Chemical tools on trial: recent misleading information cases


For this week’s blog, I have picked it a still-hot and enjoyable Nature article by Monya Baker.1

How many times have you had screening results which make no sense to you end in frustration and unexplicable conclusions? How many times have you encountered that your chemical tools (hits) are neither as you thought, behaved oddly or even conducted regular quality controls on them and enough analytical tests? Read more to recognise unexpected setbacks.

The author goes through a few examples where researchers have encountered, for example, that chemical probes hitting specific targets suddenly became inactive when alternatives suppliers came onto stage. A futher realisation that one isomer was presented in different proportions if it was mixed with its other enantiomer (mirror-image like compounds sharing the same molecular formula) altering its activity leading to discover that sometimes, researchers do not know what they have in their hands if too much trust is put on commercial sources or the lack of further structural corroborations.2

When screening large compound libraries and identifying hits, the presence of false positives, impurities, degradation, mixed-up and messed-up stocks could also lead to infructouos crusades. Especially when liquid stocks are kept for months or years, at variable temperatures, the effect of poor solubility, side-reaction impurities, solvent effects and cockails of natural product mixtures amongst others. 3

Suggested online resources like: Chemical Probes Portal, Probe Miner and Probes and Drugs Portal 4 have been created to be used as a good first port of call toolbox with advice and information on which chemicals or drugs to use as well as public assessments.

The infamous case of BOSUTINIB, an approved cancer drug which was sold by nearly 20 suppliers with the chemical substituents wrongly located (please see ‘Spot the difference’ cartoon) has created havoc. jose

Both bosutinib and the other mis-identified isomer target cell-signalling proteins but with different potencies putting under trial numerous papers which reported data on the isomer of bosutinib rather on itself.5

Another researcher, Kim Janda caused an uproar when in its group they could not synthesise a molecule described to boost cell production of a powerful natural antitumor protein, TRAIL. The distributors had perpetuated the mistake in the original publication and after even clinical trials and patents were issued, he filled a patent with the proposed new active version of the TIC10 structure. 6

Another case emphasises how activity showed a big drop after small changes in contrast with bigger changes. Scientists realised that the present of Zn in their preparation was responsible for this activity without effect from the organic molecule whatsoever. Copper or Palladium from its use in catalytic reactions have been reported showing false positives.7

Even the present of NMP (N-methyl-2-pyrrolidone) a polar solvent used in some cases for keeping chemical probes in solution has recenlty showed anticancer activity in control tests, with potential implications in misleading the potency of the substances contained on it. 8

A list of common-sense leading practises to suppress these errors are given in the paper:

  • Use and buy chemicals by their CAS number (unique identification to chemical structures)
  • Request a detailed quality control certificate from external suppliers
  • Place enquires about the synthetic method used
  • Perform independent or in-house analysis upon receipt of the starting chemicals and reagents
  • Structural forms, chiral compounds, potential ambiguity in their chemistry substitution, then determine their optical purity and apply chiral chromatography techniques to isolate single forms.
  • If possible, previous in-house synthesis and determination with structural characterization.

Mismatching results, not-well documented suppliers, dubious chemical insertions (not well validated) as well as poor purities and the presence of contaminants (even at low concentrations) are always to blame for cases like those described in the article over the years. Albeit the final responsibility lies on the chemist’s team who need to be reassured by exploring and conducting further unequivocal tests.

The views represented in this blog are the author’s own.

Blog written by Jose Gascon

References:

  1. https://www.nature.com/nature/journal/v548/n7668/pdf/548485a.pdf
  2. Huber, K. V. M. Nature, 508, 222–227 (2014).
  3. Bisson, J. et al. J. Med. Chem. 59, 1671–1690 (2016)
  4. See: Chemical Probes Portal (www.chemicalprobes.org ), Probe Miner (www.probeminer.icr.ac.uk) and Drugs Portal (www.probes-drugs.org )
  5.  https://www.chemistryworld.com/news/pfizers-response-to-compound-fraud-spotlights-quality-issues-/9234.article
  6. https://phys.org/news/2014-05-chemists-cancer-drug-candidate.html ,Oncotarget, 2014, 5(24): 12728–12737 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4350349/
  7. Hermann, J. C. et al. ACS Med. Chem. Lett. 4, 197–200 (2013)
  8.  Shortt, J. et al. Cell Rep. 7, 1009–1019 (2014).

 

 

 

 

 

 

 

 

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