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Jul
21

Wiki, Wiki, Wiki – for chemical probes

Sorry for the cheap title (for those born after the mid 80’s its a reference to a song by a funk band called Newcleus).

A very interesting commentary published today in Nature Chemical Biology by Arrowsmith et al and its all about chemical probes. Go check it out and note that it took over 50 people to put this together. I am not an expert on these things but at a guess it could have been written by a handful of authors…how many of these authors are tacked on for show?

I found out about it yesterday and was asked to comment on it for Chemistry World – I would have much preferred to have reviewed it for Nature Chemical Biology and then perhaps this would have ended up in a journal that is more appropriate based on the results it contains.

The results are a Wiki.. and so far the Wiki contains only 7 chemical probes. Yes I had to look a few times to make sure I had not gone to the wrong address today when it published – when I looked yesterday all I could find was a GoDaddy site. With over 50 authors from very distinguished labs I would have expected them to push out (or their students) a grand total of more than 7 probes. Dare I mention how many $millions these labs pull in from the tax payer to work on finding chemical probes..naming no specific names. And then there are the big pharma folks, pretty sure they have wasted a good few $billion pursuing avenues of research based on duff probes..they could have chipped in a few that actually work. Why not add them to the commentary for good measure? Yes Wiki’s take lots of effort but based on this, the wiki was an afterthought, the commentary came first. I would hazard a wild guess that there will be less than 50 people submitting probes to this wiki (outside of the authors). I hope WellcomeTrust do not look at what they have funded anytime soon – they may want to wait until the number of probes at least reaches double figures. And with that they should have published when there was something substantial to show.

I do not mean to come across as cynical because a few of the authors are widely admired (by me at least for their consistent efforts in exposing crummy molecules, probes and drugs)..Some of the authors are admired for other things that generally do not involve chemical probes or developing wiki’s.

My actual email to the reporter from Chemistry World is below – you can see how just one line was chosen out of several choice quotes – IMHO producing a database would have been ideal that is at least structure searchable (we are dealing with molecules here after all) and contained all the probes out there (good and bad).. And how can you totally ignore the massively funded NIH chemical probes effort when one of the authors is from the NIH? Why did this have to come from the Structural Genomics Consortium? The more I read it and think about it, the more questions.

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Dear Ida,

I am happy to provide some comment on reading this paper. Thank you for bringing it to my attention.

My first comment is does it really need 53 authors to preach to the choir on this topic? Or does this journal only accept mega-author papers
Many of these groups are either responsible for putting probes out there / funded to the total tune of over $500M by the NIH over the past decade, they should have thought about the consequences of what they were doing at the outset and planned a database of probes and information.

Is it me or has the definition of a probe and requirement continually shifted with each publication?

A chemical probes portal – a great idea but the url appeared to fail – did the reviewers of the article test it –(I get a godaddy site!)
Most people would write a paper after they had done something useful, perhaps it would have helped if they created the wiki first, made sure it was functional, then publish a paper on it?
 
No idea if such a portal would actually be searchable by structure – that was not suggested in the paper by the authors!

Most people would probably come across the probes with issues on “in the pipeline” blog – Derek Lowe does a good job of alerting the community anyway.

The authors did not cite our recent summary of issues with chemical probes – which is unfortunate, I know at least one of the 53 authors read it- Parallel worlds of public and commercial bioactive chemistry data. – PubMed – NCBI 

Hope that helps.

cheers
Sean

 

 

 

 

1 comment

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  1. George Dionne says:

    And I thought that you were talking about Wikipedia .. And only 7 probes with all those authors?
    Nonetheless, thanks for the information! Looking forward to your updates of your work.

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