18 February 2013

FAK This

FAK, also known as PTK2, is a well known oncology target.  Current known inhibitors can be broken into three different binding classes:   Cpds I-IV are hinge binders, the chloropyramine targets the FAK-VEGF interface, and Y15 targets the Y397 site. Cpds V and VI were recently reported as novel allosteric inhibitors of FAK.

In this paper, a group led by researchers at Merck Serono, report their discovery of a new core from an "accelerated knowledge-based fragment growing approach".  

They used a commercially available fragment library (defined as:  MW, <200 solubility="">1 μg/mL; number of hydrogen bond donors and acceptors, ≤3) was screened against the immobilized kinase domain of FAK by SPR, which allowed them to determine kinetics for most of the fragments.  Compound I (Magenta) was found to be a 43 μm inhibitor.  The X-ray structure showed it to make excellent contacts with the protein.  Addition of the spinach shown in green, afforded an order of magnitude increase in potency.  In order to facilitate better elaboration, they chose to use 7-azaindole as the scaffold.
Then, going through traditional SAR and medchem, they end up with this table.  The best compound is a single digit nanomolar inhibitor with cell-based activity. One important aspect of this work is that the lead series can induce a rare helical loop DFG conformation.  In their conclusion, they state 
it was easier to improve kinase inhibition than kinase selectivity.

The first thing that stands out here is the solubility limit.  For a 250 Da fragment, 1μg/mL corresponds to 4 μM.  To me that sounds incredibly low; is it a typo?  They don't mention who those fragments are from.  I would love to know out of sheer curiousity.   Secondly, although they talk about their accelerated fragment growing approach, they don't actually explain what they mean by that?  To the best of my reading, I don't think they have introduced anything novel here.  


Dan Erlanson said...

One thing I thought was interesting was the attempt to correlate binding kinetics with cell activity; only molecules with relatively slow off-rates showed activity in HT-29 cells. Of course, these also tended to be the most potent molecules.

Another interesting observation was that some of the molecules active by SPR showed no inhibition in a biochemical assay, which the authors suggest could be due to (extremely) low solubility.

Anonymous said...

Given a max conc of 4uM and, as stated in the article, a two-fold 10 point concentration series I have a hard time trusting their stated kinetic results (SI, page 8). Anyone else who made the same observation?