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So What Exactly is SCR7?

Those of you who are into CRISPR will likely have heard for SCR7. It’s a compound added to the system that seems to enhance its efficiency and specificity, presumably through its inhibition of DNA ligase IV. That’s all fine – the mechanism makes sense, and making CRISPR more selective is a worthy goal that any number of labs are working on. That SCR7 structure is deeply unappealing, to be sure (two Schiff bases!), although all it has to do is hang around enough in vitro to do its thing. But there seems to be a problem with SCR7 itself.

SCR7

That’s what the people at Tocris are saying. Tocris is one of the larger (and definitely one of the more reliable) companies that sell inhibitors, ligands, and preclinical compounds for all sorts of targets. They’ve noticed that the material being sold by other vendors does not seem to match the reported structure. Instead, what’s out there seems to be the related pyrazine compound (at right). It appears that the pyrazine is actually the active compound in the CRISPR system, which makes you wonder if it’s the active compound in the original 2012 paper on its use as a ligase inhibitor as well.

SCR7 pyrazine

This also brings up thoughts of quality control, since the mass of the pyrazine compound is two hydrogens off that of the original structure (which should be immediately apparent in mass spec) and even more apparent in an NMR (those imine protons should be very distinctive). One might get the impression that there are some suppliers who didn’t bother looking at either of those very closely, or who just took what they got from some other source and ran with it under their own label. Worth keeping in mind next time you’re purchasing some tool compound. . .

 

13 comments on “So What Exactly is SCR7?”

  1. MoBio says:

    Two cheers for Tocris.

    As they frequently get their material from other vendors/labs it might be useful to find out where the other vendors are getting their materials from?

  2. steve says:

    I wonder if Tocris filed a patent on the pyrazine. It’s certainly a classic methods patent situation if everyone thought the active compound was the other structure and may be quite valuable if it ends up being used in GMP processes. Or have I just become too mercenary after all these years of drug development?

  3. Peter Kenny says:

    Did the Tocris people have any views on why the tautomeric preference of of the two compounds should be so different? That said, both compounds should be tested for their ability to scavenge/quency singlet oxygen so that we know whether they should be considered to be PAINS.

    1. AVS-600 says:

      You’d expect more preference for the di-keto tautomer in the pyrazine compound because aromatic stabilization from a second fused ring is significantly less important than that of a single aromatic ring. That said, the tautomeric preference of both species, along with dimers and oligomers that have poorly-defined tautomeric states, probably depends significantly on solvent anyway.

  4. Erebus says:

    My memory is a bit hazy, but wasn’t there an article mentioned on this blog, a few years ago, where somebody tested compounds from companies like Sigma, Tocris, and others of that sort, and found that something like 30% of the items received were misrepresented in some way? (I could be way off base, but I’d swear it was something like that.)
    …Does anybody have a link to that?

  5. OldLabRat says:

    Hmmm. The disclosing synthesis patent (WO 2014006518 A, available on google) has 14 protons in the H-NMR and the appropriate -ESI mass of 333. The reaction conditions are benzaldehyde and AcOH in DMF with a 3 hour reflux. Any synthesis experts care to comment on the likelihood of thermal cyclization of the imine carbons under these conditions?

  6. Tocris says:

    We made this material ourselves and discovered that the material reported as SCR7 in fact cyclises to what we are calling SCR7 pyrazine, and we have confirmed that SCR7 pyrazine is the identity of the material used in the original paper.

    We make the vast majority of our products ourselves and always qc material thoroughly before sale, we are well aware of the potential pitfalls for biologists associated with using white powders out of vials, and our efforts to verify the contents and enlighten our audience is where our ‘definitely one of the more reliable tag’ comes from (thanks!).

    There is more information on our website and if anyone has any more questions or would like to see the analytical data, Tocris technical support will be happy to help.

  7. antiaromatic says:

    I will first say that refluxing DMF is quite unusual for an imine formation reaction, but regardless the high temperature would be very likely to induce 6pi electrocyclization that would make the subsequent oxidation facile in air.

  8. Anon says:

    Are we sure that the bis-immine can’t undergo an electrocyclization, followed by oxidation to reach the pyrazine?

    I can definitely think that this reaction could happen on standing in DMSO.

  9. Nick K says:

    I concur with the poster above who says that refluxing DMF is rather extreme for an imine formation. Was the reaction carried out under air? If so, those conditions could very well lead to 6 pi electrocyclization followed by dehydrogenation to the pyrazine.

  10. A Nonny Mouse says:

    Easier to use benzil……

  11. Antony says:

    So What Exactly is SCR7?
    here is the answer..

    SCR7 is neither a selective nor a potent inhibitor of human DNA ligase IV.

    DNA Repair (Amst). 2016 May 7;43:18-23. doi: 10.1016/j.dnarep.2016.04.004

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