Doctor of Philosophy / Department of Chemistry / Duy H. Hua / The first section of this thesis deals with the synthesis of substituted quinolines and its bioactivities against gap junction. Cancer cells are characterized by down regulated or altered gap junction intercellular communication (GJIC) activities; enhancement of GJIC would provide a pathway for the delivery of anticancer drugs. Our computational studies using Autodock found binding interactions between gap junction channels and substituted quionlines (code name PQs). Thus, a serial of PQ compounds were synthesized and their activities against GJIC were tested. Among these synthesized PQs, 6-Methoxy-8-[(3-aminopropyl) amino]-4- methyl-5-(3-trifluoromethyl- phenyloxy)quinoline (PQ1) can specifically enhance GJIC activity of T47D cells without affecting the normal MECs. The PQ1 induced apoptosis can spread throughout the gap juctions, consequently cause the decrease of cell viability and colony growth. PQ1 can attenuate tumor growth of xenograft tumors in Nu/Nu mice. Compound 7 (code PQ11) which has an IC50 of 15.6nM against T47D cancer cell, is a promising candidate for further pharmacological studies. The second section of this thesis deals with the synthesis and anticancer bioactivities of PEG-PEI based nanogels. Nanogels were synthesized, encapsulated with anticancer drugs, and loaded to stem cells. Stem cells can target at the cancer cell and release the nanogel and anticancer drug to kill the cancer cell. The nontoxic PEG-PEI nanogel which can be loaded to stem cells was successfully synthesized by doubly treatment of PEI with activated PEG. Based on this nontoxic nanogel, two other types of nanogels were synthesized. In one type of nanogel, an anticancer drug, SN38 was modified and attached to the nontoxic nanogel via a tetra-peptide linker. This tetra peptide can be recognized and cut by legumain, a protein that highly over expressed in many tumors, to release the drug to tumors. In the other type of nanogel, straptavidin was attached to the nanogel which can bind to biotin and recognized by tumor. The result indicated this type of nanogel can be loaded to stem cells within 15 minutes.

Abstract “Biomimetic Aminoacylation” Svetlana K. Tzvetkova Doctor of Philosophy, 2008 Graduate Department of Chemistry University of Toronto The accuracy of ribosomal protein synthesis depends on the fidelity of highly specific enzymes, aminoacyl tRNA synthetases, towards amino acid – tRNA pairs. These biological catalysts are responsible for activating the amino acids as aminoacyl adenylates and for their subsequent attachment to the 2’- or 3’-OH at the 3’-terminal of the correct tRNA to give aminoacyl-tRNA. Extended diversity in protein structure and function could be achieved if non-natural side chains can be introduced in protein synthesis. This requires that the acceptor stem of a tRNA molecule be synthetically aminoacylated. The most widely used methods for charging tRNA with non-natural amino acids involve multi-step synthesis of an aminoacyl-pCpA and its consequent enzymatic ligation to truncated tRNA. No direct route to these species has been reported. We have developed a method for direct biomimetic aminoacylation of the 3’-terminal hydroxyls of tRNA. Our approach shows to be promising in reactions leading to direct 2’- or 3’-O-aminoacylation of not only nucleosides and nucleotides but also RNA in general and tRNA in particular. The system we have developed provides: 1) efficient activation of the amino acids as aminoacyl phosphates, analogues of the enzymatic intermediates, and 2) specific recognition of the 3’-terminal of tRNA by lanthanide ions present in the reaction. The aminoacylating reagents used in our studies were carefully selected to provide handles to follow the reaction: UV absorbance, fluorescence spectroscopy and 19F NMR. Lanthanide (III) ions can play a role similar to a key part of the aminoacyl tRNA synthetases – they bring the aminoacyl close to the 3’-terminal of tRNA, in this case by forming a bis-bidentate complex with the aminoacyl phosphate and the 2’,3’-diol functionality of the 3’-terminal adenosine. This process relies on the specificity towards the unique 3’-terminal diol on tRNA, provided by the metal ion and the simultaneous complexation of the aminoacyl phosphate.

Hydrogen bonding interactions have been applied to the synthesis of chiral vicinal diamines and the generation of helical chirality. A stereospecific synthesis of vicinal diamines was developed by using the diaza-Cope rearrangement reaction driven by resonance-assisted hydrogen bonds (RAHBs). This process for making a wide variety of chiral diamines requires only a single starting chiral diamine, 1,2-bis(2-hydroxyphenyl)-1,2-diaminoethane (HPEN) and aldehydes. Experimental and computational studies reveal that this process provides one of the simplest and most versatile approaches to preparing chiral vicinal diamines including not only C2 symmetric diaryl and dialkyl diamines but also unsymmetrical alkyl-aryl and aryl-aryl diamines with excellent yields and enantiopurities. Weak forces affecting kinetics and thermodynamics of the diaza-Cope rearrangement were systematically studied by combining experimental and computational approaches. These forces include hydrogen bonding effects, electronic effects, steric effects, and oxyanion effects. As an example of tuning diamine catalysts, a vicinal diamine-catalyzed synthesis of warfarin is described. Detailed mechanistic studies lead to a new mechanism involving diimine intermediates. Decreasing the NCCN dihedral angle by varying the diamine structure results in an increase of the enantioselectivity up to 92% ee. Hydrogen bonds have been used to generate helical chirality in a highly stereospecific manner with a single amino acid and 2,2′-dihydroxybenzophenone. DFT computational and experimental data including circular dichroism (CD), X-ray crystallography and 1H NMR data provide insight into the origin of the stereospecificity. A signalling dizao group can be attached to the receptor for general sensing of amino acid enantiopurity.

2-(2-mandelyl)thiamin (MTh), the adduct of benzoylformate and thiamin, is an accurate model of 2-(2-mandelyl)thiamin diphosphate, the initial covalent intermediate in the decarboxylation of benzoylformate by benzoylformate decarboxylase (BFDC). The first order rate constant for spontaneous decarboxylation of MTh is about 106 times smaller than the enzymic rate (kcat) for the BFDC reaction. Based on the similarities of MTh and the corresponding enzymic intermediate, as well as the inherent nature of the intermediate, it is not obvious why the enzyme-catalyzed reaction is so much faster. However, earlier studies showed that the decarboxylation of MTh is catalyzed by protonated pyridines and this was proposed to occur through a preassociation mechanism. If this explanation is correct, then the observed 12C/13C kinetic isotope effect (CKIE) will increase in the presence of the catalyst as a more favorable forward commitment is made possible. This provides a specific model for the enzyme-catalyzed process. We developed a technique using headspace analysis and compound specific isotope analysis (CSIA) to determine the CKIE for the decarboxylation of MTh in the presence and absence of pyridinium. We found that the CKIE increases in the presence of the catalyst, as predicted for the preassociation mechanism. In a related study, we investigated the kinetics of decarboxylation of pyrrole-2-carboxylic acid, which was known to be subject to acid catalysis in highly acidic solutions. In the expected mechanism, protonation of the pyrrole ring at C2 destroys the aromaticity of the ring. C-C bond cleavage in the process of decarboxylation will re-establish the aromatic pyrrole. However, the overall reaction rate would not increase as it is counteracted by a larger concentration of the undissociated carboxyl group compared to carboxylate ion necessary for decarboxylation. Since the reaction occurs readily, there must be an alternative pathway for the acid-catalyzed reaction. This can be achieved in an associative mechanism that is initiated by addition of water to the carboxyl group of the carboxyl-protonated reactant. C-C bond cleavage results in formation of pyrrole and protonated carbonic acid, a species that has been recognized as a viable intermediate in related processes. Protonated carbonic acid is spontaneously converted to H3O+ and carbon dioxide. The associative mechanism is consistent with solvent-deuterium kinetic isotope effects and 12C/13C kinetic isotope effects.

The development of new, improved methods for forming carbon–carbon and carbon–heteroatom bonds is the basic goal in synthetic organic chemistry. In the Lautens group, many recent advances have been made using late transition metals such as rhodium and palladium. One such research project involves the synthesis of indoles through tandem C–N and C–C coupling reactions using gem-dibromoolefin starting materials, and this area serves as a starting point for the research described. Chapter 1 describes a method by which the tandem use of gem-dibromoolefins can be halted to give intramolecular monocoupling reactions, maintaining one of the carbon–bromine bonds which can serve as a useful handle for further functionalization. The use of copper as a catalyst is key to this reaction, as it features a unique mechanism for carbon–heteroatom bond formation. Benzofurans and benzothiophenes can be prepared by this method. Chapter 2 describes the synthesis of 2-bromoindoles using an intramolecular Buchwald–Hartwig amination of gem-dibromoolefins. It is found that the products are more reactive towards palladium(0) than the starting material, and the use of a bulky phosphine ligand which facilitates reversible oxidative addition is required. This represents one of the first catalytic applications of this step in synthesis. Chapter 3 further explores the concept of reversible oxidative addition in a novel carbohalogenation reaction of alkenes. Aryl iodides tethered to alkenes are treated with a palladium(0) catalysts, which can undergo the basic steps of oxidative addition, carbopalladation, and novel sp2 carbon–iodine reductive elimination. This process is remarkably simple in concept, and is a waste-free, atom economically method for preparing new carbon–carbon bonds. Chapter 4 discusses various limitations to the carbohalogenation methodology, and seeks to overcome these problems. The use of aryl bromide starting materials can be accomplished by adding an iodide source to the reaction, allowing halide exchange of palladium(II) intermediates to occur. Intermolecular and asymmetric variants are also explored. Computational studies are discussed which reveal useful mechanistic details of the catalytic cycle, and this information is used in the development of novel phosphine ligands.

This work can be separated into two parts; the first will encompass chapters one and two, which discuss the use of the Catellani reaction to access different heterocycles. The second part will encompass the remaining chapters and deals with stereoselective reactions of arynes. Chapter one outlines the development of a general and high yielding synthesis of the phenanthridine nucleus via a palladium-catalyzed domino reaction of aryl iodides with N-H or N-trimethylsilyl imines. This strategy was applied in a succinct synthesis of benzo[c]phenanthridine alkaloids nitidine and NK109. Chapter two details the development of a Catellani-type reaction of aryl iodides with 2H-azirines. Conditions were found to selectively provide access to either the indole nucleus or unusual dihydroimidazoles. The yields of the products ranged from moderate to good, however, the success of the reaction is highly dependent on the structure of the 2H-azirine. A mechanism was proposed involving oxidative addition of the azirine to generate an azaalyl intermediate. In Chapter three the foray into the area of aryne chemistry begins. A stereoselective nickel- catalyzed [2+2+2] cycloaddition of 1,6-enynes with aryne intermediates was developed. Attempts were made at the development of an asymmetric variant of the reaction, however, only low enantiomeric excess was observed. Good diastereoselectivity could be obtained when an allylic substituent was present. The yields of the products ranged from moderate to excellent. However, the yields vary greatly and in a number of cases the reactions were unsuccessful. Finally, in chapter four the development of a general and high yielding annulation strategy for the synthesis of various carbo- and heterocycles, based on an intramolecular aryne ene reaction is described. It was found that the geometry of the olefin is crucial to the success of the reaction and it that regioselective hydrogen migration occurs. Furthermore, the electronic nature of the aryne was found to be important to the success of the reaction. Deuterium labeling studies and DFT calculations provided insight into the reaction mechanism. The data suggested a concerted asynchronous transition state, resembling a nucleophilic attack on the aryne. This strategy was successfully applied to the formal synthesis of the ethanophenanthridine alkaloid (±)-crinine. In a similar vein, preliminary results demonstrating an intramolecular, formal [2+2] cycloaddition of an aryne with an S, O-ketene acetal to give interesting tricyclic benzocyclobutene products are disclosed.

A range of N-H alkynylaziridines were prepared from amphoteric unprotected aziridine aldehydes without protecting-group manipulation. Unprotected alpha -amino allenes can be obtained from these strained propargyl amines via a 9-BBN mediated hydride transfer. Further transformation of alpha -amino allenes to 2,4,6-trisubstituted pyridines was realized. We also developed another class of amphoteric molecules – alpha-boryl aldehydes, equipped with the tetrahedral MIDA boryl group. A wide range of boryl-substituted building blocks or functionalized boronic acid derivatives have been accessed from these bench-stable alpha-borylcarbonyl compounds. Further chemoselective transformations of these alpha-boryl aldehyde derived building blocks have been conducted, where alph-boryl isocyanates, alpha-aminoboronic acids, acylboronates, and borylated heterocycles were achieved through the decarboxylative functionalization of alpha-borylcarboxylic acids.

The development of a palladium-catalyzed intramolecular carboesterification of unactivated olefins is described. Olefin difunctionalization is a powerful tool for adding complexity to a molecule, and this formal [3+2] cycloaddition generates highly functionalized fused ring systems. Initially discovered by Dr. Yang Li in our group, it was found that when propiolic acids with a pendant terminal olefin were treated with 1 mol % Pd(MeCN)2Cl2, 3 equivalents of copper (II) chloride, and 3 equivalents of lithium chloride in acetonitrile at 50 °C, cyclization occurred in up to 90% yield. The optimization of this reaction and the extension to propiolamides and propargyl alcohols is described in this thesis. A mechanism involving a novel palladium-carboxylate species is proposed. Preliminary investigations into the synthesis of chiral sulfoxide pincer ligands are also described. The nucleophilic aromatic substitution of 1,3-dibromobenzene and 2,6-dichloropyridine with various thiols, followed by oxidation of the sulfides to sulfoxides is investigated as a route to the desired proligands.

scyllo-Inositol is currently in phase II clinical trials as a therapeutic for Alzheimer’s disease (AD). Previous work from our lab has shown that scyllo-inositol prevents Ab1-42 fibril formation instead leading to the formation of small Ab oligomers in vitro. To further understand the molecular details of Ab-scyllo-inositol binding interactions, a library of scyllo-inositol derivatives was prepared. A sequence of protecting group transformations afforded a hydroxylamine functionalized scyllo-inositol. Subsequent oxime formation with aromatic aldehydes generated a novel class of inositol derivatives in good yield and high purity. The effects of these compounds on the Ab aggregation cascade were evaluated by a biotin-avidin Ab1-42 oligomer assay and atomic force microscopy (AFM). Preliminary plate assay data indicated that several of these derivatives increased peptide oligomerization and the corresponding AFM images showed altered fibril formation. These results suggested that this class of scyllo-inositol derivatives is active in the Ab aggregation cascade.

Squaramides (3,4-diaminocyclobutene-1,2-diones) are known to be strong hydrogen bond donors, and recently have been demonstrated to show unusual responses to anions and the potential to adopt secondary structures. In the first part of the project, a small molecule version of a fluorene-based poly(squaramide) was synthesized to gain insights into the mechanism of the “turn-on” fluorescence response of the polymer in the presence of mono-basic phosphate anions. In the second part, mono and dipyridyl squaramides are examined. Pyridyl squaramides were discovered to form strong intramolecular hydrogen bonds, making the folding process more favorable than their urea counterparts. They are particularly interesting as their urea analogues are capable of taking up helical conformations when folded. The folding properties of these pyridyl squaramides in a range of solvents, and the influence of added anions on the folding process, are described herein.