SELEX based aptamers with diagnostic and entry inhibitor therapeutic potential for SARS-CoV-2

Abstract

Frequent mutation and variable immunological protection against vaccination is a common feature for COVID-19 pandemic. Early detection and confinement remain key to controlling further spread of infection. In response, we have developed an aptamer-based system that possesses both diagnostic and therapeutic potential towards the virus. A random aptamer library (~ 1017 molecules) was screened using systematic evolution of ligands by exponential enrichment (SELEX) and aptamer R was identified as a potent binder for the SARS-CoV-2 spike receptor binding domain (RBD) using in vitro binding assay. Using a pseudotyped viral entry assay we have shown that aptamer R specifically inhibited the entry of a SARS-CoV-2 pseudotyped virus in HEK293T-ACE2 cells but did not inhibit the entry of a Vesicular Stomatitis Virus (VSV) glycoprotein (G) pseudotyped virus, hence establishing its specificity towards SARS-CoV-2 spike protein. The antiviral potential of aptamers R and J (same central sequence as R but lacking flanked primer regions) was tested and showed 95.4% and 82.5% inhibition, respectively, against the SARS-CoV-2 virus. Finally, intermolecular interactions between the aptamers and the RBD domain were analyzed using in silico docking and molecular dynamics simulations that provided additional insight into the binding and inhibitory action of aptamers R and J.

Aptamers and Nanobodies as New Bioprobes for SARS-CoV-2 Diagnostic and Therapeutic System Applications

“…Subsequently, they conducted SARS-CoV-2 pseudovirus inhibition assay using these aptamers to identify aptamers with antiviral potential. The antiviral efficiency of the highest binding aptamers R and J (same central sequence as in R but lacking flanked primer regions) showed 95.4% and 82.5% inhibition against SARS-CoV-2, respectively [ 146 ].…”

Application and Immunogenicity of Aptamers in Cancer Therapy

“…In this situation, a new enriched reservoir of selected oligonucleotides is produced by the PCR transcription of the suitable ssDNA from the SELEX results. 42 This selected oligonucleotide resource is then used in the subsequent round of selection. To select specific aptamers for high-affinity target molecules, 6-20 rounds of the SELEX procedure are often necessary.…”