Structural insights into the binding modes of SHP2 allosteric inhibitors

Src homology region 2 -containing protein tyrosine phosphatase 2 (SHP2) is an oncoprotein and a promising target for cancer treatment. Efforts to develop SHP2 allosteric inhibitors, such as SHP099, have laid the foundation for SHP2-targeted therapeutics. However, there are few SHP2 allosteric inhibitors have reached to clinical trials up to date. SHP099, despite its high potency, has off-target effects on the human ether-a-go-go related gene (hERG) channel, increasing cardiovascular toxicity risk due to its highly basic amine group. To address these challenges, understanding the molecular interactions between SHP2 allosteric inhibitors and SHP2 is essential for advancing drug development. In a previous study, an in-silico structure-based screening identified neutral SHP2 inhibitors, including C8. This study analyzed the binding modes of ionized and neutral SHP2 allosteric inhibitors under physiological and acidic pH conditions using constant pH molecular dynamics (cpHMD) simulations. SHP099 and C8 exhibited lower free binding energies with SHP1 compared to SHP2, confirming their specificity for SHP2. The protonated tertiary amine group in SHP099 contributed significantly to ligand stability and binding to SHP2, which was not observed with the neutrally charged allosteric inhibitor (C8). Furthermore, SHP099's binding interactions with SHP2 were pH-dependent, with acidic pH conditions showing the highest binding affinity. These findings provide insights into the molecular interactions of SHP2 allosteric inhibitors under physiologically relevant conditions, which will guide the optimization of the structural design of pyrazine-class SHP2 allosteric inhibitors.

The online version contains supplementary material available at 10.1007/s40203-025-00551-x.