In silico selection of aptamers against SARS-CoV-2

• Published in: Analyst (London) Vol. 149; no. 19; pp. 4770 - 4788
• Main Authors: Akmal Shukri, Amir Muhaimin, Wang, Seok Mui, Feng, Chaoli, Chia, Suet Lin, Mohd Nawi, Siti Farah Alwani, Citartan, Marimuthu
• Format: Journal Article
• Language: English
• Published: England Royal Society of Chemistry 23.09.2024
• Subjects: Antiviral Agents - chemistry; Aptamers, Nucleotide - chemistry; Betacoronavirus - isolation & purification; Computer Simulation; Coronavirus Infections - diagnosis; Coronavirus Infections - virology; COVID-19 - diagnosis; COVID-19 - virology; Dynamic structural analysis; Humans; Molecular docking; Molecular Docking Simulation; Molecular dynamics; Molecular Dynamics Simulation; Nucleic Acid Conformation; Nucleic acids; Pandemics; Pneumonia, Viral - virology; SARS-CoV-2 - genetics; SARS-CoV-2 - isolation & purification; SELEX Aptamer Technique - methods; Severe acute respiratory syndrome coronavirus 2
• ISSN: 0003-2654; 1364-5528; 1364-5528
• DOI: 10.1039/d4an00812j

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 approaches to isolate aptamers. Impressive performances of these -derived aptamers in their respective assays have been documented thus far, bearing testimony to the huge potential of the approaches, akin to the traditional SELEX in isolating aptamers. In this study, we provide an overview of the 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 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- selection modifications were enumerated. Shedding light on the steps involved in the selection can set the stage for further improvisation to augment the functionalities of the aptamers in the future.