Computational studies in human African trypanosomiasis
- Authors: Muronzi, Tendai
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/431883 , vital:72812 , DOI 10.21504/10962/431885
- Description: Human African trypanosomiasis (HAT) is a neglected tropical disease (NTD) caused by two subspecies of the parasite, namely Trypanosoma brucei (Tb) gambiense (g-HAT) and rhodesiense (r-HAT). HAT is endemic in sub-Saharan countries, where the parasite transmission vectors, tsetse flies, breed. An estimated 70 million people remain at risk of contracting the disease, where the infection is classified as acute or chronic for g-HAT and r-HAT, respectively, with both forms ending in fatal meningoencephalitis when left untreated. Both g-HAT and r-HAT are responsible for widespread fatal epidemics throughout sub-Saharan African history, resulting from the complex molecular interplay between trypanosomes and humans through unique, innate immunity evasion mechanisms. Of interest, the Tbr subspecies expresses a serum resistance-associated protein (SRA), which binds to human serum lytic factor, apolipoprotein L1 (ApoL1), nullifying any trypanocidal activity. In response, ApoL1 (G1 and G2) variants found in humans of sub-Saharan African lineage have been cited for conferring resistance to the r-HAT infection in an interaction that is not fully elucidated In the event of successful infection, current HAT chemotherapeutics are plagued with complexity of administration, poor efficacy, toxicity, and potential drug resistance, highlighting a need for improved approaches. The parasite folate pathway provides a strategic target for alternative anti-trypanosomal drug development as trypanosomatids are folate auxotrophs, requiring host folate for growth and survival. Validated drug targets pteridine reductase (TbPTR1) and dihydrofolate reductase (TbDHFR) are essential for salvaging cofactors folate and folate biopterin crucial to parasite survival, making them viable targets for anti-folate investigation. The overall aims of this thesis were to a) provide insights into the molecular and dynamic basis of the SRA and ApoL1 interplay in HAT infection and b) identify safer and more efficient anti-folate anti-trypanosomal drug alternatives through in silico approaches. To achieve our first aim, in silico structure prediction was applied to generate 3D models of ApoL1 C-terminal variants G0, G1, G1G/M, G2 and G1G2, and four SRA variants retrieved from the NCBI database. The SRA and ApoL1 structures were inspected dynamically to identify the effect of the variants through molecular dynamics (MD) simulations. Dynamic residue network (DRN) analysis of MD trajectories was fundamental in identifying residues playing a vital role in the intramolecular communication of both proteins in the presence of mutations. Protein-protein docking was then applied to calculate plausible SRA-ApoL1 C-terminal wild-type complex structures to further elucidate the nature of SRA-mediated infection. Through MD simulations, twelve SRA-ApoL1 dimeric structures were narrowed down from five to two energetically sound complexes. The two feasible SRA-ApoL1 complexes (1 and 2) exhibited favourable communication observed through DRN analysis, including the retaining key communication residues identified in prior monomer DRN calculations. ApoL1 C-terminal variants were additionally incorporated into SRA-ApoL1 complexes 1 and 2 for further complex dynamics analysis This investigation into the nature of SRA-ApoL1 binding resulted in five primary outcomes: 1) highlighting the intramolecular effects ApoL1 variants have on the stability of the protein, 2) the identification of crucial SRA and ApoL1 communication residues in both monomeric or dimeric form, 3) the isolation of feasible SRA-ApoL1 complexes determined through global and local structural analyses 4) identification of residues crucial to the complex formation and maintenance of SRA-ApoL1, overlapping with those identified in (1), and 5) the minimal dissociative role of the G1 mutations in the complex, but compounding effect of the G2 deletion mutation. Computational modelling and drug repurposing were employed to achieve the thesis's second aim as they drastically cut down the costs involved in drug discovery and provide a more time-efficient screening method through numerous drug candidates. Using high throughput virtual screening, a subset of 2089 approved DrugBank compounds were screened against TbPTR1. The outputs were filtered to 24 viable compounds in 54 binding poses using binding energy and molecular interactions. Through subsequent MD simulations of 200ns, thirteen potential hit compounds were identified. The resultant hit compounds were subjected to further blind docking against TbDHFR and molecular dynamics to identify compounds with the potential for dual inhibition. The filtered subset was also tested in in vitro single concentration and dose-response bioassays to assess inhibitory properties against Trypanosoma brucei, complementing in silico findings. Post-molecular dynamics, four compounds exhibited high stabilities and molecular interactions with both TbPTR1 and TbDHFR, with two presenting favourable results in the in vitro assays. Three compounds additionally shared common structural moieties. In all, the in silico repurposing highlighted drugs characterised by favourable interactions and stabilities in TbPTR1, thus providing (1) a framework for further studies investigating anti-folate HAT compounds and (2) modulatory scaffolds based on identified moieties that can be used for the design of safe anti-folate trypanosomal drugs. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2023
- Full Text:
- Date Issued: 2023-10-13
- Authors: Muronzi, Tendai
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/431883 , vital:72812 , DOI 10.21504/10962/431885
- Description: Human African trypanosomiasis (HAT) is a neglected tropical disease (NTD) caused by two subspecies of the parasite, namely Trypanosoma brucei (Tb) gambiense (g-HAT) and rhodesiense (r-HAT). HAT is endemic in sub-Saharan countries, where the parasite transmission vectors, tsetse flies, breed. An estimated 70 million people remain at risk of contracting the disease, where the infection is classified as acute or chronic for g-HAT and r-HAT, respectively, with both forms ending in fatal meningoencephalitis when left untreated. Both g-HAT and r-HAT are responsible for widespread fatal epidemics throughout sub-Saharan African history, resulting from the complex molecular interplay between trypanosomes and humans through unique, innate immunity evasion mechanisms. Of interest, the Tbr subspecies expresses a serum resistance-associated protein (SRA), which binds to human serum lytic factor, apolipoprotein L1 (ApoL1), nullifying any trypanocidal activity. In response, ApoL1 (G1 and G2) variants found in humans of sub-Saharan African lineage have been cited for conferring resistance to the r-HAT infection in an interaction that is not fully elucidated In the event of successful infection, current HAT chemotherapeutics are plagued with complexity of administration, poor efficacy, toxicity, and potential drug resistance, highlighting a need for improved approaches. The parasite folate pathway provides a strategic target for alternative anti-trypanosomal drug development as trypanosomatids are folate auxotrophs, requiring host folate for growth and survival. Validated drug targets pteridine reductase (TbPTR1) and dihydrofolate reductase (TbDHFR) are essential for salvaging cofactors folate and folate biopterin crucial to parasite survival, making them viable targets for anti-folate investigation. The overall aims of this thesis were to a) provide insights into the molecular and dynamic basis of the SRA and ApoL1 interplay in HAT infection and b) identify safer and more efficient anti-folate anti-trypanosomal drug alternatives through in silico approaches. To achieve our first aim, in silico structure prediction was applied to generate 3D models of ApoL1 C-terminal variants G0, G1, G1G/M, G2 and G1G2, and four SRA variants retrieved from the NCBI database. The SRA and ApoL1 structures were inspected dynamically to identify the effect of the variants through molecular dynamics (MD) simulations. Dynamic residue network (DRN) analysis of MD trajectories was fundamental in identifying residues playing a vital role in the intramolecular communication of both proteins in the presence of mutations. Protein-protein docking was then applied to calculate plausible SRA-ApoL1 C-terminal wild-type complex structures to further elucidate the nature of SRA-mediated infection. Through MD simulations, twelve SRA-ApoL1 dimeric structures were narrowed down from five to two energetically sound complexes. The two feasible SRA-ApoL1 complexes (1 and 2) exhibited favourable communication observed through DRN analysis, including the retaining key communication residues identified in prior monomer DRN calculations. ApoL1 C-terminal variants were additionally incorporated into SRA-ApoL1 complexes 1 and 2 for further complex dynamics analysis This investigation into the nature of SRA-ApoL1 binding resulted in five primary outcomes: 1) highlighting the intramolecular effects ApoL1 variants have on the stability of the protein, 2) the identification of crucial SRA and ApoL1 communication residues in both monomeric or dimeric form, 3) the isolation of feasible SRA-ApoL1 complexes determined through global and local structural analyses 4) identification of residues crucial to the complex formation and maintenance of SRA-ApoL1, overlapping with those identified in (1), and 5) the minimal dissociative role of the G1 mutations in the complex, but compounding effect of the G2 deletion mutation. Computational modelling and drug repurposing were employed to achieve the thesis's second aim as they drastically cut down the costs involved in drug discovery and provide a more time-efficient screening method through numerous drug candidates. Using high throughput virtual screening, a subset of 2089 approved DrugBank compounds were screened against TbPTR1. The outputs were filtered to 24 viable compounds in 54 binding poses using binding energy and molecular interactions. Through subsequent MD simulations of 200ns, thirteen potential hit compounds were identified. The resultant hit compounds were subjected to further blind docking against TbDHFR and molecular dynamics to identify compounds with the potential for dual inhibition. The filtered subset was also tested in in vitro single concentration and dose-response bioassays to assess inhibitory properties against Trypanosoma brucei, complementing in silico findings. Post-molecular dynamics, four compounds exhibited high stabilities and molecular interactions with both TbPTR1 and TbDHFR, with two presenting favourable results in the in vitro assays. Three compounds additionally shared common structural moieties. In all, the in silico repurposing highlighted drugs characterised by favourable interactions and stabilities in TbPTR1, thus providing (1) a framework for further studies investigating anti-folate HAT compounds and (2) modulatory scaffolds based on identified moieties that can be used for the design of safe anti-folate trypanosomal drugs. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2023
- Full Text:
- Date Issued: 2023-10-13
Species diversity and distribution patterns of three freshwater fish genera in southern Africa
- Authors: Mutizwa, Tadiwa Isaac
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/431896 , vital:72813
- Description: Access restricted. Expected release in 2025. , Thesis (PhD) -- Faculty of Science, Ichthyology and Fisheries Science, 2023
- Full Text:
- Date Issued: 2023-10-13
- Authors: Mutizwa, Tadiwa Isaac
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/431896 , vital:72813
- Description: Access restricted. Expected release in 2025. , Thesis (PhD) -- Faculty of Science, Ichthyology and Fisheries Science, 2023
- Full Text:
- Date Issued: 2023-10-13
The electrocatalytic activity of metallophthalocyanines and their conjugates with carbon nanomaterials and metal tungstate nanoparticles
- Authors: Ndebele, Nobuhle
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/431934 , vital:72816 , DOI 10.21504/10962/431933
- Description: In this dissertation, seventeen phthalocyanine complexes were synthesised. Of these, only four are known and have been published. These complexes were synthesised using the conventional statistical condensation method that involves refluxing the phthalonitrile(s) (4-((1,3-bis(dimethylamino)propan-2-yl)oxy)phthalonitrile, 4-(4-carboxyphenoxy)phthalonitrile, 4-(4-acetylphenoxy)phthalonitrile, dimethyl 5-(3,4-dicyanophenoxy)-isophthalate, 4-(4-(tert-butyl)phenoxy)phthalonitrile, 5-phenoxylpicolinic acid phthalonitrile 4-(4-formylphenoxy) phthalonitrile, and 4-(4-(3-oxo-3-phenylprop-1-enyl) phenoxy) phthalonitrile) with the metal salt and 1,8-diazabicyclo[5.4.0]undecane as a catalyst in a high-temperature solvent. And thereafter (when necessary), isolation and purification of the target compounds were achieved through the use of silica column chromatography. These compounds were characterised using various analytical techniques such as; ultraviolet-visible absorption, mass spectroscopy, and Fourier transform infrared spectra and elemental analysis. These techniques proved that the complexes were successfully synthesised and isolated as pure compounds. Carbon-based (graphene quantum dots and nitrogen-doped graphene quantum dots) and metal oxide (bismuth tungsten oxide and nickel tungsten oxide) nanomaterials were synthesised. Together with the purchased single-walled carbon nanotubes, these nanomaterials were conjugated to some of the MPc complexes via non-covalent (carbon-based nanomaterials) and covalent (metal oxides) linkage forming hybrid materials. These nanomaterials and hybrids were characterised using various analytical methods (ultraviolet-visible absorption, X-ray diffraction, Raman spectroscopy, thermographic analysis, and dynamic light scattering). Nanomaterials were utilised herein to determine their effect on the properties of MPc complexes and provide a synergistic effect in the hope of enhancing these properties. All complexes synthesised in this work (MPcs, nanomaterials and hybrids) were employed as electrocatalysts in electrochemical sensing. These electrocatalysts were embedded onto the glassy carbon electrode via an adsorption method known as drop-casting. The modified electrode surfaces were characterised using cyclic voltammetry, electrochemical impedance spectroscopy and scanning electrochemical microscopy to determine various electrochemical parameters. These electrocatalysts were used in the detection of either nitrite, catechol and/or dopamine. The detection limits, sensitivities, kinetics and catalytic constants were among other parameters determined for each electrocatalyst. These electrocatalysts proved to be stable electrocatalysts that could potentially be used for practical applications. The determined parameters were comparable and sometimes better than those obtained in literature. , Thesis (PhD) -- Faculty of Science, Chemistry, 2023
- Full Text:
- Date Issued: 2023-10-13
- Authors: Ndebele, Nobuhle
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/431934 , vital:72816 , DOI 10.21504/10962/431933
- Description: In this dissertation, seventeen phthalocyanine complexes were synthesised. Of these, only four are known and have been published. These complexes were synthesised using the conventional statistical condensation method that involves refluxing the phthalonitrile(s) (4-((1,3-bis(dimethylamino)propan-2-yl)oxy)phthalonitrile, 4-(4-carboxyphenoxy)phthalonitrile, 4-(4-acetylphenoxy)phthalonitrile, dimethyl 5-(3,4-dicyanophenoxy)-isophthalate, 4-(4-(tert-butyl)phenoxy)phthalonitrile, 5-phenoxylpicolinic acid phthalonitrile 4-(4-formylphenoxy) phthalonitrile, and 4-(4-(3-oxo-3-phenylprop-1-enyl) phenoxy) phthalonitrile) with the metal salt and 1,8-diazabicyclo[5.4.0]undecane as a catalyst in a high-temperature solvent. And thereafter (when necessary), isolation and purification of the target compounds were achieved through the use of silica column chromatography. These compounds were characterised using various analytical techniques such as; ultraviolet-visible absorption, mass spectroscopy, and Fourier transform infrared spectra and elemental analysis. These techniques proved that the complexes were successfully synthesised and isolated as pure compounds. Carbon-based (graphene quantum dots and nitrogen-doped graphene quantum dots) and metal oxide (bismuth tungsten oxide and nickel tungsten oxide) nanomaterials were synthesised. Together with the purchased single-walled carbon nanotubes, these nanomaterials were conjugated to some of the MPc complexes via non-covalent (carbon-based nanomaterials) and covalent (metal oxides) linkage forming hybrid materials. These nanomaterials and hybrids were characterised using various analytical methods (ultraviolet-visible absorption, X-ray diffraction, Raman spectroscopy, thermographic analysis, and dynamic light scattering). Nanomaterials were utilised herein to determine their effect on the properties of MPc complexes and provide a synergistic effect in the hope of enhancing these properties. All complexes synthesised in this work (MPcs, nanomaterials and hybrids) were employed as electrocatalysts in electrochemical sensing. These electrocatalysts were embedded onto the glassy carbon electrode via an adsorption method known as drop-casting. The modified electrode surfaces were characterised using cyclic voltammetry, electrochemical impedance spectroscopy and scanning electrochemical microscopy to determine various electrochemical parameters. These electrocatalysts were used in the detection of either nitrite, catechol and/or dopamine. The detection limits, sensitivities, kinetics and catalytic constants were among other parameters determined for each electrocatalyst. These electrocatalysts proved to be stable electrocatalysts that could potentially be used for practical applications. The determined parameters were comparable and sometimes better than those obtained in literature. , Thesis (PhD) -- Faculty of Science, Chemistry, 2023
- Full Text:
- Date Issued: 2023-10-13
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