Re: A chemical substance is not a drug
I think the plan for those cases is that you document the failure, and then throw everything out. Discovery of drugs is pretty much a process of trying hundreds of molecules and hoping that one of them does more good than harm to patients with a specific set of conditions.
The usefulness of machine learning in this fields is in pointing you towards the ones that look more likely to work. That's a far cry from "AI can design drugs", but it's still a useful tool. At least in principle; it remains to be seen whether it's actually effective in suggesting molecules that, at the end of the process, actually work.