Chemotherapy is the most common cancer treatment. Traditionally, platinum-based drugs are used in chemotherapy. More recently, researchers have focused on ruthenium based compounds as a substitute for the platinum compounds. Ruthenium-based compounds appear to be less toxic to healthy cells than traditional platinum-based compounds. In this study, 7 ruthenium-based compounds were tested on HT-29 (colon) and MCF-7 (breast) human cancer cell lines with the specific aim of determining whether or not any of the ruthenium-based compounds exhibited cytotoxic properties. In addition, levels of vascular endothelial growth factor (VEGF) production were tested in supernate from the cancer cells treated with various ruthenium-based compounds to determine whether or not the ruthenium-based compounds had an effect their VEGF production. Our results indicate that none of the ruthenium based compounds tested had a cytotoxic effect on the cancer cell lines; however, some of the compounds did exhibit inhibition of cell growth. Results further indicate an initial decrease in VEGF production in the cell lines treated with the ruthenium compounds but that this effect was compound-cell line specific.

Drug based nanoparticle (NP) formulations have gained considerable attention over the past decade for their use in various drug delivery systems. NPs have been shown to increase bioavailability, decrease side effects of highly toxic drugs, and prolong drug release. Furthermore, polymer based, biodegradable nanodelivery has become increasing popular in the field of NP formulation because of their high degree of compatibility and low rate of toxicity. Due to their popularity, commercially available polymers such as poly lactic acid (PLA), poly glycolic acid (PGA) and polylactic-co-glycolic acid (PLGA) are commonly used in the development and design of new nano based delivery systems. Nonsteriodal anti-inflammatory drugs (NSAIDs) are commonly used for the treatment of pain and inflammation. NSAIDs such as diclofenac and celecoxib function by blocking cyclooxygenase expression and reducing prostaglandin synthesis. Unfortunately, the pharmacological actions of NSAIDs can lead to the development of several adverse side effects such as gastrointestinal ulceration and bleeding. The aim of this study was to formulate and optimize diclofenac or celecoxib entrapped polymer NPs using an emulsion-diffusion-evaporation technique. NP formulations were evaluated based on specific formula parameters such as particle size, zeta potential, morphology, and entrapment efficiency. Effects of stabilizer type, stabilizer concentration, centrifugal force, drug amount, and/or emulsifier (lecithin) on nanoparticle characterization were examined for formula optimization. Results of the formulation studies showed that NPs developed using polylactide-co-glycolide (PLGA) polymers and the stabilizer didodecyldimethylammonium bromide (DMAB) demonstrated enhanced stability, drug entrapment, and reduced particle size. These findings demonstrate an effective method for polymer NP formulation of diclofenac or celecoxib. Furthermore, the results reported herein support a novel method of drug delivery that may function to reduce known adverse effects of these pharmacotherapeutic agents.

Oxidative stress, the imbalance of free radical generation with antioxidant defenses, leads to cellular inflammation, apoptosis and cell death. This compromised environment results in debilitating diseases, such as oral mucositis (OM), atherosclerosis, and ischemia/reperfusion injury. Antioxidant therapeutics has been a proposed strategy to ameliorate these imbalances and maintain homeostatic environments. However, the success of these approaches, specifically curcumin, has been limited due to characteristics such as hydrophobicity and high reactivity when released as bolus doses to contest to oxidative stress induced diseases. The development of a controlled release system to aid in protection of the antioxidant capacity of curcumin, as well as a tunable system to aid in proper rate of release for disease can overcome these limitations. Previously, the use of a poly(beta-amino ester) (PBAE) chemistry has been developed in Dziubla and Hilt laboratories to provide desirable properties. The dynamic mechanical analysis and efficacy in cellular protection has been studied, yet the sensitivity and responsiveness of these polymers to abnormal environments found within oxidative stress compromised environments are unknown. In this work, a series of networks were comprised of different molar ratios of modified acrylated curcumin, poly(ethylene glycol) diacrylate, and a primary diamine crosslinker to create tunable hydrolytically degradable crosslinked hydrogels. I hypothesized a consumption rate difference of free curcumin and curcumin as a released product from the crosslinked network in the presence of a free radical generating system. After the consumption profiles of each were reported differently, the experimental data was translated into a kinetic rate model to identify quantitative consumption rate parameters of curcumin and active film degradation products. The effect on the released products arose the question of curcumin consumption in other oxidizing environments. These networks were then investigated in low concentrations of a hydrogen peroxide insult, and interestingly showed sensitivity to hydrolysis by recovering significantly more curcumin at an accelerated rate of release. Identifying the sensitivity of these tunable networks to environmental stimuli, they were then presented to a series of low pH environments, which significantly reduced the degradation time, finding a dependence of rate of release on the weight loading of curcumin present within the film. To translate these responsive materials to an application-based system, the curcumin conjugated PBAE polymers were investigated as an oral rinse drug delivery system for the treatment of radiation-induced OM in a hamster model. Radiation-induced OM onset and severity was reduced with a 20 wt% microparticle loaded mucoadhesive system that releases curcumin over 24 hours, providing promising results of a therapeutic effect from curcumin when incorporated in to a controlled release delivery system. Overall, curcumin conjugated PBAE polymers show selectivity of hydrolysis in abnormal environments related to oxidative stress. This information is beneficial to the proper design and loading of antioxidant therapeutics within crosslinked polymers, giving the ability to tune release to treat and deliver based on the environment’s insult. This can advance the potential use for antioxidant therapeutics in pharmaceutical applications in the future.

Gene therapy is an approach for the treatment of acquired cancers, infectious disease, degenerative disease, and inherited genetic indications. Developments in the fields of immunotherapies and CRISPR/Cas9 genome editing are revitalizing the efforts to move gene therapy to the forefront of modern medicine. However, slow progress and poor clinical outcomes have plagued the field due to regulatory and safety concerns associated with the flagship delivery vector, the recombinant virus. Immunogenicity and poor transduction in certain cell types severely limits the utility of viruses as a delivery agent of nucleic acids. As a result, significant efforts are being made to develop non-viral delivery systems that perform mechanistically similarly to viral delivery but lack immunogenic factors. Though safer, existing agents lack the efficacy inherent in the natural design of viral vectors. Clinical relevance of non-viral vectors will therefore depend on the ability to engineer optimized systems for cellular delivery in physiological environments. Progress in non-viral vector design for gene delivery requires a deep understanding of the various barriers associated with nucleic acid delivery, including cell surface interaction, internalization, endosomal escape, cytosolic transport, nuclear localization, unpackaging, etc. Further, it requires a knowledge of vector design properties (surface chemistry, charge, size, shape, etc.) and how these physical parameters affect interactions with the cellular environment. Of these interactions, charge is shown to govern how particles are internalized and subsequently processed, thereby affecting the intracellular fate and efficacy of delivery. Charge also affects the in-serum stability where negative zeta potential improves stability and circulation time. Therefore, it is important to understand the effects of polyplex charge and other parameters on the internalization and intracellular fate of polyplexes for gene therapy. In chapter 2, studies are performed to delineate the effects of polyplex charge on the cellular internalization and intracellular processing of polymer-mediated gene delivery. Charge is shown to affect the endocytic pathway involved in internalization, and the caveolin-dependent and macropinocytosis pathways lead to higher gene delivery efficacy, likely due to avoidance of acidified compartments such as late endosomes and lysosomes. In chapters 3-4, novel nanoparticles carrying DNA, RNA, and antioxidants are assessed for therapeutic effect with an emphasis on studying the internalization mechanisms and resulting effect on efficacy. Novel RNA delivery agents are shown to benefit from EGFR-targeting aptamer and nanoceria/PEI hybrids are demonstrated to provide simultaneous antioxidant and gene therapy. Finally, chapter 5 demonstrates the use of silencing RNA and CRISPR/Cas9 genome editing to study the prevalence of gene targets in vivo. The overall goal of this work is to contribute to the design and application of novel nanoparticles for gene delivery and offer insight into the engineering of novel polyplexes. It remains clear that route of internalization is key to successful gene delivery, and designing polyplexes to enter through non-acidified endocytic pathways is highly beneficial to transgene expression. This can be achieved through incorporation of surface chemistries that trigger internalization through targeted pathways and is the source of further work in the lab.

Overdose and addiction are two medical complications of cocaine abuse. To date, there is no FDA approved pharmacotherapy specific for cocaine abuse. Cocaine hydrolases (CocHs) have been extensively investigated for its potential in anti-cocaine therapy. Previous studies have demonstrated that CocHs efficiently hydrolyze cocaine to generate biologically inactive metabolites both in vivo and in vitro. However, it has not been studied whether there is gender difference in the therapy using CocHs. In addition, the effectiveness of CocHs is unknown for treating cocaine toxicity when alcohol is co-administered. The main purpose of this dissertation is to characterize and evaluate efficient CocHs for cocaine overdose and cocaine addiction treatment. In the first set of studies, the effectiveness of human serum albumin-fused CocH1 were studied in male and female rats. The pharmacokinetic profiles, as well as the pharmacodynamic effects of CocH1-HSA were compared in male and female rats. The obtained data clearly demonstrated that CocH1-HSA was equally effective in both genders. The second set of studies investigated the efficiency of Fc-fused CocH5 in reversing cocaine toxicity in rats receiving simultaneous administration of cocaine and alcohol. Results showed that CocH5-Fc rapidly hydrolyzed cocaine and cocaine’s toxic metabolites in rats, and demonstrated that CocH5-Fc was efficient in treating cocaine toxicity when alcohol was simultaneously administered. In later studies to investigate the effects of CocH5-Fc for the treatment of cocaine addiction, a mathematical model was developed and validated to predict the effects of CocH5-Fc on the disposition of cocaine in rat blood and brain. This model adequately described the effects of CocH5-Fc in accelerating the elimination of cocaine and its toxic metabolites in both rat blood and brain. In conclusion, the studies within the current dissertation demonstrate the clinical potential of CocHs for the treatment of both cocaine overdose and cocaine addiction.

Flexible enzymes are notoriously a bane to structure-based drug design and discovery efforts. This is because no single structure can accurately capture the vast array of conformations that exist in solution and many are subject to ligand-associated structural changes that are difficult to predict. Glutamate racemase (GR) – an antibiotic drug discovery target involved in cell wall biosynthesis – is one such enzyme that has eluded basic structure-based drug design and discovery efforts due to these flexibility issues. In this study, our focus is on overcoming the impediment of unpredictable ligand-associated structural changes in GR drug discovery campaigns. The flexibility of the GR active site is such that it is capable of accommodating ligands with very different structures. Though these ligands may bind to the same pocket, they may associate with quite dissimilar conformations where some are more favorable for complexation than others. Knowledge of these changes is invaluable in guiding drug discovery efforts, indicating which compounds selectively associate with more favorable conformations and are therefore better suited for optimization and providing starting structures to guide structure-based drug design optimization efforts. In this study, we develop a mutant GR possessing a genetically encoded non-natural fluorescent amino acid in a region remote from the active site whose movement has been previously observed to correlate with active site changes. With this mutant GR, we observe a differential fluorescence pattern upon binding of two structurally distinct competitive inhibitors known to associate with unique GR conformations – one to a favorable conformation with a smaller, less solvated active site and the other to an unfavorable conformation with a larger, more solvated active site. A concomitant computational study ascribes the source of this differential fluorescence pattern to ligand-associated conformational changes resulting in changes to the local environment of the fluorescent residue. Therefore, this mutant permits the elucidation of valuable structural information with relative ease by simply monitoring the fluorescence pattern resulting from ligand binding, which indicates whether the ligand has bound to a favorable or unfavorable conformation and offers insight into the general structure of this conformation.

The emergence and proliferation of Gram-negative bacteria expressing β-lactamases is a significant threat to human health. β-Lactamases are enzymes that degrade the β-lactam antibiotics (e.g., penicillins, cephalosporins, monobactams, and carbapenems) that we use to treat a diverse range of bacterial infections. Specifically, β-lactamases catalyze a hydrolysis reaction where the β-lactam ring common to all β-lactam antibiotics and responsible for their antibacterial activity, is opened, leaving an inactive drug. There are two groups of β-lactamases: serine enzymes that use an active site serine residue for β-lactam hydrolysis and metalloenzymes that use either one or two zinc ions for catalysis. Serine enzymes are divided into three classes (A, C, and D), while there is only one class of metalloenzymes, class B. Clavulanic acid, sulbactam, and tazobactam are β-lactam-based BLIs that demonstrate activity against class A and C β-lactamases; however, they have no activity against the class A KPC and MBLs, NDM and VIM. Avibactam and vaborbactam are novel BLIs approved in the last two years that have activity against serine carbapenemases (e.g., KPC), but do not inhibit MBLs. The overall goals of this project were to use X-ray crystallography to study the catalytic mechanism of serine β-lactamases with β-lactam antibiotics and to understand the mechanisms behind the broad-spectrum inhibition of class A β-lactamases by avibactam and vaborbactam. This project also set out to find novel inhibitors using molecular docking and FBDD that would simultaneously inactivate serine β-lactamases and MBLs commonly expressed in Gram-negative pathogenic bacteria. The first project involved examining the structural basis for the class A KPC-2 β-lactamase broad-spectrum of activity that includes cephalosporins and carbapenems. Three crystal structures were solved of KPC-2: (1) an apo-structure at 1.15 Å; (2) a complex structure with the hydrolyzed cephalosporin, cefotaxime at 1.45 Å; and (3) a complex structure with the hydrolyzed penem, faropenem at 1.40 Å. These complex structures show how alternative conformations of Ser70 and Lys73 play a role in the product release step. The large and shallow active site of KPC-2 can accommodate a wide variety of β-lactams, including the bulky oxyimino side chain of cefotaxime and also permits the rotation of faropenem’s 6-alpha-1R-hydroxyethyl group to promote carbapenem hydrolysis. Lastly, the complex structures highlight that the catalytic versatility of KPC-2 may expose a potential opportunity for drug discovery. The second project focused on understanding the stability of the BLI, avibactam, against hydrolysis by serine β-lactamases. A 0.83 Å crystal structure of CTX-M-14 bound by avibactam revealed that binding of the inhibitor impedes a critical proton transfer between Glu166 and Lys73. This results in a neutral Glu166 and neutral Lys73. A neutral Glu166 is unable to serve as a general base to activate the catalytic water for the hydrolysis reaction. Overall, this structure suggests that avibactam can influence the protonation state of catalytic residues. The third project centered on vaborbactam, a cyclic boronic acid inhibitor of class A and C β-lactamases, including the serine class A carbapenemase KPC-2. To characterize vaborbactam inhibition, binding kinetic experiments, MIC assays, and mutagenesis studies were performed. A crystal structure of the inhibitor bound to KPC-2 was solved to 1.25 Å. These data revealed that vaborbactam achieves nanomolar potency against KPC-2 due to its covalent and extensive non-covalent interactions with conserved active site residues. Also, a slow off-rate and long drug-target residence time of vaborbactam with KPC-2 strongly correlates with in vitro and in vivo activity. The final project focused on discovering dual action inhibitors targeting serine carbapenemases and MBLs. Performing molecular docking against KPC-2 led to the identification of a compound with a phosphonate-based scaffold. Testing this compound using a nitrocefin assay confirmed that it had micromolar potency against KPC-2. SAR studies were performed on this scaffold, which led to a nanomolar inhibitor against KPC-2. Crystal structures of the inhibitors complexed with KPC-2 revealed interactions with active site residues such as Trp105, Ser130, Thr235, and Thr237, which are all important in ligand binding and catalysis. Interestingly, the phosphonate inhibitors that displayed activity against KPC-2, also displayed activity against the MBLs NDM-1 and VIM-2. Crystal structures of the inhibitors complexed with NDM-1 and VIM-2 showed that the phosphonate group displaces a catalytic hydroxide ion located between the two zinc ions in the active site. Additionally, the compounds form extensive hydrophobic interactions that contribute to their activity against NDM-1 and VIM-2. MIC assays were performed on select inhibitors against clinical isolates of Gram-negative bacteria expressing KPC-2, NDM-1, and VIM-2. One phosphonate inhibitor was able to reduce the MIC of the carbapenem, imipenem 64-fold against a K. pneumoniae strain producing KPC-2. The same phosphonate inhibitor also reduced the MIC of imipenem 4-fold against an E. coli strain producing NDM-1. Unfortunately, no cell-based activity was observed for any of the phosphonate inhibitors when tested against a P. aeruginosa strain producing VIM-2. Ultimately, this project demonstrated the feasibility of developing cross-class BLIs using molecular docking, FBDD, and SAR studies.

<p>Globally of today, acquired immunodeficiency syndrome (AIDS) and malaria are two of the most threatening diseases known to mankind. The World Health Organization estimated that AIDS and malaria together claimed nearly 4 million lives in 2003 and many more were infected by the causative agent human immunodeficiency virus (HIV) and the <i>Plasmodium falciparum</i> (<i>P. falicparum</i>) parasite. Current treatment regims for HIV and <i>P. falicparum</i> infections are undermined by rapid emergence of drug-resistant strains and severe drug side-effects.</p><p>A resistance mechanism of the commonly selected K103N RT mutant towards three second generation non-nucleoside RT inhibitors (NNRTIs) is presented based on X-ray structures. Subtle changes in contacts between inhibitor and residue in position 103 aided the design of improved inhibitors. For the PR target, attempts have been made to structurally assist the development of diol-based protease inhibitors (PIs) with the aim of improving the anti-viral potency without reducing the inhibitory efficacy. It was shown that ortho- and meta-fluoro-substituted P1/P1’-benzyloxy side chains improved the anti-viral potency without affecting the accommodation to the S1/S1’ subsites. </p><p>The apparent increase in malaria resistance makes drug interventions of current targets increasingly complicated. A prominent new drug target is found in the parasite’s hemoglobin degradation pathway – the aspartic protease plasmepsin II (Plm II). The usefulness of Plm II as an anti-malarial target is presented supported by Plm II complexed with a novel inhibitor. Structurally it is shown that bulky P1- and P3-side-chains adopt a novel binding mode to the Plm II binding cleft with implications for further inhibitor development.</p>

Globally of today, acquired immunodeficiency syndrome (AIDS) and malaria are two of the most threatening diseases known to mankind. The World Health Organization estimated that AIDS and malaria together claimed nearly 4 million lives in 2003 and many more were infected by the causative agent human immunodeficiency virus (HIV) and the Plasmodium falciparum (P. falicparum) parasite. Current treatment regims for HIV and P. falicparum infections are undermined by rapid emergence of drug-resistant strains and severe drug side-effects. A resistance mechanism of the commonly selected K103N RT mutant towards three second generation non-nucleoside RT inhibitors (NNRTIs) is presented based on X-ray structures. Subtle changes in contacts between inhibitor and residue in position 103 aided the design of improved inhibitors. For the PR target, attempts have been made to structurally assist the development of diol-based protease inhibitors (PIs) with the aim of improving the anti-viral potency without reducing the inhibitory efficacy. It was shown that ortho- and meta-fluoro-substituted P1/P1’-benzyloxy side chains improved the anti-viral potency without affecting the accommodation to the S1/S1’ subsites. The apparent increase in malaria resistance makes drug interventions of current targets increasingly complicated. A prominent new drug target is found in the parasite’s hemoglobin degradation pathway – the aspartic protease plasmepsin II (Plm II). The usefulness of Plm II as an anti-malarial target is presented supported by Plm II complexed with a novel inhibitor. Structurally it is shown that bulky P1- and P3-side-chains adopt a novel binding mode to the Plm II binding cleft with implications for further inhibitor development.

The protein kinases are a large family of enzymes that play a fundamental role in propagating signals within the cell. Because of the high degree of binding site similarity shared among protein kinases, designing drug compounds with high specificity among the kinases has proven difficult. However, computational approaches to comparing the 3-dimensional geometry and physicochemical properties of key binding site residues, referred to here as substructures, have been shown to be informative of inhibitor selectivity. This thesis introduces two fundamental approaches for the comparative analysis of substructure similarity and demonstrates the importance of each method on a variety of large protein structure datasets for multiple biological applications. The Family-wise Alignment of SubStructural Templates Framework (The FASST Framework) provides an unsupervised learning approach for identifying substructure clusterings. The substructure clusterings identified by FASST allow for the automatic evaluation of substructure variability, the identification of distinct structural conformations and the selection of anomalous outlier structures within large structure datasets. These clusterings are shown to be capable of identifying biologically meaningful structure trends among a diverse number of protein families. The FASST Live visualization and analysis platform provides multiple comparative analysis pipelines and allows the user to interactively explore the substructure clusterings computed by FASST. The Combinatorial Clustering Of Residue Position Subsets (CCORPS) method provides a supervised learning approach for identifying structural features that are correlated with a given set of annotation labels. The ability of CCORPS to identify structural features predictive of functional divergence among families of homologous enzymes is demonstrated across 48 distinct protein families. The CCORPS method is further demonstrated to generalize to the very difficult problem of predicting protein kinase inhibitor affinity. CCORPS is demonstrated to make perfect or near-perfect predictions for the binding ability of 12 of the 38 kinase inhibitors studied, while only having overall poor predictive ability for 1 of the 38 compounds. Additionally, CCORPS is shown to identify shared structural features across phylogenetically diverse groups of kinases that are correlated with binding affinity for particular inhibitors; such instances of structural similarity among phylogenetically diverse kinases are also shown to not be rare among kinases. Finally, these function-specific structural features may serve as potential starting points for the development of highly specific kinase inhibitors. Importantly, both The FASST Framework and CCORPS implement a redundancy-aware approach to dealing with structure overrepresentation that allows for the incorporation of all available structure data. As shown in this thesis, surprising structural variability exists even among structure datasets consisting of a single protein sequence. By incorporating the full variety of structural conformations within the analysis, the methods presented here provide a richer view of the variability of large protein structure datasets.