Can I change the first sentence to the following sentence?
1) The cells were treated with enzyme A. -> The enzyme A was treated to the cells.
2) The protein was adsorbed to the nanoparticle. -> The nanoparticle was adsorbed with the protein.
The original sentences are correct, you should use those.
"treat to" means to give something as a gift or pay for something on someone else's behalf, e.g. "I'll treat you to dinner tonight". So "The enzyme A was treated to the cells" makes it sound like someone bought enzyme A some cells as a present.
"adsorb" means "to cause a substance, usually a gas, to form a very thin layer on the surface of another substance". So on, to or onto are the prepositions you could use. "adsorbed with" doesn't make any sense.