejamento de inibidores seletivos desta enzima como novos potenciais antimalariais. Estes potenciais inibidores são derivados do ácido 5-formil-6-hidrofólico com diferentes cargas e comprimentos de cauda. Simulações por dinâmica molecular e estimativas das energias de interação dos compostos nos sítios ativos de ambas as enzimas mostraram que os compostos com carga líquida negativa e caudas curtas ou caudas longas e anfóteras, seriam potencialmente mais seletivos em relação à enzima do parasita.

Plasmodium falciparum Serine Hydroxymethyltransferase has never been used as target for antimalarial chemotherapy, possibly because its great sequence similarity with the human enzyme. This similarity suggests implies that P. falciparum may not be able to mutate this enzyme to develop resistance for chemotherapy. In this work, we have used differences on the dynamic behavior of the active sites of the crystallographic structure of the human enzyme and a homology model of parasite's enzyme, both in complex with glycine, as N-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane] and 5-formyl-6-hydrofolic acid, to design prototypes for selective inhibitors of this enzyme as new potential antimalarials. Those potential inhibitors are 5-formyl-6-hydrofolic acid derivatives with different charges and tail lengths. Molecular dynamics simulations and interaction energy estimates of the compounds within the active sites of both enzymes showed that compounds with a negative net charge and either shorter tails or longer amphoteric tails, would be more selective towards pfSHMT.

Reativadores eficientes de Aceticolinesterase são fundamentais para o desenvolvimento de antídotos contra o envenenamento por pesticidas neurotóxicos e agentes de guerra química. Todavia, o mecanismo da reação de reativação e as características estruturais dos reativadores conhecidos são pouco compreendidos. Com o objetivo de estudar o comportamento dinâmico e o efeito da carga líquida do antídoto na reativação desta enzima, foi conduzido um estudo por dinâmica molecular da acetilcolinesterase humana inibida por tabun em complexo com o antídoto pralidoxima e com seu análogo deazapralidoxima nas formas neutra e aniônica. Os resultados mostraram que a carga positiva da pralidoxima é importrante para sua admissão e permanência dentro do sítio ativo. Além disso, os análogos, diferente da pralidoxima, quando colocados dentro do sítio ativo, se distanciam do resíduo serina fosforilado da enzima e são repelidos pelo potencial eletrostático na entrada do canal que conduz ao sítio ativo.

Efficient acetylcholinesterase reactivators are fundamental for the development of antidotes against poisoning by neurotoxic pesticides and chemical warfare agents. However, the mechanism of the reactivation reaction and the structural characteristics of the known reactivators are poorly understood. In order to study the dynamic behavior and the effect of the antidote net charge in the reactivation of this enzyme, we carried out a molecular dynamics study of human acetylcholinesterase inhibited by tabun in complex with the antidote pralidoxime and with its deaza analogues in the neutral and anionic forms. Results show that the positive charge of pralidoxime is important for its admission and permanence inside the active site. Also, the analogues, unlike pralidoxime, when forced inside the active site, move away from the phosphorilated serine residue of the enzyme and are repelled by the electrostatic potential at the entrance of the channel that conducts to the active site.