HIT101308137 and HIT104293658 nominate dual target chemotypes for PTPN1 and PTPN2 with preliminary selectivity in colorectal cancer cells

Colorectal cancer remains a major clinical challenge, and dual targeting of PTPN1 and PTPN2 represents a promising strategy to modulate conserved phosphatase signaling relevant to tumor biology and immune regulation. Here, we identified and prioritized two compounds, HIT101308137 and HIT104293658, as dual compatible chemotypes for PTPN1 and PTPN2 through a structure guided workflow integrating pocket comparison, ligand based interaction hypothesis generation, and structure based evaluation under static and dynamic conditions. Sequence and structural analyses supported high conservation of the catalytic pocket, providing a feasible basis for dual target coverage. Screening and post docking tri metric prioritization nominated three shared candidates, of which HIT101308137 and HIT104293658 were further differentiated by microsecond molecular dynamics simulations and interaction occupancy profiling. In both targets, the candidates preserved an Arg centered anchoring pattern within the P loop, while exhibiting distinct binding behaviors: HIT101308137 maintained a more co crystal like, catalytic core coupled interaction network with stronger persistence of contacts associated with the WPD region, whereas HIT104293658 displayed a more entrance biased interaction distribution consistent with increased pose reorganization. In CCK 8 viability assays, HIT101308137 and HIT104293658 produced reproducible dose dependent reductions in viability in HCT116 and SW480 cells, while showing limited effects in NCM460 and FHC cells within the same concentration window. Together, these results nominate HIT101308137 and HIT104293658 as starting points for dual target optimization and provide a mechanistic rationale to enhance cellular potency while maintaining low impact on normal colonic epithelial cells.