Elucidating the molecular docking and binding dynamics of aptamers with spike proteins across SARS-CoV-2 variants of concern

Authors: Quintela, Irwin; VASSE, TYLER - Volunteer; JIAN, DANA - Volunteer; HARRINGTON, CAMERON - Former ARS Employee; SIEN, WESLEY - Volunteer; Wu, Vivian

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 3/5/2025
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Since the emergence of SARS-CoV-2, its variants have been categorized into several key groups: variants of concern (VOCs), interest (VOIs), being monitored (VBMs), and of high consequence (VOHCs). Infection starts when the virus binds to the host’s ACE-2 receptors, which activates the spike (S) proteins and facilitates fusion of the viral and host cell membranes. As the main target for vaccine, diagnostic, and therapeutic development, S-protein has garnered great attention. Specifically, immune- and aptamer-based technologies targeting the S-protein have been explored. Mutations in the S-protein have undergone positive selection, enhancing transmissibility and immune evasion, thus complicating current mitigation strategies. This study aims to identify and develop VOC-specific DNA aptamers targeting the S-protein. Aptamers were selected through in-vitro Sequential Evolution of Ligands by Exponential Enrichment (SELEX), a technique designed to identify sequences that bind preferentially to the S-protein. SELEX rounds progressed with increasing stringency to select aptamers with high affinities. After this, the most abundant aptamers were subjected to an in-silico analysis for 2D and 3D structures predictions. The resulting 3D structures were modeled and docked with the S-protein structures of the VOCs available in the Protein Data Bank to assess potential binding interactions. Binding events were further investigated using in-vitro Enzyme-Linked Oligonucleotide Assay (ELONA), which provided dissociation constant (Kd) values for the isolated aptamers. In this study, the predominant aptamers were named Alpha Apt, Delta Apt, and Omicron Apt. Their most stable 2D structures (lowest 'G) exhibited significant thermodynamic stability, revealing key structural features such as stems and hairpin loops. Molecular docking simulations identified the highest-ranked models based on docking scores and ligand root-mean-square deviation values. The docking models displayed another layer of understanding of VOCs aptamers and S-protein interaction at the molecular level.The Kd values 193.53 ± 30.84 nM (Alpha Apt), 111.51 ± 55.41 nM (Delta Apt), and 32 ± 11.84 nM (Omicron Apt) indicate high-affinity aptamers with VOCs via the S-protein. The standard deviation for these values was less than 60%of the calculated Kd, a typical result for this type of affinity estimation. These three VOC-specific DNA aptamers are promising candidates for further development as therapeutic agents or diagnostic tools, particularly in point-of-care testing and pen-side diagnostics.