Biomimetic Scaffolds for the Controlled Release of Bioactive Molecules for Tissue Engineering Applications

The temporospatial controlled delivery of growth factors is crucial to trigger the desired healing mechanisms in target tissues. The uncontrolled release of growth factors has been demonstrated to cause severe side effects in its surrounding tissues. Thus, the first working hypothesis was to tune and optimize a newly developed multiscale delivery platform based on a nanostructured silicon particle core (pSi) and a poly (dl-lactide-co-glycolide) acid (PLGA) outer shell. In a murine subcutaneous model, the platform was demonstrated to be fully tunable for the temporal and spatial control release of the payload. Secondly, a multiscale approach was followed in a multicompartment collagen scaffold, to selectively integrate different sets of PLGA-pSi loaded with different reporter proteins. The spatial confinement of the microspheres allowed the release of the reporter proteins in each of the layers of the scaffold. Finally, the staged and zero-order release kinetics enabled the temporal biochemical patterning of the scaffold. The last step of this PhD project was to test if by fully embedding PLGA microspheres in a highly structured and fibrous collagen-based scaffold (camouflaging), it was possible to prevent their early detection and clearance by macrophages. It was further studied whether such a camouflaging strategy was efficient in reducing the production of key inflammatory molecules, while preserving the release kinetics of the payload of the PLGA microspheres. Results demonstrated that the camouflaging allowed for a 10-fold decrease in the number of PLGA microspheres internalized by macrophages, suggesting that the 3D scaffold operated by cloaking the PLGA microspheres. When the production of key inflammatory cytokines induced by the scaffold was assessed, macrophages' response to the PLGA microspheres-integrated scaffolds resulted in a response similar to that observed in the control (not functionalized scaffold) and the release kinetic of a reporter protein was preserved.

Cannabinoid system combined to classic targets for a new MTDL strategy: design and synthesis of natural inspired molecules for Alzheimer's disease

In this thesis is described the design and synthesis of potential agents for the treatment of the multifactorial Alzheimer’s disease (AD). Our multi-target approach was to consider cannabinoid system involved in AD, together with classic targets. In the first project, designed modifications were performed on lead molecule in order to increase potency and obtain balanced activities on fatty acid amide hydrolase and cholinesterases. A small library of compounds was synthesized and biological results showed increased inhibitory activity (nanomolar range) related to selected target. The second project was focused on the benzofuran framework, a privileged structure being a common moiety found in many biologically active natural products and therapeutics. Hybrid molecules were designed and synthesized, focusing on the inhibition of cholinesterases, Aβ aggregation, FAAH and on the interaction with CB receptors. Preliminary results showed that several compounds are potent CB ligands, in particular the high affinity for CB2 receptors, could open new opportunities to modulate neuroinflammation. The third and the fourth project were carried out at the IMS, Aberdeen, under the supervision of Prof. Matteo Zanda. The role of the cannabinoid system in the brain is still largely unexplored and the relationship between the CB1 receptors functional modification, density and distribution and the onset of a pathological state is not well understood. For this reasons, Rimonabant analogues suitable as radioligands were synthesized. The latter, through PET, could provide reliable measurements of density and distribution of CB1 receptors in the brain. In the fifth project, in collaboration with CHyM of York, the goal was to develop arginine analogues that are target specific due to their exclusively location into NOS enzymes and could work as MRI contrasting agents. Synthesized analogues could be suitable substrate for the transfer of polarization by p-H2 molecules through SABRE technique transforming MRI a more sensitive and faster technique.

Contribution of Non-Covalent Interactions and Electronic Effects on the Conformational Landscape and Tautomeric Equilibria of Molecules and Molecular Complexes: Structural and Dynamical Data from Rotational Spectroscopy

This thesis concerns the study of complex conformational surfaces and tautomeric equilibria of molecules and molecular complexes by quantum chemical methods and rotational spectroscopy techniques. In particular, the focus of this research is on the effects of substitution and noncovalent interactions in determining the energies and geometries of different conformers, tautomers or molecular complexes. The Free-Jet Absorption Millimeter Wave spectroscopy and the Pulsed-Jet Fourier Transform Microwave spectroscopy have been applied to perform these studies and the obtained results showcase the suitability of these techniques for the study of conformational surfaces and intermolecular interactions. The series of investigations of selected medium-size molecules and complexes have shown how different instrumental setups can be used to obtain a variety of results on molecular properties. The systems studied, include molecules of biological interest such as anethole and molecules of astrophysical interest such as N-methylaminoethanol. Moreover halogenation effects have been investigated on halogen substituted tautomeric systems (5-chlorohydroxypyridine and 6-chlorohydroxypyridine), where it has shown that the position of the inserted halogen atom affects the prototropic equilibrium. As for fluorination effects, interesting results have been achieved investigating some small complexes where a molecule of water is used as a probe to reveal the changes on the electrostatic potential of different fluorinated compounds: 2-fluoropyridine, 3-fluoropyridine and penta-fluoropyridine. While in the case of the molecular complex between water and 2-fluoropyridine and 3-fluoropyridine the geometry of the complex with one water molecule is analogous to that of pyridine with the water molecule linked to the pyridine nitrogen, the case of pentafluoropyridine reveals the effect of perfluorination and the water oxygen points towards the positive center of the pyridine ring. Additional molecular adducts with a molecule of water have been analyzed (benzylamine-water and acrylic acid-water) in order to reveal the stabilizing driving forces that characterize these complexes.

Development of synthetic methods of silicon nanocrystals functionalized with photoactive molecules

The thesis is focused on the development of a method for the synthesis of silicon nanocrystals with different sizes, narrow size distribution, good optical properties and stability in air. The resulting silicon nanocrystals have been covalently functionalized with different chromophores with the aim to exploit the new electronic and chemical properties that emerge from the interaction between silicon nanocrystal surface and ligands. The purpose is to use these chromophores as light harvesting antennae, increasing the optical absorption of silicon nanocrystals. Functionalized silicon nanocrystals have been characterized with different analytical techniques leading to a good knowledge of optical properties of semiconductor quantum dots.

Upgrading Bio-Platform Molecules in the Gas-Phase: From Levulinic Acid to Bio-Chemicals

Levulinic acid (LA) is a polyfunctional molecule obtained from biomass. Because of its structure, the United States Department of energy classified LA as one of the top 12 building block chemicals. Typically, it is valorized through chemical reduction to γ-valerolactone (GVL). It is usually done with H2 in batch systems with high H2 pressures and noble metal catalysts, making it expensive and less applicable. Therefore, alternative approaches such as catalytic transfer hydrogenation (CTH) through the Meerwein–Ponndorf–Verley (MPV) reaction over heterogeneous catalysts have been studied. This uses organic molecules (alcohols) which act as a hydride transfer agent (H-donor), to reduce molecules containing carbonyl groups. Given the stability of the intermediate, reports have shown the batch liquid-phase CTH of levulinate esters with secondary alcohols, and remarkable results (GVL yield) have been obtained over ZrO2, given the need of a Lewis acid (LASites) and base pair for CTH. However, there were no reports of the continuous gas-phase CTH of levulinate esters. Therefore, high surface area ZrO2 was tested for gas-phase CTH of methyl levulinate (ML) using ethanol, methanol and isopropanol as H-donors. Under optimized conditions with ethanol (250 ℃), the reaction is selective towards GVL (yield 70%). However, heavy carbonaceous materials over the catalyst surface progressively blocked LASites changing the chemoselectivity. The in situ regeneration of the catalyst permitted a partial recovery of the LASites and an almost total recovery of the initial catalytic behavior, proving the deactivation reversible. Tests with methanol were not promising (ML conversion 35%, GVL yield 4%). As expected, using isopropanol provided complete conversion and a GVL yield of 80%. The reaction was also tested using bioethanol derived from agricultural waste. In addition, a preliminary study was performed for the hydrogenolysis of polyols to produce bioethanol, were Pd-Fe catalyst promoted the ethanol selective (37%) hydrogenolysis of glycerol.

Advanced Luminescent Materials for Technological Applications

This thesis focusses on the study of several luminescent materials and investigates some related technological applications. It is made of six chapters. Chapter 1 introduces a brief history, basic principles and applications of photoluminescence. Chapter 2 presents the photophysical properties of five benzoheterodiazole dyes. These molecules were incorporated in PMMA- and PDMS-based LSC-PV devices to determine the emission quantum yields, transmission, re-absorption and IPCE properties. DFT calculations were performed to investigate the structures and energy levels of these dyes. Chapter 3 concerns the preparation of a luminescent film to calibrate an ESA satellite that will monitor the fluorescence of terrestrial vegetation. ZnPc was selected as suitable dye to make the film. Ferrocene was selected as quencher to control the emission intensity. An industrial printing technology was used to produce large-area calibration sheets coated with green pigment that simulates the NIR reflectance of green plants in which the ZnPc is embedded. Photophysical properties of a series of alkynyl gold NHC complexes containing naphthalimide chromophore were studied in Chapter 4. All the compounds were studied in solution and solid state. Further investigations were carried out by incorporating these compounds in PMMA matrix to make films. XRD and DFT calculations were made to determine the structures and energy levels of the complexes. In chapter 5 we studied the photophysical properties of star-shaped molecular systems which can operate as molecular motors when attached onto surface, along with those of their related ligands/moieties in tetrahydrofuran solution. The photophysical properties of these molecular systems can show if they are suitable to operate as light-triggered molecular machines. Finally, chapter 6 concerns the photoluminescence behavior of three NHC half-sandwich Ir/Rh metal complexes. The photophysical properties of these compounds were examined in CH2Cl2 solutions and PMMA films. These complexes may prove potential candidates for organic phosphorescent materials.

Multifarious tumor-oriented small molecules: development of synthetic methodologies and application for diagnostic platforms

Cancer represents one of the most relevant and widespread diseases in the modern age. In this context, integrin receptors are important for the interactions of cells with extracellular matrix and for the development of both inflammation and carcinogenic phenomena. There are many tricks to improve the bioactivity and receptor selectivity of exogenous ligands; one of these is to integrate the amino acid sequence into a cyclic peptide to restrict its conformational space. Another approach is to develop small peptidomimetic molecules in order to enhance the molecular stability and open the way to versatile synthetic strategies. Starting from isoxazoline-based peptidomimetic molecules we recently reported, in this thesis we are going to present the synthesis of new integrin ligands obtained by modifying or introducing appendages on already reported structures. Initially, we are going to introduce the synthesis of linear and cyclic α-dehydro-β-amino acids as scaffolds for the preparation of bioactive peptidomimetics. Subsequently, we are going to present the construction of small molecule ligands (SMLs) based delivery systems performed starting from a polyfunctionalised isoxazoline scaffold, whose potency towards αVβ3 and α5β1 integrins has already been established by our research group. In the light of these results and due to the necessity to understand the behaviour of a single enantiomer of the isoxazoline-based compounds, the research group decided to synthesise the enantiopure heterocycle using a 1,3-dipolar cycloaddiction approach. Subsequently, we are going to introduce the synthesis of a Reporting Drug Delivery System composed by a carrier, a first spacer, a linker, a self-immolative system, a second spacer and a latent fluorophore. The last part of this work will describe the results obtained during the internship abroad in Prof. Aggarwal’s laboratory at the University of Bristol. The project was focused on the Mycapolyol A synthesis.

Small molecules exploiting emerging therapeutic opportunities for breast cancer treatment

Among the different types of breast cancer (BC), the estrogen receptor positive (ER+) subtype, which requires estrogens for its growth and proliferation, is the most common, while triple negative BC, characterized by the absence of ER, progesterone receptor and human epidermal growth factor receptor 2, often leads to poor prognosis. First-line therapies for the treatment of ER+ BC act either by suppressing estrogen production, through the inhibition of aromatase (AR) enzyme, or by blocking estrogen prooncogenic activity, via the modulation/degradation of ERs. The serious side effects and the intrinsic or acquired resistance phenomena that arise with prolonged use of these drugs limit their therapeutic application, stimulating the search for new strategies to face this disease. In this context, the development of dual acting aromatase inhibitors, able to target both the orthosteric and the recently identified allosteric pockets of AR could be an opportunity to fight ER+ BC. Another promising strategy could be the development of multitarget compounds, targeting both AR and ERs. In this scenario, here we designed and synthesized two series of new xanthones or more flexible benzophenones as potential dual acting aromatase inhibitors. Moreover, inspired from tamoxifen metabolites and a literature compound endowed with activity on both AR and ER, different structurally related series of potential multitarget compounds were developed. The biological results showed that some of the new molecules were promising candidates for further development. It was recently observed that the lately discovered histamine H4 receptor is expressed in human breast tissue, displaying a key role in biological processes mediated by histamine such as cell proliferation, senescence, and apoptosis in malignant cells, representing a potential target in triple negative BC. Thus, a broad series of methyl quinazoline sulfonamides, carrying different functional groups on the sulfonamide moiety, were designed and synthesized as potential H4 receptor ligands.

A take on complexity: bio-molecules and human metabolism interaction modelling for health and nutrition with machine learning

The advent of omic data production has opened many new perspectives in the quest for modelling complexity in biophysical systems. With the capability of characterizing a complex organism through the patterns of its molecular states, observed at different levels through various omics, a new paradigm of investigation is arising. In this thesis, we investigate the links between perturbations of the human organism, described as the ensemble of crosstalk of its molecular states, and health. Machine learning plays a key role within this picture, both in omic data analysis and model building. We propose and discuss different frameworks developed by the author using machine learning for data reduction, integration, projection on latent features, pattern analysis, classification and clustering of omic data, with a focus on 1H NMR metabolomic spectral data. The aim is to link different levels of omic observations of molecular states, from nanoscale to macroscale, to study perturbations such as diseases and diet interpreted as changes in molecular patterns. The first part of this work focuses on the fingerprinting of diseases, linking cellular and systemic metabolomics with genomic to asses and predict the downstream of perturbations all the way down to the enzymatic network. The second part is a set of frameworks and models, developed with 1H NMR metabolomic at its core, to study the exposure of the human organism to diet and food intake in its full complexity, from epidemiological data analysis to molecular characterization of food structure.

Design, realization, and characterization of complex reaction networks in dynamic mechanically interlocked molecules

The experimental projects discussed in this thesis are all related to the field of artificial molecular machines, specifically to systems composed of pseudorotaxane and rotaxane architectures. The characterization of the peculiar properties of these mechano-molecules is frequently associated with the analysis and elucidation of complex reaction networks; this latter aspect represents the main focus and central thread tying my thesis work. In each chapter, a specific project is described as summarized below: the focus of the first chapter is the realization and characterization of a prototype model of a photoactivated molecular transporter based on a pseudorotaxane architecture; in the second chapter is reported the design, synthesis, and characterization of a [2]rotaxane endowed with a dibenzylammonium station and a novel photochromic unit that acts as a recognition site for a DB24C8 crown ether macrocycle; in the last chapter is described the synthesis and characterization of a [3]rotaxane in which the relative number of rings and stations can be changed on command.

Ions and Small Molecules as Modulators of F1FO-ATPase, Mitochondrial Bioenergetics and Cell Metabolism

The properties of the mitochondrial F1FO-ATPase activated by the natural cofactor Mg2+ or by Ca2+, were studied, mainly on heart mitochondria from swine, widely used in translational medicine. The Ca2+ driven conformational changes in the F1FO-ATPase form the mitochondrial permeability transition pore (mPTP), which triggers regulated cell death and is involved in severe pathologies. The Ca2+-activated F1FO-ATPase hydrolyzes ATP with kinetics slightly different from those of the Mg2+-ATPase. Known F1-ATPase inhibitors inhibit both the Ca2+-activated F1FO-ATPase and the mPTP formation strengthening the molecular link between them. The different Gd3+ effects on the Ca2+- and Mg2+-activated F1FO-ATPases confirm their difference as also phenylglyoxal which preferentially inhibits the Ca2+-activated F1FO-ATPase. The effects of phenylarsine and dibromobimane, which interact with differently distant Cys thiols, show that mPTP opening is ruled by nearby or distant dithiols. Bergamot polyphenols and melatonin inhibit the mPTP and ROS formation. H2S, a known cardiovascular protector, unaffects the F1FO-ATPase, but inhibits Ca2+ absorption and indirectly the mPTP, both in swine heart and mussel midgut gland mitochondria. New generation triazoles inhibit the Ca2+-activated F1FO-ATPase and the mPTP, but unaffect the Mg2+-activated F1FOATPase. In parallel, the energy metabolism was investigated in mammalian cells. In boar sperm ATP is mainly produced by mitochondrial oxidative phosphorylation (OXPHOS), even if it decreases over time because of less active mitochondria. Insufficient ATP may induce sperm dysfunction. Also, canine mesenchymal stem cells rely on OXPHOS; those from umbilical cord which produce more ATP than those from adipose tissue, seem preferable for transplant studies. The intestinal porcine enterocyte cell line IPEC-J2, used for human gut research, responds to different fetal bovine serum concentrations by remodeling OXPHOS without altering the bioenergetic parameters. The IPEC-J2 bioenergetics is modulated by Vitamin K vitamers. These data shoulder cell bioenergetics as precious tool for medical research.

Novel developments of atropisomeric organic molecules. Design of atropisomeric drugs, fluorescent compounds and investigation of reaction mechanisms.

In recent years, the study of restricted rotation bonds in organic compounds has aroused increasing interest. The reason is that this characteristic can lead to obtaining new properties in organic compounds. In this research thesis, an intense investigation was carried out using DFT calculations and experimental evaluation of the barriers to rotational energies, in order to discover new properties deriving from the restricted rotation bonds. Research has been developed in various fields of organic chemistry, ranging from drugs (the atropisomeric atorvastatin in Chapter 3) to luminescent compounds (aryls amino borane in Chapter 4). Furthermore, an organocatalytic central to axial conversion mechanism was investigated through DFT calculations, finding out interesting outcomes (Chapter 5). Finally, a project in collaboration with Dr. Farran and Prof. Vanthuyne of the Aix-Marseille University was done to investigate the interactions in transition states of rotational barriers.

Rotational and ro-vibrational analyses of molecules of astrochemical interest

The rotational and ro-vibrational spectroscopy analysis of selected molecules of astrophysical importance, namely formaldehyde, mono-deuterated hydrogen sulfide, cyanoacetylene, deuterated cyanoacetylene, aminoacetonitrile, allylimine, and 2-aza-1,3-butadiene, has been presented in this thesis. For formaldehyde and mono-deuterated hydrogen sulfide, which are well-known interstellar molecules, a detailed Measured Active Rotational–Vibrational Energy Levels (MARVEL) analysis has been performed. For both of them, the MARVEL approach has been used to accurately derive the rotational and ro-vibrational energy levels from the experimental data available in the literature combined with new millimeter-wave measurements. Overall, the MARVEL analysis span a huge frequency range, from millimeter-wave to infrared (IR). For allylimine and 2-aza-1,3-butadiene, the pure rotational spectrum has been extended to the millimeter-wave region. The outcome of these two studies is the derivation of very accurate spectroscopic parameters that allow the accurate prediction of their rotational transitions over a large frequency range. For allylimine, this line catalog allowed the tentative detection of two isomers of allylimine (Ta and Ts) towards the G+0.693 molecular cloud. In addition to rotational spectroscopy, high-resolution IR spectra of interstellar molecules play also of pivotal role for the exploration of astromomical objects. For these reasons, high-resolution IR spectra of cyanoacetylene, deuterated cyanoacetylene, and aminoacetonitrile have been investigated. The precise spectroscopic constants of several vibrational excited states of these three molecules have been derived from the assignment of newly recorded IR spectra. Given the fact that all these three molecules are potentially present in Titan’s atmosphere, their ro-vibrational transitions can be considered unvaluable tools for their search, which might also be extended to other planetary atmospheres.

Development of a porcine lactation model for the evaluation of mammary transfer of exogenous molecules - A contribution from the conception project

Around 5 million women give birth each year in Europe and, while breastfeeding, the majority of them may need to take medications, either occasionally or continuously. Unfortunately, there is often scarce evidence of trustworthy information about how a specific molecule might affect the physiology of lactation. This is the reason that brought a European public-private partnership to fund the development of a reliable platform to provide women and health-care professionals a helpful instrument to reduce uncertainty about the effects of medication used during breastfeeding. On April 1st 2019, the ConcePTION project (Grant Agreement n°821520) started to develop such envisaged platform. The 3rd Work Package was in charge of the validation of in vitro, in vivo and in silico lactation models. Between the numerous species currently used in preclinical studies, pigs’ similarities with humans’ anatomy, physiology and genomics make them extremely useful as translational models, when proper veterinary expertise is applied. The ASA team from the University of Bologna, went first to characterize the translational lactation model using the swine species, chosen upon literature review. The aim of this work was to lay the foundations of a porcine lactation model that could be suitable for application within pharmaceutical tests, to study drug transfer through milk prior approval and commercialization. The obtained results highlighted both strengths and critical points of the study design, allowing a significant improvement in the knowledge of pharmacokinetic physiology in lactating mammals. Lastly, this project allowed the assessment of microbial changes in gut resident bacteria of newborns through an innovative in vitro colonic model. Indeed, even if there were no evident adverse effects determined by drug residues in milk, possible alterations in the delicate microbial ecology of newborns’ gastrointestinal tract was considered pivotal, giving its possible impact on the individual health and growth.

Microwave and millimeter-wave spectroscopy of sulfur-containing molecules

The rotational spectroscopy of several sulfur bearing molecules and their 1:1 water complex, cysteamine, cysteamine monohydrate, 1-thioglycerol and 1-propanethiol were studied in the micro-wave and (or) millimeter-wave range. Precise laboratory spectra and conformational information were obtained. For cysteamine, the conformational space (at the B3LYP-GD3(BJ)/Def2-TZVP level) and the measurement and analysis of its rotational spectra in the 6 - 18 and 59.6 - 120 GHz are reported. The hyperfine structure of the rotational spectra was observed and analyzed for the first time. Based on the measured spectra, a search of the different conformers of cysteamine was performed toward the G+0.693-0.027 molecular cloud. We computed the upper limit of the ratio of ethanolamine to cysteamine, which is >0.8−5.3. For the cysteamine monohydrate, the conformational space was explored (at the B3LYP-GD3(BJ)/Def2-TZVP level). The rotational spectra of the cysteamine monohydrate complex have been assigned in the frequency range 6 – 18.5 GHz. The global minimum, Conf A1, was the only observed one. The 34S isotopologue of Conf A1 was observed in natural abundance, while 18O isotopologue was detected by introducing the H218O. In this conformer, the water molecule plays both proton donor and acceptor roles, forming a OHw···N interaction, a SH···Ow interaction and a CH···Ow interaction. The conformational space of 1-thioglycerol has been characterized by quantum mechanical calculation and its rotational spectrum has been recorded and analyzed in the frequency range 59.6 - 78.4 GHz. The global minimum of 1-thioglycerol is gTg’Gg’ and were detected together with gTg’Tg and gGgG’g, while the two detected conformers are g’G’gGg’ and tGgGg. The high-resolution rotational spectrum of 1-propanethiol in the frequency range 59.6 – 78.4 GHz was measured. Two conformers, Gg and Tg, were observed and their spectra were analyzed. Considering the overall conformational space calculated at the B3LYP-GD3(BJ)/Def2-TZVP level they are among the lowest energy conformers.