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Drug targets in the malaria parasite, Plasmodium falciparum
Our laboratory is interested in parasitic diseases, with a primary focus on the causative agent of severe malaria, Plasmodium falciparum. The burden of disease-causing parasites is particularly high in developing countries, and inadequate resources are directed towards the development of much-needed treatments. Complete genome sequences are available for many of these parasites, so a wealth of information is available from which to search for potential targets for chemotherapeutic interventions. We are interested in identifying and characterising promising drug targets from P. falciparum and other parasites, as well as studying the modes of action and mechanisms of resistance for existing drugs.
We use various bioinformatic methods to screen for promising drug targets, and molecular biological, and cell biological methods (confocal and electron microscopy with transgenic parasites), as well as in vitro parasite culture to characterise and test potential parasite drug targets. In collaboration with Professor Malcolm McConville, we are subjecting malaria parasites to metabolomic analyses to help understand the modes of action of existing and novel anti-malarial drugs.
The Ralph laboratory is a member of a European Union FP7-funded consortium (Mephitis) of eight laboratories studying protein translation in the apicoplast and cystosol of Plasmodium in the search for potential targets for anti-malarial drugs.
1. Aminoacyl-tRNA synthetases enzymes as drug targets
Projects on offer are aimed at characterising aminoacyl-tRNA synthetase (aaRS) enzymes as drug targets in Plasmodium. These enzymes catalyse the attachment of amino acids to their relevant tRNA molecules and are essential for protein synthesis. They have recently been recognised as promising drug targets across a broad range of microbes, and we have recently identified Plasmodium aaRSs that are potential targets for new drugs to treat malaria. Plasmodium aaRS enzymes are very different to the forms found in humans, so we hope to develop drugs that inhibit Plasmodium without affecting their human host cells. We are developing assays to measure specific inhibition of Plasmodium aaRS enzymes, and will also test inhibitors for their ability to kill Plasmodium grown in culture.
Fig. 1. A structural model of a P. falciparum aminoacyl-tRNA synthetase. aaRS enzymes have several deep substrate-binding pockets that appear to be suitable for targeting with small molecule inhibitors. Such inhibition has already been demonstrated for many bacteria, including Staphylococcus aureus (golden staph).
Gene regulation in P. falciparum
P. falciparum successfully evades the human immune system by an ingenious trick of constantly changing the surface coat to avoid detection and destruction mediated by human antibodies. This constant surface transformation is referred to as antigenic variation, and is controlled by a fascinating mechanism of genetic regulation. Many of the regulatory processes involved in this mechanism are epigenetic processes, dependent on covalent modifications of the nucleosomes that serve as a scaffold for DNA wrapping.
Fig. 2 This false-colored transmission electron micrograph shows a P. falciparum parasite, cause of the most severe form of malaria. Antigenic variation in these parasites contributes to parasite immune evasion, and compartmentalisation of silencing factors and chromatin states in the nucleus play important roles in regulating antigenic variation. In this image, the infected erythrocyte is shown in red, and the parasite is shown in purple. The dark blue highlights the condensed material at the nuclear periphery with lighter blue displaying the nuclear core
1. Chromosomal compartmentalization
Genetic elements within and adjacent to genes help regulate the covalent modifications of the nucleosomes to which they are attached. These elements also delineate where one nucleosome-modification zone ends and where the next begins. This is a phenomenon that has been very poorly studied in any microbe, but is extremely important for understanding how some genes are highly activated while others are stringently silenced. We have established genetic screens to identify these elements in P. falciparum, and will identify the proteins that recognise these elements.
2. Upstream elements regulating transcription
While much is known about the genetic elements that regulate transcription in some model organisms, transcriptional promoters are only vaguely understood in Plasmodium. The complete sequencing of the Plasmodium genome, combined with a number of whole-genome microarray experiments, now provide us with an opportunity to identify the elements that regulate timing and abundance of Plasmodium transcription. This project will combine bioinformatic analyses with parasite genetic transfection experiments to characterise transcriptional regulation.
Apicomplexan cell biology
Apicomplexan parasites possess novel organelles and cell biological structures, some of which are adaptions to intracellular parasitism, while others are vestiges of their evolutionary past. We are interested in understanding protein trafficking to the various compartments of apicomplexan parasites, and are developing bioinformatic tools to catalogue and predict protein subcellular localisation in apicomplexan parasites such as Plasmodium.
(ApiLoc is a database of published experimental sub-cellular localisations for Apicomplexan parasites.)
Dr Stuart Ralph
Dr Chaitali Dekiwadia (Research officer)
Erin Lim (Research assistant)
Dr Katherine Putnam (Research officer)
Current members of the Ralph Lab
Chaitali is a postdoctoral researcher investigating merozoite invasion of the malaria parasites Plasmodium falciparum
Florian is a graduate student researching the digestive vacuole of the malaria parasite, Plasmodium falciparum. Florian's co-supervisor is Alan Cowman at the WEHI
Michelle is an Honours student researching tRNA synthetases of Plasmodium falciparum as antimalarial drug targets
Erin is a research assistant studying epigenetic regulation and protein translation in Plasmodium falciparum
Katherine is a postdoc researching tRNA sythetases of Plasmodium falciparum as antimalarial drug targets
James is a graduate student studying the structure and function of Plasmodium falciparum tRNA sythetases. James is also investigating inhibitors of tRNA sythetases as potential anti-malarials. He is co-supervised by Matt Perugini and Renwick Dobson
Howard is an Honours student investigating falciparum-specific virulence factors. He is co-supervised by Elizabeth Hartland, Department of Microbiology and Immunology
Ben is a graduate student researching the bioinformatic prediction of subcellular localisation of proteins in apicomplexan parasites. He is co-supervised by Terry Speed at the WEHI
Lee is a graduate student studying mRNA splicing in apicomplexan parasites. He is co-supervised by Geoff McFadden and Giel van Dooren
Alumni of the Ralph Lab
Maria is now working as a bioinformatician at the Peter Mac Cancer Centre
|Nilushi De Silva
Nilushi is now a PhD student in the Department of Microbiology and Immunology at Columbia University in New York City
Robert is now completing his Masters degree at the University of Stuttgart