Nitrilases are enzymes which catalyze the hydrolysis of a nitrile into the corresponding carboxylic acid and ammonia. These enzymes are potentially applicable in biocatalysis and bioremediation because of their advantages over the conventional (chemical) methods of nitrile hydrolysis (lower demand for energy, safety, simplicity, high yields, selectivity). In this work, genome mining was used to search for the sequences of hypothetical nitrilases from filamentous fungi. The amino acid sequences of previously characterized fungal nitrilases were used as the templates. Then the new synthetic genes together with other genes from our nitrilase library were expressed in E. coli and the substrate specificities of the enzymes thus produced were compared. Significant attention was focused on the relationships between the sequence of the enzyme and its substrate specificity. The arylacetonitrilases from Arthroderma benhamiae (NitAb) and Nectria haematococca (NitNh) were purified and characterized. Their substrate specificities, kinetic parameters, pH and temperature profiles and subunit and holoenzyme size were assessed. NitAb and NitNh together with other recombinant fungal nitrilases were employed in the hydrolysis of high concentrations of (R,S)-mandelonitrile in a batch or fed-batch mode. Nitrilase from...

Le ligand Rim3, constitué d’une cavité resorcinarène fonctionnalisée par 3 groupements méthylimidazole a été synthétisé et étudié. Ce ligand est capable de coordiner différents métaux de transitions comme le zinc et le cuivre. Ces complexes possèdent des propriétés hôte-invité intéressantes et une sélectivité avec la taille de la cavité. La complexation d’invités acides nécessite l’addition d’une base exogène. De plus, la présence de base peut être nécessaire pour réaliser des réactions d’hydratation ou d’hydrolyse. Dans ce manuscrit sont présentés différents ligands cavitaires resorcinarène avec 4 imidazoles greffés. Chaque ligand et complexe associé présente des solubilités différentes. Nous étudierons d’abord la synthèse et la caractérisation des systèmes en milieu organique ou aqueux. Les études de complexation montreront la forte affinité associée à ces complexes en milieu organique. L’étude des propriétés hôte-invité montre que le complexe est capable de coordiner un invité acide de manière quantitative dans les conditions RMN. Cette coordination ne nécessite pas l’addition de base. Le 4e imidazole joue le rôle de base intramoléculaire et n’est pas nécessaire à la coordination. Deux positions labiles en cis sont également disponibles, attesté par la coordination de ligands bidentes. Le complexe zincique [Rim4ZnII(EtOH)](ClO4)2 montre des propriétés d’hydratation des nitriles. Dans l’acétonitrile avec 35% d’eau à 70°C, le complexe forme de l’acétamide de manière catalytique. L’addition de base n’est pas nécessaire et le pH n’évolue pas avec la réaction. Dans l’eau avec 10% d’acétonitrile, [WRim(OH)44 Zn(H2O)](NO3)2 catalyse l’hydratation en acétamide mais est inhibé par l’hydrolyse successive en acétate. / In this manuscript, we present the synthesis and caracterisation of three tetradentate bowlshaped ligand. These ligands are resorcin[4]arene functionnalized by four methylimidazole. Each ligand is soluble in a different medium, such as organic solvent, water and mixed solvent. The four methylimidazoles are able to coordinate several metal ions, such as zinc, copper and iron. We then present the host-guest properties of the complexes. The complexes are able to coordinate acidic guests without addition of an exogenous base, thanks to the fourth imidazole. Two labiles positions are avalaible in cis, and bidentate ligands are able to coordinate the metal ions. Finally, we present the reactivity of the complexes. The zinc complex, [Rim4Zn]2+ catalyses the acetonitrile hydration with 35% water at 70°C. In an aqueous media with 10% water,[WRim(OH)44 Zn(H2O)](NO3)2 catalyses not only the acetonitrile hydration but also it’s subsequent hydrolysis into acetate.

A enzima cruzaína é um alvo validado e promissor para a descoberta de agentes tripanossomicidas. A validação desta enzima estimulou o desenvolvimento de vários inibidores ao longo dos últimos vinte anos. A descoberta de novos compostos, provenientes de classes químicas distintas, mais seguros e eficazes representa uma importante contribuição para o desenvolvimento da quimioterapia da doença de Chagas. Dentre essas classes, encontram-se as dipeptidil-nitrilas, que apresentam alta potência contra a cruzaína e são conhecidamente inibidores covalente-reversíveis. Estudos de afinidade através de Calorimetria de Titulação Isotérmica (ITC) são fundamentais na compreensão de sistemas bioquímicos e viabilizam a determinação dos parâmetros termodinâmicos. A ITC possibilita determinar com precisão e acurácia os valores de Kd(1/Ka), ΔH,ΔG,ΔS e ΔCp e com esses parâmetros pode-se traçar facilmente o perfil termodinâmico dos ligantes. No presente trabalho, a enzima selvagem cruzaína bem como sua forma mutante C25S foram preparadas e, pela primeira vez, foi realizado o estudo de afinidade através da ITC para 16 dipeptidil-nitrilas usadas como inibidores da cruzaína. O perfil termodinâmico (TP) foi obtido e observado como entálpico-dirigido com compensação entrópica desfavorável. A fatoração da energia livre ( ΔG) de interação foi usada para avaliar os efeitos causados pelas substituições em P1, P2 e P3 na energética, sugerindo uma correlação direta entre a afinidade e a otimização entálpica/entrópica. As substituições avaliadas promoveram um aumento de 10 a 20 vezes na afinidade da cruzaína pelo inibidor. Estudos em diferentes tampões foram realizados para a determinação da influência do efeito de ionização na afinidade. Foi determinado o valor de ΔCp do complexo cruzaína-Neq0409 e a relação de ΔHITC com ΔHvH. O Neq0569 foi testado contra a proteína mutante C25A, tendo sido observada inversão da assinatura que passou a ser entropicamente dirigida. Além disso, uma redução de 176 vezes na afinidade foi observada, demonstrando a importância da ligação covalente-reversível para o aumento da afinidade. / The enzyme cruzain is a validated and promising target for the discovery of trypanocidal agents. The validation of this enzyme has stimulated the development of several inhibitors over the past twenty years. The discovery of new compounds from different chemical classes, which are safer and more effective is an important contribution to the development of chemotherapy of Chagas disease. Among known classes are the dipeptidyl nitriles that exhibit high cruzain affinity and are known to be covalent-reversible inhibitors. Molecular optimization requires a rigorous assessment of physicochemical properties, including the thermodynamic characterization of molecular forces that govern cruzain-inhibitor interactions. Affinity studies through Isothermal Titration Calorimetry (ITC) are fundamental in understanding biochemical systems and enable the determination of thermodynamic parameters. The ITC tool provides the determination of Kd values (1/Ka), ΔH, ΔG, ΔS and ΔCp accurately and precisely. These parameters can easily be used to draw the thermodynamic profile of ligands. In this study, the wild type cruzain enzyme and its mutant form C25S were prepared and, for the first time by the best of our knowledge, the study was conducted by ITC for 16 dipeptidyl nitriles used as inhibitors of cruzain enzyme, which is a hydrolase. The thermodynamic profile (TP) was obtained and observed to be enthalpy-driven with unfavorable entropic compensation. The free energy factorization (ΔG) interaction was used to evaluate the effects caused by substitutions in P1, P2 and P3 in energy, thereby suggesting a direct correlation between the affinity and the enthalpy/entropy optimization. Substitutions made possible to observe an increase of 10 to 20 times higher than the affinity for previous cruzain inhibitors. Studies on different buffers were performed to determine the influence of ionizing effect on affinity. The ΔCp value was determined for cruzain-Neq0409 complex and its ΔHITC relationship with ΔHvH was also evaluated. Neq0569 was tested against the mutant protein C25A, having been observed reversal of the signature which became entropy driven. Furthermore, a reduction of 176-fold in the affinity was observed, demonstrating the importance of covalent-reversible binding to increase affinity.

<p align=\"justify\">A necessidade urgente de descoberta de terapias mais seguras e eficazes para o tratamento da doença de Chagas e leishmanioses tem motivado a pesquisa por novos inibidores das enzimas cruzaína e CPB, as principais cisteíno proteases do T. cruzie e Leishmania spp., respectivamente. Uma série de 52 compostos nitrílicos que atuam como inibidores covalente-reversíveis de cisteíno proteases foi sintetizada no grupo NEQUIMED/IQSC/USP e avaliada quanto a sua atividade inibitória contra as enzimas cruzaína, CPB de Leishmania mexicana e catepsina L de humanos. Utilizando planejamento molecular baseado em hipótese, mapeamos as relações estrutura-atividade (SARs) desses inibidores através de variações nas posições P1, P2, P3 e P1\' do esqueleto dipeptidil nitrílico. A substituição do grupo eletrofílico (warhead) aminonitrila em P1 pelo grupo azanitrila melhorou a afinidade em duas ordens de magnitude para todos os alvos avaliados. Um dos mais potentes inibidores, o análogo azanitrila Neq0690 mostrou uma cinética de ligação lenta com valores de pKi de 8,8, 9,3 e 9,7 para cruzaína, catepsina L e LmCPB, respectivamente. A substituição bioisostérica da ligação amida entre as posições P2-P3 pelo grupo trifluoroetilamina resultou na síntese do Neq0659, um potente inibidor com um perfil de ação seletivo para as proteases de parasitos. A substituição do grupo metileno em P1 pelo ciclopropano aumentou a afinidade para todas as enzimas. Contudo, uma inibição seletiva da cruzaína e LmCPB foi associada à presença do grupo (R)-benzila como substituinte da posição P1 dos derivados CF3 substituídos. Embora os compostos substituídos com leucina, tirosina, triptofano e 3-cloro fenilalanina como substituintes da posição P2 foram relativamente bem tolerados pela cruzaína e catepsina L, uma restrita especificidade foi verificada para LmCPB com pequenos ganhos de afinidade para os inibidores que possuíam os grupos leucina e metil benzoato como substituintes dessa posição. Com relação à posição P3, a inserção do grupo 3-terc-butilpirazol e 3-bromo piridina aumentou a afinidade para todos os alvos avaliados enquanto que um ganho seletivo para a LmCPB foi observado para os compostos que possuíam o grupo bifenila nessa posição. Além disso, duas novas estruturas cristalográficas da LmCPB complexada com o Neq0690 e metil metanotiossulfonato (MMTS) foram determinadas com resoluções de 1,3 Å e 1,5 Å, respectivamente. As estruturas dos co-complexos revelaram os modos de interação (MoB) desses ligantes, bem como as principais características do processo de reconhecimento bimolecular. Isso permitirá o uso de estratégias de planejamento baseado na estrutura do alvo com translação natural para a pesquisa por novos inibidores de cisteíno proteases, com amplo espectro de ação na quimioterapia de doenças a elas relacionadas. / <p align=\"justify\">The urgent need for the discovery of safer and more effective therapies for the treatment of Chagas disease and leishmaniasis has motivated the search for new inhibitors of the enzymes cruzain and CPB, the major T. cruzi and Leishmania spp. cysteine proteases, respectively. A series of 52 nitrile-containing compounds acting as covalent-reversible inhibitors of cysteine proteases was synthesized at the NEQUIMED/IQSC/USP Medicinal Chemistry Group and evaluated for their inhibitory activity against the enzymes cruzain, Leishmania mexicana CPB and cathepsin L from humans. Using hypothesis-driven molecular design, we mapped the structure-activity relationships (SARs) of these inhibitors through variations in the P1, P2, P3 and P1\' positions of the dipeptidyl nitrile scaffold. The substitution of the aminonitrile by the azanitrile group improved the affinity by two orders of magnitude for all the evaluated targets. One of the most potent inhibitors, the azanitrile analogue dubbed Neq0690 showed a slow-binding kinetics with pKi values of 8.8, 9.3 and 9.7 for cruzain, cathepsin L and LmCPB, respectively. Bioisosteric substitution of the amide moiety between the P2-P3 positions by the trifluoroethylamine group resulted in the synthesis of Neq0659, a potent inhibitor with a selective action profile for parasite proteases. Substitution of the methylene group at P1 by cyclopropane increased the affinity for all enzymes. However, selective inhibition of cruzain and LmCPB was associated with the presence of the (R)-benzyl group as substituent of the P1 position of the substituted CF3 derivatives. Although leucine, tyrosine, tryptophan and 3-chloro phenylalanine substituted compounds as substituents of the P2 position were relatively well tolerated by cruzain and cathepsin L, a restricted specificity was verified for LmCPB with small affinity gains for the inhibitors possessing the leucine and methyl benzoate as substituents of that position. Regarding the P3 position, the insertion of the 3-tert-butylpyrazole and 3-bromo pyridine groups increased the affinity for all evaluated targets whereas a selective gain for LmCPB was observed for the compounds having the biphenyl moiety at that position. In addition, it is noteworthy that two new crystallographic structures of LmCPB complexed with Neq0690 and methyl methanethiosulfonate (MMTS) were determined with resolutions of 1.3 Å and 1.5 Å, respectively. The structures of the co-complexes revealed the modes of binding (MoB) of these ligands, as well as the main characteristics of the bimolecular recognition process. This will allow the natural translational target structure strategies for the search for new inhibitors of cysteine proteases with broad spectrum of action in the chemotherapy of related diseases.

Late transition metal complexes of silver(I), rhodium(I), ruthenium(II), palladium(II) and platinum(II) containing a nitrile-functionalized N-heterocyclic carbene ligand (C-CN) were prepared. The nitrile group on the C–CN ligand was shown to undergo hydrolysis under basic conditions, leading to a silver(I) carbene complex with a primary-amido functional group, and a trimetallic complex of palladium(II) with a partially hydrolyzed C–N–N–C donor ligand. The reduction of a nitrile-functionalized imidazolium salt in the presence of nickel(II) chloride under mild conditions yielded an axially chiral square-planar nickel(II) complex containing a unique primary-amino functionalized N-heterocyclic carbene ligand (C-NH2). A transmetalation reaction moved this chelating C–NH2 ligand from nickel(II) to ruthenium(II), osmium(II), and iridium(III), yielding important catalysts for the hydrogenation of polar double bonds. The ruthenium(II) complex, [Ru(p-cymene)(C–NH2)Cl]PF6 catalyzed the transfer and H2-hydrogenation of ketones. The bifunctional hydride complex, [Ru(p-cymene)(C–NH2)H]PF6, which contains a Ru–H/N–H couple showed no activity under catalytic conditions unless when activated by a base. The outer-sphere mechanism involving bifunctional catalysis of ketone reduction is disfavored according to experimental and theoretical studies and an inner-sphere mechanism is proposed involving the decoordination of the amine donor from the C–NH2 ligand. The ruthenium(II) complex [RuCp*(C–NH2)py]PF6 showed higher activity than the iridium(III) complex [IrCp*(C–NH2)Cl]PF6 in the hydrogenation of ketones. This ruthenium(II) complex also catalyzes the hydrogenation of an aromatic ester, a ketimine, and the hydrogenolysis of styrene oxide. We proposed an alcohol-assisted outer sphere bifunctional mechanism for both systems based on experimental findings and theoretical calculations. The cationic iridium(III) hydride complex, [IrCp*(C–NH2)H]PF6 , was prepared and this failed to react with a ketone in the absence of base. The crucial role of the alkoxide base was demonstrated in the activation of this hydride complex in catalysis. Calculations support the proposal that the base deprotonates the amine group of this hydride complex and triggers the migration of the hydride to the η5-Cp* ring producing a neutral iridium(I) amido complex. This system contains an active Ir–H/N–H couple required for the outer sphere hydrogenation of ketones in the bifunctional mechanism.

Late transition metal complexes of silver(I), rhodium(I), ruthenium(II), palladium(II) and platinum(II) containing a nitrile-functionalized N-heterocyclic carbene ligand (C-CN) were prepared. The nitrile group on the C–CN ligand was shown to undergo hydrolysis under basic conditions, leading to a silver(I) carbene complex with a primary-amido functional group, and a trimetallic complex of palladium(II) with a partially hydrolyzed C–N–N–C donor ligand. The reduction of a nitrile-functionalized imidazolium salt in the presence of nickel(II) chloride under mild conditions yielded an axially chiral square-planar nickel(II) complex containing a unique primary-amino functionalized N-heterocyclic carbene ligand (C-NH2). A transmetalation reaction moved this chelating C–NH2 ligand from nickel(II) to ruthenium(II), osmium(II), and iridium(III), yielding important catalysts for the hydrogenation of polar double bonds. The ruthenium(II) complex, [Ru(p-cymene)(C–NH2)Cl]PF6 catalyzed the transfer and H2-hydrogenation of ketones. The bifunctional hydride complex, [Ru(p-cymene)(C–NH2)H]PF6, which contains a Ru–H/N–H couple showed no activity under catalytic conditions unless when activated by a base. The outer-sphere mechanism involving bifunctional catalysis of ketone reduction is disfavored according to experimental and theoretical studies and an inner-sphere mechanism is proposed involving the decoordination of the amine donor from the C–NH2 ligand. The ruthenium(II) complex [RuCp*(C–NH2)py]PF6 showed higher activity than the iridium(III) complex [IrCp*(C–NH2)Cl]PF6 in the hydrogenation of ketones. This ruthenium(II) complex also catalyzes the hydrogenation of an aromatic ester, a ketimine, and the hydrogenolysis of styrene oxide. We proposed an alcohol-assisted outer sphere bifunctional mechanism for both systems based on experimental findings and theoretical calculations. The cationic iridium(III) hydride complex, [IrCp*(C–NH2)H]PF6 , was prepared and this failed to react with a ketone in the absence of base. The crucial role of the alkoxide base was demonstrated in the activation of this hydride complex in catalysis. Calculations support the proposal that the base deprotonates the amine group of this hydride complex and triggers the migration of the hydride to the η5-Cp* ring producing a neutral iridium(I) amido complex. This system contains an active Ir–H/N–H couple required for the outer sphere hydrogenation of ketones in the bifunctional mechanism.

Made available in DSpace on 2014-10-09T12:41:39Z (GMT). No. of bitstreams: 0 / Made available in DSpace on 2014-10-09T14:08:52Z (GMT). No. of bitstreams: 0 / Dissertação (Mestrado) / IPEN/D / Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP

Made available in DSpace on 2014-10-09T12:41:39Z (GMT). No. of bitstreams: 0 / Made available in DSpace on 2014-10-09T14:08:52Z (GMT). No. of bitstreams: 0 / Hidrogéis são membranas formadas pela reticulação de cadeias poliméricas, empregados na área farmacêutica como produtos biomédicos. Dentre os principais polímeros selecionados para a síntese de hidrogéis, destaca-se a poliacrilamida (PAAM) devido às suas propriedades como hidrofilicidade e alto grau de intumescimento. Proteínas terapêuticas e enzimas são veiculadas em hidrogéis como carreadores de fármaco ou como dispositivos para tratamento de feridas e escaras na pele. Este trabalho teve como objetivo a síntese de uma membrana à base de PAAM favorável para veiculação de proteínas. As proteínas empregadas foram papaína e albumina de soro bovino (BSA) e as etapas do processo englobaram síntese da membrana, adição das proteínas no sistema, irradiação em condições específicas e caracterização da membrana. Ao utilizar temperaturas criogênicas na síntese e na irradiação das amostras, houve predomínio de reticulação da cadeia polimérica, fato que não ocorria em temperatura ambiente. As membranas foram obtidas com incorporação dos ativos na concentração de 0,2 a 1% (p/p), obtendo-se concentração de PAAM entre 4% a 10% (p/p), as quais receberam irradiação com raios gama provenientes de uma fonte 60Co, na dose de 25 kGy. Nas condições realizadas, as membranas não apresentaram citotoxicidade nem adesão celular, o perfil de liberação das proteínas foi adequado, a papaína manteve sua bioatividade preservada apesar do decaimento biológico e, segundo estudos de carga das moléculas, a membrana possui maior afinidade com a papaína, liberando-a mais lentamente. Desta forma, o método proposto e as membranas obtidas foram apropriados para a obtenção de um biomaterial. / Dissertação (Mestrado) / IPEN/D / Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP

A enzima cruzaína é um alvo validado e promissor para a descoberta de agentes tripanossomicidas. A validação desta enzima estimulou o desenvolvimento de vários inibidores ao longo dos últimos vinte anos. A descoberta de novos compostos, provenientes de classes químicas distintas, mais seguros e eficazes representa uma importante contribuição para o desenvolvimento da quimioterapia da doença de Chagas. Dentre essas classes, encontram-se as dipeptidil-nitrilas, que apresentam alta potência contra a cruzaína e são conhecidamente inibidores covalente-reversíveis. Estudos de afinidade através de Calorimetria de Titulação Isotérmica (ITC) são fundamentais na compreensão de sistemas bioquímicos e viabilizam a determinação dos parâmetros termodinâmicos. A ITC possibilita determinar com precisão e acurácia os valores de Kd(1/Ka), &Delta;H,&Delta;G,&Delta;S e &Delta;Cp e com esses parâmetros pode-se traçar facilmente o perfil termodinâmico dos ligantes. No presente trabalho, a enzima selvagem cruzaína bem como sua forma mutante C25S foram preparadas e, pela primeira vez, foi realizado o estudo de afinidade através da ITC para 16 dipeptidil-nitrilas usadas como inibidores da cruzaína. O perfil termodinâmico (TP) foi obtido e observado como entálpico-dirigido com compensação entrópica desfavorável. A fatoração da energia livre ( &Delta;G) de interação foi usada para avaliar os efeitos causados pelas substituições em P1, P2 e P3 na energética, sugerindo uma correlação direta entre a afinidade e a otimização entálpica/entrópica. As substituições avaliadas promoveram um aumento de 10 a 20 vezes na afinidade da cruzaína pelo inibidor. Estudos em diferentes tampões foram realizados para a determinação da influência do efeito de ionização na afinidade. Foi determinado o valor de &Delta;Cp do complexo cruzaína-Neq0409 e a relação de &Delta;HITC com &Delta;HvH. O Neq0569 foi testado contra a proteína mutante C25A, tendo sido observada inversão da assinatura que passou a ser entropicamente dirigida. Além disso, uma redução de 176 vezes na afinidade foi observada, demonstrando a importância da ligação covalente-reversível para o aumento da afinidade. / The enzyme cruzain is a validated and promising target for the discovery of trypanocidal agents. The validation of this enzyme has stimulated the development of several inhibitors over the past twenty years. The discovery of new compounds from different chemical classes, which are safer and more effective is an important contribution to the development of chemotherapy of Chagas disease. Among known classes are the dipeptidyl nitriles that exhibit high cruzain affinity and are known to be covalent-reversible inhibitors. Molecular optimization requires a rigorous assessment of physicochemical properties, including the thermodynamic characterization of molecular forces that govern cruzain-inhibitor interactions. Affinity studies through Isothermal Titration Calorimetry (ITC) are fundamental in understanding biochemical systems and enable the determination of thermodynamic parameters. The ITC tool provides the determination of Kd values (1/Ka), &Delta;H, &Delta;G, &Delta;S and &Delta;Cp accurately and precisely. These parameters can easily be used to draw the thermodynamic profile of ligands. In this study, the wild type cruzain enzyme and its mutant form C25S were prepared and, for the first time by the best of our knowledge, the study was conducted by ITC for 16 dipeptidyl nitriles used as inhibitors of cruzain enzyme, which is a hydrolase. The thermodynamic profile (TP) was obtained and observed to be enthalpy-driven with unfavorable entropic compensation. The free energy factorization (&Delta;G) interaction was used to evaluate the effects caused by substitutions in P1, P2 and P3 in energy, thereby suggesting a direct correlation between the affinity and the enthalpy/entropy optimization. Substitutions made possible to observe an increase of 10 to 20 times higher than the affinity for previous cruzain inhibitors. Studies on different buffers were performed to determine the influence of ionizing effect on affinity. The &Delta;Cp value was determined for cruzain-Neq0409 complex and its &Delta;HITC relationship with &Delta;HvH was also evaluated. Neq0569 was tested against the mutant protein C25A, having been observed reversal of the signature which became entropy driven. Furthermore, a reduction of 176-fold in the affinity was observed, demonstrating the importance of covalent-reversible binding to increase affinity.

<p align=\"justify\">A necessidade urgente de descoberta de terapias mais seguras e eficazes para o tratamento da doença de Chagas e leishmanioses tem motivado a pesquisa por novos inibidores das enzimas cruzaína e CPB, as principais cisteíno proteases do T. cruzie e Leishmania spp., respectivamente. Uma série de 52 compostos nitrílicos que atuam como inibidores covalente-reversíveis de cisteíno proteases foi sintetizada no grupo NEQUIMED/IQSC/USP e avaliada quanto a sua atividade inibitória contra as enzimas cruzaína, CPB de Leishmania mexicana e catepsina L de humanos. Utilizando planejamento molecular baseado em hipótese, mapeamos as relações estrutura-atividade (SARs) desses inibidores através de variações nas posições P1, P2, P3 e P1\' do esqueleto dipeptidil nitrílico. A substituição do grupo eletrofílico (warhead) aminonitrila em P1 pelo grupo azanitrila melhorou a afinidade em duas ordens de magnitude para todos os alvos avaliados. Um dos mais potentes inibidores, o análogo azanitrila Neq0690 mostrou uma cinética de ligação lenta com valores de pKi de 8,8, 9,3 e 9,7 para cruzaína, catepsina L e LmCPB, respectivamente. A substituição bioisostérica da ligação amida entre as posições P2-P3 pelo grupo trifluoroetilamina resultou na síntese do Neq0659, um potente inibidor com um perfil de ação seletivo para as proteases de parasitos. A substituição do grupo metileno em P1 pelo ciclopropano aumentou a afinidade para todas as enzimas. Contudo, uma inibição seletiva da cruzaína e LmCPB foi associada à presença do grupo (R)-benzila como substituinte da posição P1 dos derivados CF3 substituídos. Embora os compostos substituídos com leucina, tirosina, triptofano e 3-cloro fenilalanina como substituintes da posição P2 foram relativamente bem tolerados pela cruzaína e catepsina L, uma restrita especificidade foi verificada para LmCPB com pequenos ganhos de afinidade para os inibidores que possuíam os grupos leucina e metil benzoato como substituintes dessa posição. Com relação à posição P3, a inserção do grupo 3-terc-butilpirazol e 3-bromo piridina aumentou a afinidade para todos os alvos avaliados enquanto que um ganho seletivo para a LmCPB foi observado para os compostos que possuíam o grupo bifenila nessa posição. Além disso, duas novas estruturas cristalográficas da LmCPB complexada com o Neq0690 e metil metanotiossulfonato (MMTS) foram determinadas com resoluções de 1,3 Å e 1,5 Å, respectivamente. As estruturas dos co-complexos revelaram os modos de interação (MoB) desses ligantes, bem como as principais características do processo de reconhecimento bimolecular. Isso permitirá o uso de estratégias de planejamento baseado na estrutura do alvo com translação natural para a pesquisa por novos inibidores de cisteíno proteases, com amplo espectro de ação na quimioterapia de doenças a elas relacionadas. / <p align=\"justify\">The urgent need for the discovery of safer and more effective therapies for the treatment of Chagas disease and leishmaniasis has motivated the search for new inhibitors of the enzymes cruzain and CPB, the major T. cruzi and Leishmania spp. cysteine proteases, respectively. A series of 52 nitrile-containing compounds acting as covalent-reversible inhibitors of cysteine proteases was synthesized at the NEQUIMED/IQSC/USP Medicinal Chemistry Group and evaluated for their inhibitory activity against the enzymes cruzain, Leishmania mexicana CPB and cathepsin L from humans. Using hypothesis-driven molecular design, we mapped the structure-activity relationships (SARs) of these inhibitors through variations in the P1, P2, P3 and P1\' positions of the dipeptidyl nitrile scaffold. The substitution of the aminonitrile by the azanitrile group improved the affinity by two orders of magnitude for all the evaluated targets. One of the most potent inhibitors, the azanitrile analogue dubbed Neq0690 showed a slow-binding kinetics with pKi values of 8.8, 9.3 and 9.7 for cruzain, cathepsin L and LmCPB, respectively. Bioisosteric substitution of the amide moiety between the P2-P3 positions by the trifluoroethylamine group resulted in the synthesis of Neq0659, a potent inhibitor with a selective action profile for parasite proteases. Substitution of the methylene group at P1 by cyclopropane increased the affinity for all enzymes. However, selective inhibition of cruzain and LmCPB was associated with the presence of the (R)-benzyl group as substituent of the P1 position of the substituted CF3 derivatives. Although leucine, tyrosine, tryptophan and 3-chloro phenylalanine substituted compounds as substituents of the P2 position were relatively well tolerated by cruzain and cathepsin L, a restricted specificity was verified for LmCPB with small affinity gains for the inhibitors possessing the leucine and methyl benzoate as substituents of that position. Regarding the P3 position, the insertion of the 3-tert-butylpyrazole and 3-bromo pyridine groups increased the affinity for all evaluated targets whereas a selective gain for LmCPB was observed for the compounds having the biphenyl moiety at that position. In addition, it is noteworthy that two new crystallographic structures of LmCPB complexed with Neq0690 and methyl methanethiosulfonate (MMTS) were determined with resolutions of 1.3 Å and 1.5 Å, respectively. The structures of the co-complexes revealed the modes of binding (MoB) of these ligands, as well as the main characteristics of the bimolecular recognition process. This will allow the natural translational target structure strategies for the search for new inhibitors of cysteine proteases with broad spectrum of action in the chemotherapy of related diseases.