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Oct
17

Targeting TB with an App

Its been a particularly hectic few days here because ..drumroll..I was putting together a blog and a Scimobileapps page for a brand new App. This one is called TB Mobile and came out of the work I have been leading at CDD in collaboration with many other researchers notably those at SRI. One of the little datasets we created as part of the phase I grant related to a list of molecules and their TB targets along with pathway, essentiality and other data.  Really we had combined the cheminformatics and bioinformatics data together. As this is one of the goals of the phase II project I had an aim/ deliverable to produce an app that contained this data. It is more like a foot in the water to see what other datasets we could appify. Big thanks to NIAID for the phase II grant which helped to make this freely available to anyone!

So based on the past results obtained through collaboration with Alex Clark at Molecular Materials Informatics, he was the obvious choice to put this together. A huge thank you to him for delivering on time and the app is exactly what I imagined!

So what is in it for someone using it? It is admittedly limited at present to 700 molecules with target data and more from the literature. But what really stimulated the idea to shift the data out of a database on the cloud and into your pocket was the ability to use molecule similarity to infer potential targets. For anyone doing whole cell screening against an organism like TB, you will know all to well that finding an interesting hit is only part of the story because then begins the chance to identify a target or targets and even then this may be a long and unfinished process. So for someone to input their molecule into the app (with content solely residing on your device – so nobody else can see what you are doing a search with) and get some suggestions in a few seconds is pretty close to [insert superlative here]. So obviously its not a perfect approach, its not particularly sophisticated..but it is free, it is accessible and it is here now. I look forward to any feedback.

Now if the funding organisations could do something similar to free up all the legacy (read old) TB data (in vivo and in vitro) perhaps we can stop people rediscovering compounds from the past and maybe also reinvigorate interest in some molecules that are gathering dust. We would be happy to discuss how we could appify such data. Unbelievably this is the first TB related app to our knowledge so I really hope it will stimulate interest in what can be done to raise awareness, make data visible and help researchers.

 

 

 

3 comments

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  1. John Overington says:

    This is a great initiative – I had my phone stolen, so when I get a replacement I’ll have a look at the app.

    Isn’t the last paragraph what the Gates funded with CDD a few years ago? https://www.collaborativedrug.com/buzz/2008/11/17/collaborative-drug-discovery-receives-gates-foundation-grant-to-support-the-development-of-a-database-to-accelerate-discovery-of-new-therapies-against-tuberculosis/

    If so, isn’t that data available to populate this app?

    1. sean says:

      Hi John,

      Very sorry to hear about your phone :(

      We went back about a decade on the ‘old’ TB data and mined patents upto 2010 and 1000′s of compounds came out of that (and is in CDD thanks to BMGF) but the overlap with target information was minimal (essentially what we have in this app). The app represents a way of making some of the data more visible and accessible and I do want to update it. I think digging back to the 50′s and 60′s to get at in vivo and in vitro data requires considerably more effort (but would like to hear of ways this can be done), but would be useful for correlations etc (though not for this particular app due to lack of target info back then). I have several folks interested in this. It seems 40-50 yrs ago that papers contained large numbers of compounds with in TB vivo data (albeit qualitative). Several groups (us included) have recently unearthed molecules that were first identified with TB activity in the late 60s but this was not widely known or in the databases that exist. So there is a bit of a generation gap..new data gets in databases, old data kind of languishes. Thanks for the opportunity to expand on this – I was a bit tired when I blogged before.

  2. sean says:

    Alex has just posted extensive detail on the app for anyone interested http://molmatinf.com/tbmobile.html

    please check it out!

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