Malaria is a devastating disease caused by one of the world's most pathogenic parasites, Plasmodium. Five species of Plasmodium infect humans: P. falciparum, P. vivax, P. ovale, P. malariae and P. knowlesi. P. falciparum is the most pathogenic and causes the greatest numbers of deaths. To date, no licensed vaccine against malaria is available, although there are numerous vaccine candidates in various stages of development. Pca 96 is a 96 kDa Plasmodium chabaudi adami protein shown to have a protective property in mice challenged with P. chabaudi adami. Thus, a P. falciparum orthologue of Pca 96 may be useful in vaccine development. BLAST searches with the Pca 96 amino acid and nucleotide sequences revealed proteins with high sequence identity to Pca 96 including the hypothetical P. falciparum PFC0760c and P. yoelii yoelii PY05757 proteins. A peptide sequence FKLGSCYLYIINRNLKEI was found to be conserved in all homologues of Pca 96, including PFC0760c, PY05757 and in the sequences of proteins from 5 other Plasmodium species. Bioinformatic approaches were explored to attempt to find a possible role of the protein and the possible importance of the conserved sequence. The conserved sequence was predicted to be an alpha helix and to contain possible HLA-DRB1*1101 and HLA-DRB1*0401(Dr4Dw4) T-cell epitopes (GSCYLYIINRNLKEI) in addition to a possible H2-Kd T-cell epitope (CYLYIINRNL). Protein-protein interaction predictions revealed that PFC0760c was likely to interact with proteins involved with nucleic acid binding. PFC0760c was predicted to have a domain found in proteins involved in the structural maintenance of chromosomes, which may suggest the protein is involved in chromatid cohesion during mitotic chromosome condensation. PFC0760c was also predicted to be located in the nucleus by the sub cellular prediction program, SubLoc. Anti-peptide antibodies were raised against the conserved amino acid sequence and against a peptide specific for PY05757 (SDDDNRQIQDFE). Both antibodies detected native antigens with immunofluorescence microscopy. The fluorescent signal appeared throughout the parasite cytoplasm and as an intense signal in the parasite nucleus. These immunofluorescence data supports the predicted nuclear location of the protein. A 822 bp portion of PFC0760c gene was expressed as a maltose-binding protein fusion protein (Pf33-MBP). Pf33-MBP was expressed and purified. Reducing SDS-PAGE and western blotting analysis revealed the fusion protein to be expressed at low levels as four bands (79, 60, 45 and 37 kDa). The purified fusion protein was cleaved with Factor Xa. MBP and Pf33 were of similar molecular mass after cleavage. To attempt to obtain better expression and purification, the 822 bp insert from pTS822 was sub-cloned into pGEX4T1. A glutathione-S-transferase (GST)-fusion protein (Pf33-GST) was expressed. The level of expression was poor and therefore not pursued. To take the study further, potential proteins that interact with PFC0760c and Pf33 need to be identified. In addition, immunisation of mice with the protein and subsequent Plasmodium challenge needs to be performed to ascertain the protective potential of the protein. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2011.

Malaria, caused by Plasmodium falciparum parasites remains a huge public health problem and a major cause of morbidity and mortality in sub-Saharan Africa, especially among children and infants. The parasite and its vector – the Anopheles spp mosquito - have tremendous adaptability capacities, including the acquisition of resistance to anti-malarial drugs and insecticides, making the development of new preventive tools, such as a safe and effective vaccine, a key element to counter balance this tendency. The most advanced malaria vaccine candidate, RTS,S/AS has progressed to a Phase III trial through a research and development plan as a result of an unforeseen partnership between African, European and American research institutions together with GSK Biologicals and the PATH Malaria Vaccine Initiative (MVI). This thesis describes some critical stages of the clinical development plan of this vaccine, reporting clinical trials of the RTS/AS candidate malaria vaccine conducted in Mozambican children and infants. Here we illustrates the assessment of the RTS,S/AS02D safety, humoral and cellular mediated immune responses and the duration of protection over a one year period in infants. We also provide a detailed immunogenicity data of 4 years of follow-up of children aged 1 to 4 years by the time of immunization with RTS,S/AS02A. These studies principally show that the vaccine is safe, well tolerated and highly immunogenic, eliciting both humoral and cell-mediated antibodies. The vaccine also protects children and infants against clinical malaria. Importantly, they also describe for the first time an association between the risk of clinical malaria and Plasmodium falciparum anticircumsporozoite antibody titters. The presented results support the hypothesis that developing a safe, immunogenic and efficacious malaria vaccine is feasible and, together with other studies, they should be the basis for the registry process of what should be the first generation of vaccines against malaria. / La malaria, causada por el parásito Plasmodium falciparum sigue siendo un gran problema de salud pública y una causa importante de mortalidad y morbilidad en el África Sub-Sahariana, especialmente entre los niños y lactantes. El parásito y su vector mosquito Anofeles spp. tienen una tremenda capacidad de adaptación, incluyendo la capacidad de adquirir resistencia a los fármacos antipalúdicos e insecticidas. Es por tanto prioritario desarrollar nuevas herramientas preventivas, entre las cuales una vacuna segura y eficaz, un elemento clave para contrarrestar esta tendencia. La vacuna candidata contra la malaria más avanzada, denominada RTS,S/AS, ha progresado hasta un ensayo de Fase III siguiendo un plan de investigación y desarrollo clínico resultado de una colaboración sin precedentes entre centros de investigación Africanos, Europeos y Americanos junto con la GSK Biologicals y PATH Malaria Vaccine Initiative (MVI). Esta tesis describe algunas de las fases críticas de estos logros, reportando los ensayos clínicos de la vacuna candidata contra la malaria RTS,S/AS llevados a cabo en niños y lactantes de Mozambique. Esta tesis analiza en detalle la evaluación de la seguridad de esta estrategia, la respuesta inmunológica (tanto humoral como celular) que esta vacuna confiere, y la duración de la protección durante un período de seguimiento de un año en los lactantes. Presentamos también los datos completos de 4 años de seguimiento de la inmunogenicidad de la RTS,S/AS02A administrada a niños de 1 a 4 años de edad en el momento de su primera vacunación. Estos estudios demuestran que la vacuna es segura, bien tolerada y altamente inmunogénica, produciendo respuestas tanto humorales como celulares. La vacuna también protege a los niños y lactantes contra la malaria clínica. Además se describe por primera vez una asociación entre el riesgo de malaria clínica y los niveles de anticuerpos contra la proteína de circumsporozoito del Plasmodium falciparum. Los resultados aquí presentados apoyan la tesis de que el desarrollo de una vacuna eficaz, inmunogénica y segura contra la malaria es posible, y deberá ser la base, junto con otros estudios, del proceso de registro de la que podrá ser la primera generación de vacunas contra la malaria.

No description available.

Malaria is a devastating parasitic disease in humans caused by species in the genus Plasmodium. With over 100 million cases and at least 1.5 million fatalities each year, the disease accounts for 4-5% of all fatalities in the world. A recent increase in the number of malaria cases in South Africa has imposed severe costs on the economy and public health. Immunity to malaria is a multi-component system involving both B and T celllymphocytes. Pc96 is a 96 kDa antigen identified in the mouse malaria model Plasmodium chabaudi adami. It is known to be associated with the outer membrane of mouse erythrocytes infected with the parasite and has shown protective roles in mice challenged with P. chabaudi adami. A specific T cell clone has been identified that adoptively provides protection to athymic mice infected with P. chabaudi adami. Antibodies raised against Pc96 identified proteins that induced the proliferation of the protective T cell clones. At least four other antigens of different species of. malaria share at least one cross-reactive epitope. In an attempt to identify a Plasmodiumfalciparum homologue ofPc96, the amino-acid sequence was used in a BLAST search of the P. falciparum genome database, identifying a 403 kDa protein with a high degree of homology to Pc96. Sequence alignments indicated a region spanning 90 amino acids in Pf403 that overlaps the Pc96 amino acid sequence. A 178 kDa protein in P. yoelii yoelii (Pyy178) was shown to be highly similar to Pc96. Tvcell epitope prediction programs identified putative T cell epitopes in Pc96 which appear to be conserved in Pf403 and Pyy178. A casein kinase IT phosphorylation site was also identified in this region and is conserved in both sequences. PCR primers were designed to amplify regions of the MAL3P6.11 gene coding for Pf403 from P.falciparum genomic DNA. An 817 bp region in the MAL3P6.11 gene was amplified. This codes for the region ofPf403 that shows high homology to Pc96 and contains the conserved T cell epitopes and casein kinase phophorylation site. A BamHI site was incorporated into the forward primer to facilitate in-frame ligation with cloning vectors. The PCRproduct obtained was verified by restriction analysis using HindIII and EcoRI sites within the fragment. The 817 bp peR product was cloned into the pMOSBlue vector using a blunt-endedPCR cloning kit, and transformed into MOSBlue competent cells. Recombinants were identified using the uIV complementation system, and verified by PCR, plasmid DNA isolation, and restriction digestion analysis. The insertDNA in pMOSBlue was cut out with BamHI and sub-cloned into the BamHI site in the pMAL-C2x expression vector. Sequencing ofthe construct confirmed the identity of the cloned insert and showed the sequence to be in frame with the malE gene coding for maltose binding protein (MBP). The fusion protein, MBP-Pf32 .5, was induced and expressed as a 75 kDa protein comprising ofthe 32.5 kDa region ofPf403, and MBP (42.5 kDa) and was detected by anti-MBP antibodies, by western blotting. This recombinant protein has many applications for further studies involving the characterisation of the Pf403 protein, and the determination of possible roles that the protein may have in stimulating an immune response during human malaria infections. / Thesis (M.Sc.) - University of Natal, Pietermaritzburg, 2003.

Department of Chemistry / MSc (Chemistry) / Due to the increasing incidence of Plasmodium strains that are resistant to current frontline antimalarial drugs, malaria remains a global public health challenge. In recent years, the emergence of resistance to frontline antimalarial drugs including the more recently discovered artemisinin class drugs has become one of the greatest challenges of controlling malaria incidence and mortality. There is, therefore, an urgent need to develop novel targets and antimalarial drugs that are effective against drug-resistant malarial parasites. Recent studies have demonstrated that calcium dependent protein kinases (CDPKs) regulate a variety of biological processes in the malaria parasite Plasmodium falciparum and that CDPK4 is important for parasite development. The gene disruption of CDPK4 in Plasmodium berghei, which results in major defects in sexual differentiation of the parasite has highlighted the importance of CDPK4 in Plasmodium biology and suggests that it may be used as a target for therapeutic drugs. PfCDPK4 is expressed in the gamete/gametocyte stage, and this could make PfCDPK4 an essential target for malaria drug discovery. The structure of PfCDPK4 was used as a template in the discovery of malaria drug leads and in designing chemical compounds or inhibitors that will show anti-parasitic activity against the target molecule. The model structure of PfCDPK4 was generated through homology modelling, and model structure validation confirmed that the model structure of PfCDPK4 is of stereochemical quality. The molecular modelling approach of in silico screening was utilized in this research, wherein a large library of chemical compounds, some natural chemical compounds, and clinically approved kinase inhibitors were screened against the target molecule PfCDPK4. In silico screening of the Bio-Focus library against PfCDPK4 resulted in twenty-six compounds being identified; in vitro single screening at a concentration of 5 μM confirmed that three compounds exhibit moderate antimalarial activity against the NF54 strain of Plasmodium falciparum, with the percentage inhibition ranging between 42% and 47%.

Malaria, caused by the parasite Plasmodium, continues to exact high global morbidity and mortality rate next only to tuberculosis. It causes 300-500 million clinical infections out of which more than a million people succumb to death annually. Worst affected are the children below 5 years of age in sub-Saharan Africa. Plasmodium is a protozoan parasite classified under the phylum Apicomplexa that also includes parasites such as Toxoplasma, Lankestrella, Eimeria and Cryptosporidium. Of the four species of Plasmodium affecting man viz., P. falciparum, P. vivax, P. ovale and P. malariae, Plasmodium falciparum is the deadliest as it causes cerebral malaria. The situation has worsened recently with the emergence of drug resistance in the parasite. Therefore, deciphering new pathways in the parasite for developing lead antimalarial compounds is the need of the hour. The discovery of the type II fatty acid biosynthesis pathway in Plasmodium falciparum has opened up new avenues for the design of new antimalarials as this pathway is different from the one in human hosts. Although many biochemical pathways such as the purine, pyrimidine and carbohydrate metabolic pathways, and the phospholipid, folate and heme biosynthetic pathways operate in the malaria parasite and are being investigated for their amenability as antimalarial therapeutic targets, no antimalarial of commercial use based on the direct intervention of these biochemical pathways has emerged so far. This is due to the fact that the structure and function of the targets of these drugs overlaps with that of the human host. A description of the parasite, its metabolic pathways, efforts to use these pathways for antimalarial drug discovery, inhibitors targeting these pathways, introduction to fatty acid biosynthesis pathway, discovery of type II fatty acid biosynthesis pathway in Plasmodium falciparum and prospects of developing lead compounds towards antimalarial drug discovery is given in Chapter 1 of the thesis. In the exploration of newly discovered type II fatty acid biosynthesis pathway of P. falciparum as a drug target for antimalarial drug discovery, one of the enzymes; β-hydroxyacyl- acyl carrier protein dehydratase (PfFabZ) was cloned and being characterized in the lab. The atomic structure of PfFabZ was not known till that point of time. Chapter 2 describes the homology modeled structure of PfFabZ and docking of the discovered inhibitors with this structure to provide a rationale for their inhibitory activity. Despite low sequence identity of ~ 21% with the closest available atomic structure then, E. coli FabA, a good model of PfFabZ could be built. A comparison of the modeled structure with recently determined crystal structure of PfFabZ is provided and design of new potential inhibitors is described. This study provides insights to further improve the inhibition of this enzyme. Enoyl acyl carrier protein reductase (ENR) is the most important enzyme in the type II fatty acid biosynthesis pathway. It has been proved as an important target for antibacterial as well as antimalarial drug discovery. The most effective drug against tuberculosis – Isoniazid targets this enzyme in M. tuberculosis. The well known antibacterial compound – Triclosan, a diphenyl ether, also targets this enzyme in P. falciparum. I designed a number of novel diphenyl ether compounds. Some of these compounds could be synthesized in the laboratory. Chapter 3 describes the design, docking studies and inhibitory activity of these novel diphenyl ether compounds against PfENR and E. coli ENR. Some of these compounds inhibit PfENR in nanomolar concentrations and EcENR in low micromolar concentrations, and many of them inhibit the growth of parasites in culture also. The structure activity relationship of these compounds is discussed that provides important insights into the activity of this class of compounds which is a step towards developing this class of compounds into an antimalarial and antibacterial candidate drugs. Components of the green tea extract and polyphenols are well known for their medicinal properties since ages. Recently they have been shown to inhibit components of the bacterial fatty acid biosynthesis pathway. Some selected tea catechins and polyphenols were tested in the laboratory for their inhibitory activity against PfENR. I conducted docking studies to find their probable binding sites in PfENR. On kinetic analysis of their inhibition, these compounds were found to be competitive with respect to the cofactor NADH. This has an implication that they could potentiate inhibition of PfENR by Triclosan in a fashion similar to that of NADH. As a model case, one of the tea catechins; EGCG ((-) Epigalocatechin gallate) was tested for this property. Indeed, in the presence of EGCG, the inhibition of PfENR improved from nanomolar to picomolar concentration of Triclosan.conducted molecular modeling studies and propose a model for the formation of a ternary complex consisting of EGCG, Triclosan and PfENR. Docking studies of these inhibitors and a model for the ternary complex is described in Chapter 4. Docking simulations show that these compounds indeed occupy NADH binding site. This study provides insights for further improvements in the usage of diphenyl ethers in conjugation or combination with tea catechins as possible antimalarial therapeutics. In search for new lead compounds against deadly diseases, in silico virtual screening and high throughput screening strategies are being adopted worldwide. While virtual screening needs a large amount of computation time and hardware, high throughput screening proves to be quite expensive. I adopted an intermediate approach, a combination of both these strategies and discovered compounds with a 2-thioxothiazolidin-4-one core moiety, commonly known as rhodanines as a novel class of inhibitors of PfENR with antimalarial properties. Chapter 5 describes the discovery of this class of compounds as inhibitors of PfENR. A small but diverse set of 382 compounds from a library of ~2,00,000 compounds was chosen for high throughput screening. The best compound gave an IC50 of 6.0 µM with many more in the higher micromolar range. The compound library was searched again for the compounds similar in structure with this best compound, virtual screening was conducted and 32 new compounds with better binding energies compared to the first lead and reasonable binding modes were tested. As a result, a new compound with an IC50 of 240 nM was discovered. Many more compounds gave IC50 values in 3-15 µM range. The best inhibitor was tested in red blood cell cultures of Plasmodium, it was found to inhibit the growth of the malaria parasite at an IC50 value of 0.75 µM. This study provides a new scaffold and lead compounds for further exploration towards antimalarial drug discovery. The summary of the results and conclusions of studies described in various chapters is given in Chapter 6. This chapter concludes the work described in the thesis. Cloning, over-expression and purification of PanD from M. tuberculosis, FabA and FabZ from E. coli are described in the Appendix.

MSc (Chemistry) / Department of Chemistry