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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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June 25, 2014

That's Just Too Colorful

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Posted by Derek

orange%20compound.jpgI have just made the most eyewateringly fluorescent orange compound of my entire chemical career. It's not in a structural class that normally I would be exploring, but it's been a while since I was on a normal project, so that's fine. But this thing - yikes. I keep telling myself "It's a probe, it's a tool, don't worry", as all my med-chem instincts tell me that a compound like this, whose color would blend in only with a pile of nasturtiums, cannot be clean. But it is. And those same instincts keep telling me that a compound this wildly colorful can never, ever be of any use in a biological setting. It's an irrational prejudice, but it dies hard.

Comments (57) + TrackBacks (0) | Category: Life in the Drug Labs


COMMENTS

1. CanuckGradStudent on June 25, 2014 8:38 AM writes...

What about isatins? They've been investigated for every medicinal property under the sun and they're the brightest compounds I've ever worked with. They're so highly colored we materials chem folk now co-opt them to build solar cell dyes?

Actually the brightest orange I've seen is just plain old isatin.

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2. Charlie Abrams on June 25, 2014 8:43 AM writes...

Color me confused: Azo? Methylene blue? Prontosil?

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3. Virgil on June 25, 2014 8:44 AM writes...

I guess the classic example of colored drugs gone bad would be dinitrophenol for weight loss. If IIRC it was the first ever drug banned by the FDA. In addition to having the rather undesirable side effect of death, the users steadily turned bright orange over time.

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4. Hap on June 25, 2014 8:57 AM writes...

Well, they did lose weight...even if having the thinnest corpse in the funeral home wasn't exactly what they wanted.

If it's an isatin, there's plenty of derivatization papers out there - throw in a carbonyl compound and a cinchona alkaloid, and something will probably happen. The product probably won't be colorful, though.

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5. Lias Balbes on June 25, 2014 9:00 AM writes...

Post a picture, please!

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6. Vader on June 25, 2014 9:06 AM writes...

What Charlie and Lias said.

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7. Anonymous on June 25, 2014 9:14 AM writes...

bright orange? Mutagen!

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8. MolecularGeek on June 25, 2014 9:31 AM writes...

You ought to be able to sell it to the microscopy and imaging crowds as a dye, if nothing else.

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9. pharmacologyrules on June 25, 2014 9:36 AM writes...

#3--do you think John Boehner takes diNO2phenol?

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10. MAZ on June 25, 2014 9:38 AM writes...

Oxindole RTK inhibitor?

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11. newnickname on June 25, 2014 9:38 AM writes...

#2 asked about Prontosil. Not only is the chemical a red color, but it turned the patients red! ... while also saving their lives as a side effect.

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12. Hap on June 25, 2014 9:45 AM writes...

Other than the yellow solution, it looks like a fruit-tomato juice hybrid. It's pretty, though.

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13. dlib on June 25, 2014 9:47 AM writes...

Now is the time to don the white coat, put it in a flask, light up the bunsen burner and call the marketing department's photographer ;-)

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14. TX raven on June 25, 2014 9:54 AM writes...

"It's an irrational prejudice..."

I thought they called these things "guidelines"

:-)

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15. Anonymous on June 25, 2014 9:55 AM writes...

Isn't this the stuff they put in Berocca that makes your wee fluorescent yellow?

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16. Helical Investor on June 25, 2014 10:05 AM writes...

Doc - I have some good news and bad news for you.

Patient - What's the good news?

Doc - We have an effective way of treating your ailment.

Patient - And the bad news?

Doc - Your future career opportunities may be limited to 'Oompa Loompa'.

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17. anon the II on June 25, 2014 10:05 AM writes...

Thanks for the picture. How 'bout a structure to boot?

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18. Chrispy on June 25, 2014 10:17 AM writes...

This is the kind of compound that can really show you how good your flash chromatography technique is. Nice, compact band migrating down the column? Good! Streaky, irregular glob? not so good...

Does it fluoresce as well?

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19. Hap on June 25, 2014 10:18 AM writes...

"To boot" would probably be right...I'd like to continue reading this blog, and if Dr. Lowe's unemployed, he won't have as much to blog about, and/or it would speed adoption of the "Do you like my writing? Please pay me to do it so I don't have to get out my change cup and sit in Harvard Square" blogging model.

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20. Contrarian on June 25, 2014 10:18 AM writes...

Cisplatin, doxorubicin, riboflavin, cobalamins, carotenoids, iodine, chloroquine, prussian blue, methylene blue, selenium sulfide...

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21. Vaudaux on June 25, 2014 10:22 AM writes...

Doxorubicin? Bright red in the IV tubing on the way in, also bright red on the way out an hour later.

Rifampin is pretty bright too

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22. PJ Hansen on June 25, 2014 10:29 AM writes...

If the compound a tool, and clean, then it looks like you've made enough to screen for target binding against all compounds in anyone's library. Until the end on time.

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23. CMCguy on June 25, 2014 10:35 AM writes...

Irrational or not even if biology turns out OK would suggest increases certain risks in the Clinical and Marketing aspects. Several actual drugs have been mentioned by commentators however would guess most encountered added hurdles not typically present with white crystalline products. You can always claim revisiting older classical medchem approach which was partly born out testing compounds from the dye industry.

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24. Erebus on June 25, 2014 10:37 AM writes...

Coenzyme Q10 is just slightly less orange than the stuff in the pictures. Isatin is pretty bad, itself. And emodin is basically the same sort of orange color... to say nothing of the other anthraquinones I've seen, which are all various shades of bright yellow to bright orange...

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25. Hap on June 25, 2014 10:42 AM writes...

All the cyanine dyes and dipyrroloboroles have to be colored too, so I don't imagine the color is a problem for a tool compound.

If it's bright enough, perhaps they can license it to OH for improvement of their construction signs - "Look, they're luminescent! Our drivers can't miss these, right?"

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26. Semichemist on June 25, 2014 10:46 AM writes...

I think I'm in tune with your instincts, seeing you hold a vial of something that colorful without gloves on is making me physically uncomfortable...

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27. David Formerly Known as a Chemist on June 25, 2014 10:46 AM writes...

I remember back in graduate school working for a short period on synthesizing hypericine (look it up), which was being explored by NIH as a lead for HIV (awww, the 80s, when even brick dust like hypericine could garner attention). A couple milligrams dissolved in a liter of acetone looked like whole blood.

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28. Secondaire on June 25, 2014 10:48 AM writes...

Beautiful. I was in a group that got a compound into Phase I for various stubborn cancers a while back, and that thing (with lots of conjugated heterocycles) was brown as a solid, and a lovely purple-magenta in solution.

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29. Jade_Nekotenshi on June 25, 2014 11:05 AM writes...

Doxorubicin and mitoxantrone come to mind, but then, those are really quite nastily toxic. They're just somewhat *more* toxic to the tumor than to everything else.

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30. Curryworks on June 25, 2014 11:14 AM writes...

looks like curcumin

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31. a. nonymaus on June 25, 2014 11:30 AM writes...

Bright colors, no problem. Long-lived luminescence, on the other hand... That's a good way to end up with singlet-oxygen phototoxicity. (unless you're trying to do that with some photodynamic therapy)

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32. oldnuke on June 25, 2014 11:30 AM writes...

Maybe a replacement for Red Dye No 2? gr

I'll never forget when my Dad discovered that the local market was using Red Dye #2 in their ground beef! The first clue was our Schnauzer's beard was slowly turning red.

Dad was not pleased and reported them to the USDA and State Health Dept. Fortunately, Snoopy's beard recovered. gr

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33. Derek Freyberg on June 25, 2014 11:31 AM writes...

Cyanocobalamin (injectable vitamin B-12) is a nice red.
And for orange, there are the CT scan contrast agents, which are iodinated something-or-others. Granted they put the oral one in Tang, which itself is orange, but you do pee orange as the agent makes its way through your system.

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34. Anonymous on June 25, 2014 11:34 AM writes...

Sutent is a yellow color - and also quite toxic

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35. A. Nonny Mouse on June 25, 2014 12:03 PM writes...

If it's not toxic, try dying material (or hair) with it. You could make a fortune if you've found a new family of dyes.

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36. John Wayne on June 25, 2014 12:58 PM writes...

@13 - Yeah, where are the lab tours when somebody makes something colorful?

Best be careful Derek; when this baby hits the clinic they are going to have to ground up skittles to make the placebo tablet the same color as the API.

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37. nachtmystium on June 25, 2014 1:15 PM writes...

Nasturtium would make a good metal band name...

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38. Anonymous on June 25, 2014 1:54 PM writes...

By measuring the absorption spectrum from the photo, and deconvoluting this into absorption and emission spectra of the compound, I think I've figured out that the molecular structure contains *at least* one aromatic group. Maybe more.

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39. Keiran Lee on June 25, 2014 2:14 PM writes...

@38 Dork

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40. Anonymous on June 25, 2014 2:59 PM writes...

OK I'm going to have to throw the rifamycins out there.

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41. Anonymous on June 25, 2014 4:33 PM writes...

Having worked in a manufacturing site that made large quantities of Sutent, epirubicin and doxorubicin the colour came in handy for proving product containment (or lack thereof)!

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42. Anonymous on June 25, 2014 5:16 PM writes...

Whatever the pigments are in the nasturtium are biologically relevant :)

Last year I grew nasturtiums. They taste VERY good. Kind of spicy and tangy. Intense. Great in salads.

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43. Jacob from Upstate NY on June 25, 2014 7:16 PM writes...

Back at the very beginning of my career, in my first semester in graduate school, I was sent off to make derivatives of perylene tetracarboxylic dianhydride as fluorescent probes for various things. I made one of these things and it barely dissolved in any NMR solvent except acetone-D6 and DMSO-D6. The solution was very similar in color to the red part of your picture there. So I finally got my spectra and I tossed the tube in a beaker in my cabinet and went home. The next morning, the rising sun shine into my cabinet, which lit up with an eerie green glow: that was the most fluorescent thing I've ever seen.
I then became more interested in the fluorescence than the synthesis, switched to a physical chemistry program, and became a physical inorganic chemist with a specialty in solid state NMR of aluminosilicate zeolites.
Go figure.

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44. Anonymous on June 26, 2014 1:55 AM writes...

Strongly fluorescent? Quantum yield please, 0.8-0.9 or bust.

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45. Anonymous on June 26, 2014 1:56 AM writes...

Strongly fluorescent? Quantum yield please, 0.8-0.9 or bust.

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46. elperrogrande on June 26, 2014 4:32 AM writes...

Gloves? (-;

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47. DrSnowboard on June 26, 2014 5:18 AM writes...

napthoquinone?

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48. Nekekami on June 26, 2014 6:35 AM writes...

Here's an experiment for you, Derek...

Will the smoke have that pretty orange if it goes boom?

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49. lol on June 26, 2014 11:57 AM writes...

Did you realize we can read your notebook from the reflection in that window!!! no but be careful.

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50. asd on June 26, 2014 8:57 PM writes...

Coming from a different chem background and not med chem, why is everyone worried about a little color?

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51. geekosaur on June 27, 2014 10:46 AM writes...

As a non-chemist: bright color usually means lots of electrons floating around loose, which usually means it reacts with anything it gets too close to. This is usually a liability in med chem, where off-target effects mean potential for nasty side effects.

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52. Another Kevin on June 28, 2014 12:12 PM writes...

Isn't phenazopyridine about that colour? It's even sold OTC...

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53. sepisp on June 30, 2014 6:01 AM writes...

Physically, color means that the compound has a conjugated system, and some of the resonance transitions this system has have an energy coincidentally in the visual range. For pure hydrocarbons, you need pretty big systems for this to happen, as in for instance beta-carotene. There is also a good explanation why heteroatoms can induce this even with rather small number of bonds - I've seen the article, but I'm not a quantum chemist so I can't explain it properly. It has something to do how the system is "squeezed" relative to an alkene. E.g. you get a much richer set of resonances with an azo compound vs. just an alkene. This is why you can get intense colors with something as small as a reductic acid, isatin or quinone.

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54. Cymantrene on July 2, 2014 2:20 AM writes...

My colleagues are working on a magenta dye used in printers. In solution and in thin layer it is magenta as one would expect, but in crystalline form it's metallic green with a golden hue, just like rose chaffer. It's astonishingly beautiful :-)

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55. Anonymous on July 6, 2014 12:34 AM writes...

@30 yep, I was going to say it looked like curcumin. One guy in my lab is synthesizing tetrazine compounds, which are fabulously colored: Neon red, fire engine red, orange, barbie pink, yellow; and they fluoresce yellow and orange.

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56. Gin on July 9, 2014 3:05 PM writes...

@29: mitoxantrone is a boring dark blue at physiologic pH. I've never altered pH to see if it turns orange, though.

An off the wall guess - cytochrome C? It is also beautifully orangish-red colored, although it is useful biologically so it can't be the answer.

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57. Shushu on October 15, 2014 10:12 PM writes...

I don't think that's what this is, but the coloration and its intensity looks almost exactly like the Petasis reagent in solution (http://en.wikipedia.org/wiki/Petasis_reagent).

"orange colored" doesn't do it justice. even dilute solutions of this stuff are intensely vibrant

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