MOLECULAR DOCKING

Well, common factors which affect the biological activity of a compound are temperature, pH, transporters, etc. I am not clear which specific condition you are asking about.
A compound may also get affected by the steric hindrance which it gets in the vicinity of any other compound/ligand or protein (amino acid). If you have developed any drug, then it is necessary to study its binding and the pathway to the target protein, there might be some carriers or transporters which interfere with the compound.
I hope it helps, if not, then feel free to ask again.
Thanks