About this Author
College chemistry, 1983
The 2002 Model
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: email@example.com
August 11, 2014
Via the Economist's "Free Exchange" blog comes this provocative paper (PDF) from the University of Chicago, Harvard, and MIT. Its authors are looking at the effect of patents on the oncology drug market, and they conclude that the current system is probably hurting patients (and the broader economy).
That's a big statement to make, so the first thing to do is dig into the paper and see how it was arrived at. The authors are looking at effective patent terms: how long an invention really has an exclusive market term. That's a big issue in drug development, of course, since the regulatory pathway to approval can be so long that only a few years are left on the patent by the time a drug can be sold.
. . .Since society cares about an invention’s total useful life, but private firms care only about monopoly life, a distortion emerges not just in the level of R&D (as arises in standard models), but also in the composition of R&D: society might value invention A more highly than invention B, but private industry may choose to develop B but not A. Note that, other things equal, commercialization lag lowers both monopoly life and total useful life: both society and private firms prefer inventions to reach the market quickly. But, under a fixed patent term, commercialization lag reduces monopoly life more rapidly than total useful life, hence the distortion away from inventions with both a long total useful life and a long commercialization lag.
The problem with oncology, the paper claims, is that drug firms therefore have an incentive to work on compounds whose clinical trials are shorter, because they have a better chance of a longer effective patent lifetime). Slow-moving cancers, which might be more treatable, are relatively neglected, because there is less likelihood of return from them given the patent timelines.
Cancer drug development tends to be specific to a cancer type (e.g. prostate) and stage of disease (e.g. metastatic). . .providing a natural framework for estimating how expected commercialization lags (as proxied by survival time) and R&D investments vary across different groups of patients. Aggregating survival information from patient-level cancer registry data, we document stark variation in survival times across patients of different cancer types and stages of disease. In order to measure R&D investments on cancer treatments relevant to each cancer type and stage of disease, we use newly-constructed data from a clinical trial registry that has cataloged cancer clinical trials since the 1970s. The key feature of this data which makes it amenable to our analysis is that for each clinical trial, the registry lists each of the specific patient groups eligible to enroll in the trial - thus allowing a match between our measures of expected commercialization lag (as measured by survival time) and R&D activity (as measured by clinical trial investments) across cancer types and stages of disease.
They show that there is much more clinical focus on the severe short-time-course cancers than on the slow-moving localized types, and they ascribe this to distortion caused by patent terms. But as far as I can tell, the authors don't consider some other factors, and as someone who's done drug discovery work in oncology, I'd like to bring these out as well.
There's no doubt that patent lifetimes are a factor, since these allow a company to recoup its development costs - and the costs of all the other failed projects. It's worth remembering that the overall clinical failure rate is still roughly 90%, so there are a lot of costs to be made up whenever sometime actually does work. But imagine that patent terms were suddenly doubled to forty years instead of twenty. This might bring in more investment into slower-moving long-term cancer projects, but I don't think it would be as simple as this paper's model suggests. Overall, a drug company would prefer not to tie up its time, effort, and capital for longer than necessary in the uncertain business of a clinical trial. Even with the prospect of a longer patent term reward at the end of the process, the disincentive for multiyear trials would still be there, because there are so many shorter alternatives in oncology. (That's as opposed to Alzheimer's, where it's long trials or nothing, at least until we understand a lot more about the disease). It's not like the slower-moving cancers are any easier to understand, find targets for, or progress into the clinic: they're all hard.
This is even more the case when you consider that the oncology field has a good number of small companies in it. The barriers to oncology drug development are lower than in some other areas - it's easier to identify patients, and there's a lot of unmet medical need. And those relatively short clinical trial times are another incentive: to do another thought experiment, if you suddenly required all drug companies working on oncology to work only on the slower-moving cancers, there would be far fewer drugs in development, since most of the smaller companies would drop out. They don't have the funds to keep going that long. So while short clinical trials may be a distortion in one direction, they have distorted the market in another, arguably beneficial direction as well, by bringing more companies and more ideas into the field.
I say "beneficial", because some of the drug mechanisms that are being tried on the faster-moving cancers would also be of use on the slower, more localized ones. The genomic, metabolic, and proteomic information learned by studying the faster-moving varieties (and the techniques used to do so) are immediately applicable to the slower-moving ones as well. It's not a zero-sum game.
There's also that unmet-medical-need factor to consider. It's easier for a company, especially a small one, to raise money and justify its spending to investors when it's working against form of cancer with a low survival rate and a relatively fast progression. The belief is that the regulatory barriers to approval are lower for such drugs, and that uptake by physicians would be faster if the drug gets approved. Side effects are also going to be more tolerated for more severe conditions, too, and oncology drugs, as is well known, tend to have some pretty significant ones.
The authors, after considering several alternatives, present evidence that when regulatory agencies allow surrogate endpoints as a factor for drug approval that investment in the longer-term cancers improves. They suggest that research into validated markers of this sort could have the best returns overall, compared to other possibilities (such as just lengthening patent terms, not that that's going to happen in the real world, anyway). And I agree with them there - but I also note that drug companies themselves have been seeking such surrogate endpoints on their own, for the same reasons. (These things speed up all trials, not just the longer ones). Large incentives for good clinical trial markers already exist, but such markers are pretty damned hard to come by, unfortunately.
But as for the main subject of this paper and its explanatory power, I'm not quite convinced. As far as I can see from going through the manuscript, none of the other factors mentioned above have been considered - everything is tied to the effective patent lifetime. And while that's probably real, and a partial surrogate for some of these issues, I have trouble buying it as the only thing that's going on. Now, this may be what economists do: find a correlation that is open to a mathematical treatment and run with it. But I don't see how you can make statements this sweeping without going into more of what (from my perspective) I see as the real world of drug discovery and development.
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July 21, 2014
What a mess there is in the hepatitis C world. Gilead is, famously, dominating the market with Sovaldi, whose price has set off all sorts of cost/benefit debates. The companies competing with them are scrambling to claim positions, and the Wall Street Journal says that AbbVie is really pulling out all the stops. Try this strategy on for size:
In a lawsuit filed in February, AbbVie noted it patented the idea of combining two of Gilead's drugs—Sovaldi and an experimental drug called ledipasvir, which Gilead plans to combine into one treatment—and is therefore entitled to monetary damages if Gilead brings the combination pill to market. Legally, AbbVie can't market Sovaldi or ledipasvir because it doesn't have the patents on the underlying compounds. But it is legal for companies to seek and obtain patents describing a particular "method of use" of products that don't belong to them.
Gilead disputes the claims of AbbVie and the other companies. A spokeswoman said Gilead believes it has the sole right to commercialize Sovaldi and products containing Sovaldi's active ingredient, known as sofosbuvir. An AbbVie spokeswoman said the company believes Gilead infringes its patents, and that it stands behind the validity and enforceability of those patents.
You don't see that very often, and it's a good thing. Gilead is, naturally, suing Abbvie over this as well, saying that Abbvie has knowing mispresented to the USPTO that they invented the Gilead therapies. I'm not sure how that's going to play out: Abbvie didn't have to invent the drugs to get a method-of-use patent on them. At the same time, I don't know what sort of enablement Abbvie's patent claims might have behind them, given that these are, well, Gilead's compounds. The company is apparently claiming that a "sophisticated computer model" allows them to make a case that these combinations would be the effective ones, but I really don't know if that's going to cut it (and in fact, I sort of hope it doesn't). But even though I'm not enough of a patent-law guy to say either way, I'm enough of one to say, with great confidence, that this is going to be a very expensive mess to sort out. Gilead's also in court with Merck (and was with Idenix before Merck bought them), and with Roche, and will probably be in court with everyone else before all this is over.
This whole situation reminds me of one of those wildlife documentaries set around a shrinking African watering hole. A lot of lucrative drugs have gone off patent over the last few years, and a lot of them are heading that way soon. So any new therapeutic area with a lot of commercial promise is going to get a lot of attention, and start a lot of fighting. Legal battles aren't cheap on the absolute scale, but on the relative scale of the potential profits, they are. So why not? Claim this, claim that, sue everybody. It might work; you never know. Meanwhile, we have a line forming on the right of ticked-off insurance companies and government health plans, complaining about the Hep C prices, and while they wait they can watch the companies involved throwing buckets of slop on each other and hitting everyone over the head with lawsuits. What a spectacle.
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June 20, 2014
Try this claim on for size and see how it fits:
"A method for treating a human disease state by means of inhibiting an enzyme whose functioning contributes to that disease state, said means comprising the administration of a molecule of molecular weight between 100 and 750 Daltons (composed of carbon, hydrogen, oxygen, nitrogen, and optionally sulfur and/or one or more halogen atoms) that has been determined to interact with the enzyme in such a way as to disturb, inhibit, or alter its function."
Not happening, that one, and it's a good thing. But stuff nearly that vague and idiotic is all over the software patent landscape. Such patents list a superficially impressive amount of detail about how their "invention" is to be implemented, but all too often, that scheme turns out to mean something like "Someone uses a computer to contact a web server" or "Someone turns on their mobile phone". It would be as if we in the drug industry could enable our compounds by citing a few synthetic organic chemistry textbooks - that's how you make 'em, right there!
But the Supreme Court has begun the task of diverting a river through this particular manure-laden stable in a 9-0 decision, Alice Corp. v. CLS. Justice Thomas delivered the opinion:
The patents at issue in this case disclose a computer-implemented scheme for mitigating “settlement risk” (i.e., the risk that only one party to a financial transaction will pay what it owes) by using a third-party intermediary. The question presented is whether these claims are patent eligible under 35 U. S. C. §101, or are instead drawn to a patent-ineligible abstract idea. We hold that the claims at issue are drawn to the abstract idea of intermediated settlement, and that merely requiring generic computer implementation fails to transform that abstract idea into a patent-eligible invention. . .
The opinion starts off by detailing why the patents under question are directed towards an abstract idea, and then goes on to demolish the contention that the method claims turn that into something patentable. All they do, the court says, is instruct someone to go off and use a computer to implement that idea (of an intermediated financial settlement), which in no way makes that idea eligible for a patent. Eventually, there will probably come a case that forces the court to propose a test for what constitutes an abstract idea, but I'll bet that all nine justices hope to be retired by the time that happens. Update: for more on this and other issues associated with this case, see this discussion at Patent Docs.
The opinion cites a number of other recent patent decisions by the court, such as Mayo v. Prometheus and Assoc. Mol. Pathology v. Myriad. One gets the impression that the Supreme Court is engaged in a multiyear, multicase effort to clean up some persistent problems in US patent law, and that this process will continue. More on this decision can be found at SCOTUSblog and The Economist.
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May 22, 2014
That last entry about Oncoceutics attracted a comment that caught my eye. If you go to the company's web site, and their press release page, there are some oddities. Somehow, the same robo-spammers who infect the comment sections of blogs have worked their way into the text of the company's press releases. Here are some examples (emphasis added):
"There are also claims for ONC201 to be used in combination with other anticancer drugs and to be given orally to generic cialis cheap treat brain cancers. "
"To the extent that statements in this press release are cialis online generic not strictly historical, including statements as to revenue projections, business strategy, outlook, objectives, future milestones, plans, intentions. . ."
"“We are very pleased that the patent cheap viagra canada was issued in less than two years,” said Martin Stogniew, PhD, Chief Development Officer of Oncoceutics."
"“ONC201 is an exciting small molecule that has demonstrated efficacy against therapy-resistant malignancies and has shown to possess therapeutically desirable properties such as oral activity, thermal stability, temporally sustained activity, ability to cross the blood-brain barrier, and Cure Male viagra online cheap Impotence – How to Cure Erectile Dysfunction safety, ” said Wafik El-Deiry, MD, PhD FACP, co-founder and Chief Scientific Advisor of Oncoceutics."
OK, you get the idea, but there are plenty more where those came from. The company might want to clean this stuff up, and figure out how it got into all their press releases in the first place.
Update: the cleaning has taken place! Same-day service. . .
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C&E News has a story today that is every medicinal chemist's nightmare. We are paid to find and characterize chemical matter, and to develop it (by modifying structures and synthesizing analogs) into something that can be a drug. Key to that whole process is knowing what structure you have in the first place, and now my fellow chemists will see where this is going and begin to cringe.
Shown at left are two rather similar isomeric structures. The top one was characterized at Penn State a few years ago by Wafik El-Deiry's lab as a stimulator of the TRAIL pathway, which could be a useful property against some tumor types (especially glioblastoma). (Article from Nature News here). Their patent, US8673923, was licensed to Oncoceutics, a company formed by El-Deiry, and the compound (now called ONC201) was prepared for clinical trials.
Meanwhile, Kim Janda at Scripps was also interested in TRAIL compounds, and his group resynthesized TIC10. But their freshly prepared material was totally inactive - and let me tell you, this sort of thing happens all too often. The usual story is that the original "hit" wasn't clean, and that its activity was due to metal contamination or colorful gunk, but that wasn't the case here. Janda requested a sample of TIC10 from the National Cancer Institute, and found that (1) it worked in the assays, and (2) it was clean. That discrepancy was resolved when careful characterization, including X-ray crystallography, showed that (3) the original structure had been misassigned.
It's certainly an honest mistake. Organic chemists will look at those two structures and realize that they're both equally plausible, and that you could end up with either one depending on the synthetic route (it's a question of which of two nitrogens gets alkylated first, and with what). It's also clear that telling one from the other is not trivial. They will, of course, have the same molecular weight, and any mass spec differences will be subtle. The same goes for the NMR spectra - they're going to look very similar indeed, and a priori it could be very hard to have any confidence that you'd assigned the right spectrum to the right structure. Janda's lab saw some worrisome correlation patterns in the HMBC spectra, but X-ray was the way to go, clearly - these two molecules have quite different shapes, and the electron density map would nail things down unambiguously.
To confuse everyone even more, the Ang. Chem. paper reports that a commercial supplier (MedKoo Biosciences) has begun offering what they claim is TIC10, but their compound is yet a third isomer, which has no TRAIL activity, either. (It's the "linear" isomer from the patent, but with the 2-methylbenzyl on the nitrogen in the five-membered ring instead).
So Janda's group had found that the published structure was completely dead, and that the newly assigned structure was the real active compound. They then licensed that structure to Sorrento Therapeutics, who are. . .interested in taking it towards clinical trials. Oh boy. This is the clearest example of a blown med-chem structural assignment that I think I've ever seen, and it will be grimly entertaining to see what happens next.
When you go back and look at the El-Deiry/Oncoceutics patent, you find that its claim structure is pretty unambiguous. TIC10 was a known compound, in the NCI collection, so the patent doesn't claim it as chemical matter. Claim 1, accordingly, is written as a method-of-treatment:
"A method of treatment of a subject having brain cancer, comprising: administering to the subject a pharmaceutical composition comprising a pharmaceutically effective amount of a compound of Formula (I) or a pharmaceutically acceptable salt thereof; and a pharmaceutically accepted carrier."
And it's illustrated by that top structure shown above - the incorrect one. That is the only chemical structure that appears in the patent, and it does so again and again. All the other claims are written dependent on Claim 1, for treatment of different varieties of tumors, etc. So I don't see any way around it: the El-Deiry patent unambiguously claims the use of one particular compound, and it's the wrong compound. In fact, if you wanted to go to the trouble, you could probably invalidate the whole thing, because it can be shown (and has been) that the chemical structure in Claim 1 does not produce any of the data used to back up the claims. It isn't active at all.
And that makes this statement from the C&E News article a bit hard to comprehend: "Lee Schalop, Oncoceutics’ chief business officer, tells C&EN that the chemical structure is not relevant to Oncoceutics’ underlying invention. Plans for the clinical trials of TIC10 are moving forward." I don't see how. A quick look through the patent databases does not show me anything else that Oncoceutics could have that would mitigate this problem, although I'd be glad to be corrected on this point. Their key patent, or what looks like it to me, has been blown up. What do they own? Anything? But that said, it's not clear what Sorrento owns, either. The C&E News article quotes two disinterested patent attorneys as saying that Sorrento's position isn't very clear, although the company says that its claims have been written with these problems in mind. Could, for example, identifying the active form have been within the abilities of someone skilled in the art? That application doesn't seem to have published yet, so we'll see what they have at that point.
But let's wind up by emphasizing that "skilled in the art" point. As a chemist, you'd expect me to say this, but this whole problem was caused by a lack of input from a skilled medicinal chemist. El-Deiry's lab has plenty of expertise in cancer biology, but when it comes to chemistry, it looks like they just took what was on the label and ran with it. You never do that, though. You never, ever, advance a compound as a serious candidate without at least resynthesizing it, and you never patent a compound without making sure that you're patenting the right thing. What's more, the Oncoceutics patent estate in this area, unless I'm missing some applications that haven't published yet, looks very, very thin.
One compound? You find one compound that works and you figure that it's time to form a company and take it into clinical trials, because one compound equals one drug? I was very surprised, when I saw the patent, that there was no Markush structure and no mention of any analogs whatsoever. No medicinal chemist would look at a single hit out of the NCI collection and say "Well, we're done - let's patent that one single compound and go cure glioblastoma". And no competent medicinal chemist would look at that one hit and say "Yep, LC/MS matches what's on the label - time to declare it our development candidate". There was (to my eyes) a painfully inadequate chemistry follow-through on TCI10, and the price for that is now being paid. Big time.
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May 7, 2014
There's a piece up at Vox about some changes over the last few years at the US patent office. This will probably not come as good news to those people (and I'm one of them) who think that too much crap makes it through the system as is, but it appears that the PTO is granting more applications than ever.
Vox lays the blame on the policies of David Kappos, appointed by President Obama in 2008. There certainly does seem to be an inflection point in the allowance rate. The two lines reflect the work of some researches at Virginia, who adjust for the number of re-applicant patents. That makes the real allowance rate over ninety per cent for new patents, which just has to be too high. (By the way, Vox really should rethink their tasteful color schemes; two different shades of butterscotch for a chart?)
Most pharma patents get granted already, I'd say. But that's because we're largely patenting new chemical matter, and it's a lot harder to argue about that. Patent quality has always been higher for new drugs than it is in many other areas, as disturbing a thought as that may be. So what else has been let through?
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May 6, 2014
Here's an article from the Independent on the legal battles that are underway about CRISPR technology. On one level, it can be a somewhat ugly story, but it also shows how much of a discovery the technique has been, that people are willing to fight for the rights to it so vigorously. But it's going to take a lot of straightening out:
On the one side is a consortium of world-class researchers led by French-born Professor Emmanuelle Charpentier who made a key discovery behind the Crispr gene editing technique and has been promised $25m (£16m) by a group of venture capitalists to commercialise her invention for medical use.
On the other side is her former colleague and the co-discoverer of the gene-editing process, Professor Jennifer Doudna of the University of California, Berkeley, who has joined a rival consortium of researchers with $43m in venture capital to advance the Crispr technique into the clinic.
Each group has recruited a formidable panel of senior scientists as advisers. The Charpentier team, called Crispr Therapeutics, includes Nobel Laureate Craig Mello, the co-discoverer of a gene-silencing technique known as RNAi, and Daniel Anderson of the Massachusetts Institute of Technology, who was the first person to show that Crispr can cure a genetic disease in an adult animal.
Meanwhile the Doudna team, known as Editas Medicine, includes the Harvard geneticist George Church, a pioneer in synthetic biology, and Feng Zhang of MIT and the Broad Institute, who successfully managed to get Crispr to work in human cells and was this month awarded the first US patent on the technique – much to the dismay of Professor Charpentier.
Another crack at human gene therapy, that's one of the biggest engines driving all this. I hope that the legal wrangling doesn't slow that down. . .
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May 1, 2014
Eli Lilly has been complaining the U. S. Government for a while about the Canadian regulatory authorities, after they invalidated the company's patents for Strattera and Zyprexa a few years ago. Unfortunately for them, as Ed Silverman reports, the U. S. Trade Representative has refused to put Canada on the list of countries that don't respect intellectual property treaties (and this despite several members of Congress joining in the request). The office has mentioned that the Canadian law is a bit fuzzy, and that the mechanisms to appeal it are not clear, but they're not going anywhere near as far as Lilly wanted. The company is suing the Canadian government under NAFTA provisions, but that's going to take a while to bear results, if it ever does.
So why were the patents invalidated in the first place? They're holding up everywhere else. The Canadian generic drug industry challenged them under what may be a unique provision of Canadian patent law: the "promise" doctrine. If a company files a selection patent, the basis for which is that a particular form of the invention is in fact preferable, then under Canadian law the patent can be invalidated if that "promise" is not borne out by data:
In the mid 2000s one could start to see Canadian patent cases “turning” somewhat. Before this, the general sense was that a mere scintilla of utility was enough to obtain a patent. However, if the patentee made an explicit and unequivocal “Promise” of a certain use or result, recent cases have held the patentee to this result. Eli Lilly’s selection patent for an antipsychotic agent (olanzapine) was first held invalid in 2007 (in preliminary type proceedings) (2007 FC 596). Eli Lilly’s patent promised that its compound was better than the rest. However Eli Lilly had not actually determined its Promise, nor was their Promise soundly predictable (ie. it was a guess).
I'm definitely not a patent attorney, but I don't know of any other jurisdiction that puts the bar up quite that high. My impression is that if a company has demonstrated that it's willing to go to the trouble of filing a selection patent, that this is enough of an indication that it feels that there's something special about its claims. You have to show real advantages versus the prior art (things that are presumably already known), but not against your own initial filing. We'll see how far this gets (and if any other countries are tempted to put in a promise clause of their own, as a handy tool for patent invalidation). India, with its large generic industry, might be a candidate, if they don't have something like this.
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April 8, 2014
So, can you patent naturally occurring substances, or not? That's a rather complicated question, and some recent Supreme Court decisions have recomplicated it in US patent law. Mayo v. Prometheus and Assoc. Mol. Pathology v. Myriad Genetics. The latter, especially, has sent the PTO (and the IP lawyers) back to staring out their respective windows, thinking about what to do next.
The Patent Office has now issued new guidelines for its examiners in light of these rulings, though, and things may be changing. Previous standards for patenting naturally occurring compounds have been tightened up - if I'm reading this correctly, no longer is the process of isolation and purification itself seen as enough of a modification to make a case for patentability. The four "judicial exception" categories, to be used in patentability decisions, are (1) abstract ideas, (2) laws of nature, (3) natural phenomena, and (4) natural products. And examiners are specifically asked to determine if a patent application's claims recite something "significantly different" than these.
Here's the blog of an IP firm that thinks that the USPTO has gone too far:
Now we learn that grant of these and similar patents were mistakes, that 100 years of consistent practice in the field of patents was wrong, that what was invented was no more than products of nature without significant structural difference from the naturally-occurring materials, and that the USPTO will endeavour to avoid such mistakes in future. . .
. . .Whatever workable rule of law is derivable from Prometheus, it is apparent from the opinion of Justice Breyer that it was not the Court’s intention to bring about a radical change in pharmaceutical practice. The opinion gives a warning against undue breadth:
“The Court has recognized, however, that too broad an interpretation of this exclusionary principle could eviscerate patent law. For all inventions at some level embody, use, reflect, rest upon, or apply laws of nature, natural phenomena, or abstract ideas.”
The problem (and it's the usual problem with fresh patent law) is that we really don't know what the phrases in the decisions or guidance mean, in practice, until there's been some practice. This is going to be thrashed out application by application, lawsuit by lawsuit, until some new equilibrium is reached. Right now, though, if you're trying to patent something that could be considered an isolated natural product, your life has become much more complicated and uncertain. Here's another IP law firm:
What is the "significantly different" standard? With respect to natural products, the Guidance offers that what is claimed should be "non-naturally occurring and markedly different in structure from the naturally occurring products". Again, it is unclear at this point how different "markedly different" will be. How different it needs to be will be worked out on a case-by-case basis, beginning at the level of the patent examiner at the USPTO.
So how can you protect your IP if it involves subject matter that could be considered a "product of nature" by a US examiner? Since we don't yet really know how different "markedly different" is, one prudent strategy would be to include multiple claims having varying degrees of modifications relative to the naturally occurring thing, to the extent these makes sense commercially and scientifically. The more different your claimed product is from the naturally occurring thing, the more likely it is to be considered patent eligible by the USPTO.
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January 22, 2014
I've been sent a copy of Scaffold Hopping in Medicinal Chemistry, a new volume from Wiley, edited by Nathan Brown of the Institute of Cancer Research in London. There are eighteen chapters - five on identifying and characterizing scaffolds to start with, ten on various computational approaches to scaffold-hopping, and three case histories.
One of the things you realize quickly when you starting thinking about (or reading about) that topic is that scaffolds are in the eye of the beholder, and that's what those first chapters are trying to come to grips with. Figuring out the "maximum common substructure" of a large group of analogs, for example, is not an easy problem at all, certainly not by eyeballing, and not through computational means, either (it's not solvable in polynomial time, if we want to get formal about it). One chemist will look at a pile of compounds and say "Oh yeah, the isoxazoles from Project XYZ", while someone who hasn't seen them before might say "Hmm, a bunch of amide heterocycles" or "A bunch of heterobiaryls" or what have you.
Another big question is how far you have to move in order to qualify as having hopped to another scaffold. My own preference is strictly empirical: if you've made a change that would be big enough to make most people draw a new Markush structure compared to your current series, you've scaffold-hopped. Ideally, you've kept the activity at your primary target, but changed it in the counterscreens or changed the ADMET properties. That's not to say that all these changes are going to be beneficial - people try this sort of thing all the time and wipe out the primary activity, or pick up even more clearance or hERG than the original series had. But those are the breaks.
And those are the main reasons that people do this sort of thing: to work out of a patent corner, to fix selectivity, or to get better properties. The appeal is that you might be able to address these without jettisoning everything you learned about the SAR of the previous compounds. If this is a topic of interest, especially from the computational angles, this book is certainly worth a look.
+ TrackBacks (0) | Category: Drug Development | Patents and IP | Pharmacokinetics
December 13, 2013
Here's some good news for open (free) access to chemical information. A company called SureChem was trying to make a business out of chemical patent information, but had to fold. They've donated their database to the EMBL folks, and now we have SureChEMBL. At the moment, that link is taking me to the former SureChem site, but no doubt that's changing shortly.
This will give access to millions of chemical structures in patents, a resource that's been hard to search without laying out some pretty noticeable money. This isn't just the database dump, either - the software has been donated, too, so things will stay up to date:
SureChEMBL takes feeds of full text patents, identifies chemical objects from either the in-line text or from images and adds 2-D chemical structures. This is then loaded into a database and is searchable by chemical structure, so you can do substructure, similarity searching and so forth - all the good things you'd expect from a chemical database. This chemical search functionality is unavailable from the public, published patent documents, and is really essential for anyone seriously using the patent literature. Oh, and the system does this live, so as patents are published, they are processed and added to the system - the delay between publication and structures being available in SureChEMBL is about a day when converted from text, and a few days when converted from image sources.
Chemical Abstracts, Reaxsys, and the others in that business should take note: if they want people to keep paying for their systems, they'll need to keep providing more value for the money. Good news all around.
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November 11, 2013
Here's a new paper in PlOSOne on drug development over the past 20 years. The authors are using a large database of patents and open literature publications, and trying to draw connections between those two, and between individual drug targets and the number of compounds that have been disclosed against them. Their explanation of patents and publications is a good one:
. . .We have been unable to find any formal description of the information flow between these two document types but it can be briefly described as follows. Drug discovery project teams typically apply for patents to claim and protect the chemical space around their lead series from which clinical development candidates may be chosen. This sets the minimum time between the generation of data and its disclosure to 18 months. In practice, this is usually extended, not only by the time necessary for collating the data and drafting the application but also where strategic choices may be made to file later in the development cycle to maximise the patent term. It is also common to file separate applications for each distinct chemical series the team is progressing.
While some drug discovery operations may eschew non-patent disclosure entirely, it is nevertheless common practice (and has business advantages) for project teams to submit papers to journals that include some of the same structures and data from their patents. While the criteria for inventorship are different than for authorship, there are typically team members in-common between the two types of attribution. Journal publications may or may not identify the lead compound by linking the structure to a code name, depending on how far this may have progressed as a clinical candidate.
The time lag can vary between submitting manuscripts immediately after filing, waiting until the application has published, deferring publication until a project has been discontinued, or the code name may never be publically resolvable to a structure. A recent comparison showed that 6% of compound structures exemplified in patents were also published in journal articles. While the patterns described above will be typical for pharmaceutical and biotechnology companies, the situation in the academic sector differs in a number of respects. Universities and research institutions are publishing increasing numbers of patents for bioactive compounds but their embargo times for publication and/or upload of screening results to open repositories, such as PubChem BioAssay, are generally shorter.
There are also a couple of important factors to keep in mind during the rest of the analysis. The authors point out that their database includes a substantial number of "compounds" which are not small, drug-like molecules (these are antibodies, proteins, large natural products, and so on). (In total, from 1991 to 2010 they have about one million compounds from journal articles and nearly three million from patents). And on the "target" side of the database, there are a significant number of counterscreens included which are not drug targets as such, so it might be better to call the whole thing a compound-to-protein mapping exercise. That said, what did they find?
Here's the chart of compounds/target, by year. The peak and decline around 2005 is quite noticeable, and is corroborated by a search through the PCT patent database, which shows a plateau in pharmaceutical patents around this time (which has continued until now, by the way).
Looking at the target side of things, with those warnings above kept in mind, shows a different picture. The journal-publication side of things really has shown an increase over the last ten years, with an apparent inflection point in the early 2000s. What happened? I'd be very surprised if the answer didn't turn out to be genomics. If you want to see the most proximal effect of the human genomics frenzy from around that time, there you have it in the way that curve bends around 2001. Year-on-year, though (see the full paper for that chart), the targets mentioned in journal publications seem to have peaked in 2008 or so, and have either plateaued or actually started to come back down since then. Update: Fixed the second chart, which had been a duplicate of the first).
The authors go on to track a number of individual targets by their mentions in patents and journals, and you can certainly see a lot of rise-and-fall stories over the last 20 years. Those actual years should not be over-interpreted, though, because of the delays (mentioned above) in patenting, and the even longer delays, in some cases, for journal publication from inside pharma organizations.
So what's going on with the apparent decline in output? The authors have some ideas, as do (I'm sure) readers of this site. Some of those ideas probably overlap pretty well:
While consideration of all possible causative factors is outside the scope of this work it could be speculated that the dominant causal effect on global output is mergers and acquisition activity (M&A) among pharmaceutical companies. The consequences of this include target portfolio consolidations and the combining of screening collections. This also reduces the number of large units competing in the production of medicinal chemistry IP. A second related factor is less scientists engaged in generating output. Support for the former is provided by the deduction that NME output is directly related to the number of companies and for the latter, a report that US pharmaceutical companies are estimated to have lost 300,000 jobs since 2000. There are other plausible contributory factors where finding corroborative data is difficult but nonetheless deserve comment. Firstly, patent filing and maintenance costs will have risen at approximately the same rate as compound numbers. Therefore part of the decrease could simply be due to companies, quasi-synchronously, reducing their applications to control costs. While this happened for novel sequence filings over the period of 1995–2000, we are neither aware any of data source against which this hypothesis could be explicitly tested for chemical patenting nor any reports that might support it. Similarly, it is difficult to test the hypothesis of resource switching from “R” to “D” as a response to declining NCE approvals. Our data certainly infer the shrinking of “R” but there are no obvious metrics delineating a concomitant expansion of “D”. A third possible factor, a shift in the small-molecule:biologicals