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TED WILSON BICHARA JUNIOR
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CONFORMATIONAL ANALYSIS OF THE FORM APO AND HOLO OF GLYCOSOMAL ENZYME GLYCEROL 3-PHOSPHATE DEIDROGENASE OF Leishmania mexicana ACROSS MOLECULAR DYNAMICS AND PCA.
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Data: 18/12/2017
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Leishmaniasis is protozoan caused by different species of the parasite of the genus Leishmania that present themselves in the promastigote form, when they are infecting the insect vector or amatisgota, when they are infecting a vertebrate host. The chemotherapy treatment is still the main means of fighting the disease, however due to the high cost and some unwanted side effects, it makes treatment difficult. Several proteins with enzymatic and structural functions have been identified as possible pharmacological targets against the parasite species in question due to their specific functions, cellular location and considerable phylogenetic distance. Glucosomal proteins are pharmacological targets that meet these requirements and have been targets of different studies. The glycosomal enzyme Glycerol 3-phosphate dehydrogenase (GPDH) from Leishmania mexicana has its crystallographic structure attached to the NAD+-DHAP bissubstrat (NDE), available in the Protein Data Bank (PDB). 10 residues in the active site are noted which are highly conserved and conformational changes in their structure. From this, in the present study, molecular dynamics (DM) simulations were combined with Principal Component Analysis (PCA) to verify the conformational activity in the non-bounded form (apo) and in the bound form (holo). A total of 100 ns of DM for each system were generated, as well as free energy calculations that estimated the structural mechanism by observing that the C-terminal domain moved considerably while the N-terminal remained conservated and stable. The results also show that the closed state after NDE formation is favorable for the enzymatic action process.
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AMARILIS ARAGAO DIAS
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SYNTHESIS, INTERCALATION, STRUCTURAL, CHARACTERIZATION AND BIOLOGICAL ANALYSIS OF CARRIER NANOPARTICLE OF KOJIC ACID.
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Data: 30/11/2017
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Intercalation of species with pharmacological activity in layered double hydroxides (LDHs) is a growing field in academic and industrial research, these compounds are capable of promoting the controlled release of drugs. In this work we merge the kojic acid in LDH nanoparticles of Mg2+/Al3+ by co-precipitation method. This substance has many applications in various fields of research, however it is easily susceptibile to photo-oxidation which causes organoleptic and chemical modifications of its structure. Recently kojic acid was introduced as a potent inhibitor of Leishmania cultures, we believe that the particular properties of HDL, such as photoprotection, and stabilization of the interleaved facilitate the production of a material resistant to possible applications for health. All samples were prepared by the co-precipitation method, were further characterized by X-ray diffraction, Raman, IR, UV-vis spectroscopy, thermogravimetry, and biological evaluations of Leishmania cultures. Our results demonstrate that HDL has 53.018% AK intercalated kojic acid and is able to withstand high temperatures, in addition to having an anti-leishmania potential. Keywords: layered double hydroxides nanoparticles, kojic acid, anti-leishman
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FABIO JORGE DE NAZARE FERREIRA
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COMPUTATIONALINVESTIGATION OF BROMINE-ARYLOXY-2ACETAMIDE-ETHYLBENZIMIDAZOLES AS NON-PEPTIDE INHIBITORS OF PROTEINASE CRUZAIN FROM TRYPANOSOMA CRUZI.
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Data: 17/11/2017
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Chagas’ disease is an infection caused by the Trypanosoma Cruzi flagellated protozoan transmittedbyinsects(gnat)knowninBrazilas“barbeiro”(barber).IntheAmazonregion, studies have shown that oral contamination has been frequent. The only available drugs for the treatment of Chagas’ disease - Benzonidazole (RochaganR, Roche) and Nifurtimox (LampitR, Bayer) - have shown limited efficiency and severe side effects. Cruzain is an enzyme present at all stages of the life cycle of T. cruzi and is the most abundant of the family of papain cysteine proteases found in the parasite, being a promising enzymatic target for the design and development of inhibitors against the disease. Non-peptidic noncovalently bound to the enzyme were synthesized and evaluated biologicallyin vitro andin vivo byFerreiraetal.(2014)analogsofthe8D(orB95)leadercompound(crystallographic), yielding a series of active compounds, of which the most powerful are: 8K, 8L and 8R. This work investigated the potential interactions and energies of the cruzain (PDB code: 3KKU) complexed with these four ligands by means of computational tools in order to help elucidate their potential inhibition activity in this enzyme. The computational protocol (parameters, topologies, coordinates, minimizations, thermalizations and productions) was the same for each system. In the final stage of molecular dynamics (MD) production, each system was simulated for a period of 100 ns, to which the mean square deviation (RMSD) stability values of the enzyme and the marked change in 8L ligand conformation were analyzed. The quality of the simulation was also evaluated through potential, kinetic and total energy, volume and temperature graphs. Interactions of hydrogen bonds of the ligands with some amino acid residues belonging to the catalytic site were analyzed. The interaction between the ASP161 and the 8R ligand is emphasized, being ratified by the energy decomposition by residue showing that ASP161 has the best contribution. In terms of binding free energy, the ∆Gtotal follows the experimental trend, pointing the 8R ligand as the most favorable to the reaction having a theoretical value of -30.04 kcal.mol−1. This spontaneity is ratified by means of the values obtained with the SIE method, whose theoretical value was -7.54 kcal.mol−1. The results of this work should favor the optimization of compound 8R or development of a series of analogs of this molecule in order to be used as a possible drug for the treatment of Chagas’ disease.
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JEANN RICARDO DA COSTA BAHIA
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THEORETICAL STUDY OF INTERACTIONS BETWEEN INHA INHIBITORS, ENOILACP REDUTASE OF MYCOBACTERIUM TUBERCULOSIS.
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Data: 29/09/2017
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catalase-peroxidase, KatG, which produces an isonicotinoyl-NADH adduct, INNADH, whichtargets the M tuberculosis Enoyl-ACP reductase protein, InhA, in order to disrupt thesynthesis chain of mycolic acidsResistance to isoniazid alone or in combination with otherdrugs is one of the most common forms of resistant tuberculosis and poses a threat to thecontrol of this disease. In this context, triclosan (TCL) appears as an alternative inhibitor ofthe synthesis of mycolic acids, since it is also specific to InhA. This study aims to evaluate theinteractions of inhibitors of InhA through Molecular Dynamics Simulation (DM) and proposepossible new inhibitors for this enzyme. The system used in this work was captured from thedatabase PDB, code 4TRO. Eight ligands, NADH, INNADH, and the TCL, P31, P41, P52,P61, P72 and P80 derivatives were evaluated. In the lower region of the active site of InhAwere more frequent π charge stacks made by PHE41 and PHE97 with the ligands NADH,INADH, P80, P31, P72, however P41 made a hydrogen bond (LH) with PHE41. In the centralregion of the active site, residues such as A GLY96, SER20 and ILE21 did LH with NADH,INNADH, P31, P41 and P80. In relation to the upper region of the InhA site. The PHE149performed EC-π with the INNADH and P41. Already in P31 was an LH with this residue andin P80 the energies are favorable for interaction. The free energies of each system presentedin descending order are INNADH (-72,038 kcal / mol), P80 (-45,841 kcal / mol), NADH (41,463kcal / mol), P41 (-40,178 kcal / mol), P31 (-30.614 kcal / mol), p52 (-19.475 kcal /mol) and P61 (-12.297 kcal / mol). These results highlight P80 and P41 as promisingcandidates for M. tuberculosis mycolic acid synthesis inhibitors, since being an energy profileis competitive with the values shown by NADH.
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GRACIMERY NEPOMUCENO REIS
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Intercalação de Ácido Cafeico em Hidróxidos Duplos Lamelares (HDL) de Zn/Al pelo método de Coprecipitação.
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Data: 28/09/2017
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O ácido cafeico (AC) é um composto fenólico de ocorrência natural em frutas e vegetais que atua como importante antioxidante, antimicrobiana, antivírus e apresenta diversas aplicações terapêuticas potenciais no tratamento de doenças como câncer de pele, do cólon, doenças imunorreguladoras, cardiovasculares e leishmaniose. Os hidróxidos duplos lamelares (HDL) são matrizes inorgânicas caracterizadas por uma estrutura em lamela que apresenta biocompatibilidade e pode ser utilizada como sistema de liberação controlada de fármacos. Neste estudo, o ácido cafeico (AC) foi intercalado em Zn/Al-HDL, através do método de co-precipitação a pH 6. O material híbrido obtido foi caracterizado por difração de raios-X em pó, espectroscopia infravermelho, espectroscopia Raman e microscópia eletrônica de varredura. Além disso, o teor de AC no material obtido foi determinado por espectroscopia UV-vis tendo um rendimento de 61%. O espaçamento basal de 11 Ǻ demonstrou a intercalação dos ânions AC nas lamelas do HDL. Os resultados de infravermelho confirmaram a presença de ânions de AC intercalados na estrutura da HDL através de duas bandas a 1406 e 1332 cm-1 (assimétricas e simétricas de alongamento COO-, respectivamente), o Raman complementa o resultado infravermelho apresentando o alongamento das bandas. As micrografias do HDL exibem uma morfologia com formatos hexagonal, no entanto, após o processo de intercalação, observou-se uma alteração considerável na estrutura do material, normalmente observada devido a incorporação do ácido orgânico entre as camadas do HDL. De um modo geral, os resultados sugerem que o material sintetizado nano-híbrido apresenta-se de forma cristalina e as moléculas do fármaco interagem com as camadas do HDL.
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VANEZA RODRIGUES VIEIRA
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Cytoprotective and cicatrizing activity of the species Conocarpus eretus L in gastric lesions induced in adult wistar rats
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Data: 06/09/2017
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The pharmacological research has been aimed at the knowledge of regional folk medicine, in order to establish the scientific bases of their respective pharmaceutical products’ effectiveness. Among the many natural sources used in our region are the species Conocarpus erectus L, popularly known as the "mangrove bud", belonging to the Combretaceae family. Different parts of the plant such as leaves, stems, fruits and flowers have their biological activity studied, among them the anticancer and antimicrobial effects. Ethnopharmacological reports obtained in the region of Salinópolis - PA also described a potential use in digestive disorders. Although a great advance in the drug therapy used in the cases of gastric ulcerationhas been made, it is important to carry out studies that prove its validity. This work aims to verify the cytoprotective activity and cicatrizing activity of the lyophilisatebark teaobtained by decoction of the species Conocarpus erectus L (LCE) in acute and chronic gastric lesions. The methodologies for evaluating the cytoprotective effect were acute lesions inducted by indomethacin and ethanol, while the cicatrization effect was evaluated by chronic acetic acid-induced lesions in adult Wistar rats. The intragastric pH variation was measured by the pylorus ligament assay. The lyophilizate’santioxidant activity was evaluated by the DPPH assay, as well as the lipid perioxide levels’ that were evaluated by the TBA-RS method in chronic lesions induced by acetic acid 5 and 10%. The results showed cytoprotective activity of LCE by the indomethacin induction model reduced the ulceration index (IU) in the treated group by 51,49%, omeprazole group by 51,33% and sucralfate group by 71,28%, all of them when compared to the controlled group. On the model of ethanol LCE’s induction, the area affected was reduced by 90.94%, and in the sucralfate’s induction group, by 75.88% when compared with the controlled group. The LCE’s healing effect reduced gastric lesions to 5% in 80.11%, while the on omeprazole group to 52.75% and the sucralfate group reduced to 66.33%, whereas in the 10%gastric lesionsthe LCE group reduced 72.11%, the omeprazole 57.47%, and the sucralfate group 43.77% (p>0,05Anova, post test Dunnett's and Turkey). The LCE treatment showed an increase of 39% onintragastric pH when compared to control (p>0,05Anova, post test Dunnett's e Turkey’s) and did not statistically showed any different from the omeprazol e group by themodel of pylorus ligation. The LCE antioxidant effect was confirmed by the DPPH assay, as it was diluted in 10x, 50x and 100x with a percentage of 67.65% ± 0.52, 73.22% ± 0.17 and 72.70% ± 1.39, respectively, when compared to the ascorbic acid antioxidant of 33,74% (AA) like this (p <0.05, Anova post test Dunnett). A lipid peroxidation evaluated in the lesions obtained by the 5%-acetic-acid-induction model showed that the average MDA levels in the nave group, controlled group and treated group LCE were 0.492 ± 0.0849, 1.579 ± 0.219, and 0.399 ± 0.092, respectively, showing that the LCE-treated group was able to reduce lipid peroxidation by 74.73% in comparison to the controlled group (p<0,05 Anova post test Dunnet) and it did not statisticallydiffer from the nave group. On the 10%-acetic-acid-model the average level of malonaldehyde in the nave group, controlled group and the LCE-treated group was 0.628 ± 0.042, 1.567 ± 0.234 and 0.441 ± 0.12, respectively. The LCE treated group managed to reduce by 71.85% the lipid peroxidation caused by acetic acid induced lesions when compared to the control group (p <0.05 Anova post test Dunnet).These results confirm the cytoprotective and cicatrizing effects of LCE and suggest possible action mechanisms associated with its antioxidant potential, as well as possible acid secretioninhibition.
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CLEISON CARVALHO LOBATO
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Drug candidates design with antileukemic activity (K562) based on the structure of 6α-hydroxyvouacapan-7β,17β-lactone and 16-(N,N-diethylamino)methylene-6α-hydroxyvouacapan-7β,17β-lactone
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Data: 31/08/2017
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Leukemia is a neoplasm of hematopoietic tissue originating from the bone marrow and can be classified according to the cell line involved as myeloid and lymphoid. Thus, we have acute myelogenous leukemia (AML), chronic myelogenous leukemia (CML), acute lymphoid leukemia (ALL) and chronic lymphocytic leukemia (CLL). Studies have evidenced the essential role of the control of ABL tyrosine kinase activity for the treatment of CML. In this study the main objective is the planning of compounds that act as inhibitors of ABL tyrosine kinase activity, responsible for the proliferation of these tumor cells. Among the naturally occurring compounds that have activity in K562 chronic myeloid leukemia tumor cells are 6α, 7β-Dihydroxyivoucapan-17β-oic acid (ADV) and 14 derivatives that have undergone chemical quantum studies in order to select the best Set theory-based basis to be used in future molecular modeling for these compounds. The method that presented the best results was DFT / B3LYP 631-G **. Virtual screening was also performed to obtain structures similar to ADV and derivatives with potential activity in the cells studied. The structures obtained by virtual screening were submitted to studies of predictions of pharmacokinetic and toxicological properties (ADME / Tox) as well as the molecular docking study to predict the binding affinity between the protein-ligand complexes. The compound which showed the best binding affinity was ZINC38664626, also showed excellent pharmacokinetic and toxicological parameters, showing to be a promising compound to be used as a drug.
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KELTON LUIS BELÉM DOS SANTOS
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Drug Design with anti-inflammatory activity in the A2a-adenosine receptor (A2AAR)
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Data: 31/08/2017
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Inflammation is a ubiquitous homeostatic mechanism generated to protect the body's integrity against endogenous or exogenous harmful agents. Inflammatory diseases constitute a complex and heterogeneous group of diseases, being an important cause of morbidity and mortality. Adenosine A2A receptor (A2AAR) has a considerable importance in the anti-inflammatory process. For the search of agonists with anti-inflammatory activity, the (6-(2,2-diphenylethylamino)-9-((2R,3R,4S,5S) -5-(ethylcarbamoyl)-3,4-dihydroxytetrahydrofuran-yl)-N-(2-(3-(1-(pyridin-2-yl)piperidin-4-yl)ureido)ethyl)-9H-purine-2-carboxamide) (UK-432097) and a set of 20 compounds found in the BindingDB database was analized. These compounds were used to generate several pharmacophore models. The predicted molecular properties were used for the construction of QSAR models (bi-, tri-, tetra-, penta-, hex-parametric) via Multiple Linear Regression Model for the prediction of biological activity. In addition, the PASS webserver was also used to predict activity. The best pharmacophoric model was used for commercial compounds in databases and the resulting compounds from the virtual screening were applied to the QSAR models. Following the methodological sequence, the results of the virtual screening were possible to select two compounds with promising activity to present specific characteristics delineated in the work, besides presenting satisfactory pharmacokinetic and toxicological profiles, being able to be used in future biological assays to confirm its activity and anti- inflammatory response to the A2AAR receptor.
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RAÍ CAMPOS SILVA
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PLANNING OF CANDIDATES FOR NEW DRUGS WITH POTENTIAL ANTI-CANCER ACTIVITY PROSTATE PC-3.
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Data: 30/08/2017
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Prostate cancer PC-3 is one of the leading causes of disease and death on the planet. It is characterized by excessive enlargement of the gland, with consequent decrease in the volume and intensity of the urinary stream. In the prostate and other organs, testosterone is an androgen hormone, which is converted to dihydrotestosterone by the enzyme 5α-reductase (5αR) and binds to the androgen receptor (AR). Mutations in these androgens cause reproduction of cancer cells after formation of the androgen - receptor complex. The incidence varies by 25 times worldwide, with higher numbers registered in the developed countries of the continents oceania, europe and north america. In Brazil it is the most prevalent among men in all regions, with 95.63/100 thousand inhabitants in the south, 67.59/100 thousand in the Midwest, 62.36/100 thousand in the southeast, 51.84/100 thousand in the northeast and 29.50/100 thousand in the north region. The species Pterodon Emarginatus Vogel, commonly called "White sucupira" is a vegetable with fruits, which in the form of alcoholic infusion is used in folk medicine for the treatment of various diseases. vouacapan compounds extracted from the said species, have been shown to be promising for the treatment of potent antiproliferative agents against human cancer cells, especially for PC-3 prostate cancer cells, in which experimental values of activity (GI50) described in the literature, were significant. In silico studies of compounds with PC-3 prostate cancer potential in AR, were employed to obtain the probable bioactive pose of the vouacapan derivative, via semi-empirical method (PM3) and refined with the base set 6-31+G(d, p), calculated in the DFT method through the theory level B3LYP with the software Gaussian03. Binding-based virtual screening was performed on five commercial compound bases with the ROCS and EON softwares, predictions of pharmacokinetic and toxicological properties using Qikprop and Derek, evaluation of the molecular overlap index by steric / electrostatic contribution, in addition to molecular docking studies using Pyrx, between the ligand and structures from the bases complexed with AR (PDB code: 2oz7), to verify binding affinity. Between 238,922 molecules, only eight presented good theoretical values of pharmacokinetics, toxicity, esteric/electrostatic similarity and binding affinity, were the hits (7) 10,9kcal.mol-1 as the best of the series, (1) 8,1kcal.mol-1 as less favorable. The others appear within this range (2.8 Kcal.mol-1) with their respective values, (8) 8,2 kcal.mol-1, (5) 8,2 kcal.mol-1, (4) 8,3 kcal.mol-1, (2) 8,5 kcal.mol-1, (3) 8,6 kcal.mol-1, (6) 8,8 kcal.mol-1, indicating good efficiency of the screening method used. The results in predictions for 21 pharmacokinetic properties, were within the recommended range, similar to 95% of the drugs available on the market and no toxicity warning. The selected structures presented similarity with the pivot vouacapan greater than 75%. Based on binding affinity and predictions, two molecules were considered more promising, can be indicated as candidates for studies in vitro and in vivo.
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VALERIA ARAUJO BARROS
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DESIGN, SYNTHESIS AND APPLICATIONS OF NAFTOSALICYLIC DERIVATIVES AS ANTIOXIDANTS
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Data: 30/08/2017
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Salicylate derivatives are successfully used as analgesic, antipyretic, anti-inflammatory agents and in prevention of cancer, mainly rectal colon. They reduce the risks of many diseases associated with old age. However, adverse effects related to gastrointestinal events are always associated to its main constituent (ASA). These aspects are linked to their chemical stability and affinity for biological receptors. The aim of this work are the design, synthesis and applications of naphthalene-salicylic derivatives as antioxidants. Thus, a theoretical study of the twelve studied compounds was carried out. The calculations of electronic properties such as frontier orbitals HOMO-LUMO, ionization potential (IP), bond dissociation energy of phenolic moiety (BDEOH), and spin density contributions were performed by using density functional theory (DFT) at the B3LYP/6-31G (d, p) level of theory on Gaussview and Gaussian computational packages. Some of these compounds were synthesized by using classical methods. The theoretical results showed that both additional hydroxyl or substitution on benzene ring for naphthalene increase the antioxidant capacity in the same values with small dissimilarities among acid, ester, and amide derivatives. A synergistic effect was observed when both are used together, producing the most potent molecules. In addition, spin density calculations have indicated a regioselective pathway can be gotten from monohydroxylated derivatives, with high possibility of generating of in vivo dihydroxy derivatives mainly at the para position relative to the phenolic group, through enzymatic or non-enzymatic reactions. Finally, the replacement of the naphthalene ring instead of the benzene ring increases both reactivity and chemical stability for the quinone-type intermediates, explaining how these compounds may play a role in the preventive mechanisms and way treatment of cancer. Some synthesized compounds are in anticancer and anti-inflammatory tests.
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AMANDA RUSLANA SANTANA OLIVEIRA
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Theoretical aspects of the interaction between cephalosporin compounds and Penicillin Binding Protein 5 of Escherichia coli using Molecular Dynamics
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Data: 04/08/2017
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Escherichia coli is an anaerobic gram-negative bacillus that naturally inhabits the intestines of mammals. The diseases come when the bacteria reach other organs of our body, causing infections, mainly in the urinary tract of women, due to the proximity of the female urethra with the anus. In the treatment of these infections antibiotics are used that fight the bacterium, such as antibiotics of the class of cephalosporins, that are the group with the greater number of β-lactam antibiotics in clinical use. These compounds are capable of inhibiting the enzymatic function of Penicillin-Binding Proteins (PBP), which is responsible for the final step of biosynthesis of peptidoglycan, an essential component for the survival of bacteria. In this work, the antimicrobial compounds cefoxitin, cefuroxime, cefotaxime, cephalothin, cefixime, cefmetazole and 7-aminocephalosporanic acid were chosen based on experimental studies of biological activity in the fight against the Gram-negative opportunistic pathogen Pseudomonas aeruginosa, to be studied theoretically by means of Molecular Dynamics (MD) simulations, binding free energy calculations and residue interaction energy, for the determination of their potential biological activity in inhibiting the enzymatic function of the specific E. coli PBP, Penicillin (PBP5), therefore, its inhibition leads to cell death. Free-binding energies were more favorable for the cefoxitin (crystallographic), cephalothin and cefuroxime ligands, -31.471 Kcal/mol, -34.225 Kcal/mol and -35.085 Kcal/mol, respectively, and it was observed that the catalytic residues Ser44 and His216 presented more favorable energy contributions to the system formed by the cephalothin ligand. Thus, cephalothin suggests to have excellent potential for inhibition of the enzymatic function of E. coli PBP5, responsible for the final phase of transpeptidation of the peptidoglycan layer.
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CLAUBER HENRIQUE SOUZA DA COSTA
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Conformational mechanism study of 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase (HMGR) protein with the statins and substract through of Molecular Dynamics, PCA, and Free Energy
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Data: 03/08/2017
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Conformational mechanism study of 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase (HMGR) protein with the statins and substract through of Molecular Dynamics, PCA, and Free Energy
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EDSON LEANDRO DE ARAUJO SILVA
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Simulação Computacional do Mecanismo Catalítico da Enzima Catecol-Metiltransferase.
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Data: 16/02/2017
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Reações de transferência de metil são muito importantes em sistemas biológicos. A enzima catecol O-metiltranferase catalisa a reação de transferência de um grupo metil do co-substrato S-adenosilmetionina para dopamina. Esta enzima está relacionada com a doença de Parkinson que se trata de uma doença neurodegenerativa que afeta de 7 à 10 milhões de pessoas da população mundial, principalmente a parcela com mais de 60 anos. Devido a importância da reação catalisada por esta enzima, ferramentas computacionais em conjunto com métodos da mecânica quântica foram utilizadas para o estudo do mecanismo de reação da transferência de metil da S-adenosilmetionina para dopamina. Neste estudo, a presença ou não do íon Mg2+ na reação e mudanças na estrutura da dopamina para catecol e fenol foram levadas em consideração a fim de propor a região quântica mais adequada para futuros trabalhos de simulação no meio enzimático. Os métodos utilizados incluem o método semiempírico PM6, o ab initio DFT e o de correlação MP2. O modelo de solvatação PCM foi usado com o intuito de estudar a reação de referência na água do sistema enzimático e analisar as barreiras de energia da reação na água e comparar com barreiras obtidas no gás.
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