Fragments vs MCL-1, again and again

Last year we highlighted a paper from Stephen Fesik’s group at Vanderbilt in which he used SAR by NMR and fragment merging to identify nanomolar inhibitors of the protein MCL-1, an anti-cancer target that had previously been thought to be impervious to small molecules. In a recent paper in Bioorg. Med. Chem. Lett., Andrew Petros, Chaohong Sun, and other former colleagues of Fesik at AbbVie describe two additional series of inhibitors.

The researchers started with an NMR screen using MCL-1 in which the methyl groups of isoleucine, leucine, valine, and methionine were ¹³C-labeled. Screening this against a library of 17,000 fragments in pools of 30(!) gave dozens of hits, some of which inhibited in a biochemical assay (for aficionados, they assessed binding to the BH3 domain of Noxa using fluorescence polarization as a readout).

Fragment 1 turned out to be fairly potent, though it is super-sized and violates the rule of three. The researchers were unable to get co-crystal structures of any of their fragments bound to MCL-1, but they were able to use NOE-based NMR experiments to develop a model of how fragment 1 might bind. This led them to synthesize a number of analogs such as compound 17, for which they were able to obtain a co-crystal structure with the protein, ultimately leading to the mid-nanomolar compound 24.

Fragment 2 was much less potent than the other fragment but had a considerably higher ligand efficiency. In this case simple modeling suggested growing away from the acidic portion of the molecule, leading to compound 36 (which was characterized crystallographically bound to MCL-1) and the more potent compound 44.

Overlaying the co-crystal structures of compounds 17 (blue) and 36 (red) reveals that they both bind in the same region, where Fesik’s compound 53 (green) also binds. All three molecules place a carboxylic acid in a similar position, but the two more potent molecules thrust a hydrophobic moiety deep into a pocket of the protein. It is tempting to speculate that compound 44, the more potent analog of compound 36, may also take advantage of this pocket.

Andrew Petros presented some of this work at FBLD 2012, so it is nice to see it in print. Though reasonably potent, it is worth keeping in mind that the molecules are also quite lipophilic. Perhaps it is significant that, like the Fesik paper, no cell-based data are presented. Collectively, though, these papers establish that MCL-1 is ligandable. Whether it will be druggable remains an important – and as yet unanswered – question.