Antibiotics have been extensively used to treat bacterial infections since Alexander Fleming’s discovery of penicillin 1928. Disease causing microbes that have become resistant to antibiotic drug therapy are an increasing public health problem. According to the world health organization (WHO) there are about 440 000 new cases of multidrug-resistant tuberculosis emerging annually, causing at least 150 000 deaths. Consequently there is an immense need to develop new types of compounds with new modes of action for the treatment of bacterial infections. Presented herein is a class of antibacterial ring-fused 2-pyridones, which exhibit inhibitory effects against both the pili assembly system in uropathogenic Escherichia coli (UPEC), named the chaperone usher pathway, as well as polymerization of the major curli subunit protein CsgA, into a functional amyloid fibre. A pilus is an organelle that is vital for the bacteria to adhere to and infect host cells, as well as establish biofilms. Inhibition of the chaperone usher pathway disables the pili assembly machinery, and consequently renders the bacteria avirulent. The focus of this work has been to develop synthetic strategies to more efficiently alter the substitution pattern of the aforementioned ring-fused 2-pyridones. In addition, asymmetric routes to enantiomerically enriched key compounds and routes to compounds containing BODIPY and coumarin fluorophores as tools to study bacterial virulence mechanisms have been developed. Several of the new compounds have successfully been evaluated as antibacterial agents. In parallel with this research, manipulations of the core structure to create new heterocycle based central fragments for applications in medicinal chemistry have also been performed.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

This thesis describes the synthesis and biological evaluation of highly substituted, ring-fused 2-pyridones. The utility of the bicyclic 2-pyridones to gain fundamental insights into the disease processes of bacterial infections and Alzheimer’s disease has been investigated. The 2-pyridones have mainly been studied as a new class of anti-infective agents termed pilicides. The function of the pilicides has been explored using uropathogenic E. coli (UPEC) as a prototype pathogen and urinary tract infection as a model disease. The pilicides target the infectious ability of UPEC by inhibiting key proteins (chaperones) in the so-called chaperone-usher pathway, thus preventing the assembly of bacterial surface organelles (pili/fimbriae). Synthetic pathways to aminomethylate the 2-pyridones have been developed in order to increase their aqueous solubility while retaining biological activity. Also, the importance of a carboxylic acid has been demonstrated in studies with various carboxylate derivatives and by bioisosteric replacement. Moreover, synthetic procedures to extend the backbone of the rigid, dipeptide-mimicking 2-pyridones have been established. This rendered peptidomimetic building blocks and structures that alongside their potential use as pilicides are of more general interest in peptidomimetic-related research. The potential pilicides have been screened for chaperone affinity using relaxation-edited 1H-NMR spectroscopy. In addition, their ability to inhibit pilus biogenesis in E. coli has been demonstrated by assays of hemagglutination, biofilm formation and attachment to bladder cells, as well as with electron and atomic force microscopy. Moreover, it has been confirmed that pilicides regulate the expression of pili without affecting the biofunctional properties of the pilus rod. This was verified by measurements of individual P pili, on living bacteria, using force measuring optical tweezers. The pilicide binding site was investigated using NMR spectroscopy and X-ray crystallography of a pilicide-chaperone complex. Based on the results obtained, a mechanism whereby the pilicides may inhibit pilus assembly was proposed, which was subsequently experimentally supported by surface plasmon resonance assays and genetic analysis. Finally, based on the generic 2-pyridone scaffold, a new collection of substituted compounds has been synthesized and validated as inhibitors of Amyloid β (Aβ)-peptide aggregation, which has been suggested to be involved in Alzheimer’s disease.

MSc (Chemistry) / Department of Chemistry / See the attached abstract below

Screening small molecule libraries is a powerful method for identifying biologically active substances. Current compound libraries are typically comprised of a large number of structurally similar compounds designed around bioactive core structures of known molecules. While the number of tested compounds are increasing, there has been a decline in drug-discovery success due to only a small region of chemical space being represented in these compound libraries. In addition, newly discovered biological targets tend not to be modulated by currently known natural products and molecular scaffolds. Diversity-oriented synthesis (DOS) aims to construct structurally novel and diverse products in a highly efficient manner to generate small-molecule libraries with a high degree of structural diversity and function. There is a need for new organic methodologies to access these atypical molecular scaffolds. The work presented here utilizes photochemical and titanium-mediated methodologies to access novel molecular scaffolds in two distinct directions: 1) by utilizing [2+2] photocycloaddition of pyridone-enynes to access functionalized cyclobutanoids capable of further modification and 2) by developing a novel Bredt’s rule-arrest Kulinkovich-de Meijere reaction to produce alkaloid building blocks with useful functionality. 2-Pyridones are known to undergo photo-initiated [2+2] and [4+4] cycloadditions with themselves and other conjugated -systems. These transformations provide rapid access to highly functionalized cyclobutanoid and cyclooctanoid derivatives capable of further manipulation to access both known and novel chemical space. Utilizing [2+2] photocycloaddition of pyridones conjugated with enyne partners we prepared polycyclic cyclobutanoids with excellent regio- and stereoselectivity. Further, these products were functionalized to give complex tetracyclic molecular scaffolds. The described approach to the 5-8-5 framework of the fusicoccane family features a key intramolecular [4+4] photocycloaddition of tethered pyridones. Intelligent design of the tether and proper choice of solvent affords rapid assembly of the polycyclic framework and sets the relative stereochemistry of five stereogenic centers. The strategy for construction of cyclooctanoid natural products is part of a long standing program to utilize the powerful photochemical properties of 2 pyridone. A novel approach for rapid access to a structurally diverse array of amino-ketone scaffolds employing a Kulinkovich-de Meijere reaction of inexpensive lactam-olefin building blocks has been developed. The formation of cyclopropylamines from alkenes and amides, the Kulinkovich-de Meijere reaction, involves two carbon-carbon bond-forming steps. Strategic use of a tricyclic intermediate can arrest the process if the second step requires formation of a bridgehead double bond. This intramolecular transformation results in formation of carbocyclic amino ketone building blocks. Further manipulation provides access to novel three-dimensional chemical space from these building blocks to produce a spectrum of fused bicyclic scaffolds in a divergent yet predictable manner. These products allow access to complex molecular space that can serve as a platform for medicinal and biochemical investigations. / Chemistry

There is a profound need for new antibiotics which overcome bacterial resistance. The predominant source for these is natural products; however, they are often quickly rendered ineffective due to antibiotic resistance. A proven method in drug discovery is improving the properties of natural products through diverted total synthesis (DTS). Of particular interest is promysalin, which is produced by Pseudomonas putida, and selectively inhibits the growth of Gram-negative pathogenic bacteria Pseudomonas aeruginosa at nanomolar concentrations. The work herein describes modifications to the side chain which were shown to modulate antibacterial potency and specificity. A similarly inspired approach to countering antibiotic resistance is the targeted modification of a single carbon to silicon, motivated by the proven success of this substitution shown in pharmaceuticals and amino acids. The target for this modification is albocycline, a known macrolactone antibiotic that exhibits potent antibiotic activity against S. aureus. Replacing the C4 carbon of albocycline with silicon will provide sila-albocycline with enhanced hydrogen bonding properties and altered lipophilicity due to the slight changes from the carbon to silicon atom. In addition, there is anticipated intrinsic stability of the silanol toward rearrangement reactions than carbon-based. The proposed synthesis diverts from the known total synthesis of albocycline, as reported by the Andrade Group. This work details the efforts made towards the total synthesis of sila-albocycline. Lastly, there is untapped potential for UV-promoted photochemistry to create molecular scaffolds, which may lead to novel synthetic routes to complex molecules in addition to providing new polycycles that may expand current medicinal products. The work herein describes the synthesis of tethered chloro- and methoxy-substituted benzyl alcohols to 2-pyridones and the resulting products when exposing the solution to ultraviolet light. This generated new polycycles with complex structures which have unexplored biological or medicinal properties. / Chemistry

<p>Bicyclic dihydrothiazolo fused 2-pyridones have been studied as a new class of antibacterial agents, termed pilicides, that target the formation of adhesive bacterial surface organelles (pili) in pathogenic bacteria. Synthetic methods to further functionalize the bicyclic 2-pyridone scaffold have been developed in order to increase water-solubility and thereby facilitate biological evalua-tions. This was accomplished by introducing aminomethylenes at the open position C-6. Tertiary amines were introduced via a microwave–assisted Mannich reaction and a synthetic route based on a formyl intermediate gave access to primary, secondary and tertiary amines, but also to other interesting functionalities. Biological evaluation confirmed that several of the function-alized compounds inhibited pili formation in uropathogenic <i>E. coli</i>., as dem-onstrated by assays of hemagglutination, biofilm formation and adherence to bladder cells. Co-crystallizing one of the pilicides with the target protein gave information about the binding site and based on this a mechanism of action was proposed, which was supported experimentally by surface plas-mon resonance and single point mutations in the protein.</p><p>Furthermore, the previously developed acylketene imine reaction used to prepare bicyclic thiazolo fused 2-pyridone pilicides has been developed to allow preparation of other ring-fused 2-pyridone systems. Benzo[a]quinolizine-4-ones and indolo[2,3-a]quinolizine-4-ones could be prepared in a fast and simple manner starting from dihydroisoquinolines and a β-carboline. Finally, this method could also be applied for the preparation of heteroatom analogs of the previously studied sulfur containing pilicides. Biological evaluations established that the sulfur atom can be replaced by oxygen and still maintain the ability to prevent pili assembly.</p>

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.

Bicyclic dihydrothiazolo fused 2-pyridones have been studied as a new class of antibacterial agents, termed pilicides, that target the formation of adhesive bacterial surface organelles (pili) in pathogenic bacteria. Synthetic methods to further functionalize the bicyclic 2-pyridone scaffold have been developed in order to increase water-solubility and thereby facilitate biological evalua-tions. This was accomplished by introducing aminomethylenes at the open position C-6. Tertiary amines were introduced via a microwave–assisted Mannich reaction and a synthetic route based on a formyl intermediate gave access to primary, secondary and tertiary amines, but also to other interesting functionalities. Biological evaluation confirmed that several of the function-alized compounds inhibited pili formation in uropathogenic E. coli., as dem-onstrated by assays of hemagglutination, biofilm formation and adherence to bladder cells. Co-crystallizing one of the pilicides with the target protein gave information about the binding site and based on this a mechanism of action was proposed, which was supported experimentally by surface plas-mon resonance and single point mutations in the protein. Furthermore, the previously developed acylketene imine reaction used to prepare bicyclic thiazolo fused 2-pyridone pilicides has been developed to allow preparation of other ring-fused 2-pyridone systems. Benzo[a]quinolizine-4-ones and indolo[2,3-a]quinolizine-4-ones could be prepared in a fast and simple manner starting from dihydroisoquinolines and a β-carboline. Finally, this method could also be applied for the preparation of heteroatom analogs of the previously studied sulfur containing pilicides. Biological evaluations established that the sulfur atom can be replaced by oxygen and still maintain the ability to prevent pili assembly.

New methods have been developed for the synthesis of bicyclic β-lactams and 2-pyridinones by combining acyl Meldrum’s acids and Δ2-thiazolines. The 2-pyridinones were synthesised both in solution using conventional heating or microwave assisted heating as well as by solid supported chemistry. The compounds (pilicides) were designed to interfere with the assembly of pili in uropathogenic E. coli by inhibiting the periplasmic chaperones. The affinity of the pilicides to the chaperones was investigated with surface plasmon resonance technique (Biacore) and with relaxation-edited 1H NMR spectroscopy experiments. Finally, the pilicides were investigated for their ability to inhibit pili formation in uropathogenic E. coli in a hemagglutination assay, where members of the 2-pyridinone family proved to be able to cause depiliation.