Gastrointestinal modelling and optimization of protein and phosphorus bioaccessibility by phytase in fish diets

Programa de doctorado: Acuicultura

Each one teaches one: characterizing active forms of proteins by single molecule force spectroscopy

This Ph.D. candidate thesis collects the research work I conducted under the supervision of Prof.Bruno Samor´ı in 2005,2006 and 2007. Some parts of this work included in the Part III have been begun by myself during my undergraduate thesis in the same laboratory and then completed during the initial part of my Ph.D. thesis: the whole results have been included for the sake of understanding and completeness. During my graduate studies I worked on two very different protein systems. The theorical trait d’union between these studies, at the biological level, is the acknowledgement that protein biophysical and structural studies must, in many cases, take into account the dynamical states of protein conformational equilibria and of local physico-chemical conditions where the system studied actually performs its function. This is introducted in the introductory part in Chapter 2. Two different examples of this are presented: the structural significance deriving from the action of mechanical forces in vivo (Chapter 3) and the complexity of conformational equilibria in intrinsically unstructured proteins and amyloid formation (Chapter 4). My experimental work investigated both these examples by using in both cases the single molecule force spectroscopy technique (described in Chapter 5 and Chapter 6). The work conducted on angiostatin focused on the characterization of the relationships between the mechanochemical properties and the mechanism of action of the angiostatin protein, and most importantly their intertwining with the further layer of complexity due to disulfide redox equilibria (Part III). These studies were accompanied concurrently by the elaboration of a theorical model for a novel signalling pathway that may be relevant in the extracellular space, detailed in Chapter 7.2. The work conducted on -synuclein (Part IV) instead brought a whole new twist to the single molecule force spectroscopy methodology, applying it as a structural technique to elucidate the conformational equilibria present in intrinsically unstructured proteins. These equilibria are of utmost interest from a biophysical point of view, but most importantly because of their direct relationship with amyloid aggregation and, consequently, the aetiology of relevant pathologies like Parkinson’s disease. The work characterized, for the first time, conformational equilibria in an intrinsically unstructured protein at the single molecule level and, again for the first time, identified a monomeric folded conformation that is correlated with conditions leading to -synuclein and, ultimately, Parkinson’s disease. Also, during the research work, I found myself in the need of a generalpurpose data analysis application for single molecule force spectroscopy data analysis that could solve some common logistic and data analysis problems that are common in this technique. I developed an application that addresses some of these problems, herein presented (Part V), and that aims to be publicly released soon.

Tris(trimethylsilyl)silyl stabilized phosphorus and lead clusters

Die Hypersilylgruppe (Me3Si)3Si stellt einen sehr sperrigen, Elektronen liefernden Substituenten dar und kann zur Stabilisierung niedriger Oxidationsstufen sowie ungewöhnlicher Strukturelemente dienen. Durch Reaktionen der base-freien Hypersilanide der Alkalimetalle sowie des Dihypersilylplumbandiyls mit unterschiedlichsten phosphorhaltigen Reagenzien konnten eine Reihe hypersilyl-stabilisierter Phosphor- und Bleicluster-Verbindungen erhalten werden. Kaliumhypersilanid reagiert in Toluol glatt mit weißem Phosphor bei Raumtemperatur in Toluol unter quantitativer Bildung von rotem Kalium-bis(hypersilyl)tetraphosphenid [(Me3Si)3Si]2P4K2 (1), einem Kaliumsalz des Tetraphosphens (Me3Si)3Si-PH-P=P-PH-Si(SiMe3)3. In Benzol oder Toluol steht 1 im Gleichgewicht mit dem dimeren Octaphosphanid [(Me3Si)3Si]4P8K4 (2). Bei längerem Stehen der toluolischen Lösungen zerfällt 1 langsam vermutlich in Folge einer Protolyse zum gelben Pentaphosphanid [(Me3Si)3Si]3P5K2 (4). Aus benzolischer Lösung konnte hingegen ein weiteres Oktaphosphanid, [(Me3Si)3Si]3P8K3 (5), isoliert werden. Führt man die Reaktion Kaliumhypersilanid mit P4 in stärker koordinierenden Lösungsmitteln wie Diethylether durch, so entstehen neben 1 größere Mengen des Triphosphenids [(Me3Si)3Si]2P3K (3); dieses enthält ein Triphosphaallyl-Anion mit partieller P-P-Doppelbindung. Setzt man Lithiumhypersilanid mit weißem Phosphor um, so beobachtet man eine vollständig andere Produktpallette. Als Hauptprodukte lassen Polyphosphane wie beispielsweise [(Me3Si)3Si]2P4 (6) nachweisen, das zu 1 analoge [(Me3Si)3Si]2P4Li2 (7) entsteht nur in vergleichsweise kleinen Mengen. In der Gegenwart von Hexahydro-1,3,5-trimethyl-S-triazin, entsteht aus Lithiumhypersilanid und P4 hingegen im wesentlichen [(Me3Si)3Si]2P3Li (8) neben beträchtlichen Mengen von (Me3Si)4Si. Dessen Bildung erfordert eine Si-Si-Bindungsspaltung im Verlauf der Reaktion. Die Reaktion von Natriumhypersilanid mit P4 verläuft sehr unübersichtlich, das Pentaphosphanid [(Me3Si)3Si]3P5Na2 (9) ist das einzige isolierbare Produkt. Setzt man 1 mit [(Me3Si)2Si]2Sn um, so bilden sich überraschenderweise, je nach verwendetem Solvens [(Me3Si)3Si]3P4SnK (10) oder [(Me3Si)3Si]2[(Me3Si)2N]P4SnK (11). Alle neuen Verbindungen wurden NMR-spektroskopisch charakterisiert, die Phosphenide 1, 7, 8 sowie die Phosphanide 2, 4, 5, 9, 10 darüber hinaus durch Kristallstrukturanalysen. Dihypersilylplumbandiyl und -stannandiyl reagieren bei tiefer Temperatur mit P4, MPH2 (M=Li, K), PMe3, and PH3 zu formalen Lewis-Säure-Base-Addukten. Die Addukte {[(Me3Si)3Si]2PbPH2}M [M = Li (15), K (18)], {{[(Me3Si)3Si]2Pb}2PH2}M [M = Li (19), K (20)], und [(Me3Si)3Si]2EPMe3 [E = Pb (21), Sn (22)] wurden als kristalline Feststoffe erhalten und konnten vollständig charakterisiert werden. Die metastabilen Addukte {[(Me3Si)3Si]2E}4P4 (E = Pb, Sn) und [(Me3Si)3Si]2PbPH3 konnten lediglich NMR-spektroskopisch nachgewiesen werden. Bei Raumtemperatur entstehen in Folge von Ligandenaustausch-Prozessen die kristallographisch charakterisierten Heterokubane [(Me3Si)3Si]4P4E4 [E = Pb (12), Sn (14)], das Diphosphen (Me3Si)3SiP=PSi(SiMe3)3 (13) sowie der Pb2P2-Heterocyclus [(Me3Si)3SiPbP(H)Si(SiMe3)3]2 (17). Bei tiefer Temperatur wird aus einer sehr langsamen Reaktion von Dihypersilylplumbandiyl und PH3 in sehr kleinen Ausbeuten ein weiteres, völlig unerwartetes Produkt gebildet: der Bleicluster [(Me3Si)3Si]6Pb12 (23). Er weist ein verzerrt ikosaedrisches, zentrosymmetrisches Pb12-Gerüst auf. Nach jetzigen Erkenntnissen läuft seine Bildung über das nicht fassbare Hydridoplumbandiyl HPbSi(SiMe3)3, das intermediär durch Substituentenaustausch zwischen Pb[Si(SiMe3)3]2 and PH3 entsteht. Der Ersatz des Phosphans durch andere Hydridquellen wie (Ph3PCuH)6, (iBu)2AlH, and Me3NAlH3 führt ebenfalls zur Bildung von Bleiclustern, allerdings ist jetzt der Cluster [(Me3Si)3Si]6Pb10 (24) das Hauptprodukt. Beide Cluster, 23 und 24, gehorchen den Wade-Regeln.

Abiotic and prebiotic phosphorus chemistry

The chief obstacle to understand the metabolic origin of life or RNA-based life is to identify a plausible mechanism for overcoming the clutter wrought by abiotic chemistry. Probably trough simple abiotic and then prebiotic reactions we could arrive to simple pre-RNA molecules. Here we report a possible preibiotic synthesis for heterocyclic compounds, and a self-assembling process of adenosine phosphates a constituent of RNA. In these processes we use a simple and prebiotic phosphorus cyclic compounds, as P4O10 and its derivatives. The processes are driven by the formation of hypercoordinated species that activate the processes by a factor of 106-8.

Preparation of new crystal forms via photochemical, mechanochemical and sol-gel methods

This work of thesis involves various aspects of crystal engineering. Chapter 1 focuses on crystals containing crown ether complexes. Aspects such as the possibility of preparing these materials by non-solution methods, i.e. by direct reaction of the solid components, thermal behavior and also isomorphism and interconversion between hydrates are taken into account. In chapter 2 a study is presented aimed to understanding the relationship between hydrogen bonding capability and shape of the building blocks chosen to construct crystals. The focus is on the control exerted by shape on the organization of sandwich cations such as cobalticinium, decamethylcobalticinium and bisbenzenchromium(I) and on the aggregation of monoanions all containing carboxylic and carboxylate groups, into 0-D, 1-D, 2-D and 3-D networks. Reactions conducted in multi-component molecular assemblies or co-crystals have been recognized as a way to control reactivity in the solid state. The [2+2] photodimerization of olefins is a successful demonstration of how templated solid state synthesis can efficiently synthesize unique materials with remarkable stereoselectivity and under environment-friendly conditions. A demonstration of this synthetic strategy is given in chapter 3. The combination of various types of intermolecular linkages, leading to formation of high order aggregation and crystalline materials or to a random aggregation resulting in an amorphous precipitate, may not go to completeness. In such rare cases an aggregation process intermediate between crystalline and amorphous materials is observed, resulting in the formation of a gel, i.e. a viscoelastic solid-like or liquid-like material. In chapter 4 design of new Low Molecular Weight Gelators is presented. Aspects such as the relationships between molecular structure, crystal packing and gelation properties and the application of this kind of gels as a medium for crystal growth of organic molecules, such as APIs, are also discussed.

Quantum field theory of (p,0)-forms on kaehler manifolds

In questa tesi abbiamo studiato la quantizzazione di una teoria di gauge di forme differenziali su spazi complessi dotati di una metrica di Kaehler. La particolarità di queste teorie risiede nel fatto che esse presentano invarianze di gauge riducibili, in altre parole non indipendenti tra loro. L'invarianza sotto trasformazioni di gauge rappresenta uno dei pilastri della moderna comprensione del mondo fisico. La caratteristica principale di tali teorie è che non tutte le variabili sono effettivamente presenti nella dinamica e alcune risultano essere ausiliarie. Il motivo per cui si preferisce adottare questo punto di vista è spesso il fatto che tali teorie risultano essere manifestamente covarianti sotto importanti gruppi di simmetria come il gruppo di Lorentz. Uno dei metodi più usati nella quantizzazione delle teorie di campo con simmetrie di gauge, richiede l'introduzione di campi non fisici detti ghosts e di una simmetria globale e fermionica che sostituisce l'iniziale invarianza locale di gauge, la simmetria BRST. Nella presente tesi abbiamo scelto di utilizzare uno dei più moderni formalismi per il trattamento delle teorie di gauge: il formalismo BRST Lagrangiano di Batalin-Vilkovisky. Questo metodo prevede l'introduzione di ghosts per ogni grado di riducibilità delle trasformazioni di gauge e di opportuni “antifields" associati a ogni campo precedentemente introdotto. Questo formalismo ci ha permesso di arrivare direttamente a una completa formulazione in termini di path integral della teoria quantistica delle (p,0)-forme. In particolare esso permette di dedurre correttamente la struttura dei ghost della teoria e la simmetria BRST associata. Per ottenere questa struttura è richiesta necessariamente una procedura di gauge fixing per eliminare completamente l'invarianza sotto trasformazioni di gauge. Tale procedura prevede l'eliminazione degli antifields in favore dei campi originali e dei ghosts e permette di implementare, direttamente nel path integral condizioni di gauge fixing covarianti necessari per definire correttamente i propagatori della teoria. Nell'ultima parte abbiamo presentato un’espansione dell’azione efficace (euclidea) che permette di studiare le divergenze della teoria. In particolare abbiamo calcolato i primi coefficienti di tale espansione (coefficienti di Seeley-DeWitt) tramite la tecnica dell'heat kernel. Questo calcolo ha tenuto conto dell'eventuale accoppiamento a una metrica di background cosi come di un possibile ulteriore accoppiamento alla traccia della connessione associata alla metrica.

Differential forms on Carnot groups

The main goal of this thesis is to understand and link together some of the early works by Michel Rumin and Pierre Julg. The work is centered around the so-called Rumin complex, which is a construction in subRiemannian geometry. A Carnot manifold is a manifold endowed with a horizontal distribution. If further a metric is given, one gets a subRiemannian manifold. Such data arise in different contexts, such as: - formulation of the second principle of thermodynamics; - optimal control; - propagation of singularities for sums of squares of vector fields; - real hypersurfaces in complex manifolds; - ideal boundaries of rank one symmetric spaces; - asymptotic geometry of nilpotent groups; - modelization of human vision. Differential forms on a Carnot manifold have weights, which produces a filtered complex. In view of applications to nilpotent groups, Rumin has defined a substitute for the de Rham complex, adapted to this filtration. The presence of a filtered complex also suggests the use of the formal machinery of spectral sequences in the study of cohomology. The goal was indeed to understand the link between Rumin's operator and the differentials which appear in the various spectral sequences we have worked with: - the weight spectral sequence; - a special spectral sequence introduced by Julg and called by him Forman's spectral sequence; - Forman's spectral sequence (which turns out to be unrelated to the previous one). We will see that in general Rumin's operator depends on choices. However, in some special cases, it does not because it has an alternative interpretation as a differential in a natural spectral sequence. After defining Carnot groups and analysing their main properties, we will introduce the concept of weights of forms which will produce a splitting on the exterior differential operator d. We shall see how the Rumin complex arises from this splitting and proceed to carry out the complete computations in some key examples. From the third chapter onwards we will focus on Julg's paper, describing his new filtration and its relationship with the weight spectral sequence. We will study the connection between the spectral sequences and Rumin's complex in the n-dimensional Heisenberg group and the 7-dimensional quaternionic Heisenberg group and then generalize the result to Carnot groups using the weight filtration. Finally, we shall explain why Julg required the independence of choices in some special Rumin operators, introducing the Szego map and describing its main properties.

Rare and complicated forms of infantile hemangiomas: new therapeutic outlooks

Infantile hemangiomas (IHs) are the most common benign neoplastic pathology of childhood; their natural history generally involves three phases: after the onset, which usually occurs in the first weeks of life, there is the proliferation phase where the IH reaches its maximum development and it is followed by the spontaneous involution which leads to the IH regression. The duration and the extent of these phases may vary widely even though in most of the cases the involution process begins around twelve months of life and the regression, complete or partial, is completed around seventh-ninth year of life. The majority of the IHs does not require any treatment. However, 10%-20% is likely to develop serious complications, functional impairments or aesthetic alterations and entail a timely treatment. Although there is no treatment protocol currently shared, therapies usually used in cases with a complication risk consist in: systemic or intralesional steroids as a first choice; interferon α, vincristine and/or bleomicin as second or third choice and/or surgical treatment. Propranolol, a non-selective beta-blocker, has been used for cardiovascular diseases even in childhood for decades. Since 2008 it has been widely used in the IHs treatment, although it is still "off-label". In literature there are hundreds of cases and some clinical studies that show the effectiveness and safety of this drug for this indication. Thanks to a multidisciplinary team (Dermatologists, Cardiologists, Paediatricians, and Radiologists) of S. Orsola-Malpighi Hospital, a clinical study, which has been previously approved by the ethics committee, is carried out in order to evaluate the efficacy and safety of systemic propranolol in the treatment of IHs in paediatric age. At the end of 2012, 78 patients underwent this treatment: the results we have obtained so far show a good efficacy and safety profile in agreement with the data provided by the literature.

Multifunctional water-soluble phosphorus dendrimers

Dendrimers are polymeric macromolecules with a regularly branched structure and are synthesised in an iterative fashion. Due to their monodispersity, well-defined shape and extremely high functionality, dendrimers are ideal nano-sized objects for functional and biocompatible surface coatings, biosensing and biomedicine. This dissertation describes the synthesis of ten novel water-soluble phosphorus containing dendrimers and their application in different biological and biomimetic systems. The dendrimers can be divided into two classes; the first type contains either a ferrocene at the core or 24 ferrocenes in the branches. They showed reversible reduction-oxidation behaviour and might be applied in electronic multilayered architectures. Dendrimers of the second class carry a dithiolane functionalised core that can strongly bind to noble metals, like gold substrates. Although such dendrimer coated substrates were unable to tether defect-free lipid bilayer membranes, the coatings were successfully applied for culturing Human Osteoblast cells. The cell adhesion to a coating of polycationic dendrimers was so strong that cell division could not take place, specifically evoking apoptosis. The polyanionic dendrimers, however, promoted excellent cell adhesion and proliferation. Therefore, the practical application of such macromolecular architectures can be envisioned, such as in dendrimer coatings for tissue engineering and or medical implants.

Solubility and permeability as in vitro predictors for in vivo performance of fenofibrate IR solid dosage forms

This current work focused on the simulation of in vivo dissolution and permeation in order to be able to predict the in vivo performance of orally administered fenofibrate immediate release formulations. Therefore, the effects of the formulation surfactants on in vivo solubility and permeation of fenofibrate under physiologically relevant excipient concentrations were emphasized.rnIt was shown that the surfactant sodium dodecyl sulfate (SDS) may decrease rather than increase the solubility of fenofibrate in vivo. This was related to the interference of SDS with the vesicular system of the biorelevant medium, FaSSIFmod, and therefore its solubilization capacity. rnMoreover, in vitro permeation studies revealed that SDS concentrations inversely correlated with fenofibrate permeability. Through combination of the observed permeation and solubility data a good in vitro/in vivo correlation regarding Cmax values in humans could be established for five fenofibrate formulations which were based on the same manufacturing technique.rnBesides the experimental part, the major characteristics and their potential implementation in a dissolution/permeation device were discussed based on the promising realization of the in vitro solubility and permeation methods. rn

Crystal Engineering of bright luminescent copper iodide clusters with phosphorus and nitrogen-based ligands

Copper(I) halide clusters are recently considered as good candidate for optoelectronic devices such as OLEDs . Although the copper halide clusters, in particular copper iodide, are very well known since the beginning of the 20th century, only in the late ‘70s the interest on these compounds grew dramatically due their particular photophysical behaviour. These complexes are characterized by a dual triplet emission bands, named Cluster Centred (3CC) and Halogen-to-Ligand charge transfer (3XLCT), the intensities of which are strictly related with the temperature. The CC transition, due to the presence of a metallophylic interactions, is prevalent at ambient temperature while the XLCT transition, located preferentially on the ligand part, became more prominent at low temperature. Since these pioneering works, it was easy to understand the photophysical properties of this compounds became more interesting in solid-state respect to solution with an improvement in emission efficiency. In this work we aim to characterize in SS organocopper(I)iodide compounds to valuate the correlation between the molecular crystal structure and the photophysical properties. It is also considered to hike new strategies to synthesize CuI complexes from the wet reactions to the more green solvent free methods. The advantages in using these strategies are evident but, obtain a single crystal suitable for SCXRD analysis from these batches is quite impossible. The structure solution still remains the key point in this research so we tackle this problem solving the structure by X-ray powder diffraction data. When the sample was fully characterized we moved to design and development of the associated OLED-device. Since copper iodide complexes are often insoluble in organic solvents, the high vacuum deposition technique is preferred. A new non-conventional deposition process have also been proposed to avoid the low complex stability in this practice with an in-situ complex formation in a layer-by layer deposition route.

Optimization of molecular and crystalline forms of drugs, agrochemicals, pesticides in relation to activity, bioavailability, patentability and to the fabrication of polymorphs, solvates, co-crystals with green chemistry methods

This doctorate was funded by the Regione Emilia Romagna, within a Spinner PhD project coordinated by the University of Parma, and involving the universities of Bologna, Ferrara and Modena. The aim of the project was: - Production of polymorphs, solvates, hydrates and co-crystals of active pharmaceutical ingredients (APIs) and agrochemicals with green chemistry methods; - Optimization of molecular and crystalline forms of APIs and pesticides in relation to activity, bioavailability and patentability. In the last decades, a growing interest in the solid-state properties of drugs in addition to their solution chemistry has blossomed. The achievement of the desired and/or the more stable polymorph during the production process can be a challenge for the industry. The study of crystalline forms could be a valuable step to produce new polymorphs and/or co-crystals with better physical-chemical properties such as solubility, permeability, thermal stability, habit, bulk density, compressibility, friability, hygroscopicity and dissolution rate in order to have potential industrial applications. Selected APIs (active pharmaceutical ingredients) were studied and their relationship between crystal structure and properties investigated, both in the solid state and in solution. Polymorph screening and synthesis of solvates and molecular/ionic co-crystals were performed according to green chemistry principles. Part of this project was developed in collaboration with chemical/pharmaceutical companies such as BASF (Germany) and UCB (Belgium). We focused on on the optimization of conditions and parameters of crystallization processes (additives, concentration, temperature), and on the synthesis and characterization of ionic co-crystals. Moreover, during a four-months research period in the laboratories of Professor Nair Rodriguez-Hormedo (University of Michigan), the stability in aqueous solution at the equilibrium of ionic co-crystals (ICCs) of the API piracetam was investigated, to understand the relationship between their solid-state and solution properties, in view of future design of new crystalline drugs with predefined solid and solution properties.