- Title
- A large multiscale detailed modelling of aptamers as anticancer therapeutics
- Creator
- Mokgopa, Kabelo Phuti
- Subject
- Aptamer
- Subject
- MicroRNA
- Subject
- Drug discovery
- Subject
- Python (Computer program language)
- Subject
- Molecular dynamics
- Subject
- Cheminformatics
- Subject
- Bioinformatics
- Date Issued
- 2025-04-02
- Date
- 2025-04-02
- Type
- Academic theses
- Type
- Master's theses
- Type
- text
- Identifier
- http://hdl.handle.net/10962/479174
- Identifier
- vital:78267
- Description
- Cancer remains a leading cause of death worldwide, characterized by uncontrolled cell growth and spread. The challenge of effectively treating cancer has spurred interest in novel therapeutic strategies that target specific biological or biochemical mechanisms involved in cancer progression. Although many enzymes have been labelled as inducers of cancer development, microRNAs (miRNAs) are also emerging as significant contributors to cancer progression. This is because miRNAs play a crucial role in regulating gene expression, while cancer develops and grows due to genetic mutations, variations, and alterations. Among these miRNAs, miRNA-10b is notable for its involvement in promoting cancer cell proliferation, migration, and metastasis across various cancers, including breast cancer, glioblastoma, and esophageal squamous cell carcinoma. For this reason, we propose inhibiting miRNA-10b using RNA aptamers as a novel and promising approach for developing new anti-cancer therapeutics. RNA aptamers are short, non-coded, synthetic, and single-stranded nucleic acid molecules capable of binding to a wide range of targets, including metal ions, chemical compounds, proteins, cells, and microorganisms. They are used for a range of applications due to their well-known specificity and selectivity, starting from drug delivery to diagnostics. In this project we aimed to design and discover novel RNA aptamers that can effectively inhibit miRNA-10b using advanced computational methods. However, major challenges were encountered due to the lack of databases or tools available to design and predict secondary and tertiary structures of RNA aptamers at a large scale. Furthermore, no tools were available to perform high throughput virtual screening of these aptamers against macromolecular targets at a large scale. Prompted by that, we developed the T_SELEX program, which encompasses the various algorithms and tools dedicated to designing RNA aptamer sequences, predicting their secondary and tertiary structures, and, lastly, virtually screening aptamers. These algorithms and advanced tools are designed to handle the complexities of aptamer selection and virtual screening. By employing virtual screening methods, the aptamer discovery process was streamlined, offering a cost-effective and efficient alternative to traditional SELEX techniques. Prior to the main purpose application, the T_SELEX program was tested by designing aptamers for targeting HIV-1 protease, and a few applications were also done to assess its aptamer design approach. The study explored RNA aptamer sequences, revealing important insights into nucleotide composition, sequence patterns, and their role in aptamer efficacy and design. Analysis of secondary and tertiary structure predictions showed that Minimum Free Energy (MFE) values do not always correlate with structural compactness or complexity, with aptamers of similar MFE values exhibiting variations in attributes like loop size and guanine content. A novel Sequence Similarity Check (SSC) algorithm is introduced focused on internal sequence comparisons and secondary structures, revealing that aptamers with similar base compositions could have distinct folding states and stability. The Base Randomization Algorithm (BRA) generated RNA aptamer libraries was further benchmarked, highlighting a critical threshold for aptamer length and demonstrating Gaussian distribution in base compositions. Virtual screening of aptamers using the T_SELEX program against pre-miRNA-10b and their mature 5p and 3p arm, identified aptamers557 and 899 as effective binders for the 3p and 5p arms, respectively. Extensive quantum mechanical and molecular dynamics simulations confirmed the stability of the aptamer-RNA complexes. Due to the understanding of the flexibility of these RNA-RNA complexes, we further proposed the stability matrices method as a calculus-based method to evaluate the relative stability of the complexes without being biased during MD analysis. MM-GBSA calculations supported docking results, identifying aptamers like aptamers557, aptamer274 and aptamer734 as strong inhibitors of the 3p arm. Overall, this project has proposed novel approaches for aptamer in silico design and validation, particularly in targeting miRNA-10b for cancer therapy.
- Description
- Thesis (MSc) -- Faculty of Science, Chemistry, 2025
- Format
- computer
- Format
- online resource
- Format
- application/pdf
- Format
- 1 online resource (304 pages)
- Format
- Publisher
- Rhodes University
- Publisher
- Faculty of Science, Chemistry
- Language
- English
- Rights
- Mokgopa, Kabelo Phuti
- Rights
- Use of this resource is governed by the terms and conditions of the Creative Commons "Attribution-NonCommercial-ShareAlike" License (http://creativecommons.org/licenses/by-nc-sa/2.0/)
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RU Department of Chemistry
| Thumbnail | File | Description | Size | Format | |||
|---|---|---|---|---|---|---|---|
| View Details Download | SOURCE1 | MOKGOPA-MSC-TR25-38.pdf | 7 MB | Adobe Acrobat PDF | View Details Download |