Computational Elucidation of a Monobody Targeting the Phosphatase Domain of SHP2

Src homology 2 (SH2) domain-containing phosphatase 2 (SHP2) is a key regulator in cellular signaling pathways because its dysregulation has been implicated in various pathological conditions, including cancers and developmental disorders. Despite its importance, the molecular basis of SHP2’s regulatory mechanism remains poorly understood, hindering the development of effective targeted therapies. In this study, we utilized the high-specificity monobody Mb11 to investigate its interaction with the SHP2 phosphatase domain (PTP) using multiple replica molecular dynamics simulations. Our analyses elucidate the precise mechanisms through which Mb11 achieves selective recognition and stabilization of the SHP2-PTP domain, identifying key residues and interaction networks essential for its high binding specificity and regulatory dynamics. Furthermore, the study highlights the pivotal role of residue C459 in preserving the structural integrity and functional coherence of the complex, acting as a central node within the interaction network and underpinning its stability and efficiency. These findings have significantly advanced the understanding of the mechanisms underlying SHP2’s involvement in disease-related signaling and pathology while simultaneously paving the way for the rational design of targeted inhibitors, offering significant implications for therapeutic strategies in SHP2-associated diseases and contributing to the broader scope of precision medicine.