Currently, most of the RNAs used in lab research are prepared by in vitro transcription or chemical synthesis, which can be costly. In vivo expression in bacterial cells is another approach to RNA preparation that allows large scale production at a lower cost. However, there are some obstacles in bacterial expression, including RNA degradation in host cell, as well as RNA extraction and purification. tRNA and 5S RNA have been reported as scaffolds to circumvent the degradation problem. These scaffolds can not only make the RNA product survive in the cell but also increase the stability after extraction. The packaging RNA (pRNA) of bacteriophage phi29 is a small non-coding RNA with a compact structure. The three-way junction (3WJ) region from pRNA is a thermodynamically stable RNA motif good for constructing therapeutic RNA nanoparticles. The 3WJ can not only integrate multiple RNA modules, but also stabilize them. Here I report a series of approaches made to express recombinant RNAs based on pRNA or 3WJ in bacteria, including 1) Investigating the mechanism of RNA folding in vitro and in vivo using 3WJ. 3WJ-based RNAs were expressed in E. coli using pET system. The results show that the folding of RNA is affected by both overall and regional energy landscape. 2) Expression of an RNA nanoparticle harboring multiple functional modules, a model of therapeutic RNA, in E. coli using a combination of tRNA scaffold and pRNA-3WJ. The expression was successful and all of the RNA modules were functional. 3) Expression of pRNA-based recombinant RNAs in B. subtilis. This is a novel system of expressing recombinant RNAs in Gram-positive bacteria.

Supersaturating Drug Delivery Systems (SDDS) could enhance oral bioavailability of poorly water soluble drugs (PWSD). Precipitation inhibitors (PIs) in SDDS could maintain supersaturation by inhibiting nucleation, crystal growth, or both. The mechanisms by which these effects are realized are generally unknown. The goal of this dissertation was to explore the mechanisms underpinning the effects of model PIs including hydroxypropyl β-cyclodextrins (HP-β-CD), hydroxypropyl methylcellulose (HPMC), and polyvinylpyrrolidone (PVP) on the crystal growth of indomethacin, a model PWSD. At high degrees of supersaturation (S), the crystal growth kinetics of indomethacin was bulk diffusion-controlled, which was attributed to a high energy form deposited on the seed crystals. At lower S, indomethacin growth kinetics was surface integration-controlled. The effect of HP-β-CD at high S was successfully modeled using the reactive diffusion layer theory. The superior effects of PVP and HPMC as compared to HP-β-CD at high S were attributed to a change in the rate limiting step from bulk diffusion to surface integration largely due to prevention of the high energy form formation. The effects of PIs at low S were attributed to significant retardation of the surface integration rate, a phenomenon that may reflect the adsorption of PIs onto the growing surface. PVP was selected to further understand the relationship between adsorption and crystal growth inhibition. The Langmuir adsorption isotherm model fit the adsorption isotherms of PVP and N-vinylpyrrolidone well. The affinity and extent of adsorption of PVP were significantly higher than those of N-vinylpyrrolidone, which was attributed to cooperative interactions between PVP and indomethacin. The extent of PVP adsorption on a weight-basis was greater for higher molecular weight PVP but less on a molar-basis indicating an increased percentage of loops and tails for higher molecular weight PVPs. PVP significantly inhibited indomethacin crystal growth at high S as compared to N-vinylpyrrolidone, which was attributed to a change in the growth mechanism resulting in a change in the rate limiting step from bulk diffusion to surface integration. Higher molecular weight PVPs were better inhibitors than lower molecular weight PVPs, which was attributed to a greater crystal growth barrier provided by a thicker adsorption layer.

Current smoking cessation guidelines recommend nicotine replacement therapy (NRT) to assist pregnant smokers to quit, but this is without strong evidence for effectiveness and safety. Nicotine, the main addictive component of tobacco, is known to exert physiological effects by binding to its receptor, the nicotinic acetylcholine receptor (nAChR). Recent studies have identified the presence of nAChRs in non-neuronal cells, and in macrophages, functional alteration upon stimulation with nicotine has been documented. To understand the impact of in utero nicotine exposure on various immune cell disposition and function, we designed preliminary studies using an in vivo model of P. aeruginosa infection. In this model, pregnant mice were exposed to nicotine and after weaning, offspring were infected intra-tracheally and humanely killed 5 days later. Nicotine-exposed mice had a greater weight reduction post-infection. This was accompanied by a decreased number of neutrophil, resident macrophages, and B lymphocytes in the lungs, while the number of B lymphocytes in the lymph nodes were greater than that of the control group. In the lung lavage fluids, IL-6, MCP-1, and TNFα concentrations were elevated in nicotine-exposed mice. In an in vitro system using bone marrow-derived macrophages, a significantly reduced production of IFNγ was observed in nicotine-exposed mice when cells were stimulated with LPS. To characterize and compare gene expression in macrophages isolated from neonates developmentally exposed to nicotine, we designed a clinical study to recruit pregnant mothers who 1) did not smoke during pregnancy, 2) smoked throughout pregnancy, or 3) used NRT during pregnancy. We found that successful RNA isolation can be achieved from neonatal tracheal aspirate samples and cell number and reagent volumes were important determinants of acceptable RNA quality and quantity. Together, these preliminary findings demonstrate a possible alteration in immune response as a result of in utero nicotine exposure and sets a groundwork for future studies in identifying mechanisms underlying the impact of developmental nicotine exposure.

Aspirin and other nonsteroidal anti-inflammatory drugs (NSAIDs) are currently widely used as fever and pain relief in patients with arthritis and other inflammatory symptoms. NSAIDs effect by inhibiting cyclooxygenase-1 (COX-1) and/or cyclooxygenase-2 (COX-2). COX isozymes (COXs) are key enzymes in the biosynthesis of prostaglandin H2 (PGH2) from arachidonic acid (AA). It is now clear that prostaglandin E2 (PGE2), one of the downstream products of PGH2, is the main mediator in both chronic and acute inflammation. Microsomal prostaglandin E synthase (mPGES-1) is the terminal enzyme of COX-2 in the PGE2 biosynthesis pathway. Different from other two constitutively expressed PGE2 synthase (PGES), mPGES-2 and cPGES, mPGES-1 is induced by pro-inflammatory stimuli and responsible for the production of PGE2 related to inflammation, fever and pain. For these reasons, selective inhibition of mPGES-1 is expected to suppress inflammation induced PGE2 production and, therefore, will exert anti-inflammatory activity while avoid the side effects of COXs inhibitors, such as gastrointestinal (GI) toxicity, and cardiovascular events. A combination of computational and experimental approaches was used to discovery mPGES-1 inhibitors with new scaffolds. The methods used include molecular docking, molecular dynamic simulation, molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) binding free energy calculation, and in vitro activity assays. Our large-scale structure-based virtual screening was performed on compounds in the NCI libraries, containing a total of ~260,000 compounds. 7 compounds have been determined for their IC50 values (about 300 nM to 8000 nM). What’s more, these new inhibitors of mPGES-1 identified from virtual screening did not shown significant inhibition against COX isozymes even at substantially high concentrations (e.g. 100 µM). Rational methodology for drug design and organic synthesis were applied to generate three series of mPGES-1 inhibitors with different scaffolds. In total, about 200 compounds were synthesized and tested for their in vitro inhibition against human mPGES-1. Compounds with high potency against human mPGES-1 were further screened for their inhibition against mouse mPGES-1 and selectivity of human mPGES-1 over COXs. Several compounds were identified as submicromolar inhibitors against human mPGES-1 with high selectivity over COXs. In general, we have successfully identified a library of compounds as potent mPGES-1 inhibitors without significant inhibition against COXs. Structure information and in vitro activity evaluation data generated from the virtual screening and the library of compounds will be used to guide future design and synthesis of the mPGES-1 inhibitors.

siRNA therapy is an emerging technique that reduces protein expression in cells by degrading their mRNAs via the RNA interference pathway (RNAi). Diseases such as cancer often proliferate due to increased protein expression and siRNA therapy offers a new method of treatment for those diseases. Although siRNA therapy has shown success in vitro, it often fails in vivo due to instability in the blood stream. To overcome this limitation, delivery vehicles are necessary for successful transfection of siRNA into target cells and cationic polymers have been widely studied for this purpose. However, complexes between siRNA and delivery vehicles made from cationic polymers exhibit stability issues in the blood stream which results in toxicity and low transfection. This work hypothesizes that improvement of vehicle/siRNA complex stability will improve siRNA transfection efficiency. To test this, the contributions and outcomes of poly(ethylene glycol) [PEG] shell and hydrophobic core modification to a polyethylenimine (PEI) based tethered nanoassemblies (TNAs) were examined. Initially, hydrophobic modification of palmitate (PAL) to the core of the TNA yielded improved transfection efficiency due to an enhanced endosomal escape capability. However, this modification also reduced the TNA/siRNA complex stability. This indicated that the core hydrophobicity must be balanced in order increase stability while increasing transfection efficiency. Additionally, TNAs made from PEG and PEI did not cause transfection in our initial study. The PEG shell density was found to be too great and thereby reduced transfection efficiency. Reducing the PEG density by lowering PEG molecular weight, reducing attachment percentage, and removing small PEI impurities from the synthesis stock increased overall transfection efficiency and unimolecularity of the TNA complexes. This indicated that the shell composition of the TNA must be tuned in order to improve particle design. Further study of the hydrophobically modification to TNAs yielded unintended effects on the transfection efficiency evaluation assay. These particles exhibited an siRNA independent reduction in the reporter protein used to observe transfection, or a false positive effect, that was not previously observed. It was found that this false positive was influence mainly by the hydrophobic group rather than the cationic polymer backbone. Cellular stress was observed in cells dosed with the hydrophobically modified TNAs which lead to over ubiquitination and rapid degradation of the luciferase protein. This demonstrated that core components of TNAs could cause cellular stress and influence interaction outside of the TNA. Overall, this work demonstrates that hydrophobic core and PEG shell modification require balancing and consideration to improve properties of future cationic polymer based siRNA delivery vehicle design.

Theranostics is an emerging treatment approach that combines diagnostics with therapy in order to personalize treatment regimens for individual patients and decrease cancer mortality. Previously, nanoparticles entrapping conventional fluorescent dyes were developed for cancer theranostics, but fluorescent nanoparticles did not allow clinicians to significantly improve cancer treatments. The use of fluorescent dyes that are sensitive to solvent acidity (halo-fluorochromism) and polarity (solvato-fluorochromism) may overcome the limitations of fluorescent nanoparticles and improve cancer therapy by enabling researchers to detect chemical properties within the nanoparticle core environment. The model halo- and solvato-fluorochromic dye Nile blue was attached to the core of nanoscale drug delivery systems called polymer nanoassemblies (PNAs), which were created by tethering hydrophilic polymers and hydrophobic groups to a cationic polymer scaffold. The fluorescence of empty PNAs increased by 100% at pH 5.0 compared to pH 7.4, and the fluorescence of drug-loaded PNAs increased up to 300% compared to empty PNAs. A comparison of the fluorochromic properties between PNAs with various core properties indicated that both hydrophobic pendant groups and scaffold amines contributed to the fluorochromism of PNAs. The halo-fluorochromism of PNAs allowed investigators to minimize the detection of fluorescence signals in healthy organs such as the liver. Fluorescence imaging of halo-fluorochromic PNAs diffused into tissue mimics indicated that fluorescence of PNAs in tissues increased by 100% at pH 7.0 compared to pH 7.4. In addition, halo-fluorochromic PNAs identified the acidic perimeter surrounding metastatic tumors in orthotopic metastatic tumor models. Computational simulations of metastatic lesions verified that some halo-fluorochromic PNAs accumulate in the hypoxic/acidic regions of metastatic tumors following intravenous administration. These simulations also indicated that the accumulation of PNAs in the hypoxic regions of tumors doubles at 12 hours post-treatment compared to 1.8 hours post-treatment. The solvato-fluorochromism of PNAs enabled the fluorescence-based measurement of drug release from the nanoassembly core during dialysis-based drug release measurements. Solvato-fluorochromic methods indicated faster drug release rates than HPLC-based methods. Mechanistic modeling of drug release indicated that solvato-fluorochromic methods were unaffected by released drugs that interfered with HPLC-based methods. However, mechanistic modeling also indicated that drug rebinding and diffusion did not account for all of the differences between drug release rates determined by solvato-fluorochromic- and HPLC-based methods. Based on this evidence, it was hypothesized that solvato-fluorochromic drug release methods measure drug diffusion from near the scaffold of PNAs in a small region of the nanoassembly core, and that this process contributes to overall drug release but does not indicate apparent drug release rates for PNAs. In order to develop PNAs for potential clinical applications, ionizable amines were removed from the polymer scaffold to increase drug loading and sustain the release of model drugs carfilzomib and docetaxel. The removal of primary amines decreased drug diffusivity in the core of PNAs (D from 3.9*10-18 cm2/s to 0.1*10-19 cm2/s) and increased the drug release half-life (t1/2 from 4 to 26 hours). The controlled release of carfilzomib from PNAs reduced drug metabolism by 60% for up to one hour and sustained proteasome inhibition in cancer cells at 72 h post-treatment compared to free drug. Overall, this work provides insight into the design of theranostic nanoparticles with beneficial properties for improving cancer treatment.

Natural products continue to be a major chemical lead matter for drug discovery due to their diverse chemical structures and bioactivities. Clinically significant natural products include anti-cancer and anti-infective compounds and while many more of these compounds show promising bioactivity, their clinical relevance is often limited by toxicity or poor solubility. Combinatorial biosynthesis can be employed to modify existing chemical scaffolds towards reducing these limitations. To fully take advantage of these biochemical tools, it is important to understand the biosynthesis and mechanism of action of the molecules. Saccharides in glycosylated natural products provide specific interactions with cellular targets and are often crucial for a compound’s bioactivity. Genetic engineering of sugar pathways can modify glycosylation patterns leading to the diversification of natural products. Saquayamycins (SQN) H and I are cytotoxic angucycline antibiotics containing five deoxyhexoses including the rare amino sugar rednose. Elucidating the biosynthetic pathway of rednose could add to the arsenal of combinatorial biosynthesis tools for drug development. Our research goal of investigating the rednose biosynthetic pathway was pursued through two specific aims: the identification of the Streptomyces sp. KY 40-1 gene cluster involved in the biosynthesis of SQN H and I (sqn) (specific aim 1), and the validation of the proposed L-rednose biosynthetic pathway up to the glycosyl transfer through enzymatic synthesis of NDP-3,6-dideoxy-L-idosamine (specific aim 2). The sqn gene cluster revealed deoxysugar biosynthetic genes that could be used to alter glycosylation patterns to generate novel compounds while the enzymatic synthesis afforded novel genetic engineering tools to generate novel TDP-deoxysugars that could be used to diversify compounds such as aminoglycosides to circumvent resistance mechanisms. The first step to generate TDP-glucosamine enzymatically was accomplished, however later steps were unsuccessful. The aureolic acid mithramycin (MTM) was recently tested in clinical trials for Ewing sarcoma following the discovery of MTM as a potent inhibitor of the oncogenic transcription factor EWS-FLI1 present only in Ewing sarcoma cells It is understood that MTM binds the minor groove of G/C rich DNA as an Mg2+-coordinated dimer disrupting transcription of proto-oncogenes; however, the DNA recognition rules were not completely understood, making further interrogation of MTM’s DNA binding preferences necessary. This research goal of further understanding the mechanism of action for MTM was approached through two specific aims: the investigation of the dimerization of MTM (specific aim 3), and the investigation of MTM’s DNA binding preferences (specific aim 4). This work established that MTM and its biosynthetic precursor premithramycin B (PreMTM B), and several MTM analogues with modified 3-side chains: mithramycin SDK (MTM SDK), mithramycin SA tryptophan (MTM SA-Trp), and mithramycin SA alanine (MTM SA-Ala) dimerize even in the absence of DNA under physiologically relevant conditions. The study also demonstrated that modification of the 3-side chain modulates DNA binding affinity of MTM analogues, established a minimum MTM binding site on DNA, and revealed MTM DNA recognition is driven by direct (sequence) and not indirect (conformation) readout laying the foundation for subsequent research based on the interaction between MTM, DNA, and the oncogenic transcription factor EWS-FLI1 in the rational design of new MTM analogues for the treatment of Ewing sarcoma.

This thesis aimed to elucidate the demographic characteristics associated with elevated or reduced rates of pneumococcal conjugate 13 (PCV13) vaccination. A retrospective cohort study was performed using the Truven Health MarketScan® Database. Three cohorts were created corresponding to populations for which the CDC recommends PCV13 vaccination. Cohort 1: children < 36 months of age. Cohort 2: adults 19-64 years of age with high infection risk. Cohort 3: adults > 65 years of age. Odds of having a PCV13 claim were calculated for each cohort. For Cohort 1, 78% out of a total of 353,214 subjects had a sufficient number of PCV13 doses to meet CDC recommendations. For Cohort 2, 3.7% out of a total of 673,157 subjects had a PCV13 claim. For Cohort 3, 18% of 1,262,531 subjects had a PCV13 claim. Odds of vaccination were generally lower in younger subjects, those with fewer outpatient claims, and those with residence in the Northeast and South regions. In Cohort 2, odds were reduced in subjects with generalized malignancy. Gender and urban residence were poor predictors of vaccination status. By understanding the demographic factors associated with lower rates of vaccination, clinicians may more effectively direct their efforts to increase pneumococcal vaccination coverage.

Ever since the advent of computer-aided drug design (CADD), in silico simulation methods have greatly accelerated the drug discovery process and lead to the discovery of numerous drug candidates. With the exponential growth of computational power, we nowadays simulate biologic systems at a scale unimaginable a decade ago and thus provides perspectives for drug design. In this dissertation research, combining in silico simulation methods like molecular docking and molecular dynamics (MD) simulation with organic synthesis, in vitro/in vivo experiments and clinical data mining, we developed new drug discovery strategies. These strategies were applied in our drug discovery projects and led to the discovery of inhibitors of microsomal prostaglandin E2 synthase 1 (mPGES-1) and butyrylcholinesterase (BChE) as potential drug candidates. Protein mPGES-1 is known as an ideal target for next generation of anti-inflammatory drugs without the side-effects of currently available anti-inflammatory drugs. Unfortunately, almost all the previously reported human mPGES-1 inhibitors are inactive (or possess very low activity) against mouse or rat mPGES-1 that prevents using well-established mouse/rat models of inflammation, pain, and other diseases for preclinical studies. It would be extremely challenging for the mPGES-1-based drug development to follow traditional drug discovery and development route. In order to solve this problem, we developed and applied Drug Repurposing Effort Applying Integrated Modeling-in vitro/vivo-Clinical Data Mining (DREAM-in-CDM) strategy in this project. With molecular dynamics simulation, we observed the process of how mPGES-1 adopts an alternative conformation to control the access of co-factor GSH (glutathione) and its impact on the function of the protein. Based on the simulation results, we not only found an explanation for the difference between the X-ray and CryoEM (cryogenic electron microscopy) structure of mPGES-1 but also used molecular docking method to identify FDA approved drug, lapatinib, as an mPGES-1 inhibitor by virtual screening and the subsequent in vitro experiments. By mining the available clinical trial data, we found solid evidence that lapatinib can be used to relieve various types of pain in cancer patients. Since lapatinib is very well tolerated, we expect lapatinib to be repurposed as a new treatment for cancer-related pain. BChE has been identified as an ideal drug target for the treatment of Alzheimer’s disease (AD) and heroin overdose. The selectivity of a therapeutically useful inhibitor for BChE over AChE is very important. Unfortunately, there is no good selective BChE inhibitor. With a robust and virtual screening strategy combining with in vitro experiments, we identified a series of compounds from the NCI compound depository as BChE inhibitors with novel scaffolds, high activity and selectivity at the same time. The most potent compound was re-synthesized and the enantiomers of the compound were separated for the first time. The binding mode of the most potent compound was also analyzed and the origin of its high activity and selectivity was revealed that will guide the development of BChE selective inhibitors in the future. In addition, a new tacrine-based BChE affinity chromatography resin was developed. The developed new resin has enabled us to more conveniently and efficiently purify the BChE proteins with improved high purity. In general, we have successfully developed new drug discovery strategies to identify novel inhibitors of different enzymes. With these newly developed strategies, we expect additional drug discoveries to be made in the foreseeable future.

Opioid use disorder (OUD) and opioid overdose are pervasive public health problems in the U.S. Medications for opioid use disorder (MOUD) have been shown effective to reduce OUD morbidity and mortality. Two distinct approaches to MOUD are currently used: agonist therapy (methadone or buprenorphine) or antagonist therapy (naltrexone). Limited information is available about the patterns of use, adherence to therapy, and characteristics of those who use agonist vs. antagonist therapy. The objective of this study is to assess recent trends in MOUD, adherence in use of MOUD, and the characteristics of those who use agonist vs. antagonist therapy in a nationally representative population of commercially insured patients in the U.S. This retrospective descriptive study utilized data from Truven Marketscan Commercial Claims and Encounters database from years 2011 to 2016. All individuals aged 18 years and older who have a diagnosis of OUD and utilize MOUD at any point during the study period were included. Demographic characteristics of interest included age, gender, geographic region, and type of insurance coverage. Clinical characteristics of interest included diagnosis of OUD and type of MOUD used, including extended – release naltrexone for injection, oral naltrexone, buprenorphine in combination with naloxone, and buprenorphine alone. Descriptive analyses were employed to understand utilization patterns and trends over time and proportion of days covered was used to measure adherence. Frequency and percentage are presented for categorical variables. Adherence of MOUD will be estimated by measuring proportion of days covered. As this study uses de-identified commercial health claims data, it has been determined as not human subjects research by the University of Kentucky’s Office of Research Integrity. Agonist therapy with buprenorphine or buprenorphine/naloxone was the most common treatment, representing 75.7% of those receiving treatment. Between 2011 and 2016, the percentage of individuals receiving treatment with partial agonist therapy decreased 16.5% to 9.2%, respectively. Meanwhile, the percentage of individuals receiving treatment with antagonist treatment increased from 0.1% in 2011 to 0.3% in 2016. In the analysis of proportion of days covered, all MOUD reported a decrease at both 180 and 365 days. In the commercial population, younger female patients were more likely to be treated with injectable naltrexone. Specifically, in the North Central geographic region, commercial adult patients were more likely to be treated with buprenorphine monotherapy. Overall, this study found a decrease in use of agonist therapy from 2011 through 2016, with an increase in use of antagonist therapy in the same time period. However, the increase in use of antagonist therapy does not fully account for the decrease in use of agonist therapy, suggesting that since 2011 many patients with OUD still remain untreated. All MOUD types were analyzed and saw a decrease in proportion of days covered, as a measure of adherence, from 2011 to 2016 putting patients at an increased risk for relapse, further complications, emergency visits, and hospitalizations. More information is needed about characteristics of patients who not only seek out treatment for OUD, but also maintain their treatment overtime.