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Development of a platform for rational diagnostic design using a venom-antibody model
Thesis (PhD)--Stellenbosch University, 2025.
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| Format: | Thesis |
| Language: | English |
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Stellenbosch : Stellenbosch University
2025
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| _version_ | 1867613898665885696 |
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| access_status_str | Open Access |
| author | Lermer, Anné |
| author2 | Kellermann, Tracy |
| author_browse | Kellermann, Tracy Lermer, Anné |
| author_facet | Kellermann, Tracy Lermer, Anné |
| author_sort | Lermer, Anné |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (PhD)--Stellenbosch University, 2025. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/134675 |
| institution | Stellenbosch University (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:43:27.297Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/134675 Development of a platform for rational diagnostic design using a venom-antibody model Lermer, Anné Kellermann, Tracy Ramharack, Pritika Vlok, Mare Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Medicine. Division of Clinical Pharmacology. Poisonous snakes -- Venom -- Toxicology Antivenins Antigen-antibody reactions Point-of-care testing Snakebites -- Treatment Thesis (PhD)--Stellenbosch University, 2025. Lermer, A. 2025. Development of a platform for rational diagnostic design using a venom-antibody model. Unpublished doctoral dissertation. Stellenbosch: Stellenbosch University [online]. Available: https://scholar.sun.ac.za/items/5e79dd34-3c73-4512-b14f-eec2bd2673f2 ENGLISH ABSTRACT: Snakebite envenomation poses a significant threat to human health globally, with rural populations in sub-Saharan and Southern African countries being the most vulnerable. Administration of antivenom is crucial for neutralising the effects of venom, especially in cases of potentially fatal neurotoxic venom. However, this treatment can also have severe side effects such as anaphylaxis, inflammatory responses, and serum sickness. Therefore, it is essential to quickly identify the source of envenoming to make informed decisions regarding antivenom administration. Currently, no reliable diagnostic test is available for African snake species to help identify the source of envenomation in this region. Three-finger toxins (3FTxs) comprise a family of cyto- and neurotoxins which have been identified as the leading cause of morbidity and mortality associated with envenoming by Elapid snake species. Snake venom three-finger toxins (3FTxs) have diverse molecular mechanisms. They interact with a range of targets including membrane bound structures such as nicotinic acetylcholine receptors (nAChRs), ion channels, and cell membrane structures. The diagnostic potential of targeting the three-finger toxins is of high value to prevent potential morbidity. Traditional diagnostic tests rely on antibodies as recognition elements. This research study presents a computational aptamer design approach using crosslinking mass spectrometry and computational informatics. The aim of this study is to identify Naja nivea (Cape cobra) toxins and antibody-binding sites by mapping epitopes and paratopes, and to use this information to create a platform for the development of aptamers that can differentially detect venom toxins from Naja spp. and/or toxin antibodies from a biological matrix. A combination of analytical laboratory techniques and computational informatics was used to achieve this aim. Paratopes and epitopes within the antibody-toxin complexes were determined by limited proteolysis, formaldehyde crosslinking, and analysis using high-resolution liquid chromatography-tandem mass spectrometry (HR-LC-MS/MS). Computational structural biology techniques were used to model peptide aptamers based on the interacting peptide fragments. The binding landscape of the peptide aptamers and the cytotoxins were investigated by conducting molecular dynamic simulations and free energy calculations. The molecular mechanism of interaction between peptide aptamers (PEPers) targeting cytotoxins from Naja spp. were evaluated at an atomistic level using computational molecular dynamic simulations. The binding affinity of the PEPers and anti-cytotoxin 1 (CTX1) single chain fragment variable (scFv) to the cytotoxins were studied by free energy calculations. The binding interactions between PEPer 3 and PEPer 1 with cytotoxins 3 and 4 were the strongest with a Gibbs free binding energy of -86 kcal/mol and -76 kcal/mol, respectively. The key interactions that led to the optimal binding energies were hydrogen bonds as well as the number of interacting residues and interacting areas (non-bonded interactions). The most hydrogen bonds were observed in PEPer 3-cytotoxin 3 (P01459) which stabilised the complex. Electrostatic energy contributed the most to the hydrogen bond formation for PEPer 3. Crosslinking mass spectrometry and computational structural biology offers a cost-effective and robust approach for rapidly identifying recognition molecules of N. nivea venom toxins. Of the designed PEPers, PEPer 3 showed the most favourable binding energy compared to the anti-CTX1 scFv. Based on the findings, PEPer 3 can be synthesised and tested in a laboratory setting for target specificity and sensitivity for use as a biorecognition element for snake venom cytotoxins in a point-of-care diagnostic test for envenomation by Naja spp. and other elapid snake species with cytotoxin containing venoms. AFRIKAANSE OPSOMMING: Geen opsomming beskikbaar. Doctoral 2025-12-23T07:16:52Z 2025-12-23T07:16:52Z 2025-12 Thesis https://scholar.sun.ac.za/handle/10019.1/134675 en Stellenbosch University 183 pages : illustrations application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Poisonous snakes -- Venom -- Toxicology Antivenins Antigen-antibody reactions Point-of-care testing Snakebites -- Treatment Lermer, Anné Development of a platform for rational diagnostic design using a venom-antibody model |
| title | Development of a platform for rational diagnostic design using a venom-antibody model |
| title_full | Development of a platform for rational diagnostic design using a venom-antibody model |
| title_fullStr | Development of a platform for rational diagnostic design using a venom-antibody model |
| title_full_unstemmed | Development of a platform for rational diagnostic design using a venom-antibody model |
| title_short | Development of a platform for rational diagnostic design using a venom-antibody model |
| title_sort | development of a platform for rational diagnostic design using a venom antibody model |
| topic | Poisonous snakes -- Venom -- Toxicology Antivenins Antigen-antibody reactions Point-of-care testing Snakebites -- Treatment |
| url | https://scholar.sun.ac.za/handle/10019.1/134675 |
| work_keys_str_mv | AT lermeranne developmentofaplatformforrationaldiagnosticdesignusingavenomantibodymodel |