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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: derekb.lowe@gmail.com Twitter: Dereklowe

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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

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May 21, 2012

A Molecular Craigslist?

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Posted by Derek

Mat Todd at the University of Sydney (whose open-source drug discovery work on schistosomiasis I wrote about here) has an interesting chemical suggestion. His lab is also involved in antimalarial work (here's an update, for those interested, and I hope to post about this effort more specifically). He's wondering about whether there's room for a "Molecular Craigslist" for efforts like these:

Imagine there is a group somewhere with expertise in making these kinds of compounds, and who might want to make some analogs as part of a student project, in return for collaboration and co-authorship? What about a Uni lab which might be interested in making these compounds as part of an undergrad lab course?

Wouldn’t it be good if we could post the structure of a molecule somewhere and have people bid on providing it? i.e. anyone can bid – commercial suppliers, donators, students?

Is there anything like this? Well, databases like Zinc and Pubchem can help in identifying commercial suppliers and papers/patents where groups have made related compounds, but there’s no tendering process where people can post molecules they want. Science Exchange has, I think, commercial suppliers, but not a facility to allow people to donate (I may be wrong), or people to volunteer to make compounds (rather than be listed as generic suppliers. Presumably the same goes for eMolecules, and Molport?

Is there a niche here for a light client that permits the process I’m talking about? Paste your Smiles, post the molecule, specifying a purpose (optional), timeframe, amount, type of analytical data needed, and let the bidding commence?

The closest thing I can think of is Innocentive, which might be pretty close to what he's talking about. It's reasonably chemistry-focused as well. Any thoughts out there?

Comments (19) + TrackBacks (0) | Category: Academia (vs. Industry) | Business and Markets | Drug Development | Infectious Diseases


COMMENTS

1. Sean on May 21, 2012 9:20 AM writes...

My friends at Quartzy have this feature on a smaller scale in that you can anomalously request a product from neighboring labs. I'd imagine that they will extend the feature over their entire platform at some point.

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2. Anonymous on May 21, 2012 9:45 AM writes...

Surely you would very quickly run into some IP issues with a system like this?

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3. anchor on May 21, 2012 9:47 AM writes...

In this crazy drug discovery business where we think quick rich scheme and patent first attitude, the craigslist kind of thing that is floated herein, will not work.

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4. scientistbymistake on May 21, 2012 9:49 AM writes...

I immediately thought innocentive, but it's very much monetary-reward-based.
It would be interesting to see if the ACS, RSC or someone would host it as an NFP thing to encourage innovation and collaboration in academia?

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5. WVGID on May 21, 2012 10:04 AM writes...

Check out the new science community at iAMscientist.
Potential for a "Science Craigslist"

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6. Anon on May 21, 2012 10:28 AM writes...

Check out Science Exchange which has "launched a website allowing scientists to outsource their research to 'providers' — other researchers and institutions that have the facilities and equipment to meet requesting scientists' needs."
http://www.nature.com/news/2011/110819/full/news.2011.492.html

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7. Joanne Kamens on May 21, 2012 10:28 AM writes...

Addgene has an open sharing model for plasmids. We contemplate something like this for tool compounds in future. Maybe somebody already made what you need but it is sitting in a freezer like so many other reagents. Addgene overcomes the MTA delay issues but I think having someone make something for you does create new delays.

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8. A.Postdoc on May 21, 2012 10:43 AM writes...

This would be pretty cool. Anything from biological chemistry tool compounds to some random protected sugar derivative....

I agree with anchor though. As far as anything medicinal chemistry or drug discovery, there are too many IP issues....

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9. bad wolf on May 21, 2012 11:15 AM writes...

Sounds like the research chemicals list from Aldrich, where they would evidently clean out a retiring prof's lab and list available compounds for resale. Cut out the middleman and even get something made to order!

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10. Anonymous on May 21, 2012 1:21 PM writes...

Seems to me that timeliness would be an issue as well... Making contact, working out the details, vetting, etc would add months to the process.

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11. Paul Ylioja on May 21, 2012 6:30 PM writes...

The reason we're thinking about this instead of an Innocentive like approach for our open source project is that we don't suffer from the the usual IP issues. We are already working in the open and anyone is free to use our work provided their accredit it to us. The idea would primarily be used for academic projects where a patent isn't the primary goal of the research.

We also want to encourage co-operation between groups rather than closed competition where many hours of work are wasted by teams who are not selected. The competition model works for Innocentive because the customer benefits from the choice of many good options. But open competition allows the other ideas to see the light of day and may be of benefit to others. If properly licensed, the team responsible will still get credit for their work.

It is the process of "Making contact, working out the details, vetting" that the "Craigslist" idea is designed to mitigate. If you know you have something in the freezer and you know someone wants it then why not send it to a someone when it would be wasted otherwise? If the compounds are being gifted, there is little incentive for fraudulent/incorrect compounds to be sent by the donator. There is no guarantee of compound identity even from "vetted" suppliers (e.g. the recent case of Bosutinib).

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12. Antony Williams on May 22, 2012 6:48 AM writes...

In terms of hosting the compounds and exposing them to the community etc that would be very easy to set up on ChemSpider and if someone wants to discuss how to do it please feel free to contact me. This is something we discussed before internally...the issue is never one of technology but rather the number of participants and willingness to post data.

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13. Laura on May 22, 2012 8:58 AM writes...

Interesting- the project reminds me a bit of Jean-Claude Bradley's (Drexel University) anti-malarial work (he worked with ChemSpider too didn't he?).

The molecular craigslist idea also reminds me a bit of a more flexible version of Pivot (the new name for Community of Science). If your institution has a subscription then you can use the collaborative workflow option in Pivot to identify people to work with (internal and external to your organization).

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14. Bin on May 22, 2012 11:38 AM writes...

assay depot (https://www.assaydepot.com/) does have lots of vendor information, covering pretty much all the data through the drug discovery pipeline. Atul Butte raised a very interesting topic on outsourcing in TEDMED (http://thehealthcareblog.com/blog/2012/05/18/tedmed-2012-atul-butte/).

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15. Chris Southan on May 28, 2012 11:37 PM writes...

After some initial exchanges with Mat and Paul (comments above) some time ago I wrote a blog post about the chemical supplier ecosystem in public databases and pointed to an earlier In the Pipeline post (http://cdsouthan.blogspot.se/2012/05/shop-till-you-hit-chemical-suppliers.html) I also included a short questionnaire for suppliers to offer donations or discounts to Malaria OSDD but the response has been very low. This may be because most primary suppliers are small and orders predominantly brokered via aggregating portals. This suggests supplier responses to the Craigslist might be low. However, authors and patent assignees who have at least a couple of million structures lying around as useful analogue series should be more promising.

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16. Barry Bunin on May 29, 2012 1:55 AM writes...

The key for widespread adoption is spanning the traditional, private secure, collaborative, and public modes with chemical and biological data. Then researchers can decide how much or when to collaborate. The challenge is to do this within researchers natural workflows. For an analysis of how different technologies could impact future business models, see: https://www.collaborativedrug.com/buzz/2012/04/25/collaboration-as-the-key-to-turning-around-the-drug-discovery-business-part-10-learning-from-ebay-nasdaq-airlines-hollywood/

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17. Christian Stevenson on June 1, 2012 3:34 PM writes...

As an employee of InnoCentive and the Innovation Program Manager responsible for our Novel Molecule Challenge program (https://www.innocentive.com/pavilion/novel-molecules), I would like to add a few points to this discussion. The Novel Molecule Challenge offers this exact opportunity:
1. Seekers who need molecules can broadcast their need to our worldwide network of Solvers. They can obtain compounds (either pre-synthesized or synthesized specifically in response to the Challenge) at prices comparable to buying from a standard commercial supplier.
2. Solvers (for instance, university professors, CRO’s, and small catalogue providers) can provide compounds they have or could make in response to a specific Challenge. Even more conveniently, Solvers can upload their entire compound library to our secure database and we will inform them any time a Seeker might want their compound. Additionally, we are currently offering rewards for simply uploading the structures into our database.
While this may not be exactly the forum you envision, I know this program has provided significant value for both Seekers and Solvers alike. I will monitor this discussion moving forward to answer any questions, or am happy to field questions privately at cstevenson@innocentive.com.

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18. Christian Stevenson on June 11, 2012 2:51 PM writes...

Also, for those potential molecule-Seekers who may be concerned about the price of working with InnoCentive, we have a newly launched low-cost option that I would be happy to describe if you contact me by email.

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19. Solomon on October 2, 2012 10:56 PM writes...

Derek, I recently started a scientific marketplace called labdonkey.com . It is similar to science exchange / assay depot concept (not there yet). The website does allow for "tendering process where people can post their "smileys" and chemical structures". Of course any user interface suggestions can be accommodated and I can offer that as a free service. Any comments? Solomon

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