The significance of fungal infections has been grossly underestimated. Only a few drugs are clinically available to treat life-threatening fungal infections, and resistance against these drugs is rising. Antifungal peptides (AFPs) are being actively explored as novel pharmaceuticals. PAF26 is a de novo designed hexapeptide possessing N-terminal cationic and C-terminal hydrophobic regions. Previously the roles of each of these motifs in the antifungal mode-of-action of PAF26 have indicated that it involves three stages: interaction with the plasma membrane, internalisation, and cell killing. The overall aim of my project was to obtain further insights into its mode-of-action and develop more active antifungal derivatives of PAF26. Three experimental fungal systems were used in this study: the model Neurospora crassa, the human pathogen Aspergillus fumigatus and the plant/human pathogen Fusarium oxysporum. The first objective of the study was to evaluate the impact of different fluorescent labels on the intracellular localisation and antifungal properties of PAF26. For this purpose a library of PAF26 labelled with 13 different fluorophores was synthesised. This library contained PAF26 conjugates of broad chemical and spectral diversity. These fluorescent PAF26 conjugates were analysed by live-cell imaging and tested for their antifungal activities. The different fluorescent labels were found to have significant impacts both on intracellular localisation and antifungal activities. TMR, carboxyfluorescein, NBD and DMN were found to be the best labels for live-cell imaging because they had the least influence on the intracellular localisation and antifungal activity of PAF26. The second objective was to identify target proteins of PAF26 in N. crassa cells. A large number of proteins were identified as binding to PAF26 from a protein pull-down and mass spectroscopy analysis using TMR- and fluorescein-labelled PAF26. One of these proteins was the highly abundant plasma membrane ATPase PMA-1. An in-silico analysis showed that PMA-1 is likely to be a major target protein of PAF26. The final objective was to develop novel antifungals based on PAF26 with improved activities and stability. Novel cyclic derivatives of PAF26 were designed in-silico against PMA-1. These peptides were synthesised and tested against N. crassa, A. fumigatus and F. oxysporum and were found to have higher activities (at the sub-micromolar level) and greater stability than the linear PAF26. Overall this study has provided novel mechanistic insights into the mode-of-action of PAF26 and discovered novel highly active antifungal peptides with clinical potential as therapeutics.

Thesis advisor: Larry W. McLaughlin / Nucleic acids are fundamental biomolecules responsible for all activities of a living cell. DNA serves as an instruction manual to the cell, containing blueprints and directions for all cellular processes, while RNA serves to carry out the messages held within DNA. Research into the structure, stability, and function of nucleic acids has revealed much about the origin and evolution of life. The ultimate goal of this work is to understand how molecules bind and associate within the minor groove of double stranded, helical DNA. A series of 2'-deoxyadenosine analogues are modified at the three position by replacing the N3-nitrogen with carbon. Substitution at this position is designed to emulate the effects of removing hydrogen bond acceptors, introducing steric bulk, and tethering functional groups of interest into the minor groove. These functional groups mimic small molecules that have been shown to bind within the minor groove of A-T rich sequences as well as serve as a platform for further substitution by fluorescent tags. The synthetic effort needed to obtain purine nucleosides containing each of these modifications was non-trivial. New methodologies unveiled directing and protecting strategies towards the desired isomer of these modified nucleosides in higher yields than those previously deemed acceptable. Application of these modified nucleosides into duplex DNA reveals thermodynamic parameters for how small molecules bind to the minor groove and the effects of introducing biomarkers into an unprecedented region of DNA. / Thesis (PhD) — Boston College, 2011. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

The cytoskeleton is a diverse, multi-protein framework that plays a fundamental role in many cellular activities including mitosis, cell division, intracellular transport, cell motility, muscle contraction, and the regulation of cell polarity and organization. Furthermore, cytoskeletal filaments have been implicated in the pathogenesis of a wide variety of diseases including cancer, blood disease, cardiovascular disease, inflammatory disease, neurodegenerative disease, and problems with skin, nail, cornea, hair, liver and colon. Increasing evidence suggests that the distribution and organization of the cytoskeleton in living cells are affected by mechanical stresses and the cytoskeleton determines cell stiffness. We developed a fully nonlinear, constrained mixture model for adherent cells that allows one to account separately for the contributions of the primary structural constituents of the cytoskeleton and extended a prior solution from the finite elasticity literature for use in a sub-class of atomic force microscopy (AFM) studies of cell mechanics. The model showed that the degree of substrate stretch and the geometry of the AFM tip dramatically affect the measured cell stiffness. Consistent with previous studies, the model showed that disruption of the actin filaments can reduce the stiffness substantially, whereas there can be little contribution to the overall cell stiffness by the microtubules or intermediate filaments. To investigate the effect of mechanical stretching on cytoskeletal remodeling and cell stiffness, we developed a simple cell-stretching device that can be combined with an AFM and confocal microscopy. Results demonstrate that cyclic stretching significantly and rapidly alters both cell stiffness and focal adhesion associated vinculin and paxillin, suggesting that focal adhesion remodeling plays a critical role in cell stiffness by recruiting and anchoring F-actin. Finally, we estimated cytoskeletal remodeling by synthesizing data on stretch-induced dynamic changes in cell stiffness and focal adhesion area using constrained mixture approach. Results suggest that the acute increase in stiffness in response to an increased cyclic stretch was probably due to an increased stretch of the original filaments whereas the subsequent decrease back towards normalcy was consistent with a replacement of the highly stretched original filaments with less stretched new filaments.

The cytoskeleton is a diverse, multi-protein framework that plays a fundamental role in many cellular activities including mitosis, cell division, intracellular transport, cell motility, muscle contraction, and the regulation of cell polarity and organization. Furthermore, cytoskeletal filaments have been implicated in the pathogenesis of a wide variety of diseases including cancer, blood disease, cardiovascular disease, inflammatory disease, neurodegenerative disease, and problems with skin, nail, cornea, hair, liver and colon. Increasing evidence suggests that the distribution and organization of the cytoskeleton in living cells are affected by mechanical stresses and the cytoskeleton determines cell stiffness. We developed a fully nonlinear, constrained mixture model for adherent cells that allows one to account separately for the contributions of the primary structural constituents of the cytoskeleton and extended a prior solution from the finite elasticity literature for use in a sub-class of atomic force microscopy (AFM) studies of cell mechanics. The model showed that the degree of substrate stretch and the geometry of the AFM tip dramatically affect the measured cell stiffness. Consistent with previous studies, the model showed that disruption of the actin filaments can reduce the stiffness substantially, whereas there can be little contribution to the overall cell stiffness by the microtubules or intermediate filaments. To investigate the effect of mechanical stretching on cytoskeletal remodeling and cell stiffness, we developed a simple cell-stretching device that can be combined with an AFM and confocal microscopy. Results demonstrate that cyclic stretching significantly and rapidly alters both cell stiffness and focal adhesion associated vinculin and paxillin, suggesting that focal adhesion remodeling plays a critical role in cell stiffness by recruiting and anchoring F-actin. Finally, we estimated cytoskeletal remodeling by synthesizing data on stretch-induced dynamic changes in cell stiffness and focal adhesion area using constrained mixture approach. Results suggest that the acute increase in stiffness in response to an increased cyclic stretch was probably due to an increased stretch of the original filaments whereas the subsequent decrease back towards normalcy was consistent with a replacement of the highly stretched original filaments with less stretched new filaments.

The synthesis of proteins bearing unnatural amino acids has the potential to enhance and elucidate many processes in biochemistry and molecular biology. There are two primary methods for site specific unnatural amino acid incorporation, both of which use the cell’s native protein translating machinery: in vitro chemical acylation of suppressor tRNAs and the use of orthogonal amino acyl tRNA synthetases. Total chemical synthesis is theoretically possible, but current methods severely limit the maximum size of the product protein. In vivo orthogonal synthetase methods suffer from the high cost of the unnatural amino acid. In this thesis I sought to address this limitation by increasing cell density, first in shake flasks and then in a bioreactor in order to increase the yield of protein per amount of unnatural amino acid used. In a parallel project, I used the in vitro chemical acylation system to incorporate several unnatural amino acids, key among them the fluorophore BODIPYFL, with the aim of producing site specifically fluorescently labeled protein for single molecule FRET studies. I demonstrated successful incorporation of these amino acids into the trial protein GFP, although incorporation was not demonstrated in the final target, FEN1. This also served to confirm the effectiveness of a new procedure developed for chemical acylation.

Des composés de type 3-arylpyrroles appelés pyakols ont montré une activité antimitotique sur des cellules tumorales murines, avec en particulier un effet sur les microtubules. Ce type d’activité biologique présentant un intérêt important en cancérologie, le travail présenté dans ce manuscrit est consacré à l’étude de ces hétérocycles. La première partie a pour objectif de développer une stratégie de synthèse permettant d’accéder efficacement au composé chef de file (pyakol I), basée sur la cyclisation d’intermédiaires α-amino-ynols catalysée par des complexes d’or. L’évaluation de l’activité biologique du pyakol I sur le cycle cellulaire et le cytosquelette de diverses lignées tumorales humaines a été réalisée. Les premiers résultats ont révélé une action originale du pyakol I sur le cytosquelette, provoquant une désorganisation du réseau de microtubules et un défaut de positionnement du fuseau mitotique. La séquence réactionnelle a ensuite été validée en l’appliquant pour la réalisation de modulations autour du motif 3-arylpyrrole ainsi que pour l’obtention de molécules marquées. La deuxième partie concerne un travail de méthodologie basée sur la réaction de cyclisation à l’or pour la synthèse de nouveaux pyrroles trifluorométhylés polysubstitués. La stratégie utilisant le trifluoroacétaldéhyde comme substrat de départ permet d’accéder à divers 3-trifluorométhylpyrroles avec de bons rendements, dans des conditions douces. / A family of 3-arylpyrroles named pyakols have shown antimitotic properties on murine cell lines, displaying in particular an effect on microtubules. Given the interest of these properties in cancerology, this work is focused on these heterocycles. The objective of the first part was to develop a synthetic strategy based on the gold-catalysed cyclisation of α-amino-ynols intermediates in order to access the lead (Pyakol I). Then, the evaluation of the biological activity of this molecule on the cell cycle and on the cytoskeleton of various human tumoral cell lines was carried out. The first results revealed an original effect on the organization of the microtubules network and the positioning of the mitotic spindle. The developed strategy was then validated by modulating the 3-arylpyrrole moiety on diverse positions, and used for the synthesis of labelled derivatives. The second part of this manuscript focused on the development of a methodology to synthesize new polysubstituted 3-trifluoromethylpyrroles, based on the gold-catalyzed cyclisation reaction. Using trifluoroacetaldehyde as building-block, various trifluoromethylated pyrroles were obtained in mild conditions with good yields.

Le développement de nanomédicaments pour l'imagerie et le traitement du cancer a suscité un intérêt croissant à cause de leur grand potentiel. En particulier les vecteurs à base de polymères et de micelles polymères sont très intéressants, car ils peuvent être conçus avec des fonctionnalités adaptées aux besoins.Nous avons utilisé des copolymères amphiphiles triséquencés pour développer de nouveaux nanovecteurs moléculaires (unimères) et supramoléculaires (micelles stabilisées par photo- réticulation). Nous les avons fonctionnalisés avec un marqueur fluorescent ou radioactif pour permettre leur imagerie in vitro et in vivo. Les interactions in vitro et in vivo ont été étudiées pour comprendre l'influence des propriétés des copolymères sur les interactions biologiques.Cette thèse présente le développement complet de nanovecteurs depuis les premières étapes de la caractérisation physico-chimique fondamentale jusqu'à l'évaluation de leur intérêt pour différentes applications cliniques. / The interest in developing new nanocarriers for imaging and therapy of cancer has been growing due to their high potential. Particularly nanocarriers based on polymers and polymeric micelles are very interesting because they can be tailor-made with certain functionalities to meet our needs.We have used amphiphilic triblock copolymers to develop new molecular (unimers) and supramolecular (micelles stabilized by photo cross-linking) nanocarriers. The carriers were then functionalized with fluorescent or radioactive markers to enable their in vitro and in vivo imaging. The in vitro and in vivo interactions were then studied to understand the influence of the copolymers properties on the biological interactions.This thesis presents the complete development of the nanocarriers from the early stages of fundamental physicochemical characterization up to the evaluation of their interest for different clinical applications

Fluorescent labeling is a method used for visualization of various types of biomolecules including proteins and protein complexes. However, the effect of protein labeling on protein structure and functions has not been investigated so far. The goal of the diploma thesis was to examine an influence of NHS-fluorescein binding on structure and function of human carbonic anhydrase I (hCA-I). The particular aims of this work were to prepare recombinant 15N-hCA-I which was used for NMR structure analysis of carbonic anhydrase upon fluorescent labeling. Furthermore, enzyme activity was measured in order to find out a correlation between the concentration of NHS- fluorescein and protein function. In addition, the reaction mixtures were systematically analyzed by ESI FT-ICR mass spectrometry. The analysis revealed experimental conditions for fluorescent labeling of human carbonic anhydrase I with minimal effect on protein structure and function. The results of this study show that the calculation of molar excess of NHS-fluorescein cannot rely on a simple procedure provided by manufacturer. However, due to decrease of enzyme activity upon fluorescent labeling, it is better to take into count the influence of NHS-fluorescein concentration on the relative enzymatic activity. Moreover, the calculation of molar...

Mouse NK cell receptors belonging to NKR-P1 family plays role in activation, inhibition and cytokine secretion by these cells. Aim of this thesis is preparation of extracellular parts of C57BL/6 mouse strain activating receptors mNKR-P1A and mNKR-P1C. Production vectors with coding sequences of both proteins were prepared. Next, optimization of production in E. coli was done and appropriate in vitro refolding and purification protocol were developed. Purified proteins were characterized by mass spectrometry and labeled by a fluorescent dye. Primary screening for potential ligand was performed. Further work will involve structural characterization of the receptors and identification of their ligands. These data may help to clarify the function of NK cells.

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