Proteins fold based on minimizing energy states. Any amino acid sequence (large molecules) can be folded in many different ways. For example enzymes binding to proteins can cause desired protein folding changes. Generally if a protein gets misfolded (happens all the time) it doesnt do anything, in some cases misfolding causes bad effects.

Prions misfold in a way that induces other of the normal version to misfold in the same way and therefore spread.

On the plus side prions kills pretty quickly and so there is unlikely to be much underlying mutation in their form or function.

Protein folding is incredibly complicated but I could imagine enzymes which could snip the prion or another similar protein which induces it to fold back into the preferred state. I doubt we have the science to explicitly design such a thing, but you could expose prion molecules in bacteria and put them under evolutionary pressure and they might eventually develop something that disables/fixes the prion.

You would essentially align survival of the bacteria to disruption of the prion molecule.

This link has an image of the two versions

https://www.mayoclinic.org/diseases-conditions/creutzfeldt-j...