A malária mata mais de um milhão de pessoas por ano, sendo uma das doenças infecciosas mais relevantes e um grande problema de saúde pública. Além disso, o surgimento de cepas resistentes aos quimioterápicos utilizados faz necessário o estudo de novos alvos para tratamentos contra esta doença. No nosso laboratório foi demonstrada a biossíntese de isoprenóides, em P. falciparum pela via MEP. Sabe-se que substâncias inibidoras da biossíntese de isoprenóides, dentre essas os terpenos, apresentam atividade antimalárica. Levando em consideração o anterior, nós avaliamos o potencial antimalárico do álcool perilico (POH) em P. falciparum e P. berghei. Nossos resultados demonstraram que o POH teve efeito inibitório contra o crescimento do P. falciparum in vitro, nas cepas 3D7 e K1 com uma IC50 de 4,8 ± 0,5 &mu;M, e 10,41±2,33 &mu;M, respectivamente. Além disso, o POH não teve efeito tóxico na linhagem celular Vero. Ainda, Comprovamos que o POH inibiu a farnesilação de proteinas entre 20 e 37 KDa de P. falciparum. Por outro lado, os experimentos in vivo não mostraram eficácia do tratamento do POH contra PbGFP em camundongos Balb/c. Em contraste, foi demostrada a eficácia do POH na de malária cerebral experimental (MCE), , indicando uma redução na taxa de incidência da MCE no grupo tratado com POH, comparado o não tratado ( P<0,05). Além disso, o POH reduziu a inflamação no cérebro dos animais tratados, uma vez que teve uma redução significativa na adesão de leucócitos aos vasos cerebrais (P<0.001), como também, o numero de hemorragias foi menor comparados com os animais não tratados. (P<0.0001). Portanto, os resultados obtidos nesta pesquisa abrem novas alternativas no estudo do mecanismo de ação do POH como um terpeno com grande potencial para tratar MC. / Malaria kills over one million people a year worldwide, and is one of the most important infectious diseases and a major public health problem. Furthermore, the emergence of resistant strains to chemotherapeutic agents used, make it necessary to study new targets for treatments against this disease. In our laboratory we have demonstrated the isoprenoids biosynthesis in P. falciparum, by the MEP pathway. It is known that the substances that inhibit isoprenoid biosynthesis, among these terpenes, have antimalarial activity in vitro and in vivo. Considering this, we evaluate the antimalarial potential of PA (POH) in P. falciparum and P. berghei. Our results showed that the POH had inhibitory effect against the growth of strains 3D7 and K1 of P. falciparum in vitro, with an IC50 of 4.8 &mu;M ± 0.5, and 10.41 ± 2.33 &mu;M, respectively. Furthermore, the POH had no toxic effect on cell line Vero. Moreover, the POH proved that inhibited proteins farnesylation from 20 to 37 kDa of P.falciparum. On the other hand, in vivo experiments did not show efficacy on treatment against POH PbGFP in BALB/c mice. In contrast, the effectiveness of POH in the experimental cerebral malaria (MCE) was demonstrated, indicating a reduction in the incidence rate of MCE in the group treated with POH, compared with of untreated animals (P <0.05). In addition, the POH reduced inflammation in the brain of treated animals, since it had a significant reduction in leukocyte adhesion to cerebral vessels (P <0.001), as also the number of bleeding was lower compared to untreated animals (P<0.0001). Therefore, the results obtained in this work provide new alternatives to study the POH\'s mechanism of action as a terpene with great potential to treat MC.

Le paludisme est l’une des maladies infectieuses la plus fréquente au monde avec 40% de la population mondiale exposée. En dépit des stratégies actuelles de lutte notamment la prise en charge rapide des cas, l’utilisation de matériaux imprégnés et la pulvérisation intra domiciliaire d’insecticide, le paludisme reste une des premières causes de morbidité et de mortalité notamment en Afrique subsaharienne. Cette partie du monde totalise à elle seule plus de 90% des cas de décès par paludisme dont 88% chez les enfants de moins de moins de 5 ans. En absence de vaccin utilisable en santé publique, il y a donc un besoin urgent de trouver une stratégie efficiente et simple de contrôle du paludisme. Le traitement préventif intermittent (TPI) définie comme l’administration d’un antipaludique à dose curative à des intervalles de temps prédéfinis réduit l’incidence du paludisme et apparaît aujourd’hui comme une des stratégies les plus prometteuses. Cette stratégie couplée au Programme Elargi de Vaccination (PEV) chez les enfants de moins de 1 an réduit l’incidence du paludisme de 30%. Des résultats plus importants sont obtenus chez les enfants de 0 à 5 ans voire de 0 à 10 ans lorsque la stratégie est appliquée en ciblant la saison de transmission. Nos travaux de recherche au Mali ont porté sur :- l’impact de la mise en œuvre du TPI couplé à la vaccination du PEV (TPin) sur i) la résistance P. falciparum à la Sulfadoxine pyrimethamine (SP), ii) la couverture des vaccins du PEV, iii) le taux de mortalité des enfants âgés de 4 à 18 mois.- l’efficacité du TPI chez les enfants ciblant la saison de transmission (TPIe) dans un contexte de faible et de forte couverture en des Moustiquaires Imprégnés d’Insecticides (MII). Nos résultats ont montré qu’après une année de mise en œuvre à l’échelle du district sanitaire, le TPIn a entrainé une augmentation de la couverture des vaccins du PEV. Cette couverture était de 53% en zone de non-intervention contre 69.5% en zone d’intervention (p<0.01). Il y a eu une réduction de la mortalité globale de 27% (RR= 0,73, IC95% : 0,55-0,97, p=0,029) chez les enfants âgés de 4 à 18 mois. Les fréquences des marqueurs moléculaires de la résistance de P. falciparum à SP en début et en fin la mise en œuvre et entre la zone d’intervention et la zone de non –intervention après une année de mise en œuvre étaient similaires. Deux doses de SP données en TPI à 8 semaines d’ intervalle durant la saison de transmission réduit le taux d’incidence du paludisme pendant la saison de transmission de 69,4% chez les enfants de moins de 5 ans et de 63,4% chez les enfants de 5-10 ans dans un contexte de très faible utilisation de MII (<5%). Dans une autre étude que nous avons menée, le TPI avec SP + Amodiaquine (AQ) donné en 3 occasions à un mois d’ intervalle pendant la saison de transmission a réduit le taux d’ incidence du paludisme clinique non compliqué de 82% (IC à 95%: 78%– 85%; P<0.001) et les formes graves de paludisme de 87% (IC à 95% 42% – 99%, P=0.001) chez les enfants âgés de 3 à 59 mois en dépit un taux d’utilisation des MII de plus de 99%. Nous n’avons pas documenté d’événement indésirable grave lié à l’utilisation de la SP ou de la SP + AQ en TPI durant ces deux études. Nos résultats étayent la recommandation du TPI, ciblant la saison de transmission ou couplée au PEV, pour la lutte antipaludique chez les enfants. / Malaria is one of the most common infectious diseases in the world and 40% of the world population is exposed to malaria. Despite the current control strategies such as rapid diagnosis and treatment of disease cases, use of insecticide impregnated materials and indoor residuals spraying with insecticides, malaria remained a main cause of morbidity and mortality particularly in sub Saharan Africa. More than 90% of the deaths due to malaria occurred in this region and 88% of these deaths occurred in children aged less than 5 years of age. In absence of vaccine that can be used in public health, there is an urgent need for a simple and efficient control strategy. Malaria intermittent preventive treatment (IPT) defined as the administration of curative dose of anti-malarial drug at predefined time intervals, appears as one of the most promising strategies. Given through the Expanded Program of Immunization (EPI), the strategy reduced the incidence of malaria by 30%. More drastic reductions were obtained in children aged 0-5 years and even 0-10 years when the malaria transmission season was targeted for the administration of the strategy. Our research work in Mali has assessed the following:- The impact of implementation of IPT administrated through EPI (IPTi) on: i) the resistance of P. falciparum to Sulfadoxine pyrimethamine (SP); ii) EPI vaccine coverage, and iii) mortality of children of 4-18 months of age. - The efficacy of IPT in children targeting the malaria transmission season (IPTe) in a context of low and high coverage of insecticide impregnated nets (ITN).We have found that the implementation of IPTi at the district level has resulted in an augmentation of the EPI vaccine coverage. The EPI vaccine coverage was 53% in the non-intervention zone compared to 69.5% in the intervention zone (p<0,01). There was a reduction in all cause mortality of 27% (RR= 0.73, 95% CI : 0.55-0.97, p=0.029) in children aged 4-18 months. The frequencies of molecular markers of the resistance of P. falciparum to SP were similar at the beginning and the end of the one year implementation period and between the intervention and non-intervention zones.Two doses of SP given at 8 weeks interval during the transmission season, reduced the incidence of malaria episodes during the transmission season by 69.4% in children aged less than 5 years and by 63.4% in children aged 5-10 years in a context of very low ITN use (<5%). In another study that we have conducted, IPT with SP + Amodiaquine (AQ) given at three occasions at one month interval during the transmission season reduced the incidence rate of clinical malaria by 82% (95% CI: 78%– 85%; P<0.001), and the incidence of severe and complicated malaria by 87% (95% IC 42% – 99%, P=0.001) in children aged 3 to 59 months of age despite an ITN use of greater than 99%.There was no serious adverse event related to the use of SP or SP+AQ in IPT during the two studies. Our results support the recommendation of IPT targeting the transmission season and IPT given through the EPI for malaria control in children.

Ces travaux ont consisté à optimiser une voie de synthèse des spirotétrahydro-β-carbolines. Une stratégie en trois étapes à partir du 3-(2-nitrovinyl)indole a été élaborée avec la séquence linéaire suivante : addition de Michael, réduction de la fonction nitro en amine et cyclisation de Pictet-Spengler. L’addition de Michael a été développée sans protection préalable de l’indole sous activation ultrasons. La réduction de la fonction nitro en amine a été menée en présence d’hypophosphites. Au cours de cette étude, la désoxygénation des cétones aromatiques a été identifiée comme réaction secondaire de la réduction et a fait l’objet d’un développement approfondi. Une nouvelle voie d’accès à des isatines fonctionnalisées en position C-5 par substitution des sels de diazonium a été mise au point notamment par la réaction de Heck-Matsuda qui a fait l’objet d’une étude plus complète. La réaction finale de Pictet-Spengler entre tryptamines et isatines aboutit aux spiroindolones. Finalement, l’activité biologique des dérivés spirotétrahydro-β-carbolines synthétisés a été évaluée et l’un d’entre eux a montré une très bonne activité envers le Plasmodium falciparum / The aim of this work was to optimize a new way of synthesis of spirotetrahydro-β-carbolines. A three-steps strategy from the 3-(2-nitrovinyl)indole was elaborated with the following linear sequence : Michael addition, reduction of the nitro function into amine and Pictet-Spengler cyclisation. Michael addition was developed without protection of the indole under sonication activation. Reduction of the nitro function into amine was carried out with hypophosphites. During this study, desoxygenation of aromatic ketones has been identified as a side reaction of the reduction and has been the subject of specific development. A new synthetic pathway to functionalized isatins on C-5 position via substitution of diazonium salts was developed, and Heck-Matsuda reaction has been more particularly studied. The final Pictet-Spengler reaction between tryptamines and isatins led to tetrahydro-β-carbolines. Finally, biological activity of spirotetrahydro-β-carbolines was evaluated and one of these compounds showed good activity against Plasmodium falciparum

The emergence of drug resistant strains of Plasmodium has given a new face to the old disease, malaria. One of the approaches is to block metabolic pathways of the pathogen. The current thesis describes the X-ray crystallographic analysis of two enzymes of the fatty acid biosynthesis pathway of the malaria parasite Plasmodium falciparum. In order to understand the functional mechanism and mode of inhibitor binding, enzyme-inhibitor complexes were characterized, which could help in further improvement of the efficacy of the inhibitors and hence to fight against the disease. The introductory chapter of the thesis presents a discussion on malaria and different metabolic pathways of the pathogen which could be suitable targets for novel antimalarials. In continuation to that, the pathway of our choice the fatty acid biosynthesis and an overview of the structural features of the enzymes involved in the pathway that have been characterized from different organisms are also described. The second chapter includes the tools of X-ray crystallography that were used for structural studies of the present work. It also discusses the biochemical, biophysical and other computational methods used to further characterize the enzymes under study. Triclosan, a well known inhibitor of Enoyl Acyl Carrier Protein Reductase (FabI) from several pathogenic organisms, is a promising lead compound to design effective drugs. The X-ray crystal structures of Plasmodium falciparum FabI (PfFabI), in complex with triclosan variants having different substituted and unsubstituted groups at different key functional locations, were determined and compared with triclosan binding which form the basis of chapter 3. The structures revealed that 4 and 2’ substituted compounds have more interactions with the protein, cofactor and solvent molecules as compared to triclosan. New water molecules were found to interact with some of these inhibitors. Substitution at the 2’ position of triclosan caused the relocation of a conserved water molecule, leading to an additional hydrogen bond with the inhibitor. This observation can help in conserved water based inhibitor design. 2’ and 4’ unsubstituted compounds showed a movement away from the hydrophobic pocket to compensate for the interactions made by the halogen groups of triclosan. This compound also makes additional interactions with the protein and cofactor which compensates for the lost interactions due to the unsubstitution at 2’ and 4’. In cell culture, this inhibitor shows less potency, which indicates that the chlorines at 2’ and 4’ positions increase the ability of the inhibitor to cross multilayered membranes. This knowledge helps us to modify the different functional groups of triclosan to get more potent inhibitors. Certain residues in the substrate binding tunnel of PfFabI were mutated to identify the role of these residues in substrate binding and protein stability, which forms the 4th chapter of the thesis. The substrate binding site residue Ala372 of PfFabI has been mutated to Methionine and Valine which increased the affinity of the enzyme towards triclosan to almost double, close to that of Escherichia coli FabI (EcFabI) which has a Methionine at the structurally similar position of Ala372 of PfFabI. Kinetic studies of the mutants of PfFabI and the crystal structure analysis of the A372M mutant revealed that a more hydrophobic environment enhances the affinity of the enzyme for the inhibitor. A triclosan derivative showed a 3-fold increase in the affinity towards the mutants compared to the wild type, due to additional interactions with the A372M mutant as revealed by the crystal structure. The enzyme has a conserved salt bridge which stabilizes the substrate binding loop and appears to be important for the active conformation of the enzyme. A second set of mutants generated to check this hypothesis exhibited loss of function, except in one case where, the crystal structure showed that the substrate binding loop is stabilized by a water bridge network. The main focus of chapter 5 is β-Hydroxyacyl-acyl carrier protein dehydratase of Plasmoduim falciparum (PfFabZ) which catalyzes the third and important reaction of the fatty acid elongation cycle. The crystal structure of PfFabZ was available in its hexameric (active) and dimeric (inactive) forms. However, until now PfFabZ has not been crystallized with any bound inhibitors. We have designed a new condition to crystallize PfFabZ with its inhibitors bound in the active site, and determined the crystal structures of three of these complexes. This is the first report of the crystal structures of PfFabZ with competitive inhibitor complexes and the first such study on any FabZ enzyme with active site inhibitors. These inhibitors in the active site stabilize the substrate binding loop, revealing the substrate binding tunnel with an overall shape of “U”. In the crystal structure, the residue Phe169 located in the middle of the tunnel was found to be in two different conformations, open and closed, implying that it controls the length of the tunnel and makes it suitable for accommodating longer substrates merely by changing its side chain conformation. The hydrophobic nature of the substrate binding channel signifies the specificity for the hydrophobic tail of fatty acid substrates. The volume of the active site tunnel is determined by the sequence as well as by the conformation of the substrate binding site loop region and varies between organisms for accommodating fatty acids of different chain lengths. All PfFabZ inhibitors reported here bind to the active site through specific contacts like hydrogen bonds with catalytic residues and hydrophobic interactions. This report on the crystal structures of the complexes of PfFabZ provides the structural basis of the inhibitory mechanism of the enzyme, that could be used to improve the potency of inhibitors against an important component of fatty acid synthesis common to many infectious organisms. The hot dog fold has been found in more than sixty proteins since the first report of its existence about a decade ago. The fold appears to have a strong association with fatty acid biosynthesis, its regulation and metabolism, as the proteins with this fold are predominantly coenzyme A-binding enzymes with a variety of substrates located at their active sites. We have analyzed the structural features and sequences of proteins having the hot dog fold. This study reveals that though the basic architecture of the fold is well conserved in these proteins, significant differences exist in their sequence, nature of substrate and oligomerization. Segments with certain conserved sequence motifs seem to play crucial structural and functional roles in various classes of these proteins. The analysis discussed in chapter 6, led to predictions regarding the functional classification and identification of possible catalytic residues of a number of hot dog fold-containing hypothetical proteins whose structures were determined in high throughput structural genomics projects. Rv0098, predicted to be the FabZ of Mycobacterium tuberculosis, was cloned, expressed, purified, crystallized, and X-ray diffraction data were collected. Molecular replacement trials with all “hot dog” fold proteins failed to yield any significant solution due to the low sequence similarity (<20%) of Rv0098 compared to other FabZs. During the trials of structure solution by multiple isomorphous replacement method, structure of Rv0098 was published and it was shown to be a long-chain fatty acyl-CoA thioesterase (FcoT). The crystal structure of Rv0098 did not explain the molecular basis of substrate specificity of varying chain lengths. Molecular dynamics studies were carried out, which revealed that certain residues of the substrate binding tunnel are flexible and thus modulates the length of the tunnel. Flexibility of the loop at the base of the tunnel was also found to be important for determining the length of the tunnel for accommodating appropriate substrates. The structural basis of accommodating long chain substrates by Rv0098 is discussed in chapter 7, by combining the crystallographic and molecular dynamics studies. Part of the work presented in the thesis has been reported in the following publications. Karmodiya, K., Sajad, S., Sinha, S., Maity, K., Suguna, K. and Surolia, N. (2007) Conformational stability and thermodynamic characterization of homotetrameric Plasmodium falciparum beta-ketoacyl-ACP reductase. IUBMB Life 59, 441-9. Pidugu, L. S., Maity, K., Ramaswamy, K., Surolia, N. and Suguna, K. (2009) Analysis of proteins with the 'hot dog' fold: prediction of function and identification of catalytic residues of hypothetical proteins. BMC Struct Biol 9, 37. Kapoor, N., Banerjee, T., Babu, P., Maity, K., Surolia, N. and Surolia, A. (2009) Design, development, synthesis, and docking analysis of 2'-substituted triclosan analogs as inhibitors for Plasmodium falciparum enoyl-ACP reductase. IUBMB Life 61, 1083-91. Maity, K., Bhargav, S. P., Sankaran, B., Surolia, N., Surolia, A. and Suguna, K. (2010) X-ray crystallographic analysis of the complexes of enoyl acyl carrier protein reductase of Plasmodium falciparum with triclosan variants to elucidate the importance of different functional groups in enzyme inhibition. IUBMB Life 62, 467-76. Maity, K., Banerjee, T., Narayanappa, P., Surolia, N., Surolia, A. and Suguna, K. (2010) Effect of substrate binding loop mutations on the structure, kinetics and inhibition of Enoyl Acyl Carrier Protein Reductase from Plasmodium falciparum. (Communicated) Maity, K., Bharat, S. V., Kapoor, N., Surolia, N., Surolia, A. and Suguna, K. (2010) Insights into the functional and inhibitory mechanism of the β-Hydroxyacyl-Acyl Carrier Protein Dehydratase of Plasmodium falciparum from the crystal structures of its complexes with active site inhibitors. (Communicated)

Molecular chaperones have emerged in recent years as major players in many aspects of cell biology. Molecular chaperones are also known as heat shock proteins (HSPs) since many were originally discovered due to their increased synthesis in response to heat shock. They were initially identified when Drosophila salivary gland cells were exposed to a heat shock at 37°C for 30 min and then returned to their normal temperature of 25°C for recovery. A “puffing” of genes was found to have occurred in the chromosome of recovering cells, which was later shown to be accompanied by an increase in the synthesis of proteins with molecular masses of 70 and 26 kDa. These proteins were hence named “heat shock proteins”. The first identification of a function for HSPs was the discovery in Escherichia coli that five proteins synthesized in response to heat shock were involved in λ phage growth. The products of the groEL and groES genes were found to be essential for phage head assembly while the dnaK, dnaJ and grpE gene products were essential for λ phage replication. It was later shown that GroEL and GroES are part of a chaperonin system for protein folding in the prokaryotic cytosol while DnaK is a member of the Hsp70 family that works in conjunction with the DnaJ (Hsp40) co-chaperone and the nucleotide exchange factor GrpE to promote phage replication by dissociating the DnaB helicase from the phage-encoded P protein. Since then, a large number of other proteins collectively referred to as HSPs have been discovered. However, heat shock is not the only signal that induces synthesis of heat shock proteins. Stress of any kind, such as nutrient deprivation, chemical treatment and oxidative stress among others causes increased production of HSPs and therefore, they are also known as stress proteins. The term “molecular chaperone” was originally used to describe the function of nucleoplasmin, a Xenopus oocyte protein that promotes nucleosome assembly by binding tightly to histones and donating the bound histone to chromatin. However, since then, chaperones have been defined as “a family of unrelated classes of proteins that mediate the correct assembly of other proteins, but are not themselves components of the final functional structure”. This view of molecular chaperones, though undoubtedly correct, doesn’t capture the multifaceted roles they have since been discovered to play in cellular processes. In recent years, molecular chaperones have been shown to perform other functions in addition to the maintenance of protein homeostasis: translocation of proteins across organelle membranes, quality control in the endoplasmic reticulum, turnover of misfolded proteins as well as signal transduction. As a result, many chaperones are also essential under non-stress conditions and play crucial roles in cell growth and development, cell-cell communication and regulation of gene expression. Heat shock protein 90 (Hsp90) is one of the most abundant and highly conserved molecular chaperones in organisms ranging from bacteria to all branches of eukarya. It has been shown to be essential for cell viability in Saccharomyces cerevisiae, Schizosaccharomyces pombe and Drosophila melanogaster. Although the bacterial homolog HtpG is dispensable under normal conditions, it is important for cell survival during heat shock. In addition to its role as general chaperone in protein folding following stress, Hsp90 has a more specialized role as a chaperone for several protein kinases and transcription factors. Many Hsp90 client proteins are signaling proteins involved in regulation of cell growth and survival. These proteins are critically dependent on Hsp90 for their maturation and conformational maintenance resulting in a key role for Hsp90 in these processes. Recent reports have also highlighted a role for Hsp90 in linking the expression of genetic and epigenetic variation in response to environmental stress with morphological development in Drosophila melanogaster and Arabidopsis thaliana. In Candida albicans, Hsp90 augments the development of drug resistance, implicating a role for Hsp90 in the evolution of infectious diseases. The malarial parasite, Plasmodium falciparum, is the causative agent of the most lethal form of human malaria. The parasite life cycle involves two hosts: an invertebrate mosquito vector and a vertebrate human host. As the parasite moves from the mosquito to the human body, it experiences an increase in temperature resulting in a severe heat shock. The mechanisms by which the parasite adapts to changes in temperature have not been deciphered. Our laboratory has been interested in investigating the role of heat shock proteins during acclimatization of the parasite to such temperature fluctuations. Heat shock proteins of the Hsp40, Hsp60, Hsp70 and Hsp90 families have been characterized in the parasite and are being examined in our laboratory. This thesis pertains to understanding the functional role of Plasmodium falciparum Hsp90 (PfHsp90) during adaptation of the parasite to fluctuations in environmental temperature. The parasite expresses a single gene for cytosolic Hsp90 on chromosome 7 (PlasmoDB accession no.: PF07_0029) coding for a protein of 745 amino acids with a pI of 4.94 and Mw of 86 kDa. Eukaryotic Hsp90 regulates several protein kinases and transcription factors involved in cell growth and differentiation pathways resulting in a crucial role for Hsp90 in developmental processes. A role for PfHsp90 in parasite development, therefore, seems likely. Indeed, PfHsp90 has previously been implicated in parasite development from the ring stage to the trophozoite stage during the intra-erythrocytic cycle. Pharmacological inhibition of PfHsp90 function using geldanamycin (GA), a specific inhibitor of Hsp90 activity, abrogates stage progression. These experiments suggest that PfHsp90 may play a critical role in parasite development. This is further substantiated by the fact that several pathogenic protozoan parasites such as Leishmania donovani, Trypanosoma cruzi, Toxoplasma gondii and Eimeria tenella depend on Hsp90 function during different stages of their life cycles. It appears, therefore, that a principal role of Hsp90 in protozoan parasites may be the regulation of their developmental cycles. However, the precise functions of PfHsp90 during the intra-erythrocytic cycle of the malarial parasite are not clear. In this study we have carried out a functional analysis of PfHsp90 in the malarial parasite. We have examined the role of PfHsp90 in parasite development during repeated exposure to febrile temperatures. We have investigated its involvement in parasite development during a commonly used synchronization protocol involving cyclical changes in temperature. We have examined the interaction of GA with the Hsp90 multi-chaperone complex from P. falciparum as well as the human host. Finally, we have carried out a systems level analysis of chaperone networks in the malarial parasite as well as its human host using an in silico approach. We have analyzed the protein-protein interactions of PfHsp90 in the chaperone network and predicted putative cellular processes likely to be regulated by parasite chaperones, particularly PfHsp90.

Significant advancements in genome sequencing techniques and other high-throughput initiatives have resulted in the availability of complete sequences of genomes of a large number of organisms, which provide an opportunity to study detailed biological information encoded therein. Identification of functional roles of proteins can aid in comprehension of various cellular activities in an organism, which is traditionally achieved using techniques pertaining to the field of molecular biology, protein chemistry and macromolecular crystallography. The established experimental methods for protein structure and function determination, although accurate and resourceful, are laborious and time consuming. Computational analyses of sequences of gene products and exploration of evolutionary relationships can give clues on protein structure and/or function with reasonable accuracy which can be used to direct experimental studies on proteins of interest, effectively. Moreover, with growing volumes of data, there has been a growing disparity in the number of well-characterized and uncharacterized proteins, further necessitating the use of computational methods for investigating evolutionary and structure-function relationships. The remarkable progress made in the development of computational techniques (Chapter 1) has immensely contributed to the state-of-the-art biological sequence analysis and recognition of protein structure and function in a reliable manner. These methods have largely influenced the exploration of protein sequence-structure-function space. One of the relevant applications of computational approaches is in the understanding of functional make-up of human pathogens, their complex interplay with the host and implications in pathogenesis. In this thesis, sensitive profile-based search procedures have been utilized to address various aspects in the context of three pathogens- Mycobacterium tuberculosis, Plasmodium falciparum and Trypanosoma brucei, which are causative agents of potentially life- threatening diseases. The existing drugs approved for the diseases, although of immense value in controlling the disease, have several shortcomings, the most important of them being the emergence of drug resistance that render the current treatment regimens futile. Thus, the identification of practicable targets and new drugs or new combination therapies become an important necessity. Analyses on structural and functional repertoire of proteins encoded in the pathogenic genomes can provide means for rational identification of therapeutic intervention strategies. This thesis begins with the computational analyses of proteins encoded in M. tuberculosis genome. M. tuberculosis is a primary aetiological agent of tuberculosis in humans, and is o responsible for an estimated 1.5 million deaths every year. The complete genome of the pathogen was sequenced and made available more than a decade ago, which has been valuable in determination of functional roles of its gene products. Yet, functions of many M. tuberculosis proteins remain unknown. Computational prediction of protein function is an on- going process based on ever growing information made available in public databases as well as the introduction of powerful homology recognition techniques. Hence, a continuous refinement is essential to make the most of the sequence data, ensuring its accuracy and relevance. With the use of multiple sequence and structural profile-based search procedures, an enhanced structural and functional characterization of M. tuberculosis proteins, totalling to 95% of the genome was achieved (Chapter 2). Following are the key findings. o Domain definitions were obtained for a total of 3566 of 4018 proteins. Amino acid residue coverage of >70% was achieved for 2295 proteins which constitute more than half of the proteome. o Domain assignments were newly identified for 244 proteins with domain-unassigned regions. Structure prediction for these proteins corroborated all the remote homologyrelationships recognized using profile-based methods, enhancing the reliability of the predictions. o Comparison on domain compositions of proteins between M. tuberculosis and human host, revealed presence of pathogen-specific domains that are not homologous to proteins in human. Such proteins in M. tuberculosis are mainly virulence factors involved in host-pathogen interactions such as immune-dominance and aiding entry and survival in human host macrophages, hence forming attractive targets for drug discovery. o Putative structural and functional information for proteins with no recognizable domains were inferred by means of fold recognition and an iterative profile-based search against sequence database. o Attributing putative structures and functions to 955 conserved hypothetical proteins in M. tuberculosis, 137 of which are reportedly essential to the pathogen, provide a basis to re-investigate their involvement in pathogenesis and survival in the host. Proteins with no detectable homologues were recognized as M. tuberculosis H37Rv-specific, which can serve as promising drug targets. An attempt was made to identify porin-like proteins in M. tuberculosis, considering MspA porin from M. smegmatis as a template. The difficulty in recognition of putative porins in M. tuberculosis is indicative of novel outer membrane channel proteins, not characterized yet, or high representation of ion-channels, symporters and transporters to compensate for the functional role of porins. In addition, MspA-like proteins were not readily recognized in other slow-growing mycobacterial pathogens that are known to infect human host, apart from M. tuberculosis. This indicates probable acquisition of physiological adaptations, i.e. absence of porins, to confer drug-resistance, in the course of their co-evolution with human hosts. Evolutionary relationships recognized between sequence (Pfam) and structural (SCOP) families aided in association of potential structures and/or functions for 55 uncharacterized Pfam domains recognized in M. tuberculosis. Such associations deliver useful insights into the structure and function of a protein housing the uncharacterized domain. The functional inferences drawn for M. tuberculosis proteins based on the predictions can provide valuable basis for experimental endeavours in understanding mechanisms of pathogenesis and can significantly impact anti-tubercular drug discovery programmes. An interesting outcome benefitted from the exercise of exploring relationships between Pfam and SCOP families, was the identification of evolutionary relationship between a Pfam domain of unknown function DUF2652 and class III nucleotidyl cyclases. A detailed investigation was undertaken to assess this relationship (Chapter 3). Nucleotidyl cyclases synthesize cyclic nucleotides which are critical second messengers in signalling pathways. The DUF2652 family predominantly comprises of bacterial proteins belonging to three lineages- Actinobacteria, Bacteroidetes and Proteobacteria. Thus, recognition of evolutionary relationship between these bacterial proteins and nucleotide cyclases is of particular interest due to the indispensability of cyclic nucleotides in regulation of varied biological activities in bacteria. Use of fold recognition program suggested presence of nucleotide cyclase-characteristic topological motif (βααββαβ) in all the members of the DUF2652 family. Detailed analyses on structural and functional features of the uncharacterized set of bacterial proteins corresponding to 50 bacterial genomes, using profile- based alignments, revealed presence of key features typical of nucleotidyl cyclases, including metal-binding aspartates, substrate-specifying residues and transition-state stabilizing residues. Depending on the features, 20 proteins of Actinobacteria lineage, predominantly mycobacteria, of unknown structure and function were identified as putative nucleotide cyclases, 23 proteins of Bacteroidetes lineage were associated with guanylyl cyclases, while 8 uncharacterized proteins of Proteobacteria were recognized as nucleotide cyclase-like proteins (7 adenylyl and one guanylyl cyclase). Sequence similarity-based clustering of the predicted nucleotide cyclase-like proteins with established nucleotide cyclases indicated the apparent evolutionarily distinctness of the subfamily of class III nucleotidyl cyclases predicted. Furthermore, analysis of evolutionarily conserved gene clusters of the predicted nucleotide cyclase-like proteins indicated functional associations that support the predictions on their participation in cellular signalling events. The inferences made can be experimentally investigated further to ascertain the involvement of the uncharacterized bacterial proteins in signalling pathways, which can help in understanding the pathobiology of pathogenic species of interest. The next objective was the recognition of biologically relevant protein-protein interactions across M. tuberculosis and human host (Chapter 4). M. tuberculosis is well known for its ability to successfully co-evolve with human host in terms of establishing infection, survival and persistence. The current knowledge on the mechanisms of host invasion, immune evasion and persistence in the host environment can be attributed, and is limited, to the experimental studies pursued by numerous groups. Chapter 4 presents an approach for computational identification of biologically feasible protein-protein interactions across M. tuberculosis and human host. The approach utilizes crystal structures of intra-organism protein-protein complexes which are transient in nature. Identification of homologues of host and pathogen proteins in the database of known protein-protein interactions, formed the initial step, followed by identification of conserved interfacial patch and integration of information on tissue-specific expression of human proteins and subcellular localization of human and M. tuberculosis proteins. In addition, appropriate filters were used to extract biologically feasible host-pathogen protein-protein interactions. This resulted in recognition of 386 interactions potentially mediated by 59 M. tuberculosis proteins and 90 human proteins. A predominance of host-pathogen interactions (193 protein-protein interactions) brought about by M. tuberculosis proteins participating in cell wall processes, was observed, which is in concurrence with the experimental studies on immuno-modulatory activities brought about by such proteins. These set of mycobacterial proteins were predicted to interact with diverse set of host proteins such as those involved in ubiquitin conjugation pathways, metabolic pathways, signalling pathways, regulation of cell proliferation, transport, apoptosis and autophagy. The predictions have the potential to complement experimental observations at the molecular level. Details on couple of interesting cases are presented in the chapter, one of which is the probable mechanism of immune evasion adopted by M. tuberculosis to inhibit lysozyme activity in macrophages, and second is the mechanism of nutrient uptake from host. The set of M. tuberculosis proteins predicted to mediate interactions with host proteins have the potential to warrant an experimental follow-up on probable mechanisms of pathogenesis and also serve as attractive targets for chemotherapeutic interventions. proteins known to participate in P. falciparum metabolism. Pathway holes, where evidence on metabolic step exists but the catalysing enzyme is not known, have also been addressed in the study, several of which have been suggested to play an important role in growth and development of the parasite during its intra-erythrocytic stages in human host. A subsequent objective was the recognition P. falciparum proteins potentially capable of remodelling erythrocytes to suit their niche (Chapter 7). Exploitative mechanisms are brought about by the parasite to remodel erythrocytes for growth and survival during intra-erythrocytic stages of its life-cycle, the understanding of which is limited to experimental studies. To achieve physicochemically viable protein-protein interactions potentially mediated by proteins of human erythrocytes and P. falciparum proteins, a structure-influenced protocol, similar to the one demonstrated in Chapter 4, was employed. Information on subcellular localization and protein expression is crucial especially for parasites like P. falciparum, which reside in One of the major shortcomings with current treatment regimen for tuberculosis is the emergence of multidrug (MDR) and extensively drug-resistant (XDR) strains that render first-line and second-line drug treatments futile. This entails a need to explore target space in M. tuberculosis as well as explore the potential of existing drugs for repurposing against tuberculosis. A drug repurposing strategy i.e. exploring within-target-family selectivity of small molecules, has been implemented (Chapter 5) to contribute towards time and cost-saving anti-tubercular drug development efforts. With the use of profile-based search procedures, evolutionary relationships between targets (other than proteins of M. tuberculosis) of FDA-approved drugs and M. tuberculosis proteins were investigated. A key filter to exclude drugs capable of acting on human proteins substantially reduced the chances of obtaining anti-targets. Thus, total of 130 FDA-approved drugs were recognized that can be repurposed against 78 M. tuberculosis proteins, belonging to the functional categories- intermediary metabolism and respiration, information pathways, cell wall and cell processes and lipid metabolism. The catalogue of structure and function of M. tuberculosis proteins and their involvement in host-pathogen protein-protein interactions compiled from chapters 2 and 4 served as a guiding tool to explore the functional importance of targets identified. Many of the potential targets identified have been experimentally shown to be essential for growth and survival of the pathogen earlier, thus gaining importance in terms of pharmaceutical relevance. Polypharmacological drugs or drugs capable of acting of multiple targets were also identified (92 drugs) in the study. These drugs have the potential to stand tolerance against development of drug resistance in the pathogen. Comparative sequence and structure-based analysis of M. tuberculosis proteins homologous to known targets yielded credible inferences on putative binding sites of FDA-approved drugs in potential targets. Instances where information on binding sites could not be readily inferred from known targets, potentially druggable sites have been predicted. Comparison with earlier experimental studies that report anti-tubercular potential of several approved drugs enhanced the credibility of 74 of 130 FDA-approved drugs that can be readily prioritized for clinical studies. An additional exercise was pursued to identify prospective anti-tubercular agents by means of structural comparison between ChEMBL compounds and 130 FDA-approved drugs. Only those compounds were retained that showed considerably high structural similarity with approved drugs. Such compounds with minor changes in terms of physicochemical properties provide a basis for exploration of compounds that may exhibit higher affinities to bind to M. tuberculosis targets. The set of approved drugs recognized as repurpose-able candidates against tuberculosis, in concert with the structurally similar compounds, can significantly impact anti-tubercular drug development and drug discovery. The next part of the thesis focuses on Plasmodium falciparum, an obligate intracellular protozoan parasite responsible for malaria. The parasite genome features unusual characteristics including abundance of low complexity regions and pronounced sequence divergence that render protein structure and function recognition difficult. The parasite also manifests remarkable plasticity in its metabolic organization throughout its developmental stages in two hosts-human and mosquito; thus obtaining an exhaustive list of metabolic proteins in the parasite gains importance. Considering the utility of multiple sensitive profile-based search approaches in enhanced annotation of M. tuberculosis genome, a similar exercise was employed to recognize potential metabolic proteins in P. falciparum (Chapter 6). A total of 172 metabolic proteins were identified as participants of 78 metabolic pathways, over and above 609heterogeneous environmental conditions at different stages in their lifecycle. Inclusion of such data aided in extraction of 208 biologically relevant protein-protein interactions potentially mediated by 59 P. falciparum proteins and 30 erythrocyte proteins. Host-parasite protein-protein interactions were predicted pertaining to several major strategies spanning intra-erythrocytic stages in P. falciparum pathogenesis including- gaining entry into the host erythrocytes (category: RBC invasion, protease), redirecting parasitic proteins to erythrocyte membrane (category: protein traffic), modulating erythrocyte machinery (category: rosette formation, putative adhesin, chaperone, kinase), evading immunity (category: immune evasion) and eventually egress (category: merozoite egress) to infect other uninfected erythrocytes. Elaborate means to analyse and evaluate the functional viability of a predicted interaction in terms of geometrical packing at the interfacial region, electrostatic complementarity of the interacting surfaces and interaction energies is also demonstrated. The protein-protein interactions, thus predicted between human erythrocytes and P. falciparum, have the potential to provide a useful basis in understanding probable mechanisms of pathogenesis, and indeed in pinning down attractive targets for antimalarial drug discovery. The emergence of drug resistance against all known antimalarial agents, currently in use, necessitates discovery and development of either new antimalarial agents or unexplored combination of drugs that may not only reduce mortality and morbidity of malaria, but also reduce the risk of resistance to antimalarial drugs. In an attempt to contribute towards the same, Chapter 8 explores the established concept of within-target-family selectivity of small molecules to recognize antimalarial potential of the approved drugs. Eighty six FDA-approved drugs, predominantly constituted by antibacterial agents, were identified as feasible candidates for repurposing against 90 P. falciparum proteins. Most of the potential parasite targets identified are known to participate in housekeeping machinery, protein biosynthesis, metabolic pathways and cell growth and differentiation, and thus are pharmaceutically relevant. During intra-erythrocytic growth of P. falciparum, the parasite resides within the erythrocyte, within a protective encasing, known as parasitophorous vacuole. Hence a drug, intended to target a parasite protein residing in an organelle, must be sufficiently hydrophilic or hydrophobic to be able to permeate cell membranes and reach its site of activity. On the basis of lipophilicity of the drugs, a physical property determined experimentally, 57 of 86 FDA-approved drugs were recognized as feasible candidates for use against P. falciparum during the course of blood-stages of infection, which can be prioritized for antimalarial drug development programmes. The final section of the thesis focuses on the protozoan parasite Trypanosoma brucei, a causative agent of African sleeping sickness (Chapter 9). This disease is endemic to sub-Saharan regions of Africa. Despite the availability of completely sequenced genome of T. brucei, structure and function for about 50% of the proteins encoded in the genome remain unknown. Absence of prophylactic chemotherapy and vaccine, compounded with emergence of drug-resistance renders anti-trypanosomal drug discovery challenging. Thus, considering the utility of frameworks established in earlier chapters for recognition of protein structure, function and drug-targets, similar steps were undertaken to understand functional repertoire of the parasite and use drug repurposing methods to accelerate anti-trypanosomal drug discovery efforts. Structures and functions were reliably recognized for 70% of the gene products (5894) encoded in T. brucei genome, with the use of multiple profile-based search procedures, coupled with information on presence of transmembrane domains and signal peptide cleavage sites. Consequently, a total of 282 uncharacterized T. brucei proteins could be newly coined as potential metabolic proteins. Integration of information on stage-specific expression profiles with Trypanosoma-specific and T-.brucei-specific proteins identified in the study, aided in pinning down potential attractive targets. Additionally, exploration of evolutionary relationships between targets of FDA-approved drugs and T. brucei proteins, 68 FDA-approved drugs were predicted as repurpose-able candidates against 42 potential T. brucei targets which primarily include proteins involved in regulatory processes and metabolism. Several targets predicted are reportedly essential in assisting the parasite to switch between differentiation forms (bloodstream and procyclic) in the course of its lifecycle. These targets are of high therapeutic relevance, hence the corresponding drug-target associations provide a useful resource for experimental endeavours. In summary, this thesis presents computational analyses on three pathogenic genomes in terms of enhancing the understanding of functional repertoire of the pathogens, addressing metabolic pathway holes, exploring probable mechanisms of pathogenesis brought about by potential host-pathogen protein-protein interactions, and identifying feasible FDA-approved drug candidates to repurpose against the pathogens. The studies are pursued primarily by taking advantage of powerful homology-detection techniques and the ever-growing biological information made available in public databases. Indeed, the inferences drawn for the three pathogenic genomes serve an excellent resource for an experimental follow-up. The set of protocols presented in the thesis are highly generic in nature, as demonstrated for three pathogens, and can be utilized for genome-wide analyses on many other pathogens of interest. The supplemental data associated with the chapters is provided in a compact disc attached with this thesis.

Plasmodium falciparum is responsible for the most virulent form of human malaria. The biology of the intra-erythrocytic stage of P. falciparum is the most well studied as it is this stage that marks the clinical manifestation of malaria. To establish a successful infection, P. falciparum brings about extensive remodeling of erythrocytes, its host compartment. The infected erythrocytes harbor several parasite induced membranous structures. Most importantly, pathogenesis related structures termed knobs, which impart cytoadherence, appear on the cell surface of the infected erythrocytes. For bringing about such eccentric renovations in its host compartment, the parasite exports 8% of its genome (~400 proteins) to various destinations in the host cell. Studies from our lab have shown that proteins belonging to heat shock protein40 (Hsp40) and heat shock protein70 (Hsp70) group of chaperones are also exported to the host compartment. We and others have implicated these chaperones in important processes such as protein trafficking and chaperoning assembly of parasitic proteins into the cytoadherent knobs. As detailed above, malaria parasite invests a lot of energy in exporting a large number of proteins including chaperones in the red blood cell to meet its pathogenic demands. In order to do so, it heavily relies on its secretory pathway. However, it is known that the parasite experiences a significant amount of oxidative stress on account of heme detoxification, its own metabolism and the immune system of the host. The parasite also effluxes large quantities of reduced thiols such as glutathione and homocysteine into the extracellular milieu indicative of redox perturbation. Additionally, the parasite lacks Peroxiredoxin IV, which otherwise localizes in the ER and carries out detoxification of peroxide generated as a result of oxidative protein folding. Together, these factors indicate that maintaining redox homeostasis is a challenging task for the parasite. It also implies that the ER, where the redox balance is even more critical as it requires oxidising environment for protein folding, is predisposed to stress. In light of this fact and the importance of secretory pathway in malaria pathogenesis, we decided to address the ways and mechanisms used by the parasite to tackle perturbations in its secretory pathway. Examination of a canonical unfolded protein response pathway in P. falciparum ER-stress is a condition arising whenever the load of unfolded proteins increases the folding capacity of the ER. However, eukaryotes have evolved a fairly well conserved homeostatic response pathway known as unfolded protein response (UPR) to tackle ER-stress. This signal transduction pathway is composed of three arms involving three ER-transmembrane signal transducers namely; IRE1, ATF6 and PERK. IRE1 brings about splicing of a bZIP transcription factor, XBP1/Hac1 and ATF6 becomes activated upon getting proteolytically cleaved in the Golgi. These transcription factors then migrate to the nucleus where they bind onto the ER-stress elements thereby, leading to the transcriptional up-regulation of the UPR targets such as ER chaperones and components of ER associated degradation (ERAD) pathway which rescue the function of the ER. PERK on the other hand brings about translational attenuation by phosphorylating eIF2α, thereby providing parasite the benefit of time to recover. We started our examination on UPR in Plasmodium by carrying out in silico analysis of the major components of UPR in the parasite by using Homo sapiens protein sequences as the query. We found that the parasite lacks the homologues of all the transcriptional regulators of canonical UPR. Only PERK component of the UPR was found to be present in the parasite. To rule out the existence of the canonical UPR in P. falciparum, we examined the status of UPR targets by subjecting the parasites to treatment with DTT. DTT perturbs the disulfide oxidation in the ER and thereby inhibits protein folding leading to ER-stress. Owing to the missing components of a canonical UPR, we did not find up-regulation of known UPR targets such as ER-chaperones including PfBiP, PfGrp94, PfPDI and ERAD marker Derlin1 at transcript as well as protein level. Owing to the presence of a PERK homologue, phosphorylation of eIF2α followed by attenuation of protein synthesis was observed upon subjecting the parasites to DTT mediated ER-stress. In the absence of a canonical UPR, the parasites were found to be hypersensitive to ER-stress in comparison to the mammalian counterpart. In the presence of DTT, the parasites showed perturbation in the redox homeostasis as indicated by increase in the levels of ROS. Next, we sought to examine if the parasites resorted to any alternate means of increasing the availability of chaperones in the ER. For this, we analysed the involvement of another Hsp70 family member, Hsp70-x which is homologous to BiP and which is known to traverse the ER while getting exported to the erythrocyte compartment. Interestingly, we found that upon exposure to ER-stress, the export of this protein is partially blocked and around 30% of the protein is retained in the ER. On the other hand, there was no effect on the trafficking of another exported chaperone KAHsp40. This indicates that the parasite possibly recruits this pool of retained Hsp70-x for the chaperoning of unfolded proteins in the ER. Global response to ER-stress in P. falciparum To dig deeper into the parasite specific strategies employed for dealing with ER-stress at a global level, we carried out high throughput transcriptomic and proteomic analysis upon subjecting the parasites to DTT mediated ER-stress. Microarray based gene expression profiling was carried out upon subjecting the parasites to DTT mediated ER-stress. We found that the parasite mounts a transcriptional response as indicated by up-regulation of 155 transcripts. In congruence with our biochemical analysis, we did not find up-regulation of ER chaperones as well as ERAD proteins. Functional grouping of the up-regulated genes revealed large number of hypothetical proteins in our list of differentially expressed genes. The genes encoding exported proteins represent yet another abundant class. In the course of examining the involvement of Plasmodium specific transcriptional regulators mediating response to DTT induced ER-stress, we identified 4 genes belonging to the family of AP2 transcription factors. AP2 (Apetela-2) are specific transcription factors which are possessed by apicomplexa and bring about regulation of developmental processes and stress response in plants. On comparing our list of up-regulated genes with the previously known targets of AP2 factors, we found that an entire cascade of AP2 factors is up-regulated upon DTT-mediated ER stress. Thus, AP2 factors appear to be the major stress response mediators as they are together responsible for the up-regulation of 60% of genes identified in this study. In addition, another striking observation made, was the up-regulation of a few sexual stage specific transcripts. 2D Gel electrophoresis and 2D-DIGE based Proteomic analysis indicated an up-regulation of secretory proteins and some components of vesicular trafficking and secretory machinery possibly to overcome the block in the functions of the secretory pathway. ER-stress triggers stage transition in P. falciparum Intrigued by the up-regulation of a few sexual stage specific genes, we were curious to examine if there was a functional significance of this observation. To this end, we decided to investigate the effect of ER-stress on induction of gametocytes, the only sexual stage found in humans. Indeed, we found a two fold induction in the numbers of gametocytes formed upon challenging the parasite with DTT mediated ER-stress. The induction of gametocytogenesis was also observed by using a clinical isolate of P. falciparum for the assay. The DTT treated cultures progressed through the gametocytogenesis pathway normally forming all the five morphologically distinct stages. Then we sought to examine if this phenomenon could be simulated in the physiological scenario as well. For this, we made use of a rodent model of malaria, P. berghei. Two different treatment regimes involving 1) direct injection of increasing concentration of DTT into P. berghei infected mice and 2) injection of DTT pretreated P. berghei infected erythrocytes into healthy mice were followed. In both cases, a significant increase in the gametocyte induction was observed. Having seen that Plasmodium undergoes gametocytogenesis upon exposure to ER-stress not only in in vitro cultures but also in in vivo scenario, we wanted to identify the players involved in the commitment to sexual stage. Recently, a transcription factor belonging to AP2 class of transcription factors, referred to as AP2-G has been implicated in committing the asexual parasites for transition to gametocyte stage. To examine the role of this factor in the phenotype observed by us, we looked at the effect of DTT on AP2-G. Interestingly, we found around 6 folds up-regulation in the expression of AP2-G levels under ER-stress. The downstream targets of AP2-G, many of which are the markers of gametocyte were also found to be up-regulated upon being exposed to DTT mediated ER-stress indicating the launch of a transcriptional program which together works in the direction of transition to gametocytes. Having seen that P. falciparum undergoes ametocytogenesis in response to DTT treatment both under in vitro and in vivo conditions, we sought to look for probable physiological analogue of DTT. Since glutathione is the major cellular redox buffer, critical for redox homeostasis, we quantitated the levels of both oxidized and reduced forms of this non protein thiol using Mass Spectrometric approach. We found that the levels of reduced forms of glutathione significantly increased upon treating the parasites with DTT. This indicates that the levels of glutathione could be one of the physiological triggers of gametocytogenesis. Conclusion In conclusion, our study analyses the ways and mechanisms employed by malaria parasite to cope with perturbations to its secretory pathway. We have established the absence of a canonical UPR in this parasite and our results suggest that Plasmodium has developed a three stage response to cope with ER stress: 1) an early adaptation to increase the local concentration of chaperones in the ER by partially blocking the export of a Hsp70 family member, 2) activation of gene expression cascade involving AP2 transcription factors and 3) a consequent switch to the transmissible sexual stage. Hence, our study throws light on a novel physiological adaptation utilised by malaria parasite to tackle stress to its secretory pathway. Gametocytogenesis, which can be transmitted to the mosquito vector, could hence serve as an effective means to escape ER-stress altogether. Importantly, while it is widely known that stress brings about switch towards sexual stages in P. falciparum, the molecular triggers involved in this process remain obscure in the field of malaria biology. Therefore, our findings also address this long standing question by providing the evidence of ER-stress being one such trigger required for switching to the transmissible sexual stages.

Notre étude s’est proposée d’analyser l’incidence du paludisme et son évolution dans le temps et dans l’espace, ainsi que de rechercher les facteurs de risque d’accès palustres chez les enfants d’un village du Moyen-Oyapock (Camopi), peuplé d’Amérindiens wayampi et émerillon, d’une part, et d’un village du Haut-Maroni (Antecume Pata), peuplé d’Amérindiens wayana, d’autre part. L’approche a été multiple avec, pour chacun des deux sites d’étude :- Une analyse de survie (modèle de Cox) à partir des accès palustres confirmés biologiquement dans une cohorte d’enfants de moins de sept ans régulièrement suivis, ainsi qu’un questionnaire de type Connaissances, Attitudes et Pratiques (CAP), puis les caractéristiques des habitats et la description de leur environnement immédiat.- Une analyse spatiale avec une classification de l’occupation du sol à partir d’images satellites SPOT 5, l’extraction de variables environnementales d’intérêt, l’étude de leur effet sur la transmission du paludisme et la mise au point d’une méthode objective de sélection d’un rayon d’observation autour des habitations pour la caractérisation de l’environnement.- Une étude de séries temporelles (ARIMA) afin de déterminer l’effet des évènements climatiques et hydrologiques sur le paludisme, aux niveaux local et plus global (El Niño).Les taux d’incidence d’accès palustres sur la période 2001-2009 se sont révélés particulièrement élevés chez les jeunes enfants, notamment à Camopi avec une moyenne de 773‰ par année. Une diminution brutale de l’incidence a eue lieu en 2007 sur le Haut-Maroni et ce phénomène est observé à Camopi depuis 2010. Une prémunition se développe assez rapidement au cours de la vie (2-3 ans), surtout contre les reviviscences à Plasmodium vivax. Les facteurs environnementaux se sont avérés être les plus nombreux et les plus fortement liés à l’incidence palustre. En effet, le dégagement des alentours du carbet de toute végétation et une certaine distance de celui-ci à la forêt sont des facteurs protecteurs. La composante géographique est également apparue essentielle à Camopi avec une incidence qui variait selon le fleuve d’habitation et en fonction de la distance au hameau principal. Les facteurs météorologiques locaux (température et niveau du fleuve) se sont également révélés être liés à l’incidence du paludisme à court terme (0-3 mois). Par ailleurs, nos résultats ont permis d’émettre un certain nombre d’hypothèses quant à la transmission et au(x) vecteur(s) local(ux), et notamment de suggérer la participation d’un vecteur autre qu’An. darlingi dans la transmission du paludisme à Camopi. Nous avons également prouvé par ce travail que la télédétection et les systèmes d’information géographique sont très prometteurs pour la prise en compte de la dimension spatiale et environnementale dans l’étude des maladies transmissibles, notamment dans les zones d’accès difficile de Guyane. / The aim of our study was to analyze the incidence of malaria in children and its evolution through time and space, as well as to search for risk factors in a village in Mid-Oyapock (Camopi), populated by Amerindians Wayampi and Emerillon, on the one hand, and a village in Upper-Maroni (Antecume Pata), populated by Amerindians Wayana, on the other hand. The approach was multiple with, for both study sites:- A survival analysis (Cox modelling) completed out of biologically confirmed malaria attacks in a cohort of children under seven, as well as a Knowledge, Attitudes, Practices and Behavior (KAPB) questionnaire, and also the characteristics of the houses and the description of their immediate environment.- A spatial analysis with a land cover classification from SPOT 5 satellite images, the extraction of environmental variables, the study of their effect on malaria transmission and the development of an objective method for picking the proper observation horizon around houses in order to characterize the environment.- A time series study (ARIMA) to determine the effect of climatic and hydrological events on malaria at local and global (El Niño) scales.The incidence rates of malaria attacks during the period 2001-2009 were particularly high among young children, especially in Camopi with an average of 773‰ by year. A sharp decline in incidence occurred in 2007 on the Upper Maroni and this phenomenon has been observed in Camopi since 2010. An acquired immunity develops quite rapidly during the life (2-3 years old), especially against P. vivax relapses. Environmental factors were found to be the most strongly associated with malaria incidence. Indeed, living in a hut cleared from the surrounding vegetation and at a larger distance from the forest are protective factors. The geographic component also appeared essential in Camopi with an incidence which varied with the river of living and with the distance from the main hamlet. The local meteorological factors (temperature and river level) also proved to be linked to malaria incidence in the short term (0-3 months). Moreover, our results have allowed issuing a number of assumptions about the transmission and the local vector(s), in particular to suggest the involvement of another vector than An. darlingi in the malaria transmission in Camopi. We also proved by this work that remote sensing and geographic information systems hold great promise for the inclusion of the spatial and environmental dimensions in the study of transmitted diseases, especially in areas of difficult access in French Guiana.

Platelet-mediated clumping of Plasmodium falciparum-infected erythrocytes (IEs) is a common property of field isolates associated with severe disease (Pain, Ferguson et al. 2001). Platelet receptors CD36 (Pain, Ferguson et al. 2001), P-Selectin (Wassmer, Taylor et al. 2008) and gC1qR (Biswas, Hafiz et al. 2007) mediate clumping. To characterize the molecular specificities of the clumping phenotype, I cloned clumping parasite line IT/C10 by limiting dilution. I characterized var gene expression in the IT/C10 clones using generic primers for the DBL tag region (Bull, Berriman et al. 2005). Clumping assays were conducted in the presence of specific reagents to delineate host factors hypothesized to contribute to development of the clumping phenotype. Finally, I conducted a clinical study with isolates from children with malaria in Kilifi, Kenya. This study shows that in parasite line IT/C10, platelet-mediated clumping is associated with Itvar30 suggesting a prominent role for the PfEMP-1 encoded by this var gene in development of platelet-mediated clumping. For IT/C10 parasites, platelet activation appears to be involved in platelet-mediated clumping. Platelet P-Selectin appears to mediate clumping using lectin-dependent interactions. To further elucidate the mechanisms that mediate clumping by host platelets, I have used a panel of platelet antagonists to delineate specific platelet activation pathways. Our results show that platelet activation plays an important role in platelet-mediated clumping. Finally, in this study, platelet-mediated clumping was associated with parasitaemia, but not with disease severity.

Les moustiques An. coluzzii sont des vecteurs du paludisme humain en Afrique sub- saharienne (Fontenille et al., 2003). Ils s’infectent après une prise de repas de sang chez un l’hôte humain porteur de gamétocytes. Les études sur la résistance/sensibilité d’An. coluzzii au parasite P. falciparum définissent sa compétence vectorielle (Ndiath et al., 2011 ; Fryxell et al., 2012 ; Gnémé et al., 2013 ; Boissière et al., 2013). La compétence vectorielle d’An. coluzzii au parasite P. falciparum est déterminée par des gènes pro/antiparasitaires, dont TEP1 qui montre un polymorphisme à l’origine de la résistance/sensibilité des moustiques vis-à-vis de P. berghei, parasite de rongeur (Baxter et al., 2007 ; Blandin et al., 2009). Dans nos travaux nous montrons que TEP1 est un facteur antiparasitaire majeur dans la réponse contre P. falciparum, mais n’explique pas seul la résistance/sensibilité des moustiques vis-à-vis du parasite. D’autres facteurs génétiques pro/antiparasitaires non encore déterminés seraient impliqués dans la compétence vectorielle chez les moustiques An. coluzzii. Pour identifier les gènes pro/antiparasitaires impliqués dans les interactions An. coluzzii – P. falciparum, et étudier l’effet de leur polymorphisme sur la résistance/sensibilité des moustiques vis-à-vis du parasite, nous avons réalisé sur le terrain, à Mfou au Cameroun, des infections expérimentales avec des isolats naturels de P. falciparum chez les moustiques L3-5, S1low et S1high sélectionnés pour leur résistance/sensibilité à P. berghei. Les moustiques Ngousso sont utilisés ici comme contrôle de l’infectivité des parasites. / Anopheles coluzzii mosquitoes are vectors of human malaria in sub-Saharan Africa. Still, even within a vector species, the ability of mosquitoes to carry malaria parasites varies extensively between individuals, with some mosquitoes that eliminate all parasites, and are therefore unable to transmit the disease. Polymorphism in the complement-like protein TEP1 was shown to contribute to determine mosquito susceptibility to the murine malaria parasite P. berghei (Blandin et al., 2009) as well as to the human malaria parasite P. falciparum (White et al., 2010). Still, we demonstrated that TEP1 alone could not fully explain mosquito resistance and we set up to identify additional genetic factors that determine mosquito vector competence in the Ngousso line that was recently colonised in Cameroon and whose phenotype range varies extensively when exposed to P. berghei infection. To be independent from variations in the TEP1 locus, we first selected a parental line homozygous for a single TEP1 allele, TEP1*S1, that was previously linked to mosquito susceptibility. We then created isofemale families and selected them according to their phenotype upon infection with the murine malaria parasite P. berghei over several generations to create two lines carrying either many (S1high) or few (S1low) parasites. To identify the regions of the genomes that are linked to this phenotypic difference, we performed crosses and QTL mapping. To test whether the phenotypic difference selected upon P. berghei infections was conserved for P. falciparum, we subjected our two lines to blood meals infected with natural isolates of the human parasite collected in Cameroon. Results of the selection process and field infections will be presented.