The enzyme soluble epoxide hydrolase (sEH) plays a major role in the pathogenesis and pathophysiology of neurodegenerative diseases like depression by catalyzing the hydrolysis of epoxyeicosatrienoic acids (EETs) into dihydroxyicosatrienoicacids (DHETs), its less biologically active form, influencing the anti-inflammatory system and promoting inflammation. Therefore, inhibiting sEH leads to increased levels of EETs, reducing inflammation, especially in the brain and can help mitigate neurodegenerative diseases. This study investigated sEH inhibition by a phenolic carotenoid compound, astaxanthin and its inhibitory mechanism of action. Enzyme inhibitory activity and kinetics demonstrated that astaxanthin had a half-maximal inhibitory concentration (IC50) of 26 ± 0.92 μM and is a mixed-non-competitive inhibitor of sEH. In silico ADME/tox analysis showed that astaxanthin is bioavailable, biostable, and non-toxic when taken orally. Molecular docking study demonstrated that astaxanthin binds to an allosteric site of sEH and formed a contact and clashing-only interaction with the ASP333 residue of the hydrolase pocket of sEH. In this study, we highlight the potential therapeutic application of astaxanthin as a natural sEH inhibitor in the treatment of inflammation-related diseases, particularly neurodegenerative diseases.

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In addition to its canonical role in aminoacylation, threonyl-tRNA synthetase (TARS) possesses pro-angiogenic activity that is susceptible to the TARS-specific antibiotic borrelidin. However, the therapeutic benefit of borrelidin is offset by its strong toxicity to living cells. The removal of a single methylene group from the parent borrelidin generates BC194, a modified compound with significantly reduced toxicity but comparable anti-angiogenic potential. Biochemical analyses revealed that the difference in toxicities was due to borrelidin's stimulation of amino acid starvation at ten-fold lower concentrations than BC194. However, both compounds were found to inhibit in vitro and in vivo models of angiogenesis at sub-toxic concentrations, suggesting a similar mechanism that is distinct from the toxic responses. Crystal structures of TARS in complex with each compound indicated that the decreased contacts in the BC194 structure may render it more susceptible to competition with the canonical substrates and permit sufficient aminoacylation activity over a wider concentration of inhibitor. Conversely, both borrelidin and BC194 induce identical conformational changes in TARS, providing a rationale for their comparable effects on angiogenesis. The mechanisms of TARS and borrelidin-based compounds on angiogenesis were subsequently tested using zebrafish and cell-based models. These data revealed ectopic branching, non-functional vessels, and increased cell-cell contracts following BC194-treatment or knockdown of TARS expression, suggesting a role for the enzyme in the maturation and guidance of nascent vasculature. Using various TARS constructs this function was found to be dependent on two interactions or activities associated with the TARS enzyme that are distinct from its canonical aminoacylation activity. Furthermore, observations that TARS may influence VEGF expression and purinergic signaling suggest the possibility for a receptor-mediated response. Taken together, the results presented here demonstrate a clear role for TARS in angiogenesis, independent of its primary function in translation. Although the exact molecular mechanisms through which TARS and borrelidin regulate this activity remain to be determined, these data provide a foundation for future investigations of TARS's function in vascular biology and its use as a target for angiogenesis-based therapy.

As peroxirredoxinas (Prx) são enzimas antioxidantes que se destacam pela capacidade de decompor uma grande variedade de hidroperóxidos com elevada eficiência (106-108M-1s-1), mantendo essas moléculas em níveis adequados à homeostase celular. Entretanto, já foi demonstrado que em diversos tipos tumorais os níveis de Prx são extremamente aumentados e experimentos envolvendo sua inativação resultam na diferenciação ou apoptose de células tumorais. Recentemente, foi descoberto um diterpenóide denominado adenantina que seria o primeiro inibidor para as Prx1 e Prx2 de humanos e foi demonstrada que sua aplicação em células de leucemia mieloide aguda promoveu diferenciação ou apoptose dessas células. Nesse contexto, o presente trabalho apresenta duas vertentes: 1) A caracterização das alterações estruturais e funcionais promovidas pela ligação da adenantina ao sítio ativo das Prx utilizando Tsa1 de Saccharomyces cerevisiae como modelo biológico, em função da sua alta similaridade com Prx2 de humanos; 2) Avaliação da atividade antitumoral dose dependente de adenantina sobre as linhagens celulares REH e MOLT-4 de leucemia linfoide aguda. No que concerne à primeira linha de investigação, nossos resultados revelam que Tsa1 é suscetível à inibição por adenantina, uma vez que o tratamento reduziu em ~66 % a velocidade de decomposição de peróxido de hidrogênio. Adicionalmente, a mutação da Thr44 de Tsa1, pertencente à chamada tríade catalítica, por uma Ser resultou em uma proteína mais suscetível a alterações na estrutura secundária e à inibição da atividade peroxidásica em função da ligação com adenantina, apresentando uma diminuição de ~85% na velocidade de reação. Características semelhantes foram observadas para a proteoforma Tsa2 de S. cerevisiae, que carreia naturalmente a substituição da Thr44 pela Ser. Análises de sequências de Prx em bancos de dados revelaram que majoritariamente proteínas contendo Ser são encontradas em organismos procariotos, muitos deles patogênicos. Finalmente, demonstramos por meio de ensaios citotoxicidade que as bactérias Staphylococcus aureus e Staphylococcus epidermidis, que possuem uma Ser na tríade catalítica, têm seu crescimento inibido pelo tratamento com adenantina (IC50 de 460µM e 77µM, respectivamente), enquanto que para Escherichia coli, que possui Thr nessa posição, a toxicidade da adenantina foi bastante baixa (não foi possível determinar o IC50 nas condições utilizadas). Dessa forma, os dados apresentados neste trabalho demonstram o potencial da utilização da adenantina tanto como antibiótico quanto como antileucêmico. / Peroxiredoxins (Prx) are antioxidant enzymes which stand out due the ability to decompose a wide variety of hydroperoxides with high efficiency (106-108M-1s-1) maintaining these molecules at suitable levels to cellular homeostasis and participating in several signaling events. However, it has been shown that, in many tumor types, Prx levels are extremely increased and experiments involving its inactivation have resulted in differentiation or apoptosis of tumor cells. It was recently found a diterpenoid, called adenanthin, that would be the first human Prx1 and Prx2 inhibitor and it was demonstrated that its application in acute myeloid leukemia cells was able to promote differentiation or apoptosis. In this context, this work presents two lines of research: 1) Characterization of structural and functional changes promoted by adenanthin binding to Prx active site using Tsa1 from Saccharomyces cerevisiae as biological model, due to its high similarity to human Prx2. 2) Evaluation of adenanthin dose-dependent antitumor activity over the acute lymphoid leukemia cell lines REH and MOLT-4. As regards the first line of research, our result reveal that Tsa1 is susceptible to inhibition by adenanthin, since the treatment with this binder reduced the hydrogen peroxide decomposition velocity in ~ 66%. In addition, the replacement of Thr44 from Tsa1, aminoacid belonging to the so-called catalytic triad, by a Ser resulted in a protein more susceptible to alterations in secondary structure and to peroxidase activity inhibition in function of adenanthin binding, presenting ~85% of decrease in reaction velocity. Similar characteristics were observed for Tsa2 proteoform from S. cerevisiae, which naturally carries the substitution of Thr44 by Ser. Prx sequences analyzes in databases revealed that mostly Ser-containing proteins are found in prokaryotic organisms, many of them pathogenic ones. Finally, we demonstrate through cytotoxicity assays that the bacteria Staphylococcus aureus and Staphylococcus epidermidis, which have a Ser in catalytic triad, have their growth inhibited by adenanthin treatment (IC50 of 460µM and 77µM, respectively), whereas for Escherichia Coli, which has Thr at that position, the tocyxicity of adenanthin was quite low (it was not possible to determine the IC50 under the used conditions). Regarding the second line of investigation, we found that adenanthin is able to induce the death of leukemic cell lines REH and MOLT-4, and for the last one, there was an unexpected proliferation of cells treated by the longest incubation period (72 hours), characterizing a possible indication of differentiation process. In this sense, the data presented here demonstrate the potential of adenanthin use in both antibiotic and antileukemic treatments.

The O-acetylation of peptidoglycan (PG) is currently known to occur in greater than 50 eubacterial species, including numerous pathogens. This modification, which occurs at the C-6 hydroxyl of the N-acetylmuramoyl residues within the heteropolymer’s glycan backbone, serves as a cell wall autolytic regulatory mechanism, and contributes to pathogenesis and persistence within a host. Despite these significant physiological and pathobiological roles however, the identity of the pathway(s) responsible for the modification was only recently elucidated, for which two unrelated systems were identified, viz., the O-acetylpeptidoglycan (OAP) cluster-encoded multi-component system typical of Gram-negative species and the singular OatA of Gram-positives. As part of the OAP PG O-acetylation system, our group previously identified O-acetylpeptidoglycan esterase (Ape) as an enzyme responsible for the removal of the modification, permitting the continued metabolism of the PG sacculus. Herein, studies were performed to assess the postulated viability of this class of enzyme as a novel antibacterial target. Specifically, recombinant Ape1 from Neisseria gonorrhoeae was purified to homogeneity and the inhibitory effect of purpurin, a natural product identified as such, evaluated in detail. Kinetic analysis demonstrated that the compound elicited a competitive mode of inhibition (Kic ~3.7 μM), while the in vivo treatment of an array of environmental and pathogenic species was found to result in growth arrest for those cells containing both O-acetylPG and Ape. Evaluation of modification levels, cell wall morphology, and viability indicated a bacteriostatic effect. Taken together these data provide proof of principle that this class of enzyme presents a worthy therapeutic target. In addition to the presence of an Ape, the OAP system further differs from that of OatA through the use of two PG O-acetyltransferases. While purported to be mutually exclusive and evolutionarily divergent, in silico genomic analyses indicated their potential copresence in Bacillus anthracis and other closely related organisms. Indeed, purpurin-mediated differential growth inhibition between several such isolates and other bacilli indicated Ape activity therein. To investigate this possibility, the hypothetical Ape3 protein from Bacillus cereus ATCC 10987 was overproduced, purified, and its function assessed. Data from activity assays involving natural and synthetic substrates indicated that the protein possesses basal esterase activity in vitro. Phenotypic analysis of B. anthracis mutants deficient in each of the organism’s putative integral membrane PG O-acetyltranslocases subsequently indicated that Ape3 preferentially functions as a PG O-acetyltransferase (Pat) in vivo and that the OAP-mediated system is required for the separation of daughter cells following division. In addition, the presence of an Oat homologue was also confirmed. Thus, this is the first report of a bacterium known to possess both types of PG O-acetylation systems. / Natural Sciences and Engineering Research Council of Canada (NSERC)

Orientador: Prof. Dr. Hugo Barbosa Suffredini / Dissertação (mestrado) - Universidade Federal do ABC. Programa de Pós-Graduação em Ciência e Tecnologia/Química, 2016. / O presente trabalho apresenta os estudos da determinacao de pesticidas organofosforados em um sistema interfacial do tipo agua/oleo de soja, a partir da inibicao enzimatica da Fosfatase acida co-imobilizada com Glicose Oxidase em eletrodo modificado com azul da Prussia. Testes inciais sobre a eficiencia da capacidade eletrocatalitica do filme de Azul da Prussia foram feitas a fim de se estabelecer o potencial de trabalho para as deteccoes de glicose 6-fosfato. As analises em fase aquosa retornaram limites de deteccao e quantificacao de 0,443 e 1,478 mol L-1, respectivamente. A sensibilidade do metodo foi calculada como sendo igual a 0,0445. Em relacao ao testes na interface oleo/agua, os limites de deteccao e quantificacao foram de 0,206 e 0,6872 mol L-1 e a sensibilidade do metodo foi encontrada como sendo igual a 0,035. A inibicao enzimatica foi observada a partir da exposicao do biossensor ao pesticida metil paration por 10, 20 e 30 minutos em fase aquosa e no sistema interfacial. Obervou-se nessas analises a eficiencia deste biossensor em detectar tal pesticida diretamente em oleo de soja a partir da aplicacao da tecnica eletroquimica de interface oleo/agua. / This work is related to the detection of organophosphorus pesticides in a water/oil interfacial system by determining the enzymatic inhibition of acid phosphatase co-immobilized with Glucose Oxidase in a modified electrode with Prussian blue. Initial efficiency tests concerning the electrocatalytic capacity of Prussian blue film were carried out, aiming to establish the working potential related to the detection of glucose 6-phosphate. The aqueous phase analyses returned limits of detection and quantification of 0.443 and 1.478 mol L-1, respectively. The sensitivity of the method was calculated as being equal to 0.0445. Concerning the tests in oil/water interface, limits of detection and quantification were calculated as 0.206 and 0.6872 mol L-1 and the sensitivity of the method was obtained as 0.0035. The enzymatic inhibition of the biosensor was observed after a methyl parathion pesticide exposure of 10, 20 and 30 minutes in the aqueous phase and the interfacial system. It was possible to observe that the efficiency of the biosensor on the detection of the pesticide directly into soybean usin the oil/water interface electrochemistry as the main tool.

Orientador: Prof. Dr. Wanius José Garcia da Silva / Dissertação (mestrado) - Universidade Federal do ABC, Programa de Pós-Graduação em Biotecnociência, 2016. / A hidrolise enzimatica da celulose e realizada pela acao sinergica de pelo menos tres tipos de celulases distintas: endoglucanases, exoglucanases e ¿À.glicosidases. As endoglucanases e celobiohidrolases sao frequentemente inibidas pelo aumento da concentracao de celobiose (dimero de glicose) no meio reacional. As ¿À-glicosidases sao enzimas que clivam celobiose em monomeros de glicose. Portanto, as ¿À-glicosidases sao essenciais ao processo de hidrolise da celulose por impedirem o acumulo de celobiose e, assim, evitar a diminuicao da taxa de hidrolise. Processos de pre-tratamento da biomassa lignocelulosica sao empregados, antes da reacao de hidrolise enzimatica da celulose, a fim de retirar a fracao de lignina e aumentar a taxa de conversao da celulose em glicose. Porem, estes processos de pre-tratamento da biomassa lignocelulosica nao sao 100% eficientes na remocao da lignina. Estudos previos mostraram que a adicao de lignina a celulose pura pode causar a reducao da liberacao de acucar em valores superiores a 60%. Assim, neste estudo, nos caracterizamos a adsorcao nao produtiva da enzima ¿À-glicosidase da familia GH1 da bacteria Thermotoga petrophila (TpBGL1) em ligninas extraidas de diferentes biomassas (cana-de-acucar e eucalipto). Em pH 7 e 6, nossos resultados indicaram que a repulsao eletrostatica enfraquece a adsorcao nao produtiva de TpBGL1 em ligninas. Contudo, em pH 4 a atracao eletrostatica fortalece a adsorcao nao produtiva. Alem disso, o aumento da temperatura de 25 oC para 70 oC nao resultou em um aumento significativo da adsorcao de TpBGL1 em ligninas, provavelmente porque nao ocorre um aumento significativo de regioes hidrofobicas na estrutura da enzima expostas ao solvente. Todas as informacoes obtidas neste estudo poderao ser uteis para aplicacoes biotecnologicas no campo de conversao de polissacarideos estruturais em bioenergia. / The enzymatic hydrolysis of cellulose to glucose requires at least three types of enzymes working synergistically: endoglucanases that randomly cleave the â-1,4-glycosidic linkages of cellulose, cellobiohydrolases which cleave off cellobiose units from the reducing or nonreducing end of cellulose chain, and â-glucosidases responsible for hydrolysis of the released cellobiose to glucose. Endoglucanases and cellobiohydrolases are normally inhibited by cellobiose, therefore, â-glucosidases are essential to avoid the decrease the hydrolysis rates of cellulose over time due to cellobiose accumulation. The presence of residual lignin after pretreatments may affect negatively the enzymatic hydrolysis of cellulose to glucose. Cellulases bind to lignin, deactivating the enzymes and reducing the overall enzymatic activities. In this study, we examined the non-productive adsorption of one â-glucosidase from Thermotoga petrophila, belonging to the family GH1, on the lignin preparations from both sugarcane (grasses) and eucalyptus (hardwood). GH1 â-glucosidase adsorption onto lignins was found to be strongly pH-dependent, suggesting that the adsorption is electrostatically modulated. At pH 7 and 6, electrostatic repulsion weakens the non-productive adsorption of GH1 â-glucosidase to lignins. However, at pH 4, attractive electrostatic interactions strengthen the non-productive adsorption of GH1 â-glucosidase to lignins. Finally, the increase of temperature did not result in the increase of GH1 â-glucosidase adsorption, probably because there is no significant increase in hydrophobic regions in the GH1 â-glucosidase structure. These studies can be useful in the field of plant structural polysaccharides conversion into bioenergy.

Palmitoylation refers to the covalent attachment of fatty acids, such as palmitate, onto the cysteine residues of proteins. This process may subsequently alter their localization and function. Nearly all of the enzymes that catalyze palmitoylation, zDHHC protein acyl transferases (PATs), are implicated in neurological disorders, infectious diseases, and cancer in humans. Of particular interest to those who study palmitoylation are Ras family GTPas and zDHHC9-GCP16, the zDHHC PAT that palmitoylates Ras proteins. Erf2-Erf4 is the zDHHC PAT that palmitoylates Ras proteins in Saccharomyces cerevisiae. Currently, there are no methods to therapeutically target palmitoylation for the treatment of disease. One of the barriers to identifying a modulator of palmitoylation is the lack of a reliable high-throughput screening system. To date, few assay systems have been developed to examine the kinetics and mechanism of that palmitoylation reaction. This lab has developed a fluorescence-based coupled assay to gain insight into the enzymology, biochemical mechanism, and kinetics of the palmitoylation reaction. This assay may be used to identify specific inhibitors of autopalmitoylation. In the first step of this reaction, the palmitoyl-moiety from palmitoyl-CoA is transferred to the zDHHC9 PAT cysteine side chain to form a palmitoyl:enzyme intermediate. The second step of palmitoylation is the subsequent transfer of the palmitoyl-moiety from the palmitoyl:enzyme intermediate to the cysteine residue of the substrate protein. This fluorescence-based coupled assay was utilized to screen a natural products library and a unique synthetic compound library for inhibitors of Erf2 autopalmitoylation. These screens led to the identification of fungal metabolite extracts and ten bis-cyclic piperazine compounds that inhibit Erf2 autopalmitoylation in the low micromolar range. This effect is similar to known inhibitors of palmitoylation that lack specificity for the palmitoylation reaction itself.

Abstract Metabolism is a major determinant of the pharmacokinetic properties of most drugs and is often behind bioavailability problems, drug-drug interactions, and metabolic idiosyncrasies. Cytochrome P450 (CYP) enzymes are a superfamily of microsomal hemoproteins catalysing the metabolic reactions of several exogenous compounds. The majority of crucial steps within drug metabolism are in connection with CYP enzymes. In the present study, in vivo, in vitro, and in silico approaches were applied and characterised to evaluate the effects of chemical entities on CYP-mediated metabolism. CYP2B6 was used as a target enzyme for these studies. For evaluation of the CYP inhibition potential of new chemical entities, a novel in vitro test system utilising the n-in-one approach was developed. This method proved to be robust and applicable to screening purposes. Validation of the n-in-one assay was done by comparing its performance to commonly used in vitro techniques using six structurally diverse drugs. All assay types yield remarkably similar results with the majority of the CYP forms tested. Several chemicals were screened in vitro and in silico in order to find potent and selective chemical inhibitors for CYP2B6. Ticlopidine, thioTEPA and 4-(4-chlorobenzylpyridine) were found to be highly effective inhibitors of CYP2B6. The selectivity of thioTEPA proved to be very high, whereas ticlopidine and 4-(4-chlorobenzylpyridine) also inhibited other CYPs. At a concentration level of 1 μM for ticlopidine and 0.1 μM for 4-(4-chlorobenzylpyridine), the inhibitory effect towards other CYPs was negligible. Due to wide clinical use and relevance, clopidogrel and ticlopidine were selected for further in vivo interaction studies. Both clopidogrel and ticlopidine significantly inhibited the CYP2B6-catalysed bupropion hydroxylation and patients receiving either clopidogrel or ticlopidine are likely to need dose adjustments when treated with drugs primarily metabolised by CYP2B6. The effect of impaired kidney function on CYP2B6 activity and on bupropion pharmacokinetics was also explored. In patients with kidney disease, the bupropion AUC and Cmax were significantly higher and the apparent oral clearance of bupropion was notably lower compared to healthy controls. The present results indicate that the in silico and in vitro methods used are helpful in predicting in vivo drug-drug interactions. The effective utilisation of these models in the early phases of drug discovery could therefore help to target the in vivo studies and to eliminate metabolically unfavourable drug candidates.

Parkinson's disease (PD) is a prevalent neurodegenerative disorder which affects over a million people in the United States. This disease is marked by the selective loss of dopaminergic neurons in the substantia nigra, leading to a decrease in the important neurotransmitter dopamine (DA), which is essential for the initiation and execution of coordinated movement. Currently, the pathogenesis behind PD is unknown, but there is evidence that both exogenous causes, such as pesticides and metals, as well as endogenous causes, such as reactive oxygen species or reactive metabolism intermediates, may play a role in the onset and progression of the disease. DA is catabolized by monoamine oxidase to 3,4-dihydroxyphenylacetaldehyde (DOPAL), which is further metabolized by aldehyde dehydrogenase and aldehyde reductase to the acid and alcohol products, respectively. Studies have demonstrated the reactivity of DOPAL with peptides and proteins, leading to covalent modification which may be detrimental to protein action. Furthermore, studies have shown that DOPAL is toxic, leading to a decrease in cell viability. Due to this, it was of interest to further study DOPAL and how it may play a role in the onset and progression of PD. It was of particular interest to determine protein targets of DOPAL modification. Until recently, no protein targets were identified and the cellular consequence of elevated DOPAL had not been fully studied. It has been previously shown that the important enzyme, tyrosine hydroxylase (TH) is inhibited by other catechols, including DA. This enzyme catalyzes the rate-limiting step in DA synthesis, oxidizing tyrosine to L-DOPA which is further metabolized to DA. Therefore, it was of interest to determine the effect of DOPAL on TH activity. It was hypothesized that DOPAL modifies and inhibits TH, leading to a decrease in the production of L-DOPA and DA. This work employed the use of a dopaminergic cell model (PC6-3 cells), to positively identify TH as a protein target of DOPAL modification. It also used both cell lysate as well as PC6-3 cell studies to investigate the effect of DOPAL modification on TH activity. Mass spectrometry was also utilized to determine sites of protein modification on TH. Results show that TH is potently inhibited by DOPAL modification, leading to a significant decrease in both L-DOPA and DA. Furthermore, DOPAL inhibition appears to be slowly-irreversible, with enzyme activity showing a time- and concentration dependent in recovery after preincubation with DOPAL. A novel cloning and purification procedure was used to clone human recombinant TH, which was used in mass spectrometry studies in which five sites of DOPAL modification were discovered. Furthermore, a real-time assay for TH activity was developed using a plate reader to spectrophotometrically observe the formation of L-DOPA over time. These data demonstrate the toxicity and potent enzyme inhibition by DOPAL and implicate DOPAL as a neurotoxin relevant in the pathogenesis of PD.