Made available in DSpace on 2016-04-04T12:45:11Z (GMT). No. of bitstreams: 2 ana_silva_ioc_mest_2012.pdf: 1481530 bytes, checksum: 26cfc4a55477788165190207123da53d (MD5) license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) Previous issue date: 2014 / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Rio de Janeiro, RJ, Brasil / A malária é uma doença que acomete milhões de pessoas todos os anos no planeta. No Brasil, essa doença atingiu cerca de 267 mil pessoas somente em 2011, sendo que a maior parte dos casos ocorreu na região Amazônica. Causada por protozoários do gênero Plasmodium, possui um amplo espectro clínico que vai desdeinfecções assintomáticas, malária não complicada, a malária grave ou complicada, podendo evoluir até o óbito. Estudos realizados em áreas holo e hiperendêmicas de malária, fundamentalmente no continente Africano e em Papua Nova Guiné, permitiram estabelecer que o conhecimento da população de parasitos que circulam em uma área.Este estudo se propôs a avaliar o perfil genético da infecção por P. falciparumem uma área de alto risco epidemiológico para malária e com presença de infecção assintomática no município de Barcelos, médio rio Negro, estado do Amazonas Para isso, foi estudado o gene MSP1 que codifica a Proteína de Superfície de Merozoíto 1, com o intuito de verificar a diversidade genética dos parasitos da região de Barcelos, a multiplicidade da infecção e as relações dos diferentes genótipos com o status clínico em área endêmica para malária. Foi realizada reação de polimerase em cadeia (PCR) a partir de DNA extraído de 79 amostras de sangue coletadas em indivíduos desta região. No total, foram encontrados 10 diferentes genótipos do parasito sendo que a maior parte dos indivíduos (45 pessoas, 56,96%) portava apenas um genótipo do parasito. Entre os indivíduos assintomáticos, 70,37% apresentavam um genótipo e os demais (29,63%) apresentaram dois genótipos Entre os pacientes com malária, 50% tinham apenas um genótipo, 25% tinham dois genótiposs, 19,23% apresentaram três genótipos e 5,77% portavam quatro genótipos. Em média, portadores assintomáticos possuíam 1,3 genótipos diferentes enquanto pacientes com malária tiveram em média 1,8 genótipos. Concluiu-se que na região de Barcelos circulam populações de P. falciparumconsideravelmente diversas e que as infecções múltiplas estão mais presentes em portadores de malária que em indivíduos assintomáticos / Malaria is a disease that attacks millions of people all of the years in the world . In Brazi l, it reached about 267 thousand people only in 2011 , and most of the cases was registered in the Amazonian area. Caused by protozoa of the gender Plasmodium , it possesses a wide clinical spectrum ranging from asymptomatic infections , no complicatedma laria, serious or complicatedmalaria that could develop until death. Studies accomplished in holo - and hyperendemic areas, fundamentally in t he African continent and in Papua New Guinea, allowed to establish that the knowledge of the population of parasite s that circulate in a certain area . This study intended to evaluate the genetic profile of the infection for P. falciparum in an area of high epidemic risk for malaria and with the pre sence of asymptomatic infection in the city of Barcelos, medium Rio Negro , state of Amazon as . For that, the gene MSP - 1 , that codifies the Merozoite Surface Protein 1, was studied to verify the genetic diversity of the parasites of the ar ea of Barcelos, the multiplicity of the infection and the relationships of the differen t genotypes with the clinical status in an endemic area for malaria. Polymerase Chain R ea ction (PCR) was accomplished starting from extracted DNA from blood samples collected in individuals from this area. In total, 10 different genotypes of the parasite we re found and most of the individuals (45 people, 56,96%) carried just a genotype of the parasite . Amon g the asymptomatical individuals , 70,37% introduced a genotype and the othe rs (29,63%) presented two . Among the patients with malaria, 50% had only one ge notype, 25% had two genotypes , 19,23% presented three genotypes and 5,77% carried four genotypes. On average, asymptomaticbearers possessed 1,3 genotypes while patient s with malaria had 1,8 genotypes on average. It was concluded that in the area of Barcel os diverse populations of P. falciparum circulate and that multiple infections are more present in malaria bearers tha n in asymptomatic individuals

Made available in DSpace on 2016-07-01T12:30:01Z (GMT). No. of bitstreams: 2 monica_cuero_ioc_mest_2016.pdf: 2091495 bytes, checksum: 520eacc5a4964c1f22509ada51d4d97a (MD5) license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) Previous issue date: 2016 / Made available in DSpace on 2016-07-05T23:52:44Z (GMT). No. of bitstreams: 3 monica_cuero_ioc_mest_2016.pdf.txt: 128716 bytes, checksum: 4fd30b67febb8c98bc54a69c0cccdcfd (MD5) license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) monica_cuero_ioc_mest_2016.pdf: 2091495 bytes, checksum: 520eacc5a4964c1f22509ada51d4d97a (MD5) Previous issue date: 2016 / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Rio de Janeiro, RJ, Brasil / A complexa diversidade genética do Plasmodium falciparum é em parte responsável pela evasão da resposta imune do hospedeiro, pelo surgimento da resistência aos fármacos e pela dificuldade no desenvolvimento de uma vacina anti-malárica eficaz. Estudos sobre a biologia deste parasito se concentram fundamentalmente em áreas holo e hiperendêmicas de malária na África subsaariana. Trabalhos realizados na região Amazônica, ainda são escassos no que se refere à diversidade genética de populações naturais de P. falciparum. Este estudo analisou a diversidade genética de P. falciparum isolados de indivíduos provenientes da região do médio rio Negro, Amazonas utilizando como alvo o gene que codifica para a proteína de superfície do merozoíta 2. METODOLOGIA: O estudo foi realizado em Barcelos, um município de alto risco epidemiológico para malária com uma média anual de 5.000 casos nos últimos cinco anos (IPA médio=156,4/1000). Foram avaliadas 79 amostras isoladas de indivíduos que apresentaram malária clínica ou infecção assintomática. Os DNAs genômicos extraídos foram submetidos à reação em cadeia da polimerase (PCR) para a confirmação do diagnóstico de infecção pelo P. falciparume em seguida foi feita uma PCR-nested, para amplificação da região do bloco 3 do gene msp2 para diferenciação das famílias alélicas (3D7 e FC27) e a diversidade intra-família foi observada após digestão com a enzima HinfI RESULTADOS: Só foi encontrada a familia 3D7 nas amostras estudadas. Dois diferentes genótipos foram encontrados circulando na área, caracterizados pela combinação dos fragmentos 16 pb, 108 pb, 349 (genotipo 1) e 16 pb, 108 pb, 400pb (genotipo 2). Foi observado que só dois indivíduos com malária clinica portavam os dois genótipos simultaneamente. Não foram encontradas diferenças estatisticamente significativas ao comparar a presença de genótipos com sexo, grupos de idade, área rural ou urbana, antecedentes de malária previa e o desfecho clinico dos indivíduos (p>0,05). CONCLUSÕES: O estudo do polimorfismo do gene msp2 tem se mostrado como uma ferramenta útil para o estudo da diversidade genética do P. falciparum. No município de Barcelos a diversidade genética desde parasito foi limitada mostrando só a presença de dois genótipos circulantes e em poucos casos uma multiplicidade da Infecção de dois parasitas simultáneamente / The complex genetic diversity of Plasmodium falciparum is partly responsible for the evasion of the host immune response, the emergence of drug resistance and the difficulty in developing an effective anti-malarial vaccine. Studies on the biology of this parasite are mainly concentrated in holo and hyperendemic malaria areas in sub-Saharan Africa. Research in the Amazon region, is scarce in relation to the genetic diversity of natural populations of P. falciparum. This study analyzed the genetic diversity of P. falciparum isolates from individuals of the Middle Rio Negro, Amazon in Brazil, using the gene coding for the merozoite surface protein 2 (MSP2). METHODOLOGY: The study was conducted in Barcelos, a malaria high epidemiological risk municipality, with an annual average of 5,000 cases in the last five years (mean IPA = 156.4 / 1000). We evaluated 79 samples isolated from subjects presenting clinical malaria or asymptomatic infection. The extracted genomic DNA was subjected to polymerase chain reaction (PCR) to confirm the diagnosis of infection with P. falciparum. A PCR-nested was made for amplification of the gene msp2 block 3 region for differentiation of allelic families (3D7 and FC27); intrafamily diversity was observed after digestion with the enzyme HinfI RESULTS: Only family 3D7 was observed in the samples. Two different genotypes were found circulating in the area, characterized by the combination of fragments 16 bp, 108 bp, 349 (genotype 1) and 16 bp, 108 bp, 400bp (genotype 2). It was observed that only two individuals with clinical malaria carried two genotypes simultaneously. No statistically significant differences were found when comparing the presence of genotypes with sex, age groups (p>0,05). Only two individuals carried out two different genotypes simultaneously (MOI). CONCLUSIONS: The study of polymorphism of the msp2 gene has been shown to be a useful tool for the study of genetic diversity of P. falciparum. The genetic diversity and MOI is very limited in this area with the presence of only two circulating genotypes

Glutamate dehydrogenase a (GDHa) has been suggested as a potential drug target against the malaria parasite Plasmodium falciparum. GDHa knockout cell line was generated and needed a phenotypic description by means of molecular biology and biochemistry. The knockout cell line was tested for higher oxidative stress sensitivity, levels of relevant proteins and gene transcripts were quantified. Furthermore, concentrations of two key molecules enabling redox homeostasis, glutathione and NADPH, were attempted to quantify. Finally, we attempted to disrupt a gene of another glutamate dehydrogenase, gdhb, which did not result in formation of viable parasites. In conclusion, GDHa is not a suitable drug target and GDHb needs to be further elucidated.

The asexual life cycle of Plasmodium falciparum parasites takes only 48 hours, allowing for rapid replication. The continuous infection, rupturing and re-infection of erythrocytes results in the pathogenicity of this disease. Schizogony (nuclear division) in P. falciparum parasites occurs via alternation between the S and M phases of the cell cycle where DNA synthesis occurs in the mature trophozoite and schizont stages, followed by mitosis to form daughter merozoites. Merozoites then give rise to ring stages after they have infected erythrocytes and the ring stages continue their development to trophozoites. This cyclic development, known as the intraerythrocytic developmental cycle, has a unique transcriptional regulation, which is closely linked to cell cycle regulation. However, the intricacies that these mechanisms are controlled by are still unidentified. One of the means in which the P. falciparum parasite’s complex life cycle is controlled is by means of epigenetics. Epigenetics refers to the heritable changes on a phenotypic level, which are independent of changes on a genetic level. One group of enzymes that participates in the parasite’s epigenetic control is the Plasmodium histone deacetylases. Inhibition of histone deacetylases (HDACs) results in hyperacetylation, which causes aberrant gene transcription and eventually results in parasite death. Comparative analyses of three histone isolation methods and analysis of P. falciparum parasite histones and their post-translational modifications (PTMs) by mass spectrometry techniques identified both epigenetically relevant and novel PTMs in P. falciparum parasite histones and led to the discovery of an adapted histone isolation method for investigation of histone PTM landscapes. When this modified method was used for the investigation of histones that were isolated from P. falciparum parasites treated with HDAC inhibitors compared to untreated parasites, differences were seen in the PTM landscape. Subsequent in silico screening strategies were used to identify ten compounds from the Medicines for Malaria Venture (MMV) Malaria Box, which target the active site of the zinc-requiring PfHDAC1. From these, eight compounds showed inhibition of proliferation of cultured P. falciparum parasites. Ensuing, the adaptation of an HDAC assay to investigate histone deacetylase inhibition was used to validate these compounds as possible PfHDAC1 inhibitors, with at least two of the compounds showing significant inhibition of PfHDAC1 activity, comparable to that of the known HDAC inhibitor, suberoylanilide hydroxamic acid, SAHA. The use of in silico screening of a large library of compounds, such as the MMV Malaria Box, successfully narrows down candidates for possible anti-malarials with drug-like properties by identification of their cellular targets. This work is method-based and facilitates the investigation of the epigenetic landscape of histones, and the identification of novel HDAC inhibitors. / Dissertation (MSc)--University of Pretoria, 2014. / gm2014 / Biochemistry / unrestricted

Magister Pharmaceuticae - MPharm / Plasmodium falciparum malaria continues to be a worldwide health problem, especially in developing countries in Africa and is responsible for over a million fatalities per annum. Chloroquine (CQ) is low-cost, safe and was the mainstay aminoquinoline derived chemotherapeutic agent that has been used for many years against blood-stage malaria. However, today the control of malaria has been complicated by increased resistance of the malaria parasite to existing antimalarial agents such as CQ. The primary cause of resistance is mutation in a putative ATP-powered multidrug efflux pump known as the p-glycoprotein (pGP) pump, and point mutation in P. falciparum CQ resistance transporter (PfCRT) protein. These mutations are responsible for the reduced accumulation of CQ at its primary site of action, the acidic digestive food vacuole of the parasite.To overcome the challenges of CQ resistance in P. falciparum, chemosensitiser offer an attractive approach. Chemosensitisers or reversal agents are structurally diverse molecules that are known to reverse CQ resistance by inhibiting the pGP efflux pump and/or the PfCRT protein associated with CQ export from the digestive vacuole in CQ resistant parasites. Chemosensitisers include the well-studied calcium channel blocker verapamil and antihistaminic agent chlorpheniramine. These drugs have little or no inherent antimalarial activity but have shown to reverse CQ resistance in P. falciparum when co-administered with CQ. Because of the channel blocking abilities of pentacycloundecylamines (PCUs) such as NGP1-01, it is postulated that these agents may act as chemosensitisers and circumvent the resistance of the Plasmodium parasite against CQ. Therefore as a proof of concept we conducted an experiment using CQ co- administered with different concentrations of NGP1-01 to evaluate the ability of NGP1-01 to act as a chemosensitiser.Herein, we report the ability of NGP1-01, the prototype pentacycloundecylamine (PCU), to reverse CQ resistance (> 50 %) and act as a chemosensitiser. NGP1-01 alone exhibited very low intrinsic antimalarial activity against both the resistant and sensitive strain (> 2000 nM), with no toxicity to the parasite detected at 10 µM. A statistically significant (p < 0.05) dose dependent shift was seen in the CQ IC50 values at both 1 µM and 10 µM concentration of co-administeredNGP1-01 against the resistant strain. Based on this finding we set out to synthesise a series of novel agents comprising of a PCU moiety as the reversal agent (RA) conjugated to a CQ-like aminoquinoline (AM) molecule and evaluate the potential of these PCU-AM derivatives as antimalarial- and/or reversed CQ agents. As recently shown by Peyton et al., (2012), the conjugation of a CQ-like molecule with a RA such as the chemosensitiser imipramine and derivatives thereof is a viable strategy to reverse CQ resistance in multidrug-resistant P. falciparum. The novel compounds were obtained by amination and reductive amination reactions. The synthetic procedures involved the conjugation of the Cookson’s diketone with different tethered 4-aminoquinoline moieties to yield the respective carbinolamines and the subsequent imines. This was followed by a transannular cyclisation using sodium cyanoborohydride as reducing agent to yield the desired PCU-AM derivatives. The CQ-like AMderivatives were obtained using a novel microwave (MW) irradiation method. Structure elucidation was done by utilising 1H- and 13C NMR spectroscopy as well as IR absorption spectrophotometry and mass spectrometry. Five PCU-AM reversed CQ derivatives were successfully synthesised and showed significant in vitro antimalarial activity against the CQ sensitive strain (NF54). PCU-AM derivatives 1.1 – 1.4 showed antimalarial IC50 values in the ranges of 3.74 – 17.6 ng/mL and 27.6 – 253.5 ng/mL against the CQ-sensitive (NF54) and CQ-resistant strains (Dd2) of Plasmodium falciparum, respectively. Compound 1.1 presented with the highest antimalarial activity against both strains and was found to be 5 fold more active against the resistant strain than CQ. The reversed CQ approach resulted in improved resistance reversal and a significantly lower concentration PCU was required compared to NGP1-01 and CQ in combination. This may be attributed to the improved ability of compound 1.1 to actively block the pGP pump and/or the increased permeability thereof because of the lipophilic aza-PCU moiety. Compound 1.1 also showed the lowest RMI value confirming that this compound has the best potential to act as a reversed CQ agent in the series. Cytotoxicity IC50 values observed for compounds 1.1 – 1.4 were in the low micromolar concentrations (2.39 – 9.54 µM) indicating selectivity towards P. falciparum (SI = 149 – 2549) and low toxicity compared to the cytotoxic agent emetine (IC50 = 0.061 µM).These results indicate that PCU channel blockers and PCU-AM derived conjugates can be utilised as lead molecules for further optimisation and development to enhance their therapeuticpotential as reversal agents and reversed CQ compounds.

Malaria causes nearly 3 million deaths annually. The parasite species responsible for the most lethal forms of malaria is P. falciparum (Miller et.al., 2002). Its destructive effect is most evident in the developing African countries, which lack the infrastructure and financial support to effectively control the disease. The only viable means of control at this stage is the use of antimalarial chemotherapy and –prophylaxis, but these drugs are losing their effectivity due to parasite resistance. This underlines the need for new, safe, efficient and cheap drugs as a solution to the African malaria problem. Within the validated folate metabolic pathway of P. falciparum, the identification of three new genes has provided new options for drug inhibition (Lee et.al., 2001). One of these genes encodes the bifunctional dihydrofolate synthase-folylpolyglutamate synthase (DHFS-FPGS), which is unique to P. falciparum (Salcedo et.al., 2001). When compared to human folylpolyglutamate synthase (FPGS), the parasite enzyme is an attractive drug target for selective inhibition due to the additional DHFS activity and low sequence similarity. However, to assess the value of DHFS-FPGS as a drug target and rationally design new drugs against the enzyme, large amounts of enzyme are needed for activity studies and structural determination. The heterologous expression of malaria genes often result in low expression levels, due to its high A+T content and codon bias. To circumvent this problem, a modified P. falciparum dhfs-fpgs, adapted to E.coli codon preferences and with a lower A+T content was synthesised in this study for increased expression. A two-step overlap-extension PCR method was optimised for the synthesis of the 1586bp dhfs-fpgs from only 1 pmol each of partially overlapping oligonucleotides. The use of partially overlapping oligonucleotides, lower amounts of starting material and fewer PCR cycles cut the costs of gene synthesis and the optimisation increased PCR efficiency, when compared to other gene synthesis reports (Carpenter et al., 1999; Zhang et al., 2002). The correct sequences could be obtained from the sequencing of as little as three clones. The successfully constructed dhfs-fpgs gene was expressed in a variety of E. coli expression hosts and vector systems. In all the systems, expression levels of the synthetic gene were much higher than for the native P. falciparum gene. Functional complementation of a DHFS-FPGS deficient E. coli strain verified that the DHFS and FPGS activities were encoded by the synthetic gene, that complementation was achieved to a greater extent than for native P. falciparum dhfs-fpgs and that a synthetic tagless and C-terminal Histidine-tagged DHFS-FPGS had the highest levels of DHFS and FPGS activity. Preliminary purification studies for these two constructs were performed for optimised enzyme isolation, to be followed by activity assays. These optimisations will also serve as basis for future large-scale isolation strategies to obtain sufficient amounts of protein for the structural determination of the enzyme, which would be vital to drug target verification, drug development and –design, thus paving the way for a new generation of antifolate malaria therapy. / Dissertation (MSc(Biochemistry))--University of Pretoria, 2006. / Biochemistry / unrestricted

The effect of infectious diseases on the population in the developing countries is of utmost concern. Malaria, tuberculosis (TB) and human immunodeficiency virus (HIV) are the three major infectious disease threats. They account for approximately half of the mortality caused by infectious diseases, which is almost half of the mortality in the developing countries. With no vaccine likely in the foreseeable future, drugs remain the best means of controlling infectious diseases. In the industrialized nations at the present time, some 50% of all prescribed drugs are derived or synthesized from natural products (animals, marine species, plants and micro-organisms). It has been estimated that plants are the most important source of medicine for more than 80% of the world’s population. As previous work on the leaves of Croton steenkampianus gave promising results and revealed that it still contained bioactive compounds that could be isolated, it was chosen for further work. The bioassay guided fractionation of the ethanol crude extract using silica and Sephadex column chromatography resulted in the isolation of six compounds: three flavoniods (quercetin, tamarixetin and eriodictyol), one new indane (1) (2,6-dimethyl-1-oxo-4 indanecarboxylic acid) and two new diterpenes (steenkrotin A (2) and steenkrotin B (3)) with novel skeletons. The structure of the compounds was determined using NMR, IR, UV, MS and X-ray crystallography. Ethanol crude extract, quercetin, steenkrotin A, steenkrotin B and the indane were tested against four strains of Plasmodium falciparum (D6, D10, Dd2 and W2). Quercetin showed good antiplasmodial activity against the D10 and Dd2 strains. The antiplasmodial activity of steenkrotin A and crude extract were moderate. The antimalarial activity of steenkrotin A in particular is promising, as it showed more activity against resistant strains. The indane, and steekrotin B were not active against the strains of P. falciparum used (IC50 > 10 μg/m). The IC50 of the compounds improved when they were combined with chloroquine. However, the IC50 of chloroquine was still the lowest. The compounds showed moderate bioactivity against Bacillus cereus and Escherichia coli. The three new compounds (1, 2 and 3) tested against Mycobacterium (H37Rv) were not active (IC50 > 10 μg/ml). The indane (1) showed anti-HIV activity at 50 μg/ml against reverse transcriptase. The antioxidant activity of the compounds tested ranged from weak to excellent (>280.00 μg/ml for compound 1 and 2 to 0.05 μg/ml for quercetin). The cytotoxicity of the compounds and extract were determined against Vero cells lines. Their IC50 values ranged from 34.0 to 305.9 ìg/ml, which is higher and better than that of chloroquine. The IC50 values obtained are: chloroquine (25.0), quercetin (33.6), steenkrotin A (35.0), ethanol extract (45.0), tamarixetin (53.8), indane (248.2) and steenkrotin B (305.9). / Thesis (PhD)--University of Pretoria, 2009. / Plant Science / unrestricted

Human malaria caused by Plasmodium falciparum is a major global burden killing between 700,000 and 2.7 million people every year. Africa bears the greatest portion of this burden, with over three quarters of deaths occurring in African children, accounting for 18% of all child deaths in sub-Saharan Africa. Synthesis of tetrahydrofolate through the folate biosynthetic pathway is vital for the survival of P. falciparum parasites and is lacking in the human host. As such, enzymes of this pathway have long presented attractive targets for drug therapy and although increasingly being compromised by resistance, anti-folates such as pyrimethamine and sulfadoxine are still very valuable drugs in many malaria-endemic regions.In this project, further investigation of the enzymes of the folate biosynthetic pathway has been attempted by developing protocols to quantify these proteins and others through proteomic techniques. Two quantification techniques were pursued. The first was quantification using whole, heterologously expressed, stable-isotope labelled forms of P. falciparum proteins for use as heavy standards in mass spectrometry. Great difficulty was experienced in the effort to express and purify P. falciparum enzymes in E. coli expression systems, with only one enzyme successfully expressed and purified in a 13C-labelled form. This one protein was taken forward into quantification experiments. The second quantification technique used a stable-isotope labelled ‘QConcat’ protein, consisting of a number of peptides from 12 P. falciparum proteins of interest, as a heavy standard in mass spectrometry. This was successfully expressed and purified in a 13C-labelled form from an artificial gene using an E. coli expression system. This too was taken forward into quantification experiments.Quantification experiments using the QConcat-based quantification technique were successfully performed on whole P. falciparum extract. Among the proteins quantified were SHMT and DHFR, two proteins of great interest from the folate biosynthetic pathway. Consistent with results from different expression analysis techniques in the literature, the folate enzymes were found to be of lower abundance than housekeeping enzymes and SHMT was found to be more abundant than DHFR.For deep quantitative analysis of the P. falciparum proteome, it was found that fractionation was necessary. Fractionation in this project was performed using a ZOOM™ IEF fractionator (Invitrogen), an OFFGEL™ IEF fractionator (Agilent) and 1D SDS-PAGE. It was found that by using these fractionation techniques, more proteins could be identified within the P. falciparum proteome, with all but one of the enzymes of the folate biosynthetic pathway being identified. Significant advances in the sensitivity of mass spectrometers during this project have also greatly facilitated the investigation of the proteome. In some cases, this meant that proteins which were only previously accessible by prefractionation of the proteome could be seen in whole P. falciparum extract. Unfortunately, QConcat-based quantification using both fractionation and sensitive mass spectrometry could not be successfully achieved in the time available. However, the promising results obtained suggest that, after careful optimisation, such an approach will be valuable.

The discovery of new β-haematin inhibitors has become one focus for researches in response to the resistance of P. falciparum malaria parasites that emerged towards well-known antimalarials. While hundreds of new β-haematin inhibitors have been discovered using detergent mediated high-throughput screening methods, a crucial aspect is understanding exactly how these β-haematin inhibitors behave in the malaria parasite and inhibit the formation of haemozoin. What is known, is that well-known β-haematin inhibitors like chloroquine cause increased amounts of exchangeable haem in the parasite digestive vacuole and form a Fe(III)PPIX-inhibitor complex by accumulating at high concentrations which consequently inhibits parasite growth. Another important focus is on understanding the digestion of haemoglobin and its role in haemozoin formation. This research investigates the in vitro modelling of cellular haemozoin and inhibition by various β-haematin inhibitors across different scaffolds and the role of haemoglobin degradation in P. falciparum malaria parasites. The investigated β-haematin inhibitors resulted in micromolar IC50 (NF54) values and decreased parasite growth with increases in concentration. Using a pyridine-based parasite haem fractionation plate method, these β-haematin inhibitors were shown to target haemozoin formation by causing increased amounts of exchangeable haem that corresponded to decreasing amounts of haemozoin in chloroquine-sensitive parasites. The amounts of exchangeable haem were shown to be inversely proportional to the percentage of parasite growth in the presence of these β-haematin inhibitors. It was apparent that there was a tendency for parasite growth inhibition activity to decrease as the amount of exchangeable haem present in chloroquine sensitive parasites increased, although, the trend was not statistically significant. Moreover, it was observed that experimental cellular accumulation ratio values were low in comparison to chloroquine and amodiaquine. Based on the experimental cellular accumulation ratio values, it was deduced that the accumulation of these β-haematin inhibitors was not primarily due to pH trapping and more complex than previously proposed. Further investigations into the exchangeable haem amounts as a function of intracellular test compound amounts at the IC50 values of these β-haematin inhibitors highlighted that there was an apparent 1:1 relationship with the amount of intracellular exchangeable haem, indicative of complex formation. Transmission electron microscopy images were obtained for untreated parasites that showed intact parasites inside red blood cells with clearly visible haemozoin crystals dispersed throughout the parasite digestive vacuole, whilst, treated parasites showed less defined haemozoin crystals as a result of inhibition. Moreover, electron energy-loss spectroscopy revealed that untreated parasites exhibited a strong iron signal which was associated with haemozoin in the parasite digestive vacuole with a weaker signal attributed to the red blood cell cytoplasm. Similarly, a strong iron signal was shown in the digestive vacuole of treated parasites which was associated with less defined haemozoin crystals. A halo around these haemozoin crystals was observed and was suggested to be indicative of the build-up of exchangeable haem. Additionally, a strong bromine signal attributed to a bromine-containing β-haematin inhibitor, test compound 1, was also observed in the same region as the haemozoin crystals. Overlaid signal distribution maps for iron and bromine showed direct evidence of Fe(III)PPIX and test compound 1, suggesting complexation. High-quality Raman spectra were obtained for the Fe(III)PPIX species in red blood cells, chloroquine sensitive parasites and synthetically prepared samples for the Fe(III)PPIX porphyrin dominated spectral region of 1700-500 cm-1 at an excitation wavelength of 532 nm. From the spectra, a putative Fe(III)PPIX-test compound 1 complex was identified and shown to be similar to the synthetically prepared counterpart, haematin-test compound 1 mixture. It was highlighted that a unique peak at 1080 cm-1 indicated π- π interactions between the pyrrole-imidazole ring and thus confirming that the formation of this putative Fe(III)PPIX-inhibitor complex occurs. The confocal Raman true mapping technique proved to be efficient and reliable for imaging the signal distribution of haemozoin at the Raman peak of 754 cm-1 and 1080 cm-1 for the Fe(III)PPIX-test compound 1 complex which co-localized in the digestive vacuole of chloroquine sensitive parasites. Moreover, oxy- and deoxy-haemoglobin was observed to be localized to the red blood cell, where, deoxy-haemoglobin was located on the outer parts of the parasite. Principle component analysis, based on the Raman peak positions, exhibited significant differences in the spectra for Fe(III)PPIX species in red blood cells, chloroquine sensitive parasites and synthetic samples where clusters were observed to separate mainly along principle component 1. These data proved that the spectra of the Fe(III)PPIX-test compound 1 complex was the same as its synthetically prepared counterpart but different from the remaining Fe(III)PPIX species. In comparison to the Fe(III)PPIX-test compound 1 complex, the cluster separations were observed to be significant, where, no significant separation was observed for the Fe(III)PPIX-test compound 1 complex and the haematin-test compound 1 mixture. Based on this, it was evident that a Fe(III)PPIX-test compound 1 complex existed in the digestive vacuole of treated chloroquine sensitive parasites. To fully understand the inhibition of haemozoin, the development of a haem pathway model is necessary, but, requires certain prerequisites. Bioinformatics data from PAXdb and ExPASy revealed that chloroquine resistance (Dd2) parasites, containing 1337 previously identified proteins with an average abundance-weighted molecular weight of 40,483 ± 77 g/mol. With this, the protein mass per cell for red blood cells, chloroquine-sensitive and - resistant parasites were consistent across three protein quantification methods was measured and revealed that chloroquine resistant parasites had a significantly higher protein mass per cell than chloroquine sensitive parasites and in turn a higher total number of protein molecules per cell. Aspartic proteases are 4-fold higher in concentration than cysteine proteases with histo-aspartic protease having the highest concentration in chloroquine resistant parasites. Along with these data, a time point quantification for chloroquine sensitive parasites throughout the blood-stage showed that the amount of haemoglobin decreased in a sigmoidal manner and corresponded to a linear increase in the amount of haemozoin and relatively constant exchangeable haem amount. This was consistent with Giemsa smears that showed that for early time points, large initial decreases in the amount of haemoglobin were observed between the early trophozoite to late trophozoite stage.

Chloroquine was one of the main malarial treatments until the late 1960s when resistance began to emerge. This antimalarial targets haemozoin formation which causes a cytotoxic accumulation of free haem in the malaria parasite leading to parasite death. This is still one of the most promising pathways for treatment of the most prevalent species of malaria parasite, Plasmodium falciparum to date but, owing to growing resistance to chloroquine and other current antimalarial drugs, there is a dire need for new drugs. One strategy is to investigate non-chloroquine haemozoin inhibitors. High-throughput screening (HTS) was previously used to investigate novel β-haematin (synthetic haemozoin) inhibitors with promising P. falciparum growth inhibition activities. Of the 144 330 compounds screened, two hit compounds were selected for investigation in this project with two different scaffolds, namely benzimidazole and carbazole indole. In order to preselect benzimidazole derivatives for synthesis, Discovery Studio and Pipeline Pilot where used in tandem to enumerate 325 728 in silico compounds. These were filtered according to predicted β-haematin inhibition activities, followed by predicted malaria parasite growth activities using previously developed models based on Bayesian statistics. The predicted active compounds were further subjected to an in silico aqueous solubility model and separated according to predicted solubility values however, only 68 out of the 35 124 active compounds showed moderate solubility whilst the rest were poorly soluble. From this data, eighteen compounds were chosen for synthesis with varying functional groups. Using the same Bayesian models, biological activities for seven fragment compounds derived from the benzimidazole hit compound were predicted. Six out of seven were predicted to be β-haematin inhibitors while five out of seven were predicted active against the malaria parasite growth inhibition model. Similar Bayesian predictions were carried out on the seven proposed carbazole indole compounds with three compounds predicted to be β-haematin inhibitors while six compounds were predicted to be active against the malaria parasite growth inhibition model. The eighteen benzimidazole compounds were synthesized using a two-step synthesis, via a condensation reaction using polyphosphoric acid (PPA), 4-aminobenzoic acid and o-phenylenediamine to form the primary amine benzimidazole intermediate after which ani acylation reaction with the appropriate acid chloride furnished the desired compounds. β-haematin inhibition analysis revealed a 78% hit rate compared to the Bayesian predictions which resulted in a 24-fold enrichment compared to random screening. SAR analysis revealed an activity trend related to the position of substituents on the ring system as follows: para < ortho < meta. The type of ring system was also investigated, with a trend of phenyl < furan < pyrrole < thiophene < pyridyl found. The fragment compounds were either purchased or synthesized via standard acylation conditions using acid chlorides or acetic anhydride with primary amines as before. β-haematin inhibition analysis showed all these compounds to be inactive at the 100 µM cut-off but these compounds were still carried through to the next stage of testing in spite of these results. Molecular docking was carried out on all eighteen benzimidazole compounds in Materials Studio using the (001) and (011) β-haematin crystal faces for adsorption, together with a modified CVFF force-field. This showed a correlation between adsorption energies of the (011) β-haematin crystal face with the experimental β-haematin inhibition values. This indicated that the (011) β-haematin crystal face was the most important for β-haematin inhibition. Analysis of the benzimidazole compounds and their π-π and hydrogen bonding interactions was performed. The number of π-π interactions were found to be important for β-haematin inhibition activity. Both sets of benzimidazole compounds were tested against the NF54 chloroquine sensitive malaria parasite using growth inhibition assays with a 50% hit rate shown for the benzimidazole compounds and a 71% hit rate for the fragment study leading to a 26-fold and 36-fold enrichments compared to random screening. SAR analysis of the benzimidazole compounds revealed a trend for activity in relation to substituent position of para ≈ ortho < meta and a ring system trend of phenyl < pyridyl < thiophene < furan < pyrrole. The benzimidazole compounds were further tested against the chloroquine resistant Dd2 P. falciparum strain which showed that disubstituted compounds were more active against this strain. Cellular haem fractionation studies revealed an increase in free haem and decrease in haemozoin confirming that haemozoin inhibition is the mode of action for the benzimidazole compounds. QSAR analysis of these compounds revealed a correlation between the -Log(P. falciparum IC50) which is also known as pLog(P. falciparum IC50) and 1/βhaematin IC50, number of hydrogen bond donors and molecular depth with 1/β-haematin IC50 the most dominant term. iv The first four carbazole indole compounds were synthesized using a two-step synthesis via deprotonation of carbazole and reaction with epichlorohydrin or 1,3-dibromopropane to furnish the epoxide or alkylbromine intermediates. These intermediates underwent a further SN2 reaction using deprotonated indole to furnish four final compounds. Synthesis of another three derivatives required benzyl protection of 7-hydroxyindole alcohol first, followed by reaction with the epoxide intermediates via an SN2 mechanism to furnish the final three compounds. Analysis using the turbidimetric solubility assay revealed the best aqueous solubility range of this series of compounds to be 10-20 µM (moderately soluble). β-haematin inhibition studies were carried out on this series of compounds with a 100% hit rate found when compared to the Bayesian model data which lead to 30-fold enrichment when compared to random screening. SAR analysis showed an increase in the number of hydroxyl groups led to an increase in β-haematin inhibition activity. Docking studies were performed on these seven compounds and showed that hydrogen bonding played a role in anchoring the molecules in the binding pocket on the crystal surface with increased adsorption energies seen with an increase in the number of hydroxyl groups. Malaria parasite growth inhibition studies showed no compounds to be active against the NF54 and Dd2 strains at the 2 µM cut-off. Cellular haem fractionation studies on the carbazole indole compounds showed that this series of compounds acts via a mechanism that results in inhibition of haemoglobin uptake into the food vacuole and not via haemozoin inhibition.