Innovative asymmetric organocatalytic processess: en route to the synthesis of biologically relevant compounds

This doctoral thesis deals with the development of novel organocatalytic strategies for asymmetric transformation. The intrinsic versatility of organocatalysis and the use of different activation modes have been exploited to achieve new catalytic enantioselective processes, towards the synthesis of biologically relevant scaffolds. The most investigated organocatalytic system have been those based on H-bond interaction (such as chiral thioureas or phosphoric acids) as well as the ones based on aminocatalysis. Despite conceptually distinct, the transformations detailed in this Thesis are linked together by simple and recurring modes of activation, induction and reactivity, promoted by the catalysts employed. The chemical diversity of the challenges encountered allows to get a precious overall view on organocatalysis, highlighting that enormous chemical diversity can be created by judicious choice of select catalyst.

Synthesis of constrained peptidomimetics for therapeutic, diagnostic and theranostic applications

This thesis work deals, principally, with the development of different chemical protocols ranging from environmental sustainability peptide synthesis to asymmetric synthesis of modified tryptophans to a series of straightforward procedures for constraining peptide backbones without the need for a pre-formed scaffold. Much efforts have been dedicated to the structural analysis in a biomimetic environment, fundamental for predicting the in vivo conformation of compounds, as well as for giving a rationale to the experimentally determined bioactivity. The conformational analyses in solution has been done mostly by NMR (2D gCosy, Roesy, VT, titration experiments, molecular dynamics, etc.), FT-IR and ECD spectroscopy. As a practical application, 3D rigid scaffolds have been employed for the synthesis of biological active compounds based on peptidomimetic and retro-mimetic structures. These mimics have been investigated for their potential as antiflammatory agents and actually the results obtained are very promising. Moreover, the synthesis of Amo ring permitted the development of an alternative high effective synthetic pathway for obtaining Linezolid antibiotic. The final section is, instead, dedicated to the construction of a new biosensor based on zeolite L SAMs functionalized with the integrin ligand c[RGDfK], that has showed high efficiency for the selective detection of tumor cells. Such kind of sensor could, in fact, enable the convenient, non-invasive detection and diagnosis of cancer in early stages, from a few drops of a patient's blood or other biological fluids. In conclusion, the researches described herein demonstrate that the peptidomimetic approach to 3D definite structures, allows unambiguous investigation of the structure-activity relationships, giving an access to a wide range bioactive compounds of pharmaceutical interest to use not only as potential drugs but also for diagnostic and theranostic applications.

Synthesis of carbolines and analogues via rhodhium-catalyzed [2+2+2] cycloaddition with alkynyl-ynamides : application to the total synthesis of alkaloids

The main research theme of this dissertation is the synthesis of g- and b-carbolines using a metal-catalyzed [2+2+2] cycloaddition strategy of tethered alkynyl-ynamides (diynes) with nitriles. g- and b-carbolines form the core of a large group of natural product and represent important targets for organic chemists. Many of these carbolines showed pharmacological effects ranging from anti-tumor to anxiolytic and anti-HIV activity. A model study with N-Ethynyl-N-tosyl-2-(2-phenylethynyl)aniline and methyl cyanoformate showed that rhodium-based catalysts promote efficiently the reaction. A further optimization showed that the regioselectivity of the reaction can be tuned by the choice of the solvent or by the catalytic system. Application to a larger scope of diynes showed that the regioselectivity strongly depends on the type of substitution of the alkynyl moieties, giving regioselectivities in the range g:b = 1/0 to g:b = 0/1. This [2+2+2] cycloaddition approach for the synthesis of the g- and b-carboline cores was successfully applied to the first total synthesis of Isoperlolyrine and the total synthesis of Perlolyrine. Extension of this strategy to heterocumulenes as cycloaddition partners allowed the synthesis of a g-carbolinone, a thiopyrano[3,4-b]indol-3-imine and thiopyranothiones.

New and More Sustainable Processes for the Synthesis of Phenolics: 2-phenoxyethanol and hydroxytyrosol

The research work has dealt with the study of new catalytic processes for the synthesis of fine chemicals belonging to the class of phenolics, namely 2-phenoxyethanol and hydroxytyrosol. The two synthetic procedures investigated have the advantages of being much closer to the Green Chemistry principles than those currently used industrially. In both cases, the challenge was that of finding catalysts and methods which led to the production of less waste, and used less hazardous chemicals, safer solvents, and reusable heterogeneous catalysts. In the case of 2-phenoxyethanol, the process investigated involves the use of ethylene carbonate (EC) as the reactant for phenol O-hydroxyethylation, in place of ethylene oxide. Besides being a safer reactant, the major advantage of using EC in the new synthesis is the better selectivity to the desired product achieved. Moreover, the solid catalyst based on Na-mordenite was fully recyclable. The reaction mechanism and the effect of the Si/Al ratio in the mordenite were investigated. In the case of hydroxytyrosol, which is one of the most powerful natural antioxidants, a new synthetic procedure was investigated; in fact, the method currently employed, the hydrolysis of oleuropein, an ester extracted from the waste water processing of the olive, makes use of large amounts of organic solvents (hexane, ethyl acetate), and involves several expensive steps of purification. The synthesis procedure set up involves first the reaction between catechol and 2,2-dimethoxyacetaldehyde, followed by the one-pot reduction of the intermediate to give the desired product. Both steps were optimized, in terms of catalyst used, and of reaction conditions, that allowed to reach ca 70% yield in each step. The reaction mechanism was investigated and elucidated. During a 3-month period spent at the University of Valencia (with Prof. A. Corma’s group), a process for the production of diesel additives (2,5-bis(propoxymethyl)furan) from fructose has been investigated.

Synthesis of novel cobalt and iron complexes for sustainable catalytic hydrogenations

Aim of the present work of thesis is to synthesize new non-noble metal based complexes to be employ in redox reactions by a metal-ligand cooperative mechanism. The need of replacing toxic and expensive precious metal complexes with more available and benign metals, has led to the development of new compounds based on cobalt and iron, which are the metals investigated in this study. A carbonyl-tetrahydroborato-bis[(2-diisopropylphosphino)ethyl]amine-cobalt complex bearing a PNP-type ligand is synthesized by a three-step route. Optimization attempt of reaction route were assessed in order to lowering reaction times and solvent waste. New cobalt complex has been tested in esters hydrogenation as well as in acceptorless dehydrogenative coupling of ethanol. Other varieties of substrates were also tested in order to evaluate any possible applications. Concerning iron complex, dicarbonyl-(η4-3,4-bis(4-methoxyphenyl)-2,5-diphenylcyclopenta-2,4-dienone)(1,3-dimethyl-ilidene)iron is synthesized by a three steps route, involving transmetallation of a silver complex, derived from an imidazolium salt, to iron complex. In order to avoid solvent waste, optimization is assessed. Studies were performed to assess activity of triscarbonyl iron precursor toward imidazolium salt and silver complexes.

Enantioselective synthesis of Equol with Ir-BARF and labelling with deuterium

In this project we researched and optimized an new synthetic route for R-Equol, a molecule that is attracting increasing interest for the medicine because of its phytoestrogenic properties and the chemoprevention of breast cancer. To reach this objective we start, from smaller building blocks, with the synthesis of Daidzein followed by a chemoselective borane reduction to obtain an olefin that will be hydrogenated enantioselectively with a commercial Ir-BARF catalyst. The increasing success of these catalysts even with this genre of substrates has already given good results with different catalysts in both e.e. and yield. For further researches we deuterate the Equol in the aliphatic O-ring and attempt a secondary synthetic route with an hydrogenation using QN-modified Pd.

Bottom-up solution synthesis of structurally defined graphene nanoribbons

Graphene nanoribbons (GNRs), which are defined as nanometer-wide strips of graphene, are attracting an increasing attention as one on the most promising materials for future nanoelectronics. Unlike zero-bandgap graphene that cannot be switched off in transistors, GNRs possess open bandgaps that critically depend on their width and edge structures. GNRs were predominantly prepared through “top-down” methods such as “cutting” of graphene and “unzipping” of carbon nanotubes, but these methods cannot precisely control the structure of the resulting GNRs. In contrast, “bottom-up” chemical synthetic approach enables fabrication of structurally defined and uniform GNRs from tailor-made polyphenylene precursors. Nevertheless, width and length of the GNRs obtainable by this method were considerably limited. In this study, lateral as well as longitudinal extensions of the GNRs were achieved while preserving the high structural definition, based on the bottom-up solution synthesis. Initially, wider (~2 nm) GNRs were synthesized by using laterally expanded monomers through AA-type Yamamoto polymerization, which proved more efficient than the conventional A2B2-type Suzuki polymerization. The wider GNRs showed broad absorption profile extending to the near-infrared region with a low optical bandgap of 1.12 eV, which indicated a potential of such GNRs for the application in photovoltaic cells. Next, high longitudinal extension of narrow (~1 nm) GNRs over 600 nm was accomplished based on AB-type Diels–Alder polymerization, which provided corresponding polyphenylene precursors with the weight-average molecular weight of larger than 600,000 g/mol. Bulky alkyl chains densely installed on the peripheral positions of these GNRs enhanced their liquid-phase processability, which allowed their formation of highly ordered self-assembled monolayers. Furthermore, non-contact time-resolved terahertz spectroscopy measurements demonstrated high charge-carrier mobility within individual GNRs. Remarkably, lateral extension of the AB-type monomer enabled the fabrication of wider (~2 nm) and long (>100 nm) GNRs through the Diels–Alder polymerization. Such longitudinally extended and structurally well-defined GNRs are expected to allow the fabrication of single-ribbon transistors for the fundamental studies on the electronic properties of the GNRs as well as contribute to the development of future electronic devices.

Synthesis of polyphenylene cylinders with different sizes and connectivity patterns as well as study of their linear congeners

In dieser Arbeit wird die Synthese von Polyphenylenzylindern (PPZ) und strukturell verwandten Molekülen beschrieben, die in unterschiedlichen Größen und verschiedenartigen Bindungsmustern dargestellt wurden. Aufgrund ihres Aufbaus sind sie direkte Vorläufermoleküle von Kohlenstoffnanoröhren (CNT)s. Ziel war es, zunächst zu untersuchen, ob sich PPZs darstellen lassen. In einem anschließenden Schritt wurde die nasschemische Synthese von CNTs untersucht, die auf diesem Weg bisher noch nicht erreicht werden konnte. Die hier studierten Strukturen führten zu vielversprechenden Ergebnisse auf diesem Weg, da die oxidative Cyclodehydrierung – eine intramolekulare Anellierung – zur Bildung von ca. 50% der notwendigen Bindungen führte.

Engineering the synthesis of lantibiotics in e. Coli by combining the cynnamicin and nisin modification systems.

I lantibiotici sono molecole peptidiche prodotte da un gran numero di batteri Gram-positivi, posseggono attività antibatterica contro un ampio spettro di germi, e rappresentano una potenziale soluzione alla crescente problematica dei patogeni multi-resistenti. La loro attività consiste nel legame alla membrana del bersaglio, che viene quindi destabilizzata mediante l’induzione di pori che determinano la morte del patogeno. Tipicamente i lantibiotici sono formati da un “leader-peptide” e da un “core-peptide”. Il primo è necessario per il riconoscimento della molecola da parte di enzimi che effettuano modifiche post-traduzionali del secondo - che sarà la regione con attività battericida una volta scissa dal “leader-peptide”. Le modifiche post-traduzionali anticipate determinano il contenuto di amminoacidi lantionina (Lan) e metil-lantionina (MeLan), caratterizzati dalla presenza di ponti-tioetere che conferiscono maggior resistenza contro le proteasi, e permettono di aggirare la principale limitazione all’uso dei peptidi in ambito terapeutico. La nisina è il lantibiotico più studiato e caratterizzato, prodotto dal batterio L. lactis che è stato utilizzato per oltre venti anni nell’industria alimentare. La nisina è un peptide lungo 34 amminoacidi, che contiene anelli di lantionina e metil-lantionina, introdotti dall’azione degli enzimi nisB e nisC, mentre il taglio del “leader-peptide” è svolto dall’enzima nisP. Questo elaborato affronta l’ingegnerizzazione della sintesi e della modifica di lantibiotici nel batterio E.coli. In particolare si affronta l’implementazione dell’espressione eterologa in E.coli del lantibiotico cinnamicina, prodotto in natura dal batterio Streptomyces cinnamoneus. Questo particolare lantibiotico, lungo diciannove amminoacidi dopo il taglio del leader, subisce modifiche da parte dell’enzima CinM, responsabile dell’introduzione degli aminoacidi Lan e MeLan, dell’enzima CinX responsabile dell’idrossilazione dell’acido aspartico (Asp), e infine dell’enzima cinorf7 deputato all’introduzione del ponte di lisinoalanina (Lal). Una volta confermata l’attività della cinnamicina e di conseguenza quella dell’enzima CinM, si è deciso di tentare la modifica della nisina da parte di CinM. A tal proposito è stato necessario progettare un gene sintetico che codifica nisina con un leader chimerico, formato cioè dalla fusione del leader della cinnamicina e del leader della nisina. Il prodotto finale, dopo il taglio del leader da parte di nisP, è una nisina completamente modificata. Questo risultato ne permette però la modifica utilizzando un solo enzima invece di due, riducendo il carico metabolico sul batterio che la produce, e inoltre apre la strada all’utilizzo di CinM per la modifica di altri lantibiotici seguendo lo stesso approccio, nonché all’introduzione del ponte di lisinoalanina, in quanto l’enzima cinorf7 necessita della presenza di CinM per svolgere la sua funzione.

Mission synthesis of sine-on-random excitations for accelerated vibration qualification testing

In most real-life environments, mechanical or electronic components are subjected to vibrations. Some of these components may have to pass qualification tests to verify that they can withstand the fatigue damage they will encounter during their operational life. In order to conduct a reliable test, the environmental excitations can be taken as a reference to synthesize the test profile: this procedure is referred to as “test tailoring”. Due to cost and feasibility reasons, accelerated qualification tests are usually performed. In this case, the duration of the original excitation which acts on the component for its entire life-cycle, typically hundreds or thousands of hours, is reduced. In particular, the “Mission Synthesis” procedure lets to quantify the induced damage of the environmental vibration through two functions: the Fatigue Damage Spectrum (FDS) quantifies the fatigue damage, while the Maximum Response Spectrum (MRS) quantifies the maximum stress. Then, a new random Power Spectral Density (PSD) can be synthesized, with same amount of induced damage, but a specified duration in order to conduct accelerated tests. In this work, the Mission Synthesis procedure is applied in the case of so-called Sine-on-Random vibrations, i.e. excitations composed of random vibrations superimposed on deterministic contributions, in the form of sine tones typically due to some rotating parts of the system (e.g. helicopters, engine-mounted components, …). In fact, a proper test tailoring should not only preserve the accumulated fatigue damage, but also the “nature” of the excitation (in this case the sinusoidal components superimposed on the random process) in order to obtain reliable results. The classic time-domain approach is taken as a reference for the comparison of different methods for the FDS calculation in presence of Sine-on-Random vibrations. Then, a methodology to compute a Sine-on-Random specification based on a mission FDS is presented.

Studies towards the total synthesis of penicillipyrone b via a biomimetic approach

Pennicillipyrone A and B are two novel meroterpenoids isolated from the marine-derived fungus Penicilliump sp. Although a preliminary toxicity studies demonstrated the bioactivity of penicillipyrone A to be far superior to that of its congener penicillipyrone B, we were intrigued by its structure. Moreover, it appeared as though one could design an efficient total synthesis based on chemistry that was familiar to our laboratory. The purpose of this project was the study of a new synthesis of Pennicillipyrone B by way of a doubley-biomimetic approach. The intended approach proceeds through a polyene cascade reaction terminated by a nucleophilic pyrone - a reaction not yet known in the literature for the construction of this type of scaffold. During the course of this study we have learned about the unanticipated reactivity of C2 substituted keto-dioxinones with regard to self-condensation. In addition, four new compounds were synthesized and two synthetic routes to the target molecule are presented.

Synthesis of novel ribose-based thioimidate n-oxides

This work is based on the study of new synthetic paths to obtain thioimidate N-oxides (TINOs) from D-ribose and to study their reactivity with the purpose to obtain ketonitrones. TINOs, aren’t well known molecules, but these enantiomerically pure backbones could be valuable intermediates in the synthesis of novel ketonitrones which are key intermediates in the synthesis of iminosugars. TINOs were discovered from the study of glucoraphanin, a particular glucosinolate, that unexpectedly cyclized into a TINO after desulfatation, by a spontaneous intramolecular Michael addition. The first part of this work was to synthetize the TINO 3 from D-ribose 1. The key step was the desilylative cyclisation of a suitably functionalized thiohydroximate 2. Based on precedent work developed in the laboratory, we could obtain the thiohydroximate from D-ribose. We then focused our studies on the cyclisation step trying to find the suitable substituents that could give the TINO in good yield by desilylative cyclisation. The second part of the project is to obtain ketonitrones 4 by palladiumcatalyzed coupling reaction.

Synthesis of (-)-dactylolide and 13-desmethylene-(-)-dactylolide and their effects on tubulin

An efficient new synthesis has been elaborated for non-natural (-)-dactylolide ((-)-2) and its 13-desmethylene analogue 4, employing a HWE-based macrocyclization approach with beta-keto-phosphonate/aldehyde 19 and the respective 13-desmethylene derivative as the key intermediates. Both (-)-2 and 4 as well as the corresponding C20 alcohols inhibit human cancer cell proliferation with IC(50) values in the sub-micromolar range and induce the polymerization of tubulin in vitro.

Stereoselective synthesis of a monocyclic peloruside a analogue

The stereoselective synthesis of the monocyclic peloruside A analogue 4 has been achieved, following a new efficient approach for the introduction of the side chain, involving a late-stage addition of vinyl lithium species 7a to aldehyde 8. Further key steps are a highly diastereoselective allyltitanation reaction and a RCM-based macrocyclization.