Fragments vs SHP2

One of the success stories we highlighted in last week’s summary of Fragments 2024 was the discovery of a potent inhibitor of SH2 domain-containing protein tyrosine phosphatase 2 (SHP2). James Day and colleagues at Astex and Taiho have just published the full account in J. Med. Chem.

 

Previous studies had shown that blocking SHP2 might be effective in certain cancers, particularly those dependent on mutant KRAS. As its name suggests, however, SHP2 is a phosphatase. This class of enzymes has highly charged active sites, which makes drug discovery notoriously difficult (see here for example). Indeed, a crystallographic fragment screen of the isolated phosphatase domain produced just one hit.

 

Simultaneously, the researchers performed NMR and crystallographic screens of the full-length protein, which contains two SH2 domains. This campaign was much more successful, with 88 crystallographically validated fragment hits. (Interestingly, a thermal shift assay of the same construct came up empty.) As Astex has previously reported, secondary binding sites on proteins are common, and SHP2 is no exception, with fragments binding to five sites. However, the vast majority – 83 of 88 – bound to what is called the tunnel region between the phosphatase domain and one of the SH2 domains.

 

The researchers note that “following completion of our Pyramid fragment screen, Novartis independently reported several SHP2 inhibitors” binding to the same site, which must have been both validating and irritating. Indeed, the Astex researchers did work on fragments binding to other sites, advancing one to a low micromolar inhibitor. But it’s hard to ignore a hot spot with dozens of bound fragments, and the tunnel region became their primary focus. One fragment was optimized to a low micromolar inhibitor. Another, fragment 3, had measurable affinity by ITC and respectable ligand-efficiency, and this was taken the furthest.

 

We’ve written previously about the importance of water in molecular interactions, and here the researchers performed solvent mapping molecular dynamics to identify water molecules that could be advantageously engaged. Scaffold hopping led to compound 15, and crystallography confirmed that the pyridine nitrogen forms a hydrogen bond to a water molecule. Increasing the lipophilicity around the phenyl ring and adding a basic amine to engage an electronegative region of the protein led to compound 18, with nanomolar biochemical activity and low micromolar activity in cells. Further structure-based design ultimately led to compound 28, with sub-micromolar cell activity. This compound has low efflux, low clearance and excellent oral bioavailability. When dosed orally in mouse xenograft models the molecule significantly inhibited tumor growth.

 

The exo-diastereomer of compound 28, in which the primary amine is facing down instead of up, shows interesting differences. It has a similar pKa as well as similar biochemical and cell-based activity but is plagued by high efflux and poor oral bioavailability. The researchers suggest that “steric shielding of the tropane bridge or pharmacophoric differences in efflux transporter recognition” may be responsible. There was considerable discussion at Fragments 2024 as to the precise source of the differences, but whatever the cause, this pair serves as a useful reminder that pharmacokinetics may vary dramatically even between nearly identical molecules.

 

Clinical development of SHP2 inhibitors has slowed due to a variety of reasons, including apparent on-target toxicity, but this is still a nice fragment-to-lead success story. Perhaps, as with capivasertib, it will just take time to find the right clinical strategy and patients who can benefit from these molecules.