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DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: Twitter: Dereklowe

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« Politics: Proxy Servers Revisited | Main | More Hot Air From Me on Screening »

June 18, 2009

Professors Patent Pathways and Possibly Profit? Please.

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Posted by Derek

Nature Biotechnology has a good wrap-up of the Ariad patent case, and it includes some insights into the whole "patent the pathway and profit" mindset. That was the heart of Ariad's strategy: they licensed a patent on NF-kappaB from Harvard, MIT, and the Whitehead institute, and promptly went wild threatening to sue everyone that came within a mile of its already ridiculously vast) claims.

I particularly like this description of the legal process involved:

. . .Despite the earlier jury verdict in Ariad's favor, "the federal circuit [court] treated these claims, you know, almost derisively. They just smacked them," says Minnesota patent attorney Warren Woessner, former chair of the biotech committee of the American Intellectual Property Law Association. Woessner had predicted Ariad's defeat. "They won in a jury trial—big deal. They got some Nobel prizewinners up there to say how wonderful this was, and the jury folded like a cheap lawn chair. That's not uncommon. But the [appeals judges] just demolished this."

Indeed. But the strategy isn't dead yet, unfortunately:

Companies asserting broad claims "are not going to get much sympathy" from the federal circuit, agrees (Duke's Arti) Rai. "And if they're trying to assert them against a defendant who is as willing to fight as Eli Lilly is, they're ultimately going to lose."

Many universities, however, emboldened by Ariad's 2006 district court victory, have been pressing for such broad claims. "Every professor that discovers a mechanism of action now wants you to claim it," says Woessner, who advises universities. "And it can be hard to dissuade them from that." The take-home lesson from the Ariad case, says Woessner, is that filing such broad claims, without specifying compounds, hoping that some will stand, is a risky patent strategy. "Don't try to get broad functional claims, like the Ariad claims, or the Rochester claims," he says, without describing specific pathway modulators.

Ah, but coming up with specific pathway modulators is often the job of. . .(drumroll) a drug company. One that's full of medicinal chemists who know how to try to optimize these things. Unless an academic group gets lucky in screening a smaller commercial compound collection, they're not likely to be able to show such enabling compounds. And since most academic researchers don't have access to anything like the industry's high-throughput screening technology, let alone the industry's files of plausible-looking molecules, the chances aren't good. Heck, they aren't all that good for us over here, and we have all those things. To get the full flavor, you really need to see some big HTS campaigns rummage expensively through a whopping compound collection and still come up with only 3-hydroxy-diddleysquat. . .

Comments (23) + TrackBacks (0) | Category: Patents and IP


1. Hap on June 18, 2009 8:55 AM writes...

Profs and universities want the pot of gold at the end of the rainbow, and if someone grants their patents, then they have a chance to get it. At minimum, they might be able to intimidate smaller companies into licensing their "technology", and so thereby gain a consistent stream of revenue. Only when someone spends a lot of money to kill their patent will it stop making them money. Unless the patents aren't granted in the first place (because they don't have an actual invention, or at least a way to carry it out), there isn't any reason for them to stop patenting anything under the sun.

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2. Anonymous on June 18, 2009 9:18 AM writes...

what if you identify some siRNAs that can modulate the pathway and show some activity in animals. The patent office will probably grant you composition claims for siRNAs but then can one make broader claims to the pathway itself or some method of treatment claims for using that pathway to treat a specific disease?

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3. RB Woodweird on June 18, 2009 10:56 AM writes...

I wrote my thesis on the total synthesis of 3-hydroxy-diddleysquat, you insensitive clod.

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4. Vadar on June 18, 2009 11:16 AM writes...

Appreciate your alliterative anouncement of the appropriateneness of the appeal outcome.

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5. SRC on June 18, 2009 11:31 AM writes...

Further to Derek's point, screening a library of compounds for hits is hardly the stuff of a doctoral dissertation.

Grad students accept poor pay to learn how to do research, not to do technicians' work. Any PI misusing grad students in that fashion is in need of a tete-a-tete with his dean.

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6. NJBiologist on June 18, 2009 11:32 AM writes...

@RB Woodwierd--

You must be very proud. I'm pretty sure I ran 3OHDS as a standard in a proof-of-concept study a year or two ago.

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7. Tim on June 18, 2009 12:29 PM writes...

Academics groups might not be able to run the necessary screens, but universities can. Given the enormous profits that could come from a broad "pathway patent," it seems that it would be worthwhile for big research universities to set up screening facilities on their own (or in exclusive partnerships with drug companies). And that's exactly what patent law should be promoting--more screening means more progress. Though Ariad's claims were absurdly broad and were deservedly smacked down, the panel's decision was too conclusory--we need to know where exactly the court is drawing the line. Hopefully the Fed Circuit will take Ariad en banc and provide better guidelines for future cases.

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8. DerekH on June 18, 2009 12:36 PM writes...

Universities do have screening groups and some even have lead and probe optimization groups. See the SBS website for academic screening centers.
They now have a large staff of ex-Pharma people who know what they are doing.

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9. Hap on June 18, 2009 12:41 PM writes...

Why are pathways and genes patentable rather than only specific inventions to manipulate or detect them? If you claim a pathway with little or knowledge of what it affects or how to manipulate it, how can you be considered to have an invention (what have you told anyone how to do)? If there's nothing disclosed on how to do something, then you are patenting the information itself (that pathway X causes condition Y), which I thought was not the point of patents at all and which was also not legal.

What I am missing in this?

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10. HelicalZz on June 18, 2009 12:42 PM writes...

RB Woodweird,

What a coincidence. I wrote mine on the isolation and characterization of 3-hydroxy-diddleysquat, so thank you for confirming the structure.

Of course by now you and I and NJBiologist realize that the the active material is really the epoxy-didleysquat and we all wasted out time on a red herring.


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11. Palo on June 18, 2009 1:40 PM writes...

What an obsession you have with the industry vs. academia thing, Derek. There's good and bad people in academia and industry, there's tons of unethical profit-making douchebags in pharma marketing (that you typically downplay with "of course, but not all") and there a lot of profit-seeking douchebags in academia trying to patent the sky (which you typically highlight as "oh my god, they are bad!). Enough of this. We should agree (but of course we won't): pharma is not always the cool "innovative" enterprise that the industry cheerleaders (you and most of your readers) would like to claim, and academia is not the main source of "creative" and original science that academia cheerleaders (like me) would like to believe.
Yes, "specific pathway modulators is often the job of. . .(drumroll) a drug company", but most often than not (close to 100%), pathway discovery and characterization is the job of... (drumroll) academia.
For your expertise in modulating pathways, you get paid... (drumroll) a lot more than the discoverer of a pathway. Some "discoverers" get jealous of you and want to get similar bits of money (and/or stock options) in (in my view) a greedy and unethical way (exploiting grad students and using federal money for their own profit)

PS: before pharma-cheerleaders burn me online, I left academia more than 2-years ago and I've been in a biotech company since then. My role is different, my salary is better, but my views, however, have not changed: academia is still the engine of basic discovery; pharma is the still the most efficient enterprise in bringing discovery to the market. The profits that pharma gets for that roll are, I still believe this, way out of proportion of its worth.

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12. EuroView on June 18, 2009 2:52 PM writes...

@ Hap

I don't know what the USPTO's stance on this is but I do know that at the European Patent Office you can't patent pathways and claims to just genes are expressly excluded. I see many US drafted applications entering the European regional phase after the international phase. Claims such as "an agonist for receptor Y" are shot down. You need to define what compound(s) will act as agonists and what the effect of interacting with receptor Y will be (e.g. an inotropic effect). And if your Markush formula is too broad and your effects too numerous, you'd better be ready to back it up with some decent data. It has always been difficult to explain to our US clients why you can't simply patent pathway Z. I hope after the latest Ariad decision this will become easier.

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13. milkshake on June 18, 2009 3:22 PM writes...

We have a rather large HTS screening group in our institute, in the same building with the medchem group, and their collection of commercially available compounds has few hundred thousands purified non-combichem individual compounds. The lists of hits hey produced were most impressive - much better than the industry HTS at former Pharmacia. (I worked on several HTS-derived series here and every hit that we got from the HTS got confirmed, some were even in low nanomonlar range.)

The only thing that stops academic institutions from going through massive screening assays is the funding. For example we cannot screen every target that we want (even if the assay is robot-ready) unless we secure funding for it because running the HTS campaign is somewhat costly

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14. Anonymous on June 18, 2009 4:21 PM writes...

Palo is right on, and therapeutic innovation is and will likely remain a collaboration / extension of academic research partnered with the economics of industry, of which pharma is a large part (but not the entire pie - don't neglect the technology side as well).

Few would honestly question that the Bayh-Dole act of 1980 was a huge driver for the biotechnology industry. Allowing / enabling academic researchers to patent and attempt to commercialize the results of government funded research has been essential to innovation in this industry.

It doesn't get enough credit.


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15. HelicalZz on June 18, 2009 4:25 PM writes...

For those unfamiliar with Bayh-Dole here is a fairly recent lookback commentary from Nature Biotechnology.


(sorry for not fully signing in on the last post - oops).

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16. milkshake on June 18, 2009 4:49 PM writes...

I know a little the chem-bio prof who helped to found Ariad and all this patent-trolling nonsense does not surprise me.

I worked at a combichem startup before; there are some over-active academia promoters like Richard Houghton, willing to found multiple start-ups on a paper-thin premise and they would typically stake some ridiculously-wide IP claims to impress the unsuspecting investors. Its not their money so there is very little risk for them personally when the companies go under but when they survive even with just a mediocre outcome (resulting in a break-even buyout by a bigger company) it would make them pretty rich.

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17. Norepi on June 18, 2009 5:16 PM writes...

#3, 6, 10: I prepared the 6-aza analogue of 3-hydroxydiddleysquat last year, but all the analogues of it were insoluble!

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18. SRC on June 18, 2009 5:46 PM writes...

Given the enormous profits that could come from a broad "pathway patent," it seems that it would be worthwhile for big research universities to set up screening facilities on their own (or in exclusive partnerships with drug companies).

And then say bye-bye to their tax-exempt status. The trustees of the university would probably just laugh that off.

Pathway patents are a non-starter. They may have issued, owing to short-sightedness in the PTO, but no one has successfully asserted one, although Rochester and Ariad have both tried.

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19. Tim on June 18, 2009 7:07 PM writes...


Not necessarily--a tax-exempt status has more to do with what profits are used for, not how they are obtained. As long as the revenue generated by patents is funneled back into the education and research mission of the university, it's no different from getting a big return on an endowment. Universities do this all the time with other types of patents now. As far as industry-academia partnerships go, they're also common. There's nothing wrong with a university doing the screening, getting the patent, and licensing it to a taxable corporation of which the university is the sole (or controlling) shareholder. Again, as long as the dividends are returned to the educational mission of the university, there's no tax problem. A university is allowed to be the sole shareholder in a corporation and it's allowed to license its IP -- from there, setting up the system I described is just paperwork (look at places like Harvard, MIT, Stanford, etc. to find examples of such paperwork).

True pathway patents are, at best, only the subject of every university president and biotech CEO's dreams. And rightfully so -- there's no social value derived from research organizations simply planting their flag and moving on. Nonetheless, if society values the discovery of new pathways, there's still a lot to be said for giving broad protection to the trailblazers who initiate a successful search. This issue boils down to which type of research we want the patent system to encourage: development of new modulators of existing pathways or the discovery of new pathways. Ideally, that's a question for Congress to answer. In the interim though, the Fed Circuit needs to decide it in an unambiguous way. First, they need to rule categorically on pathway patents. Because panel decisions may later be overruled by the en banc court (and they often are in the Fed Circuit, at least relative to regional circuits), all of the judges should consider this issue. Research organizations will tailor the direction of their work to the rule, so the rule needs to be final. Second, there need to be guidelines for future cases -- cases in which the claims aren't as ridiculous as Ariad's. To smack Ariad around and say "no, no, you can't make claims like this" isn't useful. Again, research will be refocused based on the rule, and it's inefficient to make researchers overly cautious simply because they don't know where the Fed Circuit will draw the line.

I certainly agree that pathway patents are both ill-advised and unenforceable at the extreme, but I believe that there is value in this sort of IP that should not be overlooked because the first few test cases failed to pass the laugh-out-loud test.

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20. Anon on June 18, 2009 8:50 PM writes...

Here's an academic screening group of 75 employees, including med chem and library synthetic groups:

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21. Anonymous BMS Researcher on June 18, 2009 9:05 PM writes...

At meetings the other day one speaker showed the SAR of sticking various groups onto each ring of 3-hydroxy-diddleysquat trying to get better potency. Unfortunately, the ones with decent potency were about as soluble as brick dust and the ones with decent solubility about as potent as lactose. My eyes do tend to glaze over after about the sixty-eighth variation.

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22. maor on June 28, 2009 4:55 PM writes...

You don't need drug companies to come up with a specific pathway modulator. A patent attorney can do that. You only need drug companies to come up with a specific pathway modulator that actually works, which isn't necessary to get a valid patent.

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