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Les histones désacétylases (HDACs) sont les principales cibles des médicaments épigénétiques anticancéreux actuellement approuvés par la FDA. Les HDACs jouent aussi un rôle important dans l'homéostasie des pathogènes eucaryotes. Par conséquent, une stratégie pour lutter contre les maladies négligées causées par ces pathogènes est de modifier les médicaments épigénétiques actuellement approuvés qui ciblent les HDACs. HDAC8 de Schistosoma mansoni (smHDAC8) est une cible médicamenteuse valable pour traiter la schistosomiase, deuxième maladie négligée mortelle après le paludisme. Les différences structurales entre les poches catalytiques des HDAC8 humaine et smHDAC8 ont permis la conception d'inhibiteurs sélectifs des schistosomes qui se lient dans une poche sélective unique à HDAC8. Ce travail de thèse montre comment cibler sélectivement des isoformes HDAC l'aide de structures à résolution atomique, et ouvre la porte à l'étude du mode d'action de HDAC8 au niveau fondamental. / Histone deacetylases (HDACs) are the major targets of currently FDA-approved anti-cancer epigenetic drugs. HDACs also play an important role in the homeostasis of eukaryotic pathogens. Hence, a strategy to tackle neglected diseases caused by these pathogens is to modify currently approved epigenetic drugs targeting HDACs. HDAC8 from Schistosoma mansoni (smHDAC8) was shown to be a valid drug target to treat schistosomiasis, second deadliest tropical disease after malaria. Structural differences between human HDAC8 and smHDAC8 catalytic pocket enabled the design of schistosome-selective inhibitors that bind in a HDAC8 selective pocket, which is unique to HDAC8 among the highly conserved HDAC isozymes. This thesis work shows how to target selectively related isoforms with the help of atomic resolution structures, and opens the door to the investigation of the mode of action of HDAC8 at the fundamental level.

Depuis sa découverte, le monoxyde d'azote n'a pas cessé d'intéresser la communauté scientifique. Sa biosynthèse est catalysée par les NO Synthases, qui est une famille de trois isoenzymes. La NOS neuronale et la NOS endothéliale sont constitutives et produisent du NO impliqué dans la neurotransmission et la vasodilatation respectivement. La NOS inductible quant à elle produit du NO impliqué dans la réponse immunitaire innée. Une surproduction de monoxyde d'azote est impliqué dans de nombreuses pathologies comme les maladies neuro-dégénératives ou les maladies chroniques à composantes inflammatoires. L'inhibition de iNOS et nNOS présente donc un grand intérêt thérapeutique. Cependant l'enjeu est de développer des inhibiteurs hautement sélectifs, afin de préserver les fonctions vitales de eNOS.Nous avons choisi de synthétiser des composés constitués d'un analogue de substrat tel que thiocitrulline et S-alkyl-isothiocitrulline auquel est ajouté, par un lien peptidique ou hétérocyclique, un résidu susceptible de se lier dans le canal d'accès du substrat, région moins conservée du site actif pouvant fournir des interactions spécifiques. La synthèse de ces composés a été réalisée sur support solide selon une méthode d'ancrage par la chaîne latérale développée au laboratoire, ou pour certains composés, selon une méthode classique d'ancrage par l'amine alpha, ces deux méthodes offrant un fort potentiel en chimie combinatoire. Les différents composés synthétisés ont été testés sur les trois isoformes recombinantes.Un second travail est brièvement exposé dans ce manuscrit. La synthèse de cyclopeptides basés sur le motif RGD impliqué dans la liaison aux intégrines a été réalisée selon un mode de cyclisation développé au laboratoire faisant intervenir la formation d'un pont guanidine qui sera ensuite diversement substitué. L'étude RMN et l'évaluation de leur activité biologique sur les récepteur opioïdes semble montrer un influence de la substitution du pont sur leur conformation et leur activité. / Since its discovery, Since its discovery, the nitric oxide did not stop interesting the scientific community. Its biosynthesis is catalyzed by NO synthases, a family of three isoenzymes. Neuronal NOS and endothelial NOS are constitutive and produce NO involved in neurotransmission and vasodilation process respectively. Inducible NOS produces NO involved in the innate immune response. An overproduction of nitric oxide is involved in many diseases such as neurodegenerative diseases or chronic diseases with inflammatory components. Thus, its inhibition should be of high therapeutical interest. However, it is necessary to develop highly selective inhibitors to preserve the vital functions of eNOS.We chose to synthesize compounds constituted of one substrate analogue as thiocitrulline or S-alkyl-isothiocitrulline which linked by a peptide bond or heterocycles to a residue able to bind into the substrate access channel, a less conserved region into the active site were specific interactions could be established. The synthesis of these compounds was performed on solid support according to an anchoring method through the side chain developed at the laboratory or, for some compounds, according to a conventional anchoring method through the alpha amine. These approaches are particulary interesting for a combinatory chemistry approach. All compounds were tested on the three recombinant isoforms.A second work is outlined in this manuscript. It consist of synthesizing cyclopeptides based on RGD motif involved in the binding to integrins and enkephalins analogues. The cyclisation method was developed in the lab and involves the formation of a guanidine bridge diversely substituted. NMR studies and biological evaluations on opioid receptor suggests that the diverse bridge substitutions could modulate the conformation and activity of the peptides.

Submitted by ALEXANDRE BORGES null (alex.brgs@hotmail.com) on 2016-06-28T19:11:21Z No. of bitstreams: 1 ESTUDOS DE MODELAGEM MOLECULAR DE LIGNANAS EM COMPLEXOS COM CICLOOXIGENASES-1 E 2.pdf: 4325586 bytes, checksum: 2f6ab56677aea7746bd28dad4b24ea23 (MD5) / Approved for entry into archive by Ana Paula Grisoto (grisotoana@reitoria.unesp.br) on 2016-06-29T17:41:12Z (GMT) No. of bitstreams: 1 borges_a_dr_ilha.pdf: 4325586 bytes, checksum: 2f6ab56677aea7746bd28dad4b24ea23 (MD5) / Made available in DSpace on 2016-06-29T17:41:12Z (GMT). No. of bitstreams: 1 borges_a_dr_ilha.pdf: 4325586 bytes, checksum: 2f6ab56677aea7746bd28dad4b24ea23 (MD5) Previous issue date: 2016-05-11 / Os inibidores seletivos da ciclooxigenase-2 (COX-2), como o rofecoxibe (2) e o celecoxibe (1), formam uma importante classe de medicamentos anti-inflamatórios desenvolvidos a partir da descoberta das duas isoformas das ciclooxigenases (COX-1 e COX-2) na década de 1979. A isoforma 1 esta relacionada com a citoproteção gástrica, agregação plaquetária e função renal e a isoforma 2 relacionada a processos inflamatórios. Estes inibidores seletivos apesar de não apresentarem os efeitos colaterais (ulceras e gastrites) dos anti-inflamatórios não esteroidais (AINEs) clássicos por inibirem apenas a COX-2, apresentam grave risco cardiovascular, o que motivou à retirada do rofecoxibe do mercado. Porém, por ser um eficiente inibidor seletivo da COX-2 a estrutura do rofecoxibe tornou-se referência no estudo de novas substâncias capazes de inibir seletivamente a COX-2. Dentre as ferramentas utilizadas na busca destas novas estruturas está a modelagem molecular através de programas como o GOLD 5.1, que foi utilizado neste trabalho. O uso do GOLD 5.1 possibilitou o estudo do comportamento das estruturas avaliadas em ligação com as ciclooxigenases. O objetivo foi obtenção de estruturas com comportamento semelhante ao rofecoxibe (em relação às COXs) como potenciais candidatos ao desenvolvimento de novos inibidores seletivos para a COX-2. O estudo foi realizado com 480 estruturas modeladas a partir de lignanas naturais como a hinoquinina, cubebina, deoxipodofilotoxina e podofilotoxina, que apresentam atividade anti-inflamatória in vivo ou in vitro, além de semelhanças estruturais com o rofecoxibe. A deoxipodofilotoxina por apresentar seletividade para a COX-2 em ensaio in vitro também foi utilizada como estrutura de referência além do rofecoxibe. Os resultados observados a partir da simulação molecular permitiram concluir que embora tanto o rofecoxibe como a deoxipodofilotoxina (3) inibam seletivamente a COX-2 in vitro, o fazem de modo diferente. Em relação a COX-2 as duas estruturas ocupam a mesma região do sítio ativo, mas o rofecoxibe apresenta interações mais fortes com o bolso hidrofílico desta isoforma (condição necessária para a inibição seletiva para os coxibes). Já para a COX-1 enquanto o rofecoxibe ocupa a porção superior do canal hidrofóbico (sítio ativo) como os demais AINEs, a deoxipodofilotoxina ocupa uma região vizinha. Pelos resultados obtidos é possível sugerir que tanto a maior flexibilidade das estruturas como a presença do anel lactônico, são importantes para um comportamento análogo ao rofecoxibe ou à deoxipodofilotoxina. Com relação à interação com o bolso hidrofílico da COX-2, os resultados sugerem que a presença de grupos aceptores de prótons menos volumosos nas posições C3 e C4, C3’ e C4’ ou C4 levam a resultados melhores que grupos aceptores de maior volume. A presença de grupos doadores de prótons apesar de permitirem forte interação com o bolso hidrofílico da COX-2 leva a resultados globais insatisfatórios, pois formam interações fortes com o resíduo Arg120 do sítio ativo da COX-1, interação considerada importante para a inibição não seletiva. Resultado semelhante à deoxipodofilotoxina foi observado apenas para a estrutura 17. As estruturas 37, 188, 266, 267, 348 e a hinoquinina (4) apresentam resultados semelhantes ao rofecoxibe, para as duas isoformas. Deste modo permite-se sugerir a partir dos resultados obtidos neste estudo que a hinoquinina (4) e as estruturas 17, 37, 188, 266, 267 e 348 apresentam-se como possíveis protótipos de fármacos que atuem como inibidores seletivos para a COX-2. / The selective inhibitors of the cyclooxygenase-2 (COX-2) as rofecoxib (2) and celecoxib (1), form an important class of anti-inflammatory drugs developed from the discovery of two isoforms of cyclooxygenases (COX-1 and COX-2) in the late 1979. Isoform 1 is related to the gastric cytoprotection, platelet and renal function and isoform 2 related to inflammatory processes. These selective inhibitors although they did not side effects (ulcers and gastritis) of the classic NSAIDs to inhibit only COX-2, have severe cardiovascular risk, which led to the withdrawal of rofecoxib from the market. However, to be an effective selective COX-2 to rofecoxib structure has a reference in the study of new substances capable of selectively inhibiting COX-2. Among the tools used in the search of these new structures is by molecular modeling program such as GOLD 5.1, which was used in this work. Using GOLD 5.1 made it possible to study the behavior of structures evaluated in binding with the cyclooxygenases. With the objective of obtaining structures with similar behavior to rofecoxib (regarding behavior with COX) as potential candidates for the development of new selective inhibitors for COX-2. The study was conducted with 480 structures modeled from natural lignans as hinokinin, cubebin, deoxypodophyllotoxin and podophyllotoxin, which have anti-inflammatory activity in vivo or in vitro as well as structural similarities with rofecoxib. The deoxypodophyllotoxin for presenting selectivity for COX-2 in the in vitro assay was also used as a reference structure beyond rofecoxib. The results observed from the molecular simulation showed that although both rofecoxib (2) as deoxypodophyllotoxin (3) selectively inhibit COX-2 in vitro, they do differently. In relation to COX-2 the two structures occupy the same region of the active site, but rofecoxib has stronger interactions with the hydrophilic pocket of this isoform (a necessary condition for the selective inhibition for coxibs). As for the COX-1 while rofecoxib occupies the upper portion of the hydrophobic channel (active site) like other NSAIDs, the deoxypodophyllotoxin occupies a neighboring region. From the results it is possible to suggest that the greater flexibility of the structures such as the presence of the lactone ring, are important for a similar behavior to rofecoxib or deoxipodofilotoxina. With respect to the interaction with the hydrophilic pocket COX-2, the results suggest that the presence of acceptors groups less bulky protons in posítions C3 and C4, C3 ' and C4' and C4 lead to better results than acceptors groups of larger volume. The presence of proton donors groups despite allowing strong interaction with the hydrophilic pocket COX-2 lead to poor overall results, since they form strong interactions with Arg120 residue of COX-1 active site, considered important interaction for inhibiting non-selective. Results similar to deoxipodofilotoxina was only observed for structure 17. Structures 37, 188, 266, 267, 348 and hinokinin (4) show results similar to rofecoxib for the two isoforSA. Thus it allows suggest from the results obtained in this study hinokinin (4) and structures 17, 37, 188, 266, 267 and 348 are shown as possible prototype drugs that act as selective inhibitors for COX-2.

Orientador: Rosangela da Silva de Laurentiz / Resumo: Os inibidores seletivos da ciclooxigenase-2 (COX-2), como o rofecoxibe (2) e o celecoxibe (1), formam uma importante classe de medicamentos anti-inflamatórios desenvolvidos a partir da descoberta das duas isoformas das ciclooxigenases (COX-1 e COX-2) na década de 1979. A isoforma 1 esta relacionada com a citoproteção gástrica, agregação plaquetária e função renal e a isoforma 2 relacionada a processos inflamatórios. Estes inibidores seletivos apesar de não apresentarem os efeitos colaterais (ulceras e gastrites) dos anti-inflamatórios não esteroidais (AINEs) clássicos por inibirem apenas a COX-2, apresentam grave risco cardiovascular, o que motivou à retirada do rofecoxibe do mercado. Porém, por ser um eficiente inibidor seletivo da COX-2 a estrutura do rofecoxibe tornou-se referência no estudo de novas substâncias capazes de inibir seletivamente a COX-2. Dentre as ferramentas utilizadas na busca destas novas estruturas está a modelagem molecular através de programas como o GOLD 5.1, que foi utilizado neste trabalho. O uso do GOLD 5.1 possibilitou o estudo do comportamento das estruturas avaliadas em ligação com as ciclooxigenases. O objetivo foi obtenção de estruturas com comportamento semelhante ao rofecoxibe (em relação às COXs) como potenciais candidatos ao desenvolvimento de novos inibidores seletivos para a COX-2. O estudo foi realizado com 480 estruturas modeladas a partir de lignanas naturais como a hinoquinina, cubebina, deoxipodofilotoxina e podofilotoxina, que apre... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The selective inhibitors of the cyclooxygenase-2 (COX-2) as rofecoxib (2) and celecoxib (1), form an important class of anti-inflammatory drugs developed from the discovery of two isoforms of cyclooxygenases (COX-1 and COX-2) in the late 1979. Isoform 1 is related to the gastric cytoprotection, platelet and renal function and isoform 2 related to inflammatory processes. These selective inhibitors although they did not side effects (ulcers and gastritis) of the classic NSAIDs to inhibit only COX-2, have severe cardiovascular risk, which led to the withdrawal of rofecoxib from the market. However, to be an effective selective COX-2 to rofecoxib structure has a reference in the study of new substances capable of selectively inhibiting COX-2. Among the tools used in the search of these new structures is by molecular modeling program such as GOLD 5.1, which was used in this work. Using GOLD 5.1 made it possible to study the behavior of structures evaluated in binding with the cyclooxygenases. With the objective of obtaining structures with similar behavior to rofecoxib (regarding behavior with COX) as potential candidates for the development of new selective inhibitors for COX-2. The study was conducted with 480 structures modeled from natural lignans as hinokinin, cubebin, deoxypodophyllotoxin and podophyllotoxin, which have anti-inflammatory activity in vivo or in vitro as well as structural similarities with rofecoxib. The deoxypodophyllotoxin for presenting selectivity for COX... (Complete abstract click electronic access below) / Doutor