Thursday, 20 September 2012

FBLD 2012 Preview

FBLD 2012 is about to happen. Although I'll not be there (and not even nearby), I thought that a preview, like the one posted recently for EuroQSAR (which I also didn't go to) might be in order.

Rod Hubbard will kick things off and he always does a great talk.  Following his contribution will be three talks from Big Pharma.  I've only ever been to one fragment conference and the Big Pharma contributions at that meeting tended to be strategy-heavy and results-light.  Hopefully things will have moved on a bit in the last three and a half years...

Were I attending the meeting, I'd be paying particularly close attention to the membrane protein talks (and might even take the opportunity to ask one of the creators of the Rule of 3 how hydrogen bond acceptors are defined when applying Ro3).  I would also be trying to learn as much as possible about newer technologies for measuring affinity.  Remember that the power of a fragment screening assay is defined by the weakness of the binding that can be detected. Although always desirable, high throughput is a secondary consideration in these assays since one rationale for screening fragments is that one doesn't need to assay as many compounds.  Expect to see at least one speaker get reminded that in SPR molecules are 'tethered' rather than 'immobilised'.

Thermodynamics and kinetics provide the focus of a few of the talks and usually one will hear about the benefits of 'enthalpy-driven' binding and slow off-rates.  My stock question for those who assert the benefits of binding that is 'enthalpy-driven' is, "how do isothermal systems sense enthalpy changes associated with binding?" and I have also made this point in print.  For a fixed Kd reducing the off-rate will also reduce the on-rate and binding kinetics have to be seen in the broader context of distribution.  If the binding is faster than distribution then on-rates and off-rates become irrelevant, except to the extent to which they determine Kd.

At a conference like this, I'd have hoped to see something along the lines of 'unanswered questions and unsolved problems'.  How predictive are fragment properties of the properties of structurally-elaborated molecules?  Just how strong is the correlation of promiscuity with lipophilicity?  Is getting structures for protein-ligand complexes still a bottleneck?

So best wishes for an enjoyable and successful meeting.  Make sure to test the wits of the speakers with some tough questions.  It's character-building for them and loads of fun for everybody else.  Meanwhile here in Brasil it is 'imunização para insetos' at my place and I've cooked up a local response to enthalpy optimisation: Termodinâmica Macumba.


Martin Andersson said...

Hi Pete, I would like to comment on your point about screening technologies. I think there has been a race for weak affinities in the last years, and people may have forgotten what fragment screening is all about: finding the most ligand efficient binders in your screening set. Hence, you need to be sure that you have a screening technology that don't miss out on small, potent binders. Having an "overly sensitive" screening technology that lets you identify the weakest binders at the expense of the more potent ones will do more harm than good. Furthermore size is equally (if not more) important, so being able to detect small binders is also a very important feature.

Pete said...

Ultimately one needs to be able to measure affinity and I would certainly be worried about screening technology that could only do this for weakest binders. I'm not aware of any technology for which this is the case and would certainly be keen to learn more.

Ligand efficiency is useful but I would not use it as the only criterion when following up the intial screen. First I'd be looking for similarity (including pharmacophoric) of fragment hits (which I refuse to call frits) to each other. Then I'd want to follow up the hits with analogs (including pharmacophoric).

It's important to remember that the denominator is abitrary(we could use the square or the square root or the square root of the number of heavy atoms) so we should use it cautiously.

Martin Andersson said...

I agree perfectly with your point on how to follow-up fragment hits. We use analogs a lot to learn more and optimize our fragments further before expanding on them. Regarding size; I did not mean to say that size is important to the calculation of ligand efficiency, but rather that the ability of your screening technology to detect binders regardless of size is important. You would not like to have your hit set enriched for the larger binders in the fragment library.
I would also argue that in an FBDD screening cascade the primary screen is often run in a mode where ligand binding is only indicated, and the actual affinity measurement is done later, during follow-up, either as a more refined experiment using the same technology or by an orthogonal technology.

The ability to detect both strong and weak binders is not so much a limitation to screening technology, but rather a limitation imposed by the way the actual assay is optmized and set up.

For an example of some NMR-based technologies that could suffer from those kind of limitations, see e.g. Kobayashi et al, 2010, J. Biomol. Screen. 15:978.

Quoting from the discussion in that paper:

"We noted a distinct lack of correlation between the binding
signal for TINS and the potency in the biological activity, whereas STD fares only marginally better. The poor correlation between the level of biological activity and the magnitude of the NMR readout is likely due to the dependence of ligand-observed NMR signals on the off rate of the ligand. During the fixed length of an NMR experiment, tighter binding ligands, which have slower off rates, will not generate as much signal amplification as weaker binding ligands. This is the likely explanation for the observation that the 2 fragments with slow kinetics in SPR and potent biological activity were only marginally detected as hits in both TINS and SPR." (I suspect this to be a typo, SPR should probably be STD)" A further issue for TINS is that for ligand screening, the parameters of the NMR experiment are optimized to detect weak binders. By shortening the T2 period during the spatially selective TINS experiment, the correlation between TINS effect and binding affinity can be improved considerably."

Hence, optimizing your screening assay to detect the weakest binders may not be optimal in every case. If you have a target with decent druggability there may be stronger binders in your library than you are anticipating, and you wouldn't want to miss those.

Pete said...

I can now see more clearly what you were getting at so thanks for the very detailed comment. I certainly agree that failing to detect stronger binders because the assay had been tuned to detect weak binders would be a problem. My take is that measurement of weak affinity is the most challenging problem which and it would probably be more correct to state that the power of the assay is defined by the weakness of the affinity that can be reliably measured. Make sure to ask lots of questions if you're going to be at FBLD.