Membrane-bound proteins such as GPCRs are often ignored by practitioners of FBLD in part because – Heptares notwithstanding – they are usually difficult to characterize structurally. This seems like a missed opportunity. A large fraction of drugs target GPCRs, and the vast majority of these were developed without crystallographic information, so why is the fragment community so fixated on structure? A paper just published in J. Med. Chem. by György Szabó, György Keserű and colleagues at Gedeon Richter, the Hungarian Academy of Sciences, and Mitsubishisi Tanabe shows how much can be done without strcutures.
The researchers were interested in metabotropic glutamate receptor 2 (mGluR2), a popular target for schizophrenia. In particular, they sought positive allosteric modulators (PAMs), which act outside the main ligand binding site to enhance signaling. A functional screen yielded compound 4 as a fairly potent fragment-sized hit. Comparison with other larger reported inhibitors suggested growing could be productive, leading to molecules such as compound 5, with sub-micromolar activity. Further optimization for potency and ADME properties led to compound 29, with low nanomolar potency.
Unfortunately, this molecule is very lipophilic (cLogP > 5), resulting in poor solubility, high plasma protein binding, and thus limited efficacy in a mouse pharmacodynamic model. All attempts to reduce lipophilicity came at the cost of potency.
To determine which elements of compound 29 were most important for binding, the researchers turned to group efficiency analyses; that is, they systematically removed different chemical groups and weighed the loss in binding energy versus the reduction in size. Even though they could not visualize precisely how each group interacted with mGluR2, the researchers could measure it. This effort revealed that the biaryl moiety was not particularly efficient, and although trimming it came at a cost in potency, this was compensated for by improved ligand efficiency. Substitution at another position off the initial fragment led to a satisfying boost in activity (compound 30). Further optimization for pharmacokinetic properties led to the fragment-sized compound 60, which is considerably less potent in vitro than compound 29 but which has better brain penetration and also better efficacy in two mouse models.
Several lessons can be drawn from this story. First, as Mike Hann warned seven years ago, molecular properties should not be ignored in the push for potency. Indeed, despite the 25-fold decrease in potency for compound 60 compared with compound 29, the smaller molecule is more effective in vivo. This is reminiscent of the Merck verubecestat story, which also involved optimization of a fragment hit to a potent but lipophilic lead that was ultimately abandoned in favor of an initially less active but more ligand-efficient series. The second lesson is that in vitro models can only take you so far. And finally, creative chemists are able to advance fragments even in the absence of structural information. Hopefully more of them will give it a try.