The emergence and spread of drug resistance in Plasmodium falciparum has consistently been a major barrier to the control and eradication of malaria. Resistance to the affordable and fast-acting former first-line drug chloroquine (CQ) was first observed in the 1950s near the Thai-Cambodian border and in South America. Resistance later spread from Asia to highly endemic regions in Africa, with reports of up to 6-fold increases in regional malaria mortality rates. The replacement drug, sulfadoxine-pyrimethamine (SP), encountered resistance within one year of clinical use. Artemisinin-(ART) based combination therapies (ACTs), which consist of a fast-acting ART derivative and a slower-acting partner drug, became the global first-line standard in 2000 and, along with mosquito vector control measures, helped decrease mortality rates by 60%. Unfortunately, parasites resistant to ART derivatives arose in Southeast Asia. This compromised the effectiveness of the ACT partner drug piperaquine (PPQ) and resistance to this drug was first reported in 2015, around a decade after the introduction of dihydroartemisinin-PPQ. By 2019, PPQ resistance, driven primarily by a series of mutations in the P. falciparum chloroquine resistance transporter (PfCRT), was widespread in Southeast Asia, resulting in >50% failure upon treatment with dihydroartemisinin-PPQ. Malaria mortality rates have surged recently, causing an estimated 619,000 deaths in 2021. Sub-Saharan Africa is most heavily affected by this disease where 78.9% of deaths are of young children. To this date, PPQ remains effective in Africa. It is a major concern that PPQ resistance will arise on this continent, however, given the importance of PPQ in current efforts to expand the range of antimalarial interventions and reverse the current rise of malaria cases in Africa. Understanding PPQ resistance mechanisms and their effect on parasite biology is critical to creating effective treatments and minimizing the impact of drug-resistant P. falciparum malaria. This thesis aims to investigate the earliest reports of PPQ resistance, to define the PPQ susceptibility and parasite fitness of contemporary SE Asian parasite strains, and to predict future dominant strains in the field to further our understanding of parasite resistance mechanisms and combat the spread of drug-resistant malaria. In Chapter 3, we show that earlier reports of PPQ resistance in Yunnan Province, China could be explained by the unique China C PfCRT variant. Using gene editing, we reveal that this variant confers a loss of fitness and parasite re-sensitization to the chemically related former first-line antimalarial CQ, while acquiring PPQ resistance via drug efflux. We employ biochemical assays to measure mutant PfCRT-mediated drug transport and molecular dynamics simulations with the recently solved PfCRT structure to assess changes in the central drug-binding cavity. This study provides impetus for adding CQ into an antimalarial treatment regimen where PPQ has lost efficacy. In response to widespread treatment failures, PPQ was removed as a first-line partner drug. Recently, additional mutations have been observed on the highly-resistant Dd2+F145I PfCRT isoform. These mutations developed in parasites in long-term in vitro culture or in Southeast Asian field isolates. In Chapter 4, I characterized the impact of these mutations on parasite fitness and antimalarial susceptibility by editing asexual blood stage parasites to express these mutant PfCRT haplotypes. Competitive growth assays with a GFP-expressing reporter line revealed that these additional mutations reduce the fitness defect imposed by F145I, likely the primary driver of their emergence. I found that these mutations differentially impact parasite susceptibility to PPQ and CQ in in vitro dose-response assays. I used proteoliposome-based drug uptake studies, molecular dynamic simulations, and peptidomics to detail the molecular features of drug resistance and parasite physiology of these lines. These experiments provide insight into parasite responses to the changing drug selective pressures in SE Asia to inform treatment strategies in this region moving forward. In Chapter 5, I sought to determine whether Asian PPQ-resistant PfCRT mutations could also mediate PPQ resistance on African PfCRT haplotypes. Using zinc-finger nuclease-based gene editing, I introduce the most common African mutant pfcrt alleles with a SE Asian PfCRT mutation into Dd2 parasites. In PPQ survival assays, these mutations only confer high-grade PPQ resistance (defined as ≥10% survival at 200 nM) on the FCB PfCRT background. I assessed the susceptibility of these gene-edited isogenic lines to other clinical antimalarials and the relative fitness of these engineered lines with in vitro assays. These experiments clearly show that there is a genetic path to PPQ resistance in African parasites; however, they also suggest that fitness costs associated with these mutations may hinder the spread of resistance. Our data provide important insights into PPQ resistance. In chapter 6, these findings are summarized along with future studies to strengthen and expand on the findings presented herein.

Plasmodium falciparum, the primary causative agent of malaria in humans, is responsible for life-threatening infections and disease in many tropical regions of the world. In 2018, there were over 228 million cases and 405,000 deaths due to malaria infection, according to World Health Organization estimates. While there has been recent progress in decreasing mortality rates attributed to malaria, the emergence of widespread antimalarial drug resistance in recent decades has endangered such progress. Therefore, there is an urgent need for new antimalarial drugs with a novel mechanism of action. Plasmodium kinases could serve as attractive drug targets due to their essential functions in all stages of the parasite’s life cycle. Plasmodium falciparum Aurora-related kinases (PfArks) have essential regulatory roles in all stages of the parasite’s asexual intraerythrocytic life cycle. As a result, it is hypothesized that PfArks are excellent potential molecular targets for novel antimalarial development. The intent of this study was to identify potent and selective inhibitors of Plasmodium from an Aurora kinase-focused commercial inhibitor library of 3,000 compounds. An initial phenotypic screen was performed at a fixed inhibitor concentration of one micromolar to identify novel compounds with potency against the P. falciparum chloroquine-resistant Dd2 strain. From this library, we have identified multiple compounds with submicromolar antiplasmodial activity in asexual intraerythrocytic life cycle stages and adequate selectivity. Additionally, this project aimed further to characterize the cellular mechanism of action of hit compounds. Multiple compounds were found to exhibit inhibitory effects against early intraerythrocytic asexual life cycle stages as well as liver stages. At this time, one hit compound (DC-6275) was found to inhibit asexual intraerythrocytic as well as liver stage parasites in addition to PfArk1 amongst other Plasmodium protein kinases tested. Overall, we believe that these identified compounds have great potential to serve as scaffolds for future antimalarial drug development.

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Malaria parasite (Plasmodium spp.) infection in the mosquito Anopheles stephensi induces significant expression of A. stephensi nitric oxide synthase (AsNOS) in the midgut epithelium as early as 6 h post-infection and intermittently thereafter. This induction results in the synthesis of inflammatory levels of nitric oxide (NO) in the blood-filled midgut that limit parasite development. However, the Plasmodium-derived factors that can induce AsNOS expression and the signaling pathways responsible for transduction in A. stephensi have not been identified until completion of the work described herein. In my studies, I have determined that P. falciparum glycosylphosphatidylinositol (PfGPIs) can induce AsNOS expression in A. stephensi cells in vitro and in the midgut epithelium in vivo. Based on related work in mammals, I hypothesized that parasite-derived AsNOS-inducing factors signal through the insulin signaling pathway and the NF-kappaB-dependent Toll and Immune deficiency (Imd) signaling pathways. In support of this hypothesis, I have determined that signaling by P. falciparum merozoites and PfGPIs is mediated through A. stephensi protein kinase B (Akt/PKB) and DSOR1 (mitogen activated protein kinase kinase, MEK)/Extracellular signal-regulated protein kinase (ERK), kinases which are associated with the insulin signaling pathway. However, signaling by P. falciparum and PfGPIs is distinctively different from signaling by insulin and these parasite signals are not insulin-mimetic to A. stephensi cells. In other studies, treatment with pyrrolidine dithiocarbamate (PDTC), an inhibitor of NF-kappaB, reduced AsNOS expression by P. falciparum merozoites in A. stephensi cells. This result suggested the involvement of Toll and Imd pathways in parasite signaling of mosquito cells. Knockout of Pelle, a proximal signaling protein in the Toll pathway, increased AsNOS expression following parasite stimulation, suggesting that the Toll pathway may negatively regulate signaling by Plasmodium-derived AsNOS-inducing factors. In contrast, knockout of TGF-beta-activated kinase 1 (Tak1), a proximal signaling protein in the Imd pathway, reduced AsNOS expression by 20% relative to the control, suggesting that the Imd pathway is required for signaling by Plasmodium-derived AsNOS-inducing factors. Despite the NO-rich environment of the midgut, Plasmodium development is not completely inhibited. This observation suggests that Plasmodium may have efficient detoxification systems during sexual development in A. stephensi. To identify Plasmodium defense genes that may defend parasites against nitrosative stress caused by AsNOS induction, expression of several antioxidant defense genes known to function in nitrosative stress defense in a variety of organisms were examined during sporogonic development. Notably, increased expression levels of P. falciparum peroxiredoxins containing 1 or 2 cysteines (1-cys or 2-cys PfPrx) were associated with periods of parasite development just prior to and during parasite penetration of midgut epithelium, an event associated with significant AsNOS induction in the midgut. The provision of N omega-L-arginine (L-NAME), a known inhibitor of NOS enzyme activity, to A. stephensi with Plasmodium culture by artificial bloodmeal significantly reduced expression of 1-cys and 2-cys PfPrx indicating that these gene products may function to protect parasites against nitrosative stress induced by AsNOS. / Ph. D.

Both vertebrates and anopheline mosquitoes inhibit <i>Plasmodium</i> spp. (malaria parasite) development via induction of nitric oxide (·NO) synthase. Expression of <i>Anopheles stephensi</i> ·NO synthase (<i>AsNOS</i>) is induced in the midgut epithelium beginning at 6 h following a <i>Plasmodium berghei</i>-infected blood meal. ·NO reacts readily with other biocompounds forming a variety of reactive nitrogen intermediates (RNIs) that may impose a nitrosative stress. These RNIs are proposed to be responsible for the AsNOS-dependent inhibition of <i>Plasmodium</i> development. In my studies, I identified several RNIs that are induced in the blood-filled midgut in response to <i>Plasmodium</i> infection. Stable end products of ·NO (NO₃⁻ and NO₂⁻), measured using a modified Griess assay, are elevated in infected midguts at 24 h post-blood meal (pBM). Further studies using chemical reduction-chemiluminescence with Hg displacement showed that infected midguts contained elevated levels of potentially toxic higher oxides of nitrogen (NO<SUB>x</SUB>), but <i>S</i>-nitrosothiol (SNO) and nitrite levels did not differ between infected and uninfected midguts at 12.5 and 24 h pBM. Thus, nitrates contributed to elevated NO<SUB>x</SUB> levels. SNO-biotin switch westerns indicated that <i>S</i>-nitrosated midgut proteins change over the course of blood meal digestion, but not in response to infection. Photolysis-chemiluminescence was used to release and detect bound ·NO from compounds in blood-filled midguts dissected from 0-33 h pBM. Results showed increased ·NO levels in <i>Plasmodium</i>-infected midgut lysates beginning at 8 h, with significant increases at 12.5-13.5 h and 24-25.5 h pBM and peak levels at 20-24 h. Photolyzed ·NO is derived from SNOs and metal nitrosyls. Since SNO concentrations did not change in response to infection, I proposed that metal nitrosyls, specifically Fe nitrosyl hemoglobin (nitrosylHb) based on the concentration of hemoglobin, were elevated in the infected midgut. At 12-24 h pBM, levels of midgut RNIs in infected mosquitoes were typical of levels measured during mammalian septic inflammation. The inverse relationship between AsNOS activity and parasite abundance indicates that nitrosative stress has a detrimental effect on parasite development. However, nitrosative stress may impact mosquito tissues as well in a manner analogous to mammalian tissue damage during inflammation. Elevated levels of nitrotyrosine (NTYR), a marker for nitrosative stress in many mammalian disease states, were detected in tissues of parasite-infected <i>A. stephensi</i> at 24 h pBM. Greater nitration of tyrosine residues was detected in the blood bolus, midgut epithelium, eggs and fat body. In the midgut, Hb remained in an oxygenated state for the duration of blood digestion. The reaction between ·NO and oxyhemoglobin (oxyHb) can result in the formation of nitrate and methemoglobin (metHb). Although nitrate levels were elevated in response to parasite infection, there was little to no metHb present in the mosquito midgut. The simultaneous presence of nitrates, nitrosylHb, oxyHb, and NTYR, together with a lack of elevated nitrites and metHb, suggested that alternative reaction mechanisms involving â ¢NO had occurred in the reducing environment of the midgut. In addition, I proposed that nitroxyl and peroxynitrite participated in reactions that yielded observed midgut RNIs. To cope with the parasite-induced nitrosative stress, cellular defenses in the mosquito may be induced to minimize self damage. I proposed that peroxiredoxins (Prx), enzymes that can detoxify peroxides and peroxynitrite, may protect <i>A. stephensi</i> from nitrosative stress. Six Prx genes were identified in the <i>A. gambiae</i> genome based on homology with known <i>D. melanogaster</i> Prxs. I identified one <i>A. stephensi</i> Prx, AsPrx, that shared 78% amino acid identity with a <i>D. melanogaster</i> 2-Cys Prx known to protect fly cells against various oxidative stresses. <i>AsPrx</i> was expressed in the midgut epithelium and is encoded by a single-copy, intronless gene. Quantitative RT-PCR analyses confirmed that induction of <i>AsPrx</i> expression in the midgut was correlated with malaria parasite infection and nitrosative stress. To determine whether AsPrx could protect against RNI- and ROS-mediated cell death, transient transfection protocols were established for AsPrx overexpression in <i>D. melanogaster</i> (S2) and <i>A. stephensi</i> (MSQ43) cells and for <i>AsPrx</i> gene silencing using RNA interference in MSQ43 cells. Viability assays in MSQ43 cells showed that AsPrx conferred protection against hydrogen peroxide, ·NO, nitroxyl and peroxynitrite. These data suggested that the ·NO-mediated defense response is toxic to both host and parasite. However, AsPrx may shift the balance in favor of the mosquito. / Ph. D.

Malaria is an infectious disease caused by Plasmodium parasites and transferred by Anopheles mosquitos. Due to Artemisinin resistance, new druggable targets identification and new drug development are urgently needed. Serine hydrolases (SHs) are one of the largest classes of enzymes having important roles in life processes. The deadliest malaria parasite, P. falciparum, encodes more than 50 SHs including proteases, lipases, esterase and others, while only several of them have been characterized. The study of uncharacterized SHs will shed light on future drug development to treat malaria. In this study, we applied chemical biology and genetic approaches to identify SHs important for the pathogenic asexual stage growth of P. falciparum parasites. We mainly focused on a depalmitoylase essential for merozoite invasion and lysophospholipases (LPLs) essential for acquiring fatty acids (FAs) from the host. Identifying essential metabolic enzymes will benefit the treatment to malaria. We focused on metabolic SHs and identified two SHs were refractory to knock out. We studied a likely essential SH named PfABHD17A, which is a human depalmitoylase homolog. PfABHD17A is localized on the rhoptry, an organelle essential for invasion. We expressed the recombinant PfABHD17A, conducted inhibitor screen and discovered that human depalmitoylase inhibitor ML211 inhibits PfABHD17A in vitro. ML211 inhibits merozoite invasion but not egress, which together with the localization of PfABHD17A on the rhoptries, suggested that PfABHD17A is essential in merozoite invasion. We also purified PfABHD17A and verified that PfABHD17A may exhibit depalmitoylase activity in vitro. LPLs are important for asexual stage parasites acquiring FAs from the host. The P. falciparum genome includes 17 putative LPLs while LPLs responsible for hydrolyzing FA from lysophosphatidylcholine (LPC) in the asexual stage are currently unknown. Using a chemical biology approach, we identified serine hydrolase inhibitor AKU-010 inhibits LPC hydrolysis effectively. Using activity-based protein profiling (ABPP) and genetic approaches, we identified that AKU-010 inhibits a series of SHs including Exported Lipases (XLs), Exported Lipases Homolog (XLH) and Plasmodium falciparum prodrug activation and resistance esterase (PfPARE). We generated a series of knockout parasite lines on the AKU-010 targets and identified that red blood cell (RBC)-localized XL2 and cytosolic XLH4 contribute to most LPC hydrolysis activity in the asexual stage. XLs and XLHs are important for parasites using LPC for growth and contribute to detoxification from accumulated LPC. XL2 and XL4 together are essential for parasite growth under high LPC concentration medium, such as human serum. XL/XLH-deficient parasites could still acquire FA from LPC, which is mainly contributed by parasite membrane- localized PfPARE. PfPARE has little impact on parasite growth and LPC metabolism with the existence of XLs and XLHs but is important after the loss of XLs and XLHs. Parasites deficient in PfPARE, XLs and XLHs have little ability to release FA from LPC and cannot use LPC as FAs source for growth. In summary, we identified metabolic SHs mediating protein depalmitoylation and lipid metabolism and in asexual stage Plasmodium falciparum, which may benefit future drug development to treat malaria. / Doctor of Philosophy / Malaria is an infectious disease caused by Plasmodium parasites and transferred by mosquitos. New druggable target identification and drug development are urgently needed to deal with the malaria issue. We focused on an understudied enzyme superfamily termed serine hydrolase (SHs), which includes more than 50 members in the deadliest malaria parasite, P. falciparum. We identified that several druggable enzymes, which can mediate protein depalmitoylation and lipid metabolism, are important for parasite growth in the pathogenic stage. Identifying essential metabolic enzymes will benefit the treatment to malaria. We screened eleven SHs and discovered that two of them are likely essential in the pathogenic stage. We focused on one human depalmitoylase homolog termed PfABHD17A. We screened the inhibitors on PfABHD17A and used the inhibitor to suggest that PfABHD17A is essential for the growth of pathogenic stage parasites. We also identified lipases important for acquiring fatty acids (FAs) from the host. Using chemical biology and genetic approaches, we discovered that three lipases are important for acquiring FAs form the host in the pathogenic stage. Inhibiting these enzymes may kill the parasite in the host.

International malaria control initiatives such as the Roll Back Malaria Initiative (RBM) and the Medicines for Malaria Venture (MMV) mobilize resources and spur research aimed at vector control as well as the treatment and eventual eradication of the disease. These efforts have managed to reduce incidence of malaria by an estimated 37% worldwide since 2000. However, despite the promising success of control efforts such as these, the World Health Organization reports a staggering 438,000 deaths from malaria in 2015. The continuing high death toll of malaria as well as emerging insecticide and antimalarial drug resistance suggests that while encouraging, success in reducing malaria incidence may be tenuous. Current vector control strategies are often complicated by ecological and behavioral heterogeneity of vector mosquito populations. As an additional obstruction, mosquito genomes are highly plastic as evidenced by the wealth or chromosomal inversions that have occurred in this genus. Chromosomal inversions have been correlated with differences in adaptation to aridity, insecticide resistance, and differences in resting behavior. However, a good understanding of the molecular mechanisms for inversion generation is still lacking. One possible contributor to inversion formation in Anopheles mosquitoes includes repetitive DNA such as transposable elements (TEs), tandem repeats (TRs) and inverted repeats (IRs). This dissertation provides physical maps for two important malaria vectors, An. stephensi and An. albimanus (Ch.2 and Ch. 3) and then applies those maps to the identification of inversion breakpoints in malaria mosquitoes. Repeat content of each chromosomal arm and the molecular characterization of lineage specific breakpoints is also investigated (Ch. 2 and Ch.4). Our study reveals differences in patterns of chromosomal evolution of Anopheles mosquitoes vs. Drosophila. First, mosquito chromosomes tend to shuffle as intact elements via whole arm translocations and do not under fissions or fusions as seen in fruitflies. Second, the mosquito sex chromosome is changing at a much higher rate relative to the autosomes in malaria mosquitoes than in fruit flies. Third, our molecular characterization of inversion breakpoints indicates that TEs and TRs may participate in inversion genesis in an arm specific manner. / Ph. D. / Malaria is a complex and devastating disease vectored by the bite of a female Anopheles mosquito. This disease claimed an estimated 438,000 lives in 2015. The mobilization of funding and resources as part of global malaria eradication initiatives have reduced the global incidence of malaria by 37% in the last 15 years. Deaths from malaria are also 60% lower vs. the year 2000. These promising gains are threatened by the ability of Anopheles mosquitoes to adapt in the face of malaria control efforts. Anopheles mosquito chromosomes are known to be highly plastic, as evidenced by numerous chromosomal inversions. Recent years have seen increases in insecticide resistance, and behavioral change in mosquito populations that allow them to avoid insecticides and remain prolific vectors of disease. This ability of mosquito vectors to adapt threatens to unravel recent progress towards a malaria free world. The projects presented in this dissertation explore mechanisms of chromosomal evolution, specifically the potential role of repetitive DNA in the generation of chromosomal inversions. The exploration of chromosomal inversions was facilitated by the creation of physical maps for Anopheles species. Prominent malaria vectors An. stephensi andAn. albimanus were physically mapped in Chapter 2 and Chapter 3 respectively. In chapter 1 and chapter 3 physical maps are utilized for the identification of chromosomal inversion breakpoints using 2 species (Ch. 2) and many species (Ch. 4). Repeat content was quantified along each chromosomal arm (Ch 2,4) and in inversion breakpoint regions (Ch 3). This dissertation presents physical maps for two important malaria species that have been applied to the study of chromosomal evolution and will also serve as community tools for further study of malaria mosquitoes. Our work on chromosomal evolution has revealed the Anopheles chromosomes tend to undergo translocations as intact elements and do not under fissions and fusions as seen in fruitflies. We also find that the malaria mosquito sex chromosome changes much more rapidly relative to the autosomes than in fruitflies. Additionally, repetitive DNA including transposable elements (TEs) and tandem repeats (TRs) may be encouraging chromosomal inversions but with differing roles on different chromosomal arms.