Maybe. [1] I have several Protease in capsule form and consume them daily. I would imagine that would have to be made into a paste to work on the boots.

Honestly I think bleach is fine. There is nothing inherently special about prions. They are just proteins and bleach will rapidly disassemble and denature proteins of any kind out of their 3D structure, some slower than others. I leave it on over night and with heat applied.

[1] - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4503822/

Most prions are characterised biochemically by their protease resistance. Proteases will not work sufficiently.