Orientadora: Profa. Dra. Káthia Maria Honório / Dissertação (mestrado) - Universidade Federal do ABC, Programa de Pós-Graduação em Ciência & Tecnologia - Química, 2014. / Este trabalho propoe o uso de tecnicas de modelagem molecular para entender os principais fatores relacionados com a interacao entre um conjunto de ligantes bioativos e o receptor TGF-¿À tipo 1 (ALK5), alvo biologico envolvido no desenvolvimento de doencas como cancer e fibrose. Para entender essas interacoes, foram utilizadas tecnicas computacionais de modelagem molecular que sao utilizadas para quantificar essas interacoes. Dentre as metodologias utilizadas neste trabalho, foram empregadas tecnicas de acoplamento molecular e analises das relacoes quantitativas tridimensionais entre estrutura quimica e atividade biologica (QSAR 3D). Dessa forma, foi estudado um conjunto de dados contendo 70 moleculas empregando tecnicas de QSAR 3D (CoMFA e CoMSIA). Os modelos CoMFA obtidos apresentaram significativos valores de validacao interna (r2 = 0,979 e q2LOO = 0,882) e externa (conjunto de predicao - r2pred = 0,998 e potencial preditivo externo . r2m= 0,998) e os modelos obtidos da analise CoMSIA tambem apresentaram valores significativos de validacao interna (r2 = 0,913 e q2LOO = 0,822) e validacao externa (conjunto de predicao - r2pred = 0,975 e potencial preditivo externo . r2m = 0,975. A analise dos mapas de contribuicoes estereoquimicas e eletrostaticas (CoMFA) e dos mapas de contribuicoes eletrostaticas e dos grupos doadores de ligacao de hidrogenio (CoMSIA) para o composto mais ativo e menos ativo foi capaz de indicar caracteristicas importantes para a inibicao do alvo biologico em estudo. Portanto, o emprego de metodologias computacionais foi de fundamental importancia para o entendimento sobre os principais fatores envolvidos na interacao entre os ligantes estudados e o receptor ALK5. / This study proposes the use of molecular modeling techniques to understand the main factors related to the interaction between a set of ligands and bioactive TGF-â receptor type 1 (ALK5), biological target involved in the development of diseases such as cancer and fibrosis. To understand these interactions, computational molecular modeling techniques were used, which are used to quantify these interactions. Among the methodologies used in this study, techniques of molecular docking and analyses of three-dimensional quantitative relations between chemical structure and biological activity (3D QSAR) were performed with the goal of understanding the main physico-chemical features related to the biological activity. Thus, we studied a data set containing 70 molecules and 3D QSAR analyses (CoMFA and CoMSIA) were carried out. The CoMFA models have good statistical parameters (r2 =0.979 and q2LOO =0.882) and a significant predictive power (r2pred=0.998 and r2m = 0.998). The CoMSIA models also showed significant values for the internal validation (r2=0.913 and q2LOO =0.822) and the external validation (r2pred=0.975 and r2m=0.975). The analysis of the steric and electrostatic contributions (CoMFA), as well as the electrostatic contributions and donor groups for hydrogen bonding (CoMSIA) for the most active and least active compounds was able to indicate important characteristics of inhibiting the biological target under study. Therefore, the use of computational methodologies was of fundamental importance to understand the main factors involved in the interaction between the studied ligands and the ALK5 receptor.

The emergence and proliferation of Gram-negative bacteria expressing β-lactamases is a significant threat to human health. β-Lactamases are enzymes that degrade the β-lactam antibiotics (e.g., penicillins, cephalosporins, monobactams, and carbapenems) that we use to treat a diverse range of bacterial infections. Specifically, β-lactamases catalyze a hydrolysis reaction where the β-lactam ring common to all β-lactam antibiotics and responsible for their antibacterial activity, is opened, leaving an inactive drug. There are two groups of β-lactamases: serine enzymes that use an active site serine residue for β-lactam hydrolysis and metalloenzymes that use either one or two zinc ions for catalysis. Serine enzymes are divided into three classes (A, C, and D), while there is only one class of metalloenzymes, class B. Clavulanic acid, sulbactam, and tazobactam are β-lactam-based BLIs that demonstrate activity against class A and C β-lactamases; however, they have no activity against the class A KPC and MBLs, NDM and VIM. Avibactam and vaborbactam are novel BLIs approved in the last two years that have activity against serine carbapenemases (e.g., KPC), but do not inhibit MBLs. The overall goals of this project were to use X-ray crystallography to study the catalytic mechanism of serine β-lactamases with β-lactam antibiotics and to understand the mechanisms behind the broad-spectrum inhibition of class A β-lactamases by avibactam and vaborbactam. This project also set out to find novel inhibitors using molecular docking and FBDD that would simultaneously inactivate serine β-lactamases and MBLs commonly expressed in Gram-negative pathogenic bacteria. The first project involved examining the structural basis for the class A KPC-2 β-lactamase broad-spectrum of activity that includes cephalosporins and carbapenems. Three crystal structures were solved of KPC-2: (1) an apo-structure at 1.15 Å; (2) a complex structure with the hydrolyzed cephalosporin, cefotaxime at 1.45 Å; and (3) a complex structure with the hydrolyzed penem, faropenem at 1.40 Å. These complex structures show how alternative conformations of Ser70 and Lys73 play a role in the product release step. The large and shallow active site of KPC-2 can accommodate a wide variety of β-lactams, including the bulky oxyimino side chain of cefotaxime and also permits the rotation of faropenem’s 6-alpha-1R-hydroxyethyl group to promote carbapenem hydrolysis. Lastly, the complex structures highlight that the catalytic versatility of KPC-2 may expose a potential opportunity for drug discovery. The second project focused on understanding the stability of the BLI, avibactam, against hydrolysis by serine β-lactamases. A 0.83 Å crystal structure of CTX-M-14 bound by avibactam revealed that binding of the inhibitor impedes a critical proton transfer between Glu166 and Lys73. This results in a neutral Glu166 and neutral Lys73. A neutral Glu166 is unable to serve as a general base to activate the catalytic water for the hydrolysis reaction. Overall, this structure suggests that avibactam can influence the protonation state of catalytic residues. The third project centered on vaborbactam, a cyclic boronic acid inhibitor of class A and C β-lactamases, including the serine class A carbapenemase KPC-2. To characterize vaborbactam inhibition, binding kinetic experiments, MIC assays, and mutagenesis studies were performed. A crystal structure of the inhibitor bound to KPC-2 was solved to 1.25 Å. These data revealed that vaborbactam achieves nanomolar potency against KPC-2 due to its covalent and extensive non-covalent interactions with conserved active site residues. Also, a slow off-rate and long drug-target residence time of vaborbactam with KPC-2 strongly correlates with in vitro and in vivo activity. The final project focused on discovering dual action inhibitors targeting serine carbapenemases and MBLs. Performing molecular docking against KPC-2 led to the identification of a compound with a phosphonate-based scaffold. Testing this compound using a nitrocefin assay confirmed that it had micromolar potency against KPC-2. SAR studies were performed on this scaffold, which led to a nanomolar inhibitor against KPC-2. Crystal structures of the inhibitors complexed with KPC-2 revealed interactions with active site residues such as Trp105, Ser130, Thr235, and Thr237, which are all important in ligand binding and catalysis. Interestingly, the phosphonate inhibitors that displayed activity against KPC-2, also displayed activity against the MBLs NDM-1 and VIM-2. Crystal structures of the inhibitors complexed with NDM-1 and VIM-2 showed that the phosphonate group displaces a catalytic hydroxide ion located between the two zinc ions in the active site. Additionally, the compounds form extensive hydrophobic interactions that contribute to their activity against NDM-1 and VIM-2. MIC assays were performed on select inhibitors against clinical isolates of Gram-negative bacteria expressing KPC-2, NDM-1, and VIM-2. One phosphonate inhibitor was able to reduce the MIC of the carbapenem, imipenem 64-fold against a K. pneumoniae strain producing KPC-2. The same phosphonate inhibitor also reduced the MIC of imipenem 4-fold against an E. coli strain producing NDM-1. Unfortunately, no cell-based activity was observed for any of the phosphonate inhibitors when tested against a P. aeruginosa strain producing VIM-2. Ultimately, this project demonstrated the feasibility of developing cross-class BLIs using molecular docking, FBDD, and SAR studies.

Docking is one of the methods in virtual screeing. Studies from around 1980 to now, many docking software have been developed, but these software have many short comings. The software currently used for docking have many disadvantage: poor efficiency, rigid structure of the proteins and the ligands, poor accuracy, without the polarization after binding, leading virtual screening is still stuck in a supporting role. Our experiment with new method improves those shortcomings of docking. With this new method, we obtain the following improvements in docking process: better efficiency, flexible structure of the proteins and the ligands, better accuracy. In the depression-related protein docked with traditional Chinese medicine test. We change the conformations of ligands with the shapes of active sites before posing, this makes the conformation of complex much more reasonable, even more complicated, large ligands. In the experiment of random sites docking, we found a possible path for compounds traveling into active sites. We illustrate a docking area by linking all possible docking sites. The lead compound may not successfully travel into active site when this area is occupied by other proteins or ligands. In the docking experiment with side-chain rotation, we rotate the torsion angle to make side chains relax. We obtained a similar result with molecular dynamics, and saved a lot of time.

A recent shift towards proteomics has seen many structural genomics initiatives set up for high-throughput structure determination using traditional methods of x-ray crystallography and NMR. The next step in the proteomic revolution focuses on the interplay of multi-protein complexes and transient protein-protein interactions, which are involved in many cellular functions. Greater understanding of protein-protein interactions will inevitably lead to better comprehension of the regulation of cellular process, which has implications in biomedical sciences and biotechnology. Even though many high-resolution initiatives focus on proteins and protein complexes, their structure-determination success rates are still low. An emerging approach uses chemical cross-linking and mass spectrometry to derive a set of sparse distance constrains, which can be used for building models of proteins and to map out residues in protein interaction interface based on partial structural information. This technique allows low-resolution identification of protein structures and their interactions in cases where traditional structure determination techniques did not produce results. Chemical cross-linkers have been successfully used for many years in identifying interacting proteins. However, recent advances in mass spectrometry have allowed the identification of exact insertion points of low-abundance cross-links and hence has opened up a new perspective on the use of cross-linkers in combination with computational structure prediction. For protein interaction studies, the approach uses chemical cross-linking information with molecular docking, so that the cross-links are treated as explicit constraints in the calculations. This study focuses on a low-cost and rapid approach to structure prediction, where partial structural information and distance constraints can be used to obtain the relative orientation of interacting proteins and domains, specifically as a rescue strategy where traditional high resolution structure determination methods were unsuccessful. This hybrid biochemical/bioinformatics approach was applied in the determination of structure of the latexin:carboxypeptidase A complex, and succeeded in achieving 4 Å rmsd compared to the crystal structure determined subsequently (Mouradov et al., 2006). Application of the bioinformatics/biochemical approach to multi-domain proteins was carried out on murine acyl-CoA thioesterase 7 (Acot7). X-ray crystallography provided structures of the two separate domains of Acot7, however the full length protein did not crystalise. Combining chemical cross-linking, mass spectrometry, molecular docking and homology modeling we were able to reconstruct how the two domains are arranged in the full length protein (Forwood et al., 2007). Limitations of this technique caused by the enormous complexity of the cross-linking reaction mixtures were identified and emphasized by analysing a large (four protein) complex of DNA polymerase III, where only one inter-protein cross-link was identified. A rapid and cost-effective method for identification of cross-linked peptides using a commercially available cross-linker was developed as part of the overall aim of streamlining the hybrid biochemical/bioinformatics in order for it to become a generally applicable technique for rapid protein structure characterisation (King et al., 2008). Finally an in-house software package was developed for assignment of cross-linked peptides based on m/z values.

A recent shift towards proteomics has seen many structural genomics initiatives set up for high-throughput structure determination using traditional methods of x-ray crystallography and NMR. The next step in the proteomic revolution focuses on the interplay of multi-protein complexes and transient protein-protein interactions, which are involved in many cellular functions. Greater understanding of protein-protein interactions will inevitably lead to better comprehension of the regulation of cellular process, which has implications in biomedical sciences and biotechnology. Even though many high-resolution initiatives focus on proteins and protein complexes, their structure-determination success rates are still low. An emerging approach uses chemical cross-linking and mass spectrometry to derive a set of sparse distance constrains, which can be used for building models of proteins and to map out residues in protein interaction interface based on partial structural information. This technique allows low-resolution identification of protein structures and their interactions in cases where traditional structure determination techniques did not produce results. Chemical cross-linkers have been successfully used for many years in identifying interacting proteins. However, recent advances in mass spectrometry have allowed the identification of exact insertion points of low-abundance cross-links and hence has opened up a new perspective on the use of cross-linkers in combination with computational structure prediction. For protein interaction studies, the approach uses chemical cross-linking information with molecular docking, so that the cross-links are treated as explicit constraints in the calculations. This study focuses on a low-cost and rapid approach to structure prediction, where partial structural information and distance constraints can be used to obtain the relative orientation of interacting proteins and domains, specifically as a rescue strategy where traditional high resolution structure determination methods were unsuccessful. This hybrid biochemical/bioinformatics approach was applied in the determination of structure of the latexin:carboxypeptidase A complex, and succeeded in achieving 4 Å rmsd compared to the crystal structure determined subsequently (Mouradov et al., 2006). Application of the bioinformatics/biochemical approach to multi-domain proteins was carried out on murine acyl-CoA thioesterase 7 (Acot7). X-ray crystallography provided structures of the two separate domains of Acot7, however the full length protein did not crystalise. Combining chemical cross-linking, mass spectrometry, molecular docking and homology modeling we were able to reconstruct how the two domains are arranged in the full length protein (Forwood et al., 2007). Limitations of this technique caused by the enormous complexity of the cross-linking reaction mixtures were identified and emphasized by analysing a large (four protein) complex of DNA polymerase III, where only one inter-protein cross-link was identified. A rapid and cost-effective method for identification of cross-linked peptides using a commercially available cross-linker was developed as part of the overall aim of streamlining the hybrid biochemical/bioinformatics in order for it to become a generally applicable technique for rapid protein structure characterisation (King et al., 2008). Finally an in-house software package was developed for assignment of cross-linked peptides based on m/z values.

Nesse trabalho, o docking e a dinâmica molecular foram utilizados como métodos de investigação das formas de interação entre um oligonucleotídeo de B-DNA e duas novas Bases de Tröger fluorescentes, com o propósito de verificar sua potencialidade como sondas biológicas. Para o docking molecular foi utilizado o protocolo descrito por Ricci et. al. (2009), que demonstrou ser um método promissor para reconhecer os modos de ligação e descrever a interação entre as Bases de Tröger e os oligonucleotídeos. Os complexos obtidos a partir dos docking foram utilizados como ponto de partida para as simulações de dinâmica molecular usando o programa GROMACS e o campo de força AMBER03, como descrito por Ricci et. al. (2010). A análise dos resultados das simulações mostraram a possibilidade, de que as Bases de Tröger podem interagir de maneiras diferentes com o oligonucleotídeo com preferência pela interação com sulco menor desse receptor. Durante todas as simulações os ligantes mantiveram-se com uma forte interação com o oligonucleotídeo, sem causar a desnaturação do mesmo. Globalmente, os resultados sugerem que as Bases de Tröger podem interagir com o sulco menor do oligonucleotídeo mas também são capazes de interagir como intercaladores. Devido as fortes interações, e també as propriedades fotofísicas (das Bases de Tröger propostas nesse trabalho), essas moléculas podem atuar como possíveis sondas biológicas. / In this work, docking and molecular dynamics simulations were used to ingestigate the interaction between a B-DNA oligonucleotide and two fluorescent Tröger´s bases, in order to verify their potential use as biological probes. For dockings was used protocol described by Ricci et. al. (2009), which proved to be a promising method to recognize the binding modes and describe the interaction between this class of compounds and the oligonucleotide. The complexes obtained from dockings were used as starting point for molecular dynamics simulations using GROMACS and the AMBER03 Force Field, as described by Ricci et. al. (2010). The analyzes of the simulation results showed the possibility that the Tröger Bases can interact in different ways with the oligonucleotide, with some preference for this receptor´s minor groove. During all simulations the ligands have maintained a strong interaction with the oligonucleotide, without causing denaturation of the same. Overall, the results suggest that Tröger´s Bases may interact with the minor groove of olinucleotide but are also able to interact as an intercalator, depending upon the substituents present. Due to the strong interactions, and also the peculiar photophysical properties, this class of molecules may act as a potential DNA probe.

As plantas medicinais são consideradas importantes fontes de compostos biologicamente ativos. Para muitas doenças crônicas, como as neurodegenerações, substâncias que apresentam atividades simultâneas em mais de um alvo relacionado à etiopatologia dessas desordens, constituem potenciais agentes terapêuticos. Nesse contexto, os objetivos deste trabalho foram a avaliação química e biológica de três espécies de samambaias de ocorrência no sul do Brasil: Blechnum binervatum, B. brasiliense e B. occidentale. O isolamento bioguiado foi utilizado para a identificação da(s) substância(s) com potencial atividade em modelos in vitro e in silico relacionados às desordens neurodegenerativas. A avaliação dos extratos e frações permitiu destacar a fração acetato de etila de B. brasiliense como a mais ativa na estabilização de radicais hidroxila (CI50: 12,5 μg/mL) e na inibição da lipoperoxidação (CI50: 10,4 μg/mL), sendo uma das mais ativas frente ao óxido nítrico (CI50: 55,6 μg/mL). Adicionalmente, na inibição da isoforma A da enzima monoamina oxidase (MAO), esta fração foi a que apresentou menor valor de CI50 (28,6 μg/mL). As frações diclorometano também apresentaram bons resultados na inibição da MAO-A, sendo algumas ativas igualmente como antioxidantes. Frente à MAO-B, os extratos e frações das três espécies vegetais demonstraram menores efeitos e foram inativos frente às enzimas acetil e butiril colinesterase, não demonstrando toxicidade em células polimorfonucleares (PMN) de ratos Wistar, na concentração de 1 mg/mL. Utilizando células-tronco cultivadas, os extratos e frações selecionadas, nas concentrações de 100 a 500 μg/mL, não afetaram a viabilidade celular e não apresentaram efeitos tóxicos. Análises químicas por cromatografia líquida de alta eficiência, acoplada a detector de arranjo de diodos e espectrometria de massas, permitiram a identificação de isômeros dos ácidos cafeoil quínico e cafeoil chiquímico nos extratos das três espécies estudadas. B. binervatum apresentou, ainda, ácido cafeico glicosilado, ácido isosalvianólico A e ácido rosmarínico sulfatado. Ácido salvianólico F foi identificado em B. binervatum e B. occidentale, bem como isômeros do ácido brainico. Ácido rosmarínico foi caracterizado em B. binervatum e B. brasiliense. Quercetina 3-O-glicosídeo e vicenina-2 também foram identificadas. As análises por cromatografia gasosa, acoplada à espectrometria de massas demonstraram que o diterpeno neofitadieno foi o composto majoritário nas frações diclorometano de Blechunm e nas frações hexano de B. occidentale e B. binervatum. Para a fração hexano de B. brasiliense, β-sitosterol foi o principal componente. A partir da fração acetato de etila de B. brasiliense foi isolado o ácido rosmarínico, o qual se mostrou ativo nos ensaios de atividade antioxidante, na inibição da catecol-O-metil transferase (CI50: 26,7 μM) e da MAO-A (CI50: 50,1 μM), sendo proposto mecanismo reversível de inibição desta enzima. Nos estudos de docking foram verificadas as interações moleculares entre o composto e as enzimas MAO-A e COMT, por ligações de hidrogênio e interações hidrofóbicas nos sítios ativos enzimáticos. O composto não apresentou efeitos tóxicos em células PMN de roedores, nas concentrações de 0,5 e 5 mM. Os ácidos rosmarínico e clorogênico isolados do extrato de B. binervatum não influenciaram na viabilidade celular e não induziram efeito tóxico sobre células-tronco (100 a 500 μM), sendo que o ácido rosmarínico foi capaz, ainda, de induzir proliferação celular. Capacidade protetora contra danos celulares causados por H2O2 (1400 μM) foi observada para ambas as substâncias, nas concentrações de 10-100 μM, sendo os resultados corroborados pelas imagens de microscopia celular. O ácido rosmarínico apresentou melhores respostas quando comparado ao ácido clorogênico, sendo mais efetivo na inibição dos danos por H2O2. O conjunto dos resultados obtidos ressalta a importância dos estudos associados químico-biológico de espécies vegetais e aponta para as potencialidades de samambaias como fontes de produtos bioativos, capazes de atuar sobre múltiplos alvos enzimáticos e não-enzimáticos relacionados a doenças neurodegenerativas. / Medicinal plants are considered important sources of biologically active compounds. For many chronic diseases, such as neurodegenerations, substances that present simultaneous activities in more than one target related to the etiopathology of these disorders are considered potential therapeutic agents. In this context, the aims of the study were the chemical and biological evaluation of three fern species, occurring in south Brazil: Blechnum binervatum, B. brasiliense and B. occidentale. The bioguided isolation was employed to identify compound(s) with potential activities at in vitro and in silico models associated to neurodegenerative disorders. The biological evaluation of extracts and fractions allowed to highlight the ethyl acetate fraction of B. brasiliense, which was the most active in the stabilization of hydroxyl radicals (IC50: 12.5 μg/mL) and on lipoperoxidation inhibition (IC50: 10.4 μg/mL), being one of the most active sample against nitric oxide (IC50: 55.6 μg/mL). Furthermore, on the inhibition of isoform A from monoamine oxidase (MAO), this fraction showed the lowest IC50 value (28.6 μg/mL). The dichloromethane fractions also presented good results in the MAO-A inhibition, being some of them active as antioxidants, too. Against MAO-B, extracts and fractions of the three species demonstrated reduced effects and all samples were inactive in the acetyl and butyryl cholinesterase inhibition, showing no toxic effects to polymorphonuclear cells (PMN) from Wistar rats, at 1 mg/mL. Using cultured stem cells, the selected extracts and fractions at 100 to 500 μg/mL did not affect cell viability and absence of cytotoxic effects was observed. The chemical analysis by high performance liquid chromatography, coupled to photodiode array detector and mass spectrometry, allowed the identification of caffeoyl quinic acid and caffeoyl shikimic acid isomers in the three studied fern species. B. binervatum presented also glycosilated caffeic acid, isosalvianolic acid A and sulphated rosmarinic acid. Salvianolic acid F was identified in B. binervatum and B. occidentale, as well as, brainic acid isomers. Rosmarinic acid was characterized in B. binervatum and B. brasiliense. Quercetin 3-O-glycoside and vicenin-2 were also found. Analysis by gas chromatography with mass spectrometry showed the diterpene neophytadiene was the major compound in dichloromethane fractions of Blechunm and in hexane fractions of B. occidentale and B. binervatum. For the hexane fraction from B. brasiliense, β-sitosterol was majority. From the ethyl acetate fraction of B. brasiliense was isolated rosmarinic acid, which was shown to be active in antioxidant assays, in the inhibition of catechol-O-methyltransferase (IC50: 26.7 μM) and MAO-A (IC50: 50.1 μM), being suggested a reversible inhibition mechanism against this enzyme. In docking studies were observed molecular interactions between the compound and MAO-A and COMT enzymes, via hydrogen bonds and hydrophobic interactions in enzyme active sites. The compound did not induce toxic effects to rodent PMN cells, at concentrations of 0.5 and 5 mM. The rosmarinic and chlorogenic acids, isolated from B. binervatum extract, did not influence cell viability and did not induce toxicity to stem cells (100 to 500 μM), the rosmarinic acid was also capable to induce cell proliferation. Protective ability against H2O2-induced cell damage (1400 μM) was observed for both substances at concentrations of 10-100 μM, and the results were supported by cellular microscopy images. Rosmarinic acid presented better responses compared with chlorogenic acid, being powerful inhibitor against H2O2-induced damage. The overall results highlights the importance of associated chemical-biological studies of plant species and points at the potential of ferns as sources of bioactive compounds, capable of modulating multiple enzymatic and non-enzymatic targets related to neurodegenerative diseases.

Neste trabalho foi realizado o estudo por docagem e simulação de dinâmica molecular de doze derivados benzazólicos fluorescentes por ESIPT, interagindo com o dodecâmero de Dickerson-Drew na forma B-DNA. Estes doze ligantes foram divididos em dois grupos (A e B), sendo o primeiro grupo composto por derivados do 2-(2’-hidroxifenil)-benzoxazol e o segundo grupo composto por três derivados do 2-(4’-amino-2’-hidroxifenil)-benzazóis, alternando entre N, S e O no anel azólico, mais três bases de Tröger derivadas dos mesmos. Na análise da docagem molecular do grupo A, os derivados com grupamento –NH2 no anel fenólico apresentaram energias de interação mais favoráveis com o DNA, verificando um favorecimento ainda maior, para os ligantes que continham –NO2 como substituinte no anel benzoxazólico. Na análise da docagem molecular para grupo B, as bases de Tröger (4ac) apresentaram interações significativamente mais favoráveis, quando comparados com seus respectivos precursores (3ac). Na análise da DM, tanto o grupo A, quanto o B, apresentaram a formação de complexos estáveis. O grupo A apresentou uma indução a alterações estruturais mínimas no DNA, sendo as maiores alterações a abertura do Rise quando os ligantes estavam intercalados, acompanhado pelo desenrolamento do parâmetro Twist. Nas interações de sulco menor, o ligante 2a foi o que formou o complexo mais estável com o DNA. Na análise da DM do grupo B, as bases de Tröger apresentaram uma preferência maior por interações do tipo intercalação que seus precursores, sendo os primeiros, os quais induziram o oligonucleotídeo a maiores alterações estruturais. Durante todas as simulações os ligantes mantiveram-se com uma forte interação com o oligonucleotídeo, sem causar a desnaturação do mesmo. Devido às interações estáveis, e também as propriedades fotofísicas peculiares dos ligantes estudados, esta classe de moléculas pode atuar como possíveis sondas biológicas. / In this work we carried out a study by docking and molecular dynamics simulations of twelve ESIPT-fluorescent benzazoles, interacting with the Dickerson-Drew dodecamer in the canonical B-DNA form. These twelve ligands were divided into two groups (A and B), with the first group consisting of derivatives of 2-(2’-hydroxphenyl)-benzoxazole and the second group consisting of three derivatives of 2-(4’-amino-2’-hydroxyphenyl)-benzazoles, alternating between N, S and O in the azole ring and three Tröger bases derived from them. In the analysis of the molecular docking of group A, the derivatives with group –NH2 in the phenolic ring presented more favorable interaction energies with the DNA, and the score was even more favorable for the ligands which contained –NO2 as substituent in the benzoxazolic ring. In the analysis of the molecular docking for group B, the Tröger bases (4ac) presented significantly more favorable interactions, when compared with their respective precursors (3ac). In the analysis of the DM, both groups A and B formed stable complexes. Group A induced only slight structural distortions in the DNA, being the largest modifications the increase of the Rise parameter when the ligands were intercalated, accompanied by the unwinding of Twist parameter. Regarding minor groove interactions, the ligand 2a formed the most stable complex with the DNA. In the analysis of the DM both groups A and B, the Tröger bases presented a greater preference for intercalation interactions than their precursors and the Tröger bases induced the largest structural changes to the oligonucleotide. During all the simulations the ligands maintained a strong interaction with the oligonucleotide, without causing the denaturation of the same. Due to the stable interactions, and also the peculiar photophysical properties of the ligands studied, this class of molecules can act as possible biological probes.

Made available in DSpace on 2014-06-11T19:27:20Z (GMT). No. of bitstreams: 0 Previous issue date: 2012-01-16Bitstream added on 2014-06-13T19:55:49Z : No. of bitstreams: 1 sabbag_mp_me_sjrp.pdf: 582990 bytes, checksum: a674199278bb87518fc43d93309aefd1 (MD5) / As infecções respiratórias agudas (IRAs) constituem a principal causa de mortalidade infantil no mundo, e o Vírus Respiratório Sincicial Humano (hRSV – Human Respiratory Syncytial Virus) é um dos principais agentes etiológicos das IRAs. Este vírus pertencente à família Paramyxoviridae, é envelopado, de simetria helicoidal, cujo genoma é RNA de fita simples não segmentada. A infectividade do vírus está relacionada com suas proteínas de membrana e dentre elas a glicoproteína G, que é responsável pela ligação do vírus à célula hospedeira e conseqüente instalação da infecção. Esta glicoproteína exerce um importante papel como antígeno de reconhecimento, sendo alvo para identificação do RSV através de anticorpos. Existem evidências de que esta proteína se liga a receptores glicosilados na célula hospedeira, porém ainda não foi descrito um receptor para a proteína G na célula. Para elucidar estes mecanismos de interação, foram realizados estudos experimentais e teóricos desta proteína. Os domínios solúveis da região N-terminal (1 a 38 aa) e C-terminal (67 a 298 aa), com 231 aminoácidos da glicoproteína G do hRSV foram clonados e a região N-terminal foi expressa em bactéria BL21 pLysS. Em paralelo, foi realizada a caracterização teórica desta proteína, e foram avaliados os possíveis sítios de interação da mesma com glicosaminoglicanos (heparina). Foram obtidos dois modelos teóricos para a proteína G do hRSV, bem como dois modelos de interação com heparina, determinando portanto, um possível sítio de ocorrência de interação. O conhecimento da estrutura da proteína G é de grande importância para elucidar a composição da estrutura e os mecanismos de interação com potenciais ligantes e deste modo, em um passo posterior, propor mecanismos de reconhecimento celular pelo hRSV, através de glicosaminoglicanos / Acute Respiratory Infections (ARI) are the leading cause of infant mortality in the world, and the Human Respiratory Syncytial Virus (hRSV) is one of the main agents of ARI. This virus belongs to Paramyxoviridae family, has a lipidic envelope, helical symmetry and its genome is a single-stranded RNA. The viral infectivity is related to its membrane proteins and among them the G glycoprotein, which is responsible for binding the virus to the host cell and consequent infection. This glycoprotein plays an important role as antigen recognition, being the target for hRSV identification through antibodies. There are evidences that this protein binds to host cell glycosylated receptors, but it has not been described a receptor for G protein in the cell yet. To elucidate these interaction mechanisms and understand the process of viral infectivity, we performed experimental and theoretical studies of this protein. The soluble domains of the N-terminal (1-38 aa) and C-terminal regions (67-298 aa), with 231 amino acids of the hRSV G glycoprotein have been cloned and the N-terminal region was expressed in BL21 pLysS bacteria. In a later trial these peptides will be purified and biophysical tests will be done. It was also performed a theoretical characterization of this protein, to assess the possible interaction sites with glycosaminoglycan (heparin). It were obtained two theoretical models for the hRSV G protein as well as two interaction models with heparin, in order to determine a possible site of occurrence of interaction. Knowledge of G protein structure is of great importance to elucidate the mechanism of viral infectivity and interaction mechanisms with potential ligants, and the results obtained in this work will allow us, in a later step, to propose mechanisms of cellular recognition by hRSV through glycosaminoglycans

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No. of bitstreams: 1 TeseNB.pdf: 25264059 bytes, checksum: f823e6e565d3555a5d49056afd7c39fe (MD5) Previous issue date: 2015-06-30 / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / In this work are presented the in silico study of the formation of complexes between organochalcogens compounds with enzymes COX-1 and COX-2 that were carried out in order to study their potential to act as selective inhibitors of COX-2 and thus as anti-inflammatories, as well as the results of in vitro and in vivo experiments of this activity. There were modeled and studied 15 organochalcogens compounds and their enantiomers, with a structure similar to that of the selective drug celecoxib. Compounds 2-(phenylseleno)-2-(2-ethyl-X)acetophenones-4’Y-substituted , with Y = H, Br, CH3, OCH3, NO2 and X = SO2, SO, S, were modeled using as starting point the crystallographic structure of the compound with Y = Br and X = SO. The three dimensional structures of the COX-1 and COX-2 enzymes were obtained from the PDB. The results of the molecular docking calculations were evaluated considering the patterns of orientations/conformations, intermolecular interactions, π interactions and scores. The results of these experiments allowed to propose a mechanism of action as well as a preferred bonding mode that would explain the activity of these compounds as possible inhibitors of COX-2, which is a condition necessary to act as anti-inflammatory. In particular, the compound where Y = OCH3 and X = SO2 (5-OCH3) being selective to COX-2 is the one with the best chances to act as an anti-inflammatory. This is because the OCH3 substituent occupied the S1 subsite of the enzyme, maintaining the interaction with His90 and the SO2 moiety interacts with the Tyr355, an important amino acid for the metabolism of the COX-2 substrate, the arachidonic acid. The other interactions made by the compound, such as π interactions, are important for fixing the ligand in the active site, although they are not directly related to its selectivity. The experiments in vitro and in vivo confirm the in silico results, as the enzyme immunoassay showed that this compound exhibits greater inhibition of COX-2 relative to COX-1. Furthermore, the activity of the 5-OCH3 compound was evaluated with the classical models of edema formation, that is the carrageenan and zymosan induced inflammation in the rat paw, resulting in a significant reduction in paw thickness after two hours and decreasing of the temperature after one hour of the application of the anti-inflammatory agent. As the best results were obtained for the model of paw edema elicited by carrageenan this suggests that the compound acts better in the case of acute inflammation. / Neste trabalho são apresentados o estudo in silico da formação de complexos entre compostos organocalcogênios e as enzimas COX-1 e COX-2 realizado com o objetivo de estudar seu potencial para atuar como inibidores seletivos da COX-2, e portanto como anti-inflamatórios, bem como os resultados dos experimentos in vitro e in vivo desta atividade. Na presente pesquisa, foram modelados e estudados 15 compostos organocalcogênios e seus enantiômeros, com estrutura similar à do fármaco seletivo celecoxibe. Os compostos da família 2-(fenilseleno)-2-(etil-X)acetofenonas-4’Y-substituídas, com Y = H, Br, CH3, OCH3, NO2 e X = SO2, SO, S, foram modelados tendo como ponto de partida a estrutura cristalográfica do composto da mesma família com Y = Br e X= SO. As estruturas tridimensionais das enzimas COX-1 e COX-2 foram obtidas no PDB. Os resultados dos cálculos de docking molecular foram avaliados considerando-se o padrão de orientações/conformações, as interações intermoleculares, as interações π e os escores. OS resultados desses experimentos permitiram propor um mecanismo de ação, bem como um modo de ligação preferencial para explicar a atuação desses compostos como possíveis inibidores da COX-2, condição necessária para atuar como anti-inflamatório. Em particular, o composto com Y = OCH3 e X = SO2 (5-OCH3) é o que apresentou o melhor potencial para atuar como anti-inflamatório, sendo seletivo à COX-2. Isto porque o substituinte OCH3 ocupou o subsítio S1 dessa enzima, mantendo a interação com a His90 e o grupo SO2, apresentou interação com a Tyr355, aminoácido importante para o metabolismo do substrato da COX-2, o ácido araquidônico. As outras interações feitas pelo composto, como as interações π, são importantes para fixação do ligante ao sítio ativo, embora não estejam diretamente ligadas com a sua seletividade. Os experimentos in vitro e in vivo permitiram confirmar os resultados dos experimentos in silico, uma vez que o ensaio imunoenzimático mostrou que este composto apresenta maior inibição da COX-2 em relação à COX-1. Ainda, a atividade do composto 5-OCH3 foi avaliada em modelo de edema de pata induzido por carragenina e zymosan, como agentes irritantes, resultando em uma diminuição significativa da espessura das patas após duas horas e diminuição da temperatura após uma hora da aplicação do agente anti-inflamatório. Uma vez que os melhores resultados foram obtidos para o modelo do edema de pata com a carragenina isto sugere o composto atua melhor no caso da inflamação aguda.