Epigenetic regulation is a complex process involving the interplay of multiple different cellular factors. Work described in this thesis concerned the characterisation of proteins involved in the binding to, and demethylation of, histone 3 (H3) tails modified by N-methylation. Initial work focussed on the biophysical characterisation of the tandem plant homeodomains (PHD) of the chromatin remodeller CHD4. NMR spectroscopy was used to investigate the solution structure of the tandem PHDs. Studies on a more native-like construct including the C terminal tandem chromodomains are also presented. Binding studies of the PHDs with H3 peptides reveal that the individual PHD fingers can independently bind a histone peptide. The remainder of the work involved characterisation of JmjC histone demethylases (KDMs), enzymes that catalyse removal of Nε-methyl groups from histone lysyl-residues. Initially, two members of the KDM7 subfamily, PHF8 and KIAA1718, were studied; a high throughput screening assay for them was developed, which enabled identification of a selective inhibitor of the KDM2/7 subfamilies of KDMs, the plant growth regulator Daminozide. A disease relevant mutation in PHF8 was studied and shown to cause mis-localisation of the enzyme to the cytoplasm, providing a potential explanation for the clinically observed phenotype. Subsequent chapters describe unprecedented activities for the JmjC KDMs. 2OG oxygenases catalyse a wide range of oxidative reactions, predominantly mediated by initial substrate hydroxylation. The activity of PHF8 with lysine analogous was tested; the results demonstrated that PHF8, and other KDMs, can oxidatively remove Nε-alkyl groups other than methyl groups, such as ethyl and isopropyl groups. The substrate scope of the JmjC KDMs thus has the potential to be wider than previously thought. Observation of β-hydroxylation of the Nε-isopropyl group of a histone peptide including Nε methylisopropyllysine by JMJD2A/E supports the presumed mechanism of histone lysine demethylation as proceeding via initial hydroxylation. This work led to the discovery that JmjC KDMs can catalyse arginine demethylation. This novel arginine demethylase activity by JmjC KDMs was characterised and the work extended to encompass potential arginine demethylase activity in cells. Biochemical characterisation of UTY, a homologue of the H3 K27 demethylases JMJD3 and UTX, which is reported to be inactive, was carried out; UTY was shown to catalyse demethylation at H3 trimethylated at K27 on peptidic substrates, albeit it at substantially lower rates than the other family members. To investigate the reason for this reduced activity, two variants were made, S1142G and P1214I; the latter variant was shown to be considerably more active than wildtype UTY, likely due to an increased peptide-binding interaction. Preliminary experiments in cells did not conclusively demonstrate histone demethylation, but a luciferase assay suggested that UTY may have catalytic activity in cells. Overall the findings in the thesis suggest that the process of cellular epigenetic regulation is likely even more complex than previously thought, with the potential that JmjC KDMs carry out multiple, context dependent functions.

The aim of this thesis was to identify and develop anti-neuroblastoma agents via two strategies. The first involves a targeted therapy approach towards the synthesis of new drug-like PTP inhibitors (Chapter 2 and 3) and the second involved devising a new versatile synthetic route to the recently established anti-tumour natural-product lead, methyl jasmonates and its analogues (Chapter 4). From a unique proprietary screening library of 5000 drug-like compounds targeted towards PTPs, three compounds from two distinct chemical series, tetrahydroquinolines P00104 and P00341, and thiobarbituric acid P00337, were identified as PTPN22 inhibitors (IC50 = 5 μM) with moderate potency in vitro. A synthetic route to each chemical series was established and optimised and the procedure was used to synthesize a series of rationally-designed analogues for detailed structure-activity relationship (SAR) studies. The compounds were tested for PTP inhibitory activity against PTPN22 via two experimentally optimised protein assays and were tested for cytotoxicity in a number of neuroblastoma cell lines. However, none of the compounds including the resynthesized hits displayed any promising biological activity, and further investigation on these chemical series was abandoned and another strategy for developing anti-neuroblastoma agents was pursued. During the last decade, many studies have reported the cytotoxic effects of methyl jasmonate, a plant stress hormone, against various tumours both in vitro and in vivo. As the research on the anti-tumour properties of methyl jasmonate is still at early stages, and also due to the lack of a versatile synthetic procedure for the preparation of its structural derivatives, detailed SAR studies of this compound have not yet been conducted. In the course of this project, a novel versatile synthetic route to methyl jasmonate and its analogues has been developed, which allows substituents to be readily introduced at the α- and β-position of cyclopentenone. This synthetic procedure will facilitate future extensive SAR studies of methyl jasmonate in tumour cells. The cytotoxic activity of the synthesized methyl jasmonate was confirmed against a range of neuroblastoma cell lines including SK-N-SH, SHSY5Y, LAN5 and the Kelly cells, and a further study on the mechanism by which methyl jasmonate induces neuroblastoma cell death is currently underway.

Caged compounds are biologically active molecules that are rendered inert by masking an important functionality with a photolabile protecting, ‘caging’, group. The caging group can be removed by irradiation with light to reveal the active compound with restored pharmacological activity with high spatial and temporal control. This technology provides an ideal tool for the study of many chemical, physiological and biological systems. This DPhil dissertation highlights several projects in which caging technology has been employed to address biological problems and questions. The first example of spatially controlled mitochondrial inactivation is reported - a tool for the study of the role of mitochondria in Ca2+ signalling. Caged TRPV1 agonists and antagonists have been developed to probe TRPV1, specifically the location of the agonist-binding site. T cell activation has been controlled with light as a tool to gain insight into the adaptive immune response. Caged sodium channel blockers have been investigated. Wavelength-orthogonal photolysis in a neuronal system has been demonstrated using the neurotransmitters glutamate and GABA - this represents a significant advancement in caging technology. This dissertation also includes investigations into the development of novel caging groups.

Dendritic cells (DC) are one of the major antigen presenting cells (APC) of the body. They, by capture of antigen and cross-presentation of these antigens, activate dormant T-cells and co-activate B-cells. As such they regulate the immune system toward either a more humoral type immune response or a more cellular type immune response. These properties have made them very studied over the past decade and many works have focus on the development of vaccine or therapeutic using DCs as a target. However, most of these actual studies have been done by injection of in vitro pre-activated DCs. The major drawback of this technique is the use of non-natural and non individual specific DCs (monocytes derived DCs and/or stem cells DCs). That is why therapeutic carrier targeting specifically DCs has to be developed. To achieve this goal, specific molecules present at the surface of DCs and involved in the activation of the immune system has to be targeted. Among them, DC-Specific ICAM-3 Grabbing Non-integrin CD209 (DC-SIGN) is very specifically expressed only on one subset of DCs called interstitial DCs. This lectin has been proven to be one of the first contacts of the DCs with T-cells and to induce one major interaction for cells proliferation of dormant T-cells. The goal of the project is to design a probe that can be used in vivo and post-mortem to target DCs via DC-SIGN. Therefore, we can use these particles as a proof of concept in vivo and in vitro, record the immune response obtained with them in vivo and in vitro and design probes that can be used to induce specific immune response for future therapy development. Lewis sugars have been shown to be quite specific to DC-SIGN. Their syntheses have been carried out in our lab with a cyanomethylthio linker at their anomeric position. This linker, once activated as a 2-imino-2-methoxyethyl moiety, has permitted the attachment of the oligosaccharides at the surface of dextran-coated iron oxide MRI nanoparticle. These particles have been chosen for their powerful properties and the advantage of the technique they are used for. Indeed, as particles their sizes mimic pathogens and DCs would interact with them, as they will with pathogen. Moreover, many copies of each oligosaccharide could be attached at their surface enhancing the interaction of the particles with the targeted lectin via a multivalent effect. As a technique, MRI has the advantage to be recorded over a long period of time (compare to ¹⁸F PET for example), with a relatively low signal/noise ratio (compare to fluorescence techniques) and without being harmful. FITC fluorescent Lewis X nanoparticles have been actually design and characterised (size by DLS, number of sugar by particles by ICP or fluorescamine fluorescence assay and binding affinity by ELISA with DC-SIGN-Fc). They have been first tested in vitro with models cells (Raji and monocytes derived DCs) for specific uptake assays, where they exhibit specific uptake and internalisation. Lewis-x nanoparticles have also been tested in vivo in a rat model and have been shown to be retained in Lymph nodes compared to control particles. Post mortem analysis appears to demonstrate that these particles were internalised by rat DCs and transported in the centre of the lymph node known as the T-cell region. Finally, cytokines and CD86 concentration measurement have shown that upon internalisation of the nanoparticles, DC maturated. In addition, an antigenic OVA peptide epitope was attached to the surface of the nanoparticles for future T-cell proliferation experiments. It will allow the determination of the immune response expected. In summary, we have developed an immunogenic MRI-active probe that can target specifically DC-SIGN via the interaction with Lewis antigens present at the surface of the probe and trigger DC maturation.

Engineered protein nanopores can be used to investigate a wide range of dynamic processes in real time and at the single-molecule level, for example covalent bond making and breaking or the interaction of ligands with their cognate binding sites. The detection of such processes is accomplished by monitoring the current carried by ions through the pore in an applied potential, which is modulated as molecules of interest interact with engineered binding sites within the pore. In contrast to ensemble measurements, where the behaviour of individual molecules is obscured by averaging, single-channel recordings can identify short-lived intermediates and rare reaction pathways, thereby adding to our understanding of fundamental processes in chemistry and biology. The goal of my thesis work was to engineer alpha-hemolysin (αHL) pores to gain insight into such processes. <b>Chapter 1</b> provides an overview of common techniques used to study single- molecule processes, in particular single channel recordings. General techniques to engineer ion channels and pores are presented, followed by examples of how the alpha-HL pore has been engineered to monitor dynamic processes at the single- molecule level. <b>Chapter 2</b> describes how alpha-HL pores can be chemically modifeed with a tridentate "half-chelator" ligand. Single channel recordings show that this modifeed pore can be used to determine rates of chelation and the stability of divalent metal ion complexes. The modifeed pore can also be used as a stochastic sensor for the detection of different divalent metal ions in solution. <b>Chapter 3</b> investigates the chelate-cooperativity between two half-chelator ligands installed in close proximity in the alpha-HL pore, as they form a full complex with a single Zn²⁺ ion. The single channel recordings reveal a two step process, in which the Zn²⁺ ion must fiferst bind to one of the two half-chelators, before the second one completes the complex. The rate constants for all the major steps of the process are determined and the extent of cooperativity between the half-chelators is quantifeed. <b>Chapter 4</b> demonstrates that genetically encoded subunit dimers of alpha-HL can be used to control the subunit arrangement in the heptameric pore. Although techniques exist to prepare heteroheptameric pores, pores containing more than one type of modifeed subunit are not commonly used because it is impossible to distinguish between the permutations of the pore. By using subunit dimers, heptamers in which two defefined subunits are adjacent to each other can be formed, which increases the range of structures that can be obtained from engineered protein nanopores. <b>Chapter 5</b> explores the possibility of following the nuclease activity of a metal complex in the alpha-HL pore at the single-molecule level. The Rh(III) complex [Rh(bpy)2phzi]²⁺ binds strongly to CC mismatches in dsDNA, and on activation with UV light promotes the cleavage of one of the two strands. To follow this reaction by single channel recording, a piece of dsDNA with the bound Rh-complex was immobilised in the HL pore and the single current changes under UV irradiation were monitored. The preliminary data indicate that the rate of the photocleavage reaction can be measured.

Single-molecule detection has provided insights into how molecules behave. Without the averaging effect of ensemble measurements, the stochastic behaviour of single molecules can be observed and intermediate steps in multistep transformations can be clearly detected. The single-molecule reactants range from small molecules (e.g. propene) to proteins of several tens of kDa (e.g. myosin). One single-molecule detection technique is single-channel electrical recording. This approach is based on the measurement of the transmembrane ionic current flowing through a nanoscale transmembrane pore under an applied potential. In this thesis, the protein α-hemolysin was employed as a nanoreactor. α-Hemolysin is a toxin secreted by Staphylococcus aureus. Its transmembrane pore (~100 Å in length and ≥14 Å in diameter) allows ions, water and small molecules to pass through its lumen. Under an applied potential, chemical changes in reactants attached to the internal wall of the pore modulate the flow of ions, leading to changes in the transmembrane ionic current. Analysis of this current provides information about the reaction kinetics and mechanisms. Chapter 1 – Single-Molecule Chemistry and α-Hemolysin is an introductory chapter that is divided into two parts. Section 1.1 provides an overview of the different techniques for the detection of chemical reactions at the single-molecule level. Section 1.2 gives a brief review of the protein pore α-hemolysin, including its structure, properties and various applications. Chapter 2 – S-Nitrosothiol Chemistry applies cysteine-containing α-hemolysins to study the biologically relevant chemistry of S-nitrosothiols (RSNO). RSNO are important molecules involved in cell signalling, which control physiological processes such as vasodilation and bronchodilation. Three reactions, namely transnitrosation (the transfer of the ‘NO’ group from RSNO to a thiol), S-thiolation (the formation of a disulfide from RSNO and thiol) and S-sulfonation (the generation of an S-sulfonate (RSSO₃⁻) from RSNO and sulfite ion), were investigated at the single-molecule level. The pH-dependency of the two competing reactions (transnitrosation and S-thiolation), the lifetime of the proposed transnitrosation intermediate, and nature of the chemical reaction between RSNO and sulfite (a bronchoconstrictor) were determined. Chapter 3 – Silver(I)-thiolate and cadmium(II)-thiolate complexes describes the kinetics of the formation and breakdown of these two metal-thiolate complexes. Ag⁺ and Cd²⁺ are commonly used in probing the membrane topology and gating properties of ion channels using the scanning cysteine accessibility method (SCAM). The binding of two Ag⁺ ions per thiol group and the stepwise build-up and dissociation of Cd²⁺-glutathione complexes were unambiguously characterized. Chapter 4 – Copper(II)-Catalyzed Diels-Alder Reactions reports the attempt to carry out copper(II)-catalyzed Diels-Alder reactions inside an engineered α-hemolysin. An iminodiacetate ligand was covalently attached within the lumen of the α-hemolysin pore. This ligand chelates Cu²⁺ ion, which can bind bidentate dienophiles and activate them towards Diels-Alder reaction with dienes. However, due to the ‘slow’ reaction rate of the Diels-Alder reaction (rate constant ~10⁻¹ M⁻¹s⁻) relative to the time-scale of the single-molecule experiment, we failed to observed chemical conversion at the single-molecule level. Nevertheless, the engineered metal-binding α-hemolysin may be useful for sensing molecules bearing metal-coordinating groups.

Diagnoses of tuberculosis, 'TB,' currently rely upon non-specific techniques such as X-ray exams and acid-fast microscopy. Improved diagnostics would preferably consider specific bacterial processes to provide real-time readouts of disease burden and response to chemotherapy. This dissertation presents the cell-wall incorporation of trehalose analogues (fluorescent and radioactive) by the mycobacterial antigen 85 enzymes as a novel method to label the causative bacteria of TB, Mycobacterium tuberculosis (Mtb). The trehalose mycolyltransesterase enzymes (antigens 85A, B, and C (Ag85)) serve as essential mediators of cell envelope function and biogenesis in Mtb. We show that the Ag85 enzymes display activities so broad that they allow added non-natural carbohydrate probes to be incorporated into Mtb growing in vitro and within macrophages. Design and synthesis of a library of structurally-diverse analogs of the sugar trehalose (Tre) revealed that Ag85-enzymes catalyze esterification of a wide variety of non-natural Tre structures, even stereoisomers and those appended with charged or bulky groups (Chapter 2). A novel mass-spectrometry based Ag85 enzyme assay was developed and employed to screen the library of compounds against all three isoforms of Ag85 (Chapter 3). This screen revealed that the Ag85 enzymes exhibit preference for dissacharides over monosaccharides and a broad tolerance for most modified trehalose compounds. This activity assay also afforded full kinetic analysis and the discovery of a novel, covalent inhibitor of the Ag85 enzymes. The Ag85 activity assay informed the design of a fluorescent trehalose-based compound (FITC-Tre), which is the first, non-toxic, selective, small molecule probe for mycobacterial infection. FITC-Tre was acylated with mycolyl esters by growing mycobacteria, anchoring the probe in the cell envelope resulting in fluorescent bacteria (Chapter 4). Adding FITC-Tre to Mtb-infected macrophages allowed selective, fluorescent tagging of Mtb in vivo (Chapter 5). Colocalization studies with antibodies against a variety of phagosomal associated components have hinted at the possibility of FITC-Tre as readout of cellular trafficking of bacteria. ¹⁸F-trehalose, biotin-trehalose and rhodamine-trehalose are also substrates of Ag85. ¹⁸F-trehalose shows promise as Mtb selective PET probe in an infected rabbit model of tuberculosis. Future work with these probes may allow for fluorescent tracking of the Mtb during the macrophage infection process, as well as the ability to label Mtb in infected tissue. The functional differences between the three isoforms of Ag85, A, B and C, are not well understood and may have implications for the survival and persistence of mycobacteria within humans. The differences in substrate specificity and catalytic activity between the Ag85 isoforms (discussed in Chapter 3) has been further investigated (Chapter 6). Mutation of three secondary site amino acids from Ag85C into Ag85B afforded nearly a twenty-fold gain in enzyme activity. Mutation of the equivalent Ag85B residues into Ag85C triggered nearly a twenty-fold loss in activity. Dissection of the roles of these three amino acids helps to explain the previously reported large differences in catalytic activity between Ag85A, B and C. Overexpression of Ag85A, B and C under tetracycline regulation revealed that these enzymes differentially modulate incorporation of mycolates into the cell wall. The Ag85 enzymes are not functionally redundant, and instead serve unique purposes in cell wall biosynthesis. In summary, this research has demonstrated that the broad substrate tolerance of Ag85 enzymes, coupled with their extracellular location, opens the door to probes of mycobacterial infection using many imaging modalities.

The Fe(II)/2-oxoglutarate (2OG) dependent oxygenases are a widespread enzyme family, which are characterised by structurally similar active sites and proposed to employ a common reaction mechanism. The work described in this thesis concerned kinetic and biophysical studies on 2OG oxygenases, with a particular focus on the hypoxia-inducible transcription factor (HIF) hydroxylases and mechanistic aspects of their reaction with oxygen. The four human HIF hydroxylases regulate cellular levels and transcriptional activity of HIF by catalysing its post-translational hydroxylation in response to changes in oxygen availability. The three prolyl hydroxylase domain enzymes (PHDs1-3) and factor inhibiting HIF (FIH) are proposed to act as cellular oxygen sensors and provide a direct link between oxygen availability and the hypoxic response. Previous transient kinetic studies have shown that PHD2 (the most important human PHD isoform) reacts slowly with oxygen, a factor proposed to be related to its oxygen-sensing role. The molecular mechanisms for the slow PHD2 reaction with oxygen were investigated using a range of kinetic and biophysical techniques to probe the effects of key active site substitutions. The studies reveal that a conservative substitution to an Fe(II)/H₂O binding residue results in 5-fold faster reaction with oxygen, suggesting a role for H₂O release from the active site in limiting the ability of oxygen to react with PHD2. This thesis also describes the first transient kinetic studies of FIH. The obtained results show that the rate of the FIH reaction with oxygen was significantly faster than for PHD2. Further, FIH catalyses hydroxylation not only of HIF-&alpha;, but also of proteins containing ankyrin repeat domains (ARD). The rate of the FIH reaction with oxygen was shown to be substrate dependent; faster oxygen activation of the reaction in the presence of ARD compared with HIF substrates was observed. Mechanistic studies were performed to investigate a report that PHD2 is involved in the enzymatic oxidation of an oncometabolite (R)-2-hydroxyglutarate (2HG) to give 2OG, in what would be an unprecedented reaction for a 2OG oxygenase. This work found that 2HG does not substitute for 2OG in PHD2 catalysis. Instead, the non-enzymatic transformation of 2HG to 2OG was observed, which could potentially contribute to the reported 2HG-dependent PHD activation in vivo. The biophysical and transient kinetic techniques used for studying the HIF hydroxylases were also applied to study the mechanism of deacetoxycephalosporin C synthase (DAOCS, the enzyme catalysing penicillin N ring expansion). Previously, it has been suggested that the DAOCS mechanism differs from the consensus 2OG oxygenase mechanism. The results described in this thesis provide strong evidence that DAOCS employs the consensus ordered mechanism characteristic of 2OG oxygenases, supporting the proposal that the consensus mechanism is a common feature of the 2OG oxygenase family. Overall, the work described in this thesis is supportive of the proposal that most, if not all, 2OG oxygenases employ a common mechanism. However, the differences in the kinetics of their reaction with oxygen, presented throughout the thesis, suggest that different 2OG oxygenases have different rate-limiting steps. Thus, the kinetics of specific oxygenases may be adapted to their biological function, in particular that of PHD2 as the key cellular O₂ sensor.

Every cell is enclosed by a membrane which gives structure to the cell and allows for the passage of nutrients and wastes into and out of the cell. Membranes are made up of amphiphilic lipid molecules, with one water-soluble end, and one hydrophobic end. Naturally occurring and synthetic membranes are made up of double-chained amphiphiles derived from hydrocarbons. Recently, a novel class of amphiphilic molecules derived from fluorocarbons have been reported. The properties of fluorinated amphiphiles are very different to that of hydrocarbon based amphiphiles. Fluorinated amphiphiles have been previously reported to be useful in the studies of membrane proteins. In this thesis, we explore some novel uses of fluorinated amphiphiles. <b>Chapter one</b>: Provides a comprehensive review of the properties of fluorocarbon-based amphiphiles and discusses the existing uses of fluorinated amphiphiles in biochemical and biomedical research. <b>Chapter two</b>: Describes some of the important materials and methods used in this thesis including a detailed description of the proteins used and the working principles behind the techniques used in the study. <b>Chapter three</b>: Looks at the stability of pre-formed planar lipid bilayers in the presence of fluorinated amphiphiles (F-amphiphiles), and characterizes the behaviour of alpha-haemolysin and other proteins in liposomes and planar lipid bilayers in the presence of F-amphiphiles. We found that F-amphiphiles have an inhibitory effect on the insertion of protein into lipid bilayers, and this property has been exploited to control the number of proteins in the bilayer. <b>Chapter four</b>: Using droplet interface bilayers, we investigate the electrical properties and behaviour of protein(s) in bilayers formed by F-amphiphiles. The results obtained with fluorinated bilayers are compared with results obtained in conventional DPhPC lipid bilayers. This is the first ever report to carry out such an investigation and it provides insights into the formation, stability and utility of fluorinated bilayers. <b>Chapter five</b>: In Chapter five, we explore another aspect of droplet interface bilayers: the feasibility of using droplet interface bilayers to screen for membrane protein libraries. I have chosen to focus on certain fundamental aspects of the screening process that are sufficient to establish the feasibility of the method and to act as the proof of concept. <b>Chapter six</b>: Summarizes all the important results in the thesis and discusses some possible future directions of this project.

Thesis advisor: Eranthie Weerapana / Cysteine residues on proteins play important catalytic and regulatory roles in complex proteomes. These functional residues can be modified under physiological conditions by posttranslational modifications (PTMs) to regulate protein activities and modulate cysteine reactivity. Many PTMs are highly labile and dynamic, rendering it difficult to detect modified proteins within complex systems. To contribute to the chemical-proteomic methods currently available, chemical probe-Mass Spectrometry (MS) platforms were developed to study oxidative cysteine modifications. A MS platform for the assessment of S-nitrosation in vitro identified Cys329 of Cathepsin D (CTSD) as highly sensitive to S-nitrosothiol formation. To achieve a more physiological relevant representation of S-nitrosation, this platform was later adapted for study in live cells using a caged electrophile, Caged BK. Additionally, oscillation of cysteine oxidation as a function of circadian rhythm in Drosophila melanogaster and human samples was explored. As a compliment to these MS platforms, a 4-aminopiperidine-based cysteine-reactive probe library was developed. These probes have been used to target specific reactive cysteines as an alternate way to regulate protein function and can be used as tools to provide insight into the roles of these residues in protein activities. / Thesis (PhD) — Boston College, 2016. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.