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Topic: Markush Structures in Patents  (Read 5263 times)

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Offline curiouscat

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Markush Structures in Patents
« on: December 04, 2012, 08:25:36 AM »
How broad are Markush structures allowed to be in  Patents? I often see patents use them but the examples hardly cover a small subset of the potential combinations? That seems broad and unfair.

Anyone know what the typical rules are?

Offline discodermolide

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Re: Markush Structures in Patents
« Reply #1 on: December 04, 2012, 08:28:46 AM »
They can probably be as broad or as narrow as you wish.
However, too broad and you may shoot yourself in the foot for any other patents in the same class of molecule.
Too narrow and the competition can spring in and gatecrash your patent. A discussion with your patent dept. usually helps.

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Offline curiouscat

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Re: Markush Structures in Patents
« Reply #2 on: December 04, 2012, 08:38:17 AM »
Quote
Too narrow and the competition can spring in and gatecrash your patent.

Yes. This I can see.

However, too broad and you may shoot yourself in the foot for any other patents in the same class of molecule.
Hmm...I didn't get this part. Why would you want a separate patent if you already have one that covers it? For time-extension purposes? 

I was thinking the strategy was "As broad as you can without the patent examiner objecting"

Quote
A discussion with your patent dept. usually helps.
Sure. :) I don't have any good ideas just yet.

The question was perhaps academic; had to read through a lot of patents last week.

Offline discodermolide

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Re: Markush Structures in Patents
« Reply #3 on: December 04, 2012, 08:52:50 AM »
Perhaps one of the compounds in the "broad patent" shows unexpected activity in a different direction. Then you can't really protect it except as a use patent and it can be very hard to break out of the series. But once again the competition can spring in. We often were faced with this problem in Pharma. When to patent, how broad the scope, if to patent at all.
We always went through the competition's patents to find uncovered compounds.
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Offline curiouscat

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Re: Markush Structures in Patents
« Reply #4 on: December 04, 2012, 09:05:14 AM »
Perhaps one of the compounds in the "broad patent" shows unexpected activity in a different direction. Then you can't really protect it except as a use patent and it can be very hard to break out of the series. But once again the competition can spring in. We often were faced with this problem in Pharma. When to patent, how broad the scope, if to patent at all.
We always went through the competition's patents to find uncovered compounds.

I hadn't thought about these angles at all. Thanks.

I was merely thinking how far does the patent office allow you to extrapolate? Often the patents seemed like they tested 3 compounds and claimed patents over 30.  If heptanol works for an application is it obvious to claim octanol will too? Something like that.

Offline discodermolide

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Re: Markush Structures in Patents
« Reply #5 on: December 04, 2012, 09:34:55 AM »
No I don't think that if hexanol works that you can claim octanol.
The invention must be something that the expert would not expect from the series of compound.
Now if hexanol clears your stops your headache and octanol does as well then you can't patent octanol separately. But, if octanol suddenly shows anti-cancer activity then you can claim for that because it is unexpected.
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Offline orgopete

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Re: Markush Structures in Patents
« Reply #6 on: December 04, 2012, 09:47:04 AM »
When a patent is published, it is considered valid on its face. Howevwer it is really like a contract, it is only as valid as its provisions provide. So as disco noted, if a patent is a use patent rather than a composition of matter patent, then the provisions are only as valid as the stated use is present.

For example, if you had applied for a patent on acetyl salicylic acid as an analgesic, you would want to cover the salts as well, thinking they are a different way to administer the active ingredient, the acid. So you proceed to cover the group I salts, group II, salts, group III, etc. Because you know the bond strength of the higher group salts will not be the same as the alkali metal salts, you would separate these into different claims. There will become a point at which you cannot make and test everything you will have claimed to have analgesic properties, some of your claims will be false or invalid.

If someone were to make a silver salt and discover it did not have any analgesic activity, they could render that claim of your patent invalid and unenforceable. You will find this claim to be among the broadest of claims only. There would be subsequent narrower and more specific claims that would remain enforce.

This is generally how all patents are structured. They are like an inverted pyramid, with very broad claims on top and very narrow claims on the bottom. Very broad claims may or may not be enforceable. This will depend upon the claims, the use, the market, the obviousness, and the wills of the patent holder and infringer. A patent covering a multibillion dollar product will result in greater opposition than an idle patent.

At the discovery end, I did not worry greatly if a compound was covered in some generic Markush claim. However, that could be a major hurdle if the compound were to become a potential commercial product. It is difficult to predict how a generic claim may affect enforceability. Pharmaceutical chemistry appears to allow more "me too" patents than other areas. Your mileage may vary.
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Offline curiouscat

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Re: Markush Structures in Patents
« Reply #7 on: December 04, 2012, 09:53:47 AM »

If someone were to make a silver salt and discover it did not have any analgesic activity, they could render that claim of your patent invalid and unenforceable. You will find this claim to be among the broadest of claims only. There would be subsequent narrower and more specific claims that would remain enforce.


But what would the competitor's incentive be then to follow up and invalidate a claim that is anyways useless to him. i.e. if the Silver salt doesn't work what's the good to getting it stricken out of your claim.

Wouldn't it make more sense to invalidate the whole patent if a subsumed  claim was patently false? That'd be a good incentive two ways: (1) To prevent inventors from filing overly broad claims (2) To incentivize reproduction and invalidation of untrue claims by competitors?

What do people think? Maybe I don't understand the intricacies.

I'm just frustrated reading patents with broad claims that don't seem to necessarily follow from their examples at all.

Offline orgopete

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Re: Markush Structures in Patents
« Reply #8 on: December 04, 2012, 04:17:51 PM »
No, we only want the claim to be invalid. We don't want to allow others to profit from any oversights of the patentee. We don't want to allow the entire patent to be overturned just so a competitor could make and sell the sodium or potassium salt because they discovered any example of the broadest claims to be invalid. We also don't want to limit the patentee from claiming a salt that might only have 3/4 of the activity in fear that could invalidate a patent, yet still have marketable activity. The borders are gray. If a claim seems overly broad, it probably is. It may be there to frighten a novice away. You should not fear those broad claims unnecessarily. However, if the broad claims actually cover the kernel of the patent, you would be infringing upon that patent.

If you discovered the silver salt made a superior imaging agent, I doubt a generic claim in an analgesia patent would be an impediment. I doubt the patent holder would sue for infringement. You should read the claims more strictly. If it is a broad claim to analgesic activity, then it is also not a claim as an imaging agent. Again, it is difficult to generalize, but I would not be too worried about broad generic claims, except if your objective is to subvert the patentee's claims. For the purpose of this forum, I don't expect that is anyone's desire.

Patent claims work two ways. To me the surprising aspect is how similar many pharmaceutical patents are to prior art. I sometimes wonder if any generic claims are upheld. If you discovered and commercialized a drug, wouldn't you be frustrated if a competitor made and commercialized a methyl or chloro analog? I think part of the similarity of drugs is embodied in the obviousness. They probably argue that a particular compound is not obvious that it should have the activity it does. Adding a substituent can also have significant negative effects, so an improvement may be unobvious.

The current patent structure really has a simple consolidating effect. An alternative would require multiple single compound patents which would contain a great deal of redundancy. I think the question that should be asked is how any alternate monopolistic license system can serve the public good.
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Offline fledarmus

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Re: Markush Structures in Patents
« Reply #9 on: December 05, 2012, 08:38:51 AM »
There are some relatively simple rules that govern how broad a patent can be. In terms of Markush structures, the following rules tend to be the ones that cause problems:

1) the invention must be enabled by the patent specification. That means that a skilled person in your field must be able to practice your invention relying only on your patent and his basic knowledge of the field without having to carry out more than a modest amount of experimentation. If you claim new compounds that are useful for new treatments, you also have to describe how to make those compounds and how to use them for treatments. In general, the more compounds you claim, the more specific examples you have to provide to demonstrate that your synthetic techniques are sufficient to enable a good synthesist to make any compound that you claim.

2) the claims must specifically describe the limits of the invention. This means that a skilled person in your field must be able to read your patent and know exactly which compounds are being claimed. With Markush claims, if you write them broadly enough, the number of compounds covered becomes enormous, and the examiner at some point will decide that it wouldn't really be possible to determine what compounds were not covered.

And of course the two most people are familiar with:

3) the invention must be novel. This means that none of the possible variants of the compounds you have put into your Markush structure can already exist, if you are claiming those structures as your invention. This can require some very careful patent writing to be sure that as many novel compounds are included without including anything in the prior art.

4) the invention must be non-obvious. This is a really tough one. Is simple replacement of a methyl group with a chloro group obvious? In some cases, maybe yes, in some cases, maybe no. If your patent is written as broadly as it should be, there will almost always be some back-and-forth with the examiner on this point. The examiner's job is to act on behalf of the American people. In return for you making your magnificent new invention public, the American people will give you a short term exclusive right to the invention, but the examiner tries to ensure that you aren't getting exclusive rights to something the public already owns.

Another rule that can sometimes be a nightmare to work around -

5) You only get one invention per patent. That doesn't necessarily mean only one compound, nor does it mean that the invention can't be used in different ways, but if your claims start to get too out of hand, the examiner may limit the amount of material you can include in a single patent by issuing a restriction requirement. The examiner divides your material up into the different inventions he sees in the material, then forces you to select one invention that will be examined for the patent. If you want to patent the other inventions, you are allowed to file additional patent applications (called Divisional Applications, or divisionals) to cover those additional inventions.

One that has been alluded to previously on this thread:

6) the invention has to be useful. That means it has to actually work! If you can't demonstrate to the examiner that your invention is good for something, it can't get patented. That doesn't mean that finding one example in a broad claim that doesn't work is enough to invalidate the patent, but if you are trying to patent a process to produce aspirin and it doesn't in fact produce aspirin, then it will not receive a patent. If you are trying to patent a perpetual motion machine or a free energy machine, you will be required to actually build one and prove that it works before you will get a patent. (Incidentally, treatments for baldness used to be in this list, until one was actually found!)

To Orgopete's point about the generic claims covering prior art - a good patent application will be written with claims going from very broad to very narrow. You try to include as much in your invention as you can in the very broad claims, and in the very narrow claims you include as exact a description as possible of the commercial embodiment of your invention, if you know what that will look like. Then the examiner will decide that your broadest claim is anticipated by the prior art (meaning that somewhere in the prior art, compounds which are exactly like the ones you claim have already been made), that some of your narrower claims are made obvious by the prior art (meaning that any skilled worker would have known to make the compounds without seeing your patent, just based on the prior art), and possibly that your narrowest claims are allowable, (meaning that they are novel, non-obvious, useful, enabled by your specification, and clear as to the limits of the invention). There then follows a series of negotiations with the patent examiner in the form of Office Actions and Responses by which you try to prove that your rejected claims are in fact patentable and the examiner describes in great detail why they are not, and if you can come to an agreement, you get a patent. If you can't, there is an appeal board within the patent office where you can go to try to get the examiner overruled, and if that doesn't work, you go to the Federal Court system.

The point of that last paragraph is that if you read published patent applications rather than actual patents, you will see claims that are far broader than anything which can possibly be allowed. In drug patents especially, you may see claims that would cover millions of individual chemical structures in the broadest claim. Even though there may be a couple of hundred individual examples of compounds listed in the specification, that is usually only sufficient to claim a couple of thousand compounds in an allowed patent unless it is completely virgin territory synthetically. In many countries outside the United States, it is even tighter - in some places, you actually have to prove that you have synthesized every compound that you claim. That means you need to show an example for every possible structure in your Markush space. These makes it almost impossible to prevent a competitor in those countries from making very close analogues to your compounds - it just isn't possible to make and characterize every compound in any chemical class.

Wow, this got long, didn't it? Let me just make one more point. Even if the very broad generic claims in a patent are not allowed, they are still prior art for any other patent that comes along. You may not get the patent yourself on your broadest claim, but if it is sufficiently enable, you will prevent anybody else from getting a patent based on your prior publication as a patent application.

I hope some of this is useful.




Offline curiouscat

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Re: Markush Structures in Patents
« Reply #10 on: December 05, 2012, 09:49:23 AM »
Quote
I hope some of this is useful.

All of it. Thank you!

Offline orgopete

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Re: Markush Structures in Patents
« Reply #11 on: December 05, 2012, 01:12:18 PM »

The point of that last paragraph is that if you read published patent applications rather than actual patents, you will see claims that are far broader than anything which can possibly be allowed. In drug patents especially, you may see claims that would cover millions of individual chemical structures in the broadest claim. Even though there may be a couple of hundred individual examples of compounds listed in the specification, that is usually only sufficient to claim a couple of thousand compounds in an allowed patent unless it is completely virgin territory synthetically. In many countries outside the United States, it is even tighter - in some places, you actually have to prove that you have synthesized every compound that you claim. That means you need to show an example for every possible structure in your Markush space. These makes it almost impossible to prevent a competitor in those countries from making very close analogues to your compounds - it just isn't possible to make and characterize every compound in any chemical class.

Wow, this got long, didn't it? Let me just make one more point. Even if the very broad generic claims in a patent are not allowed, they are still prior art for any other patent that comes along. You may not get the patent yourself on your broadest claim, but if it is sufficiently enable, you will prevent anybody else from getting a patent based on your prior publication as a patent application.


Note that fledarmus has written as one experienced in the art and I agree with. See the highlighted text. Generic structures help provide some protection. While patents do have their limitations, they are also useful publications and one should not fear them nor their generic claims. Again, reflect on the highlighted text.
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Offline curiouscat

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Re: Markush Structures in Patents
« Reply #12 on: December 05, 2012, 01:27:03 PM »
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If you are trying to patent a perpetual motion machine or a free energy machine, you will be required to actually build one and prove that it works before you will get a patent. (Incidentally, treatments for baldness used to be in this list, until one was actually found!)

Outside of these exceptions, though, there's no validation of the data presented in a patent, right? One just believes that the patentee got the results and yields that he claims he did?

Offline fledarmus

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Re: Markush Structures in Patents
« Reply #13 on: December 05, 2012, 02:55:32 PM »
Quote
If you are trying to patent a perpetual motion machine or a free energy machine, you will be required to actually build one and prove that it works before you will get a patent. (Incidentally, treatments for baldness used to be in this list, until one was actually found!)

Outside of these exceptions, though, there's no validation of the data presented in a patent, right? One just believes that the patentee got the results and yields that he claims he did?

Well, yes and no. The patent examiner is supposed to be an expert in the field he or she is examining, and if the science in the patent flies in the face of everything that is known in the field, the standard of proof can be quite a bit higher, even up to requiring a working model of the invention. In general, however, that proof is simply an affidavit from the inventor or sometimes from a second expert in the field that has replicated the inventor's work. The examiners do not actually replicate any of the work themselves to check it.

Remember, though, that the patent has to be enabling - that means that the material in the patent has to work, without any excessive experimentation, in the hands of another person skilled in the field. A patent can be declared invalid in a court of law if the invention doesn't actually work, if anybody is willing to go through the time and money to challenge it. If the only person that can get it to work is the inventor, then obviously he has left something out of the patent that is required for it to be enabled.

Offline curiouscat

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Re: Markush Structures in Patents
« Reply #14 on: December 06, 2012, 02:09:35 AM »
Well, yes and no. The patent examiner is supposed to be an expert in the field he or she is examining, and if the science in the patent flies in the face of everything that is known in the field, the standard of proof can be quite a bit higher, even up to requiring a working model of the invention.

Sure, I get what you mean. I didn't have an obviously bogus or wacky invention in mind.

Here's the sort of case I had in mind: Let's say there's a lot of interest in finding a catalyst that will convert A to B at room temperatures. Based on the underlying science it is clear that some metal catalyst class X is likely to work at least in theory. Of course, one can't know until one really tests so it isn't "obvious" but no one has tried it before so it if X does indeed work it will be both novel and useful.

A couple of competitors start working on this but the experimental program is expected to take ~2 years.

With this background what stops Competitor-Foo from proactively filing a patent with essentially reasonable-looking but made-up data claiming X actually works well and then keep continuing its search.

That X might work is indeed reasonable; so nothing flies in the way of known science even to the patent examiner. If X does indeed work, no one is the wiser and Foo gets to enjoy the patent.

In case it turns out later that X does not work what incentive will the competitors have to litigate against Foo and get the speculative claim struck down? After all, they all now know that X is a dud. Ok, say even out of pure spite they did prosecute the claim, Foo forgoes the patent. No fines, no penalty, no downside.

Isn't early filing on speculative or made-up data a win win situation in such cases? Is the affidavit the only thing stopping this sort of skulduggery?

PS.

This isn't entirely hypothetical. I've had several occasions when I tried setting up an experiment based on the conditions mentioned in a Patent but got yields no where close to what they had reported. Of course, knowing how finicky these things can be I assumed it was something wrong in my setup, reagents etc.  But in hindsight, I wonder what if the patent had it wrong?

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