I've already spoken of my disdain for "method of treatment" patents, the claiming of entire biochemical pathways for their medical use. It's something that you never used to see, even though US patent law has long allowed it. But in recent years, an increasing number of these applications have shown up, and they're starting to become issued patents. One of them issued on Tuesday. It's a big one, and it's going to cause a massive legal tangle.

I want to distinguish such patents from the standard "use patents" that companies file on a compound class when they discover a new use. I've no problem with that at all, since it relates to specific chemical entities and what they're good for. A patent claim that "3-aminothingamabobs are useful for the inhibition of whateverase enzyme" is fine with me, as is one that says that "3-aminothingamabobs are useful for the treatment of diabetes." Such patents will have to enable the claims, by backing them up with data showing that the compounds really do inhibit the enzyme, or really do lower blood sugar.

But the kinds of claims that are sending us toward a huge intellectual-property train wreck read like this: "Treatment of disease through inhibition of whateverase enzyme." Note that this claim doesn't address any chemical matter at all - it's similar to a business-method patent of the kind that have been driving technology companies crazy. In effect, this claim says "If you come up with a drug that works through this pathway, you infringe our patent. It doesn't matter if you were looking for something that worked that way or not. It doesn't matter if your compound has six other modes of action. And it doesn't matter if you even knew how it worked when you developed it."

Such patents have come to the drug industry's attention over the last few years, and there have been some local legal skirmishes. But this latest one could start the all-out battle. It covers the use of a cell signaling protein called NF-kappaB (NF-kB, with that "k" more properly in a Greek font.) That one's involved in regulation of genes that are extremely important in inflammation, cell death, and cancerous states. The list of diseases that have an NF-kB component is therefore impressive: cancers of various types, atherosclerosis, osteoporosis, arthritis and sundry other autoimmune diseases, septic shock, and so on. Here's a diagram of its main functions that will be impressively incomprehensible without some cell biology background, and here's a more extended review of the field if you're up for it.

I've no idea of how many academic research groups are working on this, but it's a heap. And in industry? How many drug companies have compounds that hit NF-kB? Well, that figure has been more exactly determined for us by the sole licensee of the new patent, Ariad Pharmaceuticals. They have sent letters to over 50 companies whose marketed or developmental compounds appear to work (at least partially) through that pathway. And they want money from all of them. Right now.

This patent's history goes back to 1986 - the earliest filing in its history is from January of that year, although the issued patent, for reasons that make my head hurt to go into, has an official filing date of 1995. That's an awful long time for an application to be kicking around the patent office; the file wrapper dealing with its prosecution history must be something to see. And I can guarantee that plenty of people are going to ask to see it, starting with the legal department at Eli Lilly.

Ariad had a lawsuit fueled and on the pad, and as soon as their patent was issued, they launched. In fact, the Business Wire press release about the lawsuit went out before the one about the patent, which shows you where Ariad's priorities are. They claim that two of Lilly's biggest products, Evista for osteoporosis and Xigris for sepsis, both work through NF-kB (and there's little doubt that they do, at least partially.) Therefore they're demanding royalties, and pronto. Lilly had ignored Ariad's previous requests for a licensing deal, according to the Wall St. Journal, which moved them up to the exalted position of First Target. The other fifty companies can presumably expect the same treatment if they don't get on Ariad's good side.

Is this going to work? I fervantly hope not, but it's anyone's guess. Almost all my colleagues that I spoke to today said "Oh, come on" to the idea that anyone could legitimately patent all the NF-kB pathways, but the patent runs to a relentless 203 issued claims. It was written carefully and comprehensively. My informal survey group didn't think much of Ariad's chances in court, either. But the company points out, correctly, that they'd be foolish to go ahead without some informed legal opinion saying that they can win.

Ariad's CEO, Harvey Berger, has this to say on their web page:

"We are focusing in 2002 on realizing the value of our intellectual property portfolio,
especially our patents related to NF-kB. . . We are the exclusive licensee
of this pioneering technology and are committed to creating value for the distinguished
team of inventors including two Nobel laureates, their institutions - The Whitehead
Institute, M.I.T., and Harvard University - and our stockholders. Our share of the potential
revenues generated from such efforts should ultimately help underwrite the cost of
developing and commercializing our promising portfolio of breakthrough medicines."

I'd like to furnish my own translation of this statement: "We are focusing in 2002 on shaking down every company we can find, by whacking them over their heads with our mighty patent. This IP windfall could provide us with the huge sums needed to get some of our own ideas to work. But for now, we're going to enjoy stripping the cash from people who have actually been able to develop useful drugs."

Well, as far as I'm aware, I don't know anyone at Ariad. I'm sure that there are some good people there, and I'm sure that some of them are working hard on good ideas. But for now, their company is devoted to a strategy that I think can only hinder medical progress and lead the pharmaceutical industry into a destructive, wasteful, patent war. Ariad should be ashamed, and MIT, Harvard and the Whitehead Institute, the assignees of the patent, should be ashamed to let them go out and do the dirty work for them. Because if they win this, everyone's going to follow suit. They'll have to. And I'm not sure I'm going to be able to stand working in an industry that looks like what that will lead to.