Aspergillus fumigatus is a globally present pathogen capable of inflicting debilitating and life-threatening opportunistic infections in individuals, primarily those who are immunocompromised. Diagnosing A. fumigatus infections is often difficult, leading to a delay in treatment which can greatly impact patient outcomes. Furthermore, our lessening of antifungal development combined with increasing resistance generates a feasible scenario where only last resort options are viable. This has prompted the World Health Organization (WHO) to declare this pathogen a "critical priority" due to increased resistance and rising mortality rates. Azoles are utilized as primary treatment options for Aspergillus fumigatus infections such as voriconazole (VRC), itraconazole (ITC), and posaconazole (POS) with a reserve of Amphotericin B (AmB). In the past two decades, the emergence of resistance to azoles has contributed to a 90% mortality rate in resistant cases globally. In this report, we investigated the MedChem Express (MCE) Drug Repurposing Compound Library (4,226 compounds) in conjunction with itraconazole at 0.06 µg/mL against A. fumigatus CDC #738. After the initial screening, we identified compounds known to be antifungals or antiseptics and deselected them. The remaining thirty selected compounds were evaluated through published literature and clinical trial data to determine those candidates with favorable characteristics/properties. Criteria for candidate selection consisted of evaluating the compounds; plasma concentration peak, the time to reach peak, protein binding, oral availability, and drug class. Six candidates were ranked the highest of the previous round –surprisingly 50% of those compounds were HIV drugs, cobicistat, elvitegravir, lopinavir. The remaining three selected compounds are penfluridol, rilapladib, and rolapitant. The combination of itraconazole (ITC), posaconazole (POS), and voriconazole (VRC), with the identified compounds demonstrated promising amounts of synergy, in resistant and susceptible isolates. Further investigation revealed novel properties of ITC and POS when in combination with our compounds of interest. Rilapladib was able to reverse POS, ITC, and VRC resistant strain(s) to a sensitive profile. Growth kinetic assays demonstrate potent anti-germination properties not seen before in the sub-inhibitory doses of azoles. This work demonstrates that high-throughput screening as a viable technique to identify robust antifungal synergizers, allowing for tenable translation to a clinical setting. / Master of Science / Aspergillus fumigatus is a worldwide fungal organism capable of causing disease, particularly in immunocompromised individuals. Infections primarily occur when individuals inhale spores that can remain dormant until the person's immune system is weakened, via disease, cancer, or prescribed drug for surgery. When the immune system is weakened, the spores are more effective at lung colonization. Aspergillus fumigatus infections can be combatted with voriconazole (VRC), itraconazole (ITC), or posaconazole (POS). However, in the past two decades, some fungi have started to develop resistance to azoles, necessitating the use of amphotericin B (AmB), a highly intolerable and final treatment option. In this report, we challenged A. fumigatus CDC isolate #738 with compounds from the MedChem Express (MCE) Drug Repurposing Compound Library (4,226 compounds) with itraconazole at 0.06 µg/mL, an ineffective concentration. We selected combinations and compounds that negated 90% of fungal growth those combinations that contained a known antifungal or antiseptic agent; once identified we deselected any known antifungal or antiseptic agents. The remaining selected compounds were evaluated for favorable drug properties, by reviewing published literature and clinical reports to determine those candidates with favorable characteristics/properties. The combination of ITC, POS, and VRC with the identified compounds demonstrated antifungal enhancement in resistant and susceptible isolates. We observed the reversal of resistance to POS, ITC, and VRC in several isolates when the drug combinations were applied. This demonstrates the importance of evaluating approved and under current review drugs to identify novel properties to aid our dwindling number of effective antifungals. This study provides promising combinational therapies for further evaluation in combating resistant A. fumigatus infections.

Neisseria gonorrhoeae, the causative agent of gonorrhea, is the second most prevalent sexually transmitted infection that leads to substantial morbidity and economic burden worldwide. Improperly treated or untreated gonorrhea can lead to severe and life-threatening complications, including abortion, infertility, pelvic pain, and maternal death. Neisseria gonorrhoeae has developed resistance to the formally and currently used antibiotics. The Centers for Disease Control and Prevention (CDC) have listed multi-drug resistant N. gonorrhoeae as an urgent threat that promptly requires the development of novel therapeutic agents. Traditional drug discovery and development is a time-consuming and costly process associated with high risks. To address the dire need to replenish the dry pipeline of anti-gonorrhea medications, drug repurposing is a promising approach. In this study, an FDA-approved drug library was screened, and 14 drugs were found to exhibit promising anti-gonococcal activity. Interestingly, three extremely potent and narrow-spectrum novel candidates, itraconazole, isavuconazole, and ravuconazole, are azole antifungals, and their activities were further investigated in vitro. Of the three azoles, ravuconazole displayed the most potent activity against N. gonorrhoeae clinical isolates. The time-kill assay revealed that the three azoles showed bactericidal activity. All three azole drugs showed a low frequency of resistance. Besides, isavuconazole and ravuconazole have a longer post-antibiotic effect than azithromycin. All three azoles cleared the burden of intracellular N. gonorrhoeae completely, which is superior to ceftriaxone. In conclusion, itraconazole, isavuconazole, and ravuconazole merit future investigation for the development of anti-gonorrheal therapeutics. This study provided unexplored avenues and promising opportunities that can be further evaluated to combat N. gonorrhoeae infection. / Master of Science / Neisseria gonorrhoeae, the causative agent of gonorrhea, is the second most prevalent sexually transmitted infection that leads to substantial morbidity and economic burden worldwide. Improperly treated or untreated gonorrhea can lead to severe and life-threatening complications, including abortion, infertility, pelvic pain, and maternal death. Due to the increasing prevalence of drug resistance against the formally and currently used antibiotics, the Centers for Disease Control and Prevention (CDC) have classified multi-drug resistant N. gonorrhoeae as an urgent-threat pathogen. Therefore, the discovery of new anti-gonorrheal therapeutics is an urgent need. Drug repurposing is the process of discovering new therapeutic uses for approved or investigational drugs that go beyond the original medical indication. To address the dire need to replenish the dry pipeline of anti-gonorrheal drugs, repurposing FDA-approved drugs is a promising approach as it significantly reduces the time and expense associated with traditional drug development. By screening an FDA-approved drug library, 14 drugs were found to display promising anti-gonococcal activity. Interestingly, three (itraconazole, isavuconazole, and ravuconazole) out of 14 identified drugs were azole antifungal drugs, and their activities were further investigated in vitro. All three azole drugs showed bactericidal activity, meaning that they killed bacteria, had a low propensity to develop resistance, and completely cleared the burden of intracellular N. gonorrhoeae. Besides, our findings suggested that isavuconazole and ravuconazole possessed exceptional activity in the suppression of bacterial growth following brief antibiotic exposure. In conclusion, the three azole drugs exhibited potent anti-gonococcal activity and merited further investigation. This study provided unexplored avenues and promising opportunities that can be further evaluated to combat multidrug-resistant N. gonorrhoeae. Neisseria gonorrhoeae, the causative agent of gonorrhea, is the second most prevalent sexually transmitted infection that leads to substantial morbidity and economic burden worldwide. Improperly treated or untreated gonorrhea can lead to severe and life-threatening complications, including abortion, infertility, pelvic pain, and maternal death. Due to the increasing prevalence of drug resistance against the formally and currently used antibiotics, the Centers for Disease Control and Prevention (CDC) have classified multi-drug resistant N. gonorrhoeae as an urgent-threat pathogen. Therefore, the discovery of new anti-gonorrheal therapeutics is an urgent need. Drug repurposing is the process of discovering new therapeutic uses for approved or investigational drugs that go beyond the original medical indication. To address the dire need to replenish the dry pipeline of anti-gonorrheal drugs, repurposing FDA-approved drugs is a promising approach as it significantly reduces the time and expense associated with traditional drug development. By screening an FDA-approved drug library, 14 drugs were found to display promising anti-gonococcal activity. Interestingly, three (itraconazole, isavuconazole, and ravuconazole) out of 14 identified drugs were azole antifungal drugs, and their activities were further investigated in vitro. All three azole drugs showed bactericidal activity, meaning that they killed bacteria, had a low propensity to develop resistance, and completely cleared the burden of intracellular N. gonorrhoeae. Besides, our findings suggested that isavuconazole and ravuconazole possessed exceptional activity in the suppression of bacterial growth following brief antibiotic exposure. In conclusion, the three azole drugs exhibited potent anti-gonococcal activity and merited further investigation. This study provided unexplored avenues and promising opportunities that can be further evaluated to combat multidrug-resistant N. gonorrhoeae.

The Norrbotnia Line Dance project focuses on the expansion and densification of Piteå, a small city in northern Sweden. To accommodate the expected population growth, the thesis explores interventions to urban sprawl by reorganizing existing buildings along Kyrkbrogatan, a main street in the city. The interventions proposed are: "Repurposing," which integrates a train station within a supermarket; "Addition," involving a shift and addition of a public building to enhance its urban presence; and "Relocation," relocating a villa to a new site and utilizing its space for apartment buildings. Through the exploration of architectural expressions and the integration of dualities, the interventions propose innovative solutions that contribute to the city's future growth and development while preserving its unique identity. By seeing buildings as free of its site the project aims to counter urban sprawl and promote a sustainable urban fabric. Drawing inspiration from Piteå's history, including its Roman-influenced city plan and previous relocations of buildings. From residential, the relocation, my thesis Norrbotnia Line Dance moves along Kyrkbrogatan through Public Offices, shifting and adding towards the beginning and end of the city at the Train Station, with its repurposing, while facing the issues of continuity as we go down the line.

京都大学 / 0048 / 新制・課程博士 / 博士(薬科学) / 甲第22752号 / 薬科博第126号 / 新制||薬科||14(附属図書館) / 京都大学大学院薬学研究科薬科学専攻 / (主査)教授 金子 周司, 教授 土居 雅夫, 教授 竹島 浩 / 学位規則第4条第1項該当 / Doctor of Pharmaceutical Sciences / Kyoto University / DFAM

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Ces travaux de thèse s’intéressent à une stratégie de fin de vie naissante : le repurposing. Nous le définissons comme un processus industriel par lequel des produits en fin d’usage sont réutilisés dans des applications distinctes. À la fin de leur premier usage, les produits sont réintégrés dans la chaine industrielle en vue d’une nouvelle utilisation dans une autre application. On parle également d’utilisations en cascade. Le but avoué est la conservation de la valeur-ajoutée des produits, aussi longtemps que possible. Cette stratégie s’inscrit aux côtés d’autres stratégies de réutilisation plus connues telles que le réemploi et le remanufacturing.L’illustration principale de la littérature, qui constitue également notre terrain d’étude, concerne les batteries au lithium. Utilisées initialement dans les véhicules électriques, elles sont aujourd’hui recyclées lorsque leurs capacités de stockage diminuent de 20 à 30%. Prolonger leur durée de vie par une seconde application, e.g. un usage stationnaire, permettrait de différer les étapes de recyclage tout en maximisant le maintien de la valeur ajoutée lors de la fabrication. Malgré ces avantages, les exemples de transformations de produits pour des applications en cascade restent à l’état de démonstrateurs, en particulier parce qu’aujourd’hui ces produits et leur chaine de valeur ne sont pas conçus avec des stratégies supportant leur réutilisation.L’objectif de ces travaux est d’apporter aux équipes de conception une vision claire de ce qu’est la stratégie de réutilisation en cascade, de comment l’intégrer lors des étapes amont du processus de conception et de guider l’évaluation environnementale correspondante, afin de les accompagner pour une réelle industrialisation des produits repurposés. En ce sens, nous émettons trois propositions.La première consiste en une classification des caractéristiques propres aux solutions en cascade selon trois axes : le produit, le processus de (re)fabrication et le modèle d’affaire envisagé. À travers ce cadre, nous décrivons les dimensions et les caractéristiques des offres de produits repurposés. Elles sont alors utilisables pour l’établissement de compromis dès les phases amont de conception. Celles-ci sont issues d’une étude bibliographique couplée à des études de terrain.Notre deuxième proposition concerne le processus de conception de tels produits. En effet, plusieurs spécificités sont à prendre en compte en comparaison d’une activité de conception classique : récupération du produit en fin d’usage, applications ultérieures pas ou peu définies, besoins flous, usage influençant les performances, etc. Une étape de conception pour les produits repurposés devra donc être intégrée en amont du processus de repurposing afin d’optimiser les solutions ultérieures. En complément, plusieurs recommandations pour la conception d’un produit repurposé sont formulées. Intégrées au plus tôt, elles visent à faciliter la réutilisation des produits en tenant compte des parties-prenantes, des phases du cycle de vie, des aspects temporels et en gérant mieux l’information.Enfin, un cadre générique structurant la réalisation d’analyses du cycle de vie de ces solutions est proposé. Les ACVistes pourront ainsi plus facilement tenir compte des spécificités de ces stratégies, car la complexité des modélisations ACV pour les produits aux applications en cascade nécessite davantage de rigueur et de précision que pour des produits à application unique. Pour supporter ce cadre, trois recommandations à destination des équipes de conception sont émises. Elles permettent la formalisation d'éléments de contexte pour améliorer la comparaison avec d’autres études et d’informations en vue des analyses de sensibilité.Ces trois propositions sont implémentées sur deux cas d’étude ‘batterie’, au cours de séances de travail regroupant des parties-prenantes de l’ensemble du cycle de vie : commanditaire, équipes de conception, logisticiens, recycleur, etc. / This PhD dissertation focuses on an innovative end-of-life strategy: repurposing. We define ‘repurposing’ as a manufacturing process through which products nearing their end-of-life are reused in different applications. At the end of their intended use, products are reintegrated into the manufacturing chain and adapted for their next application. We also refer to this strategy as cascading application reuse (CAR). The main purpose of CAR is the preservation of the added-value of such products. This strategy is in line with other reuse strategies such as direct reuse and remanufacturing.The central illustration in our case study addresses lithium-ion batteries used in electric vehicles, which are recycled when the battery’s charging capacity falls below 80%. Extending the component lifespan with a second application, e.g. stationary application, postpones introduction into the waste stream, retaining the added-value from the original manufacturing process. Despite these advantages, examples of product adaptation for CAR remain at a proof-of-concept scale - currently these products and their value chains are not yet designed with strategies supporting reuse.The objective of this research is to provide a clear vision to design teams about repurposing strategies, how to integrate the strategies during the upstream stages of the design process and how to facilitate the corresponding lifecycle assessment. The objective is to support designers during the manufacturing of repurposed products. We make three proposals.The first consists of classifying the characteristics specific to the repurposing strategy according to three axes: the product, the (re)manufacturing process and the business model. Through this framework, we describe the dimensions and characteristics of what the repurposed product offers, which are integral during the design activity. These attributes are the result of a study of the relevant literature coupled with several field investigations.Our second proposal concerns the design process for such products. Indeed, several differences with classical design practices appear: the need for product recovery at the end of use, subsequent applications and needs not fully defined, which affect performance, etc. A design stage for repurposed products must therefore be integrated before subsequent applications in order to optimise redesign solutions. Integrated as early as possible, they aim to facilitate product reuse by taking into account stakeholders, life cycle phases, time aspects and better information management.Finally, a generic framework structuring the carrying out of life cycle analyses of repurposing is proposed. This will simplify the inclusion of their specificities for life cycle assessments (LCA) practitioners. Indeed, the complexity of LCA modelling for cascading applications products requires more rigour and precision than single application products. To support this framework, three recommendations for design teams are made, the objective of which is to better formalise the information from the design process. These recommendations support the formalisation of contextual elements to improve comparison with other studies and the organisation of information for sensitivity analyses.These three proposals are implemented on two battery case studies, during working sessions involving stakeholders representing the complete life cycle: sponsor, design teams, logisticians, recycler, etc.

Recent attempts to reprogram a Roomba to be used as a simple agent have led to interesting behavior. Observation has shown that the behavior of the Roomba is not only dependent on the precepts of the Roomba, but also relies heavily on the uncontrollable environmental conditions that the Roomba is placed in. Ultimately this makes the Roomba a great platform to test and teach aspects of artificial intelligence. This paper will show how most of the tested environmental conditions are mitigated by a learning agent that will adjust behavior dependent on the precepts that are received.

A quimioterapia disponível para o tratamento das leishmanioses conta com um número reduzido de fármacos, com efeitos adversos severos e progressivo aumento de resistência. O reposicionamento de fármacos oferece uma grande oportunidade para introdução de novas terapias. Antidepressivos orais têm demonstrado eficácia tanto in vitro quanto in vivo contra espécies de Leishmania spp. Neste estudo, o antidepressivo sertralina (SRT), e o fármaco ciclobenzaprina (CBP), um relaxante muscular de estrutura tricíclica análoga a antidepressivos, foram avaliados quanto a atividade contra Leishmania (L.) infantum. Estudos metabolômicos não dirigidos utilizando multiplataforma analítica, foram combinados a análises de parâmetros celulares, essenciais para obtenção de uma ampla descrição dos mecanismos de ação. A CBP mostrou uma atividade leishmanicida in vitro, com valor de CE50 de 4,3 ?M contra formas promastigotas e 8,6 ?M contra formas amastigotas intracelulares. O fármaco apresentou uma citotoxicidade (CC50) de 70,6 ?M em células NCTC, e um índice de seletividade similar a miltefosina. Os estudos de mecanismo de ação, sugeriram que a CBP se difunde pela membrana plasmática, causando diminuição do ??p e no interior citoplasmático, parece induzir um estresse do RE com liberação de Ca+2; concomitantemente, induz um desacoplamento brando da cadeia respiratória mitocondrial e depleção dos níveis de ATP. Com o efeito prolongado, a liberação de Ca+2 parece ativar a autofagia, e seu influxo para a mitocôndria potencializar os efeitos deletérios, diminuindo o ??m e aumentando a produção de ROS. A longo prazo, o CBP induz uma extensa alteração metabólica, caracterizada aumento dos níveis da maioria dos metabólitos identificados e atividade desregulada de transportadores de membrana, gerando alto gasto energético associado a condições insuficientes de produção de energia mitocondrial, resultando em morte celular. A sertralina também apresentou atividade leishmanicida in vitro, com valor de CE50 de 2 ?M contra formas promastigotas e 3,9 ?M contra formas amastigotas intracelulares. Sua toxicidade em células NCTC foi de 19,6 ?M, resultando em um índice de seletividade similar a miltefosina. Nossos estudos confirmaram a mitocôndria de Leishmania como alvo primário e, o efeito de desacoplamento da cadeia respiratória associado ao colapso energético, estresse oxidativo seguido da despolarização do ??m como a possível origem desta disfunção mitocondrial. Estudos metabolômicos evidenciaram que a extensão do desarranjo metabólico, abrange diminuição da capacidade de detoxificação do metabolismo tiol-redox, uma severa depleção do pool intracelular de aminoácidos e poliaminas, evidenciando uma completa deterioração do metabolismo energético, por meio de um mecanismo multialvo direcionado a vias metabólicas essências do parasita. Finalmente, este estudo descreve a atividade anti-Leishmania de dois fármacos orais aprovados, com mecanismos de ação letais e irreversíveis no parasita, encorajando o prosseguimento para futuros estudos pré-clínicos na leishmaniose visceral americana / The available chemotherapy for the treatment of leishmaniasis has a reduced number of drugs, with severe adverse effects and progressive increase of resistance. The drug repurposing offers a great opportunity for the introduction of new therapies. Oral antidepressants have been demonstrated efficacy both in vitro and in vivo against Leishmania spp. In this study, the antidepressant sertraline (SRT), and the drug cyclobenzaprine (CBP), a muscle relaxant with tricyclic structure analogous to antidepressants, were evaluated against Leishmania (L.) infantum. Untargeted metabolomic studies using multiplataform analysis were combined to cellular parameters to a broad description of the mechanisms of action. Cyclobenzaprine showed an in vitro leishmanicidal activity with an EC50 value of 4.3 ?M against promastigotes and 8.6 ?M against intracellular amastigote forms. The drug showed a cytotoxicity (CC50) of 70.6 ?M in NCTC cells, and a selectivity index similar to miltefosine. Mechanism of action studies suggested that CBP diffuses through the plasma membrane, causing a decrease of the ??p and inside the cytoplasm, the drug seems to induce an ER stress, with release of Ca+2; concomitantly, it induces a mild decoupling of the mitochondrial respiratory chain and depletion of ATP levels. With the prolonged effect, a release of Ca+ 2 appears to activate an autophagy, and its mitochondrial influx results in a potentiation of deleterious effects as decreasing of ??m and increasing ROS production. In long term, CBP induces an extensive metabolic alteration, characterized increased levels of most of the identified metabolites and unregulated activity of membrane transporters. These generates a high energy expenditure associated to limited conditions of mitochondrial energy production, resulting in the cellular death. Sertraline also showed in vitro leishmanicidal activity, with an EC50 value of 2 ?M against promastigotes and 3.9 ?M against intracellular amastigote forms. Its toxicity in NCTC cells was 19.6 ?M, resulting in a selectivity index similar to miltefosine. Our studies confirmed the mitochondria of Leishmania as the primary target, and the uncoupling of the respiratory chain associated with energy collapse, oxidative stress, and the depolarization of ??m as the possible origin of this mitochondrial dysfunction. Metabolomics evidenced an extended metabolic disarray caused by SRT encompassing a decrease in the scavenging capacity of the thiol-redox metabolism and a severe depletion of the intracellular pool of amino acids and polyamines. The complete deterioration of energetic metabolism was evident through a multi-target mechanism, affecting the main metabolic pathways of the parasite. Finally, this study describes an anti-Leishmania activity of two approved oral drugs with lethal and irreversible mechanisms of action in the parasite, encouraging future preclinical studies in American visceral leishmaniasis.

Healthcare big data are a growing source of real-world data with which to identify and validate medications with repurposing potential. Previously, we developed a claims-based workflow to evaluate medications with potential to treat stimulant use disorders. In order to test the workflow, the framework was applied in the context of opioid use disorders (OUDs), for which there are medications with known efficacy. Using the Truven Marketscan Commercial Claims Database, a nested case-control analysis was conducted to determine the association between OUD medications (buprenorphine, naltrexone) and remission. Cases were defined as enrollees with a remission diagnosis and matched (1:4) to controls (individuals without remission) using incidence density sampling, with age group, sex, region, and index year as additional matching variables. After adjusting for behavioral health visits, polysubstance use disorders, and psychiatric disorders using conditional logistic regression, the odds of OUD medication exposure were 3.8 (99% confidence interval: 3.0 – 4.9) times higher in cases than controls. Evaluation of angiotensin converting enzyme inhibitors (e.g. lisinopril) as a negative control revealed no significant association between the medication and remission. This work demonstrates the feasibility of using administrative health claims data to evaluate the effectiveness of medications to treat substance use disorders.

Drugs exert their (therapeutic) effects via molecular-level interactions with proteins and other biomolecules. Computational prediction of drug-protein interactions plays a significant role in the effort to improve our current and limited knowledge of these interactions. The use of the putative drug-protein interactions could facilitate the discovery of novel applications of drugs, assist in cataloging their targets, and help to explain the details of medicinal efficacy and side-effects of drugs. We investigate current studies related to the computational prediction of drug-protein interactions and categorize them into protein structure-based and similarity-based methods. We evaluate three representative structure-based predictors and develop a Protein-Drug Interaction Database (PDID) that includes the putative drug targets generated by these three methods for the entire structural human proteome. To address the fact that only a limited set of proteins has known structures, we study the similarity-based methods that do not require this information. We review a comprehensive set of 35 high-impact similarity-based predictors and develop a novel, high-quality benchmark database. We group these predictors based on three types of similarities and their combinations that they use. We discuss and compare key architectural aspects of these methods including their source databases, internal databases and predictive models. Using our novel benchmark database, we perform comparative empirical analysis of predictive performance of seven types of representative predictors that utilize each type of similarity individually or in all possible combinations. We assess predictive quality at the database-wide drug-protein interaction level and we are the first to also include evaluation across individual drugs. Our comprehensive analysis shows that predictors that use more similarity types outperform methods that employ fewer similarities, and that the model combining all three types of similarities secures AUC of 0.93. We offer a first-of-its-kind analysis of sensitivity of predictive performance to intrinsic and extrinsic characteristics of the considered predictors. We find that predictive performance is sensitive to low levels of similarities between sequences of the drug targets and several extrinsic properties of the input drug structures, drug profiles and drug targets.