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Submitted by Jorge Silva (jorgelmsilva@ufrrj.br) on 2021-10-24T05:51:05Z No. of bitstreams: 1 2019 - Sheisi Fonseca Leite da Silva Rocha.pdf: 3059409 bytes, checksum: 78e70249053e5be917fab9c80bc8a3b5 (MD5) Made available in DSpace on 2021-10-24T05:51:05Z (GMT). No. of bitstreams: 1 2019 - Sheisi Fonseca Leite da Silva Rocha.pdf: 3059409 bytes, checksum: 78e70249053e5be917fab9c80bc8a3b5 (MD5) Previous issue date: 2019-01-29 CAPES - Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior Shp2, along with Shp1, forms a small family of protein tyrosine phosphatases. Studies suggest that although inhibition of Shp2 is advantageous for the treatment of some types of cancer, inhibition of Shp1 may have the opposite effect because it acts as a tumor suppressor. In this way, we sought to develop an in silico methodology capable of identifying more selective Shp2 inhibitors. In this work, we showed that in spite of the thermodynamic complexity involved in the enzyme/inhibitor interaction, it was possible to correlate the selectivity of two series (76 compounds) with the difference of the enthalpy of interaction calculated in both enzymes. The interaction profile of the inhibitors with Shp2 and Shp1 were initially obtained by molecular docking. After the refinement of the geometries of the enzyme / inhibitor complexes with the semi-empirical molecular orbital PM7 method, the enthalpy values of the interaction were obtained. For the series 1, composed of 52 selective inhibitors of Shp2, we demonstrated that the enthalpy of interaction can be used as a reliable criterion for the identification of selective inhibitors for Shp2, since it was significantly more favorable for Shp2 than for Shp1 with a confidence level of 99%. For series 2, composed of 24 compounds, a satisfactory correlation (R = 0.70) could be obtained between the selectivity and the relative percentage difference of the calculated enthalpies of interaction in both enzymes. Another objective of this work was to construct a model of prediction of the activity of inhibitors of Shp2 using as empirical basis the series 1 to validate it later with the series 2. Due to the presence of negatively charged inhibitors within the series, it was necessary to consider the electrolytic effect, correcting the experimental values of inhibitory activity, since such data refer to formal concentrations and the thermodynamic constant involves effective concentrations. For this it was necessary to calculate the ionic strength of the reaction medium and to estimate the activity coefficients of the species involved in the enzyme /inhibitor dissociation equilibrium through the Guntelberg equation. The construction of the model was based on literature proposals on the use of thermodynamic cycles to calculate the free energy of interaction between ligands and enzymes. In this sense, terms related to the enthalpy of interaction of the enzyme / inhibitor complex, the energy of solvation of the ligand and the entropic losses due to rotational restrictions were obtained after their interaction with the enzyme. These terms were correlated through linear multiple regression with experimental data of inhibition. In this way it was possible to develop a prediction model of the activity of inhibitors of Shp2 with good correlation with experimental data (R = 0.83). This model was validated satisfactorily (R = 0.73) with series 2 and used in the prediction of the relative activity of new compounds. A Shp2, juntamente com a Shp1, forma uma pequena fam?lia de prote?nas tirosina fosfatases. Estudos sugerem que, embora a inibi??o da Shp2 seja vantajosa para o tratamento de alguns tipos de c?ncer, a inibi??o da Shp1 pode ter o efeito oposto, pois atua como supressora de tumores. Desta forma, buscou-se desenvolver uma metodologia in silico capaz de identificar inibidores da Shp2 mais seletivos. Neste trabalho, mostramos que apesar da complexidade termodin?mica envolvida na intera??o enzima/inibidor, foi poss?vel correlacionar a seletividade de duas s?ries (76 compostos) com a diferen?a das entalpias de intera??o calculadas em ambas as enzimas. Os perfis de intera??o dos inibidores com a Shp2 e a Shp1 foram inicialmente obtidos por docagem molecular. Ap?s o refinamento das geometrias dos complexos enzima/inibidor com o m?todo do orbital molecular semi-emp?rico PM7, foram obtidos os valores de entalpia de intera??o. Para a s?rie 1, composta por 52 inibidores seletivos da Shp2, demonstramos que a entalpia de intera??o pode ser usada como um crit?rio confi?vel para a identifica??o de inibidores seletivos para a Shp2, pois foi significativamente mais favor?vel para Shp2 do que para a Shp1 com um n?vel de confian?a de 99%. Para a s?rie 2, composta por 24 compostos, uma correla??o satisfat?ria (R = 0,70) p?de ser obtida entre a seletividade e a diferen?a percentual relativa das entalpias de intera??o calculadas em ambas as enzimas. Outro objetivo deste trabalho foi construir um modelo de predi??o da atividade de inibidores da Shp2 utilizando como base emp?rica a s?rie 1 e posteriormente, validar com a s?rie 2. Devido ? presen?a de inibidores carregados negativamente dentro das s?ries estudadas, foi necess?rio considerar o efeito eletrol?tico, corrigindo os valores experimentais de atividade inibit?ria (CI50), uma vez que tais dados se referem a concentra??es formais e a constante termodin?mica envolve concentra??es efetivas. Para isso foi necess?rio calcular a for?a i?nica do meio reacional e estimar os coeficientes de atividade das esp?cies envolvidas no equil?brio de dissocia??o enzima/inibidor atrav?s da equa??o de Guntelberg. A constru??o do modelo se baseou em propostas da literatura sobre o uso de ciclos termodin?micos para se calcular a energia livre de intera??o entre ligantes e enzimas. Neste sentido, foram obtidos termos referentes ? entalpia de intera??o do complexo enzima/inibidor, a energia de solvata??o do ligante e as perdas entr?picas devido a restri??es rotacionais ap?s a intera??o do mesmo com a enzima. Estes termos foram correlacionados atrav?s de regress?o m?ltipla linear com dados experimentais de inibi??o. Desta forma foi poss?vel desenvolver um modelo de predi??o da atividade de inibidores da Shp2 com boa correla??o com dados experimentais (R= 0,83). Este modelo foi validado de forma satisfat?ria (R=0,73) atrav?s da s?rie 2 e utilizado na predi??o da atividade relativa de novos compostos.

Submitted by Sandra Pereira (srpereira@ufrrj.br) on 2020-11-19T13:29:49Z No. of bitstreams: 1 2014 - Sheisi Fonseca Leite da Silva Rocha.pdf: 988981 bytes, checksum: 49abe58d9422ae29356979cf6629dec8 (MD5) Made available in DSpace on 2020-11-19T13:29:49Z (GMT). No. of bitstreams: 1 2014 - Sheisi Fonseca Leite da Silva Rocha.pdf: 988981 bytes, checksum: 49abe58d9422ae29356979cf6629dec8 (MD5) Previous issue date: 2014-04-15 Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior, CAPES, Brasil. Urease is an important enzyme for the research in agriculture, environment and medicine. This enzyme catalyzes the hydrolysis of urea to ammonia and carbamate, which decomposes spontaneously, yielding a second molecule of ammonia, causing a significant increase of pH solution. In order to develop theoretical models for the prediction of activities of urease inhibitors, we initially studied the enzyme?s spin multiplicity, which contains two Ni(II) ?ons, and the state of protonation of the oxygen located between the nickel ions. The results indicate that the system is best represented by the triplet or quintet state and the oxygen atom located between the nickel ions, probably is a hydroxyl ion. Based on these results, the construction of the models was based on literature proposals about the use of thermodynamic cycles for the calcultation of the free energy of binding between ligands and enzymes. In the present work, parameters such as the interaction enthalpy, the Gibbs free energy required for the inhibitor to go from the aqueous phase to the interior of the enzyme and the entropic losses associated to the freezing of bonds after the binding of the inhibitors to the enzyme were used to develop correlations with the measured experimental Ki values. The quantification of these parameters for some phosphinic acids derivatives from the literature allowed us to obtain a good empirical model for the correlation between experimental activity data and the theoretical parameters (r=0.92). The model was employed for the prediction of the relative activity of a series of new proposed compounds by the organophosphorous synthesis group of UFRRJ. It was possible to identify which compounds are the most promising and which are the main factors that should be modified in order to optimize the urease inhibition profile by these compounds. A urease ? uma enzima importante para as pesquisas relacionadas com a agricultura, meio ambiente e medicina. Ela catalisa a rea??o de hidr?lise da ur?ia para formar am?nia e carbamato, o qual se decomp?e espontaneamente, produzindo uma segunda mol?cula de am?nia e di?xido de carbono, provocando um significativo aumento do pH da solu??o. Com o objetivo de desenvolver modelos de predi??o da atividade de inibidores da urease, estudou-se inicialmente a multiplicidade de spin da enzima, que cont?m dois ?ons Ni(II), e o estado de protona??o do oxig?nio localizado entre estes ?ons. Os resultados indicaram que o sistema ? melhor representado pelo estado tripleto ou quinteto e o oxig?nio localizado entre os ?ons de n?quel provavelmente ? um ?on hidroxila. A partir destes resultados, a constru??o dos modelos se baseou em propostas da literatura sobre o uso de ciclos termodin?micos para se calcular a energia livre de intera??o entre ligantes e enzimas. No presente estudo, foram combinados termos referentes ? entalpia de intera??o entre o inibidor e a enzima, a energia livre de Gibbs necess?ria para o inibidor passar do meio aquoso para o interior da enzima e as perdas entr?picas devido a restri??es rotacionais ap?s a intera??o do mesmo com a enzima para se obter fun??es de correla??o com constantes inibit?rias (Ki) obtidas experimentalmente. A quantifica??o destes par?metros para alguns derivados do ?cido fosf?nico da literatura nos possibilitou o desenvolvimento de um modelo para determina??o da atividade com boa correla??o com dados experimentais (r=0,92). Este modelo foi utilizado na predi??o da atividade relativa de novas dialquilfosforilidrazonas, sintetizadas pelo grupo de s?ntese de organofosforados da UFRRJ. Foi poss?vel identificar quais compostos s?o os mais promissores da s?rie proposta e quais fatores devem ser alterados para otimizar o perfil de inibi??o da urease.