This dissertation presents the theory and practice of designing, synthesizing and using peptidomimetics to disrupt protein-protein interactions. Our general strategy is to design and synthesize peptidomimetics that will mimic peptide secondary structures (alpha-helices and beta-sheets). Chapter One is a theoretical examination of the feasibility of using beta-sheet mimics called molecular clamps to inhibit substrate-receptor interactions by blocking the substrate rather than the receptor or enzyme. Several natural and synthetic examples of this approach are given in support of this concept. We also present the results of a kinetic modeling study and a consideration of which types of systems would be the best candidates for a substrate-targeted inhibitor approach. Chapter Two relates a continuation of previous work in our lab to synthesize five novel beta-protected hydrazino amino acids. These hydrazines are essential precursors for synthesizing constrained beta-strand mimetics. We showed that we could selectively deprotect the alpha-nitrogen of the hydrazines, and we synthesized several novel examples of polar beta-protected hydrazino amino acids. Chapter Three discusses the design and synthesis of small-molecule and peptidomimetic MDM2 inhibitors, including our work on synthesizing a new class of alpha-helix mimics that have improved water solubility compared with previously reported examples of alpha-helix mimics. As with the constrained beta-strand mimics described in Chapter Two, the synthesis of novel hydrazino amino acid precursors is a key step in synthesizing our alpha-helix mimics. One isoleucine hydrazine derivative was synthesized, and progress was made toward synthesizing two other hydrazines from tryptophan. In addition, the synthesis of three potential small-molecule inhibitors of MDM2 is described. Chapter Four describes the use of the GLIDE program to design and evolve an alpha-helix mimic that will interact with the pro-apoptotic protein Bax. Progress toward the synthesis of this compound is also reported.

The Mevalonate Pathway: A Potential Therapeutic Target for JAK2-driven Myeloproliferative Neoplasms Lori Nicole Griner Abstract Myeloproliferative neoplasms (MPNs) are diseases of hematopoietic stem cell origin and are characterized by uncontrolled growth of cells of the myeloid compartment. The Philadelphia chromosome negative classical MPNs, including polycythemia vera, essential thrombocythemia, and myelofibrosis, are diseases of dysregulated JAK2 signaling. In fact, the majority of MPN patients have activating mutations in JAK2 (e.g JAK2-V617F), a tyrosine kinase that contributes to the growth and survival of myeloid cells. While MPNs were first described over sixty years ago, a significant need remains to develop therapeutic strategies for them. Inhibitors of JAK2 are currently being developed, and one inhibitor, ruxolitinib, was recently approved for certain MPN patients. Ruxolitinib has made profound impacts on improving splenomegaly and constitutional symptoms in MPN patients, but it and other JAK2 inhibitors have not significantly reduced the JAK2 mutant allele burden, and thus such inhibitors have not induced remission in these patients. The current consensus in the MPN field supports JAK inhibition for the treatment of patients, but a further understanding of MPNs and JAK2 signaling, as well as improved JAK2 inhibitors, may be necessary for treating MPN patients. The work described in this dissertation has uncovered novel requirements for JAK2-V617F-driven signaling and transformation. We demonstrate that JAK2-V617F co-localizes with lipid rafts, cholesterol-rich microdomains within the plasma membrane that function to serve as platforms for signaling complex formation. Signaling complex formation is a necessary component for dysregulated signaling induced by JAK2-V617F. We provide evidence that cholesterol altering-lipid raft disrupting agents attenuate JAK2-V617F-driven signaling. We also show that cholesterol-lowering statins are effective at downregulating JAK2 signaling and inducing apoptosis in JAK2-V617F-driven cell lines. Importantly, we show that statins, inhibitors of the mevalonate pathway, inhibit the growth of primary MPN cells, while the same statin doses have no effect on healthy controls. Impressively, we demonstrate that statins cooperate with multiple JAK inhibitors, including ruxolitinib, to inhibit cell growth and induce apoptosis of JAK2-V617F-driven cells. This report establishes statin-mediated inhibition of the mevalonate pathway as a potential approach to improve MPN therapeutics. We propose future studies with statins and JAK2 inhibitors in the treatment of MPNs.

Spinosyn A is a particularly interesting natural product due to its structural complexity and potent insecticidal activity. The biosynthetic pathway of spinosyn A is interesting as it has two unusual features, the SpnF-catalyzed (4+2) cycloaddition and the SpnL-catalyzed cyclization to produce the perhydro-as-indacene core. The work described in this dissertation focuses on elucidating the mechanisms of the SpnF- and SpnL-catalyzed reactions. SpnF has attracted significant interest as a possible Diels-Alderase. To explain how SpnF catalyzes the formation of cyclohexene ring, three plausible mechanisms have been proposed, the Diels-Alder reaction mechanism, the ionic rearrangement mechanism, and the biradical rearrangement mechanism. Kinetic isotope effect studies were performed using four deuterium-labeled mechanistic probes, specially the C4-D, C7-D, C11-D, and C12-D analogs. Currently, the ionic rearrangement mechanism can be excluded, based on the results using the C4-D and C7-D analogs. In addition, how SpnF accelerates the reaction was studied to assess the contribution of an entropic x preorganization compared to enthalpic transition state stabilization. To measure the relative rate enhancements due to structural perturbations, three mechanistic probes were synthesized, the linear analog, the C13-14 Unc analog, and the C2-3 Unc analog. Unfortunately, the linear analog and C13-14 Unc analog didn’t show any turnover activity under either non-enzymatic or enzymatic conditions. Thus, no conclusion could be drawn from incubation with these substrate analogs. Mechanistic studies of SpnL-catalyzed cyclization were devoted to differentiating between the Rauhut-Currier type mechanism and the Michael addition mechanism. Biochemical studies using the C13-F analog as a mechanism-based inhibitor showed the formation of a covalent adduct with SpnL, which is consistent with the Rauhut-Currier type mechanism. Additional experimental data obtained from isotope trace experiments and kinetic isotope effect studies using C12-D analog supports the Rauhut-Currier type mechanism. Biochemical studies concerning the role of SAM in SpnF and SpnL showed that SAM is required for the activity of SpnL, and were inconclusive for SpnF. SpnL mutant studies showed that Cys60 and Glu96 may be important for the catalysis of SpnL. Chemoenzymatic total synthesis of spinosyn A was completed by chemical etherification of 17-pseudoaglycone and D-forosamine. / text

Amine degradation in aqueous amine scrubbing systems for capturing CO₂ from coal fired power plants is a major problem. Oxygen in the flue gas is the major cause of solvent deterioration, which increases the cost of CO₂ capture due to reduced capacity, reduced rates, increased corrosion, solvent makeup, foaming, and reclaiming. Degradation also produces environmentally hazardous materials: ammonia, amides, aldehydes, nitramines, and nitrosamines. Thus it is important to understand and mitigate amine oxidation in industrial CO₂ capture systems. A series of lab-scale experiments was conducted to better understand the causes of and solutions to amine oxidation. This work included determination of rates, products, catalysts, and inhibitors for various amines at various conditions. Special attention was paid to understanding monoethanolamine (MEA) oxidation, whereas oxidation of piperazine (PZ) and other amines was less thorough. The most important scientific contribution of this work has been to show that amine oxidation in real CO₂ capture systems is much more complex than previously believed, and cannot be explained by mass transfer or reaction kinetics in the absorber by itself, or by dissolved oxygen kinetics in the cross exchanger. An accurate representation of MEA oxidation in real systems must take into account catalysts present (especially Mn and Fe), enhanced oxygen mass transfer in the absorber as a function of various process conditions, and possibly oxygen carriers other than dissolved oxygen in the cross exchanger and stripper. Strategies for mitigating oxidative degradation at low temperature, proposed in this and previous work are less effective or ineffective with high temperature cycling, which is more representative of real systems. In order of effectiveness, these strategies are: selecting an amine resistant to oxidation, reduction of dissolved metals in the system, reduction of the stripper temperature, reduction of the absorber temperature, and addition of a chemical inhibitor to the system. Intercooling in the absorber can reduce amine oxidation and improve energy efficiency, whereas amine oxidation should be considered in choosing the optimal stripper temperature. In real systems, 2-amino-2-methyl-1-propanol (AMP) is expected to be the most resistant to oxidation, followed by PZ and PZ derivatives, then methyldiethanolamine (MDEA), and then MEA. MEA oxidation with high temperature cycling is increased 70% by raising the cycling temperature from 100 to 120 °C, the proposed operational temperature range of the stripper. PZ oxidation is increased 100% by cycling to 150 °C as opposed to 120 °C. Metals are expected to increase oxidation in MEA and PZ with high temperature cycling by 40 - 80%. Inhibitor A is not expected to be effective in real systems with MEA or with PZ. MDEA is also not effective as an inhibitor in MEA, and chelating agents diethylenetriamine penta (acetic acid) (DTPA) and 2,5-dimercapto-1,3,4-thiadiazole (DMcT) are only mildly effective in MEA. Although MEA oxidation in real systems cannot be significantly reduced by any known additives, it can be accurately monitored on a continuous basis by measuring ammonia production from the absorber. Ammonia production was shown to account for two-thirds of nitrogen in degraded MEA at low temperature and with high temperature cycling, suggesting that it is a reliable indicator of MEA oxidation under a variety of process conditions. A proposed system, which minimizes amine oxidation while maintaining excellent rate and thermodynamic properties for CO₂ capture would involve use of 4 m AMP + 2 m PZ as a capture solvent with the stripper at 135 °C, intercooling in the absorber, and use of a corrosion inhibitor or continuous metals removal system. Reducing (anaerobic) conditions should be avoided to prevent excessive corrosion from occurring and minimize the amount of dissolved metals. This system is expected to reduce amine oxidation by 90-95% compared with the base case 7 m MEA with the stripper at 120 °C. / text

The investigations conducted within this dissertation centers around the use of electric cell-substrate impedance sensing (ECIS). This system is able to characterize in real-time analysis, the adhesion of cells to their substrate and neighboring cells. With this, valuable information can be gathered with in-vitro experiments regarding a tissue culture's response to physiological stimulation. This dissertation has taken advantage of ECIS' ability to analyze toxicology, barrier function, and cancer invasion on a tissue culture. With proper analysis modifications, trans-epethelial resistance (TER) can be used as a cytotoxicity assay with higher sensitivity than previously thought. In vitro assessment of cytotoxicity based on TER needs more quantitative methods to analyze the alteration of cell morphology and motility. Here, we applied ECIS to evaluate dose-dependent responses of human umbilical vein endothelial cells (HUVEC) and mouse embryonic fibroblasts (NIH 3T3) exposed to cytochalasin B and protein kinase inhibitor H7. To detect subtle changes in cell morphology, the frequency-dependent impedance data of the cell monolayer were measured and analyzed with a theoretical cell-electrode model. To detect the alternation of cell micromotion in response to cytochalasin B and H7 challenge, time-series impedance fluctuations of cell-covered electrodes were monitored and the values of power spectrum, variance, and variance of the increment were calculated to verify the difference. While a dose-dependent relationship was generally observed from the overall resistance of the cell monolayer, the analysis of frequency-dependent impedance and impedance fluctuations distinguished cytochalasin B levels as low as 0.1µM and H7 levels as low as 10 µM for HUVEC and 3T3 layers. Even though overall resistance values are relatively small for 3T3 layers, and frequency scan measurements are negligible, impedance fluctuation analysis reveals significant micromotion for cytotoxic detection. Our results show that cytochalasin B and H7 causes a decrease of junctional resistance between cells and an increase of membrane capacitance. Cigarette smoke is cytotoxic and tumorigenic. Initial studies were conducted to evaluate the cytotoxicity of cigarette smoke condensate (CSC) on HUVEC layers. The focus was then turned to investigations involving in vitro cancer invasion assays with CSC on HUVEC layers. ECIS is an excellent investigative device that can be utilized to observe cancer invasion on normal tissue cultures due to the significantly higher impedance signature of cancer cells. The investigation in this dissertation focused on cigarette smoke's influence on cellular mechanics of endothelial cells and the invasive potential of two ovarian cancer cell lines (ALST and OVCA429) against a fully active endothelium. The HUVEC cultures responded to CSC with an increase in junctional binding, where as ALST and OVCA429 relieved adhesion thereby providing an improved motility when evaluated in wound healing assays. Transmigration of the HUVEC layer by ALST cells exhibit a pre-CSC exposure time-dependence affecting the effectiveness of ALST transmigration. The HUVEC layer's decreased tight junction binding that resulted from CSC exposure, allowed for a more aggressive ALST layer formation that occurred during simulated intravasation. Increased HUVEC layer tight junction binding that occurred in the first five hours in response to CSC during extravasation contributes to impeding ALST transmigration at high concentrations of CSC. Overall, CSC has an impeding effect on ALST transmigration during extravasation while causing aggressive transmigration during intravasation.

Sarcomas are rare mesenchymally-derived tumors with limited treatment options. Tyrosine kinases may serve as potential targets for sarcoma therapy because many are mutated or overexpressed in sarcomas and cell lines. One potential molecular target for sarcoma treatment is the Src tyrosine kinase. Three independently synthesized Src kinase inhibitors were evaluated in human sarcoma cell lines. Of the three, dasatinib, provided promising results as a potential sarcoma therapy. Until this study, dasatinib activity had not been characterized in sarcoma cells. Based on our previous findings of Src activation in human sarcomas, we evaluated the effects of dasatinib in twelve sarcoma cell lines. Dasatinib inhibited Src activity and downstream signaling at nanomolar concentrations. Inhibition of Src signaling was accompanied by blockade of cell migration and invasion. Moreover, apoptosis was induced in a subset of bone sarcomas at nanomolar concentrations of dasatinib. Inhibition of Src protein expression by siRNA also induced apoptosis, indicating that these bone sarcoma cell lines are dependent on Src activity for survival. These results demonstrate that dasatinib inhibits migration and invasion of diverse sarcoma cell types, and selectively blocks the survival of bone sarcoma cells. Therefore dasatinib may provide therapeutic benefit by preventing the growth and metastasis of sarcomas. Microarray analysis of the sarcoma cell lines lead to the identification of a molecular signature that successfully predicts response to dasatinib by induction of apoptosis. Components of this molecular signature are expressed in primary human sarcomas. Furthermore, expression of the molecular signature in sarcomas can be utilized to cluster tumors based on theoretical response to dasatinib. While the prediction of response in tumors is theoretical, there is encouraging evidence to support further endeavors into validating the potential of this molecular signature to predict response in patients.Together, these studies reveal that, in cell lines, both constitutive Src activation and the presence of a molecular signature that predicts response to dasatinib are important parameters to consider when selecting dasatinib as a treatment for. Furthermore, novel therapeutic approaches that inhibit Src signaling may selectively induce apoptosis in tumor cells and sensitize to chemotherapy those tumors that contain the relevant molecular signature.

Work in the Turos group over the past five years has focused on the development of N-alkylthio beta-lactams, which show antibacterial activity against Staphylococcus (including MRSA), Bacillus, and others. These compounds do not function in the manner of the traditional beta-lactam antibiotics, but were thought to undergo an intracellular thiol-transfer to coenzyme A. In expanding the SAR of these novel compounds, it was found that N-alkylthio-2-oxazolidinones also exhibit antibacterial activity. Although CoA acts as the thiol-redox buffer in the genera most susceptible to the N-alkylthio beta-lactams, studies on Coenzyme A disulfide reductase (CoADR) show that the redox buffer is not affected by these compounds. However, the recent finding that fatty acid synthesis is affected by the N-alkylthio beta-lactams led to the discovery that these compounds act as prodrugs, and that the asymmetric CoA disulfides produced by in vivo thiol transfer are potent inhibitors of beta-ketoacyl-acyl carrier protein synthase III (FabH) through a novel thiol-disulfide exchange with the active site cysteine. Lactams 2a and 2g were also found to be potent inhibitors of this enzyme. In an effort to produce a CoA mixed-disulfide mimic which could cross the cell membrane, a series of simple aryl-alkyl disulfides were synthesized and tested against E. coli, S. aureus, and B. subtilis. Several of these compounds were found to be very potent antibacterials both in vitro and in vivo, with MICs less than 0.125 micrograms/mL. Comparison of the activities of these disulfides with those of acyl-CoA analogs and CoA mixed disulfides support the assertion that FabH is indeed the cellular target of these potent new compounds.

Targeted therapies have begun to be developed and approved in the clinic over the past several decades to treat cancers with specific genetic alterations. In non-small cell lung cancer (NSCLC), patients harboring EGFR activating mutations often respond to the EGFR inhibitors gefitinib/erlotinib, exhibiting down-regulation of central oncogenic pathways and dramatic tumor regressions. Despite initially promising results, the vast majority of patients develop resistance to targeted therapies. Thus far, several mechanisms of resistance including T790M mutation in EGFR, amplification of the MET receptor tyrosine kinase (RTK), activating mutations in downstream signaling molecules, and loss of negative regulators have been identified. As a result, next generation inhibitors and combination therapies continue to be developed and tested in the clinic. There are still many cases in which the cause of resistance to a particular targeted therapy is unknown, or the subset of patients most likely to benefit has not been identified. This thesis describes the ability of the MET ligand, HGF, to activate PI3K signaling and cause gefitinib resistance in EGFR-driven cancers. In addition, detection of a preexisting subpopulation of MET amplified cells (present before treatment with an EGFR inhibitor) is shown to successfully predict the development of MET amplification as a resistance mechanism. These results suggest that it may be possible to prospectively identify patients who will benefit from combined MET/HGF and EGFR inhibitors as initial therapies. Further, this thesis highlights the importance of both PI3K/AKT and MEK/ERK signaling as drivers of cell proliferation and viability, and describes a novel feedback network regulating these pathways. In multiple cancer models, treatment with a single agent MEK inhibitor leads to feedback up-regulation of ERBB3/PI3K/AKT signaling. The mechanism for this feedback involves loss of an inhibitory threonine phosphorylation in the conserved juxtamembrane domains of EGFR and HER2 following MEK inhibition, which leads to increased ERBB receptor activation. These results further elucidate the complex feedback networks that regulate signaling in cancer cells, and suggest possible limitations for the efficacy of single agent RAF/MEK pathway inhibitors. Collectively, this work describes multiple resistance mechanisms to kinase inhibitors, and suggests new biomarkers to define those patients who are likely to benefit from specific targeted therapies.

Ebolavirus (EboV) is a highly pathogenic enveloped virus that causes outbreaks of zoonotic infection in Africa. The clinical symptoms are manifestations of the massive production of pro-inflammatory cytokines in response to infection and in many outbreaks, case fatality rate exceeds 75%. The unpredictable onset, ease of transmission, rapid progression of disease, high mortality and lack of effective vaccine or therapy have created a high level of public concern about EboV. Here we report the properties of a benzylpiperazine adamantane diamide-derived compound identified in a screen for inhibitors of EboV infection. We found that the inhibitor is specific, reversible, and that the target(s) for inhibition are present in cells and not in virus particles. The compound is not an inhibitor of acid pH-dependent endosome protease activity, which is required for EboV infection. Treatment of cells with this compound causes accumulation of cholesterol in late endosomes and lysosomes (LE/LY), suggesting it inhibits one or more proteins involved in regulation of cholesterol uptake into cells. Using mutant cell lines and informative derivatives of the inhibitor, we found the inhibitor target is the endosomal membrane protein Niemann-Pick C1 (NPC1). NPC1 is a polytopic LE/LY membrane protein that mediates uptake of lipoprotein-derived cholesterol into cells. We find that NPC1 is essential for EboV infection, that NPC1 binds to the protease-cleaved GP1 subunit of the EboV glycoprotein, and that the anti-viral compound inhibits infection by targeting NPC1 and interfering with binding to GP1. Furthermore, analysis of viral variants resistant to the anti-viral compound revealed that the residues which confer resistance are located on the surface of the receptor binding domain of GP1. Combined with the results of previous studies of GP structure and function, our findings support a model of EboV infection in which cleavage of the GP1 subunit by endosomal cathepsin proteases removes heavily glycosylated domains to expose the N-terminal domain, which is a ligand for NPC1 and regulates membrane fusion by the GP2 subunit. Thus, NPC1 is essential for EboV entry and a target for anti-viral therapy.

Immunotherapy has been proposed as an alternative to conventional cancer therapies due to its reduced toxicity and ability to induce long-lasting anti-tumor immune responses. Dendritic cell (DC) vaccination is one immune-based anti-cancer strategy that has received attention due to the ability of DC to process and present antigen to T lymphocytes to initiate immune responses. However, the clinical efficacy of DC-based immunotherapy against established cancers in humans has been extremely low and despite recent advances, objective response rates in DC vaccine trials are rarely above 10%. This lack of efficacy is due in part to immunosuppressive factors, such as transforming growth factor &beta (TGF-&beta), present in the tumor microenvironment that promote tumor immune escape. Therefore, TGF-&beta represents a major barrier to effective cancer immunotherapy and strategies to neutralize this cytokine may lead to more efficacious DC vaccines.In this study, we employed two small molecule transforming growth factor &beta receptor type I (T&betaRI/ALK5) kinase inhibitors (HTS466284 and SM16) in combination with DC vaccines to treat established TGF-&beta-secreting 4T1 mammary tumors. The results demonstrate that while both inhibitors blocked the effects of TGF-&beta in vitro, HTS466284 by itself or in combination with DC vaccination was unable to consistently control the growth and metastasis of established 4T1 tumors. In contrast, SM16 inhibited the growth of established tumors when delivered orally and suppressed the formation of pulmonary metastases when delivered orally or via daily intraperitoneal (i.p.) injection. The efficacy of SM16 was dependent on cellular immunity as this drug had no effect in immunodeficient SCID mice. Furthermore, orally delivered SM16 in combination with DC vaccination led to complete tumor regression in several mice that correlated with increased T cell infiltration of the primary tumor and enhanced in vitro IFN-gamma production and tumor-specific cytolytic activity by splenocytes. Finally, a suboptimal dose of SM16 that failed to control primary tumor growth on its own synergized with DC vaccination to inhibit the growth of established 4T1 tumors. These findings suggest that blockade of TGF-&beta signaling using a small molecule T&betaRI/ALK5 kinase antagonist may be an effective strategy to bolster the efficacy of DC-based cancer vaccines.