Abstract The enzyme phenylethanolamine N-methyltransferase (PNMT) catalyses the biosynthesis of adrenaline. Although adrenaline is a significant central nervous system (CNS) neurotransmitter, and has been associated with various physiological processes such as the control of blood pressure and the neurodegeneration observed in Alzheimer’s disease, its exact role in the CNS is unclear. As part of an international collaborative effort, this project aimed to develop PNMT inhibitors suitable for probing the role of CNS adrenaline, and to generate novel drug leads. Towards the goal of developing potent and selective PNMT inhibitors, this thesis utilised three general approaches. The first approach involved classical structure-guided drug discovery using X-ray crystallography, and is described in Chapter 2. Characterisation of the PNMT pharmacophore provided results that led to a new understanding of how PNMT recognises inhibitors. Structures described in this thesis revealed a cryptic binding pocket that is only revealed on binding of inhibitors that were predicted to be too large to interact with PNMT. The findings therefore demonstrated an extraordinary degree of flexibility inherent to the PNMT binding pocket, and emphasise the need to include greater protein flexibility in inhibitor design strategies. Secondly, this thesis investigated the catalytic mechanism of PNMT, described in Chapters 3 and 4. This research characterised the binding of substrates to wild type and variant PNMT, including the physiological substrate noradrenaline, and model substrates as well as substrate-analogue inhibitors of the enzyme. PNMT catalyses the methylation of a range of substrates. However, differential substitutions to these substrates can dictate the ligand binding position and thereby determine whether methyl transfer will occur. Additionally, the results provided new lessons for the routine use of point mutations in the study of enzymes, because changes are not always simply an indication of the difference in the residue functionality. I found, for example, that single site mutations can induce large movements in enzyme. Therefore structural characterisation of enzyme variants is an important addition to kinetic studies to enable a comprehensive examination of catalytic function. Finally, I have implemented a fragment based screening (FBS) approach to the discovery of novel lead compounds that inhibit PNMT, described in Chapters 5 and 6. The FBS approach has many advantages over existing drug discovery methods including higher hit rates, higher efficiency hits, and the ability to sample a larger range of chemical space. This thesis describes the application of FBS by X-ray crystallography to PNMT. The approach was used to screen a library of 384 compounds yielding 12 novel PNMT fragment leads. Furthermore, chemical elaboration and kinetic evaluation of these hits was performed in Chapter 7. In summary, this thesis has made a significant contribution to our understanding of the chemistry, kinetics and structure of PNMT. This understanding will be important in ongoing efforts to develop potent, selective, and CNS-active inhibitors of the enzyme.

Diss. (sammanfattning) Uppsala : Univ., 2004. / Härtill 5 uppsatser.

Diss. (sammanfattning) Uppsala : Uppsala universitet, 2005. / Härtill 4 uppsatser.

Thesis (Ph.D.). / Written for the Dept. of Biochemistry. Title from title page of PDF (viewed 2008/01/11 ). Includes bibliographical references.

Thesis (M.S.)--University of North Carolina at Wilmington, 2004. / Includes bibliographical references (leaves : [74]-76).

Thesis (Ph. D.)--University of Washington, 2007. / Vita. Includes bibliographical references (leaves 93-109).

As doenças tropicais têm sido alvo de constantes pesquisas nos últimos anos, em diversos centros em todo o mundo. A procura por novos tratamentos eficazes contra estas desordens estimula a identificação de novos alvos moleculares. A esquistossomose é uma doença parasitária crônica, que afeta cerca de 200 milhões de indivíduos em todo o mundo, causada pelo platelminto trematodo do gênero Schistosoma. No Brasil, a única espécie encontrada é o Schistosoma mansoni. Neste trabalho de mestrado, a enzima purina nucleosídeo fosforilase (PNP, EC 2.4.2.1) do parasita Schistosoma mansoni foi selecionada como alvo molecular para a identificação de novos inibidores e sua caracterização cinética através de potência biológica, seletividade e mecanismo de ação. Adicionalmente, dois complexos cristalográficos foram obtidos na presença de inibidores potentes da PNP, tornando-se assim parâmetros para a modelagem molecular empregando a técnica de docagem. Os estudos computacionais permitiram boa compreensão das interações intermoleculares, fornecendo as bases para um estudo detalhado das relações entre a estrutura e atividade destes compostos. Esse conjunto de informações será de grande utilidade nas etapas de planejamento de novas moléculas bioativas mais potentes e seletivas, candidatas a agentes quimioterápicos contra a esquistossomose. / Tropical diseases have been a target of constant research for several years. The search for new efficient treatments against these parasitic diseases has been stimulating the identification of new molecular targets and new drug candidates. Schistosomiasis is a chronic parasitic disease, which affects about 200 million people in the world, caused by a trematode worm of Schistosoma genus. In Brazil, Schistosoma mansoni is the only specie found. In this Master´s dissertation, the enzyme purine nucleoside phosphorylase (PNP, EC 2.4.2.1) from S. mansoni was selected as a molecular target for the identification and kinetic characterization, including potency, affinity and mechanism of action, of new inhibitors from two chemical classes. In addition, two complexes enzyme-inhibitor were characterized by X-ray diffraction, and were useful for molecular modeling studies employing the docking method. These provided important insights about the main intermolecular interactions responsible for the process of molecular recognition and enzyme inhibition. The information gathered in this work should be useful for future medicinal chemistry efforts in the design of new inhibitors of S. mansoni PNP having increased potency and affinity.

As ferramentas computacionais de modelagem molecular e de QSAR estão integradas ao processo de planejamento de fármacos na busca inesgotável por novas moléculas bioativas de elevado interesse terapêutico. O trabalho em Química Medicinal realizado nesta dissertação de mestrado envolveu o estudo das relações entre a estrutura e atividade de inibidores da enzima purina nucleosídeo fosforilase (PNP) bovina e de Schistosoma mansoni. A potência de uma série de inibidores da PNP de S. mansoni foi determinada experimentalmente através da medida de valores de 1C50, empregando um ensaio cinético padronizado e validado. Conjuntos de dados padrões para inibidores da enzima PNP bovina e de S. mansoni foram organizados, contendo os dados de estrutura e atividade correspondentes. Estes conjuntos formaram a base científica para o desenvolvimento dos modelos preditivos de QSAR 2D, empregando o método holograma QSAR. Os modelos finais de HQSAR desenvolvidos possuem alta consistência interna e externa, apresentando bom poder preditivo. Estes modelos, em conjunto com as informações obtidas dos mapas de contribuição de HQSAR, são guias químico-medicinais importantes no planejamento de inibidores mais potentes e seletivos, candidatos a protótipos de novos fármacos na quimioterapia segura das doenças alvo deste trabalho / Computational tools for molecular modeling and QSAR are well-integrated into the drug design process in the search for new bioactive molecules of significant therapeutic interest. The Medicinal Chemistry work done in this dissertation involved structure-activity studies of inhibitors of bovine and Shistosoma mansoni purine nucleoside phosphorylase (PNP). The potency of a series of S. mansoni inhibitors was experimentally determined through measurements of IC50 values, employing a standard validated kinetic assay. Data sets for bovine and S. mansoni PNP were organized, encompassing the structural information and corresponding biological data. These data sets established the scientific basis for the development of the predictive QSAR models using the hologram QSAR method. The final HQSAR models generated possess both good internal and external consistency with good correlative and predictive power. These models and the information obtained from the HQSAR contribution maps should be useful in guiding future medicinal chemistry efforts designed to discover novel potent and selective inhibitors as drug candidates for the chemotherapy of the target diseases of this work

A malária é a doença tropical com maior taxa de mortalidade global. O surgimento de resistência às terapias de primeira linha reforça a necessidade do desenvolvimento de novos candidatos a fármacos. O objetivo deste trabalho foi a descoberta de inibidores e otimização da atividade destas moléculas como candidatos a compostos líderes para o desenvolvimento de novos agentes antimaláricos. Nesse sentido, realizamos a triagem da coleção Malaria Box e identificamos 11 moléculas de diferentes classes químicas como candidatos a inibidores da enzima enolase de Plasmodium falciparum (Pfeno). Em seguida, determinamos a potência inibitória contra a enzima alvo (IC50 entre 11 – >1.000 μM), atividade antiplasmodial in vitro contra a forma eritrocítica do parasito (EC503D7 entre 5,6–1.600 nM) e citotoxicidade (MCL50 > 19 μM) do subconjunto de 11 compostos do Malaria Box (1–11). Ensaios de combinação com o antimalárico artesunato e estágio de ação foram conduzidos para avaliar o potencial de associação e qual fase do ciclo eritrocítico seria mais suscetível as moléculas desse subconjunto. Os resultados obtidos indicam que alguns compostos apresentam caráter aditivo (2 e 9) ou antagônico (1, 3–8, 10 e 11) em relação ao artesunato e ação rápida (1–3, 5, 7, 9–11) ou lenta (4, 6 e 8) no desenvolvimento do parasita. Diante desses resultados, um conjunto de critérios estruturais e de atividade biológica foi estabelecido para a seleção de um candidato para estudos de relação estrutura-atividade (SAR). O derivado de hidrazinobenzimidazol (4) foi selecionado como hit inicial e 24 derivados (12–35) foram planejados, sintetizados e tiveram a atividade de inibição enzimática (IC50 entre 44 – >200 μM), atividade antiplasmodial contra cepas sensível (EC503D7 entre 0,19–14 μM) e resistente (EC50K1 entre 0,15–2,4 μM) e citotoxicidade (MCL50 > 3,7 μM) determinadas no primeiro ciclo de SAR. Os dados obtidos sugerem que a enzima Pfeno não é o alvo principal de ação dos derivados hidrazinobenzimidazol, contudo, a atividade antiplasmodial da série indicou razoável distribuição em termos de potência e variabilidade estrutural que permitiram a construção de um modelo HQSAR (q2= 0,64 e r2 = 0,93) adequado para o planejamento e predição da atividade inibitória de oito novos derivados hidrazinobenzimidazol (36–43). Os novos derivados foram sintetizados e tiveram sua atividade antiplasmodial (EC503D7 entre 0,10–2,3μM), citotoxicidade (MCL50 > 3 μM) e seletividade (SI > 5) determinadas. Os dados de validação prospectiva do modelo indicaram boa correlação entre a atividade real e predita para os novos derivados. Além disso, neste segundo ciclo de SAR foi descoberto o composto 41 como o mais potente (EC50 = 0,1 μM) e seletivo (SI > 2.000) da série investigada neste trabalho. Nossos resultados indicam que os derivados hidrazinobenzimidazol são moléculas atrativas para a descoberta de compostos líderes para o desenvolvimento de candidatos a fármacos antimaláricos. / Malaria is the tropical disease with the highest overall mortality rate. The emergence of resistance to first-line therapies reinforces the need for the development of new drug candidates. The main goal of this work was the discovery and optimization of these molecules as lead candidates for the development of new antimalarial agents. In this sense, we screened Malaria Box collection and identified 11 molecules from different chemical classes as inhibitor candidates of Plasmodium falciparum enolase enzyme (Pfeno). Then, we determined the inhibitory potency against the target enzyme (IC50 between 11 – >1.000 μM), in vitro antiplasmodial activity against the erythrocytic form of the parasite (EC503D7 between 5,6–1.600 nM) and cytotoxicity (MCL50 > 19 μM) of the 11 compounds subset from Malaria Box (1–11). Combination with artesunate and stage of action assays were conducted to evaluate the potential of association and which erythrocytic stage would be more susceptible to the molecules of this subset. The results obtained indicate that some compounds showed additive (2 and 9) or antagonistic (1, 3–8, 10 and 11) effect with artesunate and fast (1–3, 5, 7, 9–11) or slow (4, 6 and 8) acting on parasite development. In view of these, a set of structural and biological activity criteria was established for the selection of a candidate for structure-activity relationship (SAR) studies. The hydrazinobenzimidazole derivative (4) was selected as hit and 24 derivatives (12–35) were designed, synthesized and had the enzyme inhibitory activity (IC50 between 44 – >200 μM), antiplasmodial activity against sensitive strains (EC503D7 between 0,19–14 μM) and resistant (EC50K1 between 0,15–2,4 μM) and cytotoxicity (MCL50 > 3,7 μM) determined in the first round of SAR. The collected data suggest that Pfeno is not the main target of the hydrazinobenzimidazole derivatives. However, the antiplasmodial activity of the series indicated a reasonable distribution in terms of potency and structural variability which allowed us the development of a HQSAR model (q2 = 0,64 and r2 = 0,93) suitable for the design and prediction of the inhibitory activity of eight new hydrazinobenzimidazole derivatives (36-43). The new derivatives were synthesized and had the antiplasmodial activity (EC503D7 between 0,10–2,3μM), cytotoxicity (MCL50 > 3 μM) and selectivity (SI > 5) evaluated. The prospective validation of the HQSAR model indicated good correlation between the actual and predicted activity for the new derivatives. Moreover, in the second round of SAR, compound 41 was discovered as the most potent (EC50 = 0,1 μM) and selective (SI > 2,000) in these series. Our results indicate that the hydrazinobenzimidazole derivatives are attractive molecules for the discovery of new lead compounds for the development of antimalarial drug candidates.

Orientador: Jörg Kobarg / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-21T00:18:21Z (GMT). No. of bitstreams: 1 Moraes_EduardoCruz_M.pdf: 2623796 bytes, checksum: 858f8566bae7879895e451ce06ad3bfb (MD5) Previous issue date: 2012 / Resumo: Cinases desempenham um papel importante na ativação de vias bioquímicas em células eucarióticas. Neks (NIMA related kinases) são uma família conservada de proteínas cinases relacionadas à progressão do ciclo celular e divisão celular, contendo em torno de 40% de identidade no domínio catalítico N-terminal com a proteína NIMA (Never in Mitosis, gene A) de Aspergillus nidulans. As cinases Neks são também descritas como relacionadas a patologias, particularmente câncer. Por estas características, as Neks são alvos potenciais para o tratamento de cânceres e desenvolvimento de drogas anti-câncer. Neste trabalho foram selecionados compostos em uma biblioteca de 87 compostos para os domínios de cinase mutados de hNek1, hNek2, hNek6, hNek8 e hNek9 e o domínio de cinase selvagem de hNek7, através de um ensaio de deslocamento térmico. Neste ensaio, foi identificado pelo menos um composto com um deslocamento da Tm significativo para a hNek1 ('delta'262-1258)-(T162A), E08 ('delta'Tm = 4.0ºC); outro, E04 ('delta'Tm = 6.5ºC) para a hNek6(S206A), e vários compostos para a hNek7wt e hNek2(_272-445)-(T175A). Destes compostos, B03 e F04 foram validados por docking no sítio de ligação de ATP da hNek7wt, enquanto B08 e E03 foram validados por reduzir a atividade da hNek7wt até 26,4% e 43,3%, respectivamente, na concentração de 312,5 nM. Além disso, o composto E04 foi capaz de reduzir a atividade da hNek6(S206A) pela metade com um IC50 próximo de 1,25 ?M. São necessários experimentos funcionais adicionais para validação desses dados, e estudos estruturais com resolução atômica serão importantes para caracterizar a associação de hNek1('delta'262-1258)-(T162A), hNek6(S206A) e hNek7 selvagem com esses e outros compostos / Abstract: Kinases play an important role in the activation of biochemical pathways in eukaryotic cells. Neks (NIMA related kinases) are a conserved kinase protein family related to cell cycle progression and cell division, containing about 40% identity in the N-terminal catalytic domain with the protein NIMA (Never in Mitosis, gene A) of Aspergillus nidulans. Nek kinases are also described as related to pathologies, particularly cancer. For these characteristics, Neks are potential targets for treatment of cancers and development of anti-cancer drugs. Here we screened the recombinant activation loop mutant kinase domains of hNek1, hNek2, hNek6, hNek8 and hNek9 and wild-type hNek7 against 87 compounds using thermal shift denaturation and identified at least one compound with significant Tm shift for hNek1('delta'262-1258)-(T162A), E08 ('delta'Tm = 4.0ºC), another one, E04 ('delta'Tm = 6.5ºC) for hNek6(S206A), but not for the other hNek6 variants, and several hit compounds for hNek7wt and hNek2('delta'272-445)-(T175A). From these, compounds B03 and F04 were validated by docking into the ATP-binding site of hNek7wt, while B08 and E03 were validated by reducing hNek7wt activity up to 26.4% and 43.3%, respectively, at a 312.5 nM concentration. We also found that mutant hNek6, without the activation loop conserved phosphorylation, is a better target for inhibitor stabilization than an activated more phosphorylated hNek6 kinase. Moreover, compound E04 was later confirmed to reduce hNek6(S206A) activity by half with IC50 near to 1.25 ?M. Further functional experiments in living cells are required to validate this findings, and structural studies with atomic resolution will be important to characterize the association of hNek1('delta'262-1258)-(T162A), hNek6(S206A) and wild-type hNek7 with these and other compounds / Mestrado / Bioquimica / Mestre em Biologia Funcional e Molecular