Characterization of binding interactions of SARS-CoV-2 spike protein and DNA-peptide nanostructures

Abstract

Binding interactions of the spike proteins of the severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) to a peptide fragment derived from the human angiotensin converting enzyme 2 (hACE2) receptor are investigated. The peptide is employed as capture moiety in enzyme linked immunosorbent assays (ELISA) and quantitative binding interaction measurements that are based on fluorescence proximity sensing (switchSENSE). In both techniques, the peptide is presented on an oligovalent DNA nanostructure, in order to assess the impact of mono- versus trivalent binding modes. As the analyte, the spike protein and several of its subunits are tested as well as inactivated SARS-CoV-2 and pseudo viruses. While binding of the peptide to the full-length spike protein can be observed, the subunits RBD and S1 do not exhibit binding in the employed concentrations. Variations of the amino acid sequence of the recombinant full-length spike proteins furthermore influence binding behavior. The peptide was coupled to DNA nanostructures that form a geometric complement to the trimeric structure of the spike protein binding sites. An increase in binding strength for trimeric peptide presentation compared to single peptide presentation could be generally observed in ELISA and was quantified in switchSENSE measurements. Binding to inactivated wild type viruses could be shown as well as qualitatively different binding behavior of the Alpha and Beta variants compared to the wild type virus strain in pseudo virus models.

A community effort to discover small molecule SARS-CoV-2 inhibitors

“…Fortunately, His-tagged Ace2 did provide good binding curves with a K D of 4.25 ± 1.52 nM (over 6 runs performed during the 3 days of assay measurements, see Supporting Information Section 4.3.2). This is stronger binding than previous measurements performed by Surface Plasmon Resonance 76 that showed 94.6 ± 6.5 nM for (monomeric) SARS-CoV-2-S1, but can be explained by multivalency of the trimer as shown by Kruse et al 77 . All 152 compounds were first analyzed using 8-point dilution series between 50 nM and 100 µM concentrations, revealing 7 compounds to be potential binders.…”

A community effort in SARS‐CoV‐2 drug discovery

“…Fortunately, His-tagged Ace2 did provide good binding curves with a K D of 4.25 � 1.52 nM (over 6 runs performed during the 3 days of assay measurements, see Supporting Information Section 4.2.3). This is stronger binding than previous measurements performed by Surface Plasmon Resonance [90] that showed 94.6 � 6.5 nM for (monomeric) SARS-CoV-2-S1, but can be explained by multivalency of the trimer as shown by Kruse et al [91]. All 152 compounds were first analyzed using 8point dilution series between 50 nM and 100 μM concentrations, revealing 7 compounds to be potential binders.…”

Integration of functional peptides into nucleic acid-based nanostructures

“…Compared to the conjugation of only one SBP1-peptide per DNA nanostructure, the affinity to recombinantly produced, full-length spike protein homotrimers was significantly enhanced for three SBP1-peptides per nanostructure. 126 More recently, Issmail et al demonstrated that the above-mentioned concept is also applicable for respiratory syncytial viruses (RSV). 128 Notably, while the previously described studies focused on binding of the peptide-DNA structures to viral proteins or whole viruses, this study showed that the structures are also capable of acting as an effective RSV entry inhibitor in vitro .…”

“…Two recent publications by Kruse et al utilized fluorescence proximity sensing, a technology called switchSENSE 124 to investigate the binding of peptide-decorated DNA trimeric structures to influenza A virus (IAV) 125 and severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2). 126 For IAV, the peptide PeB was used, which has been designed to interfere with the function of IAV's Hemagglutinin (HA) protein. It was observed that three PeB peptides linked to DNA structures showed oligovalent binding to different strains of IAV.…”