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<p>Small molecule metabolites have important and diverse roles in every major cellular function. To study the activities of metabolites and the biological processes in which they are involved, it is important to be able to detect their levels within cells. Technologies that measure the concentrations of small molecules within the context of living, growing cells are highly advantageous but are challenging to produce. In this thesis, a novel class of intracellular small molecule sensors is produced, characterized and applied to address novel and relevant research questions. These sensors detect a specific target molecule within bacterial cells using RNA regulatory elements known as riboswitches and one of many possible reporter proteins. In addition to a project that yielded new methodology to create custom riboswitches, two projects that assess the capabilities of sensors that detect an active form of vitamin B12 are described. These projects present an abundance of data that provide novel insights into the transport and metabolism of vitamin B12 in <em>E. coli</em> cells. Overall, the results presented indicate that riboswitch-based sensors represent valuable and unique tools for the study of microbial biology. The thesis is concluded with a discussion that describes design strategies and several exciting potential applications for future riboswitch sensors.</p> / Doctor of Philosophy (PhD)

Obesity and its comorbidities have emerged as serious healthcare concerns in the western world due to increased prevalence of nutritional overabundance and decreased physical activity. Due to the significant population affected and economic burden placed on national healthcare systems, there is a demonstrated need for effective weight management therapeutics. Obesity presents clinically diverse phenotypes that increase a person's susceptibility to comorbidities that commonly result in deteriorated health (cardiovascular disease, diabetes mellitus, hypertension, etc). A comorbidity of specific relevance is non-alcoholic fatty liver disease (NAFLD) and its advanced disease state known as non-alcoholic steatohepatitis (NASH), as it has had a documented rise in prevalence parallel to that observed with obesity. Currently there are no FDA approved therapeutics for NAFLD or NASH, with the majority in clinical development aiming to mitigate the effects caused by accumulation of adipose tissue in the liver known as steatosis. An alternative therapeutic approach is to use small molecules to uncouple oxidative phosphorylation in the mitochondria by passively shuttling protons from the mitochondrial inner membrane space into the mitochondrial matrix. Mitochondrial uncoupling results in the disruption of the proton motive force leading to an upregulation of metabolism (i.e., decrease in steatosis). Small molecule mitochondrial uncouplers have recently garnered great interest for their potential in treating the advanced disease state of NASH. In this study, we report the structure-activity relationship (SAR) profiling of a 6-amino-[1,2,5]oxadiazolo[3,4-b]pyrazin-5-ol core, which utilizes the hydroxy moiety as the proton transporter across the mitochondrial inner membrane. We demonstrated that a wide array of substituents are tolerated with this novel scaffold that increased cellular metabolic rates in vitro using changes in oxygen consumption rate as a read-out. In particular, compound SHS4121705 (2.12i) displayed an EC50 of 4.3 M in L6 myoblast cells and excellent oral bioavailability and liver exposure in mice. In the preclinical stelic animal model (STAM) mouse model of NASH, administration of 2.12i at 25 mg kg-1day-1 resulted in decreased liver triglyceride levels and improved liver enzymes, NAFLD activity score, and fibrosis without affecting body temperature or food intake. Overall, our initial studies showcased the promise of mitochondrial uncouplers toward the treatment of NASH. While initial results were promising, the lead compound 2.12i had reduced potency compared to the alkyl derivatives reported in the SAR, unfortunately alkyl derivatives suffered from poor physiochemical properties, possibly due to metabolism of the alkyl chain. We hypothesized that addressing metabolic liabilities of these compounds could lead to increased potency with maintained efficacy in the STAM mouse model of NASH. Herein, we detail the SAR profiling of a 6-amino-[1,2,5]oxadiazolo[3,4-b]pyrazin-5-ol core derivatized with 1,1'-biphenyl anilines capable of eliciting mild mitochondrial uncoupling. A wide array of substituents are tolerated, and demonstrated sustained and stable increases in ¬cellular oxygen consumption rates over a broad concentration range. In particular, compound SHS4091862 (3.9b) displayed an EC50 of 2.0 μM in L6 myoblast cells with a pharmacokinetic profile of Cmax = 46 μM and t1/2 = 4.7 h indicating excellent oral bioavailability. Administration of 3.9b at 60 mg kg-1 day-1 in the STAM mouse model of NASH decreased fibrosis, steatosis, and hepatocellular ballooning to result in a 1.9-point decrease in NAFLD activity score (NAS) compared to vehicle. No changes in food intake, body weight, alanine transaminase (ALT) or aspartate transaminase (AST) levels were observed with 3.9b. Positive control Resmetirom afforded a 1.2-point decrease in NAS score, but increased ALT levels. Cumulatively, our work demonstrates the therapeutic potential of small molecule mitochondrial uncouplers to address metabolic diseases, namely NAFLD. / Doctor of Philosophy / There has been a significant increase in the population suffering from metabolic diseases in the western world. Among the most concerning metabolic diseases are obesity and nonalcoholic fatty liver disease, which have been shown to arise from excessive consumption of calorie dense food and limited physical activity. A novel approach to combat these diseases is to use mitochondrial uncouplers that disrupt the body's natural process for ATP production, causing an increase in metabolism. This increase in the metabolic rate results in the reduction of fat mass including in organs such as the liver. This work describes the design, development, and biological study of mitochondrial uncouplers capable of producing an increase in metabolism; specifically, SHS4121705 (2.12i) and SHS4091862 (3.9b) were shown to be potent uncouplers in vitro and were active in mouse models of fatty liver disease.

Discovered in 1980, HTLV-1 (Human T-cell Leukemia Virus-1), was the first identified human retrovirus and is shown to be associated with a variety of diseases including: adult T-cell leukemia lymphoma (ATLL), tropical spastic paraparesis/HTLV-1 associated myelopathy (TSP/HAM), chronic arthropathy, uveitis, infective dermatitis, and polymyositis. The mechanism by which the virus causes disease is still unknown. HTLV- 1 infection has been reported in many regions of the world but is most prevalent in Southern Japan, the Caribbean basin, Central and West Africa, the Southeastern United States, Melanesia, parts of South Africa, the Middle East and India. Approximately 30 million people are infected by HTLV-1 worldwide, although only 3-5% of the infected individuals evolve Adult T-cell Leukemia (ATL) during their life and the prognosis for those infected is still poor. The retroviral proteases (PRs) are essential for viral replication because they process viral Gag and Gag-(Pro)-Pol polyproteins during maturation, much like the PR from Human Immunodeficiency Virus-1 (HIV-1). Various antiviral inhibitors are in clinical use and one of the most significant classes is HIV-1 PR inhibitors, which have used for antiretroviral therapy in the treatment of AIDS. HTLV-1 PR and HIV-1 PR are homodimeric aspartic proteases with 125 and 99 residues, respectively. Even though substrate specificities of these two enzymes are different, HTLV-1 PR shares 28% similarity with HIV-1 PR overall and the substrate binding sites have 45% similarity. In addition to the 125-residue full length HTLV-1 PR, constructs with various C- terminal deletions (giving proteases with lengths of 116, 121, or 122 amino acids) were made in order to elucidate the effect of the residues in the C-terminal region. It was suggested that five amino acids in the C-terminal region are not necessary for the enzymatic activity in Hayakawa et al. 1992. In 2004 Herger et al. had suggested that 10 amino acids at the C-terminal region are not necessary for catalytic activity. A recent paper suggested that C-terminal residues are essential; and that catalytic activity lowers upon truncation, with even the last 5 amino acids necessary for full catalytic activity (1). The mutation L40I has been made to prevent autoproteolysis and the W98V mutation was made to make the active site of HTLV-1 PR similar to HIV-1 PR. We have characterized C-terminal amino acids of HTLV-1 PR as not being essential for full catalytic activity. We have discovered potential new inhibitors by in silico screening of 116-HTLV-1 PR. These small molecules were tested kinetically for various constructs including the 116, 121 and 122-amino acid forms of HTLV-1 PR. Inhibitors with the best inhibition constants were used in HTLV-1 infected cells and one of the inhibitors seems to inhibit gag processing.

Yes / The first use of a dinuclear UIII/UIII complex in the activation of small molecules is reported. The octadentate Schiff-base pyrrole, anthracene-hinged ‘Pacman’ ligand LA combines two strongly reducing UIII centres and three borohydride ligands in [M(THF)4][{U(BH4)}2(m-BH4)(LA)(THF)2] 1-M, (M ¼ Li, Na, K). The two borohydride ligands bound to uranium outside the macrocyclic cleft are readily substituted by aryloxide ligands, resulting in a single, weakly-bound, encapsulated endo group 1 metal borohydride bridging the two UIII centres in [{U(OAr)}2(m-MBH4)(LA)(THF)2] 2-M (OAr ¼ OC6H2tBu3-2,4,6, M ¼ Na, K). X-ray crystallographic analysis shows that, for 2-K, in addition to the endo-BH4 ligand the potassium countercation is also incorporated into the cleft through h5-interactions with the pyrrolides instead of extraneous donor solvent. As such, 2-K has a significantly higher solubility in non-polar solvents and a wider U–U separation compared to the ‘ate’ complex 1. The cooperative reducing capability of the two UIII centres now enforced by the large and relatively flexible macrocycle is compared for the two complexes, recognising that the borohydrides can provide additional reducing capability, and that the aryloxide-capped 2-K is constrained to reactions within the cleft. The reaction between 1-Na and S8 affords an insoluble, presumably polymeric paramagnetic complex with bridging uranium sulfides, while that with CS2 results in oxidation of each UIII to the notably high UV oxidation state, forming the unusual trithiocarbonate (CS3)2 as a ligand in [{U(CS3)}2(m-k2:k2-CS3)(LA)] (4). The reaction between 2-K and S8 results in quantitative substitution of the endo-KBH4 by a bridging persulfido (S2)2 group and oxidation of each UIII to UIV, yielding [{U(OAr)}2(m-k2:k2-S2)(LA)] (5). The reaction of 2-K with CS2 affords a thermally unstable adduct which is tentatively assigned as containing a carbon disulfido (CS2)2 ligand bridging the two U centres (6a), but only the mono-bridged sulfido (S)2 complex [{U(OAr)}2(m-S (LA)] (6) is isolated. The persulfido complex (5) can also be synthesised from the mono-bridged sulfido complex (6) by the addition of another equivalent of sulfur. / EPSRC, European COST network

<p dir="ltr">Post-translational modifications (PTMs) play a crucial role in regulating protein function and location. Protein AMPylation, the addition of adenosine monophosphate (AMP), significantly influences protein trafficking, stability, and pathogenic virulence. The Fic Domain family of proteins targets hydroxyl-containing amino acid residues (Ser, Thr, or Tyr), catalyzing the addition of various phosphate-containing moieties such as nucleoside monophosphates (NMPs), phosphocholine, and phosphate. Using gene mining techniques, Dr. Seema Mattoo’s group has identified a clade of Fic domain containing proteins typified by the enzyme originating from <i>Bordetella bronchiseptica</i> (BbFic) which prefers utilizing guanosine triphosphate (GTP) as a substrate over other nucleotides. To understand the physiological role of GMPylation, identifying the proteins modified by BbFic is a first critical step and can be accomplished via mass spectrometry-based proteomics. For a low stoichiometry PTM like GMPylation, however, there is a need to develop chemical tools that enable the targeted enrichment of modified protein. Identifying key interactions between substrate proteins and the BbFic nucleotide binding site will enable development of highly specific molecular tags for Fic substrates.</p><p dir="ltr">The goal of this research project, therefore, is to design chemical probes to tag Fic enzyme substrates, thereby facilitating the identification of GMPylated proteins in chemical proteomics workflows. A set of ATP and GTP analogues carrying either alkyne or azide handles were proposed as possible probes. While 8-azido guanosine showed a high docking score in our in-silico study, literature reports highlight its chemical instability upon exposure to air and light. An alternative probe, the 8-ethynyl guanosine, also showed a high docking score and docks in the same position and orientation as guanosine (the natural ligand) but necessitates synthetically challenging via cross-coupling reactions.</p><p dir="ltr">We considered multiple GMP analogues as potential molecular tags with the assistance of molecular docking with the BbFic enzyme. With predicted binding affinities in hand, we prioritized candidate GTP analogs for synthesis to probe the BbFic-mediated protein GMPylation process. While N6 propargyl guanosine serves as a lead probe for AMPylation, computational analysis reveals challenges with O6 due to its altered hydrogen bond donor/acceptor presentation. The distinctive chemical properties of guanosine, compared to adenosine, require a thorough evaluation of protective group strategies, as not all synthetic methodologies used for ATP analogue synthesis are applicable to GTP analogues. Isolating the triphosphate analogue proved challenging, although purification of the monophosphorylated counterpart is feasible. The Protide analogue benefits from phosphate charge masking, which facilitates purification. While much work remains until the physiological role of GMPylation can be determined, important progress has been made in the design and synthesis of chemical tools for studying this newly discovered PTM.</p>