The rapid increase of multi-drug resistant bacteria and associated deaths has stimulated research into the development of novel therapeutic options. Antimicrobial peptides (AMPs) display a high therapeutic potential in solving this problem. Research focuses on new ways to enhance the antibacterial activity of AMPs and this includes the amidation of the C-terminus. Once the structure of an AMP is altered it is altered it is necessary to revaluate the properties of this AMP compared to the unaltered peptide. In this study, a peptide fragment Os(3-12), based on a defensin from the tick Ornithodoros savignyi, was amidated at the C-terminus. The effect of C-terminal amidation on the structural, antibacterial, cytotoxic and antioxidant activities of Os(3-12)NH2 was investigated and compared to Os(3-12) as well as the parent peptide Os. Mode of action related to membrane permeabilization was evaluated. The effect of serum and on the antibacterial activity of Os(3-12)NH2 was also determined. Circular dichroism experiments indicated Os(3-12) and Os(3-12)NH2 to be unstructured in sodium dodecyl sulphate micelles and 50% trifluoroethanol, unlike Os which was predominantly α-helical. Although still less potent than Os, the determined minimum bactericidal concentration (MBC) for each peptide indicated that amidation increases the bactericidal activity of Os(3-12) by 16-fold against Escherichia coli and by 8-fold against both Pseudomonas aeruginosa and Bacillus subtilis. In comparison amidation enhanced the activity of the peptide towards Staphylococus aureus by only 2-fold. The kinetics of bactericidal activity revealed that Os(3-12)NH2 killed E. coli within 10 minutes and B subtilis within 60 minutes. SYTOX green was applied to evaluate the effects of the peptides on the membrane integrity of the bacterial cells. LL-37, a peptide known to disrupt microbial membranes, induced membrane permeabilization of both E. coli and S. aureus membranes. Both Os and Os(3-12)NH2 were found to also cause membrane permeabilization of these bacteria, albeit not to the same extent as LL-37, thus suggesting possible internal targets subsequent to membrane permeabilization. In the presence of 30% human serum and a physiological salt mixture comprising of 145 mM NaCl, 2.5 mM CaCl2 and 1 mM MgCl2 the bactericidal activity of Os(3-12)NH2 was lost. The amidated peptide was found to be non-toxic towards human erythrocytes and Caco-2 cells. Os(3-12)NH2 showed strong antioxidant activity and was found to be 15-fold more active than glutathione (GSH), a known antioxidant. In conclusion Os(3-12)NH2 has been identified as a multifunctional AMP that is nontoxic to mammalian cells. However the therapeutic potential of Os(3-12)NH2 may be restricted to topical applications due to the peptide’s inactivity under physiological conditions. Although Os(3-12)NH2 causes membrane permeabilization, indications are that there are additional intracellular targets that need to be identified. / Dissertation (MSc)--University of Pretoria, 2016. / Biochemistry / Unrestricted

La rhéologie et la photonique de divers systèmes biologiques complexes allant des protéines jusqu'aux bactéries et cellules ont été étudiées dans cette thèse. Ces travaux se basent sur deux grands thèmes, où le premier traite la modification des surfaces solides avec des molécules biologiques tandis que le second se concentre sur l'étude des effets des différentes drogues sur des cellules malignes, et non malignes par des techniques microscopiques complémentaires. Dans ce travail, des matrices orientées de films de polyélectrolytes/membrane pourpre ont été produites et étudiées en fonction de différentes conditions physico-chimiques. Des peptides spécifiques présentant de propriétés de reconnaissance de surface pour le ZnSe et le Si ont été isolées par la technologie de Phage Display. Le peptide de Si a été utilisé dans la détection des molécules avec une microcavité de silicium poreux, et ceci a montré un meilleur seuil de détection comparé à celui des autres méthodes classiques de fonctionnalisation. Le peptide spécifique de ZnSe a été utilisé afin de démontrer son utilité pour la préservation de l'activité et structure secondaire native des biomolécules adsorbées. Concernant les cellules, une différence de réponse, entre deux types de cellules épithéliales mammaires malignes MCF-7 et non-malignes HMEC184A1, sous traitement avec la curcumine, a été démontrée sur les cellules vivantes et fixées. Après, une évaluation des forces d'interaction entre un agent clinique anticancéreux cetuximab (CET) et EGFR (Epidermal Growth Factor Receptor) sur la surface des cellules de carcinome épithéliales A431 a été réalisé via la microscopie à force atomique en mode force. Une différence sur l'élasticité des cellules et sur les forces de liaison EGFR-CET a été notée quand le CET a été combiné avec d'autres drogues thérapeutiques. Les résultats de nos études d'imagerie fonctionnelle pourraient ouvrir de nouvelles voies dans la recherche de traitements contre le cancer. / The rheology and photonics of various complex biological systems ranging from proteins to bacteria and cells have been studied in this thesis. The work is organized around two major themes where the first one deals with surface modifications for adsorption of biological molecules while the second one focuses on comparative studies of non-malignant and cancerous cells under the effect of various drugs, using complementary microscopic techniques. In this work, oriented polyelectrolyte/purple membrane matrices have been produced and studied under different physico-chemical conditions. Peptides with surface recognition properties for the ZnSe and Si semiconductors have been isolated by Phage Display technology. The Si specific peptide has been used in detection of molecules with a porous silicon microcavity, providing a considerably enhanced detection resolution compared to traditional functionalization methods. The specific peptide of ZnSe has been used to demonstrate its utility in preservation of activity and native secondary structure of biomolecules in their adsorbed form. In the second part of my work concerning the cells, a different response (in morphology and elasticity) under treatment with curcumin, for two types of malignant MCF-7 and non-malignant HMEC184A1 mammary epithelial cells was demonstrated on living and fixed cells. Then, an evaluation of binding interactions between a clinical anticancer agent Cetuximab (CET) and the Epidermal Growth Factor Receptor (EGFR) on the surface of epithelial carcinoma A431 cells was performed via force mode atomic force microscopy. A difference was noted on the elasticity of cells and also on the EGFR-CET binding forces when CET was combined with other therapeutic drugs. The results of our functional imaging studies might open new avenues in the research for treatments against cancer.

La glycoxydation est un processus délétère directement impliqué dans la pathologie diabétique. Ce phénomène touche principalement les protéines circulantes. Une des cibles majoritaires de ce phénomène est l'albumine, protéine plasmatique la plus abondante. L'objectif de ce travail de thèse vise une meilleure compréhension du phénomène de glycoxydation dans le diabète. Pour cela, les conséquences fonctionnelles et physiologiques liées aux altérations structurales et biochimiques de l'albumine glyquée ont été étudiées, à travers la comparaison d'un modèle d'albumine glyquée in vivo purifiée de patients diabétiques avec celui correspondant à la protéine glyquée par un processus in vitro. Notre étude montre des modifications de type structural et oxydatif attestées par des mesures de fluorescence (accessibilité du tryptophane) et de groupements spécifiques comme les fructosamines, les amines primaires, résidus thiols et carbonyles. D'un point de vue fonctionnel, l'albumine glyquée purifiée de patients diabétiques exerce, sur des cultures cellulaire, un effet proinflammatoire et prooxydant, encore plus marqué que ne le fait l'albumine glyquée in vitro. Également, les capacités de liaison de l'albumine avec les médicaments ainsi que l'activité estérase diminuent avec le phénomène de glycation. Les résultats de cette étude apportent de nouveaux éléments de compréhension sur le phénomène de glycation de l'albumine tel qui pourrait apparaitre dans la pathologie diabétique et ouvre de nouvelles pistes d'études sur l'impact réel des AGEs issus de l'albumine dans des désordres physiologiques inhérents à cette pathologie. / Albumin constitutes the major circulating protein in blood and represents a very beneficial biological actor through its multifunctional properties such as antioxidant activities and drug binding capacities. But, in hyperglycemic conditions, such as those encountered in diabetes, albumin can undergo glycoxidative modifications which may impact the protein quality. Objectives of my thesis were to clarify the impact of glycoxidative modification of albumin on its structure and its functions and to determine whether such impairments may be encountered in albumin purified from diabetics. The occurrence of structural and oxidative modifications were found to be enhanced in in vitro glycoxidized HSA and albumin purified from diabetics, after determination of their free thiol group content, relative electrophoretic migration, carbonyl content, fructosamines and antioxidant activities. In addition, glycoxidized albumins exhibited impaired pharmaceutic molecule binding capacities and reduced esterase activities. Also, cells treated with glycoxidized albumin purified from diabetics, exhibited a proinflammatory state even more exacerbated than those incubated with in vitro glycated albumins. We evidenced the triggering action of metals (copper and iron) on glycoxidative-induced modifications in albumin. This work needs further studies and opens doors to many perspectives aiming to reach a better understanding of glycoxidative modification of albumin in diabetic patients.

Made available in DSpace on 2017-07-24T19:38:06Z (GMT). No. of bitstreams: 1 Cibeli May Villalba.pdf: 4939252 bytes, checksum: 5a6b5eaea0352844ad9868a7a9b79f0b (MD5) Previous issue date: 2012-03-13 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Proteins are the most abundant biomolecules in living organisms; they are present in all parts of a cell. They have different functions; their structural study is important because it brings greater insight into its functions and allows us to understand how they interact to each other and with the other molecules. Protein structures can be studied experimentally especially by the X-ray diffraction technique and computationally by homology modeling. Thus, in this work, structural studies were made with the alpha-amylase inhibitor from rye (Secale cereale), which inhibits the activity of amylase and then can be used in the treatment of Diabetes mellitus, obesity, pest control, amongst other applications. Through chromatographies, two different inhibitors could be separated, namely A2 and B2, which were crystallized, but did not show a minimum X-ray diffraction quality. Thus, a structural study was performed with data from a twinned crystal previously obtained, yet current refinement programs can now deal with such data. The structure was refined and compared with the alpha-amylase inhibitor 0.19 from wheat. Then, structural studies were also performed for the YchF GTPase and enolase from Trypanosoma cruzi; both have been studied with the possibility of being used as a target in the treatment of Chagas' disease. Initially, trials to express heterologously and to purify them for crystallization trials were performed; yet those were unsuccessful, a computational work was pursued, in which alignments and homology modelling for both proteins were made. The computational work was continued for Trypanosoma cruzi enolase,in which comparisons with the Homo sapiens enolase to seek and plan inhibitors for the former, through literature and data bank searches, were made; thus, docking of these was performed, which pointed more favorable binding energies for the substrates, phosphoenolpyruvate (PEP) and 2-phosphoglycerate (PG2), for the inhibitor phosphonacetohydroxamate (PAH) and for the compound coded ZINC25695689 from the ZINC (ZINC Is Not Commercial) data bank. Also, from the experimental position of the PAH inhibitor (deposited in the PDB, code 2PTZ), the interaction energies for these searched and planned molecules were estimated,through the AMBER molecular dynamics program, and, apparently, the presence of a chlorine atom conveniently bound to the inhibitor could promote an improvement of the interaction energy. / As proteínas são as biomoléculas mais abundantes nos seres vivos, estando presentes em todas as partes de uma célula. Elas possuem diferentes funções no organismo; seu estudo estrutural é importante, pois traz maior conhecimento sobre suas funções e possibilita entender como interagem entre elas e com outras moléculas. A estrutura de proteínas pode ser estudada experimentalmente principalmente por meio da técnica de difração de raios X e computacionalmente por meio da modelagem por homologia. Sendo assim, realizaram-se neste trabalho estudos estruturais com o inibidor de alfa-amilase do centeio (Secale cereale), que inibem a atividade amilásica e que podem ser utilizados em tratamento de Diabetes mellitus, obesidade, controle de pragas, entre outros usos. Por meio de cromatografias, puderam-se separar dois diferentes inibidores, denominados A2 e B2, que foram cristalizados, mas não apresentaram mínima qualidade de difração de raios X. Assim, realizou-se um estudo estrutural com dados de difração obtidos anteriormente para um cristal geminado, dada a possibilidade atual dos programas de refinamento de tratarem este problema. A estrutura foi refinada e comparada com o inibidor de alfa-amilase 0,19 do trigo. Em sequência, estudos estruturais também foram realizados para a proteína YchF da família das GTPases e para a enolase de Trypanosoma cruzi; ambas vêm sendo estudadas com a possibilidade de serem usadas como alvo no tratamento da doença de Chagas. Inicialmente tentou-se expressá-las de maneira heteróloga e purificá-las para a realização de ensaios de cristalização; com o insucesso disto, partiu-se para um trabalho computacional em que se fizeram alinhamentos e modelos por homologia para as duas proteínas. O trabalho computacional foi continuado para a enolase de Trypanosoma cruzi, comparando-a com a enolase de Homo sapiens para se buscar e planejar inibidores para a primeira, por meio de pesquisa na literatura e em bancos de dados; assim, fez-se a alocação ("docking") destes, obtendo-se energias de ligação mais favoráveis para os substratos, fosfoenolpiruvato (PEP) e 2-fosfoglicerato (PG2), para o inibidor fosfonacetohidroxamato (PAH) e para o composto codificado ZINC25695689 do banco de dados ZINC (ZINC Is Not Commercial). Também, a partir da posição experimental do inibidor PAH (depositada no PDB, código 2PTZ) estimaram-se as energias de interação para as moléculas pesquisadas e planejadas, através do programa de dinâmica molecular AMBER e, aparentemente, a presença de um átomo de cloro convenientemente ligado ao inibidor poderia promover melhoria da energia de interação.

Die Systematische Toxikologische Analyse (STA) stellt auf Grund der großen Vielfalt und der ständigen Zunahme an toxikologisch relevanten Substanzen eine der größten Herausforderungen in der chemischen Analyse dar. In der vorliegenden Arbeit wurde daher die Eignung der Flüssigchromatographie in Kombination mit der Hybrid-Quadrupol-Flugzeitmassenspektrometrie (LC-QTOF-MS) für diesen Zweck untersucht. Dazu wurden eine Datenbank mit über 7360 und eine CID-Spektrenbibliothek mit mehr als 2720 toxikologisch relevanten Substanzen erstellt und geeignete Probenvorbereitungsmethoden entwickelt. Die Erprobung der Methoden erfolgte an dotierten Blut- und Haarproben. Hierbei zeigte sich, dass die Analyse im Auto-MS/MS-Modus (Messzyklen von MS- und MS/MS-Spektren) eine Identifizierung basischer Substanzen mittels CID-Spektren zwischen 0,5 und 2 ng/ml im Blut ermöglichte. Die Nachweisgrenzen der für 24 Wirkstoffe validierten Methode in Haaren lagen bei 3 bis 15 pg/mg. Die Eignung der LC-QTOF-MS zur STA von Haarproben wurde an 30 Drogentodesfällen und 60 Todesfällen mit bekannter chronischer Medikamenteneinnahme zu Lebzeiten sowie an 77 Blutproben nachgewiesen. Für die Suche nach Metaboliten wurde ein Metaboliten-Tool entwickelt. In der praktischen Anwendung auf Datenfiles von Blut- und Haarproben erwies sich das Tool als wertvolles Hilfsmittel zur Identifizierung unbekannter Peaks und zur Bestätigung von Suchergebnissen in der Datenbank. Zur automatischen Konzentrationsabschätzung identifizierter Substanzen wurde ein Tool „Estimate Concentration“ geschaffen. Die Überprüfung des Verfahrens an realen Blut- und Haarproben durch Vergleich mit HPLC-DAD- und GC-MS-Ergebnissen wies eine gute Übereinstimmung der Konzentrationen auf. Insgesamt zeigten die Untersuchungen, dass die LC-QTOF-MS zurzeit die am besten geeignete Methode für die STA darstellt. Auch bei einem erst später aufkommenden Verdacht kann eine gezielte Suche in dem bereits gemessenen Datenfile durchgeführt werden. / Due to the large variety and the steady increase of toxicologically relevant substances, systematic toxicological analysis (STA) is one of the most difficult tasks in analytical chemistry and, therefore, a steady topic of research and methodical improvement. For this reason, the suitability of liquid chromatography in combination with hybrid quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) for STA was investigated. For this purpose, a database of more than 7360 and a CID spectra library of more than 2720 toxicologically relevant substances and suitable methods for sample preparation were developed. The application was evaluated at spiked blood and hair samples. It was found that the analysis in Auto-MS/MS mode (alternating measurement cycles of MS and MS/MS spectra) allowed substance identification in blood using CID spectra between 0.5 and 2 ng/ml for basic substances. The detection limits of the validated method in hair ranged from 3 to 15 pg/mg for 24 drugs. The suitability of LC-QTOF-MS for STA was tested for hair samples from 30 drug-related death cases and from 60 death cases with known chronic medication as well as for 77 blood samples. For the search of metabolites, a metabolite tool was developed. In the practical application to data files from blood and hair samples, the tool proved to be very helpful for identification of unknown peaks and for confirmation of results obtained only from the database without CID spectra. A tool "Estimate Concentration" was created for automatic estimation of concentrations of identified substances. The application to real blood and hair samples and the comparison of the concentrations with results from HPLC-DAD and GC-MS showed good agreement. Overall, these investigations showed that LC-QTOF-MS is currently the most favorable method for STA. Because of the comprehensive registration of all substances in a sample, the data files can be checked for the presence of certain poisons even later without new measurements.