Diss. (sammanfattning) Stockholm : Karol. inst., 2004. / Härtill 5 uppsatser.

Submitted by Ana Maria Fiscina Sampaio (fiscina@bahia.fiocruz.br) on 2012-06-05T21:05:38Z No. of bitstreams: 1 Bruno de Bezerril Andrade - 2010.pdf: 74164438 bytes, checksum: a1cccf3d1f924ff7710fc4a73a190f0a (MD5) / Made available in DSpace on 2012-06-05T21:05:38Z (GMT). No. of bitstreams: 1 Bruno de Bezerril Andrade - 2010.pdf: 74164438 bytes, checksum: a1cccf3d1f924ff7710fc4a73a190f0a (MD5) / Universidade Federal da Bahia. Centro de Pesquisas Gonçalo Moniz. Salvador, Bahia, Brasil / A malária é considerada uma das mais importantes doenças infecciosas do mxmdo. Esta doença é causada por diversas espécies do protozoário Plasmodium sp., principalmente o Plasmodium falciparum e o Plasmodium vivax, transmitido por mosquitos do gênero Anopheles. Apesar dos esforços governamentais e privados para o desenvolvimento de estratégias para o controle da doença, o panorama atual da malária está piorando, muito em razão do aparecimento de cepas de parasitas resistentes aos medicamentos. Os casos fatais são relatados principalmente na Áfiica e são causados pelo Plasmodium falciparum. Apesar de ser menos letal, a malária causada pelo Plasmodium vivax é mais amplamente distribuída e pode apresentar também alta morbidade e mortalidade. Na maioria das áreas endêmicas, estudos têm identificado vários fatores relacionados à imunidade clínica ou susceptibilidade aos parasitas. Assim, pelo menos quanto à malária causada pelo Plasmodium falciparum, idade, polimorfismos genéticos e exposição repetida ao parasita são considerados importantes determinantes da evolução da doença. Infelizmente, pouco tem sido feito na identificação de fatores preditores consistentes que poderiam ser usados para avaliação clínica. Este quadro é ainda pior para malária causada pelo Plasmodium vivax, provavelmente porque muitos pesquisadores consideram que é uma doença benigna. Além disso, como a maioria do conhecimento atual sobre a patogênese da malária não ajudou a reduzir a ocorrência da infecção e suas complicações, novas abordagens são necessárias para superar este cenário desfavorável. Esta Tese reúne um conjunto de seis manuscritos que visam identificar potenciais determinantes da gravidade da malária em uma área endêmica da Amazônia Ocidental Brasileira. Em primeiro lugar, um método preciso e eficaz para o diagnóstico da malária foi rastreado através da comparação de vários testes, incluindo um software baseado em redes neurais artificiais. O ensaio molecular mostrou-se o mais eficiente para o diagnóstico da malária sintomáticos e assintomáticos. Além disso, a utilização racional de um teste rápido para diagnóstico da malária pode ser promissora em áreas onde há dificuldade na formação continuada dos técnicos diagnósticos. A rede neural artificial indicou que o balanço de citocinas é um forte determinante do quadro clínico. Em outro estudo, uso de sorologia para mensuração de anticorpos IgG contra o sonicado de glândula salivar do vetor Anopheles darlingi mostrou-se útil para a avaliação da exposição ao Plasmodium vivax e também para estimar a imunidade clínica á malária. Em um terceiro estudo com foco na identificação de outros fatores relacionados à imunidade clínica, a exposição natural ao vírus da hepatite B mostrou-se associada à redução da gravidade clínica da malária causada tanto pelo Plasmodium vivax quanto pelo Plasmodium falciparum. No que diz respeito exclusivamente à malária vivax, os casos graves apresentaram uma intensa e desregulada resposta inflamatoria sistêmica. Nestes pacientes, a enzima antioxidante superóxido dismutase-1 surgiu como um excelente marcador da gravidade e mostrou-se envolvida na patogênese da doença grave, na qual há uma liberação de grandes quantidades de heme livre. Em conjunto, os manuscritos desta tese adicionam importantes informações no entendimento dos mecanismos determinantes da gravidade da malária, extremamente / Malaria is considered one of the most important infectious diseases that ever threaten the world. This disease is caused mainly by the infection with Plasmodium falciparum or Plasmodium vivax transmitted by Anopheles mosquitoes. Despite governmental and private efforts for the development of key strategies for the disease control, the actual panorama of the Plasmodium infection is getting worse due to the emergence of drug resistMt parasite strains. The lethal cases are reported mostly in Africa and are caused by Plasmodium falciparum. Albeit being less lethal, Plasmodium vivax infections are more widely distributed can cause high morbidity and eventually death. In most endemic areas, studies have indentified a number of factors related to clinical immunity or susceptibility to the parasites. Thus, at least regarding the falciparum malaria, age, genetic polymorphisms and repeated exposure to Plasmodium are considered most important determinants of the disease outcome. Unfortunately, little has been made in the screening of reliable predicting factors that could be ultimately used for clinical evaluations. This landscape is even worse for vivax malaria, probably because many researches consider it as a benign disease. Moreover, as most of the current knowledge about the malaria pathogenesis did not truly help to relieve the disease burden, new insights are necessary to overcome this unfavorable scenario. This thesis brings together a set of six manuscripts that aim to identify potential determinants of the disease severity linked to the immunopathogenesis in an endemic area from the western Brazilian Amazon. First, a precise and effective method for malaria diagnosis was screening by comparing multiple tests, including a software based of artificial neural networks. The molecular assay showed to be the most efficient for the diagnosis of symptomatic and asymptomatic malaria. In addition, the rational use of a rapid test for the diagnosis of malaria may be promising in areas where there is difficulty in continued training of technical human resources. The artificial neural network indicated that the cytokine balance is a strong determinant of the clinical presentation. In another study, the use of serology for measuring IgG antibodies against the sonicate salivary gland of Anopheles darlingi vector is a promising marker of exposure to Plasmodium vivax and can also estimate the clinical immunity. Intriguingly, the natural exposure to the hepatitis B virus appeared as an important factor associated with reduced clinical severity for both vivax and falciparum malaria. Concerning solely the vivax malaria, severe cases have an intense and unregulated inflammatory response. In these patients, the antioxidant enzyme superoxide dismutase-1 has emerged as an excellent marker of severity and was involved in the pathogenesis of the severe disease in which there is a release of large amounts of free heme. Together, the manuscripts of this thesis add important information in understanding the mechanisms that determine the severity of malaria.

Submitted by Nuzia Santos (nuzia@cpqrr.fiocruz.br) on 2013-01-25T16:12:26Z No. of bitstreams: 1 Bernardo Simões Franklin.pdf: 11748497 bytes, checksum: e1831598c734af4113b0028438c1b84f (MD5) / Made available in DSpace on 2013-01-25T16:12:26Z (GMT). No. of bitstreams: 1 Bernardo Simões Franklin.pdf: 11748497 bytes, checksum: e1831598c734af4113b0028438c1b84f (MD5) Previous issue date: 2009 / Desde sua descoberta, os receptores do tipo Toll (TLRs) têm sido envolvidos em quase todas as doenças que afetam a saúde humana. Seu papel na proteção contra vários patógenos, incluindo protozoários está bem estabelecido. Entretanto, pouco se sabe sobre o papel dos TLRs na malária. No presente estudo, investigamos o papel dos TLRs durante a malária murina e humana. Nossos resultados mostraram que camundongos com deficiência para MyD88, um adaptador essencial para a sinalização dos TLRs, produzem níveis de citocinas pró-inflamatórias significativamente menores e apresentam sintomas mais amenos durante a infecção por Plasmodium chabaudi. Entretanto, estes animais retêm a capacidade de controlar a parasitemia sugerindo que os TLRs possuam um papel na patogênese e não na proteção contra a malária. Posteriormente, mostramos que ambas, a infecção natural humana por P. falciparum e a experimental murina por P. chabaudi, aumentam a expressão e a responsividade dos TLRs nas células do sistema imune inato. O estado hiper-responsivo das células durante a malária é derivado da ativação de TLR9 e a produção de IFN por células T, levando a uma alta susceptibilidade ao choque séptico durante a malária aguda. Finalmente, em colaboração com a EISAI Research Institute, desenvolvemos um antagonista de TLR9 e testamos seu efeito na Malária Cerebral (CM), uma das manifestações clínicas mais graves da malária. O tratamento oral com este composto inibiu os sintomas, tais como extravasamento vascular cerebral, protegendo camundongos da morte por CM. Em conjunto, nossos resultados mostram um importante papel dos TLRs, especialmente TLR9, na patogênese da malária e que a intervenção na função destes receptores é uma potencial quimioterapia anti-inflamatória contra essa doença. / Toll-like receptors (TLRs) have been involved in almost every know disease that afflict human health so far and their role in resistance to several pathogens, including protozoan parasites, has been well established. The role of TLRs in malaria, however, still remains to be elucidated. Here we studied the role of TLRs in experimental and naturally acquired malaria infection. We showed that mice with deficiency to MyD88, an essential adaptor to TLRs signaling, produce significant lower levels of proinflammatory cytokines and commensurate better clinical outcome upon infection with Plasmodium chabaudi. Nevertheless, these mice can still control parasite loads suggesting that TLRs are involved in pathogenesis rather than protection during malaria. We further studied cellular responsiveness of innate immune responses during human and murine malaria. We showed that both natural acquired P. falciparum infection in humans and experimental infection of mice with P. chabaudi increase TLR expression in innate immune cells causing pro-inflammatory priming of TLR responses. The cellular hyper-responsiveness during Malaria is caused by TLR9 activation and IFN production by T cells conferring high susceptibility to septic shock during the acute disease. Finally, in collaboration effort with EISAI Research Institute, we develop and tested an antagonist of TLR9, on Cerebral Malaria (CM), one of the most severe manifestations of malaria. Oral treatment of mice with this compound inhibited CM symptoms, such as vascular leakage, and prevented death from CM. All together our results show an important role of TLRs, especially TLR9, in malaria pathogenesis and that the therapeutic targeting of TLRs is a potential anti-inflammatory chemotherapy against malaria.

Submitted by Izabel Franco (izabel-franco@ufscar.br) on 2016-09-20T14:33:37Z No. of bitstreams: 1 TeseDSC.pdf: 4230414 bytes, checksum: d505357e4ed13e446578eb00507beec7 (MD5) / Approved for entry into archive by Marina Freitas (marinapf@ufscar.br) on 2016-09-21T12:36:04Z (GMT) No. of bitstreams: 1 TeseDSC.pdf: 4230414 bytes, checksum: d505357e4ed13e446578eb00507beec7 (MD5) / Approved for entry into archive by Marina Freitas (marinapf@ufscar.br) on 2016-09-21T12:36:19Z (GMT) No. of bitstreams: 1 TeseDSC.pdf: 4230414 bytes, checksum: d505357e4ed13e446578eb00507beec7 (MD5) / Made available in DSpace on 2016-09-21T12:36:27Z (GMT). No. of bitstreams: 1 TeseDSC.pdf: 4230414 bytes, checksum: d505357e4ed13e446578eb00507beec7 (MD5) Previous issue date: 2015-06-16 / Não recebi financiamento / Malaria is an acute febrile disease caused by protozoan parasites of the genus Plasmodium, being the species P. falciparum responsible for the most severe forms and deaths caused by the disease. These parasites have developed resistance to commonly used drugs and therefore there is a need to develop new antimalarial agents. Aryltetralone lignans are compounds that show antiplasmodial activity in vitro against P. falciparum, but its mechanism of action is still not fully understood. In this work, we postulate a plausible mode of action of some aryltetralone lignans and according to the obtained results we suggest modifications to the ligands for a better biological activity. In order to achieve our objectives we first performed a search for similar chemical compounds, for which their macromolecular targets were known. From the results obtained, P. falciparum tubulin was selected as a potential target for these lignans. Since there is no experimentally determined three-dimensional structure for this protein, we performed a molecular homology modeling of P. falciparum tubulin and the structure of bovine tubulin complexed with colchicine was selected as template. The analysis of the obtained model showed that the three dimensional structure of Plasmodium tubulin is conserved in relation to the bovine tubulin with some important substitutions occurring in the colchicine binding site region: Ala250B by Ser248B, Ala316B by Cys314B and Ile318B by Met316B. Then, molecular docking of the aryltetralone lignans, colchicine and podophyllotoxin was performed in the modeled P. falciparum tubulin. The docking calculations results allowed to conclude firstly that, although the amino acid substitutions in the binding site, the colchicine binding mode in the P. falciparum tubulin is exactly the same as that already described in the literature for bovine tubulin. As for podophyllotoxin, a different binding mode from that described in the literature for bovine tubulin was obtained due to the replacement of Ala250B by Ser248B and the Val318B by Met316B. For the aryltetralone lignans studied, three different binding modes were obtained: one exhibited by compounds 1, 2 and 3, another by 4 and 6, and a third one by 5. The lignans 1, 2 and 3 are oriented in a way so that the C ring containing the dimethoxy or methylenedioxy group is positioned in the same region obtained for the ring containing the trimethoxy group in the case of colchicine and podophyllotoxin, performing a C-H...π interaction with Leu246B. Lignans 4 and 6 orient themselves with the aromatic ring C between Ala180A and Leu246B and being held in this position by C-H...π interactions. Lignan 5 is oriented with the aromatic ring C between Leu246B and Leu253B, performing C-H...π interactions with these residues, in a similar way to what was obtained with colchicine in this site. So the likely mechanism of action of the aryltetralone lignans studied here would be their binding to the same colchicine binding site in the tubulin protein of P. falciparum and thereby interrupting the divisions and other cellular functions. / A malária é uma doença febril aguda causada por protozoários parasitas pertencentes ao gênero Plasmodium, sendo a espécie P. falciparum a responsável pela maioria das formas severas e mortes pela doença. Estes parasitas desenvolveram resistência aos fármacos comumente utilizados e, portanto, existe a necessidade de se desenvolver novos agentes antimaláricos. Lignanas ariltetralônicas são compostos que apresentam atividade antiplasmodial in vitro contra o P. falciparum, porém seu mecanismo de ação ainda não é totalmente compreendido. Neste trabalho, conseguimos postular o modo de ação de algumas lignanas ariltetralônicas e, a partir dos resultados obtidos, sugerimos modificações nestes compostos de modo a obter uma melhoria na sua atividade biológica. Para isso, primeiramente foi realizada uma busca por compostos químicos semelhantes, cujos alvos macromoleculares eram conhecidos. A partir dos resultados obtidos, selecionou-se a tubulina do P. falciparum como potencial alvo para estas lignanas. Como não há estrutura tridimensional determinada experimentalmente para esta proteína, foi realizada a modelagem molecular por homologia da tubulina do P. falciparum, selecionando como molde a estrutura da tubulina bovina complexada com colchicina. A partir da análise do modelo construído, verificou-se que a estrutura tridimensional da tubulina do Plasmodium é conservada em relação à tubulina bovina e que ocorrem algumas substituições importantes na região do sítio de ligação da colchicina: Ala250B por Ser248B, Ala316B por Cys314B e Ile318B por Met316B. Em seguida, foi realizado o docking molecular das lignanas ariltetralônicas, da colchicina e da podofilotoxina na tubulina do P. falciparum. Os resultados do docking permitiram concluir primeiramente que, embora ocorram algumas substituições de aminoácidos no sítio, o modo de ligação da colchicina na tubulina do P. falciparum é exatamente o mesmo ao já descrito na literatura para a tubulina bovina. Já para a podofilotoxina, foi obtido um modo de ligação diferente do descrito na literatura para a tubulina bovina, devido à substituição da Ala250B pela Ser248B e da Val318B pela Met316B. Para as lignanas ariltetralônicas estudadas, foram obtidos três modos de ligação diferentes: um exibido pelos compostos 1, 2 e 3, outro para 4 e 6 e um terceiro modo exclusivo para 5. As lignanas 1, 2 e 3 orientam-se de modo que o anel C, que contém o grupo dimetóxi ou metilenodióxi, se posiciona na mesma região do sítio obtida para o anel contendo o grupo trimetóxi da colchicina e da podofilotoxina, realizando uma interação C–H...π com a Leu246B. As lignanas 4 e 6 orientam-se com o anel aromático C entre a Ala180A e a Leu246B, sendo mantido nesta posição por interações C–H...π. No caso da lignana 5, esta se orienta com o anel aromático C entre a Leu246B e Leu253B, realizando interações C– H...π com estes resíduos, semelhante ao que foi obtido para a colchicina neste sítio. Assim, o mecanismo provável de ação das lignanas ariltetralônicas aqui estudadas passaria pela sua ligação ao mesmo sítio de ligação da colchicina na proteína tubulina do P. falciparum e, com isso, interrompendo as divisões e outras funções celulares.

Heat Shock 40 kDa proteins (Hsp40s) partner with heat shock 70 kDa proteins (Hsp70s) in facilitating, among other chaperone activities; correct protein transport, productive protein folding and assembly within the cells; under both normal and stressful conditions. Hsp40 proteins regulate the ATPase activity of Hsp70 through interaction with the J-domain. Plasmodium falciparum Hsp70s (PfHsp70s) do not contain a Plasmodium export element (PEXEL) sequence although PfHsp70-1 and PfHsp70-3 have been located outside of the parasitophorous vacuole. Studies reveal that a type I P. falciparum (PfHsp40) chaperone (PF14_0359) stimulates the rate of ATP hydrolysis of the cytosolic PfHsp70 (PfHsp70-1) and that of human Hsp70A1A. PFE0055c is a PEXEL-bearing type II Hsp40 that is exported into the cytosol of P. falciparum-infected erythrocytes; where it potentially interacts with human Hsp70. Studies reveal that PFE0055c associates with structures found in the erythrocyte cytosol termed “J-dots” which are believed to be involved in trafficking parasite-encoded proteins through the erythrocyte cytosol. If P. falciparum exports PFE0055c into the host cytosol, it may be proposed that it interacts with human Hsp70, making it a possible drug target. The effect of PFE0055c on the ATPase activity of human Hsp70A1A has not been previously characterised. Central to this study was bioinformatic analysis and biochemical characterisation PFE0055c using an in vitro (ATPase assay) approach. Structural domains that classify PFE0055c as a type II Hsp40 were identified with similarity to two other exported type II PfHsp40s. Plasmids encoding the hexahistidine-tagged versions of PFE0055c and human Hsp70A1A were used for the expression and purification of these proteins from Escherichia coli. Purification was achieved using nickel affinity chromatography. The urea-denaturing method was used to obtain the purified PFE0055c whilst human Hsp70A1A was purified using the native method. PFE0055c could stimulate the ATPase activity of alfalfa Hsp70, although such was not the case for human Hsp70A1A in vitro.

This thesis is divided into two distinct sections which can be combined under the broad umbrella of structural bioinformatics studies related to drug discovery. The first section involves the establishment of an online South African natural products database. Natural products (NPs) are chemical entities synthesised in nature and are unrivalled in their structural complexity, chemical diversity, and biological specificity, which has long made them crucial to the drug discovery process. South Africa is rich in both plant and marine biodiversity and a great deal of research has gone into isolating compounds from organisms found in this country. However, there is no official database containing this information, making it difficult to access for research purposes. This information was extracted manually from literature to create a database of South African natural products. In order to make the information accessible to the general research community, a website, named “SANCDB”, was built to enable compounds to be quickly and easily searched for and downloaded in a number of different chemical formats. The content of the database was assessed and compared to other established natural product databases. Currently, SANCDB is the only database of natural products in Africa with an online interface. The second section of the thesis was aimed at performing structural characterisation of proteins with the potential to be targeted for antimalarial drug therapy. This looked specifically at 1) The interactions between an exported heat shock protein (Hsp) from Plasmodium falciparum (P. falciparum), PfHsp70-x and various host and exported parasite J proteins, as well as 2) The interface between PfHsp90 and the heat shock organising protein (PfHop). The PfHsp70-x:J protein study provided additional insight into how these two proteins potentially interact. Analysis of the PfHsp90:PfHop also provided a structural insight into the interaction interface between these two proteins and identified residues that could be targeted due to their contribution to the stability of the Hsp90:Hop binding complex and differences between parasite and human proteins. These studies inspired the development of a homology modelling tool, which can be used to assist researchers with homology modelling, while providing them with step-by-step control over the entire process. This thesis presents the establishment of a South African NP database and the development of a homology modelling tool, inspired by protein structural studies. When combined, these two applications have the potential to contribute greatly towards in silico drug discovery research.

Human malaria is an economically important disease caused by single-celled parasites of the Plasmodium genus whose biology displays great evolutionary adaptation to both its mammalian host and transmitting vectors. This thesis details the 70 kDa heat shock protein (Hsp70) and J protein chaperone complements in malaria parasites affecting humans, primates and rodents. Heat shock proteins comprise a family of evolutionary conserved and structurally related proteins that play a crucial role in maintaining the structural integrity of proteins during normal and stress conditions. They are considered future therapeutic targets in various cellular systems including Plasmodium falciparum. J proteins (Hsp40) canonically partner with Hsp70s during protein synthesis and folding, trafficking or targeting of proteins for degradation. However, in P. falciparum, these classes of proteins have also been implicated in aiding the active transport of parasite proteins to the erythrocyte cytosol following erythrocyte entry by the parasite. This host-parasite “cross-talk” results in tremendous modifications of the infected erythrocyte, imparting properties that allow it to adhere to the endothelium, preventing splenic clearance. The genome of P. falciparum encodes six Hsp70 homologues and a large number of J proteins that localize to the various intracellular compartments or are exported to the infected erythrocyte cytosol. Understanding the Hsp70-J protein interactions and/or partnerships is an essential step for drug target validation and illumination of parasite biology. A review of these chaperone complements across the Plasmodium species shows that P. falciparum possesses an expanded Hsp70-J protein complement compared to the rodent and primate infecting species. It further highlights how unique the P. falciparum chaperone complement is compared to the other Plasmodium species included in the analysis. In silico analysis showed that the genome of P. falciparum encodes approximately 49 J proteins, 19 of which contain a PEXEL motif that has been implicated in routing proteins to the infected erythrocyte. Most of these PEXEL containing J proteins are unique with no homologues in the human system and are considered as attractive drug targets. Very few of the predicted J proteins in P. falciparum have been experimentally characterized. To this end, cell biological and biochemical approaches were employed to characterize PFB0595w and PFD0462w (Pfj1) J proteins. The uniqueness of Pfj1 and the controversy in literature regarding its localization formed the basis for the experimental work. This is the first study showing that Pfj1 localizes to the mitochondrion in the intraerythrocytic stage of development of P. falciparum and has further proposed PfHsp70-3 as a potential Hsp70 partner. Indeed, attempts to heterologously express and purify Pfj1 for its characterization are described. It is also the first study that details the successful expression and purification of PfHsp70-3. Further, research findings have described for the first time the expression and localization of PFB0595w in the intraerythrocytic stages of P. falciparum development. Based on the cytosolic localization of both PFB0595w and PfHsp70-1, a chaperone – cochaperone partnership was proposed that formed the basis for the in vitro experiments. PFB0595w was shown for the first time to stimulate the ATPase activity of PfHsp70-1 pointing to a functional interaction. Preliminary surface plasmon spectroscopy analysis has revealed a potential interaction between PFB0595w and PfHsp70-1 but highlights the need for further related experiments to support the findings. Gel filtration analysis showed that PFB0595w exists as a dimer thereby confirming in silico predictions. Based on these observations, we conclude that PFB0595w may regulate the chaperone activity of PfHsp70-1 in the cytosol while Pfj1 may play a co-chaperoning role for PfHsp70-3 in the mitochondrion. Overall, this data is expected to increase the knowledge of the Hsp70-J protein partnerships in the erythrocytic stage of P. falciparum development, thereby enhancing the understanding of parasite biology.

Malaria is a major public health problem that affects millions of lives globally. The increased burden of malaria requires new interventions that will address the eradication of the disease. Current interventions include vector control by using insecticide-treated bed nets and indoor residual spraying, and antimalarial drugs to control the parasite. Parasite resistance has been reported for the currently used effective antimalarial drugs. To pre-empt the impact of parasite resistance a continued development of new antimalarial drugs that have novel mechanisms of action should be pursued. Antimalarial drug discovery requires that potential antimalarial drugs should have different drug targets to those already targeted, to lower the chances of resistance. Potential antimalarial drugs should preferably provide a single radical cure to prevent reproduction at all life cycle stages. This study tested the effects of in silico designed compounds targeting plasmodial Ca2+- dependent protein kinases (CDPK) 1 & 4, FIKK kinases and bromodomain proteins on the Plasmodium parasite. These enzymes are involved in gene regulation and are important factors during gene transcription. In P. falciparum the gatekeeper kinases contain small hydrophobic pockets near the ATP-binding site. These hydrophobic pockets allow for selective inhibition of these proteins at the ATP-binding site. The compounds were tested in vitro to determine their antiplasmodial activity. These compounds are shown to be potential inhibitors of the intra-erythrocytic P. falciparum parasites as three of the compounds showed selective cytotoxic activity at less than 1 μM against the chloroquine sensitive laboratory strains (3D7 and NF54). Even though the proteins targeted by these compounds have been previously indicated to play a role at specific stages during the parasite’s life cycle, the compounds tested here were not able to target the sexual gametocyte stages of the Plasmodium parasite. Further optimisation of these compounds should be performed to improve activity against both the asexual and sexual stages of the parasites. / Dissertation (MSc)--University of Pretoria, 2017. / Pharmacology / MSc / Unrestricted

PhD (Biochemistry) / Department of Biochemistry / Malaria is a parasitic disease that accounts for more than 660 thousand deaths annually, mainly in children. Malaria is caused by five Plasmodium species P. ovale, P. vivax, P. malariae, P. falciparum and P. knowlesi. The most lethal cause of cerebral malaria is P. falciparum. The parasites have been shown to up-regulate some of their heat shock proteins (Hsp) in response to stress. Heat shock protein 70 (called DnaK in prokaryotes) is one of the most prominent groups of chaperones whose role is central to protein homeostasis and determines the fate of proteins. Six Hsp70 genes are represented on the genome of P. falciparum. The Hsp70 genes encode for proteins that are localised in different sub-cellular compartments. Of these two occur in the cytosol, PfHsp70-z and PfHsp70-1; two occur in the endoplasmic reticulum, PfHsp70-2 and PfHsp70-y; one in the mitochondria, PfHsp70-3 and one exported to the red blood cell cytosol, PfHsp70-x. PfHsp70-1 is a well characterized canonical Hsp70 involved in prevention of protein aggregation and facilitates protein folding. Little is known about PfHsp70-z. PfHsp70-z was previously shown to be an essential protein implicated in the folding of proteins possessing asparagine rich repeats. However, based on structural evidence PfHsp70-z belongs to the Hsp110 family of proteins and is thought to serve as a nucleotide exchange factor (NEF) of PfHsp70-1. The main aim of this study is to elucidate the functional roles of PfHsp70-z as a chaperone and its interaction with PfHsp70-1. In the current study, PfHsp70-z was cloned and expressed in E. coli JM109 cells. This was followed by its purification using nickel chromatography. The expression of PfHsp70-z in parasites cultured in vitro was investigated and its association with PfHsp70-1 was explored using a co-immuno precipitation assay. PfHsp70-z expression in malaria parasites is up regulated by heat stress and the protein is heat stable based on investigations conducted using Circular Dichroism. Furthermore, the direct interaction between recombinant forms of PfHsp70-z and PfHsp70-1 were investigated using slot blot and surface plasmon resonance assays. PfHsp70-z was observed to exhibit ATPase activity. In addition, the direct interaction between PfHsp70-z and PfHsp70-1 is promoted by ATP. Based on limited proteolysis and tryptophan fluorescence analyses, PfHsp70-z binds ATP to assume a unique structural conformation compared to the conformation of the protein bound to ADP or in nucleotide-free state. PfHsp70-z was able to suppress the heat-induced aggregation of malate dehydrogenase and luciferase in vitro. Interestingly, while ATP appears to modulate the conformation of PfHsp70-z, the chaperone function of PfHsp70-z was not influenced by ATP. Altogether, these findings suggest that Characterization of Heat Shock Protein 70-z (PfHsp70-z) from Plasmodium falciparum iii PfHsp70-z serves as an effective peptide substrate holding chaperone. In addition, PfHsp70-z may also serve as the sole nucleotide exchange factor of PfHsp70-1. The broad spectrum of functions of this protein, could explain this PfHsp70-z is an essential protein in malaria parasite survival. This is the first study to show that PfHsp70-z possess independent chaperone activity and that it interacts with its cytosolic counterpart, PfHsp70-1 in a nucleotide dependent fashion. Furthermore, the study shows that PfHsp70-z is a heat stable molecule and that it is capable of forming high order oligomers.

Malaria is prevalent in over 100 countries which is populated by half of the world’s population and culminates in approximately one million deaths per annum, 85% of which occurs in sub-Saharan Africa. The combined resistance of the mosquitoes and parasites to the currently available pesticides and antimalarial chemotherapeutic agents requires the concerted effort of scientists in the malaria field to identify and develop novel mechanisms to curb this deadly disease. In this study, a thorough understanding of the role players in the polyamine pathway of the parasite was obtained, which could aid future studies in the development of novel inhibitory compounds against these validated drug targets. The uniquely bifunctional S-adenosylmethionine decarboxylase/ornithine decarboxylase (AdoMetDC/ODC) of Plasmodium falciparum forms an important controlling node between the polyamine and methionine metabolic pathways. It has been speculated that the unique bifunctional association of the rate-limiting enzymes allows for the concerted regulation of the respective enzyme activities resulting in polyamine synthesis as per requirement for the rapidly proliferating parasite while the methionine levels are strictly controlled for their role in the methylation status. The results of this study showed that the enzyme activities of the bifunctional complex are indeed coordinated and subtle conformational changes induced by complex formation is suggested to result in these altered kinetics of the individual AdoMetDC and ODC domains. Studies also showed that the identification of the interaction sites between the domains, which allows for communication across the complex, may be targeted for specific interference with the enzyme activities. Furthermore, these studies showed that the current knowledge on the different subclasses of the AdoMetDC family should be re-evaluated since P. falciparum AdoMetDC shows diverse properties from orthologues and therefore points towards a novel grouping of the plasmodial protein. The extensive biochemical and biophysical studies on AdoMetDC has also provided important avenues for the crystallisation and solving of this protein’s 3D structure for subsequent structure-based identification of drug-like lead compounds against AdoMetDC activity. The application of structure-based drug design on malarial proteins was additionally investigated and consequently proved that the rational design of lead inhibitory compounds can provide important scaffold structures for the identification of the key aspects that are required for the successful inhibition of a specific drug target. Spermidine synthase, with its intricate catalytic mechanism involving two substrate binding sites for the products of the reactions catalysed by AdoMetDC/ODC, was used to computationally identify compounds that could bind within its active site. Subsequent testing of the compounds identified with a dynamic receptor-based pharmacophore model showed promising inhibitory results on both recombinant protein and in vitro parasite levels. The confirmation of the predicted interaction sites and identification of aspects to improve inhibitor interaction was subsequently investigated at atomic resolution with X-ray protein crystallography. The outcome of this doctoral study shows the benefit in applying a multidisciplinary and multinational approach for studying drug targets within the malaria parasite, which has led to a thorough understanding of the targets on both biochemical and structural levels for future drug design studies. / Thesis (PhD)--University of Pretoria, 2011. / Biochemistry / unrestricted