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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

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June 18, 2010

What Has Bioinformatics Ever Done For Us?

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Posted by Derek

A reader points me to this discussion, which is trying to figure out what the most useful discovery made via bioinfomatics is so far. There's a $100 prize for the winning suggestion, just to keep the discussion moving (and no, I don't anticipate offering cash bounties around here any time soon!) The early going seems to have ended up in the "Hold it, that's not bioinformatics, is it?" ditch, but that's not a useless discussion, either.

So if you have some suggestions, hop over there and add them to the fray, or vote for the ones that you like so far. I'm racking my brain a bit myself.

Comments (11) + TrackBacks (0) | Category: In Silico


COMMENTS

1. MLBpitcher_and_OrganicChemist on June 18, 2010 7:06 AM writes...

Wouldn't targeted drugs like imatinib and erlotinib count?

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2. Keith Robison on June 18, 2010 7:10 AM writes...

At one level, I'm tempted to throw back the question "what is the greatest thing in chemistry ever discovered with solvents?". Bioinformatics is so foundational to so much of modern biology -- imagine how useless any DNA sequence (particularly entire ones) would be without the tools to explore them.

I also suspect that some will argue that some of the discoveries listed below fall into some other discipline. By my reckoning, if the computational comparison of data played a critical role in making a biological discovery, then it is fair game.

An early notable discovery is the fact that one of the enzymes of the Krebs Cycle doubles as the intracellular sensor for iron. I believe that was strictly an informatics discovery; nobody went looking for this reuse.

The finding that what were called "bacteria" fell into two anciently-diverging clades (Eubacteria and Archea) came purely from sequence. And then the discovery that Archea are really more eukaryote-like in much of their machinery (I was scooped on this by about 6 months) came purely from looking at sequences cloned for other reasons.

Informatics pretty much nailed down the endosymbiont hypothesis of chloroplast & mitochondrial formation. Computational comparisons are also the best evidence for a common ancestor.

Microarray analysis has parsed some previously indistiguishable cancers into finer and finer categories, with some clinical impact (e.g. diffuse large B-cell lymphoma).

Just throwing out examples -- I fully expect someone else to find something better, though the "Archea have a lot in common with Eukaryota" is a pretty big one.

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3. CompChemist on June 18, 2010 7:40 AM writes...

The answer is no, of course not, it would be a misunderstanding of the discipline to suggest otherwise. Maybe there are 1 or 2 extremely unusual case examples but it should not be the aim of the discipline.

The computational tools simply aid the design and discovery of new therapeutic agents. To expect any more is to totally miunderstand the science (although many a good theoretical scientist often gets carried away with his claims of what the tools can do).

Bioinformatics has never discovered a drug, nor has computational chemistry. But then again, medicinal chemistry alone has never discovered a drug, it needs good biology and you could easily state it the reverse way round.

However, do away with computational tools and you will never be able to process the huge amount of information the discovery process now generates. they are an essential part of it.

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4. Keith Robison on June 18, 2010 9:43 AM writes...

Another is the entire modular structure of proteins, particularly signalling proteins. Looking at oncogenes after Src and realizing they had "homology domains" SH1 (kinase domain), SH2 & SH3 -- and then needing to know what those SH2 & SH3 domains were up to.

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5. RKN on June 18, 2010 1:43 PM writes...

The question is poorly cast - it would be analogous to ask for a ranking of discoveries enabled by statistics.

The obvious answer, already put forth, is BLAST and the insights that followed into sequence similarity. But perhaps the most important insight attributable to bioinformatics lies in the name itself, that biology is information. In fifty years or less I expect biology and bioinformatics will be synonymous.

Permalink to Comment

6. Anonymous BMS Researcher on June 19, 2010 6:59 AM writes...

Well, to name one specific practical item with which I have direct firsthand knowledge, none of the antiviral drugs approved in the last decade would be on the market without bioinformatics to analyze resistance mutation data.

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7. retread on June 19, 2010 4:19 PM writes...

#2 "what is the greatest thing in chemistry ever discovered with solvents?". Easy. Valproic acid (aka Depakene), a commonly used anticonvulsant when I was practicing. The brain is mostly fat, and drugs getting into it must be fairly lipid soluble, usually meaning that they are poorly soluble in water. The bioassay for anticonvulsant activity was how much current it took to throw a hapless rabbit into convulsions (this is what happens in electroconvulsive therapy).

Valproic acid (2 n-propyl 1 - pentanoic acid) was used as such a solvent. Fortunately someone had the brains to do a control, and it turned out to be the active principle in whatever they were studying. It certainly wasn't found from first principles, or a clear understanding of the neurophysiologic mechanisms behind epilepsy.

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8. Eddie Paulos on June 20, 2010 10:26 PM writes...

Bio-info could be useful during early stages of drug discovery when instead of wet-lab the computation lab would help us see the direction we would like to take, but again Bio-info in itself can never do the discovery since what happens in silico need not happen in vivo lest we would have all the Sci-Fi movies translating in real life!

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9. Burkhard Heil on June 21, 2010 7:11 AM writes...

Strange question, since nobody would challenge e. g. PCR in that way. Bioinformatics is an excellent way to sort out dead ends (at the expense of some none-dead ends). Are there any modern discoveries that were made without bioinformatics or - to get rid of the term bioinformatics - without the application of computational methods on biological data?

Permalink to Comment

10. Eddie Paulos on June 21, 2010 10:36 PM writes...

The following link throws more light:
Hammami, R. Current trends in antimicrobial agent research: chemo- and bioinformatics approaches, Drug Discov Today (2010), doi:10.1016/
j.drudis.2010.05.002

Permalink to Comment

11. Ben on June 28, 2010 8:27 AM writes...

The aquaduct?

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