Macrocyclic ligand-complexed transition metal-oxo intermediates are the active oxidizing species in a variety of important biological and catalytic oxidation reactions. Many transition metal catalysts have been designed to mimic the predominant oxidation catalysts in nature, namely the cytochrome P450 enzymes. Iron porphyrin complexes have been the center of research as catalysts. In this study 5,10,15,20- tetramesitylporphyrin (H2TMP) and its corresponding iron complexes FeIII(X)TMP (X= Cl, ClO4, ClO3, NO3, NO2, and BrO3) have been successfully synthesized and fully characterized by UV-vis and NMR spectroscopies. For the catalytic selective oxidation of organic sulfides, the potential of iron(III) porphyrin complexes with iodobenzene diacetate [PhI(OAc)2] have been investigated. Iodobenzene diacetate was found to be an efficient oxygen source in the iron(III) porphyrin-catalyzed oxidation of sulfides to sulfoxides. Iron(III) porphyrin catalysts show an excellent conversion and selectivity for the sulfoxidation reactions. Reaction conditions and environments that effect the catalytic sulfoxidation including solvent, catalytic amount, axial ligand, water, and thioanisole substrates, have been investigated to identify the optimal conditions and the substrate scope. Under optimized conditions, excellent substrate conversions (up to 100%) as well as product selectivies (sulfoxide:sulfone > 95:5) have been achieved. To probe the nature of the oxidizing species in above catalytic sulfoxidations, iron(IV)-oxo porphyrin radical cations model of Compound I were chemically produced from the corresponding iron(III) tetramesitylporphyrin precursors with excess amounts of PhI(OAc)2 (20-50 equivalents) in CH3CN solvent. All O=FeIV(X)TMP·+ (X= Cl, ClO4, ClO3, and NO3) show weaker Soret band and broader Q band that are characteristic of Compound I analogues. A new photochemical method that led to generation of the iron(IV)-oxo porphyrin radical cations was also successfully developed. Iron(IV)-oxo porphyrin radical cations were generated by irradiation of iron(III) porphyrin chlorate or bromate complexes that result in heterolytic cleavage of the O-X bond in the axial ligand.

Advancements in nanoparticle drug delivery of anticancer agents require mathematical models capable of predicting in vivo formulation performance from in vitro characterization studies. Such models must identify and incorporate the physicochemical properties of the therapeutic agent and nanoparticle driving in vivo drug release. This work identifies these factors for two nanoparticle formulations of anticancer agents using an approach which develops mechanistic mathematical models in conjunction with experimental studies. A non-sink ultrafiltration method was developed to monitor liposomal release kinetics of the anticancer agent topotecan. Mathematical modeling allowed simultaneous determination of drug permeability and interfacial binding to the bilayer from release data. This method also quantified the effects of topotecan dimerization and surface potential on total amount of drug released from these liposomal formulations. The pH-sensitive release of topotecan from unilamellar vesicles was subsequently evaluated with this method. A mechanistic model identified three permeable species in which the zwitterionic lactone form of topotecan was the most permeable. Ring-closing kinetics of topotecan from its carboxylate to lactone form were found to be rate-limiting for topotecan drug release in the neutral pH region. Models were also developed to non-invasively analyze release kinetics of actively-loaded liposomal formulations of topotecan in vivo. The fluorescence excitation spectra of released topotecan were used to observe release kinetics in aqueous solution and human plasma. Simulations of the intravesicular pH in the various release media indicated accelerated release in plasma was a consequence of increased intravesicular pH due to ammonia levels in the plasma instead of alterations in bilayer integrity. Further studies were performed to understand the roles of dimerization, ion-pairing, and precipitation on loading and release kinetics obtained from actively-loaded topotecan. Extension of this type of modeling for other types of nanoparticles was illustrated with doxorubicin-conjugated polymeric micelles. Mathematical modeling of experimental studies monitoring doxorubicin release identified conjugation stability during storage, hydrazone hydrolysis kinetics, and unconjugated doxorubicin partitioning affected micellar doxorubicin release. This work identifies several of the key parameters governing drug release from these liposomal and micellar nanoparticles and lays the framework for future development of in vivo release models for these formulations.

The development of novel imidazopyridines, which includes both tetrahydroimidazo[1,5-a]pyridine (rIMP) and imidazo[1,5-a]pyridine (IMP) was investigated using conventional and microwave induced procedures that afforded compounds at high yield of 88-96%. rIMP was synthesized using a two-step procedure that involved the microwave synthesis of IMP, then the reduction of the pyridine moiety of the fused imidazopyridine rings using 10% Pd/C and hydrazine monohydrate. The microwave synthesis of imidazopyridines involved the one pot reaction of 2-benzoylpyridine, substituted benzaldehyde and ammonium formate in acetic acid under open vessel microwave conditions, which resulted in products within 40 minutes. Novel PEG-IMP development, involved the synthesis of ethylene glycol tethered benzaldehydes and IMPs using traditional Williamson etherification synthesis, which afforded products at a high yield of 92-95%. We have then shown IMP and rIMP roles in its antiproliferative property towards PCa cells, specificity in inhibiting PI3K isoforms, and structural motif’s interaction with different residues in the kinase binding domain of the class I PI3K isoforms. The antiproliferative property towards PC3 cells shows increased activity with compounds containing pyridyl group on carbon 3 of the imidazo[1,5-a]pyridine parent moiety with signs of toxicity to PC3 within 24 hours of incubation and at 1 μM of the parent compound. Furthermore, the IMPs were tested against five prostate cellular lines: PC3, RWPE1, D145, LNCaP and LNCaP C81. IMPs showed little activity towards RWPE1 and increased activity towards PC3 cells. We determined that functionalizing the phenyl group at position 1 increased the efficacy of rIMP compared to the IMP. After showing increased toxicity to PC3 cells, it was important to investigate the mechanism in which IMP pose toxicity towards PC3 cells. The biochemical assay showed that rIMP was more effective in inhibiting PI3Kα isoform compared to both pan inhibitor wortmannin and IMP. Both IMP and rIMP inhibited more than 60% of PI3Kγ isoform activity at nanomolar concentrations. After showing IMPs affinity to PI3K isoforms, we investigated the binding interactions rIMP and IMP towards the PI3K isoforms using MOE molecular modeling software.

Analyzing protein tertiary structure is an effective method to understanding protein function. In my thesis study, I aimed to understand how surface features of protein can affect the stability and specificity of enzymes. I focus on 2 proteins that are involved in human disease, Profilin (PFN1) and APOBEC3A (A3A). When these proteins are functioning correctly, PFN1 modulates actin dynamics and A3A inhibits retroviral replication. However, mutations in PFN1 are associated with amyotrophic lateral sclerosis (ALS) while the over expression of A3A are associated with the development of cancer. Currently, the pathological mechanism of PFN1 in this fatal disease is unknown and although it is known that the sequence context for mutating DNA vary among A3s, the mechanism for substrate sequence specificity is not well understood. To understand how the mutations in Profilin could lead to ALS, I solved the structure of WT and 2 ALS-related mutants of PFN1. Our collaborators demonstrated that ALS-linked mutations severely destabilize the native conformation of PFN1 in vitro and cause accelerated turnover of the PFN1 protein in cells. This mutation-induced destabilization can account for the high propensity of ALS-linked variants to aggregate and also provides rationale for their reported loss-of-function phenotypes in cell-based assays. The source of this destabilization was illuminated by my X-ray crystal structures of several PFN1 proteins. I found an expanded cavity near the protein core of the destabilized M114T variant. In contrast, the E117G mutation only modestly perturbs the structure and stability of PFN1, an observation that reconciles the occurrence of this mutation in the control population. These findings suggest that a destabilized form of PFN1 underlies PFN1-mediated ALS pathogenesis. To characterize A3A’s substrate specificity, we solved the structure of apo and bound A3A. I then used a systematic approach to quantify affinity for substrate as a function of sequence context, pH and substrate secondary structure. I found that A3A preferred ssDNA binding motif is T/CTCA/G, and that A3A can bind RNA in a sequence specific manner. The affinity for substrate increased with a decrease in pH. Furthermore, A3A binds tighter to its substrate binding motif when in the loop region of folded nucleic acid compared to a linear sequence. This result suggests that the structure of DNA, and not just its chemical identity, modulates A3 affinity and specificity for substrate.

In the past, aminocyclohexanol rings have been successfully utilized as pH-triggered molecular switches in various trans-2-aminocyclohexanol derivatives. By changing the groups on the amine nitrogen, these models provided a wide pH range in which a switch can occur. The pH-induced switch of conformation was monitored by 1H-NMR spectroscopy. The models were also incorporated into the bilayer membrane of liposome structures and tested for their ability to disrupt their membrane upon their conformational flip induced by a decrease in pH. In this work, the amide bond has been studied as a molecular switch and various amide derivatives have been tested for their potential as lipid-like compounds that also exhibit a pH-sensitive conformational flip. The conformational analysis of these compounds was achieved by various NMR techniques and NMR acid-base titration studies were utilized to estimate the pKa of a number of the compounds described.

The dissociative photoionization reactions of two small, oxygenated organics, namely 1,3-dioxolane and methyl vinyl ketone, were studied by photoelectron photoion coincidence (PEPICO) spectroscopy. Experiments involving 1,3-dioxolane were carried out in the photon energy range of 9.5‒13.5 eV. The statistical thermodynamics model shows that a total of six dissociation channels are involved in the formation of three fragment ions, namely C3H5O2+ (m/z 73), C2H5O+ (m/z 45) and C2H4O+ (m/z 44), with two channels contributing to the formation of each. By comparing the results of ab initio quantum chemical calculations to the experimentally derived appearance energies of the fragment ions, the most likely mechanisms for these unimolecular dissociation reactions are proposed, including a description of the relevant parts of the potential energy surface.In the case of methyl vinyl ketone, an important atmospheric intermediate in the oxidation of isoprene, between 9.5‒13.8 eV four main fragment ions were detected at m/z 55, 43, 42, and 27 aside from the parent ion at m/z 70. The m/z 55 fragment ion (C2H3CO+) is formed from ionized MVK by direct methyl loss, while breaking the C–C bond on the other side of the carbonyl group results in the acetyl cation (CH3CO+, m/z 43) and the vinyl radical. The m/z 42 fragment ion is formed via a CO loss from the molecular ion after a methyl shift. The lightest fragment ion, the vinyl cation (C2H3+ at m/z 27), is produced in two different reactions: acetyl radical loss from the molecular ion and CO-loss from C2H3CO+. Their contributions to the m/z 27 signal are quantified based on the acetyl and vinyl fragment thermochemical anchors and quantum-chemical calculations. Based on the experimentally derived appearance energy of the m/z 43 fragment ion, a new, experimentally derived heat of formation is proposed for gaseous methyl vinyl ketone (ΔfH0K = −94.2 ± 4.8 kJ mol−1; ΔfH298K = −110.4 ± 4.8 kJ mol−1), together with cationic heats of formation and bond dissociation energies.

Opioid-induced constipation (OIC) is one of the major adverse effects of opioid analgesics used by millions of patients each year. While progress has been made, there remains a significant unmet medical need in the treatment of OIC. Major gaps remain in our understanding of the role of the gastrointestinal tract and central nervous system (CNS) in precipitating OIC. For the last four decades, numerous investigations to study the sites of action of opioid analgesics have utilized peripherally acting mu-opioid receptor antagonists (PAMORAs), which have been incorrectly believed to have limited penetration across the blood-brain barrier (BBB). Several preclinical and clinical reports indicate that significant amounts of PAMORAs penetrate the BBB quite readily. As a result, the usage of current PAMORAs have resulted in misunderstandings of the role of the CNS and gastrointestinal tract in causing side effects such as opioid-induced constipation (OIC). We have developed a transthyretin-based novel drug delivery approach for restricting the passage of small molecules across the BBB. Our approach involves endowing the opioid agonist/antagonist with the selective transthyretin ligand, AG10. The newly synthesized naloxone- and oxycodone-based conjugates have demonstrated superior peripheral selectivity, improved pharmacokinetics, and efficacy in rats compared to other clinically used PAMORAs. Here we present chemical synthesis, in vitro binding and stability studies, as well as pharmacokinetic and pharmacodynamic evaluations of the AG10-opioid conjugates in rats. Our AG10-based PAMORA allowed us to obtain new insights into the important role of mu-opioid receptors in the central nervous system (CNS) in causing constipation. Additionally, our results demonstrate for the first time that synergy between mu-opioid receptors in the central nervous system and the gastrointestinal tract is crucial to the understanding of OIC and the development of effective treatment regimens. These findings contradict prior ideas that OIC was caused by a mechanism that involves primarily the gastrointestinal mu-opioid receptors. Moreover, we confirmed our findings by a AG10-oxycodone conjugate, a peripherally restricted opioid agonist. This molecule demonstrated the predominant role of CNS in OIC precipitation. The newly synthesized AG10-opioid conjugates represent a novel class of pharmacological probes that will aid in our understanding of OIC and other undesirable adverse effects of opioids. In addition, these conjugates have been evaluated for their potential therapeutic value in the preclinical studies. Collectively our approach to limit the BBB penetration of opioids will contribute to develop safer and more effective opioid medications.

Photoelectron Photoion Coincidence (PEPICO) Spectroscopy studies on two unsaturated hydrofluorocarbons (HFCs), also known as hydrofluoroolefines (HFOs), are presented here. Previously, the Sztáray group has studied the dissociation of trans-1,3,3,3-tetrafluoroprop-1-ene (ElixClean), which is a fourth-generation refrigerant and propellant and has lower global warming potential than its precursors. My study is an extension of the ElixClean study as it aims to explore how the different number of fluorine atoms impact the dissociation reactions of these molecules. Both 3,3,3-trifluoropropene (TFP) and cis-1,2,3,3,3- pentafluoropropene (PFP) are also utilized as propellants and refrigerants.Measurements were carried out with remote access to the CRF-PEPICO (combustion reactions followed by photoelectron photoion coincidence spectroscopy) endstation of the vacuum-ultraviolet (VUV) beamline at the Swiss Light Source (SLS). Gas phase samples were intersected with tunable vacuum ultraviolet synchrotron light to create photoions and photoelectrons which are then detected in coincidence. Breakdown diagrams were then obtained by integrating the photoelectron-photoion coincidence signal for times of flight corresponding the precursor and fragment ions and plotting their fractional abundances at each photon energy. Analysis of these dissociation mechanisms was aided by ab initio calculations. Dissociative photoionization of TFP was studied over the photon energy range of 11.8–16.0 eV. Besides the molecular ion (m/z 96), there were four main fragment ions detected: m/z 95 (H-loss), 77 (F-loss), 46 (CF2-loss), 27 (CF3-loss). The experimental data for the dissociative photoionization of PFP was taken over the photon energy range of 12.0–16.5 eV and indicated the formation of m/z 113(F-loss), m/z 82 (CF2-loss), m/z 69 (C2HF2-loss), and m/z 51 (C2F3-loss), but an H-loss is not detected. Quantum-chemical calculations at the B3LYP level were used to explore the potential energy surface and identify the most likely structures that play a role in the dissociative photoionization processes of these fluorinated propenes. The energies of the most relevant stationary points were refined utilizing G4 composite method. The dissociation/isomerization pathways of energy-selected TFP and PFP ions will be explored, and I will discuss the most likely mechanisms that lead to the lowest-energy products.

Lysophosphatidic acid (LPA) influences many physiological processes, such as brain and vascular development. It is associated with several diseases including ovarian cancer, breast cancer, prostate cancer, colorectal cancer, hepatocellular carcinoma, multiple myeloma atherosclerotic diseases, cardiovascular diseases, pulmonary inflammatory diseases and renal diseases. LPA plasma and serum levels have been reported to be important values in diagnosing ovarian cancer and other diseases. However, the extraction and quantification of LPA in plasma are very challenging because of the low physiological concentration and similar structures of LPA to other phospholipids. Many previous studies have not described the separation of LPA from other phospholipids, which may make analyses more challenging than necessary. We developed an SPE extraction method for plasma LPA that can extract LPA at high purity. We also developed an HPLC post-column fluorescence detection method that allows the efficient quantification of LPA. These methods were used in a clinical study for ovarian cancer diagnosis to help validate LPA as a biomarker of ovarian cancer. Moreover, molecular imprinted polymers (MIPs) were designed and synthesized as material for the improved extraction of LPA. Compared to the commercially available materials, the MIP developed shows enhanced selectivity for LPA. The extraction was overall relatively more efficient and less labor-intensive.

Part I. The reaction between chiral acyl chlorides and trans -2-substituted-cyclohexanols proceeds diastereoselectively, i.e. produces mixtures of unequal amounts of diastereomers. We found for the first time that addition of pyridine or diisopropylethylamine accelerates the acylation, and unexpectedly for some substituents (RX) may completely invert its diastereoselectivity. These observations have been rationalized in terms of a stereoselective intramolecular assistance by the RX group to the acylation of the neighboring hydroxyl ("bait-and-hook" mechanism). A series of trans -2-substituted-cyclohexanols were synthesized and acylated with a racemic reagent in presence and absence of pyridine. The results showed that the presence of a nucleophilic group on the second carbon allowed for the preferred formation of one of the diastereomers in the absence of pyridine. However, in the presence of pyridine, the diastereoselectivity would inverse, and the reaction would favor the formation of the other diastereomer. To test the intramolecular acyl transfer hypothesis in detail a series of thioglucosides has been synthesized. Part II. The synthesized thioglucosides were tested as inhibitors of fungal glycosidases. Two compounds showed greater than 80% inhibition values in excess of the activity of β-D-glucosidases. More interestingly, the same compounds showed a marked enhancement of α-D-galactosidase activity by as much as 35%.