Humans are incredibly complex systems (and systems of systems) and our knowledge of how these systems work and interact is very limited despite the amount of work put into improving our understanding of them.

We can try to simulate the interaction between a drug and a protein, but most of the time the data to say what the downstream effects (if any) are simply does not exist. This is further complicated by the fact that these downstream effects can be extremely varied depending on both the tissue/disease you are targeting and the person you are treating.

Of course we are always generating more data from more diverse populations and more conditions, but there is a very very long way to being able to simulate drug trials like this.