Determina??o de energia livre de liga??o por m?todos in silico para ligantes da enzima InhA (EC 1.3.1.9) de Mycobacterium tuberculosis
Ano de defesa: | 2016 |
---|---|
Autor(a) principal: | |
Orientador(a): | |
Banca de defesa: | |
Tipo de documento: | Dissertação |
Tipo de acesso: | Acesso aberto |
Idioma: | por |
Instituição de defesa: |
Pontif?cia Universidade Cat?lica do Rio Grande do Sul
|
Programa de Pós-Graduação: |
Programa de P?s-Gradua??o em Biotecnologia Farmac?utica
|
Departamento: |
Faculdade de Farm?cia
|
País: |
Brasil
|
Palavras-chave em Português: | |
Área do conhecimento CNPq: | |
Link de acesso: | http://tede2.pucrs.br/tede2/handle/tede/6877 |
Resumo: | Tuberculosis is an infectious disease responsible for about 1.3 million deaths annually worldwide. Despite the appearance of multi-resistant strains of Mycobacterium tuberculosis (Mtb), since the 80?s there is a gap in the development of new antimicrobials. With the advent of bioinformatics and computational molecular biophysics, became possible to test, from a established molecular target, numerous molecules, especially associated with the prediction of binding free energy. In the current dissertation, were selected 14 compounds with recognized activity against the enzyme 2-trans-enoil-ACP redutase (InhA, EC 1.3.1.9) of Mtb. These molecules were divided into three groups. Set 1: 5 compounds with distant values of binding free energy. Set 2: 9 compounds with close binding free energy values and similar molecular structures (derived from Genz 10850). Set 3: 14 ligands, corresponding to the sum of the set?s 1 and 2. Sampling obtained from molecular dynamics and 2 ns of simulations, in explicit solvent, allowed to estimate the free energy of bind associated with the methods MM/GBSA, MM/PBSA, (QM)MM/GBSA, LigScore, DrugScore, AutoDock and SQM. The ranking of the compounds were based in the correlation (R2) between the predicted and experimental values. Results showed similar values of R2 in all tested methods. More accurate methods, such as SQM and (QM)/MM/GBSA, not obtained better correlations in comparison with simplified methods, as LigScore and DrugScore. In general, Set 1 obtained a moderate correlation (R2 of 0.00-0.80). Set?s 2 and 3, showed weak correlation (R2 < 0.40). Despite the satisfactory results of Set 1, the tested methods presented limitations in the ranking of compounds with close values of experimental binding free energy and similar molecular structures, as Set 2. |
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Souza, Osmar Norberto de486.043.996-15http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4781658Z2Bachega, Jos? Fernando Ruggierohttp://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4258467P3025.849.010-13http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4413803U1Migott, Gustavo Bellani2016-08-03T18:19:52Z2016-02-29http://tede2.pucrs.br/tede2/handle/tede/6877Tuberculosis is an infectious disease responsible for about 1.3 million deaths annually worldwide. Despite the appearance of multi-resistant strains of Mycobacterium tuberculosis (Mtb), since the 80?s there is a gap in the development of new antimicrobials. With the advent of bioinformatics and computational molecular biophysics, became possible to test, from a established molecular target, numerous molecules, especially associated with the prediction of binding free energy. In the current dissertation, were selected 14 compounds with recognized activity against the enzyme 2-trans-enoil-ACP redutase (InhA, EC 1.3.1.9) of Mtb. These molecules were divided into three groups. Set 1: 5 compounds with distant values of binding free energy. Set 2: 9 compounds with close binding free energy values and similar molecular structures (derived from Genz 10850). Set 3: 14 ligands, corresponding to the sum of the set?s 1 and 2. Sampling obtained from molecular dynamics and 2 ns of simulations, in explicit solvent, allowed to estimate the free energy of bind associated with the methods MM/GBSA, MM/PBSA, (QM)MM/GBSA, LigScore, DrugScore, AutoDock and SQM. The ranking of the compounds were based in the correlation (R2) between the predicted and experimental values. Results showed similar values of R2 in all tested methods. More accurate methods, such as SQM and (QM)/MM/GBSA, not obtained better correlations in comparison with simplified methods, as LigScore and DrugScore. In general, Set 1 obtained a moderate correlation (R2 of 0.00-0.80). Set?s 2 and 3, showed weak correlation (R2 < 0.40). Despite the satisfactory results of Set 1, the tested methods presented limitations in the ranking of compounds with close values of experimental binding free energy and similar molecular structures, as Set 2.A tuberculose ? uma doen?a infectocontagiosa respons?vel por cerca de 1,3 milh?o de mortes anualmente a n?vel mundial. Apesar do aparecimento de cepas multirresistentes de Mycobacterium tuberculosis (Mtb), desde a d?cada de 80 se observa uma lacuna no desenvolvimento de novos antimicrobianos. Com o advento da bioinform?tica e biof?sica molecular computacional, tornou-se poss?vel, a partir de um alvo molecular preestabelecido, testar in?meros candidatos a f?rmacos, com destaque para a predi??o da energia livre de liga??o. Nesta disserta??o, foram selecionados 14 compostos com conhecida atividade frente a enzima 2-trans-enoil-ACP redutase (InhA, EC 1.3.1.9) de Mtb. Estas mol?culas foram divididas em 3 grupos. Grupo 1: 5 compostos com valores esparsos de energia livre. Grupo 2: 9 compostos com valores similares de energia livre e derivadas do composto Genz-10850. Grupo 3: 14 compostos correspondendo ? uni?o dos Grupos 1 e 2. Amostragens por simula??es de din?mica molecular de 2 ns, em solvente expl?cito, permitiram estimar os valores da energia livre de liga??o destes compostos com os m?todos MM/GBSA, MM/PBSA, (QM)MM/GBSA, LigScore, DrugScore, AutoDock e SQM. O ranqueamento dos compostos foi baseado na correla??o (R2) entre valores experimentais e estimados de energia livre. Os resultados apontaram valores de R2 similares entre os m?todos testados. T?cnicas mais robustas, como SQM e (QM)MM/GBSA, n?o obtiveram resultados mais acurados em compara??o ?quelas mais simples, como LigScore e DrugScore. No geral, foram obtidos valores moderados de correla??o (R2 de 0,00-0,80) para o Grupo 1. Os Grupos 2 e 3 exibiram correla??es fracas (R2 <0,40). Apesar dos resultados satisfat?rios para o Grupo 1, os m?todos utilizados apresentaram limita??es e n?o foram capazes de predizer e ranquear corretamente compostos com valores pr?ximos de energia livre e estruturas moleculares similares, como os do Grupo 2.Submitted by Setor de Tratamento da Informa??o - BC/PUCRS (tede2@pucrs.br) on 2016-08-03T18:19:52Z No. of bitstreams: 1 DIS_GUSTAVO_BELLANI_MIGOTT_COMPLETO.pdf: 6201853 bytes, checksum: 70237f84b98539735536877e1ffbc4e7 (MD5)Made available in DSpace on 2016-08-03T18:19:52Z (GMT). No. of bitstreams: 1 DIS_GUSTAVO_BELLANI_MIGOTT_COMPLETO.pdf: 6201853 bytes, checksum: 70237f84b98539735536877e1ffbc4e7 (MD5) Previous issue date: 2016-02-29application/pdfhttp://tede2.pucrs.br:80/tede2/retrieve/165902/DIS_GUSTAVO_BELLANI_MIGOTT_COMPLETO.pdf.jpgporPontif?cia Universidade Cat?lica do Rio Grande do SulPrograma de P?s-Gradua??o em Biotecnologia Farmac?uticaPUCRSBrasilFaculdade de Farm?ciaMEDICAMENTOS - DESENVOLVIMENTOTUBERCULOSEENZIMAS - FARMACOLOGIABIOTECNOLOGIA - F?RMACOSBIOLOGIA MOLECULARCIENCIAS DA SAUDE::FARMACIADetermina??o de energia livre de liga??o por m?todos in silico para ligantes da enzima InhA (EC 1.3.1.9) de Mycobacterium tuberculosisinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesis2304961219518893267600600600-83806546368433781166997636413449754996info:eu-repo/semantics/openAccessreponame:Biblioteca Digital de Teses e Dissertações da PUC_RSinstname:Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)instacron:PUC_RSTHUMBNAILDIS_GUSTAVO_BELLANI_MIGOTT_COMPLETO.pdf.jpgDIS_GUSTAVO_BELLANI_MIGOTT_COMPLETO.pdf.jpgimage/jpeg3046http://tede2.pucrs.br/tede2/bitstream/tede/6877/5/DIS_GUSTAVO_BELLANI_MIGOTT_COMPLETO.pdf.jpgcf8ef190a8ef030d88b4ac7337089a97MD55TEXTDIS_GUSTAVO_BELLANI_MIGOTT_COMPLETO.pdf.txtDIS_GUSTAVO_BELLANI_MIGOTT_COMPLETO.pdf.txttext/plain154862http://tede2.pucrs.br/tede2/bitstream/tede/6877/4/DIS_GUSTAVO_BELLANI_MIGOTT_COMPLETO.pdf.txt80059a844f0c2f35987461920d8142b1MD54LICENSElicense.txtlicense.txttext/plain; charset=utf-8610http://tede2.pucrs.br/tede2/bitstream/tede/6877/3/license.txt5a9d6006225b368ef605ba16b4f6d1beMD53ORIGINALDIS_GUSTAVO_BELLANI_MIGOTT_COMPLETO.pdfDIS_GUSTAVO_BELLANI_MIGOTT_COMPLETO.pdfapplication/pdf6201853http://tede2.pucrs.br/tede2/bitstream/tede/6877/2/DIS_GUSTAVO_BELLANI_MIGOTT_COMPLETO.pdf70237f84b98539735536877e1ffbc4e7MD52tede/68772016-08-03 20:00:29.547oai:tede2.pucrs.br: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Biblioteca Digital de Teses e Dissertaçõeshttp://tede2.pucrs.br/tede2/PRIhttps://tede2.pucrs.br/oai/requestbiblioteca.central@pucrs.br||opendoar:2016-08-03T23:00:29Biblioteca Digital de Teses e Dissertações da PUC_RS - Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)false |
dc.title.por.fl_str_mv |
Determina??o de energia livre de liga??o por m?todos in silico para ligantes da enzima InhA (EC 1.3.1.9) de Mycobacterium tuberculosis |
title |
Determina??o de energia livre de liga??o por m?todos in silico para ligantes da enzima InhA (EC 1.3.1.9) de Mycobacterium tuberculosis |
spellingShingle |
Determina??o de energia livre de liga??o por m?todos in silico para ligantes da enzima InhA (EC 1.3.1.9) de Mycobacterium tuberculosis Migott, Gustavo Bellani MEDICAMENTOS - DESENVOLVIMENTO TUBERCULOSE ENZIMAS - FARMACOLOGIA BIOTECNOLOGIA - F?RMACOS BIOLOGIA MOLECULAR CIENCIAS DA SAUDE::FARMACIA |
title_short |
Determina??o de energia livre de liga??o por m?todos in silico para ligantes da enzima InhA (EC 1.3.1.9) de Mycobacterium tuberculosis |
title_full |
Determina??o de energia livre de liga??o por m?todos in silico para ligantes da enzima InhA (EC 1.3.1.9) de Mycobacterium tuberculosis |
title_fullStr |
Determina??o de energia livre de liga??o por m?todos in silico para ligantes da enzima InhA (EC 1.3.1.9) de Mycobacterium tuberculosis |
title_full_unstemmed |
Determina??o de energia livre de liga??o por m?todos in silico para ligantes da enzima InhA (EC 1.3.1.9) de Mycobacterium tuberculosis |
title_sort |
Determina??o de energia livre de liga??o por m?todos in silico para ligantes da enzima InhA (EC 1.3.1.9) de Mycobacterium tuberculosis |
author |
Migott, Gustavo Bellani |
author_facet |
Migott, Gustavo Bellani |
author_role |
author |
dc.contributor.advisor1.fl_str_mv |
Souza, Osmar Norberto de |
dc.contributor.advisor1ID.fl_str_mv |
486.043.996-15 |
dc.contributor.advisor1Lattes.fl_str_mv |
http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4781658Z2 |
dc.contributor.advisor-co1.fl_str_mv |
Bachega, Jos? Fernando Ruggiero |
dc.contributor.advisor-co1Lattes.fl_str_mv |
http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4258467P3 |
dc.contributor.authorID.fl_str_mv |
025.849.010-13 |
dc.contributor.authorLattes.fl_str_mv |
http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4413803U1 |
dc.contributor.author.fl_str_mv |
Migott, Gustavo Bellani |
contributor_str_mv |
Souza, Osmar Norberto de Bachega, Jos? Fernando Ruggiero |
dc.subject.por.fl_str_mv |
MEDICAMENTOS - DESENVOLVIMENTO TUBERCULOSE ENZIMAS - FARMACOLOGIA BIOTECNOLOGIA - F?RMACOS BIOLOGIA MOLECULAR |
topic |
MEDICAMENTOS - DESENVOLVIMENTO TUBERCULOSE ENZIMAS - FARMACOLOGIA BIOTECNOLOGIA - F?RMACOS BIOLOGIA MOLECULAR CIENCIAS DA SAUDE::FARMACIA |
dc.subject.cnpq.fl_str_mv |
CIENCIAS DA SAUDE::FARMACIA |
description |
Tuberculosis is an infectious disease responsible for about 1.3 million deaths annually worldwide. Despite the appearance of multi-resistant strains of Mycobacterium tuberculosis (Mtb), since the 80?s there is a gap in the development of new antimicrobials. With the advent of bioinformatics and computational molecular biophysics, became possible to test, from a established molecular target, numerous molecules, especially associated with the prediction of binding free energy. In the current dissertation, were selected 14 compounds with recognized activity against the enzyme 2-trans-enoil-ACP redutase (InhA, EC 1.3.1.9) of Mtb. These molecules were divided into three groups. Set 1: 5 compounds with distant values of binding free energy. Set 2: 9 compounds with close binding free energy values and similar molecular structures (derived from Genz 10850). Set 3: 14 ligands, corresponding to the sum of the set?s 1 and 2. Sampling obtained from molecular dynamics and 2 ns of simulations, in explicit solvent, allowed to estimate the free energy of bind associated with the methods MM/GBSA, MM/PBSA, (QM)MM/GBSA, LigScore, DrugScore, AutoDock and SQM. The ranking of the compounds were based in the correlation (R2) between the predicted and experimental values. Results showed similar values of R2 in all tested methods. More accurate methods, such as SQM and (QM)/MM/GBSA, not obtained better correlations in comparison with simplified methods, as LigScore and DrugScore. In general, Set 1 obtained a moderate correlation (R2 of 0.00-0.80). Set?s 2 and 3, showed weak correlation (R2 < 0.40). Despite the satisfactory results of Set 1, the tested methods presented limitations in the ranking of compounds with close values of experimental binding free energy and similar molecular structures, as Set 2. |
publishDate |
2016 |
dc.date.accessioned.fl_str_mv |
2016-08-03T18:19:52Z |
dc.date.issued.fl_str_mv |
2016-02-29 |
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info:eu-repo/semantics/masterThesis |
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http://tede2.pucrs.br/tede2/handle/tede/6877 |
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http://tede2.pucrs.br/tede2/handle/tede/6877 |
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por |
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por |
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2304961219518893267 |
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600 600 600 |
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6997636413449754996 |
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Pontif?cia Universidade Cat?lica do Rio Grande do Sul |
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Programa de P?s-Gradua??o em Biotecnologia Farmac?utica |
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PUCRS |
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Brasil |
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Faculdade de Farm?cia |
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Pontif?cia Universidade Cat?lica do Rio Grande do Sul |
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