Investigating novel treatment approaches to combat Clostridioides difficile Rusha Pal ABSTRACT Clostridioides difficile is the leading cause of antibiotic-induced diarrhea and colitis in hospitals and communities worldwide. The enteric pathogen, classified to be an "urgent threat" by the United States Center for Disease Control and Prevention (CDC), capitalizes on disrupted intestinal microbiome to establish infection with disease symptoms ranging from mild diarrhea to potentially fatal conditions. Disruption of the intestinal microbiome, caused mostly by antibiotic use, enables C. difficile to colonize and proliferate within the host. Paradoxically, antibiotics are used to treat C. difficile infection. These antibiotics decimate the gut microbial community further, thus priming the gastrointestinal tract to become more prone to recurrence of infection. To tackle this clinical setback, we utilized a combination of traditional and non-traditional drug discovery approaches and identified chemical entities and targeted treatment options effective against this toxin-producing intestinal pathogen. Herein, we exploited the strategy of high-throughput screening to identify leads that harbor anticlostridial activity. Our primary phenotypic screen of FDA-approved drugs and natural product libraries led to the identification of novel molecules that were further characterized for their anticlostridial efficacy both in vitro and in vivo. The most potent scaffolds identified were those of mitomycin C, mithramycin A, aureomycin, NP-003875, NAT13-338148, NAT18-355531, and NAT18-355768. Of these, mithramycin A, aureomycin, and NP-003875 were also found to harbor anti-virulence properties as they inhibited toxin production by the pathogen. Furthermore, natural product NP-003875 could confer protection to 100% of the infected mice from clinical manifestations of the disease in a primary infection model of C. difficile. Our final approach has been to develop targeted therapeutics called peptide nucleic acids (PNAs). PNAs are antisense agents capable of inhibiting gene expression in bacteria. In this study, antisense inhibition of the RNA polymerase  subunit gene (rpoA) of C. difficile was found to be bactericidal for the pathogen and could also inhibit the expression of its virulence factors. Additionally, antisense inhibition of the C. difficile rpoA gene was found to be non-deleterious for the tested commensal microflora strains. Given their intriguing anticlostridial properties, it can be concluded that our research opened exciting possibilities that can be further evaluated to uncover new treatments for CDI. / Doctor of Philosophy / Investigating novel treatment approaches to combat Clostridioides difficile Rusha Pal LAYMAN LANGUAGE ABSTRACT Clostridioides difficile is a prominent human pathogen that can colonize the gut and cause fatal infections. C. difficile is the most common cause of microbial healthcare-associated infection and results in substantial morbidity and mortality. The "most urgent worldwide public health threat" label has been assigned to C. difficile by the United States Centers for Disease Control and Prevention (CDC). There is a pressing need to develop new classes of antibiotics with improved efficacy to treat C. difficile infections (CDI). To address the need for novel strategies to combat the growing problem of CDI, we screened FDA-approved drugs and natural products library in search of novel drugs that possess potent and specific anticlostridial activity. Several promising hits were identified and evaluated successfully both in vitro and in vivo. The most potent and novel hits that displayed exceptional activity were mitomycin C, mithramycin A, aureomycin, NP-003875, NAT13-338148, NAT18-355531, and NAT18-355768. Furthermore, a murine model of C. difficile infection revealed that compound NP-003875 conferred 100% protection to the infected mice from clinical manifestations of the disease. Interestingly, these compounds were non-toxic to the gut microflora and human cells. Our final approach has been to develop non-traditional therapeutics to target specific genes in C. difficile. These novel therapeutics are called peptide nucleic acids (PNA). Herein, we designed a PNA targeting RNA polymerase  subunit gene (rpoA) of C. difficile. The designed PNA could successfully inhibit the growth of the pathogen and expression of its virulence factors. In conclusion, our research opened exciting possibilities that can be further evaluated to uncover new treatments for CDI.

Current high-throughput screening (HTS) tools (i.e., single-use 96-well filter plate) are limited to the few membrane types that are sold commercially, restricting the ability to screen membrane materials for targeted applications. In this thesis, a multi-well device capable of screening any flat-sheet membrane was designed, where multiple devices can be stacked for extensive HTS (>32 experiments). Confocal imaging of a Natrix Q cross-section – a membrane type not sold in a commercial filter plate – was carried out after 24 h in contact with green fluorescent protein to visually confirm protein-membrane interactions. The static binding capacity (SBC) of bovine serum albumin (BSA) and Herring testes DNA was found for specific parameters: membrane type (Mustang Q, Sartobind Q, Natrix Q, Durapore), salt concentration (0, 50, 100 mM NaCl), and contact time (1 min, 4 h, 8 h, 24 h). Considering solution conditions, the highest BSA SBC was observed with Natrix Q at 0 M NaCl with a contact time of 24 h. The DNA and BSA SBC values for Natrix Q were the highest among the membrane types evaluated, demonstrating consistency with literature trends. These findings suggest that SBC experiments can predict promising membrane materials for scaled-up applications. Finally, the chromatography process was replicated in this multi-well device (Natrix Q), showing 50% BSA elution from the membrane. The results of this thesis confirmed this ability to accommodate any membrane adsorber, simultaneously compare different membrane materials, and extract the membrane for post-experimental analysis. This work’s significance was emphasized in its future potential to aid with membrane material selection, particularly with exploring the properties of next-generation membrane materials (e.g., 3D-printed membranes). Three future areas for optimization with this multi-well device were highlighted: biotherapeutic purification, sequencing of membrane materials within a process, and applying it as a tool to understand ion selectivity. / Thesis / Master of Applied Science (MASc) / Membranes are used in many industries, such as water treatment, environmental remediation, and biopharmaceuticals. In the biopharmaceutical industry, high-throughput screening (HTS) tools (e.g., filter plates), which allow for miniaturized experiments, are used to perform extensive experimental analysis to determine optimal solution conditions (e.g., pH) for biomolecule binding. Unfortunately, commercial filter plates are limited in customizability for HTS of membrane materials. To address these limitations, this thesis focuses on designing and validating a multi-well device capable of incorporating any membrane adsorber. Different biomolecules (proteins, DNA), solution conditions, and membrane materials were evaluated. The results of this thesis confirmed this ability to accommodate any membrane adsorber, simultaneously compare different membrane materials, and extract the membrane for post-experimental analysis. This work also discussed using this device for future rapid membrane material selection in multiple industries (e.g., biotherapeutics, ion extraction).

No description available.

<p>The 20^th century introduction of antibiotics made once fatal infectious diseases readily treatable. This taken-for-granted therapy is now threatened by rising antibiotic resistance. The ability of pathogens to acquire numerous simultaneous resistance mechanisms has given rise to an alarming number of increasingly difficult to treat multi-drug resistant infections. When coupled with a sharp decline in development of novel antibiotic therapies, health practitioners today are left with limited therapeutic options. Several alternative methodologies have been employed to find novel therapeutics, including new techniques in natural product isolation and the production of semi-synthetic and synthetic antibiotics; however, there has been limited focus on targeting antibiotic resistance mechanisms directly to create synergistic therapies. We demonstrate the potential in using small molecules to target antibiotic kinases, thereby rescuing the antibiotic action of aminoglycosides and macrolides when used in combination. We conducted a thorough examination of these enzymes including: kinetic analysis; an assessment of phosphate donor specificity; and in-depth structural comparison, including a case study on the structure-function relationship of APH(4)-Ia. This analysis culminated in an intensive screening initiative of fourteen antibiotic kinases against a set of well defined protein kinase inhibitors. From this work, we have identified several inhibitors that have the potential for use in future combination therapeutics. This study illustrates the benefit of a structure-activity based approach to drug discovery, an important tool at a time when novel therapeutic strategies are required.</p> / Doctor of Philosophy (PhD)

<p>The current rise in multi-drug resistant Gram-negative bacterial infections is of particularconcern. Gram-negative pathogens are difficult to treat due to their intrinsic resistome.The outer membrane (OM) of Gram-negative bacteria serves as a permeability barrier tomany antibiotics, due in large part to the lipopolysaccharide (LPS) component that isunique to these organisms, and in addition to, the OM is lined with a number of multidrugresistant efflux pumps. As the clinical effectiveness of first line therapies declines inthe face of this resistance, novel strategies to discover new antibiotics are required. Theidentification of new antibiotic targets is one method currently being applied to meet thischallenge. This work examines the permeability barrier of Escherichia coli as a possibletarget for antibiotic adjuvants. A structure-function analysis of GmhA and GmhB, whichcatalyze the first and third conserved steps in LPS ADP-heptose biosynthesis, wasperformed. The active site residues of each of these enzymes were identified viacrystallographic, mutagenic, and kinetic analyses. Potential mechanisms have beenproposed, offering insight into the function of these potential adjuvant targets. In addition,a whole screen of E. coli was performed to identify compounds that potentiatenovobiocin, an antibiotic with limited activity against Gram-negative pathogens due toOM permeability. Four small molecules were found that were able to synergize withnovobiocin. One of these, A22, is known to alter bacterial cell shape, suggesting a newpathway for antibiotic adjuvants to combat Gram-negative infection. Together, thesestudies highlight the varied targets available for novel therapeutic strategies.</p> / Doctor of Philosophy (PhD)

<p>The human interactome presents a goldmine of potentially powerful therapeutic targets, yet very few small molecule modulators of protein-protein interactions (PPI) have been identified. PPI pose a particular challenge for drug discovery, and one of the major obstacles to fully exploiting these interactions is a lack of appropriate technologies to screen for modulating compounds. This thesis aims to address the need for function- based approaches that target PPI by using magnetic beads (MB) and mass spectrometry (MS) to develop efficient assays to monitor these interactions and their modulation by small molecules. The work begins with the validation of a novel magnetic “fishing” assay, which uses affinity-capture MB to isolate intact complexes of a “bait” protein from solution. By monitoring the recovery of the secondary binding partner, this assay was used to functionally screen a library of 1000 compounds for small molecule modulators of a calmodulin/melittin (CaM/Mel) model system. The versatility of magnetic “fishing” is clearly demonstrated during a study of a more relevant CaM-based system, which uncovered a novel mode of interaction for the CaM-binding domain of transcription factor SOX9. In addition to the MB-based approach, a simple MS-based competitive displacement assay is developed to identify minimal inhibitory fragments of a target complex as indicators of potential ‘hot-spots’. The assay was used to probe a DNA repair complex of XRCC4/ligaseIV, and identified a short helix that can be used as a more defined target surface for future high-throughput screening and rational drug design. The functional MS-based assays herein are highly adaptable tools to monitor PPI, and will facilitate the study of these and other important biomolecular interactions.</p> / Doctor of Philosophy (PhD)

Carla Abarca Ph.D. Thesis / The selective separation of valuable minerals by froth flotation is a critical unit operation in mineral processing. Froth flotation is based on the ability of chemical reagents, called collectors, to selectively lower the surface energy of valuable mineral particles, facilitating attachment of the modified mineral particles to air bubbles in the flotation cell. The mineral laden bubbles rise to the surface forming a froth phase that can be isolated. Novel cationic polystyrene nanoparticle collectors have been developed recently to be used as effective flotation collectors, aiming to recover challenging nickel sulfide ores that respond poorly to conventional molecular flotation collectors. However, optimizing nanoparticle flotation collectors is a challenge. An effective nanoparticle collector candidate should meet three requirements: (1) it should be colloidally stable in the flotation media; (2) it should be hydrophobic enough to change the mineral surface and induce an air bubble-mineral particle attachment; and (3) specifically and strongly bind to metal-rich minerals. Producing nanoparticles that are simultaneously colloidally stable and sufficiently hydrophobic presents a problematic task. Thus, a delicate balance of nanoparticle properties is required for commercially viable nanoparticle collectors. This thesis presents a promising approach for discovering and characterizing novel nanoparticle collectors by using high throughput screening techniques. Developed was a workflow for fast fabrication and testing of nanoparticle candidates, including: (1) parallel production of large nanoparticle libraries covering a range of surface chemistries, (2) a high throughput colloidal stability assay to determine whether a nanoparticle type is stable in flotation conditions; (3) an automated contact angle assay to reject nanoparticles that are not hydrophobic enough to induce efficient bubble-particle attachment, and; (4) a laboratory flotation test in sodium carbonate (pH~10) with the best nanoparticle candidates. The automated colloidal stability assay was based on the optical characterization of diluted nanoparticle dispersions in multiwell plates, yielding critical coagulation concentrations (CCCs) of sodium carbonate. To pass this screening test, the CCC of candidate nanoparticles must be greater than the effective carbonate concentration in commercial flotation cells. Since the nanoparticle size affects the intrinsic light scattering properties of the nanoparticles, two routes were developed. The colloid stability assay was suitable for nanoparticles ranging between 50 nm and 500 nm, since nanoparticle size. The automated contact angle assay used a miniature 16-well plate format where flat glass slides were exposed to 200 μL nanoparticle dispersions. The cationic nanoparticles formed a saturated adsorbed monolayer on the glass, and after rinsing and drying, the water contact angle was automatically measured. Effective nanoparticle candidates had contact angles greater than 50 degrees, a criterion developed with model experiments. During the development of the automated workflow platform, a series of nanoparticles with methyl-ended PEG-methacrylate monomers were prepared. Although the PEG chains greatly enhanced colloidal stability, the particles were too hydrophilic to be effective collectors. Interestingly, nanoparticles with long PEG chains acted as froth modifiers, giving wetter and more robust foams as well as increased entrainment of materials that did not adhere to bubbles. Conventional laboratory scale latex synthesis methodologies are far too inefficient to generate large library of candidate nanoparticles. Instead, we started with a few parent nanoparticle types and then used Click chemistry to generate a large range of surface chemistries. Specifically copper-mediated azide alkyne cycloaddition reaction was used to functionalize the surface of azide nanoparticles with different chemical groups, ranging from hydrophilic amine-terminated PEG chains, to hydrophobic hexane-terminated materials. The Click library exhibited an extensive range of critical coagulation concentrations and contact angle values. For example, for a given parent azide nanoparticle, the contact angles ranged from 62 to 101 degrees, depending upon the density and type of click reagent. A novel paper chromatographic method was developed for the quantitative determination surface azide. This assay was critical for determining the surface density of functional groups from the click reactions. Overall, high throughput screening techniques were designed and applied to the development of nanoparticle collectors for froth flotation. Automated screening assays of critical coagulation concentration and contact angle proved to be effective in obtaining flotation domain maps, and finding the most promising nanoparticle collectors for froth flotation. I believe the work in this thesis is one of the first reported uses of high throughput methodologies for the development of mineral flotation reagents. / Thesis / Doctor of Philosophy (PhD) / Novel cationic polystyrene nanoparticle collectors have been developed to be used as effective flotation collectors, aiming to recover challenging nickel sulfide ores that respond poorly to conventional molecular flotation collectors. However, optimizing nanoparticle flotation collectors is a challenge. This thesis presents a promising approach for discovering and characterizing novel nanoparticle collectors by using high throughput screening techniques and click chemistry. Development of nanoparticle libraries and automated screening assays of critical coagulation concentration and contact angle proved to be effective in obtaining flotation domain maps, and finding the most promising nanoparticle collectors for froth flotation.

The antimicrobial resistance (AMR) crisis, where new antibiotic discovery is not keeping pace with the emergence of resistant pathogens, is driven by mobile genetic elements (MGEs). MGEs can autonomously transfer between bacteria, along with AMR genes. The widespread use of antibiotics in the clinic, in agriculture, and animal husbandry, has accelerated the MGE-mediated transfer of AMR genes in the environment. However, despite playing such an important role in the AMR crisis, the dynamics and mechanisms behind the transmission of genes are poorly understood. Furthermore, which natural and man-made compounds inhibit or promote their movement in these environments is unknown. One method to combat the rise in AMR is to identify small molecules as probes to understand the molecular basis of transmission and apply this information to prevent MGE-mediated resistance dissemination. Since conjugation is the main mechanism for AMR gene transfer, targeting MGEs that use conjugation, such as conjugative plasmids (e.g. Tn1549) and conjugative transposons (e.g. F plasmid), has the potential to prevent the emergence of multi-drug resistant pathogens. In this work, a high throughput assay modeled after Tn1549 excision was screened against a library of known bioactive compounds to find modulators of the integrase and excisionase activity. Several fluoroquinolone antibiotics including ciprofloxacin were identified as dose-dependent inhibitors of excision, which acted by changing supercoiling levels in the cell. Ciprofloxacin enhanced conjugation frequency of Tn1549 at sub-MIC concentrations relative to an untreated control and inhibited conjugation frequency at higher concentrations. A second project was focused on a high throughput conjugation assay based on the separation of the lux operon between a donor and recipient cell, such that only transconjugants produce luminescence to reflect active gene transfer. This work furthers our understanding of the development of assays to target MGEs and screening for inhibitors of their movement. / Thesis / Master of Science (MSc) / Antibiotics are small molecules that cure bacterial infections. However, their efficacy is fading as a result of the ability of mobile genetic elements (MGEs) to spread antimicrobial resistance genes between bacteria. Conjugative plasmids (CPs) and conjugative transposons (CTns) are two of the major types of MGEs that contribute to the dissemination of antimicrobial resistance in pathogens. The goal of this research is to search for inhibitors of CTns and CPs in order to prevent the emergence of multi-drug resistant bacteria. High throughput assays were designed to model both a CTn (Tn1549) and a CP (F plasmid) to find small molecules targeting their movement. A screen of the Tn1549 excision assay identified fluoroquinolone antibiotics that inhibit excision in a dose-dependent manner and indirectly inhibit the integrase used to excise the CTn. Ciprofloxacin, a fluoroquinolone, inhibited the conjugation frequency of Tn1549. Future work will focus on identifying new inhibitors of these MGEs and their characterization.

Coenzyme nicotinamide adenine dinucleotide (NAD, including the oxidized form-- NAD+ and reduced form--NADH) and the phosphorylated form--nicotinamide adenine dinucleotide phosphate (NADP, including NADP+ and NADPH) are two of the most important biological electron carriers. Most NAD(P) dependent redox enzymes show a preference of either NADP or NAD as an electron acceptor or donor depending on their unique metabolic roles. In biocatalysis, the low enzymatic activities with unnatural coenzymes have made it difficult to replace costly NADP with economically advantageous NAD or other biomimetic coenzyme for catalysis. This is a significant challenge that must be addressed should in vitro biocatalysis be a viable option for the practical production of low-value biocommodities (i.e., biohydrogen). There is a significant need to first address the coenzyme selectivity of the NADP-dependent dehydrogenases and evolve mutated enzymes that accept biomimetic coenzymes. This is a major focus of this dissertation. Establishment of efficient screening methods to identify beneficial mutants from an enzymatic library is the most challenging task of coenzyme engineering of dehydrogenases. To fine tune the coenzyme preference of dehydrogenases to allow economical hydrogen production, we developed a double-layer Petri-dish based screening method to identify positive mutant of the Moorella thermoacetica 6PGDH (Moth6PGDH) with a more than 4,278-fold reversal of coenzyme selectivity from NADP+ to NAD+. This method was also used to screen the thermostable mutant of a highly active glucose 6-phosphate dehydrogenase from the mesophilic host Zymomonas mobilis. The resulting best mutant Mut 4-1 showed a more than 124-fold improvement of half-life times at 60oC without compromising the specific activity. The screening method was further upgraded for the coenzyme engineering of Thermotaga maritima 6PGDH (Tm6PGDH) on the biomimetic coenzyme NMN+. Through six-rounds of directed evolution and screening, the best mutant showed a more than 50-fold improvement in catalytic efficiency on NMN+ and a more than 6-fold increased hydrogen productivity rate from 6-phosphogluconate and NMN+ compared to those of wild-type enzyme. Together, these results demonstrated the effectiveness of screening methods developed in this research for coenzyme engineering of NAD(P) dependent dehydrogenase and efficient use of the less costly coenzyme in ivSB based hydrogen production. / Ph. D.

Compartmentalisation and metabolism are two universal features observed among all living organisms. Their emergence and harmonious functioning are considered critical for the emergence of life. In an attempt to understand the chemical processes that may have resulted in the emergence of life, origin(s)-of-life researchers have investigated 1. possible mechanisms of prebiotic compartmentalisation and 2. plausible protometabolic reactions as precursors to metabolic chemistry. Historically, these two aspects of origin(s)-of-life research have been investigated in isolation. However, there is a growing consensus regarding the necessity of investigating prebiotic compartmentalisation and protometabolic reactions in tandem. Prebiotic compartmentalisation via formation of lipid vesicles have long been regarded as a general route for protocell formation. However, modern views on protocell formation suggest that such structures might be insufficient, in the absence of specialised transport proteins, to efficiently create suitable environments for sustaining out-of-equilibrium reactions, necessary for the emergence of life. This, coupled with the discovery of membrane-less organelles, formed through liquid-liquid phase separation (LLPS) in modern cells, and their ever increasingly identified roles in biology, has sparked renewed interest among origin(s)-of-life researchers in the synergy between prebiotic reactions and Oparin’s hypothesis of prebiotic compartmentalisation via coacervation. To date, most of the work, investigating the effect of coacervation on chemical reactions, have focused on biochemical reactions catalysed by complex biomolecules such as proteinaceous enzymes and ribozymes. Moreover, historically, the phenomenon of complex coacervation has primarily been associated with long-chain polymers. However, recent demonstrations of complex coacervation among several prebiotically relevant metabolites necessitates the need for developing experimental strategies that can comprehensively investigate complex coacervation, in terms of phase diagrams, involving such prebiotically relevant metabolites. Such understanding is essential to enhance the design of experiments that aim to combine protometabolic reactions and complex coacervation. To this end, the research presented in this thesis, at first, demonstrates a highthroughput screening methodology for complex coacervate formation, in chapter 2, using automated liquid handling strategies and random forest classifier machine learning algorithm based classification of bright-field microscopy images. This methodology has then been utilised to obtain the conditions in which oxidised and reduced nicotineamide adenine dinucleotide (NAD+ and NADH) form coacervate with 50-mer poly-lysine and poly-arginine. Further, the precipitation properties of 50-mer poly-arginine in sodium bicarbonate solution have been investigated. In chapter 3, incorporation of complex coacervation in three different protometabolic reactions in three different ways have been exhibited. In “Protometabolic NAD+ reduction using pyruvate”, NADH, which is the product of the reaction, participates in coacervation with 50-mer poly-arginine. In “Coenzyme A catalysed peptide ligation”, the catalyst of the reaction, coenzyme A contributes to coacervation with 10-mer polyarginine. In “Heme catalysed oxidation of Amplex Red”, the coacervate is formed form polymers, such as carboxymethyl dextran and poly-diallyldimethylammonium, that are not reactants, products or catalyst of the studied reaction. It has been further shown that the incorporation of coacervation, to “Protometabolic NAD+ reduction using pyruvate”, results in the enhancement of NADH formation by 2.5 times in comparison to the amount of NADH produced in the absence of any poly-cations. Preliminary results also suggest that the presence of coacervation resulted in the suppression of both “Coenzyme A catalysed peptide ligation” and “Heme catalysed oxidation of Amplex Red”. This study elucidates an unprecedented methodology for screening of coacervate formation as well as highlighting the various ways in which coacervation of prebiotically relevant metabolites can be embedded into protometabolic reactions. Further, this study also sheds light on the influence of coacervation on protometabolic reactions, revealing patterns that were previously primarily observed in biochemical reactions catalysed by enzymes (or ribozymes).