The serine hydrolase (SH) enzyme superfamily is one of the largest and most diverse enzyme classes in eukaryotes and prokaryotes. The most virulent human malaria parasite Plasmodium falciparum has over 40 predicted serine hydrolases (SH). Prior investigation on a few of these have suggested their critical role in parasite biology. The majority of the SHs in P. falciparum have not been functionally characterized. Investigation of these uncharacterized SHs will provide new insights into essential features of parasite metabolism and possibly lead to new antimalarial targets. In this study, we have employed activity-based protein profiling (ABPP) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to functionally characterize SHs. In our effort to profile plasmodial SHs using ABPP, we have identified a human erythrocyte SH, acylpeptide hydrolase (APEH) in the developing parasites. This finding is the first report of internalization of host hydrolytic enzyme by the parasite. Treatment of parasites with an APEH specific triazole urea inhibitor, AA74-1, caused growth inhibition in parasites with poor potency in the first replication cycle, however, the potency dramatically increased in the second cycle. We show that this unique growth inhibition profile is due to the inability of AA74-1 to inhibit parasite-internalized APEH in vivo. These findings suggest that internalization of active APEH by the parasite is essential for parasite survival. Lipases catalyze the hydrolysis of ester bonds of lipid species such as neutral lipids and phospholipids. Although roles of lipases in propagation, as well as virulence in various organisms, have been acknowledged, in P. falciparum lipases remain understudied. We combined LC-MS/MS with the SH-directed ABPP to identify lipases of SH superfamily in P. falciparum. We have identified 16 plasmodial SHs with putative lipase activity. Bioinformatics analysis of our identified lipases is consistent with our findings. We have screened a panel of various classes of SH inhibitors in a competitive ABPP. A plasmodial putative lipase was potently and specifically inhibited by human monoacylglycerol lipase inhibitor. This inhibition profile suggests it as a monoacylglycerol lipase which plays a role in releasing fatty acids from neutral lipid. This finding shows that how inhibitor screening can aid in building hypotheses on biological roles of an enzyme. Altogether, in this dissertation, we have presented a robust strategy of identifying and functionally characterizing SHs in P. falciparum, which opens the door to the discovery of new biological processes. / Doctor of Philosophy / Malaria contributed to nearly a half a million deaths in 2017. The vast majority of malaria-related deaths are due to the parasite Plasmodium falciparum. This parasite resides inside human red blood cells (erythrocytes) and grows rapidly during a 48 hour cycle. There are over 40 serine hydrolase (SH) superfamily proteins in the parasite. Biological functions of the majority of SHs in the parasite remains unknown. Study on these SHs will provide new insights into parasite biology, and possibly present new antimalarial drug targets. We used chemical biology techniques to identify and functionally characterize parasite SHs. In one study, we show the parasite intenalized a human erythrocyte SH, acylpeptide hydrolase (APEH). We used an APEH-specific inhibitor to investigate the biological significance of internalized APEH in parasite biology. Treatment of the parasite with the inhibitor resulted in parasite growth inhibition suggesting internalization of APEH is essential for parasite survival. Lipases are enzymes that aid in break down of lipids and have shown to be crucial for growth and pathogenicity in various organisms. Lipases and lipid catabolism remain understudied in the malaria parasite. We used mass spectrometry in our approach to identify 16 lipases in asexual parasites. We have also shown that screening with highly specific inhibitors can help in predicting biological function of a particular enzyme. In summary, in this body of work, we have presented an approach of studying SHs in the malaria parasite, which will provide new insights into parasite biology.

Despite our growing knowledge of virus biology they continue to present a problem to global public health. This problem arises from their high mutation rates that allow them to evade antiviral therapies that we have developed to date. An alternative solution for developing antiviral therapies could be to target host cell factors that are hijacked by the virus. The basis of this hypothesis is that if we can stop the virus from using host cell machinery or from evading host immune mechanisms we could treat the infection more efficiently. With the major research focus being on viral proteins and how we can prevent their functions, there is a lot of work to be done in finding host factors that could be the key to treating an infection. The three themes presented in this thesis broadly focus on this goal. The first theme looks at miRNAs, their interacting partners, and their dysregulation during HCV infection. A microRNA is identified from a small molecule screen of miRNAs that are dysregulated during HCV infection and its role in liver immunometabolism is examined to determine its antiviral potential and identify host factors that could be of interest to target with antiviral therapeutics. The second theme examines the potential of activity-based protein profiling techniques for complementing existing antiviral therapies. An azauracil probe is characterized to examine its ability to interact with viral polymerases and its suitability as a building block for antiviral research or therapies. The final theme uses activity-based protein profiling techniques to study a novel carbamate-hydrazone chemotype and establish its suitability as a chemical probe. The hydrazone probe’s reactivity with the mammalian proteome was determined and its interacting partners were identified using chemoproteomic techniques with an overall goal of examining its suitability for antiviral research. Overall, this thesis uses chemical and molecular biology techniques to present three differing perspectives on how to approach the discovery of host factors and develop novel antiviral therapies.

La tuberculose (TB) reste la maladie infectieuse la plus meurtrière au monde. L’absence de développement de médicaments accompagnée de l'émergence de la résistance aux molécules existantes se traduit principalement par l'échec du traitement et la mort. M. tb infecte l'homme par l'inhalation. Le patient peut rester en bonne santé sans aucun symptôme, on parle alors de tuberculose latente. Dans ce cas, la bactérie résider dans le macrophage. La principale caractéristique de M. tb est de rester cacher à l'intérieur de ces cellules, puis se réactiver lorsque le système immunitaire s’affaibli.Mon travail a été consacrée à l'étude de nouveaux analogues de Cyclophostin / Cyclipostins (CyCs) et Oxadiazolone. Nombreuses molécules présentaient des activités antibactériennes lorsque la bactérie était cultivée dans le milieu liquide ou à l'intérieur du macrophage sans aucun effet toxique sur les macrophages.En utilisant le meilleur inhibiteur de CyC17, nous avons identifié 23 protéines cibles potentielles, étant impliquées dans le métabolisme des lipides de M. tb et / ou dans la biosynthèse des lipides de la paroi cellulaire. Parmi ces cibles, Ag85C et TesA, ont été caractérisées biochimiquement et structurallemnent.De plus, nous avons établi que les CyC sont des inhibiteurs puissants et sélectifs de la croissance des mycobactéries. De manière intéressante, ces composés étaient également actifs contre de nombreuses souches cliniques de M. abscessus, un pathogène opportuniste également appelés « cauchemars pour les antibiotiques », ouvrant ainsi la voie à la recherche de solutions alternatives pour lutter contre les souches mycobactériennes résistantes. / Tuberculosis (TB) is one of the deadliest infectious diseases worldwide. The stagnation in drug development accompanied with the emergence of drug resistance mainly results in treatment failure and death. M. tb infect human through inhalation. Patient can remains healthy without any symptom in which case it is known as latent TB. In latent TB, the bacteria is known to be reside in the macrophage - a type of white blood cell of the immune system, that engulfs and digests infected microorganisms. The famous characteristic of M. tb is the ability to stay inside and avoid to be killed by these cells, then reactivate when the immune system is weak.My work was devoted to the study of two series of new compounds, namely analogs of Cyclophostin/Cyclipostins (CyCs) and Oxadiazolone (OXs). Many molecules exhibited antibacterial activities when the bacteria was grown in the liquid medium or inside the macrophage without any toxic effect to the macrophages.Using the best CyC17 inhibitor, we identified 23 potential candidate target proteins, being involved in M. tb lipid metabolism and/or in cell wall lipid biosynthesis. Among these targets, two important protein, i.e. Ag85C and TesA, were biochemically and structurally characterized.Moreover, we clearly established that the CyCs are powerful and selective growth inhibitors of mycobacteria, with no effect on Gram-negative or Gram-positive bacteria. Interestingly, these compounds were also active against numerous M. abscessus clinical strains, an opportunistic pathogens also called “nightmare for antibiotic”, thus opening the way to find alternative solutions to fight against resistant mycobacterial strains.

Herkömmliche Zytostatika greifen vornehmlich in den Zellzyklus ein und somit werden Zellen mit hoher Proliferationsrate geschädigt. Allerdings fallen hierunter nicht ausschließlich Krebszellen, sondern auch gesunde, schnell proliferierende Gewebearten. Auf Grund dessen verursacht eine klassische Chemotherapie schwerwiegende Nebenwirkungen. Neuere Therapieansätze greifen daher geno- sowie phänotypischer Unterschiede zwischen malignen und gesunden Zellpopulationen auf und können selektiv den zytotoxischen Wirkstoff in die Tumorpopulation einbringen. Dazu werden sogenannte Prodrug-Konzepte verfolgt, bei denen ein möglichst „untoxisches” Prodrug gezielt im entarteten Gewebe enzymatisch zum zytotoxischen Wirkstoff (Drug) aktiviert wird. In diesem Rahmen werden Substrate für die Antibody-Directed Enzyme Prodrug Therapy (ADEPT) hergestellt. Bei diesem Konzept wird eine hohe Tumorspezifität durch Konjugate aus Enzymen und Antikörpern erlangt, indem das Immunglobulin selektiv an tumorassoziierte Antigene bindet und durch das konjugierte Enzym die Drugfreisetzung ermöglicht wird. Die natürlichen zytotoxischen Antibiotika (+)-CC 1065 und (+)-Duocarmycin SA dienen hierbei als Leitstrukturen für die Synthese entsprechender Prodrugs. Im Rahmen der vorliegenden Arbeit wurden insgesamt zwei neue Duocarmycin-analoge Prodrugs sowie neun neue seco-Drugs synthetisiert, wobei vier Vertreter eine terminale Alkinfunktion aufweisen. Für die Darstellung der Prodrugs wurden auf die Galaktose als Glykosideinheit zurückgegriffen. Zudem wurde ein neuartiges dimeres seco Drug hergestellt, das aus zwei pharmakophoren Einheiten sowie einem verbrückenden Linker mit Alkineinheit besteht. Die jeweiligen Substanzen wurden auf ihre In-vitro-Zytotoxizitäten sowie die Eignung für eine Anwendung im ADEPT-Ansatz evaluiert. Neun der neuen Duocarmycin-Analoga wurden in Form von seco- und Prodrugs wurden im Rahmen des aktivitätsbasierten Protein-Profilings untersucht. Hierbei konnte die Aldehyddehydrogenase 1 als wichtiges Angriffsziel der Duocarmycin-Familie verifiziert werden.