One Solution for All: Searching for Universal Aptamers for Constantly Mutating Spike Proteins of SARS‐CoV‐2

Abstract

Aptamers that can recognize the spike (S) protein of SARS-CoV-2 with high affinity and specificity are useful molecules towards the development of diagnostics and therapeutics to fight COVID-19. However, this S protein is constantly mutating, producing variants of concern (VoCs) that can significantly weaken the binding by aptamers initially engineered to recognize the S protein of the wildtype virus or a specific VoC. One strategy to overcome this problem is to develop universal aptamers that are insensitive to all or most of the naturally emerging mutations in the protein. We have recently demonstrated this concept by subjecting a pool of S protein-binding DNA aptamers for one-round parallel-SELEX experiments targeting 5 different S protein variants for binding-based sequence enrichment, followed by bioinformatic analysis of the enriched pools. This effort has led to the identification of a universal aptamer that recognizes 8 different variants of the spike protein with equally excellent affinity.

Comparative Characterization of Diverse DNA Aptamers for Recognition of Spike Proteins of Multiple SARS‐CoV‐2 Variants

“…One strategy to overcome this problem is to develop universal aptamers that are insensitive to all or most of the emerging mutations in the S-protein by conducting parallel-SELEX experiments targeting different S-protein variants with equally excellent affinity, as we have done for the discovery of MSA52. [48,63] In addition, it is necessary to determine the binding sites of these aptamers with the S-protein (vide infra) so that specific aptamers can be chosen to target the S-protein of future variants of concern.…”

“…This insensitivity most probably reflects the unique selection method used to derive MSA52 via parallel-SELEX experiments targeting different S-protein variants. [48,63] We also conducted competition assays to determine if the 9 aptamers competed with each other for the same binding site. Based on the competition results and the nature of the targets used for the aptamer selection experiments, we make the following predictions: (1) the aptamers CoV2-6 and Aptamer-1 bind the RBD domain of S1 and their binding sites partially overlap with each other; (2) the binding site of the non-RBD-targeting aptamer SP6 partially overlaps with the binding site of MSA52; (3) MSA52 partially recognizes the RBD domain of S1 and partially recognizes non-RBD domain of S1 and the two-site recognition causes the binding site of MSA52 to partially overlap with CoV2-6 (or Aptamer-1) and SP6; (4) AR10 recognizes a distinctive non-RBD domain of S1.…”

“…Among these aptamers, MSA52 shows the least variation in K d values for the free S‐proteins and the S‐proteins on PV (Tables 1 and 2). This insensitivity most probably reflects the unique selection method used to derive MSA52 via parallel‐SELEX experiments targeting different S‐protein variants [48,63] …”

MLCNN‐COV: A multilabel convolutional neural network‐based framework to identify negative COVID medicine responses from the chemical three‐dimensional conformer

“…Negative medicine responses are unwanted, adverse, and unfavorable effects. Because of COVID, global public health will face significant problems and health concern issues in the near future [4][5][6], so the development of effective medicines (drugs) is essential. Predicting adverse COVID medicine reactions is critical to the medicines development pipeline.…”

Three on Three: Universal and High-Affinity Molecular Recognition of the Symmetric Homotrimeric Spike Protein of SARS-CoV-2 with a Symmetric Homotrimeric Aptamer

“…An extensive array of MREs have been investigated for SARS-CoV-2 research since the onset of the pandemic. − Among these MREs, nucleic acid aptamers have stood out as a promising option. − Aptamers are short, single-stranded oligonucleotides that demonstrate high binding affinity and selectivity toward a specific substrate. − Their binding affinity can be further enhanced by creating multimeric aptamers by joining two or more monomeric substituents together, typically by linking monomers together in series to form a linear multimer. ,− However, such an arrangement may result in one or more monomers being inaccessible to the target, particularly if the trimer is immobilized on a surface through a terminal end, as the innermost monomer closest to the surface would likely not be accessible for binding to the spike protein. Linear trimers may also be unable to align correctly with the three-fold symmetric spike protein, preventing the full enhancement of affinity.…”