Selection and Characterization of SARS-CoV-2 Spike Binding Clickmers

Area of Science:

• Biochemistry
• Molecular Biology
• Chemical Biology

Background:

• Expanding the chemical diversity of aptamers is crucial for enhancing their diagnostic capabilities.
• Aptamers offer a promising alternative to antibodies for molecular recognition applications.

Purpose of the Study:

• To develop chemically modified DNA aptamers (clickmers) targeting the SARS-CoV-2 spike glycoprotein using click-SELEX.
• To evaluate the binding affinity and specificity of generated clickmers against various SARS-CoV-2 variants.

Main Methods:

• Click-systematic evolution of ligands by exponential enrichment (SELEX) was employed to generate clickmers.
• Binding affinities were assessed using flow cytometry, surface plasmon resonance (SPR), and microscale thermophoresis (MST).
• Structure-function analysis identified key modification sites and evaluated truncated variants.

Main Results:

• Two distinct clickmer families targeting SARS-CoV-2 spike protein were generated, functionalized with benzofuran or indole moieties.
• Lead candidates (BF1 and N2) exhibited nanomolar affinity for wild-type SARS-CoV-2 spike protein.
• Clickmers demonstrated maintained binding to Alpha, Delta, and Mu variants, with a truncated N2 variant showing enhanced binding to Omicron.

Conclusions:

• The click-SELEX platform is versatile for generating chemically modified aptamers against clinically relevant targets.
• Developed clickmers show potential for SARS-CoV-2 diagnostics, with promising affinity and variant coverage.
• Truncated clickmer variants can retain or enhance binding, offering opportunities for optimized aptamer design.