Dissertations / Theses on the topic 'Diversity-oriented synthesi'

La seguente dissertazione è un riassunto di un progetto di dottorato della durata di tre anni, condotto con lo scopo di esplorare nuove regioni dello spazio chimico, che potrebbero contenere interessanti molecole bioattive. Infatti, al giorno d’oggi, solo una porzione molto limitata dello spazio chimico è stata investigata. Oltretutto, tale porzione diventa ancora più ristretta se si considerano solo molecole caratterizzate da attività biologica. In questa tesi sono state considerate due diverse strategie per consentire un’ulteriore esplorazione dello spazio chimico: si tratta della diversity-oriented synthesis (DOS) e di un particolare approccio chemoenzimatico, sviluppato durante sei mesi trascorsi presso l’Università di Warwick (UK), sotto la supervisione della Professoressa Manuela Tosin. Capitolo 1. Il primo capitolo della tesi contiene un’introduzione generale ai principi della diversity-oriented synthesis, che costituirà il tema principale della dissertazione. Successivamente viene presentata una overview dettagliata, riguardante un approccio DOS sviluppato negli ultimi anni nel gruppo Passarella. Tale approccio si basa sull’utilizzo del 2-piperidinetanolo (1) come precursore per ottenere una libreria di derivati piperidinici diversificati. Alla fine del capitolo, viene presentata la progettazione di un’ulteriore espansione di tale libreria, tramite la sintesi dei prodotti riportati in Figura 1 (La figura può essere visionata nella versione dell'abstract riportata nel file della tesi). Capitolo 2. Questo capitolo riguarda la sintesi enantioselettiva di otto prodotti polieterociclici, caratterizzati da tre scaffolds altamente diversificati. La diversificazione strutturale è stata ottenuta a partire da un intermedio comune, sfruttando la diversa reattività dei suoi diastereoisomeri syn e anti, che, posti nelle medesime condizioni di reazione, hanno portato a prodotti strutturalmente diversi. In tal modo, analoghi di alcaloidi naturali sono stati ottenuti. Capitolo 3. In questo capitolo viene presentata la sintesi di una libreria di potenziali inibitori dell’hedgehog signalling pathway. La struttura degli inibitori è stata disegnata sulla base di studi di docking, prendendo ispirazione da una classe di prodotti naturali, i withanolidi. Gli elementi chiave del design sviluppato sono un carbammato biciclico, ottenibile da 1, e un lattone α,β-insaturo. La struttura presenta tre stereocentri e, ad oggi, due su quattro stereoisomeri racemi sono stati sintetizzati. I test biologici hanno rivelato due intermedi attivi, che sono stati sintetizzati anche in versione enantiopura. Inoltre, studi preliminari, volti allo sviluppo di inibitori di seconda generazione, sono attualmente in corso. Capitolo 4. In questo capitolo viene presentata la sinesi di un prodotto naturale, la (-)-anaferina, ottenuta come ulteriore ramificazione del nostro approccio DOS. L’idea è nata prendendo ispirazione dall’intermedio 10, già usato per la sintesi degli inibitori hedgehog. Infatti, il suo alcol omoallilico può essere convertito in un lattame α,β-insaturo (usando una procedura analoga a quella impiegata per la sintesi del primo prodotto presente nel riquadro rosa in Figura 1). Una volta ottenuto il lattame, questo può essere ridotto a piperidina. La successiva ossidazione del ponte 2-idrossipropanico a chetone permette poi di completare la sintesi della (-)-anaferina. Il Capitolo 5 riporta la sintesi di coniugati bivalenti, potenzialmente in grado di interagire con le tubuline in modo sinergico. Gli elementi chiave di tali coniugati sono un composto ibrido, precedentemente sintetizzato nel gruppo Passarella a partire da 1, e la N-10-deacetiltiocolchicina, noto legante di β-tubulina. Il prodotto ibrido contiene invece i motivi fondamentali della struttura della pironetina, noto legante di α –tubulina. Le due funzionalità attive sono state connesse da linkers diversi. Tuttavia i test biologici hanno evidenziato come la scelta di impiegare linkers lipofilici abbia reso i nostri coniugati migliori substrati per la P-glicoproteina, coinvolta nello sviluppo della resistenza ai farmaci, sviluppata da diverse cellule tumorali. Per questo motivo, nuovi coniugati verranno presto prodotti nel nostro laboratorio, testando linkers diversi. Infine, il Capitolo 6 ha riguardato la generazione di versioni non naturali e diversificate di due antibiotici, lasaloside A e salinomicina. A tal fine, un approccio simile alla mutasintesi, basato sulla somministrazione di probes chimiche, mimiche del malonato, ai microrganismi produttori di tali antibiotici, è stato impiegato. In particolare, diverse strategie, per un facile recupero e analisi dei prodotti non naturali presenti nei complessi brodi di fermentazione, sono state considerate. Quattro probes sono state sintetizzate e diversi esperimenti sono stati sviluppati per verificare la loro applicabilità in tale contesto.
This dissertation is an overview of a three-years project, aimed at the exploration of new regions of the chemical space, that could contain new unusual bioactive compounds. The already discovered small molecules cover only a small portion of the chemical universe, that becomes even narrower when bioactive compounds are considered. In this context, two different strategies for the investigation of the chemical space have been considered: the diversity oriented-synthesis (DOS), that constitute the major topic of the work, and a chemoenzymatic approach, developed during a period spent at the University of Warwick (UK), in the laboratory of Professor M. Tosin. Chapter 1 deals with the general principles of the DOS approach, focusing then the attention on a library of piperidine-based compounds previously synthesised in Professor Passarella’s research group, starting from a common precursor, 2-piperidine ethanol (1). An overview of the main results previously accessed in this field is reported. At the end of the chapter, the planning of a further expansion of this library is presented. The structure of the newly accessed piperidine-based products is appreciable in Figure 1 (see Figure 1 in the abstarct version reported in the thesis file); their obtainment was the main goal of this thesis. Chapter 2 is focused on the stereoselective synthesis of eight highly diversified polyheterocyclic compounds, characterized by three different scaffolds. In particular, the different scaffolds were originated by the same precursor, considering that its different syn- or anti- stereocenter configuration, influenced the reaction outcome. This project opens the possibility of accessing analogs of some natural products, such as lupin and lycopodium alkaloids. Chapter 3 concerned the obtainment of a library of potential Hedgehog (Hh) signalling pathway inhibitors, rationally designed exploiting docking simulations and taking inspiration from a class of natural products, the withanolides. The designed scaffold contains two key motif, a bicyclic carbamate and an α,β-unsaturated lactone, and presents three stereocenters. So far, two out of the four racemic isomers have been accessed and biological evaluation revealed two interesting intermediates, that have been synthesised also as separate enantiomers. Moreover, preliminary studies toward the obtainment of 2nd generation inhibitors have been performed in our laboratory. Biological evaluation of these compounds is currently in progress and will orient the future development of this work. Chapter 4 is aimed at the synthesis of (-)-anaferine as an unexpected further ramification of our DOS approach. Key intermediate 10, already exploited for the synthesis of the inhibitors of chapter 3, has been employed as starting material, converting its homoallylic alcohol into an α,β-unsaturated lactam. To this extent, the same approach used in chapter 1, to transform 9 into a similar lactam (left compound in the pink box of Figure 1) was applied. After that, the synthesis of (-)-anaferine was accomplished in few steps, reducing the lactam to piperidine and oxidizing the 2-hydoxypropane bridge to the corresponding ketone. Chapter 5 deals with the synthesis of thiocolchicine-based bivalent compounds, possibly acting as microtubules binders. A hybrid compound, bearing the key structural features of pironetin (one of the few known α-tubulin binder), previously synthesised on our laboratory from 2-piperidine ethanol, was exploited as key building block. In fact, it was connected through different linkers to N-10-deacteyl-thiocolchicine, a model of β-tubulin binder. Biological tests revealed that the lipophilic nature of the linkers rendered our conjugates better substrates for P-glycoprotein, leading to a drop in activity on resistant cancer cells. Therefore, new bivalent compounds will be soon produced in our laboratory, changing linkers chemo-physical properties. Structures of the new compounds resulting from the expansion of the DOS-approach from 2-piperidine ethanol 1. Finally, chapter 6 concerned a project aimed at the generation of unnatural, diversified derivatives of lasalocid A and salinomycin, through feeding experiments of malonate-mimicking chemical probes to the natural Streptomyces producers, in an approach resembling mutasynthesis. The efforts were focused on the devopment of different strategies for an easier recovery and analysis of the unnatural products from the complex mixtures of the fermentation broths. To this extent, four chemical probes have been synthesised and proof on concept experiments were performed to verify their applicability in this field.

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.

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 Torilis japonica, exhibits a range of biological activities including testosterone 5α-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[5.3.0.01,5.02,4]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 is divided into three separate parts with amino alcohols as the common feature. The first part describes the development of a novel three-component approach to the synthesis of α-hydroxy-β-amino esters. Utilizing a highly diastereoselective Rh(II)-catalyzed 1,3-dipolar cycloaddition of carbonyl ylides to various aldimines, syn-α-hydroxy-β-amino esters formed in high yields and excellent diastereoselectivities. This methodology was also applied in a short enantioselective synthesis of the C-13 side-chain of Taxol.

The second part of the thesis describes a total synthesis of D-erythro- Sphingosine based on a cross-metathesis approach to assemble the polar head group and the aliphatic chain.

The last part deals with the application of amino alcohols as scaffolds in a diversity-oriented protocol for the development of libraries of small polycyclic molecules. The design of the libraries is based on the iterative use of two powerful ring-forming reactions; a ring-closing metathesis and an intramolecular Diels-Alder reaction, to simultaneously introduce structural complexity and diversity.

This thesis describes the development of a novel methodology to allow the synthesis of skeletally diverse alkaloid-like unnatural compounds. Enantiomerically enriched building blocks are iteratively assembled onto a purification handle using reliable coupling reactions. Subsequently, ring-opening-ring-closing metathesis cascade reactions are used as a complexity generating step to restitch the molecular framework. Chapter 1 introduces the concept of diversity-oriented synthesis, with particular emphasis on strategies used to introduce skeletal diversity. The conceptual idea behind the project is explained, and placed into context using leading examples as the benchmark for success in diversity-oriented synthesis. Chapter 2 describes the synthesis of a range of building blocks, many of which are enantiomerically enriched, on multigram scale. The design of a solid phase 'linker' is described in Chapter 3, as are the solution phase studies used to explore suitable methodologies to couple the building blocks. The use of solid phase chemistry is described in Chapter 4, as well as the use of light fluorous tags as an alternative purification handle. Chapter 5 describes the synthesis and subsequent metathesis of a range of fluorous-tagged metathesis substrates using one building block iteration. The Thesis concludes with the preparation of 45 metathesis precursors using combinations of two building blocks assembled onto a fluoroustagged linker in Chapter 6. Metathesis cascades were carried out, allowing the isolation of 33 complex and skeletally diverse products.

This thesis describes a novel approach to diversity-oriented synthesis. The approach involves the iterative assembly of building blocks onto a purification handle using temporary diisopropylsilylene tethers; this approach yields substrates for a ring-c1osing-ring-opening olefin metathesis cascade. The metathesis cascade results in a skeletal transformation and a range of scaffolds have been generated using only a few simple building blocks and a small number of common reactions. The use of a fluorous tag as a purification handle minimised labour-intensive purification steps and rendered the approach appropriate for library synthesis. The structures ofthe diverse final compounds are reminiscent ofpolyketide natural products. Chapter 1 describes alternative approaches for varying molecular scaffolds and places our generic approach in context. In Chapter 2, .the syntheses of.enant.iome~cally enriched building . blocks are described in· which an enzymatic desymmetrisation· is often used to induce asymmetry. Our investigations to conduct our methodology on solid support our described in Chapter 3. The potential of individual building blocks to participate in simple metathesis cascades is described in Chapter 4. In addition, this Chapter describes our studies to optimise the formation of unsymmetrical silaketals using diisopropylsilyl ethers as storable precursors. The thesis culminates with the preparation of36 metathesis substrates in which pairs of building blocks have been appended to the fluorous tag. The metatheses of some ofthese substrates are described and leads to natural product-like ligands.

There is a growing interest in using diversity-oriented synthesis (DOS) to generate small molecule libraries that are inspired by bioactive natural products. Over the years they have proven to be quite valuable chemical probes for understanding protein functions. Of particular interest is the design of natural product-like chiral scaffolds in which one could explore the three dimensional space around the building block by having several chiral diversity sites. A novel synthesis to reach an indoline scaffold is described. This template is then utilized to synthesize a seven-membered ring tricyclic derivative through an olefin ring-closing metathesis (RCM) approach. As well, asymmetric diversity-oriented reactions (e.g. asymmetric benzenethiol addition and intramolecular free radical cyclization) were explored with the tricyclic compound with the intention of utilizing these reactions on solid phase for generating a library.

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

The ever-increasing demand for new drugs drives the need to explore new areas of biologically-relevant chemical space. Drug targets, largely the active sites of proteins, have three-dimensional shape. However, chiefly for reasons of synthetic tractability, the screening libraries that are extensively used for high throughput screening (HTS) drug discovery are mostly composed of flat aromatic and heteroaromatic compounds.1 This has resulted in a trend towards flatness in drug candidates, limiting the possibilities in the navigation of three-dimensional biological space. A variety of approaches, such as diversity-oriented synthesis (DOS),2, 3 target-oriented synthesis (TOS),2, 4 function-oriented synthesis (FOS),5 and biology-oriented synthesis (BIOS)6, 7 have emerged to address this issue. Natural products are a source of therapeutically useful compounds with high success rates in drug discovery.8 They tend to be highly saturated, and therefore non-flat, molecules with chiral centres. These features of natural products arise from interaction with the active sites of proteins involved in biosynthetic pathways. Inspired by natural products, we sought to identify three-dimensional (3D) molecular scaffolds embedded in natural products with the aim of producing focused synthetic libraries that explore new biological profiles.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Natural Sciences
Science, Environment, Engineering and Technology
Full Text

Over the years, it has been shown that natural products that act as highly specific modulators of protein function are complex in nature, highly functionalized and contain few stereogenic centers. There are several examples in literature, where benzopyran-based natural products have been utilized as small molecule chemical probes in understanding protein function. Inspired by the "privileged benzopyrans", the studies reported in this thesis are centred on the development of a novel method leading to the synthesis of functionalized benzopyran-derived scaffolds. Further, several attempts have been made to obtain natural product-like polycyclic compounds as derivatives of these scaffolds. Our approach has been to develop the synthetic methods initially by solution synthesis. In one case, a partial solid phase synthesis has been achieved that could further be extended to library generation. The synthetic efforts to obtain several benzopyran-based analogs are reported. These include the development of a novel, stereoselective synthetic route to obtain functionalized benzopyran templates (71a,b) and further extensions leading to diverse tricyclic derivatives having medium sized rings with few asymmetric diversity sites. An intramolecular Mitsunobu-based approach was explored to obtain benzopyran-derived tricyclic derivatives having a cis- and trans-fused lactone moiety ( 72, 73). Although we were successful in making the amino acid conjugates (387, 392, 395), we were not successful in making their tricyclic derivatives. Several ring closing metathesis (RCM)-based approaches were also developed to obtain benzopyran-based tricyclic derivatives having functionalized 6- and 8-membered rings, and were successful in making the polyethers ( 74, 75). Also reported in this chapter is the preliminary work on solid phase synthesis in which benzopyran-based tricyclic compounds with 6- and 8-membered rings were obtained by a RCM approach (541a,b).

Les pochonines A-F sont six molécules récemment décrites appartenant à la famille des lactones résorcyliques à 14 chaînons et qui présentent une activité contre le virus de l’herpès. Notre intérêt initial pour ces dérivés était fondé sur l’observation que plusieurs autres lactones résorcyliques sont connues pour leur potentiel biologique comme inhibiteurs de kinases ou d’ATPases. Par ailleurs le radicicol, de structure proche, est un puissant inhibiteur de la protéine de choc thermique HSP90, cible privilégiée pour la chimiothérapie en raison de son rôle fondamental dans la maturation fonctionnelle de nombreux oncogènes. Une synthèse de la pochonine C et sa conversion en radicicol ont été réalisées en respectivement sept et huit étapes, à partir de trois fragments facilement accessibles. Des synthèses alternatives de ces composés ont également été réalisées en utilisant des réactifs supportés et des réactions sur phase solide. A partir d’une analyse théorique de la dynamique moléculaire du radicicol et de ses analogues connus, une corrélation entre l’inhibition de HSP90 et l’énergie libre du conformère bioactif a été établie, permettant ainsi l’identification de la pochonine D comme inhibiteur potentiel de cette protéine. La synthèse totale de la pochonine D en utilisant des réactifs supportés a permis de confirmer cette hypothèse et de montrer que celle-ci est quasiment aussi active contre HSP90 que le radicicol (IC50 (radicicol) = 20 nM, IC50 (pochonine D) = 80 nM). Considérant les similarités structurales entre les pochonines D et A, nous avons également synthétisé la pochonine A pour son évaluation en tant qu’inhibiteur de HSP90, celle-ci présentant effectivement une activité de l’ordre du nanomolaire. La chimie développée à l’aide de réactifs supportés pour la synthèse des pochonines naturelles (A et D en particulier) nous a ensuite permis de préparer une banque de molécules fondée sur le même squelette et présentant cinq points de diversité, de manière à étudier les relations structure-activité sur différentes cibles. L’évaluation biologique de cette bibliothèque de 100 molécules pour l’inhibition d’un panel de 24 kinases et de HSP90 a révélé plusieurs composés actifs et sélectifs, démontrant ainsi le potentiel de la famille des lactones résorcyliques pour l’inhibition de kinases et d’ATPases
Pochonins A − F are six new members of the 14-membered resorcylic acid lactones (RALs) family which were identified in a Herpes Simplex Virus replication assay. Our interest in the pochonins stems from the observation that several other RALs are known to inhibit ATPases or kinases. Among them, radicicol was shown to be a potent inhibitor of HSP90 (Heat Shock Protein 90) whose activity is required for the functional maturation of a number of oncogenes, thus making this protein an attractive target for chemotherapy. A modular synthesis of pochonin C and its conversion to radicicol is presented. Both natural products are prepared in seven and eight steps, respectively, from three readily available fragments. Alternative syntheses of these compounds were also achieved using a combination of polymer-bound reagents and reactions on solid phase. Based on a molecular dynamics/minimization of radicicol and several known analogs, a correlation between the HSP90-inhibitory activity and the free energy of the bioactive conformer was established, leading to the identification of pochonin D as a potential inhibitor of HSP90. Its synthesis using polymer-bound reagents allowed us to confirm this finding and pochonin D was shown to be nearly as potent an HSP90 inhibitor as radicicol. Considering their closely-related structure, pochonin A was also synthesized and tested for HSP90 inhibition. The polymer-assisted chemistry developed for the pochonins syntheses enabled us to prepare a library based on the pochonin scaffold bearing five points of diversity, allowing us to extend beyond the modifications of the natural resorcylic acid lactones. Testing the library for its inhibition against a panel of 24 kinases at 10 µM and against HSP90 reveals several hits, thereby demonstrating the potential of the resorcylides towards the inhibition of therapeutically relevant kinases and ATPases. These syntheses of the pochonins were also the first reported in the literature allowing us to confirm structural assignments and to provide optical rotations as well as to define the stereochemistry of pochonin C’s carbon bearing the chlorine atom

La découverte de nouvelles entités naturelles est un processus particulièrement long et coûteux ; il faut donc réussir le plus tôt possible à détecter les composés connus dans les matrices étudiées, afin de ne pas les ré-isoler inutilement. C’est tout l’enjeu de l’annotation (c’est-à-dire l’identification partielle mais rapide de composés) et de la déréplication (autrement dit, l’application de l’annotation en vue d’écarter les molécules déjà connues du processus d’isolement).Grâce à sa sensibilité inégalée et à l’avènement de l’ère du « big data », la chromatographie liquide à haute performance couplée à la spectrométrie de masse tandem (CLHP-SM/SM) s’est imposée comme l’un des outils de référence dans cette démarche. En effet, son utilisation implique bien souvent le recours à des méthodes de traitement informatiques, comme le « molecular networking », de par la quantité considérable de données générées.La thèse se présente donc en deux parties : la première, portée sur l'extraction de nouveaux composés à partir d'une plante de la famille des Apocynaceae déjà très étudiée, Picralima nitida. La seconde propose une application des réseaux moléculaires à de la chimie biomimétique en mélanges, autour des alcaloïdes de type « 3-alkylpipéridines »
The discovery of new natural products is a very long and expensive process ; it is therefore important to detect previously known compounds in the studied matrices, to avoid an useless second isolation. This is the aim of annotation (partial but quick identification of compounds) and of dereplication (application of annotation to avoid reisolation).Thanks to its unequaled sensibility and to the "big data" era, the high performance liquid chromatography hyphenated to tandem mass spectrometry has become a reference technique in this field. Indeed, its use is generally implemented by informatic tools, as "molecular networking", because of the large amount of generated data.This thesis is divided into two parts : the first one deals with extraction of new compounds from a very well-known Apocynaceae plant, Picralima nitida. The second one is about the application of "molecular networking" to biomimetic chemistry in mixtures, especially about "3-alkylpiperidines" alkaloids

Multi ring-fused 2-pyridones have shown interesting activity in a variety of biological systems. It would be of great interest to explore the biological application of even more multi heterocyclic ring fused 2-pyridones. ‘Diversity oriented synthesis’ is an excellent concept emerged in recent years to access compounds with structurally and stereochemically diverse skeletons. This served as an efficient avenue for synthesizing various ring fused 2-pyridones using formyl, chloromethylene substituted 2-pyridone ( 6) as a starting compound. By treating the starting material (6) with various nucleopliles, different sized heterocyclic ring fused 2-pyridones has been synthesized. Additionally, an improved methodology for the synthesis of naphthyridones was presented.

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

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.

The generation of new chemical entities (NCEs) for use in chemical biology and drug discovery is of wide interest to both academia and the pharmaceutical industry. In order to generate NCEs, this project focused on development of new synthetic methodologies using transition-metal mediated [2+2+2] cyclotrimerisation of alkynes and unsaturated molecules to form bi- and tricyclic heterocyclic derivatives, some with structural resemblance to the quinocarcin family of natural products. Three different dialkynes (1,5-di(prop-2-yn-1-yl)pyrrolidin-2-one 2.117a, 1,6-di(prop-2-yn-1-yl)piperidin-2-one 2.118a and 4-benzyl-1,6-di(prop-2-yn-1-yl)piperazin-2-one 2.120a) were successfully synthesised. Several cyclotrimerisations were attempted, with the best yields being obtained when diethylacetylene dicarboxylate 2.113a was used as the monoalkyne and Cp*Ru(cod)Cl as the catalyst in refluxing toluene. New heterocyclic compounds with potential for diversification were synthesised using a diversity-oriented synthesis approach; specifically the build/couple/pair strategy for the synthesis of small molecules. Racemic nitrogen and oxygen building blocks were coupled with acrylonitrile, bromoacetonitrile and acyl chlorides. The pair step involved the intramolecular ring closure using transition-metal catalysed [2+2+2] cyclotrimerisations using microwave assisted radiation. The best catalyst for this approach was found to be CpCo(CO)2 at 150 ºC (300 W) in chlorobenzene. This provided a new methodology with potential for synthesising a diverse set of small molecules for biological testing. 20 compounds were subjected to chemosensitivity testing using the MTT assay. Several compounds were shown to possess activity in bladder (RT112) and breast (MCF-7) cancer cell lines. As these two cell lines are known to express extra-hepatic cytochromes P450 enzymes, it is possible that these are involved in generating cytotoxic metabolites that may damage DNA.

La nécessité grandissante de disposer d’une large librairie de diverses petites molécules pour le screening biologique constitue une puissante force motrice pour les chimistes organiciens et requiert en amont le développement de méthodologies rapides et efficaces. Dans ce cadre, nous nous sommes plus particulièrement intéressés à la fonctionnalisation d’énamides qui représentent des blocs moléculaires intéressants permettant d’introduire des fonctionnalités aminées dans des systèmes variés. Notre objectif a été de synthétiser des petites bibliothèques de molécules azotées à partir de substrats communs tout en mettant en oeuvre les différentes stratégies de la synthèse orientée vers la diversité et en s’attachant à respecter les règles suivantes : économie d’atomes, processus catalysés, synthèses rapides en peu d’étapes et contrôle de la stéréoselectivité. Dans un premier temps, nous avons principalement synthétisé divers énamides, nous permettant par la suite de développer des méthodologies innovantes et d’accéder à des « structures privilégiées » ou des fragments clés présents dans des produits naturels ou dans des substances potentiellement biologiquement actives en mettant en jeu des processus variés telles que des réactions d’aza-Michael, d’oxyamidation ou en cascade et la chimie du palladium avec de la CH insertion, des dioxoazoborocanes ou encore l’utilisation de l’auxiliaire chiral SAMP
The continuing demand to synthesize new and original collections of small molecules for the biological screening is an attractive subject for organic chemists and requires upstream the development of fast and easy synthetic methods. In this context, we decided to focus particularly on the functionalization of enamides which represent valuable building blocks in order to introduce nitrogen based functionality into various organic systems. Our objective was to synthesize new nitrogen containing compound libraries starting from common substrates by applying Diversity-Oriented Synthesis strategy and following these rules: atom economy, catalyzed reactions, fast synthesis in few steps and control of stereoselectivity. Firstly we mainly synthesized enamides. Thereafter, we developped efficient methodologies giving access to motifs frequently found in “privileged structures” or key scaffolds present in natural products or potential bioactive compounds thanks to various processes like aza-Michael, oxyamidation or cascade reactions, palladium chemistry with CH activation, dioxoazoborocanes or chiral auxiliary SAMP

Type-1 diabetes is caused by the autoimmune destruction of insulin-producing beta cells in the pancreas. Beta-cell apoptosis involves a complex set of signaling cascades initiated by \(interleukin-1\beta (IL-1\beta)\), \(interferon-\gamma (IFN-\gamma)\), and \(tumor necrosis factor-\alpha (TNF-\alpha)\). \(IL-1\beta\) and \(TNF-\alpha\) induce \(NF\kappa B\) expression, while \(IFN-\gamma\) induces STAT1 activation. These cytokines lead to a decrease of beta-cell function. The goal of this thesis is to identify small-molecule suppressors of cytokine-induced beta-cell apoptosis using high-throughput screening approach. Using the rat INS-1E beta-cell line, I developed an assay to measure cellular viability after 48 hours of cytokine treatment. I screened 29,760 compounds for their ability to suppress the negative effects of the cytokines. I identified several compounds to be suppressors of beta-cell apoptosis. These efforts led to the discovery of \(GSK-3\beta\) and HDAC3 as novel targets for suppressing beta-cell apoptosis. I also followed up on BRD0608, a novel suppressor that increased ATP levels and decreased caspase activity in the presence of cytokines. To follow up this compound, 35 analogs related to BRD0476 were synthesized using solid-phase synthesis and tested for their protective effects in the presence of cytokines. A structurally related analog, BRD0476, was found to be more potent and active in human islets, decreasing caspase activation and increasing insulin secretion after a 6-day treatment. I performed gene-expression profiling of INS-1E cells treated with the cytokine cocktail in the absence or presence of \(10\mu M\) BRD0476. Gene-set enrichment analysis revealed that the gene sets most significantly changed by BRD0476 involved cellular responses to \(IFN-\gamma\). I therefore assessed the effects of BRD0476 on STAT1 transcriptional activity. Cytokine treatment increased the reporter-gene luciferase activity, while co-treatment with BRD0476 reduced this activity significantly. To identify the intracellular target(s) of BRD0476, I collaborated with the Proteomics Platform in Broad Institute using SILAC (stable isotope labeling by amino acids in cell culture). SILAC is a mass spectrometry-based method to identify proteins that bind a small molecule attached to a bead. Deubiquitinase USP9X was pulled down by BRD0476. Knock-down of USP9X by siRNA phenocopied the protective effects of BRD0476. Binding assays were performed to identify interactions between BRD0476 and USP9X.
Chemistry and Chemical Biology

Chemical biology encompasses the study and manipulation of biological system using chemistry, often by virtue of small molecules or unnatural amino acids. Much insight has been gained into the mechanisms of biological processes with regards to protein structure and function, metabolic processes and changes between healthy and diseased states. As an ever expanding field, developing new tools to interact with and impact biological systems is an extremely valuable goal. Herein, work is described towards the synthesis of a small library of heterocyclic-containing small molecules and the mechanistic details regarding the interesting and unexpected chemical compounds that arose; an alternative set of non-toxic copper catalyzed azide-alkyne click conditions for in vivo metabolic labelling; and the synthesis of an unnatural amino acid for further chemical modification via [3+2] cycloadditions with nitrones upon incorporation into a peptide of interest. Altogether, these projects strive to supplement pre-existing methodology for the synthesis of small molecule libraries and tools for metabolic labelling, and thus provide further small molecules for understanding biological systems.

Les protéines BET, modules impliqués dans la régulation épigénétique, jouent un rôle essentiel dans le développement du cancer. Actuellement plusieurs inhibiteurs de protéines BET font l'objet d'essais cliniques pour le traitement de différents types de cancer. Une des limitations au développement clinique est l'impact général de la modulation génique induite par des inhibiteurs de type ‘pan-BET’ non sélectifs. Un ciblage individuel des protéines BET et la discrimination des domaines BD1 et BD2 conduiraient à un effet transcriptionnel plus spécifique limitant les effets secondaires et l’apparition de résistance. Le criblage d’une chimiothèque focalisée sur les interactions protéine-protéine a permis d’identifier deux molécules avec des profils de sélectivité uniques. Une étude de SAR a révélé le fragment minimal nécessaire à l’interaction ligand-protéine. La résolution de la structure cristallographique en complexe avec Brd4(BD1) a permis de valider nos interprétations et de développer des inhibiteurs BET plus puissants et sélectifs. Une stratégie de synthèse originale orientée vers une diversité structurale (DOTS) combinant le criblage virtuel et l’élaboration automatisée de bibliothèques focalisées a été utilisée. Ce travail a découvert un inhibiteur optimisé de BD1 avec une affinité de 100x supérieure à la molécule initiale et un ratio de sélectivité BD1 vs BD2 égale à 300. L’activité cellulaire d’inhibition du pro-oncogène c-Myc, au µM, a permis de valider le composé en tant que sonde moléculaire. Des études in vitro et in vivo permettront d'élucider le rôle biologique individuel de chaque BD et de valider l'intérêt de leurs développement en clinique
BET-proteins, acting as epigenetic readers, play an essential role in cancer development. To date, numerous potent inhibitors disrupting BET functions have been discovered, including several of them that are undergoing clinical trials for the treatment of different types of cancer. The common drawback limiting their use in clinical practice is an inability to distinguish between BET-members that may cause side effects and resistances. The selective targeting of individual BET and the discrimination between BD1 and BD2 present an opportunity to achieve more selective transcriptional effect. A midthroughput screening of previously designed chemical library allowed identification of two molecules with unique profiles of selectivity that have never been observed. An undertaken structure-based program revealed a minimum scaffolds necessary for binding. Taking together with resolved X-Ray structures it allowed the development of more potent and selective BET inhibitors by DOTS (diversity oriented target focused synthesis) strategy, combining virtual screening and diversity oriented library design. This optimization led to a potent inhibitor with up to 100-fold improvement of affinity to the target and up to 300-fold selectivity toward BD1. Dose-response downregulation of c-Myc levels in low micromolar range in cell assays allowed the validation of the identified molecule as a chemical probe. Further comprehensive in vitro and in vivo evaluations of this compound will enable elucidating the biological role of each bromodomain and a validation of the interest toward the development of selective inhibitors in clinic

Allylboration reactions have been thoroughly utilized in organic chemistry since it was discovered that they could add in a nucleophilic fashion to aldehydes and ketones in 1964. Modification of allylboronates and the substrates that they can react with has been the focus of many research groups over the past three decades. Recent works have made use of catalysis to promote the addition of allylboronates that are generally otherwise unreactive toward various electrophiles. Chapter 2 will discuss the discovery that Brnsted acids can catalyze the addition of unreactive 2-alkoxycarbonyl allylboronates to aldehydes and that the diastereoselectivity of the reaction is determined by the electronic nature of the aldehyde. Ketones and imines are much less reactive than aldehydes towards allylboronates due to steric and electronic factors. As a result, new conditions are often required to promote the allylboration reaction of ketones and imines. Chapter 3 will briefly discuss the challenges that ketones present as substrates for allylboration reactions and show my attempts at achieving this transformation. Chapter 4 will describe imines and their associated challenges as substrates for allylboration reactions. However, once harnessed, these substrates provide easy access to -methylene -lactones when a 2-alkoxycarbonyl allylboronate is used as the allylating reagent. The modification of important or interesting molecules by making major or minor changes to a common core structure is the basis of diversity-oriented synthesis of combinatorial libraries. -Alkylidene -lactones and -alkylidene -lactams are biologically interesting compounds present in numerous natural products. Chapter 5 will discuss how the title compounds were modified by various metal-catalyzed coupling reactions to provide a diversity-oriented combinatorial library of -lactones and -lactams. Since -lactones are prevalent in many natural products, the application of 2-alkoxycarbonyl allylboronates to a target-oriented synthesis was intriguing. Unlike diversity-oriented synthesis, target oriented synthesis aims at synthesizing a single compound through any number of controlled steps, arriving at one specific product that is obtained as a pure isomer. Access to highly complex -lactones is often tedious, however, Chapter 6 will discuss how a simple, one-step allylboration reaction of a complex aldehyde with a 2-alkoxycarbonyl allylboronate can lead to a highly substituted -lactone. This -lactone can be further modified and transformed into chinensiolide B, a biologically active natural product isolated from a plant found in various locations in China.

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.
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Thesis (Ph. D.)--University of Alberta, 2010.
Title from pdf file main screen (viewed on June 25, 2010). In the title, the words alpha and gamma are represented by the Greek letters. A thesis submitted to the Faculty of Graduate Studies and Research in partial fulfillment of the requirements for the degree of Doctor of Philosophy, Department of Chemistry, University of Alberta. Includes bibliographical references.

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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.

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.

碩士
國立交通大學
應用化學系碩博士班
105
First part:One-pot, three step synthesis of 3-(1-propyl-1H- benzo[d]imidazol-2-yl)-2H-chromen-2-one, using 2-cyano-N-(2-(propylamino)phenyl)acetamide compound 11 under p-toluene sulfonic acid catalyst to undergo intramolecular cyclization to form 2-(1-propyl-1H-benzo[d]imidazol-2-yl)acetonitrile compound 12, then add proper triethylamine to undergo Knoevenagel condensation reaction to get intermediate 14, and finally add 1N HCl to provide compound 15. Second part: Compounds 12 obtained in the first part of the study can further synthesize polycyclic structures to increase their biological activity and diversity, such as pyrazole. The compound 12, benzaldehyde 18 and piperidine are reacted in toluene to form the olefinic compound 23 and reacted with the phenylhydrazine compound 17 and cesium carbonate in an ethanol solution to give the product 1H-benzo [d] imidazole-1,3-diphenyl-1H-pyrazol-5-amine. Part 3: Synthesis of 2-aza-7-arylpyrrolidine alkaloid derivatives using a single non-mirror optical isomer. The intermediate 5-aryl thiohydantain 30 was first reacted with L-ester-based amino acid 32 and isothiocyanate 33 at room temperature for 30 minutes, followed by the addition of malononitrile , Benzaldehyde and piperidine at room temperature for 12 hours to give the product 2-aza-7-arylpyrrolididine 31.