Now that it's been publicized, it's just a matter of innovators running the program against their own methods and patenting the computer-generated work-arounds. In a sense it's now going to be harder for creative medicinal chemists to work around patents.

I came here to say this. However, I think the FDA will put up more of a barrier to "alternatives" than any patent. It doesn't matter if software says that an alternative drug is effective, the only way that they can be sold is if they are tested. Testing is supposed to be the most expensive part of producing a new drug. The software might have other applications besides medicine though.