Verdedigde doctoraten

Priyanka Shaw

• 21/12/2021
• 1 p.m.
• Venue: Campus Drie Eiken, O.02
• ​Online PhD defence
• You must present a valid Covid Safe Ticket and ID to attend this defence
• Supervisors: Annemie Bogaerts, Evelien Smits & Angela Privat-Maldonado
• Department of Chemistry

Abstract

Reactive oxygen and nitrogen species (RONS) generated by cold atmospheric plasma (CAP) can activate discrete signaling transduction pathways or disrupt redox cellular homeostasis, depending on their concentration. This makes that CAP possesses the therapeutic potential for wound healing, cancer, and other diseases. In order to effectively use CAP in the clinic, a clear understanding of the interaction of RONS with biomolecules (lipids, proteins, and nucleic acids) from the atomic to the macro scale, and their biological significance, is needed.

In this work, I have therefore studied the dual role of CAP-derived RONS, i.e., (i) in the signaling pathways involved in wound healing, and (ii) in their reaction with biomolecules to cause oxidation-mediated damage. I performed computer simulations to provide fundamental insight about the occurring processes that are difficult or even impossible to obtain experimentally. Furthermore, next to computational studies, I used both 2D and 3D tissue cultures. The 3D model allows proliferation in a more physiologically relevant geometry that stimulates the production of extracellular matrix proteins.

I investigated the treatment of human gingival fibroblasts with low doses of CAP-generated RONS. This treatment demonstrated that it can inhibit colony formation but does not induce cell death, induce the expression of metalloprotease proteins, induce extracellular matrix degradation, and promote cell migration, which could result in enhanced wound healing.

In contrast, at high concentrations, RONS can disrupt the cell membrane integrity and induce cancer cell death through oxidative stress-mediated pathways. I discovered how oxidation of the cell membrane (lipid-peroxidation) can facilitate the access of a drug (Melittin) into cancer cells, and in this way, reduce the required therapeutic dose of Melittin in melanoma and breast cancer cells (demonstrated using in vitro, in ovo and in silico approaches). Furthermore, I studied how excessive lipid-oxidation in chemoresistant pancreatic cancer cells promotes ferroptotic cell death. This was due to the stimulation of the iron-dependent Fenton reaction by targeting a redox-specific signaling network. However, upon oxidative stress, cells protect themselves via a sophisticated intracellular antioxidant system that involves the regulation of glutathione/glutathione peroxidase 4 (lipid repair enzyme). Cancer cells exhibited increased levels of intracellular RONS due to their hypermetabolism, leading to high expression of anti-oxidant systems. I, therefore, focus on the effect of reactive species on the intracellular anti-oxidant system and corresponding DNA damages in both temozolomide-sensitive as well as temozolomide-resistant glioblastoma spheroids, in a 3-dimensional tumor model with a more complex tumor microenvironment than cell monolayers.

Jonathan Bogaerts

• 04/11/2021
• 4 p.m.
• Venue: Campus Middelheim, G0.10
• You must present a valid Covid Safe Ticket and ID to attend this defence
• ​Online PhD defence
• Supervisor: Christian Johannessen
• Department of Chemistry

Abstract

The importance of molecular structure determination is well recognized by scientist within a wide range of disciplines, including organic and physical chemists as well as pharmacists. The reason hereof is that information on the molecular structure can for example provide insight in the mode of action, create a better understanding on reaction mechanisms or can help in the rational design of new drug scaffolds. Fortunately, today many different techniques are available to help scientists in this quest. X-ray crystallography and Nuclear magnetic resonance (NMR) spectroscopy are probably the most wide-spread techniques for this purpose as they can provide structural information at atomic resolution. However, as one technique seldom permits to obtain all pieces of the structural puzzle, in most cases a combination of techniques are employed. Therefore, it is of utmost importance to understand what information can be extracted using a specific technique and understand its complementarity with regards to other methods.

This thesis focusses on exploring the application of the vibrational spectroscopic technique Raman optical activity (ROA) to determine the molecular structure of a molecule in solution. ROA is a so-called chiroptical method and is measured as the difference in right- and left circular polarized components of the Raman scattered light by a chiral molecule. In other words, ROA spectroscopy combines the wealth of structure sensitive bands present in a Raman vibrational spectrum with the sensitivity towards chirality. In the past, this unique combination has proven to be particularly useful in the study of the conformational behaviour of biomacromolecules such as proteins and carbohydrates. However, the application of ROA for molecular structure determination beyond these is rather limitedly examined and, consequently, not fully understood yet.

To start bridging this gap, in this thesis ROA was applied to a wide variety of chiral molecular to create a better understanding of both opportunities/strengths and weaknesses/limitations of ROA spectroscopy towards its applicability for structure determination.

Rani Moons

• ​23/09/2021
• 4 p.m.
• ​Online PhD defence
• Venue: CGB, U.024
• You must present a valid Covid Safe Ticket and ID to attend this defence
• Supervisors: Frank Sobott & Stuart Maudsley
• Department of Chemistry

Abstract

Over the last years the use of mass spectrometry (MS) in the structural biology field has significantly increased. Native MS approaches, structure-sensitive digestion and fragmentation, crosslinking and labeling techniques coupled to MS gained their position in the structural MS field. The information obtained includes the protein mass, subunit stoichiometry of protein complexes, which protein regions are solvent exposed or buried inside the structure, ligands interacting with the protein, ligand stoichiometry, ligand binding sites, general shape and conformational changes of the protein, protein-protein interaction sites and the protein sequence with eventual mutations or post translational modifications (PTMs). An important class of proteins are intrinsically disordered proteins (IDPs), that account for over 30% of all eukaryotic proteins. With a (partial) natively disordered structure these proteins are very challenging to characterize, due to their dynamic and heterogeneous conformational ensemble. Development and use of structural MS is important to further elucidate IDP structure since MS methods can cope with their flexible and dynamic nature.

In this thesis the IDP alpha synuclein (α-syn) is investigated using various MS approaches, to further characterize this protein and show the possibilities of MS as a structural technique in the challenging field of IDP characterisation. α-syn consists of 140 amino acids, is mainly expressed in presynaptic nerve terminals and plays a major role in the development of Parkinson’s disease (PD). α-syn monomers can aggregate and form intermediate structures such as oligomers, which then further aggregate and form mature α-syn fibrils. Various factors, e.g. mutations, PTMs, ligands, pH, presence of biological membranes, can affect this aggregation pathway. It is important to know how these changes occur at the molecular level to gain more understanding about aggregate formation and how this might be tackled.

Using native and ion mobility (IM) MS it was investigated if we can characterize interactions and conformational changes of α-syn monomers, and we show how instrumental advances in MS contribute to the structural IDP field. Native IM-MS was also used to determine possible structural effects of disease related mutations and relevant PTMs of α-syn. Finally we show that MS-based techniques can bridge the gap between molecular events that determine monomer conformations and the resulting aggregate structures. In general the value, relevance and importance of using MS-based techniques in the structural biology field to study challenging systems such as IDPs to characterize their full conformational ensemble and aggregation pathway is highlighted.

Nick Sleegers

• ​20/09/2021
• 2 p.m.
• ​Online PhD defence
• Supervisor: Karolien De Wael
• Department of Chemistry

Abstract

Unnecessary exposure of bacteria to antibiotics accelerates antimicrobial resistance and thereby comprising the effectiveness of antibiotic treatments. Therefore, there is a need for better surveillance of antibiotics when released in the environment. Monitoring of antibiotic levels discharged in waste waters is one of many necessary measures. The use of electrochemistry is an inviting approach to address this surveillance need and, in general, it allows a fast, on-site and sensitive detection of low concentrations. The aim of this PhD thesis is to gain comprehensive insight in the voltammetric behavior of the cephalosporin antibiotics. Therefore, four cephalosporin antibiotics and the two main intermediates, were subjected to an electrochemical fingerprinting study. Oxidation signals of the core structure and the different side chains were elucidated. Their respective signals were further exploited to allow simultaneous detection of different cephalosporins in a single analysis below one minute. In parallel, investigations into the oxidation products were undertaken for all the redox centers of the cephalosporins. A combination of small scale electrolysis and liquid chromatography coupled to quadrupole-time-of-flight mass spectrometry was used to produce and identify the products formed during oxidation of the redox centers, which were subsequently fitted into the electrochemical frameworks provided by voltammetric analysis. This combined strategy allowed the identification of the mechanisms behind the oxidation of the three redox centers in cephalosporins. In order to develop a monitoring strategy for cephalosporins, the influence of the degradation on the electrochemical fingerprint had to be taken into account as degradation is employed to reduce antibiotic levels in industrial effluents before their release into the environment. Therefore, the changes of the voltammetric fingerprints upon degradation were investigated. It was shown that the characteristic voltammetric signals of the cephalosporin core structure disappeared upon hydrolysis. Additional oxidation signals that appeared after degradation were elucidated and linked to different inactive degradation products. Lastly, the research activity was directed towards the coupling of electrochemistry at screen printed electrodes to HPLC analysis. Essentially, the knowledge gained in the electrochemical fingerprints of cephalosporins was exploited and applied into the field of chromatographic analysis. Hereby, generating an extra dimension of separation to electrochemical analysis which will aid in the analysis of complex mixtures and matrices. The approach gave promising results as 15 antibiotics from four different classes were detected at low ppb-level.

Elise Daems

• 03/06/2021
• 4 p.m.
• ​Online PhD defence
• Supervisors: Karolien De Wael & Frank Sobott
• Department of Chemistry

Abstract

Aptamers are short, synthetic DNA or RNA molecules that are characterized by a specific 3D conformation which enables specific target recognition. Aptamers are promising tools in many application fields from sensing to therapeutics. One of the major challenges in the aptamer field is understanding the relationship between the sequence and what determines the higher-order structure and specific interactions with targets. Therefore, this PhD thesis focuses on the use of different mass spectrometry (MS) based approaches to characterize aptamers and their interactions. Several of these approaches are already widely applied to study other biomolecules, such as proteins, but are still largely unexplored for aptamers and oligonucleotides in general. ​ ​

A first focus was put on obtaining information on the higher-order structure and conformational stability of aptamers using a combination of MS and with ion mobility (IM) spectrometry by performing collision-induced unfolding (CIU) experiments. CIU was shown to hold great promise to analyze the conformational dynamics and gas-phase stabilities of aptamers.

Next, the capabilities and limitations of native IM-MS for the analysis of noncovalent interactions of aptamers were demonstrated. The conformational behavior and interactions of cocaine-binding aptamers were studied and it was found that relative binding affinities of aptamers that only differ slightly in sequence and structure can be determined using native MS. Moreover, native IM-MS allowed the detection of small conformational changes upon binding of a target, which were found to be dependent on the binding mode of the aptamer. An adaptive binding mechanism was suggested for flexible aptamers that require more reorganization upon binding. ​ ​

In the final part of this thesis, the importance of thoroughly characterizing and validating aptamer-target interactions before using them in an application was emphasized. Moreover, the gathered insights were applied in our own development of a proof-of-concept aptamer-based sensor. This was shown by investigating the interactions of ampicillin aptamers which were found to not bind the target they were selected for in the first place. A multi-analytical approach combining complementary techniques was used for this purpose since no single technique is generally applicable to characterize all aptamers and their interactions and to obtain a comprehensive picture of the aptamer-target interactions. Furthermore, such multi-analytical approach was used to characterize a testosterone-binding aptamer while developing an aptamer-based electrochemiluminescent sensing strategy for this target. This shows the importance of native MS, in combination with other techniques, to thoroughly understand the aptamer-target interactions in the development of a designed application.

Nick Hoeven

• 18/02/2021
• 2 p.m.
• ​Online PhD defence
• Supervisor: Pegie Cool
• Department of Chemistry

Abstract

The earth has been warming up at an unprecedented pace during the last decades, which is majorly caused by increasing greenhouse gases. High CO2 concentrations in the atmosphere led to worldwide awareness of environmentally conscious thinking and acting to reduce this compound and other greenhouse gases. CO2 conversion makes valorization possible through valuable chemicals and fuels. This cradle-to-cradle philosophy is necessary in our current society, both reducing atmospheric greenhouse gases and simultaneously partly responding to the need for alternative fuels. This is fundamental as continuous increase of anthropogenic greenhouse gases are one of the most important issues of this and future generations.

In this thesis, the photocatalytic reduction of CO2 with H2 in the gas phase over modified Ti-Beta zeolites is studied. The goal of this thesis is the development of improved photocatalytic materials for CO2 applications in the gas phase and to overcome limitations posed by the use of TiO2 and classical semiconductors.

Different methods for CO2 utilization and conversion have been discussed. Furthermore, an overview on the mechanism of photocatalysis and the limitations of the use of TiO2, as well as the strategies to overcome those limitations have been described. In particular, the superior photocatalytic activity of isolated tetrahedrally coordinated Ti-species in combination with the high surface area of zeolites has been highlighted. The importance of a well-designed photocatalytic reactor and its influence on the turnover frequencies (TOFs) of the reaction products are also described. The experimental work focusses on the optimization of the synthesis method and the Ti loading of the Ti-Beta zeolites. Next, the synthesized zeolites are tested in a photocatalytic reactor and the influences of the material properties on the product TOFs are discussed. In order to further enhance the photocatalytic properties and the product selectivities of the catalysts, noble metal nanoparticles (Pt and Pd) are deposited onto the Ti-Beta zeolites. Finally, alternative catalysts (e.g. 3D printed structures and Z-scheme catalysts) are tested in the photocatalytic reactor and compared to the highest performing Ti-Beta catalysts.

In conclusion, this PhD has put a step forward in the development of novel and highly active photocatalytic materials, with improved performance compared to classical pure TiO2, for the photocatalytic reduction of CO2 in the gas phase.

Sumit Srivastava

• 15/02/2021
• 1 p.m.
• ​Online PhD defence
• Supervisor: Pegie Cool
• Department of Chemistry

Abstract

The main objective of this work was to contribute towards the co-utilization of CO2(g) and residues from metallurgical industries to produce Fe-carbonate bonded monoliths that are free from cement clinker. While excessive CO2 is considered a significant problem due to the increased global warming and its associated effects, Fe-rich metallurgical wastes are still used for low-value applications or are landfilled. Moreover, due to the volume of their use, construction materials production accounts for 7-8% of total CO2-emissions. Therefore, the co-utilization of slag and CO2 to produce construction materials has significant potential to contribute towards achieving future sustainability goals. In this study, Fe(0) is initially chosen as a model system to understand the feasibility of producing FeCO3-bonded monoliths under the desired reaction conditions (<100 °C, and <25 bar CO2-pressure). In addition to demonstrating the feasibility of FeCO3-cementation, the underlying reaction mechanisms are also discussed. Since the dissolution of Fe-sources is usually known to be the rate-limiting step, Fe-dissolution in dilute conditions is studied as a function of temperature, CO2-pressure, and time. Similar to the dissolution studies on Fe(0), dissolution studies in dilute solutions are also extended to the Fe-Si rich non-ferrous slags as a function of temperature, CO2-pressure, and time. In both the studies, it is shown that high temperature and CO2-pressure are conducive towards the dissolution of Fe(0) and Fe-rich slags. To transfer the knowledge of FeCO3-cementation from the model Fe(0) system to the sources in which Fe co-exists with Ca, FeCO3-cementation in CO2-H2O-Fe(0)-Ca(OH)2 systems is also studied. The importance of microstructures of the products, and the formation of mixed (Ca, Fe)-carbonates is pointed in this study. Finally, it is shown that the non-ferrous slags can be co-utilized with ferrous metallurgical slags rich in Ca to produce carbonate-bonded monoliths with high mechanical strength. It is shown that the carbonation of the non-ferrous slags as mixes with ferrous slags can lead to a significant decrease in environmental leaching. With more than 575 million tonnes of metallurgical slags produced every year, they offer an opportunity for significant CO2-mineralization as well as to produce low-carbon construction materials.

Jeroen Bomon

• 02/02/2021
• 16.00 uur
• ​Online doctoraatsverdediging​
• Promotor: Bert Maes
• Departement Chemie

Abstract

De noodzaak om CO2 uitstoot terug te dringen, de prijsstijging van aardolie en de krimpende voorraden ervan maken het voor de maatschappij noodzakelijk om te investeren in de ontwikkeling van nieuwe, duurzamere manieren om te voldoen aan de noden van een continu groeiend bevolkingsaantal. De fabricage van producten gebaseerd op (bio)hernieuwbare grondstoffen is een mogelijke manier om dit aan te pakken. Als voorbeeld werden producten afgeleid van (hemi)cellulosereeds veelvuldig onderzocht en worden zelfs reeds toegepast in de industrie. Deze biopolymeren bevatten echter geen aromatische eenheden, wat bij voorkeur ander plantaardig materiaal vereist om deze belangrijke bouwstenen beschikbaar te maken voor de chemische industrie.

In dit Doctoraatsproefschrift werd het gebruik van hernieuwbare substraten, dewelke in hun structuur aromatische eenheden bevatten, vooropgesteld voor chemische omzetting. Bijvoorbeeld, biopolymeer lignine, de grootste bron aan bioaromatische verbindingen op aarde is potentieel een geschikte bron aan startmateriaal. Verscheidene routes zijn gekend om lignine the depolymeriseren in moleculen met een laag moleculair gewicht, waarvan een overzicht wordt weergegeven in Hoofdstuk 1. In Hoofdstukken 2-4 werd een waaier aan substraten afgeleid van lignine omgezet in waardevolle producten d.m.v. functionaliseringen en defunctionaliseringen. Naast lignine zijn ook ferulazuur en eugenol, respectievelijk bekomen uit rijstzemelen en kruidnagel, nuttige substraten in dit onderzoek. ​ ​

In Hoofdstuk 2 wordt een goekope methode, enkel gebruik makend van een sterk zuur en heet water onder druk, voorgesteld om deze monomeren te defunctionaliseren op zowel koolstof- als zuurstofatomen van de dialkoxyareen-eenheden, hetgeen aanleiding geeft tot vorming van een hydroxybenzeen (fenol, catechol, pyrogallol en afgeleide isomeren) als product. Gelijkaardige omstandigheden, gebaseerd op het gebruik van hetzelfde sterk zuur of een heterogeen alternatief worden beschreven in Hoofdstuk 3 omtrent selectieve defunctionalisering op zuurstofatomen in de monomeren, hetgeen leidt tot vorming van C-gealkyleerde hydroxybenzenen. Naast deze werkwijzen voor defunctionalisering, wordt functionalisering van biohernieuwbaar substraat met stikstofatomen beschreven in Hoofdstuk 4, gezien dit element cruciaal is in de productie van verbindingen met farmaceutische of agrochemische toepassing. 

Het gebruik van een biohernieuwbare grondstof is één van de 12 Principes van Groene Chemie. Om te analyseren of de ontwikkelde reactiecondities eveneens kunnen beschouwd worden als “groen”, werd de CHEM21 Green Metrics Toolkit toegepast op zowel de nieuwe ontwikkelde methoden als op literatuurprocedures voor dezelfde reactie of voor de synthese van hetzelfde product, hetgeen ons toelaat een nuttige vergelijking te maken. Het resultaat van deze analyse wordt beschreven in Hoofdstuk 5. 

Yannick Engelmann

• 12/01/2021
• 3 p.m.
• ​Online PhD defence​
• Supervisors: Annemie Bogaerts & Erik Neyts
• Department of Chemistry

Abstract

CO2 conversion, CH4 conversion and NH3 synthesis are three essential processes that can help to reduce greenhouse gas emissions. However, these processes typically require harsh reaction conditions when performed thermally, because of the strong chemical bonds of the reactants. Plasma catalysis can provide alternative methods to activating chemical bonds at ambient conditions. Due to the complexity of plasma-catalytic systems, fundamental understanding of the underlying mechanisms is still lacking, impeding the optimization of the technology and holding back its full potential. The aim of this dissertation is to provide fundamental understanding, needed to unlock the full potential of plasma catalysis.

As a tool to acquire the fundamental understanding, we introduced microkinetic modelling to provide detailed information on reaction mechanisms, kinetics and thermodynamics of the processes. In this way, we identified the limitations of thermal processes, but also unraveled if and how plasma-catalytic processes can overcome these limitations. The main difficulty of CO2 hydrogenation is to selectively produce CH3OH at sufficient rates. In plasma catalysis, the contribution of the plasma is twofold: excitation of the reactant molecules, lowering the barrier of dissociation and increasing the conversion rates of the thermal pathways, and generation of reactive radicals and intermediates, allowing new, unique pathways that potentially lead to CH3OH (often in a much faster way).

In the study on the conversion of CH4, we showed the limitations of transition metal catalysts to produce C2-hydrocarbons under thermal conditions. Thermally, the more noble catalysts are not able to dissociate the strong chemical bonds of the CH4 molecule, while the less noble catalysts suffer from cokes formation. In plasma catalysis, dissociation rates on noble catalysts can be increased by vibrationally exciting the reactants, or catalytic dissociation can be avoided by adsorption of plasma-generated radicals. Whether the adsorbed species couple directly to C2-hydrocarbons or undergo further dehydrogenation before coupling, can be controlled by the catalyst binding strength.

Lastly, the potential of the plasma-catalytic NH3 synthesis is locked in the enhanced catalytic rates, caused by plasma-induced excitation and plasma-generated radicals. Again, both vibrationally excited species and plasma-generated radicals are found to improve the NH3 synthesis rates. Due to the contribution of ER reactions, rates are not only increased on noble catalysts, but also on more strongly binding catalysts, making the choice of the catalyst material much less impactful.