Thesis advisor: Amir H. Hoveyda / The possibility of accessing altered frameworks wherein the spatial relationship between several organic fragments can be controlled can notably impact drug discovery and development. In this context, we introduce a strategy that can be used for programmable and divergent synthesis of a diverse and otherwise difficult-to-prepare set of cyclic amines and bridged bicyclic enamines wherein up to four exit vectors can be altered accordingly. Central to the approach is a catalytic multicomponent reaction that merges a nitrile, a trisubstituted allenylboronate and a silyl hydride, delivering multifunctional 1,4-aminoboronates that contain a versatile and stereochemically defined trisubstituted alkenyl boronate. We show that the products can be modified to afford an assortment of complex, drug-like, polycyclic amines. What is more, a new cyclization strategy, involving the triflic anhydride-mediated reaction of a trisubstituted alkene and a nearby amide, was developed for synthesis of the corresponding bridged bicyclic scaffolds. These resulting bridged enamines and various derivatives are evocative of the 1-azabicyclo[3.2.1]octane core, found in a variety of bioactive alkaloids. / Thesis (PhD) — Boston College, 2023. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

A four component reaction involving the coupling of functionalized aldehydes, amines, acid chlorides, and [pi]- and organometallic nucleophiles has been developed to prepare multifunctional substrates that may be employed in subsequent ring-forming reactions to generate diverse arrays of functionalized heterocyclic scaffolds. Allyl metals, Grignard reagents, silyl ketene acetals, silyl enol ethers, and silyloxy furans have been utilized as the nucleophile in the four component reaction (4CR). The 4CR has been sequenced with intramolecular Heck reactions, Diels-Alder and [3+2] cycloadditions, ring closing metathesis (RCM), and Dieckmann condensations to provide a number of diverse heterocyclic structures. The practical utility of this approach to diversity-oriented synthesis (DOS) was further exemplified by its application to the first total synthesis of the isopavine alkaloid roelactamine, which was completed in only four steps from commercially available materials. The application of this methodology towards the synthesis of the Aspidosperma alkaloids rosicine and pseudotabersonine is also presented. To this end, an imine pentadienylation/double RCM strategy has been adopted to rapidly access the pentacyclic core of the aspidospermine alkaloids. This sequence involved the use of a pentadienyl aluminum reagent, which was found to react with aryl imines to give branched products in good yields. / text

Thesis advisor: Marc L. Snapper / Cyclobutadiene cycloadditions provide rapid access to rigid polycyclic systems with high strain energy and unusual molecular geometries. Further functionalization of these systems allows entry into unexplored chemical space. A tricarbonylcyclobutadiene iron complex on solid support enables exploration of these cycloadditions in a parallel format amenable to diversity oriented synthesis. Modeling of the cycloaddition transition states with density functional calculations provides a theoretical basis for analysis of the regioselectivity observed in generation of these substituted bicyclo[2.2.0]hexene derivatives. The high strain energy accessible in cyclobutadiene cycloadducts and their derivatives renders them useful synthons for access to medium-ring natural products through ring expansion. Torilin, a guaiane sesquiterpene isolated from extracts of the fruits of <italic>Torilis japonica</italic>, exhibits a range of biological activities including testosterone 5&alpha;-reductase inhibition, hKv1.5 channel blocking, hepatoprotective, anti-inflammatory and anti-cancer effects. These activities are reviewed and analyzed from the perspective of a common biochemical target. Tandem oxidation and acid-catalyzed rearrangement of a highly strained tetracyclo[5.3.0.0<super>1,5</super>.0<super>2,4</super>]decane in the presence of tetrapropylammonium perruthenate provides the bicyclo[5.3.0]decane core of this natural product with complete control of relevant stereochemistry. The complex precursor required for this rearrangement is rapidly accessed by cyclopropanation of an intramolecular cyclobutadiene cycloadduct. Synthetic studies are reported which provide preliminary access to 8-deoxytorilolone. / Thesis (PhD) — Boston College, 2010. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

This thesis explores two approaches to fragment-based drug discovery. First, protein target CK2 was chosen due to its importance in the cancer phenotype. A literature fragment, NMR154L, proved to be a promising compound for fragment development, due to its binding at the interface site of the protein rather than the highly conserved ATP pocket. Analogues were synthesised of this fragment leading to a candidate with a better IC50. Additionally, computer modelling of the interface site suggested that a series of spirocyclic compounds would inhibit this protein. These were synthesised and tested in vitro. Results from these tests were analysed and informed the synthesis of new inhibitors with the aid of crystal structures and computer modelling. Secondly, to address the lack of spirocyclic scaffolds in fragment screening libraries a number of diversity-orientated synthetic campaigns were undertaken. The first of these utilised glycine as starting material. Two terminal alkenes were installed. The alkenes were linked and the amino and acidic residues cyclised. This allowed for the formation of a diverse range of spirocyclic scaffolds from this one starting material. Having established chemistry for linking amino and acidic residues a campaign with dehydroalanine was under taken. This would allow for the installation of the second ring by pericyclic chemistry as well as using chemistry previously established. This pericyclic chemistry was also applied to synthesising spirocycles from rings with exocyclic double bonds. These being readily installed from Wittig chemistry, this allowed utilisation of starting materials which contained a cyclic ketone. Of these azetidinone was a good candidate due to the fact it was a commercially available building block and allowed access to spirocycles containing a 4-membered ring; an underrepresented ring size. Finally, computation analysis was carried out on the library to assess it diversity and any potential biological targets which these fragments may inhibit.

In efforts to search for tool compounds that are capable of probing normal and disease-associated biological processes, both quality and identity of the screening collection are very important. Towards this goal, diversity-oriented synthesis (DOS) has been explored for a decade, which aims to populate the chemical space with diverse sets of small molecules distinct from the traditional ones obtained via combinatorial chemistry. In the practice of DOS, macrocyclic ring-closing metathesis (RCM) reactions have been widely used. However, the prediction and control of stereoselectivity of the reaction is often challenging; chemical transformation of the olefin moiety within the product is in general limited. Chapter I of this thesis describes a methodology that addresses both problems simultaneously and thus extends the utility of the RCM reactions. By installing a silyl group at the internal position of one of the olefin termini, the RCM reaction could proceed with high stereoselectivity to afford the (E)-alkenylsiloxane regardless of the intrinsic selectivity of the substrate. The resulting alkenylsiloxane can be transformed to a variety of functionalities in a regiospecific fashion. The conversion of the (E)-alkenylsiloxanes to alkenyl bromides could proceed with inversion of stereochemistry for some substrates allowing the selective access of both the E- and Z-trisubstituted macrocyclic alkenes. It was also found that the silyl group could trap the desired mono-cyclized product by suppressing nonproductive pathways. Chapter II of this thesis describes the application of the concept of DOS in the area of fragment-based drug discovery. Most fragment libraries used to date have been limited to aromatic heterocycles with an underrepresentation of chiral, enantiopure, \(sp^3\)-rich compounds. In order to create a more diverse fragment collection, the build/couple/pair algorithm was adopted. Starting from proline derivatives, a series of bicyclic compounds were obtained with complete sets of stereoisomers and high \(sp^3\) ratio. Efforts are also described toward the generation of diverse fragments using methodology described in Chapter I. The glycogen synthase kinase \((GSK3\beta)\) was selected as the proof-of-concept target for screening the DOS fragments. / Chemistry and Chemical Biology

Verdazyl radicals are a family of multicoloured stable free radicals. Aside from the defining backbone of four nitrogen atoms, these radicals contain multiple highly modifiable sites that grant them a high degree of derivatization. Despite having been discovered more than half a century ago, limited applications have been found for the verdazyl radicals and little is known about their chemistry. This thesis begins with an investigation to determine whether verdazyl radicals have a future as mediating agents in living radical polymerizations and progresses to their application as substrates for organic synthesis, an application that to date has not been pursued either with verdazyl or nitroxide stable radicals. The first part of this thesis describes the successful use of the 1,5-dimethyl-3-phenyl-6-oxoverdazyl radical as a mediating agent for styrene and n-butyl acrylate stable free radical polymerizations. The study of other verdazyl derivatives demonstrated the impact of steric and electronic properties of the verdazyl radicals on their ability to mediate polymerizations. The second part of this thesis outlines the initial discovery and the mechanistic elucidation of the transformation of the 1,5-dimethyl-3-phenyl-6-oxoverdazyl radical into an azomethine imine, which in the presence of dipolarophiles, undergoes a [3+2] 1,3-dipolar cycloaddition reaction to yield unique pyrazolotetrazinone structures. The reactivity of the azomethine imine and the scope of the reaction were also examined. The third part of this thesis describes the discovery and mechanistic determination of a base-induced rearrangement reaction that transforms the verdazyl-derived pyrazolotetrazinone cycloadducts into corresponding pyrazolotriazinones or triazole structures. The nucleophilicity, or the lack thereof, of the base employed leading to various rearrangement products was examined in detail. The final part of this thesis demonstrates the compatibility of the verdazyl-initiated cycloaddition and rearrangement reactions with the philosophy of diversity-oriented synthesis in generating libraries of heterocycles. A library of verdazyl-derived heterocycles was generated in a short amount of time and was tested non-specifically for biological activity against acute myeloid leukemia and multiple myeloma cell lines. One particular compound showed cell-killing activity at the 250 mM range, indicating future potential for this chemistry in the field of drug discovery.

Verdazyl radicals are a family of multicoloured stable free radicals. Aside from the defining backbone of four nitrogen atoms, these radicals contain multiple highly modifiable sites that grant them a high degree of derivatization. Despite having been discovered more than half a century ago, limited applications have been found for the verdazyl radicals and little is known about their chemistry. This thesis begins with an investigation to determine whether verdazyl radicals have a future as mediating agents in living radical polymerizations and progresses to their application as substrates for organic synthesis, an application that to date has not been pursued either with verdazyl or nitroxide stable radicals. The first part of this thesis describes the successful use of the 1,5-dimethyl-3-phenyl-6-oxoverdazyl radical as a mediating agent for styrene and n-butyl acrylate stable free radical polymerizations. The study of other verdazyl derivatives demonstrated the impact of steric and electronic properties of the verdazyl radicals on their ability to mediate polymerizations. The second part of this thesis outlines the initial discovery and the mechanistic elucidation of the transformation of the 1,5-dimethyl-3-phenyl-6-oxoverdazyl radical into an azomethine imine, which in the presence of dipolarophiles, undergoes a [3+2] 1,3-dipolar cycloaddition reaction to yield unique pyrazolotetrazinone structures. The reactivity of the azomethine imine and the scope of the reaction were also examined. The third part of this thesis describes the discovery and mechanistic determination of a base-induced rearrangement reaction that transforms the verdazyl-derived pyrazolotetrazinone cycloadducts into corresponding pyrazolotriazinones or triazole structures. The nucleophilicity, or the lack thereof, of the base employed leading to various rearrangement products was examined in detail. The final part of this thesis demonstrates the compatibility of the verdazyl-initiated cycloaddition and rearrangement reactions with the philosophy of diversity-oriented synthesis in generating libraries of heterocycles. A library of verdazyl-derived heterocycles was generated in a short amount of time and was tested non-specifically for biological activity against acute myeloid leukemia and multiple myeloma cell lines. One particular compound showed cell-killing activity at the 250 mM range, indicating future potential for this chemistry in the field of drug discovery.

No / Since the development of the first cytotoxic agents, synthetic organic chemistry has advanced enormously. The synthetic and medicinal chemists of today are at the centre of drug development and are involved in most, if not all, processes of drug discovery. Recent decreases in government funding and reformed educational policies could, however, seriously impact on drug discovery initiatives worldwide. Not only could these changes result in fewer scientific breakthroughs, but they could also negatively affect the training of our next generation of medicinal chemists.

Le concept de la DOS (Diversity-Oriented Synthesis) est une nouvelle approche qui vise à générer des collections de petites molécules avec des hauts degrés de diversité et de complexité structurale. Diverses stratégies ont été mises en place pour y parvenir de manière la plus efficace possible à partir de simples substrats de départ.Dans ce contexte, ce travail de thèse a permis de montrer comment un processus domino avait tout le potentiel à être exploité en tant que formidable outil dans le cadre d’une approche DOS, générateur à la fois de complexité mais également de diversité structurale. Un précurseur connu et largement étudié pour son caractère exceptionnellement versatile a été valorisé dans ce contexte : la 3-formylchromone. Dans ce manuscrit, nous montrerons comment il est possible de moduler le cours d’un processus domino pour atteindre de hauts degrés de diversité structurale, à partir des chromones accepteurs de Michael-1,6 et d’amines primaires. Nous verrons en particulier comment le contrôle d'une ou de plusieurs étapes clefs des séquences réactionnelles impliquées peut être réalisé selon :(I) la modulation pertinente d’une ou plusieurs unité(s) de structure au sein des substrats de départ, (II) la modulation des paramètres réactionnels (solvants, température, additifs), et(III) l’induction d’un changement de réactivité au sein d’un intermédiaire réactionnel par addition d’un agent externe. / In the early 2000s a general consensus has emerged in which the molecular diversity within a given library of small molecules, rather than its size, has been recognized as a crucial requirement. Diversity-oriented synthesis (DOS) has emerged from this new paradigm. This novel approach aims to generate collections of small molecules with high degrees of structural diversity, in the most efficient way, starting from simple building-blocks. Since the generation of collections of structurally diverse small molecules in a DOS-driven approach constitutes a real challenge, diverse strategies have been set up for this purpose.In this line, this work has shed light on the great potential of a domino process as a valuable tool in a DOS-driven strategy, capable of generating both molecular diversity and architectural complexity. This study has been focused on the 3-formylchromone building block, a particular framework which has already proven being an exceptionally versatile precursor of molecular diversity. In this manuscript, we will highlight how it is possible to modulate the course of a domino process to achieve high degrees of molecular diversity, starting from the chromone based 1,6-Michael acceptors platform and primary amines as reaction partners. In particular we will show how it is feasible to control the course of particular steps involved in the domino process through: (I) the pertinent modulation of the Michael acceptors and the primary amines structures, (II) the modulation of the reaction parameters (solvent, temperature, additives), and (III) the tuning of the reactivity within a key reaction intermediate induced by the introduction of an external agent.

There are many applications of small organic compounds, e.g. as drugs or as tools to study biological systems. Once a compound with interesting biological activity has been found, medicinal chemists typically synthesize small libraries of compounds with systematic differences to the initial “hit” compound. By screening the new ensemble of compounds for their ability to perturb the biological system, insights about the system can be gained. In the work presented here, various ways to synthesize small libraries of ring-fused 2‑pyridones have been developed. Members of this class of peptidomimetic compounds have previously been found to have a variety of biological activities, e.g. as antibacterial agents targeting virulence, and as inhibitors of the aggregation of Alzheimer b‑peptides. The focus in this work has been to alter the core skeleton, the central fragment, of the previously discovered biologically active 2‑pyridones and evaluate the biological effects of these changes. Several new classes of compounds have been constructed and their preparations have included the development of multi-component reactions and a method inspired by diversity-oriented synthesis. Some of the new compounds have been evaluated for their effect on the fibrillation of different amyloid proteins. Both the Parkinson-associated amyloid protein a-synuclein and the bacterial protein CsgA that is involved in bacterial biofilm formation are affected by subtle changes of the compounds’ central fragments. This is an example of the usefulness of central-fragment alterations as a strategy to probe structure-activity relationships, and the derived compounds may be used as tools in further study of the aggregation of amyloid proteins.