Yup. From hazy chemistry degree knowledge, we don't know how most drugs actually work. Designing drugs based on the shapes or proteins etc is pretty cutting edge stuff.
And also the nature of organic chemistry is that even if a drug does work a certain way, it probably has several other pathways it can go down. That is, only a certain (probably low) percentage of the drug will actually have the effect you want, the rest will take part in other reactions.
command + shift + ?