- Title
- Screening drug candidates for sars-cov-2 spike protein variants within the SANCDB (South African Natural Compounds Database) and drug bank
- Creator
- van der Merwe, Vicky
- Subject
- COVID-19 (Disease)
- Subject
- Vaccines -- Development
- Subject
- Viral vaccines
- Date Issued
- 2024-12
- Date
- 2024-12
- Type
- Master's theses
- Type
- text
- Identifier
- http://hdl.handle.net/10948/69499
- Identifier
- vital:77263
- Description
- The WHO declared the Coronavirus Infectious Disease 2019 (COVID-19) pandemic as over on the 5th of May 2023. However, the Severe Acute Respiratory Syndrome Coronavirus 2 Virus (SARS-CoV-2) is still prevalently spread within populations, causing hospitalization and death in serious infections. Most anti-COVID-19 agents are weakly or conditionally or even strongly recommended against in non-severe cases with low to medium risk of hospitalisation and further highlight the significance of effective treatments for SARS-CoV-2 infected patients. The host’s Angiotensin-Converting Enzyme 2 (ACE2) interaction with the viral spike protein’s Receptor-Binding Domain (RBD) of SARS-CoV-2 leads to the subsequent infection, viral replication, and further propagation of the virus. This establishes the spike protein’s RBD as a vital target for drug design. Through HADDOCK and AlphaFold driven structural refinement, the then novel SARS-CoV-2 delta [3.34 Å (PDB ID: 7WBQ)] and omicron [3.00 Å (PDB ID: 7WBP)] crystalline structures of the variants’ RBD, in complex with its host receptor human ACE2, were modelled to improve the low-resolution starting structures. Models predicted by HADDOCK independently yielded refined structures with improved resolutions of 2.49 Å (delta) and 2.41 Å (omicron). SARS-CoV-2 spike protein RBD of delta and omicron variants were screened for less frequently considered allosteric binding sites that could block ACE2-RBD engagement. Eight potential allosteric binding sites were identified through CavityPlus for both variants, with a single best druggable potential allosteric site identified for each. The search for potential inhibiting hit compounds involved using the SANCDB and DrugBank databanks and screening both the allosteric and orthosteric binding sites through molecular docking. Despite differences in mutated interacting residues and bond interactions, a lead compound for orthosteric binding sites (SANC00290) and potential allosteric modulators of both delta and omicron (SANC00746 and DB01029) were found. These compounds show promise in blocking ACE2-RBD engagement to potentially reduce viral interaction and infection of, and potentially withstanding further mutational residues. This study contributes to further investigation of affordable SA natural compound COVID-19 treatment and a starting point for in vitro analysis studies.
- Description
- Thesis (MSc) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Format
- computer
- Format
- online resource
- Format
- application/pdf
- Format
- 1 online resource (104 pages)
- Format
- Publisher
- Nelson Mandela University
- Publisher
- Faculty of Science
- Language
- English
- Rights
- Nelson Mandela University
- Rights
- All Rights Reserved
- Rights
- Open Access
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- Visitors: 5
- Downloads: 0
Collections
NMU School of BioMolecular and Chemical Sciences
| Thumbnail | File | Description | Size | Format | |||
|---|---|---|---|---|---|---|---|
| View Details Download | SOURCE1 | VAN DER MERWE, V.pdf | 2 MB | Adobe Acrobat PDF | View Details Download |