In silico selection of aptamers against SARS-CoV-2
Aptamers are molecular recognition elements that have been extensively deployed in a wide array of applications ranging from diagnostics to therapeutics. Due to their unique properties as compared to antibodies, aptamers were also largely isolated during the COVID-19 pandemic for multiple purposes....
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Published: |
Royal Society of Chemistry
2024
|
| Online Access: | http://psasir.upm.edu.my/id/eprint/118520/ |
| _version_ | 1848867763740737536 |
|---|---|
| author | Akmal Shukri, Amir Muhaimin Wang, Seok Mui Feng, Chaoli Chia, Suet Lin Mohd Nawi, Siti Farah Alwani Citartan, Marimuthu |
| author_facet | Akmal Shukri, Amir Muhaimin Wang, Seok Mui Feng, Chaoli Chia, Suet Lin Mohd Nawi, Siti Farah Alwani Citartan, Marimuthu |
| author_sort | Akmal Shukri, Amir Muhaimin |
| building | UPM Institutional Repository |
| collection | Online Access |
| description | Aptamers are molecular recognition elements that have been extensively deployed in a wide array of applications ranging from diagnostics to therapeutics. Due to their unique properties as compared to antibodies, aptamers were also largely isolated during the COVID-19 pandemic for multiple purposes. Typically generated by conventional SELEX, the inherent drawbacks of the process including the time-consuming, cumbersome and resource-intensive nature catalysed the move to adopt in silico approaches to isolate aptamers. Impressive performances of these in silico-derived aptamers in their respective assays have been documented thus far, bearing testimony to the huge potential of the in silico approaches, akin to the traditional SELEX in isolating aptamers. In this study, we provide an overview of the in silico selection of aptamers against SARS-CoV-2 by providing insights into the basic steps involved, which comprise the selection of the initial single-stranded nucleic acids, determination of the secondary and tertiary structures and in silico approaches that include both rigid docking and molecular dynamics simulations. The different approaches involving aptamers against SARS-CoV-2 were illuminated and the need to verify these aptamers by experimental validation was also emphasized. Cognizant of the need to continuously improve aptamers, the strategies embraced thus far for post-in silico selection modifications were enumerated. Shedding light on the steps involved in the in silico selection can set the stage for further improvisation to augment the functionalities of the aptamers in the future. |
| first_indexed | 2025-11-15T14:41:40Z |
| format | Article |
| id | upm-118520 |
| institution | Universiti Putra Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-15T14:41:40Z |
| publishDate | 2024 |
| publisher | Royal Society of Chemistry |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | upm-1185202025-08-07T07:11:05Z http://psasir.upm.edu.my/id/eprint/118520/ In silico selection of aptamers against SARS-CoV-2 Akmal Shukri, Amir Muhaimin Wang, Seok Mui Feng, Chaoli Chia, Suet Lin Mohd Nawi, Siti Farah Alwani Citartan, Marimuthu Aptamers are molecular recognition elements that have been extensively deployed in a wide array of applications ranging from diagnostics to therapeutics. Due to their unique properties as compared to antibodies, aptamers were also largely isolated during the COVID-19 pandemic for multiple purposes. Typically generated by conventional SELEX, the inherent drawbacks of the process including the time-consuming, cumbersome and resource-intensive nature catalysed the move to adopt in silico approaches to isolate aptamers. Impressive performances of these in silico-derived aptamers in their respective assays have been documented thus far, bearing testimony to the huge potential of the in silico approaches, akin to the traditional SELEX in isolating aptamers. In this study, we provide an overview of the in silico selection of aptamers against SARS-CoV-2 by providing insights into the basic steps involved, which comprise the selection of the initial single-stranded nucleic acids, determination of the secondary and tertiary structures and in silico approaches that include both rigid docking and molecular dynamics simulations. The different approaches involving aptamers against SARS-CoV-2 were illuminated and the need to verify these aptamers by experimental validation was also emphasized. Cognizant of the need to continuously improve aptamers, the strategies embraced thus far for post-in silico selection modifications were enumerated. Shedding light on the steps involved in the in silico selection can set the stage for further improvisation to augment the functionalities of the aptamers in the future. Royal Society of Chemistry 2024 Article PeerReviewed Akmal Shukri, Amir Muhaimin and Wang, Seok Mui and Feng, Chaoli and Chia, Suet Lin and Mohd Nawi, Siti Farah Alwani and Citartan, Marimuthu (2024) In silico selection of aptamers against SARS-CoV-2. Analyst, 149 (19). pp. 4770-4788. ISSN 0003-2654; eISSN: 1364-5528 https://pubs.rsc.org/en/content/articlelanding/2024/an/d4an00812j 10.1039/D4AN00812J |
| spellingShingle | Akmal Shukri, Amir Muhaimin Wang, Seok Mui Feng, Chaoli Chia, Suet Lin Mohd Nawi, Siti Farah Alwani Citartan, Marimuthu In silico selection of aptamers against SARS-CoV-2 |
| title | In silico selection of aptamers against SARS-CoV-2 |
| title_full | In silico selection of aptamers against SARS-CoV-2 |
| title_fullStr | In silico selection of aptamers against SARS-CoV-2 |
| title_full_unstemmed | In silico selection of aptamers against SARS-CoV-2 |
| title_short | In silico selection of aptamers against SARS-CoV-2 |
| title_sort | in silico selection of aptamers against sars-cov-2 |
| url | http://psasir.upm.edu.my/id/eprint/118520/ http://psasir.upm.edu.my/id/eprint/118520/ http://psasir.upm.edu.my/id/eprint/118520/ |