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No description available.

Matrix Metalloproteinase-13 (MMP-13) belongs to a large family of proteolytic enzymes which are characterized by their ability to degrade the extracellular matrix components. MMP-13 appears to have a critical role in tumor invasion and metastasis. In this study, several fluorogenic probes specific for MMP-13 were designed and characterized. These synthesized probes could be modified with chelators to be applied for imaging MMP-13 in breast cancer and/or multiple myeloma models. The activity and selectivity of MMP-13 and other MMPs against these probes were studied through two approaches. It was found that these probes were cleaved by all MMPs, but MMP-13 showed the highest activity and selectivity towards these peptides. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2020. / FAU Electronic Theses and Dissertations Collection

Chemical labeling is an important tool for understanding protein structure and function. Biological research often requires the use of molecular labels that are covalently attached to facilitate detection or purification of the labeled protein and its binding partners. Although the number of probes have been developed for labeling of specific residues of proteins is substantial, there is still a need for new reagents with better reactivity, and selectivity. Moreover, these chemical probes should be able to label the protein of interest under mild biologically relevant conditions. Aryl diazonium salts have been utilized for selective modification of tyrosine residues. However, most diazonium compounds need to be generated in situ under strongly acidic conditions due to their instability1. Our group has previously shown that triazabutadienes can be used as precursors that can generate diazonium under mild acidification2 or photo-irradiation3. Current reported systems for bioconjugation of tyrosine require an additional step for fluorescent labeling4. To address this issue and reduce background fluorescence that is associated with fluorescent labeling, coumarin triazabutadiene-based fluorogenic probes were synthesized and tested for tyrosine specific labeling of proteins under mild acidic condition or photo-irradiation. Furthermore, a coumarin triazabutadiene-based cross-linker was synthesized with an azide functionality that can be used to attached the coumarin triazabutadiene warhead onto the surface of a protein. Upon the activation of the triazabutadiene group, by light or lowering the pH, this system can generate a coumarin diazonium salt on the surface of the protein. Such a system can find application in the study of protein-protein interactions and virus-protein interactions. A cyclooctyne triazabutadiene was synthesized to attach a cyclooctyne group on the tyrosine residues of proteins in biologically relevant pH, and 3-azido 7-hydroxy coumarin was made as a fluorogenic partner of the cyclooctyne triazabutadiene. It was demonstrated that this system can label tyrosine residue followed by a copper-free click reaction with the azido coumarin fluorophore. This system has been tested on model proteins and can be consider as one the first fluorogenic triazabutadiene systems that can be utilized for labeling of tyrosine under mild conditions. In conclusion, this dissertation demonstrates progress in developing fluorescent and fluorogenic triazabutadienes systems for labeling of tyrosine residues of proteins as well as fluorophore triazabutadiene cross-linker that can be used for studying protein-protein interaction, and virus-protein interactions. These systems offer a convenient tool to those wishing to study proteins, protein-protein interactions, and virus-protein interactions.

Fluorescent protein labelling is a powerful tool for the sensitive visualization of proteins in living cells, allowing the elucidation of their localization, trafficking and ultimately their cellular function. We have developed a novel labelling technique based on the genetic fusion of a protein of interest to a small helical peptide sequence containing two Cys residues (dC10). This tag can undergo an efficient reaction with small fluorogenic labelling agents composed of a fluorophore and a dimaleimide core (dM10) that confers high reaction specificity, and quenches the latent fluorescence through photo-induced electron transfer, until both of its maleimide groups have formed robust covalent bonds with the tag Cys thiol groups. Our initial efforts at intracellular protein labelling demonstrated the importance of the selectivity of the labelling reaction, which is dependent on the reactivity of the dC10 tag. To that end, we re-engineered the dC10 tag through rational protein design. Mutant libraries were prepared through combinatorial mutation at specific positions of the helical tag sequence, and screened for their fluorogenic reactivity. In this way, we identified a novel sequence for a next-generation dC10 tag that confers 10-fold greater selectivity that we then applied to in cellulo labelling. Subsequent mechanistic studies revealed the basis for this dramatic increase in reactivity. Current applications of this powerful labelling technique, including the site-specific chelation of lanthanide ions for NMR spectroscopy and site-specific covalent heavy-atom labelling for X-ray crystallography, will also be discussed.

Visualizing proteins in living cells without perturbing biological function remains a key challenge in chemical biology. A chemical approach to this problem is the synthesis of small molecule fluorophores that react specifically with a protein of interest (POI). We have developed a site-specific labelling method based on a Fluorogenic Addition Reaction (FlARe). The FlARe probe’s fluorescence is quenched until it undergoes thiol addition with a small, genetically encoded dicysteine peptide tag fused to the POI. Recent blue coumarin probes were shown to be highly selective for target proteins over other cellular thiols; however, fluorogens that can label in the red and green channels of the fluorescence microscope are more desirable for cellular imaging, as red light is lower in energy and therefore less photo-toxic. In the work presented herein, we use DFT calculations to guide the design of red-shifted, PeT-quenched BODIPY based dimaleimide fluorogens. Driven by the preliminary results of a FlARe probe (YC29) that emitted in the red channel, we attempted to prepare the hit compound through a new synthetic approach to further evaluate kinetics and in cellulo labelling. Given the time available, this compound was unable to be synthesized through an SNAr or Pd-catalyzed approach. Alternatives probes lacking the red-shifting substituent were synthesized and evaluated in vitro and in cellulo. The fluorescent enhancement and reaction kinetics of these probes were evaluated in detail, in order to determine the suitability of their application to cellular labelling. A green-BODIPY fluorogen was synthesized that exhibits suitable kinetics for labelling and a dramatic fluorescent enhancement of ~800-fold upon tagging. This probe was successfully applied to the specific, fluorescent labelling of a nuclear histone protein in cellulo.

This dissertation is composed of two research projects. The first research project is aimed at using synthetic fluorogenic probes to study the possible or dominant linkages in biomass. These probes that mimic the linkages found in lignin-cellulosic biomass are designed to select the optimal fungi from direct evaluation process or could be tested against other microbials to screen candidates which can break ligno-hemicellulose bonds. For the first stage, these probes would be tested against white rot fungi extract. The white rot fungi are used for the first stage to see if releasing or degrading carbohydrates while keeping lignin largely intact is possible or not. These probes can help to answer fundamental questions, such as what could be the dominant linkages between lignin and hemicellulose, and what are the possible mechanisms for the cleavage of carbohydrates in biomasses. Understanding the linkages in these biomass will enable high efficient degradation or release of carbohydrates, primarily hemicelluloses, from biomass. The second project is focused on synthesizing new aminoglycoside analogs and exploring the potential to revive traditional antibacterial kanamycin as new types of antifungal agents. Aminoglycosides are widely used broad spectrum antibiotics. Although mainly used as antibacterial agents, there have been studies to show amphiphilic aminoglycoside derivatives could be possibly employed as antifungal agents. A concise and novel method for site-selective alkylation of tetra-azidokanamycin has been developed that leads to the divergent synthesis of three classes of kanamycin derivatives. These new amphiphilic kanamycin derivatives bearing alkyl chains length of 4, 6, 7, 8, 9, 10, 12, 14，16 have been synthesized and tested against bacteria and fungi. Surprisingly, the antibacterial effect of the synthesized kanamycin derivatives decline or disappear compared with the original kanamycin A, but some of the compounds show very strong activity as antifungal agents.

Despite major advances in the diagnosis and treatment of cancer, there remains a paucity of biomarkers for early detection (poor selectivity and specificity). Legumain [asparaginyl endopeptidase (AEP); EC 3.4.22.34] is a potential cancer biomarker and molecular target for imaging and therapy. Legumain is a lysosomal protease, active at acidic pH (4.0 - 6.5) with a remarkably restricted substrate specificity, uniquely cleaving an asparagine (Asn) at the P1 position, and is overexpressed in various solid tumours. A novel legumain-targeted first generation fluorogenic rhodamine-B based peptide substrate Rho-Pro-Ala-Asn~PEG-AQ (SM9) has been developed for diagnostic application in the early detection of tumours, which exploits the enzyme's proteolytic specificity. The fluorogenic probe SM9 is an efficient FRET substrate, in which an aminoanthraquinone acts as a ‘black hole' quencher of rhodamine fluorescence that is restored on incubation with recombinant (rh)-legumain. Importantly, confocal microscopy studies have revealed localization of SM9 in the lysosomes of PC3 prostate cancer cells. The design principles have been extended to a second generation orthogonally functionalised, legumain-activated dual fluorogenic gadolinium-based magnetic resonance imaging (MRI) contrast agent Rho-Pro-Ala-Asn~Lys-[DOTA-(Gd3+)]-PEG-AQ (SM32). Furthermore, towards the development of selective and targeted theranostic (therapeutic and diagnostic) anticancer agents, a novel third generation fluorogenic legumain substrate prodrug Rho-Pro-Ala-Asn~Propyl-Pip-Propyl-AQ (ALS5) that incorporates a cytotoxic, lysosomotropic anthracenedione ALS1, has been designed. Activation of prodrug ALS5 by rh-legumain in vitro directly afforded the cleavage product and active drug ALS1. Confocal microscopy studies have shown that ALS5 and active ALS1 (at 1 μM) were also localized in the lysosomes of PC-3 cells. Furthermore, ALS1 induced morphological changes and apoptosis in PC-3 cells, as measured by fluorescence microscopy, and staining with Annexin V and DAPI using flow cytometry. All novel legumain-activated oligopeptide substrates and intermediate compounds have been fully characterised by high resolution mass spectrometry and NMR spectroscopy. Selected compounds have been further characterised by HPLC. The molecular probes and prodrugs have the potential to be used as diagnostic tools to define the legumain expression in tumour biopsies and provide prognostic information of value in determining patient-focussed treatment options, with extension to therapeutic strategies to improve tumour targeting.

L'étude de la dynamique des protéines est essentielle pour comprendre les processus biologiques. Notre laboratoire a développé une nouvelle classe de protéines fluorescentes semi-synthétiques, appelée Fluorescence-Activating and absorption-Shifting Tag (FAST). Cette thèse de doctorat présente le développement de nouveaux systèmes FAST avec diverses propriétés pour l'imagerie multiplexée. Nous avons développé une série de fluorogènes permettant de modifier la couleur de FAST de vert-jaune à orange et rouge. Au delà de l’application de l’imagerie multi-couleurs, ces fluorogènes permettant un échange dynamique des couleurs grâce à la liaison réversible de FAST, ouvrant de nouvelles perspectives pour le développement de méthodes d’imagerie sélective reposant sur la dynamique de systèmes réactifs. Pour étendre davantage les propriétés spectrales de FAST vers le rouge lointain, nous avons développé une nouvelle série de fluorogènes rouges, pour lesquels nous avons sélectionné par une stratégie d'évolution dirigée basée sur le yeast display et la cytométrie en flux de nouveaux tags protéiques capables d’interagir avec ces fluorogènes et d’activer leur fluorescence. Nous avons enfin développé de nouveaux fluorogènes capables de former des complexes fluorescents avec FAST, mais incapables de traverser la membrane plasmique, ce qui permet de détecter sélectivement les protéines membranaires. / Studying protein activities could help us to understand the complex mechanisms controlling cells and organisms. Our laboratory recently developed Fluorescence-Activating and absorption-Shifting Tag (FAST), a small fluorogen-based reporter enabling to fluorescently label fusion proteins in living cells. My PhD thesis presents the developments of new FAST systems with various properties for multiplexed imaging. We report a collection of fluorogens enabling to tune the fluorescence color of FAST from green-yellow to orange and red. Beyond allowing multicolor imaging of FAST-tagged proteins in live cells, these fluorogens enable dynamic color switching because of FAST’s reversible labeling, opening great prospects for the design of selective imaging methods relying on dynamic systems. In order to further expand the spectral properties of FAST to red, we also designed and developed a library of red fluorogenic dyes, for which we engineered specific protein binders by applying a directed evolution strategy based on the yeast display technology and high-throughput fluorescence activating cell sorting (FACS). We finally developed novel fluorogens able to form fluorescent complexes with FAST, but incapable of crossing the plasma membrane, which makes it possible to selectively detect FAST-tagged cell-surface proteins.

La presente tesis doctoral titulada "Sondas moleculares y complejos de rutenio (II) y osmio (II) para la detección cromo-fluorogénica de especies cargadas y monóxido de carbono" se centra en el desarrollo de sensores químicos moleculares. El trabajo realizado se puede dividir en dos partes: (i) síntesis y caracterización de sondas moleculares multifuncionales para la detección óptica de aniones y cationes metálicos y, (ii) preparación de complejos de rutenio (II) y osmio (II) para la detección cromo-fluorogénica de monóxido de carbono. La primera familia de sondas moleculares, a la cual se hace referencia en el capítulo 2, se basa en el uso de imidazoantraquinonas como subunidad indicadora. Empleando este fragmento molecular se prepararon y caracterizaron cuatro sondas (2a-2d). De todos los aniones que se ensayaron, sólo el fluoruro es capaz de inducir la aparición de una banda de absorción (lo cual se refleja en diferentes cambios de color) y bandas de emisión desplazadas hacia el rojo. Estos cambios se atribuyen a la desprotonación del grupo N-H del anillo de imidazol inducida por el fluoruro. También los cationes Fe3+, Al3+ y Cr3+ son capaces de producir desplazamientos moderados hacia el azul de las bandas de absorción de los cuatro receptores, así como una desactivación marcada de la emisión a causa de su coordinación (con los átomos de oxígeno y nitrógeno del cromóforo imidazoantraquinona). El segundo capítulo también está dedicado al estudio del comportamiento de coordinación frente a aniones y cationes de una segunda familia de sondas (3a-3d) basadas en derivados de imidazoquinolina. Nuevamente el anión fluoruro promueve la desprotonación de estos compuestos, lo cual se refleja en la aparición de bandas de absorción y de emisión desplazadas hacia el rojo. En cuanto a la respuesta óptica en presencia de cationes metálicos es muy poco selectiva, observándose cambios en las bandas UV-visible y una desactivación de las bandas de emisión en presencia de Hg2+, Cu2+, Co2+, Fe3+, Fe2+, Zn2+, Pb2+, Cd2+, Cr3+ y Al3+. A lo largo del capítulo 3 se presenta la síntesis, caracterización y comportamiento cromo-fluorogénico frente al monóxido de carbono de dos conjuntos de complejos de rutenio (II) y osmio (II) que tienen en su esfera de coordinación los fluróforos 2,1,3-benzotiadiazol (BTD) y 5-(3-tienil)-2,1,3-benzotiadiazol (TBTD). En la primera parte de este capítulo se prepararon ocho compuestos con el ligando BTD (1-8). Al burburjearles CO, las disoluciones de cloroformo de dichos complejos mostraron notables cambios de color. Además, su emisión se vio incrementada debido a la coordinación de los complejos con el CO y el desplazamiento del fluoróforo BTD. Por otro lado, la adsorción de los complejos en sílice dio lugar a sólidos que presentaron importantes cambios de color permitiendo la detección de CO en fase gas a simple vista y con alta selectividad y sensitividad. El segundo conjunto de complejos de rutenio (II) y osmio (II) contiene el fluróforo TBTD (3-7). Éstos también son capaces de detectar CO cuando se encuentran disueltos en cloroformo y adsorbidos en sílice a través de cambios de color y fluorescencia. Por otra parte, se prepararon dos nuevos complejos (8 y 9) funcionalizados con una cadena de polietilenglicol. Ambos complejos son solubles en agua y permiten la detección de CO en este disolvente altamente competitivo. Además, los compuestos 8 y 9 no son tóxicos y se emplearon con éxito en la detección de CO en células HeLa. / The present PhD thesis entitled "Molecular probes and ruthenium (II) and osmium (II) complexes for the chromo-fluorogenic sensing of charged species and carbon monoxide" is focused on the development of molecular chemosensors. More in detail, the work carried out is clearly divided into two independent parts: (i) the synthesis and characterization of multifunctional molecular probes for the optical detection of anions and metal cations and, (ii) the preparation of ruthenium (II) and osmium (II) complexes for the chromo-fluorogenic sensing of carbon monoxide. The first family of molecular probes, reported in chapter 2, is based on the use of imidazoanthraquinone as signaling subunit. Using this molecular fragment four probes (2a-2d) are prepared and characterized. Of all the anions tested, only fluoride is able to induce the appearance of red-shifted absorption (reflected in marked color changes) and emission bands. These changes are ascribed to a fluoride-induced deprotonation of the N-H moiety of the imidazole ring. Also Fe3+, Al3+ and Cr3+ were able to induce moderate blue-shifts of the absorption bands of the four receptors upon coordination (with the oxygen and nitrogen atoms of the imidazoanthraquinone chromophore) and marked emission quenching. The second chapter is also devoted to study the coordination behavior toward anions and cations of a second family of probes (3a-3d) containing imidazoquinoline derivatives. Again, fluoride anion promoted the deprotonation on the probes that are reflected in the apperacence of red-shifted absorption and emission bands. The optical response in the presence of metal cations is quite unselective and UV-visible shifts and emission quenchings are observed in the presence of Hg2+, Cu2+, Co2+, Fe3+, Fe2+, Zn2+, Pb2+, Cd2+, Cr3+ and Al3+. Chapter 3 presents the synthesis, characterization and chromo-fluorogenic behavior toward of carbon monoxide of two set of ruthenium (II) and osmium (II) complexes bearing 2,1,3-benzothiadiazole (BTD) and 5-(3-thienyl)-2,1,3-benzothiadiazole (TBTD) fluorophores. Eight complexes functionalized with BTD ligand (1-8) are prepared in the first part of this chapter. Chloroform solutions of the complexes underwent remarkable color changes when CO is bubbled. Also, significative emission enhancements are obserbed due to coordination of CO and displacement of BTD fluorophore. Besides, the adsorption of the complexes on silica yielded solids that presented remarkable color changes that allowed a naked eye detection of CO in gas phase. The second set of ruthenium (II) and osmium (II) complexes contains TBTD fluorophore (3-7). Also these complexes are able to detect CO in chloroform solution and in gas phase when adsorbed on silica through color and fluorescence changes. Moreover, two new complexes (8 and 9) containing a poly(ethylene) glycol chain are prepared. Both complexes are water soluble and allowed CO detection in this highly competitive solvent. Besides, 8 and 9 are non-toxic and are successfully used for CO detection in HeLa cells. / La present tesi doctoral titulada "Sondas moleculars i complexos de ruteni (II) i osmi (II) per a la detecció cromo-fluorogènica d'espècies carregades i monòxid de carboni" es centra en el desenvolupament de sensors químics moleculars. El treball realizat es pot dividir en dues parts: (i) síntesi i caracterització de sondes moleculars multifuncionals per a la detecció òptica d'anions i cations metàli·lics i, (ii) preparació de complexos de ruteni (II) i osmi (II) per a la detecció cromo-fluorogènica de monòxid de carboni. La primera família de sondes moleculars, a la qual es fa referència en el capítol 2, es basa en l'ús d'imidazoantraquinones com a subunitat indicadora. Emprant aquest fragment molecular es van preparar i caracteritzar quatre sondes (2a-2d). De tots els anions que es van assajar, només el fluorur és capaç d'induir l'aparició d'una banda d'absorció (la qual cosa es reflecteix en diferents canvis de color) i bandes d'emissió desplaçades cap al roig. Aquestos canvis s'atribuïxen a la desprotonació del grup NH de l'anell d'imidazol induïda pel fluorur. També els cations Fe3+, Al3+ i Cr3+ són capaços de produir desplaçaments moderats cap al blau de les bandes d'adsorció dels quatre receptors, així com una desactivació marcada de l'emissió a causa de la seua coordinació (amb els àtoms d'oxigen i nitrogen del cromòfor imidazoantraquinona). El segon capítol també està dedicat a l'estudi del comportament de coordinació en presència d'anions i cations d'una segona família de sondes (3a-3d) basades en derivats d'imidazoquinolina. Novament l'anió fluorur promou la desprotonació d'aquestos compostos, la qual cosa es reflecteix en l'aparició de bandes d'absorció i d'emissió desplaçades cap al roig. Quant a la resposta òptica en presència de cations metàl·lics és molt poc selectiva, observant-se canvis en les bandes UV-visible i una desactivació de les bandes d'emissió en presència de Hg2+, Cu2+, Co2+, Fe3+, Fe2+, Zn2+, Pb2+, Cd2+, Cr3+ i Al3+. Al capítol 3 es presenta la síntesi, caracterització i comportament cromo-fluorogènic en presència de monòxid de carboni de dos conjunts de complexos de ruteni (II) i osmi (II) que tenen a la seua esfera de coordinació els fluoròfors 2,1,3-benzotiadiazol (BTD) i 5-(3-tienil)-1,2,3-benzotiadiazol (TBTD). A la primera part d'aquest capítol es van preparar huit compostos amb el lligant BTD (1-8). Al bambollejar-les CO, les dissolucions de cloroform d'aquestos complexos van mostrar notables canvis de color. A més, la seua emissió es va veure incrementada a causa de la coordinació dels complexos amb el CO i el desplaçament del fluoròfor BTD. D'altra banda, l'adsorció dels complexos en sílice va donar lloc a sòlids que van presentar importants canvis de color premetent la detecció de CO en fase gas a simple vista i amb alta selectivitat i sensitivitat. El segon conjunt de complexos de ruteni (II) i osmi (II) conté el fluoròfor TBTD (3-7). Aquestos també són capaços de detectar CO quan es troben dissolts en cloroform i adsorbits en sílice a través de canvis de color i fluorescència. D'altra banda, es van preparar dos nous complexos (8 i 9) funcionalitzats amb una cadena de polietilenglicol. Ambdós complexos són solubles en aigua i permeten la detecció de CO en aquest dissolvent altament competitiu. A més, els compostos 8 i 9 no són tòxics i es van emprar amb èxit en la detecció de CO en cèl·lules HeLa. / Marín Hernández, C. (2017). Molecular probes and ruthenium (II) and osmium(II) complexes for the chromofluorogenic sensing of charged species and carbon monoxide [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/95407 / TESIS