In Silico analysis of Spermidine, Spermine and Putrescine interaction with selected heat shock proteins from Plasmodium falciparum 3D7 towards malaria drug development
- Authors: Godlo, Sesethu
- Date: 2022
- Subjects: Heat shock proteins , Malaria vaccine , Plasmodium falciparum
- Language: English
- Type: Master'stheses , text
- Identifier: http://hdl.handle.net/10353/27709 , vital:69395
- Description: Malaria is a mosquito-borne disease that affects around half of the world's population. It is one of the most common parasite infections that endangers human life. One of the most serious issues in malaria therapy is the emergence and spread of antimalarial drug-resistant Plasmodium parasites. This is due to the Plasmodium parasite's constant evolution and development of new methods of surviving medication toxicity. Studies of antimalarial drug development have been focused on polyamine biosynthesis by targeting precursors such as ornithine decarboxylase, adenosylmethionine decarboxylase, and spermidine synthase and protein-protein interactions between Plasmodium falciparum chaperones spotting out Hsp90, Hsp70, and Hsp40 as potential targets with little attention being paid to the interaction between polyamines and molecular chaperones. Therefore, this study seeks to identify interactions between polyamines and molecular chaperones present in the malarial parasite Plasmodium falciparum 3D7. The identification of these interactions might lead to the design of effective drugs to treat and eliminate malaria. Using computational analysis, this study aims to find interactions between polyamines and molecular chaperones found in the malarial parasite Plasmodium falciparum 3D7. The sequences of the selected heat proteins retrieved, and the 3D structures predicted and validated. These structures were docked with polyamines retrieved from PubChem and MD simulations on the docked interactions were performed. Docking revealed common amino acid residues with hydrogen bonds and salt bridges between all receptors and ligands, with glutamine and aspartic acid standing out. MD simulations revealed that when HSP20 and HSP40 transport the ligands, they pop up or are released too quickly. However, HSP60, HSP70, and HSP90 provide optimism since the ligands remain attached to the proteins for a specific amount of time. To further understand and confirm these interactions wet laboratory studies may be carried out in future. , Thesis (MSci) -- Faculty of Science and Agriculture, 2022
- Full Text:
- Date Issued: 2022
- Authors: Godlo, Sesethu
- Date: 2022
- Subjects: Heat shock proteins , Malaria vaccine , Plasmodium falciparum
- Language: English
- Type: Master'stheses , text
- Identifier: http://hdl.handle.net/10353/27709 , vital:69395
- Description: Malaria is a mosquito-borne disease that affects around half of the world's population. It is one of the most common parasite infections that endangers human life. One of the most serious issues in malaria therapy is the emergence and spread of antimalarial drug-resistant Plasmodium parasites. This is due to the Plasmodium parasite's constant evolution and development of new methods of surviving medication toxicity. Studies of antimalarial drug development have been focused on polyamine biosynthesis by targeting precursors such as ornithine decarboxylase, adenosylmethionine decarboxylase, and spermidine synthase and protein-protein interactions between Plasmodium falciparum chaperones spotting out Hsp90, Hsp70, and Hsp40 as potential targets with little attention being paid to the interaction between polyamines and molecular chaperones. Therefore, this study seeks to identify interactions between polyamines and molecular chaperones present in the malarial parasite Plasmodium falciparum 3D7. The identification of these interactions might lead to the design of effective drugs to treat and eliminate malaria. Using computational analysis, this study aims to find interactions between polyamines and molecular chaperones found in the malarial parasite Plasmodium falciparum 3D7. The sequences of the selected heat proteins retrieved, and the 3D structures predicted and validated. These structures were docked with polyamines retrieved from PubChem and MD simulations on the docked interactions were performed. Docking revealed common amino acid residues with hydrogen bonds and salt bridges between all receptors and ligands, with glutamine and aspartic acid standing out. MD simulations revealed that when HSP20 and HSP40 transport the ligands, they pop up or are released too quickly. However, HSP60, HSP70, and HSP90 provide optimism since the ligands remain attached to the proteins for a specific amount of time. To further understand and confirm these interactions wet laboratory studies may be carried out in future. , Thesis (MSci) -- Faculty of Science and Agriculture, 2022
- Full Text:
- Date Issued: 2022
A novel, improved throughput bioassay for determining the delative speed of antimalarial drug action using fluorescent vitality probes
- Authors: Laming, Dustin
- Date: 2020
- Subjects: Plasmodium falciparum , Malaria -- Treatment -- Africa , Antimalarials , Malaria vaccine
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/139902 , vital:37810
- Description: Malaria is one of the most prevalent diseases in Africa and Plasmodium falciparum is widely accepted as the most virulent of the malaria parasite species, with a fatality rate of 15 – 20 % of reported cases of infection. While various treatments have been accepted into early stage clinical trials, there has been little progress towards a proven vaccine. Pending a long-term solution, endemic countries rely heavily on the development of innovative drugs that are not only efficacious but are also quick acting. Traditional methods of evaluating antimalarial killing speeds via morphological assessments are inherently flawed by tedious, subjective interpretations of the heterogenous parasite morphology encountered in routine parasite culture conditions. This has led to the introduction of alternative assay formats to determine how rapidly compounds act on parasites in vitro: a parasite reduction ratio (PRR) assay that measures the recovery of parasite cultures from drug exposure; determining the shift in IC50 values of compounds when dose-response assays are carried out for different time periods; a bioluminescence relative rate of kill (BRRoK) assay that compares the extent to which compounds reduce firefly luciferase activity in transgenic parasites. Recent whole cell in vitro screening efforts have resulted in the generation of chemically diverse compound libraries such as the Medicines for Malaria Venture’s Pathogen Box, which houses 125 novel compounds with in vitro antiplasmodial activity. Assessing the relative killing speeds of these compounds would aid prioritizing fast-acting compounds that can be exploited as starting points for further development. This study aimed to develop a bioassay using the calcein-acetoxymethyl and propidium iodide fluorescent vitality probes, which would allow the relative speed of drug action on Plasmodium falciparum malaria parasites to be assessed and ranked in relation to each other using a quantitative, improved throughput approach. Initially applied to human (HeLa) cells, the assay was used to compare the relative speeds of action of 3 potential anti-cancer compounds by fluorescence microscopy. Subsequently adapted to P. falciparum, the assay was able to rank the relative speeds of action of standard antimalarials by fluorescence microscopy and two flow cytometry formats. Application of a multiwell flow cytometer increased throughput and enabled the assessment of experimental compounds, which included a set of artemisinin analogs and 125 antimalarial compounds in the MMV Pathogen Box. The latter culminated in the identification of five rapidly parasiticidal compounds in relation to the other compounds in the library, which may act as benchmark references for future studies and form the basis of the next generation of fast acting antimalarials that could be used to combat modern, resistant malaria.
- Full Text:
- Date Issued: 2020
- Authors: Laming, Dustin
- Date: 2020
- Subjects: Plasmodium falciparum , Malaria -- Treatment -- Africa , Antimalarials , Malaria vaccine
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/139902 , vital:37810
- Description: Malaria is one of the most prevalent diseases in Africa and Plasmodium falciparum is widely accepted as the most virulent of the malaria parasite species, with a fatality rate of 15 – 20 % of reported cases of infection. While various treatments have been accepted into early stage clinical trials, there has been little progress towards a proven vaccine. Pending a long-term solution, endemic countries rely heavily on the development of innovative drugs that are not only efficacious but are also quick acting. Traditional methods of evaluating antimalarial killing speeds via morphological assessments are inherently flawed by tedious, subjective interpretations of the heterogenous parasite morphology encountered in routine parasite culture conditions. This has led to the introduction of alternative assay formats to determine how rapidly compounds act on parasites in vitro: a parasite reduction ratio (PRR) assay that measures the recovery of parasite cultures from drug exposure; determining the shift in IC50 values of compounds when dose-response assays are carried out for different time periods; a bioluminescence relative rate of kill (BRRoK) assay that compares the extent to which compounds reduce firefly luciferase activity in transgenic parasites. Recent whole cell in vitro screening efforts have resulted in the generation of chemically diverse compound libraries such as the Medicines for Malaria Venture’s Pathogen Box, which houses 125 novel compounds with in vitro antiplasmodial activity. Assessing the relative killing speeds of these compounds would aid prioritizing fast-acting compounds that can be exploited as starting points for further development. This study aimed to develop a bioassay using the calcein-acetoxymethyl and propidium iodide fluorescent vitality probes, which would allow the relative speed of drug action on Plasmodium falciparum malaria parasites to be assessed and ranked in relation to each other using a quantitative, improved throughput approach. Initially applied to human (HeLa) cells, the assay was used to compare the relative speeds of action of 3 potential anti-cancer compounds by fluorescence microscopy. Subsequently adapted to P. falciparum, the assay was able to rank the relative speeds of action of standard antimalarials by fluorescence microscopy and two flow cytometry formats. Application of a multiwell flow cytometer increased throughput and enabled the assessment of experimental compounds, which included a set of artemisinin analogs and 125 antimalarial compounds in the MMV Pathogen Box. The latter culminated in the identification of five rapidly parasiticidal compounds in relation to the other compounds in the library, which may act as benchmark references for future studies and form the basis of the next generation of fast acting antimalarials that could be used to combat modern, resistant malaria.
- Full Text:
- Date Issued: 2020
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