Rare diseases caused by single-gene mutations affect almost one million Canadians. According to the Online Mendelian Inheritance in Man database, ~4,500 rare monogenic diseases have a known cause; but less than 5% of patients have access to disease-modifying drugs. The dearth of accessible drugs for patients suffering from rare genetic diseases is partly due to the astronomical costs of traditional drug development which, when combined with the small target population, make rare disease therapeutics unattractive ventures for the pharmaceutical establishment. The paucity of cost-effective treatments for rare diseases has resulted in the promotion of clinic-ready drug repurposing as a tenable strategy for rare disease therapeutics. To identify repurposed candidates for rare neurogenetic diseases, I conducted a transcriptome-wide drug screen in mouse primary cerebrocortical cultures. RNA sequencing was used to develop a database of transcriptome-wide differential expression for 218 clinic-tested drugs. The “Neuron Screen” database was queried to identify drugs that upregulate ~60 rare neurogenetic disease genes (type I hits). Gene set enrichment pathway analysis by Ingenuity Pathway Analysis (IPA) was used to identify network associated drug-gene interactions (type II hits). Both types of drug-gene hits were further assessed in vitro and in vivo by qRT-PCR and western blot analysis. This analysis showed that the IPA-based network-associated approach reduces the false positive rate when identifying differentially expressed genes in transcriptome-wide data-sets. The analysis also identified two drug-gene interactions with genes that cause rare neurogenetic disease, thyroid hormone-Pmp22 and dexamethasone-Mfsd2a, that merit further investigation. This work proves the utility of the Neuron Screen database to connect rare disease genes with transcript-modulating drugs and provides a starting point to understand the transcriptional effects of pharmacologic agents on the mammalian brain.

Indiana University-Purdue University Indianapolis (IUPUI) / Background: Alzheimer’s disease (AD) is the third leading cause of death for the older demographic in the United States, just after heart disease and cancer. However, unlike heart disease and cancer, the death rates for AD are increasing. Despite extensive research, the cause or origin of AD remains unclear and there is no existing cure. However, with the improvement of single-cell RNA-sequencing (scRNA-seq) technologies and drug repurposing tools, we can further our knowledge of AD and its pathogenesis. Method: Our primary aim was to identify repurposable drug and compound candidates for AD treatment and identify significant cell types and signaling pathways using two scRNA-seq datasets from cortex samples of AD patients and controls. To achieve this aim, we generated differential gene expression profiles, calculated log fold-changes, and estimated standard errors to make pairwise comparisons between the diseased and healthy samples. We used the 21,304 drugs/compounds with response gene expression profiles in 98 cell lines from the LINCS L1000 project to detect consistent differentially expressed genes (DEGs), that were either i) up-regulated in cells of diseased samples and down-regulated in cells with treatment, or ii) down-regulated in cells from diseased samples but up-regulated in cells with treatment. To evaluate these identified drugs, we compared the p-value, false discovery rate (FDR) and A Single-cell Guided Pipeline to Aid Repurposing of Drugs (ASGARD) drug score for each cell type. We further annotated and assessed doublet cell types within the Grubman et al. dataset using cell type proportions. Result: The analysis provided several potential therapeutic treatments for AD and its target genes and pathways as well as important cell type interactions. Notably, we identified an interaction between endothelial cells and microglia, and further identified drug candidates to target this interaction. Conclusion: We identified repurposable drugs/compounds candidates in each dataset which were also identified in literature. We further identified doublet cell type interactions of interest and drugs that target this interaction.

A comprehensive framework is presented for the integration of electrified transportation and renewable energy through repurposing batteries of plug-in electric vehicles towards a sustainable energy future. The framework considers future market penetration scenarios of plug-in electric vehicles, availability of batteries at their vehicular end of life, and the storage capacity required to generate base-load wind power in the region of study. The objective is to develop a model that can be used as a policy tool to investigate how different scenarios and pertinent parameters can effectively meet the challenges of sustainability in the energy and transportation sectors when the ultimate goal is to simultaneously displace fossil fuels with new generation of low-cost intermittent renewable energy. A sample case study is performed for Canada to investigate and verify the performance of the model. The analysis shows that the proposed approach can further improve the energy sustainability performance of Canada in 2050 by 1.65–4.11%, depending on the confidence level and in addition to electrification of transportation. In the framework, a statistical algorithm is developed to calculate the capacity of an energy storage system required for delivering base-load electricity for a wind farm in the future electric grids. The algorithm contributes towards the goal of utilizing low- cost intermittent wind energy to base-load power generation in the future electric grids. The introduced algorithm presents three methods to perform the sizing calculations each representing a scenario associated with the stages of the wind energy industry. The results of the studied case are applied to estimate the cost of wind energy to produce rated power at different confidence levels, which show cost-effectiveness and less intermittency on the power systems allowing for larger penetrations of renewables. Advanced statistical methods are used to more accurately characterize the operational wind power output versus manufacturer’s power curve. This is essential for effective integration of wind power into the power systems. Four parametric and nonparametric models are applied to estimate the power curve of wind turbines based on the available operational wind power data. The results of this study suggest that the penalized spline regression method presents a better performance over the other analyzed methods. Finally, an experimental testing is performed in laboratory to show the proof of concept of the capacity degradation of used batteries of plug-in electric vehicles in stationary applications using a 25 kWh repurposed energy storage system obtained from a taxi fleet in their “as-is” condition. The proposed comprehensive framework herein presents an approach leading to a sustainable transportation system by providing low-cost renewable energy, and can be used as a gold standard to compare other policies like hydrogen energy technologies. / October 2015

Through interviews and writing sample analysis of two secondary students who are fan fiction writers, this article examines the tensions between curricular writing and extracurricular fan fiction writing. This study finds students have rich extracurricular writing lives, and they repurpose familiar practices from fan fiction writing for the classroom. This study further discusses the role of genre in effective repurposing. This study argues students who develop genre awareness repurpose their extracurricular writing more effectively to fulfill curricular assignments.

Lynching photographs and images of spectacle lynching were originally produced to commemorate and celebrate lynching. Through processes of rhetorical re-circulation and repurposing of lynching photographs by those in the anti-lynching movement, lynching and visual representations of it became socially unacceptable. The rhetorical strategies concerning the display of images of violence toward African Americans developed in the anti-lynching movement became one of the most important means of protesting civil rights violations in the United States. This study examines three cases of repurposing lynching photographs during the peak of the anti-lynching movement in the 1930’s. The first is the NAACP sponsored Art Commentary on Lynching. I examine four pieces of art in this exhibition that violate the conventions of lynching photography by representing the lynching in other visual mediums that allow the artists to manipulate the lynching scene. The second chapter examines the generation and circulation of an anti-lynching pamphlet featuring a photograph of the lynching of Rubin Stacy. The photograph is repurposed through the interaction of text and image in the pamphlet in a series of rhetorical questions, details of the case, and general information about lynching. The third case is the song, “Strange Fruit.” The song conjures an image through its use of ekphrasis, and suggests a particular reading of that image throughout the performance of the song. I focus on Billie Holiday’s rendition of the song, but draw conclusions about the song and its various performances and recordings. I argue that the use and manipulation of lynching photographs raised social consciousness and public awareness in opposition to spectacle lynching, and re-articulated the meaning of violence, and representations of violence, toward African Americans in the public sphere.

The traditional view of drug design is that a single drug should interact with a single molecular target. As science progressed, there was an understanding that most drugs interact with more than one target and that multiple targets may be responsible for either adverse effects or additional therapeutic effects. The idea of polypharmacology, which suggests that the focus of drug design should shift from a single drug that interacts with a single target to a single drug that can have interactions with multiple targets and multiple therapeutic effects, revolutionized the drug discovery process. Discovering new drugs is a long and costly process with years of research and development and clinical trials required before the drugs reach the market for much needed therapeutic applications. By repurposing drugs that are already on the market for a new therapeutic target, the discovery process is accelerated significantly. One such a target disease, for which there is a great need for new effective therapies, is Parkinson’s disease (PD). PD is a progressive neurodegenerative disease that is caused by the death of dopaminergic neurons in the substantia nigra with the resulting loss of dopamine from the striatum. Degeneration in PD leads to varying degrees of motor difficulty and disability, along with other symptoms. Current therapies are focussed on symptomatic management and an improvement of the quality of life of patients, rather than on a cure. There are several therapeutic targets that are currently used in the treatment of PD. One of those targets is the monoamine oxidase (MAO) enzymes, in particular the MAO-B isoform. The MAO enzymes are responsible for the metabolism of amine neurotransmitters, such as dopamine, and inhibition of MAO-B has proven to be an effective strategy to increase the dopamine levels in the brain. Clinically, selective MAO-B inhibitors are administered concurrently with levodopa (a precursor of dopamine) to increase the levels of dopamine derived from levodopa. This approach prolongs the beneficial effects of levodopa. Because MAO-A is responsible for the breakdown of noradrenalin, adrenalin, serotonin and tyramine, non-selective and selective MAO-A inhibitors have therapeutic applications in other neurological and psychiatric disorders such as depression. MAO-A inhibitors, particularly irreversible inhibitors, are also notable from a toxicological point of view. Irreversible MAO-A inhibitors may lead to potentially dangerous effects when combined with serotonergic drugs and certain foods containing tyramine, such as cheeses and processed meats. Selective MAO-B inhibitors and reversible MAO-A inhibitors appear to be free of these interactions. Based on the considerations above, this study aimed to identify clinically used drugs which also inhibit the MAO enzymes as a secondary pharmacological property. Such drugs may, in theory, be repurposed as MAO inhibitors for therapeutic use in the treatment of PD and depression. The identification of potential MAO-A inhibitory properties among clinically used drugs are of further importance since the irreversible inhibition of MAO-A may lead to dangerous effects when combined with certain drugs and foods. To screen clinically used drugs for potential MAO-A and MAO-B inhibitory activities, a pharmacophore approach was followed. A pharmacophore model is a virtual 3D representation of the common steric and electrostatic features of the interaction between an enzyme and a ligand. By identifying hydrogen bond acceptor, hydrogen bond donor and hydrophobic interactions between a reference ligand and an enzyme, a model is created that can search databases for other molecules that would have similar interactions with the enzyme and arguably also act as ligands. This enables the screening of a large amount of molecules in a short amount of time. To assist in the identification of MAO inhibitors, pharmacophore models of the MAO enzymes were constructed using the known crystallographic structures of MAO-A co-crystallized with harmine, and MAO-B cocrystallized with safinamide. The Discovery Studio® software package (Accelrys) was used for this purpose. In this study, virtual libraries of United States Food and Drug Administration (FDA) approved drugs and the United States Environmental Protection Agency (EPA) maximum daily dose databases were screened with pharmacophore models of MAO-A and MAO-B. Among the hits, 26 drugs were selected on the basis of availability and cost, and were subjected to in vitro bio-assays in order to determine their potencies (IC50 values) as inhibitors of recombinant human MAO-A and/or MAO-B. Among the drugs tested, 6 compounds exhibited inhibitory activity towards the MAO enzymes. Of the 6 compounds, pentamidine (IC50 = 0.61 μM for MAO-A and IC50 = 0.22 μM for MAO-B) and phenformin (IC50 = 41 μM for MAO-A) were selected for further analysis. An examination of the recoveries of the enzymatic activities after dilution and dialysis of the enzyme-inhibitor complexes showed that both pentamidine and phenformin interact reversibly with the MAO enzymes. A kinetic analysis suggests that pentamidine acts as a competitive inhibitor with estimated Ki values of 0.41 μM and 0.22 μM for the inhibition of MAO-A and MAO-B, respectively. An analysis of the available pharmacokinetic data and typical therapeutic doses of phenformin and pentamidine suggests that the MAO inhibitory potencies (and reversible mode of action) of phenformin are unlikely to be of pharmacological relevance in humans. Pentamidine, on the other hand, is expected to interact with both MAO-A and MAO-B at typical therapeutic doses. Because of its MAO-A inhibitory activity, pentamidine may thus, in theory, lead to a tyramine-associated hypertensive crisis when combined with tyramine-containing foods. However, pentamidine is unlikely to inhibit central MAO since it does not appear to penetrate the central nervous system to a large degree. In an attempt to gain further insight into the mode of binding to MAO, pentamidine and phenformin were docked into models of the active sites of MAO-A and/or MAO-B. An analysis of the interactions between the enzyme models and the ligands were carried out and the results are discussed in the dissertation. The results of this study show that the pharmacophore model approach may be useful in identifying existing drugs with potential MAO inhibitory effects. The search for new therapeutic MAO inhibitors, that can be used in the treatment of certain neurological disorders, including PD and depression, may be accelerated by employing a virtual screening approach. Such an approach may also be more cost effective than the de novo design of MAO inhibitors. / MSc (Pharmaceutical Chemistry), North-West University, Potchefstroom Campus, 2014

The traditional view of drug design is that a single drug should interact with a single molecular target. As science progressed, there was an understanding that most drugs interact with more than one target and that multiple targets may be responsible for either adverse effects or additional therapeutic effects. The idea of polypharmacology, which suggests that the focus of drug design should shift from a single drug that interacts with a single target to a single drug that can have interactions with multiple targets and multiple therapeutic effects, revolutionized the drug discovery process. Discovering new drugs is a long and costly process with years of research and development and clinical trials required before the drugs reach the market for much needed therapeutic applications. By repurposing drugs that are already on the market for a new therapeutic target, the discovery process is accelerated significantly. One such a target disease, for which there is a great need for new effective therapies, is Parkinson’s disease (PD). PD is a progressive neurodegenerative disease that is caused by the death of dopaminergic neurons in the substantia nigra with the resulting loss of dopamine from the striatum. Degeneration in PD leads to varying degrees of motor difficulty and disability, along with other symptoms. Current therapies are focussed on symptomatic management and an improvement of the quality of life of patients, rather than on a cure. There are several therapeutic targets that are currently used in the treatment of PD. One of those targets is the monoamine oxidase (MAO) enzymes, in particular the MAO-B isoform. The MAO enzymes are responsible for the metabolism of amine neurotransmitters, such as dopamine, and inhibition of MAO-B has proven to be an effective strategy to increase the dopamine levels in the brain. Clinically, selective MAO-B inhibitors are administered concurrently with levodopa (a precursor of dopamine) to increase the levels of dopamine derived from levodopa. This approach prolongs the beneficial effects of levodopa. Because MAO-A is responsible for the breakdown of noradrenalin, adrenalin, serotonin and tyramine, non-selective and selective MAO-A inhibitors have therapeutic applications in other neurological and psychiatric disorders such as depression. MAO-A inhibitors, particularly irreversible inhibitors, are also notable from a toxicological point of view. Irreversible MAO-A inhibitors may lead to potentially dangerous effects when combined with serotonergic drugs and certain foods containing tyramine, such as cheeses and processed meats. Selective MAO-B inhibitors and reversible MAO-A inhibitors appear to be free of these interactions. Based on the considerations above, this study aimed to identify clinically used drugs which also inhibit the MAO enzymes as a secondary pharmacological property. Such drugs may, in theory, be repurposed as MAO inhibitors for therapeutic use in the treatment of PD and depression. The identification of potential MAO-A inhibitory properties among clinically used drugs are of further importance since the irreversible inhibition of MAO-A may lead to dangerous effects when combined with certain drugs and foods. To screen clinically used drugs for potential MAO-A and MAO-B inhibitory activities, a pharmacophore approach was followed. A pharmacophore model is a virtual 3D representation of the common steric and electrostatic features of the interaction between an enzyme and a ligand. By identifying hydrogen bond acceptor, hydrogen bond donor and hydrophobic interactions between a reference ligand and an enzyme, a model is created that can search databases for other molecules that would have similar interactions with the enzyme and arguably also act as ligands. This enables the screening of a large amount of molecules in a short amount of time. To assist in the identification of MAO inhibitors, pharmacophore models of the MAO enzymes were constructed using the known crystallographic structures of MAO-A co-crystallized with harmine, and MAO-B cocrystallized with safinamide. The Discovery Studio® software package (Accelrys) was used for this purpose. In this study, virtual libraries of United States Food and Drug Administration (FDA) approved drugs and the United States Environmental Protection Agency (EPA) maximum daily dose databases were screened with pharmacophore models of MAO-A and MAO-B. Among the hits, 26 drugs were selected on the basis of availability and cost, and were subjected to in vitro bio-assays in order to determine their potencies (IC50 values) as inhibitors of recombinant human MAO-A and/or MAO-B. Among the drugs tested, 6 compounds exhibited inhibitory activity towards the MAO enzymes. Of the 6 compounds, pentamidine (IC50 = 0.61 μM for MAO-A and IC50 = 0.22 μM for MAO-B) and phenformin (IC50 = 41 μM for MAO-A) were selected for further analysis. An examination of the recoveries of the enzymatic activities after dilution and dialysis of the enzyme-inhibitor complexes showed that both pentamidine and phenformin interact reversibly with the MAO enzymes. A kinetic analysis suggests that pentamidine acts as a competitive inhibitor with estimated Ki values of 0.41 μM and 0.22 μM for the inhibition of MAO-A and MAO-B, respectively. An analysis of the available pharmacokinetic data and typical therapeutic doses of phenformin and pentamidine suggests that the MAO inhibitory potencies (and reversible mode of action) of phenformin are unlikely to be of pharmacological relevance in humans. Pentamidine, on the other hand, is expected to interact with both MAO-A and MAO-B at typical therapeutic doses. Because of its MAO-A inhibitory activity, pentamidine may thus, in theory, lead to a tyramine-associated hypertensive crisis when combined with tyramine-containing foods. However, pentamidine is unlikely to inhibit central MAO since it does not appear to penetrate the central nervous system to a large degree. In an attempt to gain further insight into the mode of binding to MAO, pentamidine and phenformin were docked into models of the active sites of MAO-A and/or MAO-B. An analysis of the interactions between the enzyme models and the ligands were carried out and the results are discussed in the dissertation. The results of this study show that the pharmacophore model approach may be useful in identifying existing drugs with potential MAO inhibitory effects. The search for new therapeutic MAO inhibitors, that can be used in the treatment of certain neurological disorders, including PD and depression, may be accelerated by employing a virtual screening approach. Such an approach may also be more cost effective than the de novo design of MAO inhibitors. / MSc (Pharmaceutical Chemistry), North-West University, Potchefstroom Campus, 2014

The number of known monogenic rare diseases (~7000) exceeds the number of effective treatments (~500) by more than an order of magnitude underlining the pressing need for generalizable therapeutic approaches for this class of conditions. In this regard, the majority of recessive and x-linked recessive disorders are caused by missense mutations encoding proteins that frequently have residual function but are rapidly degraded by the 26S proteasome. Bortezomib is a small molecule that inhibits the 26S proteasome and has been approved for use in patients for an unrelated condition; multiple myeloma. Previous work has shown that, for a small number of disorders, bortezomib can inhibit the degradation of the mutant protein, thereby increasing the protein level and activity, holding out the promise of a beneficial therapeutic effect by the repurposing of this agent. We present here a high level western blot based survey of nine recessive disorders to characterize the general effectiveness of such an approach. Thirteen patient fibroblast cell lines comprising 9 different diseases with 19 known mutations were selected on the basis of missense mutations protein expression data when available. The cell lines were incubated with bortezomib (10 nM and 50 nM; 24 hrs) and levels of the mutated protein were quantified by western blot. Unfortunately, no consistent, appreciable increase was observed for any of the conditions tested. The general therapeutic value of re-purposing bortezomib for recessive and x-linked diseases appears limited at best. The few reported cases of bortezomib successfully working in increasing mutated protein levels appear to be the exceptions and not the norm. Moreover successes are more often limited to cell lines carrying a transgene expressing the mutated protein rather than endogenous mutated protein in patient cell lines.

Chronic obstructive pulmonary disease (COPD) is a progressive lung disease characterized by breathlessness due to airflow obstruction. COPD is the third leading cause of death worldwide. So far, none of the existing pharmacological treatments for COPD can stop the progressive decline in lung function. Drug repurposing is the application of existing approved therapeutic compounds for new disease indications, which may reduce the cost and time of new drug development. So far, there is not any systematic multi-omics data integration for drug repurposing in COPD. The goal of this project is to develop a systems biology pipeline for the identification of biological-relevant gene targets with drug repurposing potential for COPD treatment using multi-omics integration. Here we implemented a computational methodology to identify drug repurposing targets for COPD. We integrated multi-omics COPD data including, genome, transcriptome, proteome, metabolome, interactome data, and drug-target information. A distance-based network model was created to rank the potential candidate genes. Fifty genes were prioritized as COPD signature genes for their overall proximity to signature genes identified at all omics levels. Forty of them may be considered as “druggable” targets. Literature search reported CRCX4 – Plerixafor as one prioritized targets-gene pair for drug repurposing. The bone marrow stimulant Plerixafor is currently being evaluated for COPD treatment in clinical trials, suggesting that our pipeline is finding promising drug repurposing targets. Our work, for the first time, applied a systematic approach integrating multiple omics data to find drug repurposing targets for COPD. / Pharmaceutical Sciences

This dissertation argues that Digital Natives, rather than employing novel ways of thinking (such as those suggested by Walter Ong's concept of Second Orality), are in fact employing a way of thinking that has always existed: repurposing. Ruth Oldenziel discusses how, historically, women used "a kind of mental quality" enabling them to re-use objects in novel ways to accomplish more of life's tasks. My research led me to investigate how a wide variety of people, especially historically marginalized people, used this kind of mental quality. This dissertation explores repurposing's real world uses as well as its uses in narratives, specifically dystopia and apocalyptic narratives. Within these narratives, repurposing plays a similar role to repurposing in the real world, filling the gap between a survival mode of life and a science/technology driven society. The last part of this dissertation explores the place of repurposing among a myriad of current concepts concerning creativity.