Decoding C-SH2 Domain/Peptide Interactions in SH2 Domain-Containing Tyrosine Phosphatase 2: A Molecular Framework for Rational Inhibitor Design

SH2 domain-containing tyrosine phosphatase 2 (SHP2), encoded by <i>PTPN11</i>, plays a crucial role in multiple cellular processes, including proliferation and differentiation. Mutations in <i>PTPN11</i> are implicated in various developmental disorders and hematological diseases, while wild-type (WT) SHP2 is a pivotal target in cancer therapy. SHP2 comprises two Src-homology 2 domains (N-SH2 and C-SH2), followed by a protein tyrosine phosphatase (PTP) catalytic domain. Under basal conditions, the N-SH2 domain autoinhibits SHP2 by blocking access to the catalytic site. An allosteric transition controls the detachment of the N-SH2 domain from the active site (and thus catalytic activity) and the affinity of the N-SH2 domain for its binding partners. We recently introduced the inhibition of protein-protein interactions (PPIs) of SHP2 as a novel, promising pharmacological strategy, an alternative to active site or allosteric inhibition. While our past efforts have focused on targeting the N-SH2 domain, this strategy shows limited efficacy against WT SHP2, where the autoinhibited conformation prevails, and the N-SH2 domain binding site is mostly unavailable. Conversely, the C-SH2 domain is not allosterically regulated, and its binding site is always accessible in both the active and inactive states of SHP2. Targeting this domain represents an alternative strategy to block SHP2 PPIs, allowing inhibition of the WT protein and weakly activated mutants. In this study, by performing molecular dynamics (MD) simulations of selected C-SH2/peptide complexes and by critically analyzing the available data from peptide libraries, the sequences of high-affinity ligands, both natural and artificial, and the experimental structures, we defined the features governing the C-SH2 binding affinity and specificity. Our analysis reveals that residues at positions +1 and +3, relative to the pY, provide hydrophobic stabilization, while polar residues are suitable at +2. The presence of a cationic residue at position +4 allows a gain in selectivity for the C-SH2 domain with respect to N-SH2. Finally, a cationic or aromatic residue at position +5 may contribute to binding affinity and selectivity. Notably, our MD simulations reveal transient but relevant interactions involving N-terminal residues that are not detectable in crystallographic structures. These findings lay the groundwork for designing peptide inhibitors that specifically target the C-SH2 domain of SHP2.