Full Text Available
Note: Clicking the button above will open the full text document at the original institutional repository in a new window.
Kinetic characterisation and mathematical modelling of the coenzyme A biosynthesis salvage pathway in Mycobacterium tuberculosis
Thesis (PhD)--Stellenbosch University, 2023.
Saved in:
| Main Author: | |
|---|---|
| Other Authors: | |
| Format: | Thesis |
| Language: | en_ZA |
| Published: |
Stellenbosch : Stellenbosch University
2023
|
| Subjects: | |
| Tags: |
No Tags, Be the first to tag this record!
|
| _version_ | 1867613911307517952 |
|---|---|
| access_status_str | Open Access |
| author | Mocke, Leanie Mocke, Leanie |
| author2 | Snoep, Jacob Leendert |
| author_browse | Mocke, Leanie Snoep, Jacob Leendert |
| author_facet | Snoep, Jacob Leendert Mocke, Leanie Mocke, Leanie |
| author_sort | Mocke, Leanie |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (PhD)--Stellenbosch University, 2023. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/128450 |
| institution | Stellenbosch University (South Africa) |
| language | en_ZA |
| last_indexed | 2026-06-10T12:43:40.048Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/128450 Kinetic characterisation and mathematical modelling of the coenzyme A biosynthesis salvage pathway in Mycobacterium tuberculosis Mocke, Leanie Mocke, Leanie Snoep, Jacob Leendert Strauss, Erick Stellenbosch University. Faculty of Science. Dept. of Biochemistry. Mycobacterium tuberculosis Coenzymes -- Mechanism of action Enzyme kinetics Coenzyme A -- Synthesis Biosynthesis -- Mathematical models UCTD Thesis (PhD)--Stellenbosch University, 2023. ENGLISH ABSTRACT: Mycobacterium tuberculosis, the bacterium responsible for tuberculosis (TB), is becoming increasingly resistant to the current arsenal of anti-TB drugs, lead- ing to an increase in multi-drug resistant disease cases and death, particularly in developing countries. There is an urgent need to discover new anti-TB drugs that target pathways different from the current treatments. A possible target is the biosynthesis salvage pathway of Coenzyme A (CoA). By constructing, validating and analysis of a mechanistic mathematical model for this pathway, based on the enzyme kinetic characteristics, a rational approach is used for drug target identification in the pathway. A detailed kinetic model for the three enzyme pathway was constructed and validated. The workflow for the construction uses classic initial rate kinetics as a first step, followed by progress curve analysis for the individual enzymes and final modelling of intermediate dynamics for the complete reconstituted pathway. For initial rate kinetics, the enzymes of interest were firstly expressed and purified and parameters experimentally determined to describe each step with a parameterised rate equation. The in silico model was built by linking the three steps with ordinary differential equations. Model construction is fol- lowed by validation by comparing in vitro fluxes with model simulated fluxes. After construction and validation, the model was deemed able to describe the system behaviour. With the reconstituted pathway, different metabolic control analysis sim- ulations were evaluated to determine how control is distributed within the pathway. Experimental and model predictions of the reconstituted salvage pathway were used for metabolic control analysis. Reconstitutions were made with enzyme ratios chosen to reflect in vivo enzyme ratios. It was observed that not the PanK which is usually indicated as “the rate-limiting-step” but rather DPCK seems to have the highest control. AFRIKAANSE OPSOMMING: Mycobacterium tuberculosis, die bakterie verantwoordelik vir tuberkulose (TB), raak toenemend weerstandbiedig teenoor die huidige arsenaal van anti-TB mid- dels, wat lei tot ’n toename in multi-middel-weerstandige siektegevalle en dood, veral in ontwikkelende lande. Daar is ’n dringende nood aan die ontwikkeling van nuwe anti-TB-middels wat wee¨ anders as die huidige behandelings teiken. ’n Moontlike teiken is die biosintese-herwinningsweg van Koe¨nsiem A (KoA). Deur ’n meganistiese wiskundige model vir hierdie pad te konstrueer, te vali- deer en te ontleed gebaseer op die ensiem kinetiese kenmerke, word ’n rasionele benadering gebruik vir geneesmiddelteiken-identifikasie in die padweg. ’n Gedetailleerde kinetiese model vir die drie ensiem padweg is gekonstru- eer en gevalideer. Die werkvloei vir die konstruksie maak gebruik van klassieke aanvanklike tempokinetika as ’n eerste stap, gevolg deur vorderingskurwe- analise vir die individuele ensieme en ’n finale intermediere dinamika vir die volledige hersaamgestelde padweg. Vir aanvanklike tempokinetika is die en- sieme van belang eerstens uitgedruk en gesuiwer en parameters eksperimenteel bepaal om elke stap met ’n geparameteriseerde tempovergelyking te beskryf. Die in silico-model is gebou deur die drie stappe met eenvoudige differensi- aalvergelykings te koppel. Modelkonstruksie word gevolg deur validering deur in vitro fluksies met model simuleerde fluksies te vergelyk. Na konstruksie en validering is die model in staat geag om die stelselgedrag te beskryf. Met die hersaamgestelde pad is verskillende metaboliese beheer analise si- mulasies gee¨valueer om te bepaal hoe beheer in die pad versprei word. Eksperi- mentele en modelvoorspellings van die hersaamgestelde reddingspad is gebruik vir metaboliese beheeranalise. Rekonstitusies is gemaak met ensiemverhou- dings wat gekies is om in vivo ensiemverhoudings te weerspiee¨l en daar is waargeneem dat nie die PanK wat gewoonlik as "die tempo-beperkende-stap- aangedui word nie, maar eerder DPCK skynbaar die hoogste beheer uitoefen. Doctorate 2023-03-05T07:18:53Z 2023-08-30T13:09:25Z 2023-03 2023-03-05T07:18:53Z 2023-08-31T09:18:45Z 2023-03-05T07:18:53Z 2023-08-31T09:18:45Z Thesis https://scholar.sun.ac.za/handle/10019.1/128450 en_ZA Stellenbosch University application/pdf xv, 101 pages : illustrations (some color) application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Mycobacterium tuberculosis Coenzymes -- Mechanism of action Enzyme kinetics Coenzyme A -- Synthesis Biosynthesis -- Mathematical models UCTD Mocke, Leanie Mocke, Leanie Kinetic characterisation and mathematical modelling of the coenzyme A biosynthesis salvage pathway in Mycobacterium tuberculosis |
| title | Kinetic characterisation and mathematical modelling of the coenzyme A biosynthesis salvage pathway in Mycobacterium tuberculosis |
| title_full | Kinetic characterisation and mathematical modelling of the coenzyme A biosynthesis salvage pathway in Mycobacterium tuberculosis |
| title_fullStr | Kinetic characterisation and mathematical modelling of the coenzyme A biosynthesis salvage pathway in Mycobacterium tuberculosis |
| title_full_unstemmed | Kinetic characterisation and mathematical modelling of the coenzyme A biosynthesis salvage pathway in Mycobacterium tuberculosis |
| title_short | Kinetic characterisation and mathematical modelling of the coenzyme A biosynthesis salvage pathway in Mycobacterium tuberculosis |
| title_sort | kinetic characterisation and mathematical modelling of the coenzyme a biosynthesis salvage pathway in mycobacterium tuberculosis |
| topic | Mycobacterium tuberculosis Coenzymes -- Mechanism of action Enzyme kinetics Coenzyme A -- Synthesis Biosynthesis -- Mathematical models UCTD |
| url | https://scholar.sun.ac.za/handle/10019.1/128450 |
| work_keys_str_mv | AT mockeleanie kineticcharacterisationandmathematicalmodellingofthecoenzymeabiosynthesissalvagepathwayinmycobacteriumtuberculosis AT mockeleanie kineticcharacterisationandmathematicalmodellingofthecoenzymeabiosynthesissalvagepathwayinmycobacteriumtuberculosis |