Structure-based identification of liensinine as a natural allosteric SHP2 inhibitorwith anti-proliferative activity in HepG2 cells

SHP2, encoded by the PTPN11 gene, is a non-receptor tyrosine phosphatase that plays a key role in oncogenic Ras/MAPK signaling. Aberrant SHP2 activity contributes to the progression of various cancers, including liver cancer. In this study, we used an AI-based virtual screening platform (HyperLab) to evaluate 127 natural compounds for SHP2 allosteric inhibition. Liensinine, a bisbenzylisoquinoline alkaloid from Nelumbo nucifera, was identified as a top candidate with strong predicted binding to the SHP2 allosteric tunnel site. This tunnel-shaped pocket is located at the interface between the N-SH2, C-SH2, and PTP domains, where allosteric inhibitors stabilize SHP2 in its closed, inactive conformation by preventing domain rearrangement. Docking analyses using HyperLab and CB-Dock2 consistently supported its interaction with key regulatory residues. Biochemical assays confirmed that Liensinine inhibits SHP2 phosphatase activity in a dose-dependent manner, with an IC₅₀ of ~5.2 μM. In HepG2 cells, Liensinine reduced cell viability to approximately 70% at 20 μM and 50% at 50 μM, indicating a concentration-dependent cytotoxic effect. Additionally, RNA-seq data analysis revealed upregulated PTPN11 expression in hepatocellular carcinoma tissues compared to normal liver. These quantitative findings strengthen the experimental evidence for Liensinine's inhibitory potential. Together, these findings suggest that Liensinine may serve as a natural SHP2 allosteric inhibitor with anticancer potential.