You have to be an expert in patent law to really understand the subtleties here. Even though I am a lawyer with some experience in intellectual property, I can't say much with confidence about this. But here is what I can say without much confidence:
Inter Partes Review is a controversial new procedure that has been used to aggressively invalidate patents, and has provided significant relief to practitioners dealing with patent trolls. The Supreme Court agreed last month to hear whether IPR is constitutional (the legal risk is that IPR impairs property rights with inadequate procedural protections).
So at a superficial level, using IPR to invalidate ChromaDex's patent (which they licensed from Dartmouth) on the method of producing NR seems like a great idea. Digging deeper, there are several problems for Elysium.
First, as you point out, IF the claim is that NR isn't patentable because it is a naturally occurring substance, that won't matter because the invention that the patent is protecting is a particular method of synthesizing NR, not the molecule itself.
Second, IPR works great against patent trolls, but maybe not in a competitor case, which this is. (What "competitor case" means is that ChromaDex is actually using the patent to run a business, not merely extorting royalties from someone else who is trying to run a business. Patent Trolls, by contrast, are "non-practicing entities" (NPEs).)
Third, IPR hasn't been as harsh to patent holders in the Pharma space as elsewhere (possibly because the patent owners are more frequently practitioners).
Fourth, IPR itself might be unconstitutional, and the shadow of the Supreme Court's cert-grant might reduce the Appeal Board's tendency to nullify patents wantonly.
In general, it seems to me that if Elysium has a satisfactory alternative to NR -- efficacious and affordable -- then they would not be messing with IP litigation, which is expensive. So the presence of this Inter Partes Review proceeding is an indication of Elysium's poor position.
As always, I think Elysium promised to use science to clean up the supplement industry, which would have been an incredibly valuable service, and instead they appear to be focusing more on using litigation to try to improve their profits, which ought to have already led to the dissolution of their Nobel Prize winning advisory board, which can't give them any useful advice about litigation. [If they had some Nobel Prize winning lawyers on their advisory board, they wouldn't have gotten themselves into this position in the first place.]
