Merge and grow: Fragment-based activators of SOS1

The RAS family of proteins is implicated in roughly one third of cancers, and as such has been a long-standing target for drug discovery. Earlier this year we highlighted how covalent fragment-based approaches were instrumental in discovery of direct KRAS inhibitors. A recent paper in J. Med. Chem. by Stephen Fesik and colleagues at Vanderbilt University takes a more unusual approach.

RAS proteins are activated when guanine exchange factors (GEFs) such as Son of Sevenless 1 (SOS1) exchange GDP for GTP. Clinical compounds bind to a mutant form of KRAS and block this process. Previous high-throughput screening in Fesik’s group had found molecules that bind to and activate SOS1-mediated nucleotide exchange. While it might seem counterintuitive to activate a known oncogene, these molecules can actually block downstream RAS signaling by inducing a feedback mechanism. Here, the researchers used fragment screening to look for a new series.

The catalytic core of SOS1 is ~65 kD, relatively large for the protein-detected NMR methods beloved of the Fesik group, so they produced proteins in which the methyl groups of Ile, Val, Leu, and Met were ¹³C-labeled. Selective Ile to Ala mutations allowed them to assign the various methyl groups. An ¹H-¹³C HMQC screen of nearly 14,000 fragments yielded 59 hits (~0.1%), all quite weak: only five had dissociation constants better than 1 mM. Crystal structures were obtained for 16, revealing that all of them bind in the same site previously identified (see also here for similar work from a different group).

Fragments F-4 and F-7 bound in similar positions as each other and also as the HTS-derived compounds, so the researchers merged them to yield molecules such as compound 1b, with improved affinity and ligand efficiency.

Crystallography suggested that a nearby aspartic acid residue could be engaged through fragment growing, leading to molecules such as compound 2d. In addition to low micromolar affinity, this molecule also activated SOS1-mediated nucleotide exchange. In a cell-based assay, the compound caused enhanced phosphorylation of downstream target ERK at low concentrations and decreased phosphorylation at high concentrations, similar to what had been seen for the earlier series of molecules. Presumably, the biphasic response is due to a negative feedback loop that ultimately clamps down RAS signaling.

This is a nice example of structurally enabled fragment-merging and growing, assisted by knowledge of other ligands. While the compounds are probably not sufficiently potent to serve as chemical probes, they could be useful starting points. Activating the RAS pathway may or may not be a good approach for treating cancer, and we need suitable chemical tools to answer this question.