06 May 2015

More Notes from DDC 2015

Dan and I both gave our thoughts on the conference last week.  But there was more than just the talks.  There were roundtables.  I chaired one on using kinetics and thermodynamics to drive medchem for the PPI track.  It was a lively discussion.  It was agreed that dyed in the wool enzymologists are priceless.  Kinetics is useless if clearance is the driving force, so this becomes a PK/PD issue.  But does it always have to be?  Paul Belcher from GE shared the On/off rate map (Figure 1) that shows what realm of binding you are in depending on your reates.  Paul also mentioned that Tony Gianetti, formerly of Genentech, used HSA and SPR to assess a more realistic picture of how compounds interact in plasma.  In terms of earlier phase uses, one of the round table attendees mentioned that she had seen talks of people using kinetic data to drive medchem.  She couldn't recollect who, so if any of our astute readers have references please share.  We also discussed using kinetic data to rank compounds with similar IC50.  A question was raised whether or not kinetics can be a good surrogate for receptor occupancy? 

Figure 1.  On/off Rate Map: A = affinity limited efficacy, B= on rate limited efficacy, C= rapid off rate limited, D= slow off protected efficacy
So, what about thermodynamics?  By and large, this was viewed as retrospective only.  Paul from GE did share that they have an app note of using SPR to generate thermodynamic data (I can't figure out how to link it, so if you want it contact me (or Paul) and we can send it). 

The main thrust was that neither kinetics nor thermodynamics are used to make prospective medchem decisions, rather they are used to justify in retrospection. Specifically for PPIs, the consensus was that the focus should be on on rate because you have to the compound in there when you can (i.e. when the complex is "open" enough). 

Derek Cole of Takeda led one of the FBDD round tables: Practical Aspects of Fragment Screening. Here is a picture, courtesy of Bjorn Walse of Saromics.  
His notes are replicated below:
Round table became figure 8 with two tables, with 2-3 deep seats and 40 -50 participants. FBDD expertise from novice to experts, including Teddy Zartler, Dan Erlanson, Gregg Siegal, and Andrew Petros. Large attendance highlights the number of newcomers to FBDD, confirmed by Dan Erlanson during opening when 2/3 of attendees indicated this was their first CHI FBDD meeting. Very lively debate/discussion covering 4 primary targets.

1. Designing and building and storing libraries. Discussed size of library i.e. 1000 or 40K. Agreed that a good library of 1000 should yield lots of high quality hits. Best to keep HA low, 10 - 16 (majority in 12 - 14 range). Discussed 3D vs. flat fragments. Flat give higher hit rate and should be major part of library. 3D likely give lower hit rate but may yield very exciting hits. Discussed complexity and the need for fragments to have enough complexity, but not two pharmacophores. (ref. Astex work). IF just starting out, best to buy a vendor library, e.g. Maybridge or others, which are fully characterized.

2. Screening techniques. NMR and SPR most common. Both very good. Tm - fast, inexpensive and can correlate with x-ray. What to do if no biochemical activity. Might be fine if below sensitivity of biochemical assay, i.e. very small fragment, however if larger fragment, need to understand why not being detected.

3. Potential pitfalls. Make sure library is soluble above assay conditions, i.e. > 1 mM in aqueous buffer (1 - 2% DMSO). Check for aggregation. Run SPR clean screen.

4. Fragment hit follow up. Think of fragments as seeds to identify protein compatible pharmacophore. SAR by catalog of similar fragments or fragments which present a similar pharmacophore is of great value. May find fragments which are much more potent, efficient, or which crystallize (if original was unsuccessful). Good to design diverse library, but similarity in fragments is different than similarity in large molecules, small 1-atom changes can have profound effect on binding mode, potency, etc.
 
If I missed any other highlights, please add them in the comments, or email me and I can add it in.  

4 comments:

Anonymous said...

With respect to thermodynamics and its prospective vs retrospective use, please check also out the following:
http://wavefunction.fieldofscience.com/2015/05/thermodynamics-in-protein-ligand.html

Dr. Teddy Z said...

Anonymous, you beat me to it.

iceobar said...

Link to the Van Hoff SPR analysis that Teddy mentioned http://www.gelifesciences.co.jp/technologies/biacore/pdf/B05_AN80_28-9214-28AA.pdf

Anonymous said...

Please could you explain how the table was derived and if there are any relevant references.

Many thanks