Polypharmacology for Kinases

We've been a roll with epigenetics and PPIs lately.  So, its a nice break when a kinase paper comes out.  But, in keeping with the theme of hard targets, today's paper is about a tyrosine kinase.  We've started to see more and more FBDD on TKs.  One problem is that TKs can acquire resistance to drugs, quickly eliminating their therapeutic usefulness.  One way around this is to use polypharmacology: "optimized inhibitory profiles for critical disease-promoting kinases, including crucial mutant targets."  In this work, they are targeting RET and VEGFR2 dual inhibitor using a in silico/fragment approach.  

Compound design was largely based upon homology modeling the "DFG-out" RET structure utilizing the VEGFR2 structure as a template.  Their Kinase Directed Fragments (KDF) are shown in Figure 1.

Figure 1.

Their fragment design rationale makes some interesting comments.  They state that a "hinge binding" fragment alone can aggregate at high concentrations needed to achieve activity in a biochemical screen.  So, their fragments have an additional moiety that interact with the lipophilic or ribose pocket.  

Accordingly, KDFs have larger molecular weights and are generally more active than the fragments contained in traditional libraries, permitting screening in the micromolar range.

I would say the first statement is conjecture and the second untrue.  17 heavy atoms is squarely in the regime of what people consider "fragment" sized.  I think instead the authors are using the wrong tool for the job.  Using a biochemical screen to find fragment actives is akin to hammering a nail with a screwdriver.  Sure, you can do it, but why would you?  

Rather expectedly, they identified compound 1 as a promising starting platform.  Of course, the criteria for selecting this compound are kept highly secret.  It did "effectively" inhibit RET at 100 (63%) and 20 uM (28%) in the presence of 190 uM ATP [Km for RET 12uM].  It had VEGFR2 activity of 59% at 100 uM. 

Add caption

Modeling allowed them to generate the compounds showed in Figure 2.

Figure 2. 

Pz-1 had activity less than 1 nM against RET, RET(V804M/L)[a gatekeeper mutant],  and VEGFR2.  This equipotency was also demonstarted in cell-based assays.  Against a panel of 91 other kinases at 50 nM, Pz-1 had significant activity against 7 others (TRKB, TRKC, GKA, FYN, SRC, TAK1, MUSK).  So, in the end using primarily modeling and a biochemical assay they were able to generate a polypharmacological TK inhibitor.  I leave it to those more well versed in the biology whether or not those 7 other kinases pose a potential problem.  I however would argue that they generated an agent with polypharmacology against 9 kinases not 2.