There's another aspect to pharmaceutical patenting that you really only find in the US, among major countries: "method of treatment" patents. I don't care for them, myself, but before I explain why, it'll help to see what the usual patents cover.
The traditional drug patent is for composition of matter - you've made some new chemical compound, and you're claiming it as your own. If your new compound is too close to someone else's claims, they can come after you (via the "doctrine of equivalents,") but generally that's not a problem. If it's really new, it's yours if you want it. A footnote for the future: as chemistry advances, we keep having to push into new territory to find patentable material, and some day it's going to be a real problem. For now, finding new stuff is often just an inconvenience, but ask me in twenty years, and I might word things more strongly.
What if you've found something useful, but someone else already owns it? Then you can get a "use patent" - you claim this compound (or class of compounds) for the particular use. If the compound itself - the composition of matter - belongs to someone, then the two of you are in a standoff. They own the compound, but they can't use it. You can use it, but you don't own it. That's the time to have your people contact their people, and hammer something out.
Similarly, if the compound you've found is something that was already known in the literature (or from an expired patent,) then no one can claim composition of matter, and a use patent is the best you can do. It sure beats nothing.
Now for method of treatment claims. These claim the use of some compound (any compound!) that works by some mechanism you've discovered, to treat some disease. That sounds innocuous, but it can spray down a whole field of research. If I'm the first person to discover that blocking the whateverase enzyme is good for treating allergies, say, then I write a patent claiming whatever compounds I've discovered to do it (composition of matter,) the use of those compounds to inhibit whateverase, and the treatment of allergies by using anything that blocks it.That last one is the medical treatment claim. It means that if you go find a compound (a totally different compound,) that does the same thing, then you can patent it until you turn blue. But you can't use it. I've got the medical treatment patented.
The European patent office won't allow those claims, at least not in so many words. They hold that such claims are an unlawful restraint on medical practitioners. There's a tricky technique known as a "Swiss Claim," where you write things up like this: "We claim the process of producing compounds such as Structure I, which are useful for the treatment of allergies through inhibition of whateverase." You didn't claim the treatment per se;you claimed a process of making a compound. But you worked in the whole purpose of making the compounds, and if you've written things in a convoluted enough form, it can be very hard to disentangle the two. A good Swiss claim is virtually a guarantee of a prolonged court fight.
I'd prefer to see the whole business disappear. Medical treatment claims have become more and more popular in recent years, and they're driving everyone in the drug industry nuts. It's turned into a mutually-assured-destruction game: "So, you claim all that stuff! Hah! I claim all this!" If we keep this up, we're going to end up with a medical landscape made up of Balkanized patches, with barbed wire and wasteland in between.
But what to do about it? As these things show up, researchers that wouldn't have thought about writing such claims feel forced to keep up. As long as they're possible, they'll be used. It may take a few years, but I think that we could be heading for some interesting situations if some of the sealed-off treatments look like they could turn into blockbusters.