Discovery of Aptamers Targeting the Receptor-Binding Domain of the SARS-CoV-2 Spike Glycoprotein

Abstract

The World Health Organization has declared the outbreak of a novel coronavirus (SARS-CoV-2 or 2019-nCoV) as a global pandemic. However, the mechanisms behind the coronavirus infection are not yet fully understood, nor are there any targeted treatments or vaccines. In this study, we identified high-binding-affinity aptamers targeting SARS-CoV-2 RBD, using an ACE2 competition-based aptamer selection strategy and a machine learning screening algorithm. The K d values of the optimized CoV2-RBD-1C and CoV2-RBD-4C aptamers against RBD were 5.8 nM and 19.9 nM, respectively. Simulated interaction modeling, along with competitive experiments, suggests that two aptamers may have partially identical binding sites at ACE2 on SARS-CoV-2 RBD. These aptamers present an opportunity for generating new probes for recognition of SARS-CoV-2 and could provide assistance in the diagnosis and treatment of SARS-CoV-2 while providing a new tool for in-depth study of the mechanisms behind the coronavirus infection.

A serological aptamer-assisted proximity ligation assay for COVID-19 diagnosis and seeking neutralizing aptamers

“…These results conrm that the accuracy of our Apt-PLA method is as good as that of the commercial ELISA kit but possesses remarkable merits of short sample-to-result time ($2 hours) in a homogeneous format. Since in vitro selection can obtain aptamers selective for many COVID-19-related associated antigens, such as the recently reported aptamers targeting SARS-CoV-2 RBD, 45 the method demonstrated here can expand this powerful Apt-PLA system signicantly to many other targets and thus provide a new toolbox for the diagnosis of COVID-19.…”

“…This competition may be due to the binding of aptamers to several amino acid residues of RBD that are key to ACE2 binding. 45 In addition, given the fact that the whole workow could be nished within 2 hours in a homogeneous format, the proposed PLA system holds great promise for simple and rapid screening of various neutralizing candidates.…”

SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations

“…As an alternative to antibodies, SELEX (systematic evolution of ligands by exponential enrichment)-based strategies are useful in identifying affinity ligands such as aptamers specific to SARS-CoV-2. Recently, aptamers target the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein [109]. Aptamers are significantly easier and cheaper to produce in comparison to antibodies.…”

Advances in detection of infectious agents by aptamer-based technologies

“…The aptamer-based Western blot analysis was verified by regular ELISA to be a rapid and sensitive method in the detection of SARS-CoV protein for infection validation. With an illustration of spike protein 3D crystal structure [43] and being familiar with the aptamer-based biosensor technologies [17], aptamer against the receptor-binding domain of the SARS-CoV-2 spike glycoprotein has been already identified [8], and an aptamer-based novel detection could be developed for the investigation of ongoing COVID-19 pandemics and clinical service.…”

“…The novel modification makes the obtained aptamer more specific, the selection process more efficient, cost-effective, and greatly reduces time consumption [7]. Specific aptamers for infectious microorganisms in the event of new epidemic outbreaks can be quickly obtained through efficient SELEX technology, such as the recent specific aptamers of SARS-CoV-2 have been obtained rapidly [8]. Once the specific aptamers of pathogenic microorganisms or their toxic molecules are identified, a variety of detection schemes can be designed based on the aptamers, including chemiluminescent, electrochemical or fluorescent detection according to the different detection signals [9][10][11][12].…”