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

« Funding in the EU: The Simple Way | Main | Another Alzheimer's Compound Goes Down »

June 27, 2008

Unknown - But You Can Buy It

Email This Entry

Posted by Derek

I sketched out a rather small molecule the other day, a perfectly reasonable looking thing, which nonetheless had absolutely no references in Chemical Abstracts. (I’d certainly like to be able to put up a drawing of the structure, but it’s something that I have a work-related interest in, so it has to stay under wraps). But it’s something with only a dozen or so heavy atoms, most of them flat and aromatic – you’d certainly expect something to have been made like it, but apparently not.

This has happened to me many times over the years. Now, you can obviously get into unknown territory immediately if you start looking for bizarre compounds: I don’t happen to have SciFinder access here on the train this morning, but I’m willing to bet that (for example) three-membered rings with one carbon, one boron, and one silicon are pretty wide open for some brave weirdo to explore. Enjoy!

But you don’t have to go that crazy to leave the paved roads behind. Many reasonable low-molecular-weight areas are only very lightly explored. You can get out of the universe of known compounds very quickly, for example, by searching for spirocycles, particularly with an oxygen or nitrogen or two scattered into the rings. Most of these would surely be interesting scaffolds for drug discovery libraries, if there were reasonable chemistry to explore them with. Even some perfectly normal looking substitution patterns of monocyclic compounds haven’t been looked into – I dreamed up a series of oxazole derivatives not long ago that no one’s ever made, and there’s nothing odd about them at all.

As you’d expect, there’s a commercial niche here. Novelty is a key requirement for patentability, so seeing no references turn up around your interesting structure is good news from an IP standpoint. (It may be bad news from a laboratory standpoint, though, because sometimes these things are unknown for a reason). But not always: there are companies that pride themselves on being able to supply such unknown scaffolds and libraries. bicyclo.gifThe perfectly reasonable-looking diazabicyclo compound shown here, for example, has no references in SciFinder, but can be purchased on a multigram scale. (There are about fifty derivatives of that bare scaffold known in the literature, which makes it pretty much uncleared ground compared to the absolutely pulverized IP landscape around, say, piperazine). Next time you're searching for such things, refine your answer set to give only those compounds with no references, and take a look at how many of them are commercially available anyway. . .

Comments (10) + TrackBacks (0) | Category: Patents and IP | The Scientific Literature


1. weirdo on June 27, 2008 10:01 AM writes...

It's kind of nice when the material truly is available.

But nothing is more annoying when, about half the time, it's just paper chemistry and the molecule is not actually available. So this darn company has polluted the IP waters without having the decency to make the molecule first. A particular French company is notably efficient at doing this. Many of us will never order from them, that's for sure, so it's unclear what they thought could accomplish . . . .

Permalink to Comment

2. John Spevacek on June 27, 2008 10:36 AM writes...

The "Lamentations on Chemistry" blog had a post on this over the weekend. CAS did a structural search over all many simple rings and found that most of the space was unexplored which begs the question you raised: is it because no one is interested or is no one interested because it is too difficult?

Permalink to Comment

3. Sili on June 27, 2008 10:39 AM writes...

I remember my supervisor being surprised that NC-CH(CONH2)2 was unknown, while (NC)2CH-CONH2 is old as the hills.

(Technically their anions. I did manage to crystallise the last one but never got round to writing it up before I fled uni. Didn't isolate the first one from the Cu complex, though. Never got around to it. I've prolly been 'scooped' by now.)

Permalink to Comment

4. Jose on June 27, 2008 1:04 PM writes...

It is amazing how sparse some simple polysub benzenes are: 5-Fluororesorcinol has 18 refs and 2 preps; 3-Fluoro-5-iodoaniline has a handful and refs and a single prep.

Permalink to Comment

5. andenbe on June 29, 2008 3:41 AM writes...

as for the N- respectively O-containing spirocycles you might want to check out this recent paper produced by the Carreira group in collaboration with Roche:

Spirocyclic Oxetanes: Synthesis and Properties
Angew. Chem. Int. Ed. 2008, 47, 4512.

Permalink to Comment

6. Panoramix on June 29, 2008 2:33 PM writes...

There is also this weird benzoxaborole aka boron-oxygen heterocycle for the treatment of fungal infections. No the kind of ring you see daily in drugs.
doi: 10.1021/jm0603724

Permalink to Comment

7. zugor on June 30, 2008 11:42 AM writes...

Someone somewhere must have made this molecule.
True, this small molecule you are after may have been made, it may also be commercially available
but you don't know it. And you maybe never will.
Developing & making new building blocks & scaffold with IP potential is the easy part for the synthetic chemists. Finding the right route to market is not. Put your molecule on a commercial databases (Scifinder, Beilstein emolecules..) and it will instantly lose 90% of its value. Same for anonymous mailshots.
Too much market visibility for your new product will indeed lower its value (you lose that semi-exclusivity factor). Too little visibility and you will not be able to reach the medicinal chemists currently looking for compounds similar to yours...

Permalink to Comment

8. Nathan on June 30, 2008 11:44 AM writes...

The problem is that even when you find a novel scaffold type, it's entirely possible that it has been unintentionally (or intentionally) generically covered by someone else’s IP. Then what do you do? The scaffold has not been exemplified, but it has been claimed!
Any insights? I think this would be a nice topic for a post Derek!

Permalink to Comment

9. Anonymous on July 1, 2008 8:57 AM writes...

2. John Spevacek: "... is it because no one is interested or is no one interested because it is too difficult?"

Don't programs exist that assess the synthetic difficulty of molecules? Won't that tell you if it's too difficult to build? In orgo class, we heard of E.J. Corey's LHASA program and that's 40 year old!

Permalink to Comment

10. Fred on August 21, 2008 7:58 PM writes...

Indeed an available chemical directory will contain some compounds not found in CAS or elsewhere (although some will not actually be available). Another place to check your substructures is PubChem ( These have actually been synthesized and bio data are often available.

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