Dual Allosteric Targeting of SHP2: Development of Bivalent Inhibitors with Enhanced Potency for Cancer Treatment

SHP2 is an attractive anticancer target due to its pivotal role in oncogenic signaling. Although combination therapies involving SHP2 inhibition are promising, none have yet advanced to clinical approval, highlighting the need for innovative SHP2-targeted approaches. Herein, we developed a series of bivalent allosteric inhibitors by linking two distinct ligands targeting the tunnel and latch sites. SDUY127 demonstrated the most potent enzymatic inhibition (IC50 = 16 nM), representing a 3-fold improvement over the parent compounds. We developed new site-specific biotinylated probes and AlphaScreen-based assays to confirm the dual engagement of both allosteric pockets. Molecular dynamics simulations further established that SDUY127 stably occupied both sites in a 1:1 stoichiometry. Additionally, SDUY127 exhibited improved antiproliferative efficacy against MV4–11 cells through more sustained suppression of MAPK signaling compared to monotherapy or combination treatments. This work identifies SDUY127 as the first bivalent SHP2 inhibitor and presents a framework for designing and validating dual-site small-molecule modulators of phosphatases.