As an example of exploitation see the statin drugs used to lower cholesterol. These were originally isolated from an ancient Chinese herbal "red yeast rice" and found to be effective. So some company patented the molecule, did clinical trials, and profit! I chose this one because I have personal experience getting dramatic reduction in my cholesterol from taking red-yeast-rice. It's also a nice example of how the system is broken. We all could have benefited from trials proving that red-yeast-rice reduces cholesterol, but that's not what happened. The company would not have funded the trials if they couldn't patent the molecule.
IMHO if clinical trials were cheaper there would be no need for granting monopolies (via patents) to cover the costs. I also don't see why trials are so expensive. There are plenty of doctors treating plenty of patients that are willing to try things. All we really need is a set of rules to protect people from irresponsible trials, and formal study procedures to document results and determine efficacy. It doesn't seem too complicated right?
Company: "But that's a naturally occurring virus, we can't patent that so we're not interested. Do something else, or find a way to 'make it better' so we we can patent it and make money."
True story. Now imagine this:
Researcher: "I've found that this rhinovirus is devastating to certain kinds of tumors when injected into them... in mice. We need to do more testing, and in humans."
Oncologist at major center: "We've seen a number of terminal patients with that type of cancer, current treatments don't work especially at stage 4. We could test that virus on a number of people if they were willing to try it."
Cancer Patient "Sign me up!"
There has to be a way to make this work, and it should cost far less than the current approach. I'd argue that it would cost the government less to fund the studies than to pay medicaid costs for the patented treatments. Sure, change would need to happen but it would happen fast, and in the mean time nobody would eliminate current treatments - they're already established and profitable.
There was a paper from one of the Fed branch offices about this. It turns out that the US has two independent mechanisms to help pharma companies make money: patents and FDA-granted exclusivity. It's unclear that patents are needed.
I admit I don't know much about the latter, but what about international markets?
However I do agree that profit is a very powerful motivator, and I see no easy way to make sure the money is better spent otherwise (although there's no reason for all research to be profit driven, publicly funded research can definitely be good thing even if only as competition).
However I get the impression that we're at the point where there are so many things that can be cured if money is no objection that money is starting to become an objection, and nobody seems to be prepared to do what is essentially putting a price on human life.
Pharma?
It's trendy to pretend that pharma patents are the Devil incarnate because they enable exploitative pricepoints by the patent-holder, but the fact is that's what enables the profit motive for the research in the first place. (At least, I've never seen a serious argument against this, only righteous blustering.)
(The fact that US pharma companies spend more on advertising than on research, has no bearing here.)