26 October 2012

What is FBDD, and how pure is your library?

The most recent post on the newest biophysical technique for fragment screening coincides with a talk I heard yesterday and some thoughts I have been having recently.  Barry Morgan of GSK gave a talk on DNA Encoded Libraries, which is a Screen for Drug paradigm, as opposite from FBDD as you can go.  The problem I have with such highly elaborated molecules (4-5 synthons) is that they are Screening for Drug, rather they are Screening for Drug Affinity and unless they get extraordinarily lucky, they will still have to medchem to optimize everything else, and maintaining affinity.  I had some interesting discussions at the breaks with Dr. Morgan and a scientist from Vipergen as to the utility of this.  Dr. Morgan agreed that they now mostly focus on libraries of 2-3 synthons (which by and large would fit the definition of fragments (especially if you ignore the linker and humongous amount of DNA sticking off the molecule).  For the GSK work, their method detects signals on as little as 1000 molecules in 25 uL (~66 attoM) and the effective concentration of each molecule in each reaction is much less than 1 pM.  So, this got me to thinking about how pure this combi-chem libraries are (and combi-chem by any other name is still combi-chem)? But, it doesn't matter, aborted chemistry (e.g. 2 synthons instead of 3 synthons) will still be detected.  In fact, this is exactly where some of the power of this technique comes in.  So, is DEL technology FBDD by with an extraordinarly sensitive detection technique?
Don Huddler of GSK gave a talk right before me (and I swear we didn't coordinate our titles) about the FBDD work in his group.  When discussing the GSK library, Don mentioned that their purity cutoff is 95%.  Of course, this is pretty low for a High Concentration Screen (a 5% impurity would be present at 50uM!).  I would prefer to see a 99% cutoff for purity, but how realistic is that?  Additionally, some people use methods that don't detect strong binders or use a HCS % inhibition cutoff for their first triage.  So, a 50uM impurity (worst case for most libraries) would probably not even register as a hit in the primary screen.  But, I am curious what levels of purity people use for their fragment libraries (if any).  I somehow can't seem to get a poll to look right with the new blogger interface, so please post your comments (anonymously if you need to) and tell me what you think.


Dan Erlanson said...

These are good questions, and not surprisingly both of them came up at FBLD 2012. Indeed, they are somewhat related, since the question “what is FBDD” gets to the issue of the “purity” of the discipline.

Regarding what constitutes FBDD, I personally take a rather catholic view: if it borrows concepts from FBDD, it is FBDD. That said, I also like Mark Whittaker’s idea of FADD (fragment-assisted drug discovery) as a broader category that includes approaches that purists might not consider FBDD.

In terms of library purity, it is important to remember that stated purity levels may not be accurate, as they are usually based on NMR or HPLC, which don’t detect everything. Heavy metals can be particularly insidious: we mentioned silver here, and at FBLD 2012 Charles Wartchow described a project at Roche in which a fragment screen produced lots of hits, but many of them turned out to be due to contaminating zinc.

Chris said...

I guess purity required may be dependent on the detection technology? Would X-ray allow the identification of the impurity, if F-NMR unless the impurity contained F it would not be seen etc.