Dual ACE2 epitope-based biomimetic receptors for selective sensing of SARS-CoV variants

Abstract

Abstract We report a combinatorial approach to design peptide-based biomimetic sensors for detecting β-type coronaviruses with high sensitivity and selectivity. We selected three peptide epitopes from key regions of the ACE2 receptor that are involved in viral binding to different variants and immobilized them individually or in binary combinations on gold sensor chips. Using Surface Plasmon Resonance (SPR), we found that single-epitope sensors displayed nanomolar dissociation constants to three RBD variants (SARS-CoV-2 Delta < SARS-CoV-2 Alpha < SARS-CoV-1) and a KD = 1.2 ± 0.4 nM to the full SARS-CoV-2 Alpha spike protein, with negligible binding to the a-coronavirus hCoV-NL63 spike protein. Molecular dynamics simulations revealed that the tightest binding epitope closely mimics ACE2 interactions with β-coronaviruses, explaining its superior performance. In contrast, dual epitope systems exhibited a reversed variant preference, with a pronounced affinity enhancement for SARS-CoV-1 (KD = 6 ± 2 nM). This was attributed to cooperative epitope interactions that could restrict the conformational flexibility of the longer epitope, favoring the effective intermolecular contacts that strengthen the interaction with the RBD. These findings suggest a time-saving approach for developing sensitive and selective sensors for rapidly mutating viruses.