Identification of selective novel hits against Mycobacterium tuberculosis KasA potential allosteric sites using bioinformatics approaches
- Authors: Hare, Fadzayi Faith
- Date: 2022-10-14
- Subjects: Tuberculosis , Docking , Molecules Models , Virtual screening , Multidrug-resistant tuberculosis , Fatty acids Synthesis , Drugs Design
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/362842 , vital:65367
- Description: Tuberculosis (TB) is a global health threat that has led to approximately 1.5 million deaths annually. According to the World Health Organization (WHO), TB is among the top ten deadly diseases and is the leading cause of death due to a single infectious agent. The main challenge in the effective treatment and control of TB is the ongoing emergence of resistant strains of Mycobacterium tuberculosis (Mtb) which lead to multi-drug resistant (MDR) and extensive-drug resistant (XDR) TB. Hence, the identification and characterization of novel drug targets and drugs that modulate the activity of the pathogen are an urgent priority. The current situation even necessitates the reengineering or repurposing of drugs in order to achieve effective control. The β-ketoacyl-acyl carrier protein synthase I (KasA) of Mycobacterium tuberculosis is an essential enzyme in the mycobacterial fatty acid synthesis (FAS-II) pathway and is believed to be a promising target for drug discovery in TB. It is one of the five main proteins of the FAS-II pathway and catalyzes a key condensation reaction in the synthesis of meromycolate chains, the precursors of mycolic acids involved in cell wall formation. Although this protein has been extensively studied, little research has been devoted to the allosteric inhibition of potential drug compounds. The main aim of this research was to identify the allosteric sites on the protein that could be involved in the inhibition of substrate binding activities and novel drug compounds that bind to these sites by use of in-silico approaches. The bioinformatics approaches used in this study were divided into four main objectives namely identification of KasA homolog sequences, sequence analysis and protein characterization, allosteric site search and lastly virtual screening of DrugBank compounds via molecular docking. Fifteen homolog sequences were identified from the BLASTP analysis and were derived from bacteria, fungi and mammals. In order to discover important residues and regions within the KasA proteins, sequence alignment, motif analysis and phylogenetic studies were performed using Mtb KasA as a reference. Sequence alignment revealed conserved residues in all KasA proteins that have functional importance such as the catalytic triad residues (Cys171, His311 and His345). Motif analysis identified 18 highly conserved motifs within the KasA proteins with structural and functional roles. In addition, motifs unique to the Mtb KasA protein were also identified and explored for inhibitor drug design purposes. Phylogenetic analysis of the homolog sequences showed a distinct clustering of prokaryotes and eukaryotes. A distinctive clustering was also observed for species belonging to the same genus. Since the mechanism of action of most drugs involves the active site, allosteric site search was conducted on Mtb KasA and the human homolog protein using a combination of pocket detection algorithms with the aim of identifying sites that could be utilized in allosteric modulator drug discovery. This was followed by the virtual screening of 2089 FDA approved DrugBank compounds against the entire protein surfaces of Mtb KasA and Hsmt KasA, performed via molecular docking using AutoDock Vina. Screening of the compounds was based on the binding energies, with more focus on identifying ligands that bound exclusively to the acyl-binding tunnel of Mtb KasA. This reduced the data set to 27 promising drug compounds with a relatively high binding affinity for Mtb KasA, however, further experiments need to be performed to validate this result. Among these compounds were DB08889, DB06755, DB09270, DB11226, DB00392, DB12278, DB08936, DB00781, DB13720 and DB00392, which displayed relatively low binding energies for Mtb KasA when compared to the human homolog protein. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
- Date Issued: 2022-10-14
- Authors: Hare, Fadzayi Faith
- Date: 2022-10-14
- Subjects: Tuberculosis , Docking , Molecules Models , Virtual screening , Multidrug-resistant tuberculosis , Fatty acids Synthesis , Drugs Design
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/362842 , vital:65367
- Description: Tuberculosis (TB) is a global health threat that has led to approximately 1.5 million deaths annually. According to the World Health Organization (WHO), TB is among the top ten deadly diseases and is the leading cause of death due to a single infectious agent. The main challenge in the effective treatment and control of TB is the ongoing emergence of resistant strains of Mycobacterium tuberculosis (Mtb) which lead to multi-drug resistant (MDR) and extensive-drug resistant (XDR) TB. Hence, the identification and characterization of novel drug targets and drugs that modulate the activity of the pathogen are an urgent priority. The current situation even necessitates the reengineering or repurposing of drugs in order to achieve effective control. The β-ketoacyl-acyl carrier protein synthase I (KasA) of Mycobacterium tuberculosis is an essential enzyme in the mycobacterial fatty acid synthesis (FAS-II) pathway and is believed to be a promising target for drug discovery in TB. It is one of the five main proteins of the FAS-II pathway and catalyzes a key condensation reaction in the synthesis of meromycolate chains, the precursors of mycolic acids involved in cell wall formation. Although this protein has been extensively studied, little research has been devoted to the allosteric inhibition of potential drug compounds. The main aim of this research was to identify the allosteric sites on the protein that could be involved in the inhibition of substrate binding activities and novel drug compounds that bind to these sites by use of in-silico approaches. The bioinformatics approaches used in this study were divided into four main objectives namely identification of KasA homolog sequences, sequence analysis and protein characterization, allosteric site search and lastly virtual screening of DrugBank compounds via molecular docking. Fifteen homolog sequences were identified from the BLASTP analysis and were derived from bacteria, fungi and mammals. In order to discover important residues and regions within the KasA proteins, sequence alignment, motif analysis and phylogenetic studies were performed using Mtb KasA as a reference. Sequence alignment revealed conserved residues in all KasA proteins that have functional importance such as the catalytic triad residues (Cys171, His311 and His345). Motif analysis identified 18 highly conserved motifs within the KasA proteins with structural and functional roles. In addition, motifs unique to the Mtb KasA protein were also identified and explored for inhibitor drug design purposes. Phylogenetic analysis of the homolog sequences showed a distinct clustering of prokaryotes and eukaryotes. A distinctive clustering was also observed for species belonging to the same genus. Since the mechanism of action of most drugs involves the active site, allosteric site search was conducted on Mtb KasA and the human homolog protein using a combination of pocket detection algorithms with the aim of identifying sites that could be utilized in allosteric modulator drug discovery. This was followed by the virtual screening of 2089 FDA approved DrugBank compounds against the entire protein surfaces of Mtb KasA and Hsmt KasA, performed via molecular docking using AutoDock Vina. Screening of the compounds was based on the binding energies, with more focus on identifying ligands that bound exclusively to the acyl-binding tunnel of Mtb KasA. This reduced the data set to 27 promising drug compounds with a relatively high binding affinity for Mtb KasA, however, further experiments need to be performed to validate this result. Among these compounds were DB08889, DB06755, DB09270, DB11226, DB00392, DB12278, DB08936, DB00781, DB13720 and DB00392, which displayed relatively low binding energies for Mtb KasA when compared to the human homolog protein. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
- Date Issued: 2022-10-14
Experiences of patients on short term drug resistant tuberculosis regimen at Nelson Mandela District TB Specialist Hospital
- Authors: Sempe, Thabo Benedict
- Date: 2021-08
- Subjects: Multidrug-resistant tuberculosis
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10353/22940 , vital:53224
- Description: The purpose of this research study was to explore and describe the experiences of patients on short-term drug resistant TB treatment in a TB specialist hospital situated in Nelson Mandela District. Patients on XDR-TB treatment face many challenges which include side effects which they find hard to tolerate and they end up stopping the treatment. Socio-economic difficulties of concern include delayed social assistance from the government to support their families, particularly when they are breadwinners. A qualitative, descriptive, explorative contextual design was used in this research study. A non-probability convenience sampling method was employed. The target population for this study consisted of those DR-TB patients who were on short-term regimen and semi-structured individual interviews were conducted. There were twelve participants who voluntary participated in the research study although the first interview was a pilot study. Ethical principles were adhered to throughout the study. A total of seven themes and twenty-seven sub-themes arose during the data analysis and were fully discussed. Confidentiality and anonymity was ensured throughout this research. The research findings showed that the participants shared positive experiences in as far as being able to easily access the health care service. Most participants were moved through a range of emotions which included shock. They felt heartbroken about the devastation and the disruptive nature of this illness to themselves and their family lives and, more seriously, were fearful of the morbidity and mortality thoughts which pervaded their thoughts but their health improved when drug resistant TB treatment was initiated. Many of the participants found it easy to disclose to their friends as they knew they could count on their support at the best and worst of times in their treatment journey. In conclusion the participants provided suggestions regarding their support needs on the journey to recovery from DR-TB. The researcher provided certain recommendations as far as the challenges expressed by the participants and these will contribute to strengthening the DR-TB adherence strategies. , Thesis (MPH) -- Faculty of Health Sciences, 2021
- Full Text:
- Date Issued: 2021-08
- Authors: Sempe, Thabo Benedict
- Date: 2021-08
- Subjects: Multidrug-resistant tuberculosis
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10353/22940 , vital:53224
- Description: The purpose of this research study was to explore and describe the experiences of patients on short-term drug resistant TB treatment in a TB specialist hospital situated in Nelson Mandela District. Patients on XDR-TB treatment face many challenges which include side effects which they find hard to tolerate and they end up stopping the treatment. Socio-economic difficulties of concern include delayed social assistance from the government to support their families, particularly when they are breadwinners. A qualitative, descriptive, explorative contextual design was used in this research study. A non-probability convenience sampling method was employed. The target population for this study consisted of those DR-TB patients who were on short-term regimen and semi-structured individual interviews were conducted. There were twelve participants who voluntary participated in the research study although the first interview was a pilot study. Ethical principles were adhered to throughout the study. A total of seven themes and twenty-seven sub-themes arose during the data analysis and were fully discussed. Confidentiality and anonymity was ensured throughout this research. The research findings showed that the participants shared positive experiences in as far as being able to easily access the health care service. Most participants were moved through a range of emotions which included shock. They felt heartbroken about the devastation and the disruptive nature of this illness to themselves and their family lives and, more seriously, were fearful of the morbidity and mortality thoughts which pervaded their thoughts but their health improved when drug resistant TB treatment was initiated. Many of the participants found it easy to disclose to their friends as they knew they could count on their support at the best and worst of times in their treatment journey. In conclusion the participants provided suggestions regarding their support needs on the journey to recovery from DR-TB. The researcher provided certain recommendations as far as the challenges expressed by the participants and these will contribute to strengthening the DR-TB adherence strategies. , Thesis (MPH) -- Faculty of Health Sciences, 2021
- Full Text:
- Date Issued: 2021-08
Resilience of the partners of long term hospitalised patients with multidrug-resistant (MDR) and extreme drug-resistant (XDR) tuberculosis (TB)
- Authors: Smith, Louise
- Date: 2013
- Subjects: Multidrug-resistant tuberculosis , Health Belief Model , Hospital patients
- Language: English
- Type: Thesis , Masters , MA
- Identifier: vital:10007 , http://hdl.handle.net/10948/d1020913
- Description: Patients diagnosed with Multidrug-resistant(MDR) and Extreme drug-resistant (XDR) tuberculosis (TB) have to be hospitalised for a period of six to twelve months, according to the MDR/XDR Policy Guidelines on the treatment of drug-resistant TB – until the patient recovers, and is no longer infectious. There are factors associated with both the patients’ and their partners’ (spouses) resistance to long-term hospitalisation. This has resulted in several acts of violence against the hospital property and members of the health-care team. However, there are a small number of partners who assist the health-care team – by ensuring compliance from the patients and providing their continued support to the patient – despite their own risk of being infected with MDR and XDR TB. This qualitative study was aimed at exploring and describing the resilience factors that have been observed amongst a small number of partners of patients with MDR and XDR TB at an in-patient treatment centre in Port Elizabeth. The research design was exploratory, descriptive and contextual in nature; and the researcher interviewed eight spouses or live-in partners of patientsfor this study, until data saturation was achieved. The data were collected through semi-structured interviews; and the data analysis was conducted, according to the eight steps proposed by Tesch model of data analysis (in Creswell, 1998).Guba’smodel of trustworthiness was used to assess the data collected during the interviews. The findings from this study will inform the health-care team on methods of how the support of the patients’ partners could be mobilised in the holistic treatment plan of MDR and XDR TB patients in an in-patient treatment centre.
- Full Text:
- Date Issued: 2013
- Authors: Smith, Louise
- Date: 2013
- Subjects: Multidrug-resistant tuberculosis , Health Belief Model , Hospital patients
- Language: English
- Type: Thesis , Masters , MA
- Identifier: vital:10007 , http://hdl.handle.net/10948/d1020913
- Description: Patients diagnosed with Multidrug-resistant(MDR) and Extreme drug-resistant (XDR) tuberculosis (TB) have to be hospitalised for a period of six to twelve months, according to the MDR/XDR Policy Guidelines on the treatment of drug-resistant TB – until the patient recovers, and is no longer infectious. There are factors associated with both the patients’ and their partners’ (spouses) resistance to long-term hospitalisation. This has resulted in several acts of violence against the hospital property and members of the health-care team. However, there are a small number of partners who assist the health-care team – by ensuring compliance from the patients and providing their continued support to the patient – despite their own risk of being infected with MDR and XDR TB. This qualitative study was aimed at exploring and describing the resilience factors that have been observed amongst a small number of partners of patients with MDR and XDR TB at an in-patient treatment centre in Port Elizabeth. The research design was exploratory, descriptive and contextual in nature; and the researcher interviewed eight spouses or live-in partners of patientsfor this study, until data saturation was achieved. The data were collected through semi-structured interviews; and the data analysis was conducted, according to the eight steps proposed by Tesch model of data analysis (in Creswell, 1998).Guba’smodel of trustworthiness was used to assess the data collected during the interviews. The findings from this study will inform the health-care team on methods of how the support of the patients’ partners could be mobilised in the holistic treatment plan of MDR and XDR TB patients in an in-patient treatment centre.
- Full Text:
- Date Issued: 2013
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