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Here is the virus in "closed" (teal) and "open" (green) form. In "open" form, it binds to ACE2. ACE2 also blocks the ideal neutralizing antibody sites, and binds with extremely high, picomolar affinity (similar binding strength to many strongly binding antibodies).
The "closed" variant is the Veesler Lab cryo-EM structure (biorxiv.org/content/10.110…). The "open" variant is the SWISS-MODEL simulated spike protein structure (swissmodel.expasy.org/repository/spe…). I did the ACE2 docking myself, before we had binding data of pocket.
Ligandal peptide nanoscaffolds are designed to interfere with ACE2-spike binding, while also promoting a strong immune response against the correct receptor-binding domain component for antibody generation. This means that you can give the nano-scaffold before or after infection.
Here is PDB structure 6WPT, showing a truncated antibody (just the antigen-binding fragment, or Fab, in orange) bound to the spike protein (teal; with one of the trimers in "open" conformation), with the "open" conformation spike bound to ACE2 (red)
Here are the same structures as above, with an overlay this of an entire antibody (PDB ID 6C6Z against MERS-CoV) so you can visualize how big the spike protein is compared to ACE2 and an antibody.
Now, imagine that you have 1000 of these spikes on each virion, and that any one of the spikes has 3 components as part of a "trimer," where one of the chains can "open" up and bind to ACE2. ACE2 is a sophisticated cloaking and immune evasion mechanism, by virtue of this.
Furthermore, see all those little sugar molecules? I've colored them yellow here. These are sugars that the virus incorporates into its protein chain, which change the surface behavior of the virus. Without the sugars, your immune response will not be the same towards the spike.
Moderna, Oxford, DNA and RNA vaccines all lack these sugar modifications and, worse yet, they present the spike protein in a random fashion without it being upon the surface of a virus, where at least the thing points the right way when fully formed. Many wrong responses result.
So, what is Ligandal doing differently? Our "nano-scaffolds" knock the ACE2 off, and are designed to generate ultra-specific antibody responses against *just* the antibody-binding motif of the virus. You should be able to administer these nano-scaffolds before or after infection.
Now, the virus is naked and exposed, and cannot bind to ACE2. Furthermore, the scaffolds present multiple spots for antibodies to bind to, and also bolster T cell receptor maturation through presenting key epitopes.
If you've already been infected, the "antidote" component will kick in, preventing ACE2 cloaking, and enhancing your immune system's ability to sense and build a response to the virus.
Note: in the beginning of this thread, I refer to the "virus." I am actually referring to the spike protein of the virus.
Antibody-dependent enhancement is a major concern when the neutralizing antibody site is so tightly bound to ACE2 that antibodies cannot readily bind to the site. This is particularly a concern with “spike protein” vaccines that present a lot of surface area for the wrong Abs.
Correction: there are probably closer to 100 spikes per virion.
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