This thesis describes our examination of the reactivity of allenylpalladium intermediates generated from the reaction of palladium(0) with propargylic electrophiles. Chapter 1 provides a general overview of the literature reported to date concerning the nature and reactivity of allenylpalladium intermediates. The coupling of a variety of propargylic electrophiles with aryl boronic acids to form allenes is examined in Chapter 2. However, when employing diastereomerically pure electrophiles, some erosion of stereochemistry was observed in the allene products. This effect was examined further, and epimerisation of the allene product was found to be the origin of the loss of stereochemistry. Evidence for the species likely responsible for this epimerisation is presented. The serendipitous formation of tetrahydrofurans (THFs) from propargylic 7-membered cyclic carbonates prompted an in-depth examination of this reactivity, as described in Chapter 3. The reaction of these cyclic carbonates was rendered stereoselective and the stereochemical outcome of the reaction elucidated. The methodology was extended to propargylic acyclic carbonates which allowed the formation of tetrahydropyrans (THPs). The effect of ring-size and substituents on the cyclisations was examined, culminating in the formation of two rings in a single step from diol-containing bis-carbonates. Chapter 4 describes the extension of this methodology to the formation of azacyclic products. This built upon foundation work conducted by a Part II student within the group, and further improved the selectivity of the reaction. Two diverse azacyclic skeletons could be formed from the same substrate by the employment of different bidentate phosphine ligands, and a variety of substrates were examined under these conditions. Chapter 5 draws general conclusions and sets out possible future directions for the methodology, and full experimental details are outlined in Chapter 6.

Lysine acetylation is a widespread protein post-translational modification that influences diverse cellular processes. An association between acetylation of histone N-terminal tails and transcriptional activation has been recognised since the 1960s. However, it has only become apparent since 2000 that many of the effects of histone acetylation are mediated by proteins that bind to acetyl-lysine through a specialised acetyl-lysine recognition domain, the bromodomain. Small-molecule inhibitors of bromodomain-histone interactions can greatly assist studies into the functions of bromodomain-containing proteins, and show promise as treatments for several diseases, including cancers. Herein I describe the discovery and development of a novel chemical series of bromodomain-binding ligands containing the 3,5-dimethyisoxazole moiety. This heterocycle acts as an acetyl-lysine bioisostere, mimicking key interactions formed between acetyl-lysine and the bromodomain. Optimised compounds show sub-micromolar affinities for bromodomains of the BET family, a class of transcriptional co-regulators. Crystallographic and structure-activity relationship studies shed light on the structural requirements for potent and selective BET ligands. Furthermore, the compounds show cellular effects consistent with BET bromodomain inhibition: cytotoxicity studies in a range of cell lines, including the NCI-60 human tumour cell line screen, reveal differential activity, with leukaemias showing particular sensitivity. 3,5-Dimethylisoxazole-containing compounds were also shown to downregulate known BET target genes. Further studies investigated the effect of modifying or replacing the methyl groups of 3,5-dimethylisoxazole on BET bromodomain affinity, which indicated that the 3-methyl group is necessary for affinity. Finally, three novel isoxazole-containing amino acids were synthesised and incorporated into histone peptides as potential bromodomain-binding, non-hydrolysable, acetyl-lysine mimics. These amino acids might be useful in uncovering the function of individual acetylated lysine residues. The identification of methyl-isoxazoles as acetyl-lysine-mimetic bromodomain ligands represents a significant advance in our understanding of structure-activity relationships for these important proteins. The confirmed cellular activity of these compounds will enable their use in future biological studies.

A brief summary of the use of palladium as a catalyst, the characteristic reactivity of palladium complexes and the commonly used palladium-catalysed cross coupling reactions is given, with a special focus on the palladium-catalysed α-arylation of enolates and its application to the synthesis of aromatic heterocycles. The synthesis of aromatic heterocycles via both traditional methods and more recent metal-catalysed approaches is discussed in the context of isoquinolines. The palladium-catalysed oxidation of dihydrofurans bearing an ortho-bromophenyl group at the 2-position to the corresponding 2-phenyl furans is disclosed along with some preliminary mechanistic investigations. A novel synthetic route to isoquinolines is detailed involving the palladium-catalysed α-arylation of ketone enolates with an appropriate ortho-substituted aryl halide to furnish a protected 1,5-dicarbonyl intermediate. The versatility of these intermediates is demonstrated with their conversion into isoquinolines, isoquinoline N-oxides and naphthols. The scope of the synthetic procedure is fully exemplified across more than 30 different scaffolds covering the full spectrum of electron-rich to electron-deficient moieties. The intermediates were shown to be amenable to functionalisation with electrophiles, leading to isoquinolines bearing additional substitution at the C4 position. Sequential one-pot procedures were developed allowing three and four component couplings to directly deliver highly-substituted isoquinolines from commercially available starting materials. This methodology was utilised in the total synthesis of the natural product berberine in 26% overall yield and a longest linear sequence of six steps.

Tunicamycin nucleoside antibiotics were the first known to target the formation of peptidoglycan precursor lipid I in bacterial cell wall biosynthesis. They have also been used extensively as inhibitors of protein N-glycosylation in eukaryotes, blocking the biogenesis of early intermediate dolichyl-pyrophosphoryl-N-acetylglucosamine. Despite their unusual structures and useful biological properties, little is known about their biosynthesis. Elucidating the metabolic pathway of tunicamycins and gaining an understanding of the enzymes involved in key bond forming processes would not only be of great academic value in itself, it would also unlock a comprehensive toolbox of biosynthetic machinery for the production of tunicamycin analogues which have the potential to act as novel therapeutic antibiotics or as specific inhibitors of medicinally important NDP-dependent glycosyltransferases. I – Cloning the tunicamycin biosynthetic gene cluster. We report identification of the tunicamycin biosynthetic genes in Streptomyces chartreusis following genome sequencing and a chemically-guided strategy for in silico genome mining that allowed rapid identification and unification of an operon fractured across contigs. Heterologous expression established a likely minimal gene set necessary for antibiotic production, from which a detailed metabolic pathway for tunicamycin biosynthesis is proposed. II – Natural product isolation and degradation. We have developed efficient methods for the isolation of tunicamycins from liquid culture in preparative quantities. A subsequent relay synthesis furnished advanced biosynthetic intermediates for use as precursors in the production of tunicamycin analogues and as substrates for the in vitro characterisation of individual Tun enzymes. III – Functional characterisation of tun gene products. Individual tun gene products were over-expressed and purified from recombinant E. coli hosts, allowing in vitro functional studies to take place. An NMR assay of biosynthetic enzyme TunF showed it acted as a UDP-GlcNAc-4-epimerase. Putative glycosyltransferase TunD showed hydrolytic activity towards substrate UDP-GlcNAc but failed to accept to the expected natural acceptor substrate, providing unexpected insights into the ordering of biosynthetic events in the tunicamycin pathway. Initial studies into the over-expression of the putative sugar N-deacetylase TunE were also described. IV – Towards synthesis of tunicamycin fragments. Investigations into a novel synthesis of D-galactosamine – a structural motif within tunicamycin – led to the unexpected observation of inverted regioselectivity upon RhII-catalysed C-H insertion of a D-mannose-derived sulfamate. This was the first example of N-insertion at the beta- rather than gamma-C-H based on conformation alone and warranted further investigation. The X-ray structure of a key sulfamate precursor offered valuable insights as to the source of this unique selectivity.

Caged compounds are a class of photosensitive reagents used to stimulate cells with spatial control down to a sub-cellular level, and millisecond temporal control. They comprise of biologically important molecule which is modified with a photolabile protecting group. In the absence of light, caged compounds are physiologically silent but irradiation with light induces the release of biologically active species. Illumination under two-photon conditions is particularly advantageous as it enables restriction of the photolysis volume to ~1 fL and it provides deeper penetration into scattering samples. This thesis reports the development of new protecting groups for two-photon uncaging in neuroscience. Mechanistically, the deprotection in these novel groups is designed to operate via an intramolecular photoinduced electron transfer (PeT) between the absorbing unit (electron-donor) and the release module (electron-acceptor). The modular design of these cages ensures separation of absorption and release steps, and allows each process to be tuned and optimized independently. Chapter 1 provides an introduction to the two-photon absorption phenomenon and a historic overview of the uncaging technique. It also discusses recent advances in the development of two-photon sensitive probes used in neuroscience. Chapter 2 describes the exploration of molecular designs for novel protecting groups. A two-photon absorbing dye (electron-donor; fluorene dye) and three different release units (electron-acceptors; nitrobenzyl, pyridinium and phenacyl) were identified as suitable building blocks for the current project. Efficiency of the intramolecular electron transfer between chosen units was evaluated using model dyads which constitute covalently linked electron-donor and acceptor species. Chapter 3 is devoted to the synthesis and photophysical evaluation of nitrobenzyl-based protecting group. Chapter 4 describes the preparation of pyridinium-derived protecting group and demonstrates PeT-mediated release of tryptophan and GABA under one- and two-photon excitation. Hydrolytic instability of pyridinium esters is highlighted. Chapter 5 reports the synthesis, hydrolytic stability and one-photon uncaging efficiency of phenacyl-based derivatives. Chapter 6 discusses properties of developed caged compounds and compares them with other compounds reported in literature. It contains overall conclusions and outlook for the current project. Chapter 7 details the experimental procedures and the characterization of compounds synthesized during this work.

The primary objective of this research project was to develop a novel protocol for the synthesis of densely functionalized optically enriched indanes through a chiral cation directed 5-endo-trig ring closure. In chapter two, a convergent strategy for the construction of the cyclization precursors is reported, which employs two easily adapted fragments. In chapter three, a range of quaternary ammonium salts are screened to establish the optimal phase-transfer conditions for this system. A variety of substrates were evaluated to probe the scope and limitations of this methodology. Finally, two potential mechanistic pathways for this enigmatic process are outlined and discussed in chapter four.

This thesis is concerned with the development of transannular iodoamination methodology for the synthesis of pyrrolizidine, indolizidine and tropane alkaloids. Chapter 1 introduces the concept of a ‘transannular cyclisation’ and outlines the utility of such cyclisations in the synthesis of a range of [x.y.z]-azabicyclic alkaloids. Chapter 2 describes the development of a three step lithium amide conjugate addition, ring-closing metathesis and transannular iodoamination protocol for the preparation of the pyrrolizidine scaffold ([3.3.0]-azabicycle). Cyclisation of a hexahydroazocine occurs with concomitant N-debenzylation to give a single diastereoisomer of the corresponding C(7)-iodopyrrolizidine product, which is then elaborated to the known pyrrolizidine, (−)-7a-epi-hyacinthacine A1. Chapter 3 delineates an extension of the methodology described in Chapter 2, and an investigation into accessing alternate diastereoisomeric pyrrolizidine scaffolds via the transannular iodoamination process. These studies culminate in the synthesis of two pyrrolizidine alkaloids, (−)-hyacinthacine A1 and (−)-hyacinthacine A2. Chapter 4 details investigations into the further elaboration of the C(7)-iodopyrrolizidine scaffold synthesised in Chapter 2. A nucleophilic displacement reaction with azide leads to the synthesis of novel 7-deoxy-7-aminoalexine analogues, whilst radical-mediated substitution of the iodide by oxygen allows the synthesis and isolation of the pyrrolizidine alkaloid (−)-1-epi-alexine. Chapter 5 outlines the development of the transannular iodoamination reaction to facilitate the synthesis of the tropane architecture ([3.2.1]-azabicycle). A tandem lithium amide conjugate addition and aldol reaction sequence is followed by ring-closing metathesis to give the required aminocycloheptene. Subsequent treatment with iodine results in transannular cyclisation to give a single iodotropane product which, following elaboration culminates in the synthesis of (+)-pseudococaine. Chapter 6 contains full experimental procedures and characterisation data for all compounds synthesised in Chapters 2, 3, 4 and 5.

trans-2,5-Disubstituted-tetrahydrofurans (THFs) are a common structural motif in many biologically active natural products, particularly in the Annonaceous acetogenins. This thesis develops a new route for their synthesis and applies it to the total synthesis of the Annonaceous acetogenin sylvaticin. Chapter 1: Introduction – Synthetic routes to trans-2,5-substituted tetrahydrofurans This chapter reviews methods for the synthesis of trans-2,5-THFs that have been applied to natural products synthesis. Chapter 2: Results & Discussion – A Novel Route to trans-THFs The rearrangement of activated 2,5-disubstituted cis-THFs is reviewed and is developed into a new synthetic method for the synthesis of trans-THFs. The reaction proceeds via a hydride shift mechanism to form an oxonium ion. Intramolecular reduction by a tethered hydrosilane stereoselectively forms the trans-THF. The mechanism of the rearrangement is investigated with the use of different stereoisomers and a deuterium labelling study. A cross-over study is carried out which confirms the reaction occurs via the proposed hydride shift mechanism. Chapter 3: Introduction – The Annonaceous Acetogenins This chapter introduces the Annonaceous acetogenins, a biologically active class of natural products often found with THF rings in their structure. The three key areas for their synthesis are explored- the synthesis of the THF core, the synthesis of the butenolide ring, and their coupling. Chapter 4: Results & Discussion – The Synthesis of Sylvaticin The Annonaceous acetogenin sylvaticin is introduced, and its isolation in nature and biological activity reviewed. With the aid of a model system study to extend the scope of the reaction, the methodology developed in Chapter 2 is then applied to the synthesis of sylvaticin. The synthesis, the first to be reported, is completed in a total of 19 linear steps starting from commercially available tetradecatetraene. In order to prove the obtained structure is that found in nature, a comprehensive investigation is undertaken using Mosher ester derivatives and the synthesis of its bis-epimer, 4,36-epi,epi sylvaticin. Chapter 5: Experimental Full experimental procedures and characterisation of compounds are reported.

This thesis describes the synthesis and reactivity of previously unprecedented bicyclic methylene aziridines via rhodium(II) catalysed cyclisation of α-allenic N-tosyloxycarbamates. These aziridines undergo reaction with organocuprates to give cis- disubstituted oxazolidinones by nucleophillic attack at the vinylic centre; plausible mechanisms for this process are discussed. Similar rhodium(II) catalysed cyclisations of β-allenic sulfamates afford cyclic enamines, aminocyclopropanes or bicyclic methylene aziridines; the product ratio depends on the allene substitution pattern. Suitably-designed substrates undergo trapping of the proposed intermediate amino allyl cation by internal nucleophiles or by cycloaddition. Finally, thermally-induced intramolecular cycloadditions of γ-allenic azides are described that give triazolines or [1,2,3]-triazoles.

This work describes the extension of rhodium-catalysed intermolecular hydroacylation to encompass some tandem catalytic processes, wherein a further catalytic process is enacted on the product of an intermolecular hydroacylation reaction in “one pot”. Chapter 1 entails an overview of the development of hydroacylation chemistry, with a focus on the different types of catalytic systems which have been used to facilitate this transformation. A brief description of some precedented examples of tandem catalytic processes which include a hydroacylation reaction is also included. Chapter 2 describes the intermolecular hydroacylation of chelating aldehydes and propargylic alkynes to form γ-hydroxy-α,β-enones, and their subsequent acid-catalysed cyclisation to form substituted furans in a "one-pot" procedure. Additionally, a tandem intermolecular hydroacylation/double-bond isomerisation protocol for the synthesis of 1,4-dicarbonyl compounds is detailed, and the subsequent transformation of this class of compounds to heterocycles is included. Chapter 3 focuses on the development of tandem catalytic hydroacylation/reductive processes, wherein a hydroacylation product undergoes a reduction which is catalysed by the hydroacylation catalyst. Chapter 4 describes an attempt to utilise the rhodium-catalysed conjugate addition of arylmetal species to enomes to create a tandem alkyne hydroacylation/conjugate addition process. Chapter 5 encompasses the use of a small range of different solvents in rhodium-catalysed hydroacylation, in an attempt to find higher-boiling alternatives to acetone and a "green" alternative to the commonly used DCE.