- Title
- Exploring the involvement of the SARS-CoV-2 Replicase in the synthesis of polyamines and heat shock proteins
- Creator
- Mthembu,Yamkela
- Subject
- Post COVID-19 condition (Disease)
- Subject
- COVID-19 (Disease)
- Subject
- Polyamines in the body
- Date Issued
- 2023-07
- Date
- 2023-07
- Type
- Master's theses
- Type
- text
- Identifier
- http://hdl.handle.net/${Handle}
- Identifier
- vital:74275
- Description
- A disease named COVID-19 almost destroyed the human population. It is caused by the SARS CoV 2 virus which emerged in 2019 and rapidly spread worldwide forcing all countries to shut down. This virus uses non-structural proteins to complete its invasion and development inside the host. The non-structural protein 2 NSP2 defined as the RNA binding protein involved in coronavirus genome replication and decreases the human immune response is key for this virus’s development and invasion. It is believed that the NSP2 associate themselves with polyamines and heat shock proteins inside the host cell, to proceed with the viral development and this study aimed to investigate how SARS CoV 2 virus key non-structural proteins NSP2 utilizes polyamines and heat shock proteins using the molecular docking approach and molecular dynamics MD. In this present study a docking approach was used. The dockings were done on ClusPro, and analysis was done on Discovery Studio, chimera, and PyMOL. One of the enzymes that are involved in the regulation of polyamine biosynthesis, adenosylmethionine decarboxylase AdoMetDC was used in investigating the polyamine binding to the viral NSP2, and major heat shock proteins HSPs HSP40, HSP70, and HSP90 were used in the investigation of the binding of HSPs to viral non-structural proteins NSP2. The results obtained show that 32 interactions were formed when docking heat shock protein 40 HSP40 with the SARS CoV 2 NSP2, but the area that has the highest interactions was from amino acid Ala554 to His557. Asp553 plays a very crucial role in this interaction forming six interactions. Heat shock protein 70 produced about 28 interactions when docked with the SARS CoV 2 NSP2. But the section with the most bonds was from position 550 to 560 of the ligand. Human heat shock protein 90 HSP90 formed 19 interactions when docked with the SARS CoV 2 viral NSP2. MD revealed Arg458, Asn508, Met297, Arg301 and Tr417 active residues. And pharmacophore modeling indicated zinc inhibitors as crucial for inhibiting this virus. Enough interactions were produced with ideal bonds lengths, and it can be said that the functioning of the SARS CoV2 viral non-structural proteins functioning majorly depends on the presence of the heat shock proteins at hand for proper formation and depends on polyamines for complete development and correct functioning.
- Description
- Thesis (MSc) -- Faculty of Science and Agriculture, 2023
- Format
- computer
- Format
- online resource
- Format
- application/pdf
- Format
- 1 online resource (88 leaves)
- Format
- Publisher
- University of Fort Hare
- Publisher
- Faculty of Science and Agriculture
- Language
- English
- Rights
- University of Fort Hare
- Rights
- All Rights Reserved
- Rights
- Open Access
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Collections
UFH Department of Biochemistry & Microbiology
| Thumbnail | File | Description | Size | Format | |||
|---|---|---|---|---|---|---|---|
| View Details Download | SOURCE1 | MTHEMBU YAMKELA MASTERS DISSERTATION FINAL.pdf | 32 MB | Adobe Acrobat PDF | View Details Download |