Here goes ...
Even with the suggestion in #1 it's still not clear what you are actually trying to say.
If "that" refers to "the concept of cell-cycle-mediated resistance", then the sentence now reads:
"Contrary to the concept of cell-cycle-mediated resistance of drug E, the concept of cell-cycle-mediated resistance to drug T is well defined",
which is contrasting "of" with "to".
Do you mean
... the concept of cell-cycle-mediated drug resistance is well defined for drug T but not for drug E
... the concept of cell-cycle-mediated drug resistance to drug T is well defined but not the concept of cell-cycle-mediated drug resistance to drug E.
or simply
... cell-cycle-mediated drug resistance is well described for drug T but not for drug E.
KISS