Malaria is a terrible disease caused by a protozoan parasite within the Plasmodium genus, claiming the lives of hundreds of thousands of people yearly, the majority of whom are children under the age of five. Of the five species of Plasmodium causing malaria in humans, P. falciparum is responsible for most of the death toll. An increase in malaria cases was detected between the years 2016 to 2017 according to the World Malaria Report of 2017, despite control efforts. The rapid development of resistance within P. falciparum against antimalarials has led to the use of artemisinin combinational therapy as the current gold standard for malaria treatment. Yet decreased parasite clearance demonstrates that using combination therapy is insufficient in maintaining current antimalarials’ effectiveness against these resistant parasites. Hence, novel compounds with a mode of action (MoA) different than current antimalarials are required. Though phenotypic screening has delivered thousands of promising hit compounds, hit-to-lead optimisation is still one of the rate-limiting steps in pre-clinical antimalarial drug development. While knowing the exact target or MoA is not required to progress a compound in a medicinal chemistry program, identifying the MoA early can accelerate hit prioritization, hit-to-lead optimisation and preclinical combination studies in malaria research. In this study, we assessed machine learning (ML) approaches for their ability to stratify antimalarials based on transcriptional responses associated with the treatments. From our results, we conclude that it is possible to identify biomarkers from the transcriptional responses that define the MoA of compounds. Moreover, only a limited set of 50 genes was required to build a ML model that can stratify compounds with similar MoA with a classification accuracy of 76.6 ± 6.4%. These biomarkers will help stratify new compounds with similar MoA to those already defined with our strategy. Additionally, the biomarkers can also be used to monitor if the MoA of a compound has changed during hit-to-lead optimisation. This work will contribute to accelerating antimalarial drug discovery during the hit-to-lead optimisation phase and help the identification of compounds with novel MoA. / Dissertation (MSc)--University of Pretoria, 2019. / Biochemistry / MSc / Unrestricted

ABSTRACT Malaria is considered by many to be the most important infectious diseases a of humans in the world. Since the dawn of civilization, malaria has left it detrimental fingerprints all over history. The World Health Organization reports an estimated 300 million people infected with the protozoan parasite worldwide and a mortality rate that claims more than one million victims annually. Of the four species known to infect huinans with malaria, Plasmodium falciparum is by far the most pathogenic and efforts to inhibit its ~idespread epidemiology have been minimal. Only a handful of antimalarials are currently available to combat the disease and even they are loosing efficacy due to the increased prevalence of drug resistance. Therefore, it is important to discover new modes of treatment. Inhibitors of protein prenylation have been identified by our laboratory to have the potential to be a new class of antimalarials. Protein prenylation is a relatively new research interest that studies the functional significance of famesyl (C15) and geranylgeranyl (C20) posttranslational modifications in a variety of cellular regulatory processes. These prosthetic groups are thought to be absolutely essential for the activity and cellular localization of prenylated proteins. Inhibitors of protein prenylation act through perturbation of the subcellular localization of these important proteins. In an effort to understand the mechanism of action of prenyl transferase inhibitors, it is important to characterize malarial prenylated proteins. This thesis initiated studies in characterizing putative prenylated proteins and has focused on three P.falciparum proteins, PfPTP, PtRab6, and PfDnaJ. Attempts have been made to clone and over-express recombinant proteins and generate antibodies for functional analysis.

Raman micro-spectroscopy provides a non-destructive probe with potential applications as a diagnostic tool for cellular disorders. This study presents micro-Raman spectra of live erythrocytes infected with a malaria parasite and investigates the potential of this probe to monitor molecular changes which occur during differentiation of the parasite inside the cell. At an excitation wavelength of 633 nm the spectral bands are dominated by hemoglobin vibrations yielding information the on structure and spin state of the heme moiety. It also demonstrates the novel use of silica capillaries as a viable method for studying the erythrocytes in an environment that is much closer to their native state, thus opening the possibility of maintaining the cell in vivo for long periods to study the dynamics of the parasite's growth.

La malaria est une maladie endémique qui a affecté 212 millions de personnes en 2015, et fait plus de 429 000 morts. Parmi les espèces causant la malaria humaine, Plasmodium falciparum est celle qui est associée au plus haut taux de morbidité et de mortalité. L’invasion du globule rouge par le parasite de la malaria, P. falciparum, est une étape clé qui est médiée par la sécrétion coordonnée de différentes protéines contenues dans les organites du complexe apical : les rhoptries, les micronèmes et les granules denses. La biogenèse de ces organites et le transport des différentes protéines apicales sont des phénomènes encore mal compris et peu étudiés. Des travaux ont montré que des microdomaines présents dans la membrane de l’appareil de Golgi possèderaient une composition lipidique et protéique distincte et seraient impliqués dans la sélection différentielle des protéines destinées aux organites du complexe apical. Cependant, la façon dont ces microdomaines sont discriminés l’un de l’autre et les mécanismes régissant leur transport à partir de l’appareil de Golgi vers le complexe apical sont présentement inconnus. Nous avons donc entrepris d’identifier les différents acteurs moléculaires impliqués dans ce trafic différentiel des protéines apicales. Les travaux réalisés dans le cadre d’un premier projet ont permis de démontrer que la sortiline, un récepteur de cargo conservé chez les eucaryotes, joue un rôle essentiel dans le transport de protéines vers les différents organites apicaux. Nous avons également démontré que la sortiline interagit avec le complexe de protéines RAMA/RAP afin d’assurer leur transport spécifique vers les rhoptries. L’analyse du phénotype en situation de « knock-down » de la sortiline a révélé à la fois un rôle essentiel de la sortiline dans la biogenèse des organites du complexe apical, mais aussi dans le processus de cytokinèse lors de la division cellulaire. Ces résultats mettent en évidence un rôle central et essentiel de la protéine escorte sortiline dans le système de transport protéique chez le parasite de la malaria P. falciparum. Dans le cadre d’un second projet, nous avons caractérisé une potentielle protéine de rhoptries (PRP2) identifiée chez Plasmodium berghei et chez Toxoplasma gondii. Nous avons cependant démontré que chez P. falciparum, cette hypothétique protéine de rhoptries est plutôt localisée à l’appareil de Golgi et n’est pas impliquée dans les évènements d’invasion. De ce fait, nous avons renommé cette protéine « Golgi protein 1 » (GP1) . Nous avons également découvert que GP1 interagit avec une protéine transmembranaire non caractérisée (« Golgi protein 2 », GP2). Nos travaux ont donc mené à la découverte d’un nouveau complexe de protéines situé dans l’appareil de Golgi et important pour la survie du parasite.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2009. / Härtill 6 uppsatser.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2007. / Härtill 4 uppsatser.

Diss. (sammanfattning) Stockholm : Karol. inst., 2005. / Härtill 5 uppsatser.

Plasmodium falciparum 1–deoxy–D–xylulose–5 phosphatereductoisomerase (PfDXR) plays a role in isoprenoid biosynthesis in the malaria parasite and is absent in the human host, making this parasite enzyme an attractive target for antimalarial drug design. To characterize PfDXR, it is necessary to produce large quantities of the enzyme in a soluble and functional form. However, the over–production of malarial proteins in prokaryotic host systems often results in the formation of truncated proteins or insoluble protein aggregates. A heterologous expression system was developed for the production of active PfDXR using codon harmonization and tight control of expression in the presence of lac repressor. Yields of up to 2 mg/l of enzyme were reported using the optimised expression system, which is 8 to 10– fold greater than previously reported yields. The kinetic parameters Km, Vmax and kcat were determined for PfDXR; values reported in this study were consistent with those reported in the literature for other DXR enzymes. A three–dimensional model of the malarial drug target protein PfDXR was generated, and validated using structure–checking programs and protein docking studies. Structural and functional features unique to PfDXR were identified using the model and comparative sequence analyses with apicomplexan and non–apicomplexan DXR proteins. Residues Val44 and Asn45, essential for NADPH binding; and catalytic hatch residues Lys224 and Lys226, which are unique to the species of Plasmodium, were mutated to resemble those of E. coli DXR. Interestingly,these mutations resulted in significant reductions in substrate affinity, when compared to the unmutated PfDXR. Mutant enzymes PfDXR(VN43,44AG) and PfDXR(KK224,226NS) also demonstrated a decreased ability to turnover substrate by 4–fold and 2–fold respectively. This study indicates a difference in the role of the catalytic hatch of PfDXR with regards to the way in which it captures substrates. The study also highlights subtle differences in cofactor binding to PfDXR, compared with the well characterized EcDXR enzyme. The validated PfDXR model was also used to develop a novel efficient in silico screening method for potential tool compounds for use in the rational design of novel DXR inhibitors. Following in silico screening of 46 potential DXR inhibitors, a two–tiered in vitro screening approach was undertaken. DXR inhibition was assessed for the 46 novel compounds using an NADPH– ependant DXP enzyme inhibition assay and antimalarial potential was assessed using P.falciparum–infected erythrocyte growth assays. Select compounds were tested in human cells in order to determine whether they were toxic to the host. From the parallel in silico and in vitro drug screening, it was evident that only a single compound demonstrated reasonable potential binding to DXR (determined using in silico docking), inhibited DXR in vitro and inhibited P. falciparum growth, without being toxic to human cells. Its potential as a lead compound in antimalarial drug development is therefore feasible. Two outcomes were evident from this work. Firstly, analogues of known antimalarial natural products can be screened against malaria, which may then lead towards the rational design of novel compounds that are effective against a specific antimalarial drug target enzyme, such as PfDXR. Secondly, the rational design of novel compounds against a specific antimalarial drug target enzyme can be untaken by adopting a coupled in silico and in vitro approach to drug discovery.

Malaria is still a significant public health problem in the Tropics, with an estimated 200 million cases a year and more than 1 million deaths, mostly in young children in sub-Saharan Africa. Plasmodium falciparum is the parasite responsible for the majority of the morbidity and mortality due to malaria. We know from the historical use of malaria to treat neurosyphilis that there were several different strains of P. falciparum, some of which were more pathogenic and had higher multiplication rates than others. High multiplication rates of P. falciparum isolates have been associated with severe disease in Thailand, but not in Kenya or Mali. In determining what differences exist between fast- and slow-growing malaria parasites, and understanding their relationship with clinical outcome, we may discover a way of targeting those parasites that cause most disease. This thesis describes a genetic analysis of the determinants of growth and pathogenicity in the rodent malaria parasite, Plasmodium chabaudi. The use of rodent malaria parasite strains for genetic analysis has several experimental, ethical and financial advantages over the use of human malaria parasites. In addition, rodent malaria parasite strains also vary significantly in their growth and pathogenicity, making them excellent candidates for a genetic analysis of these characteristics. The first section of this thesis is concerned with the characterisation of the growth, pathogenicity and transmissibility of two strains, DS and DK, of the rodent malaria parasite P. c. adami. The DS strain is fast-growing, pathogenic, non-selective in its invasion of red blood cells and a poor transmitter to mosquitoes. The DK strain is slow-growing, non-pathogenic, selective in its invasion of red blood cells and a good transmitter to mosquitoes. In the second section of this thesis is a detailed study of the growth characteristics of DS and DK in mixed infections, relative to their growth in single infections. Both sections provide information relevant for the main objective of this thesis, but also contribute to the body of work on pathogenicity and transmissibility, and pathogenicity and strain behaviour in mixed infections, which has been carried out in rodent malaria parasites to-date. The third section of the thesis contains the results of a genetic analysis of the difference in growth between P. c. adami strains DS and DK, using the Linkage Group Selection (LGS) technique. On several occasions, DS and DK were crossed in the mosquito vector and, following selection for fast growth in mice, the cross progeny were initially screened with genome-wide, quantitative AFLP markers. Markers specific to the slow-growing parent DK which were greatly reduced in intensity after selection were found on P. chabaudi chromosomes 6, 7 and 9. This result suggests that the difference in growth between the two strains is determined by multiple genetic loci. The selection on chromosomes 7 and 9 was then looked at in greater detail, using SNP-based markers quantified by Pyrosequencing™. It was found, consistently, that a region at one end of DS chromosome 9 was inherited as a single, non-recombining unit in cross progeny selected for fast growth. As this was the region most strongly selected against, it suggests that a gene (or genes) in this region has a major role in the determination of growth characteristics, and therefore pathogenicity, in P. c. adami. Narrowing down this region further, in order to identify the candidate gene(s), remains a key future objective.

Plasmodium falciparum is the etiological agent of severe human malaria. The virulence of the parasite is dependent on a complex life cycle supported by a diverse repertoire of stage specific surface antigens. Notably, members of the 6-Cys s48/45 protein family are differentially presented on the parasite surface of each life cycle stage and known to play important biological roles, though the underlying molecular mechanisms are not well understood. Of the 6-Cys antigens, Pf41 is localized to the surface of the blood-stage merozoite through its interaction with Pf12 and is a target of the host immune system; accordingly, Pf41 is one of the five top-ranked potential malaria vaccine candidates. Pfs47 is localized to the surface of the sexual-stage gametocyte through its glycophosphatidylinositol-anchor and is currently being investigated as a transmission blocking vaccine. Intriguingly, both Pf41 and Pfs47 are predicted to adopt a three domain architecture. Prior to the studies presented here, only a single two domain 6-Cys protein had been structurally characterized. During my graduate studies, the structure of Pf41 was also determined by Dr. Michelle Parker in the Boulanger lab and I was able to perform the structural interpretation. Structural analysis revealed an unexpected topology where domains 1 and 2 are juxtaposed and the predicted central domain, which was largely proteolyzed during the crystallization process, is inserted as an extended loop in domain 1. Data from my ITC binding studies and protease protection assays suggest this inserted domain-like region (ID) plays an essential role in promoting assembly with Pf12. Despite several attempts, I was unable to crystallize Pfs47. Thus, to obtain architectural information describing Pfs47, a chemical cross linking experiment coupled with mass spectrometry was performed. The resulting data led me to predict that Pfs47 also incorporates an ID (Ser155 to Gln267) within D1. An engineered Pfs47 construct lacking the predicted ID was purified as a monomer, indicating that the predicted ID is expendable for stability of the overall structure. Collectively, these data provide important insight into the overall architecture of the biologically important Plasmodium 6-Cys proteins, which enables us to support ongoing collaborative vaccine design efforts. / Graduate