About this Author
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

Chemistry and Drug Data: Drugbank
Chempedia Lab
Synthetic Pages
Organic Chemistry Portal
Not Voodoo

Chemistry and Pharma Blogs:
Org Prep Daily
The Haystack
A New Merck, Reviewed
Liberal Arts Chemistry
Electron Pusher
All Things Metathesis
C&E News Blogs
Chemiotics II
Chemical Space
Noel O'Blog
In Vivo Blog
Terra Sigilatta
BBSRC/Douglas Kell
Realizations in Biostatistics
ChemSpider Blog
Organic Chem - Education & Industry
Pharma Strategy Blog
No Name No Slogan
Practical Fragments
The Curious Wavefunction
Natural Product Man
Fragment Literature
Chemistry World Blog
Synthetic Nature
Chemistry Blog
Synthesizing Ideas
Eye on FDA
Chemical Forums
Symyx Blog
Sceptical Chymist
Lamentations on Chemistry
Computational Organic Chemistry
Mining Drugs
Henry Rzepa

Science Blogs and News:
Bad Science
The Loom
Uncertain Principles
Fierce Biotech
Blogs for Industry
Omics! Omics!
Young Female Scientist
Notional Slurry
Nobel Intent
SciTech Daily
Science Blog
Gene Expression (I)
Gene Expression (II)
Adventures in Ethics and Science
Transterrestrial Musings
Slashdot Science
Cosmic Variance
Biology News Net

Medical Blogs
DB's Medical Rants
Science-Based Medicine
Respectful Insolence
Diabetes Mine

Economics and Business
Marginal Revolution
The Volokh Conspiracy
Knowledge Problem

Politics / Current Events
Virginia Postrel
Belmont Club
Mickey Kaus

Belles Lettres
Uncouth Reflections
Arts and Letters Daily
In the Pipeline: Don't miss Derek Lowe's excellent commentary on drug discovery and the pharma industry in general at In the Pipeline

In the Pipeline

« More "More Scientists" Debate | Main | Watch Your Cell Assays »

June 18, 2012

What Compound Are You Trying to Patent, Again?

Email This Entry

Posted by Derek

I sure hope that Sanofi doesn't really want to own these compounds in this recent patent filing. (Thanks to a reader at another company for sending this along!) But what are the odds of that, given that they went to all the trouble of filing on them?
The reason I say that is while the compounds are drawn correctly in the experimental section (the part that was done by the chemists), the description and the claims (which were done by the lawyers) have the wrong structure in them. Wrong, as in doesn't match the experimentals, and wrong as in doesn't exist, either. The patent is directed towards indolizine derivatives, but the drawings in the claims are not indolizines, but are rather some sort of charged species whose name I do not exactly have at the tip of my tongue. Not that they're drawn any charges on anything, naturally, even though all those nitrogens have four bonds on them.

Does this invalidate the patent? Probably not, although I am most certainly not a lawyer. The names, as written, still seem to be fine. Does this complicate efforts to defend the chemical matter? You'd have to think so. Does it make people at Sanofi look like they either don't know much chemistry, aren't paying much attention, or both? Absolutely.

Comments (25) + TrackBacks (0) | Category: Patents and IP


1. Will on June 18, 2012 9:16 AM writes...

The general standard for correcting an error in the specification is whether the intended structure would have been readily apparent to an ordinary chemist. If the experimental section does in fact show more legitimate structures, it should not be too big a problem to convince an examiner to allow the change. Much mischief could be wrought though, if a patent issuing from this gets into litigation,

Permalink to Comment

2. DLIB on June 18, 2012 9:42 AM writes...

Will is spot on....when the rubber hits the road in litigation you would not want to deal with this.

Permalink to Comment

3. Rick Wobbe on June 18, 2012 9:45 AM writes...

Bear in mind that this is an application, not an issued patent, and the rules for making corrections would allow this unfortunate error to be fixed with no damage to the strength of the eventual patent(s). Sad to say, mistakes like this happen all the time. Perhaps if more were called out like this, however, they would get less common.

Permalink to Comment

4. kissthechemist on June 18, 2012 9:49 AM writes...

I've contributed to patents and I know how there's just endless reams of seemingly meaningless detail to check, but what do you look like if the FRONT PAGE with the BIG STRUCTURE ON IT is wrong? Feeling smart? Probably not.

Note to self. Check everything. Done checking? OK now check the REALLY OBVIOUS bits again.

Permalink to Comment

5. PPedroso on June 18, 2012 9:57 AM writes...


that's a good use to all the mediocre chemists out there, just give them patents and ask them if the intended structure are apparent to them!

Permalink to Comment

6. NoDrugsNoJobs on June 18, 2012 10:09 AM writes...

Is that a tautomer of the protonated form of the indolizine?

Permalink to Comment

7. newnickname on June 18, 2012 10:15 AM writes...

At companies that use outside law firms, stuff like this sometimes results from shifting work to the brother or niece or cousin of the Chief [Pick Any] Officer. Probably not the case at Sanofi.

I always asked to proof read the patents before filing. There were ALWAYS horrendous chemistry errors. Things I had already asked to be corrected would come back unchanged or changed for the worse. Of course, the lawyers were getting $N per hour to do the writing, I was getting around $(N/15) per hour to correct their mess. Probably even less as it wasn't "work" so I was doing the proofing after hours.

But it was always a pleasure to talk with them about their mistakes ... in six minute increments.

(At one place I worked, we spent more on lawyers than on research. That strategy did not keep us in business.)

Permalink to Comment

8. Will on June 18, 2012 10:22 AM writes...

what's especially shameful is that most chem drawing programs will automatically insert a positive charge on the nitrogen or otherwise indicate the valency is incorrect, you'd have to take affirmative steps to "clean up" the error in the structure

Permalink to Comment

9. gya on June 18, 2012 10:45 AM writes...

along the lines of structural errors. check out pg 1 of RB Woodward's phd thesis-second paragraph total 'sythesis'
pg 2-in the third structure drawn...oesterone contains the famous 'texas carbon'. whoops!
and that's just 2 pgs in. even the great ones make mistakes.

stoltz has the link to his thesis here:

Permalink to Comment

10. Chris on June 18, 2012 11:06 AM writes...

Just out of curiosity (and not for this particular example) would this sort of error mean that the erroneous structure was now in the public domain and no longer patentable?

Permalink to Comment

11. NoDrugsNoJobs on June 18, 2012 11:27 AM writes...

#10 (Chris) - Most likely not. First of all, if we accept the structure is essentially untenable as written, then it is not enabled such that one of ordinary skill in the art can make and use it. Further, although utility is presumably established for the actual compounds made in the application, one could presumably not assume a credible utility for the funky structure (tautomer?) shown.

Permalink to Comment

12. Will on June 18, 2012 11:52 AM writes...

@ 10 and 11 - For a claim to the compound itself, utility is a not relevant in an anticipation analysis. The Sanofi application presumably doesn't describe how to make the quaternary compound, and so, as 11 points out, the question of novelty would hinge on whether an ordinary chemist could make the disclosed compound without undue experimentation.

Permalink to Comment

13. Kevin on June 18, 2012 12:48 PM writes...

My favorite claim section from a collaborator:

"... wherein R1, R2, R3, R4, R5, R6, R7 and R8 independently comprise: H, substituted or non-substituted alkyl, substituted or non-substituted alkoxy, a halogen (F, Cl, Br, I, and At)..."

So, um, who wants to demonstrate the chemistry on the At compound?

Permalink to Comment

14. anon on June 18, 2012 12:52 PM writes...

Is the pictured drug molecule a radiopharmaceutical? Kinda scary with that Americium atom attached.

Permalink to Comment

15. Patentguy on June 18, 2012 1:10 PM writes...

@14 Not sure if I am being whooshed here, but the specification describes the "Am" moiety as a substituted pyrrolidinyl or piperidinyl. These are therapeutics.

Permalink to Comment

16. petros on June 18, 2012 1:34 PM writes...

While Am may be defined as a substituted pyrrolidinyl or piperidinyl group Markush definitions should not include Atomic symbols!

Permalink to Comment

17. Jimmy on June 18, 2012 4:14 PM writes...

@ petros: Thanks for pointing out the obvious for those of us not familiar with the Actinides. I couldn't see why the actual structures didn't fall under the general structure otherwise.

Permalink to Comment

18. McChemist on June 18, 2012 7:21 PM writes...

I think that moiety is "A-r-n", written in a font with bad kerning. Not "A-m".

Permalink to Comment

19. McChemist on June 18, 2012 7:23 PM writes...

Whoops, going into the text, I see it is actually "A-m". Never mind.

Permalink to Comment

20. scrabbler on June 19, 2012 3:11 AM writes...

In the US, they can make the "obvious" correction. In Europe, they're probably screwed.

Permalink to Comment

21. scrabbler on June 19, 2012 3:12 AM writes...

In the US, they can make the "obvious" correction. In Europe, they're probably screwed.

Permalink to Comment

22. Thoryke on June 19, 2012 9:34 AM writes...

Isn't Sanofi the place where the CEO told the scientists they weren't really all that important, and they needed to get over thinking they were so essential to the enterprise?

Nice to see that showing up in the wash so quickly...

Permalink to Comment

23. The Heterocyclist on June 19, 2012 11:49 AM writes...

Just for fun... taking a stab at the compounds shown, crazy though they may be. Assuming one has a positive charge on the nitrogen, the compounds drawn would be formally derived by protonation of an indolizine at the bridgehead carbon, position 8a. I suppose you could call the compounds shown 8aH-indolizine salts (8aH-indoliziums?) They'd likely be highly acidic, donating the 8a proton to go back to the aromatic indolizine. This is analogous to protonation/deprotonation of pyrrole at C2.

Permalink to Comment

24. Nick K on June 19, 2012 2:51 PM writes...

Strange to see Sanofi is still interested in indolizines. Over twenty years ago they bought a Belgian firm called Labaz to acquire the rights to an indoizine-based calcium antagonist called fantofarone (SR 33557). Needless to say, the Belgian site was closed down a few years later.

Permalink to Comment

25. overthetop on June 20, 2012 7:48 AM writes...

Depending on where they are in the PCT process, this error is probably correctable with an Article 34 amendment. Since the species list and the reaction scheme are all correct, they probably can meet the burden that amendment corrects an obvious error and does not add new matter. If they can't amend the PCT, they certainly can amend the genus claim during US prosecution.

Permalink to Comment


Remember Me?


Email this entry to:

Your email address:

Message (optional):

The Last Post
The GSK Layoffs Continue, By Proxy
The Move is Nigh
Another Alzheimer's IPO
Cutbacks at C&E News
Sanofi Pays to Get Back Into Oncology
An Irresponsible Statement About Curing Cancer
Oliver Sacks on Turning Back to Chemistry