The indictment makes it obvious that this started long before Daraprim was in the news. I'd say this isn't politically motivated, at least not for that reason alone.
Remember, they got Al Capone in the 1930s for tax evasion - not all the other things he was certainly guilty of. Several other gangsters were convicted of things like mail fraud.
If you're guilty, or even just under investigation, don't paint a target on your back. A smart person would know to lay low. Schkreli ... didn't.
I would note that I have no knowledge of the investigation beyond what's being reported (and only a cursory knowledge of that). I could be totally wrong. Maybe these charges were immediately obvious to investigators and it's just taken them almost a year to get their ducks in a row. I'm just theorizing here based on some historical knowledge of famous criminals and how they were eventually brought down (see my comments above on gangsters in the 20s and 30s).
That this question even has any legitimacy is troubling in and of itself.
Both matters pre-date Skreli's national notoriety, because it was his new, post-Retrophin firm that made him "famous" for price gouging.