#BadBosutinib: It's not paranoid if the molecules are really out to get you

Would you have caught this problem?
Credit: Chemical and Engineering News

a.k.a. Don't take the bad bosutinib!

From the pages of Chemical and Engineering News, a synthetic mystery story by Bethany Halford that is so freaky, you'll go back to your lab and try not to put every bottle through a full characterization study:

Some bad bosutinib is going around. Scientists who have purchased the compound may have actually received an isomer rather than the genuine molecule. 

Bosutinib, also known as SKI-606, is currently in Phase III clinical trials to treat chronic myeloid leukemia. Officials at Pfizer, the company sponsoring the clinical trials, say that only genuine bosutinib has been administered to patients. However, as a selective kinase inhibitor, the compound is also used in medical and basic research. The news that researchers may have unwittingly been using an isomer of bosutinib instead of using the genuine compound threatens to invalidate research efforts around the world. 

The first inklings that there may be problems in the bosutinib supply were discovered in December, when Nicholas M. Levinson, a postdoc at Stanford University, noticed something funny in the Protein Data Bank. A structure recently deposited by Stefan Knapp, Frank von Delft, and coworkers at England’s Oxford University was supposed to show bosutinib bound to a kinase, but the arrangement of one of the ligand’s atoms was wrong. 

It was a subtle difference. Bosutinib has a chloro group on the 2-position of its aniline subunit, but this was missing in the Oxford structure. Instead, this molecule appeared to have a chlorine in the 3-position, where bosutinib has only a hydrogen. (Emphasis CJ's)  

Levinson had been working on the structure of bosutinib bound to a different kinase, and when he saw this new structure, it convinced him that what had been a nagging inconsistency in his own work was actually a widespread problem. 

Levinson and Boxer put their publication on hold, ordered bosutinib from a different vendor, and did a battery of tests to determine which material was the genuine bosutinib. They soon figured out the original compound they had done all their research on turned out not to be bosutinib. “We had wasted a huge amount of time and money on the wrong isomer,” Boxer says. On the basis of multidimensional nuclear magnetic resonance (NMR) experiments, Boxer and Levinson believe that this isomer not only has a chlorine at the 3-position rather than the 2-position, but also that the chloro and methoxy groups that appear in the 4- and 5-positions, respectively, in bosutinib’s aniline moiety have been switched. (Emphasis CJ's)

What I find interesting is that the relevant company (LC Pharmaceuticals) that sold the research sample to Stanford has started blogging about this issue, and in a February report, he raises questions about Wyeth/Pfizer's own characterization of the compounds:

 Bosutinib (of empirical formula C26H29Cl2N5O3) could be taken to be one or more of:
(i) a particular arrangement of those atoms and bonds depicted graphically, such as in Figure 2, as was published in the 2001 J. Med. Chem. article. 

(ii) a substance in a bottle at Wyeth-Ayerst (the company that originated bosutinib and was later acquired by Pfizer) at the time that company first made the compound;

(iii) a substance made by a particular synthetic sequence and reaction conditions, such as in J. Med. Chem., op. cit. or by one of the three other published synthetic routes that we are aware of; 

(iv) a substance with (i) certain specific inhibitory potencies or inactivities when tested on a panel of eleven rat and human kinases [Cancer Res. 66: 11314-11322 (2006)] or (ii) other activity profiles as measured in other set(s) of bioassays;

or, a new, very important alternative: 

(v) the substance that is being administered to human patients in Pfizer-sponsored clinical trials.

In Bethany Halford's article, Pfizer makes very clear statements that only the correct bosutinib has been given to patients. Boy, for their sake, I sure hope they're right.

As a synthetic chemist (and someone who used to make molecules for sale to researchers), I'm in profound sympathy with LC Pharmaceuticals. I would like to think that I would have caught the weird NMR issues (Figure S2, Word document) and I would have noticed that things that weren't symmetrical were acting symmetrically. I hope that I am right.

Finally, I believe that this mistake could have happened to anyone. However, the fact that the incorrect compounds came to LC Pharmaceuticals by way of Chinese manufacturers cannot escape anyone's notice nor improve their reputation (or lack thereof) for quality.

Readers, would you have caught this? What, if anything, would you do to make sure this didn't happen to you?