04 November 2013

Biophysics Conference (pt 3)

I have been giving my thoughts on the Novalix Conference on Biophysics in DD here and here.  Today's installment is on the "Emerging Technologies" and "Hits and Leads" section of the conference.  

Stefan Duhr- NanoTemper: Microscale Thermophoresis (MST) has been discussed here previously. Both Dan and I really like this technology.  This talk was an excellent overview of the theory.  Nanotemper claims that it has a dynamic range up to the mM range, however in their talk all of the examples were relatively, or very, tight binding complexes.  It has definite advantages in that it only uses 4 uL of sample/data point and it takes 40s/data point.  

There were a variety of talks on technologies that are definitely cool in a "Amazing they can do that" sort of way.  However, as an application to drug discovery, not so much.  There was a talk about Backscattering Interferometry (BSI), a switchable DNA chip (definitely cool tech, but with no discernible advantage over similar technology), Cryo-TEM (!), most of these talks I could not figure out how you would use in screening/FBHG.  However, the point of emerging technology is to emerge, so maybe in the near future there will be pretty boxes that have notable, robust discovery uses.

Chris Marshall -UToronto: This talk and Till's (below) were about GTPases.  This talk focused on a NMR-based GTPase assay.  What was particularly interesting was that they tethered their GTPase (Rheb) to a nanodisc, which should tumbling properties semi-independent of the nanodisc. This is a much more "biological" condition that many people typically use.  Other than that, this was a decidely academic talk.  In an organization with unlimited resources, and no time lines, you might follow the same approach as this group did.  In reality, I can't imagine you would.

Helena Danielson - Uppsala U/Beactica: This was a very interesting talk (per usual).  One key comment she made was: ease of use of a technology is NOT the same as ease of implementation.  In terms of Beactica's fragment library: 2000 compounds (from her slide) that are largely Voldemort Rule compliant.  It is enriched in known drug frameworks with diversity and scaffold representation (I am not sure what is meant by that).  For her first case study, they only used 930 fragments.  She didn't mention why a subset of the entire library was used.  She mentioned that they use an early biochemical screen as an orthogonal assay.  She spent a lot of time discussing the deconstruction of sensorgrams, in particular, if you have specific and non-specific binding contributing.  She also presented a case study against a GABA-A like receptor.  She then spent the rest of her talk discussing Chemodynamics: varying sample conditions, like temperature or pH. For BACE, for example, compounds need to bind at neutral and then acidic pH. 

Till Maurer- Genentech:  Till's talk was on k-RAS by NMR.  (As an aside, k-RAS has become a "hot" target largely due to this work.  Way back in 2003, we published a new method for NMR screening using k-RAS as one of our targets because it was so interesting we knew legal would let it go.)  Their fragment library had 3285 fragments (it is now 5000) biased towards high solubility for X-ray follow up in mixtures of 5.  Of 3285 fragments they found 1092 with a S/N >5.  Of these 266 confirmed (higher S/N threshold and other criteria) and were followed up by H-N HSQC.  Of 25 confirmed by HSQC, 6 produced crystals. 

Johannes Ottl- Novartis: The last talk of the conference was another really nice overview of the various biophysical methods and how they are applied in a few different case studies. 

So, what was the take home of this conference?  Biophysics is a rich and diverse toolbox.  However, in many cases we still don't know how to use these powerful tools prospectively, rather they are much more used retrospectively. 


Dan Erlanson said...

The Genentech Ras work is really interesting (I blogged about it last year here), but Ras has been "hot" for much longer; Fesik had an independent effort that found fragments that bind to the same site (see here).

Peter Kenny said...


Dr. Teddy Z said...

I knew that would bring you out Pete.

Anonymous said...

Nanotemper does look really good, but throughput is a huge issue as you can only load 16 samples at a time and the last time I checked the loading was a manual process (don't know if it can be automated now?)

If there was a 96 or 384 plate based version, it would be much more practical.

Ford@NanoTemper said...

Hi. NanoTemper Technologies now has an automated instrument for increased throughput. The array of capillaries fit into a 384 well plate, and the instrument can be integrated with liquid handling. We have an application note for fragment screening with MEK1 protein, carried out in collaboration with Sanofi. And we recently won the BioProcess International award (Analytical- best technology application)!

-Nicole Ford
Application Scientist, NanoTemper Technologies

Ford@NanoTemper said...

Link for automated instrument from NanoTemper: http://www.nanotemper-technologies.com/products/monolith-series/monolith-ntautomated/