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

## TL;DR

This study explores how to design inhibitors that target the C-SH2 domain of SHP2, a protein involved in cancer and other diseases, to improve therapy options.

## Contribution

The study introduces a novel framework for designing inhibitors targeting the C-SH2 domain of SHP2, based on molecular dynamics and peptide library analysis.

## Key findings

- Residues at positions +1 and +3 provide hydrophobic stabilization for C-SH2 binding.
- A cationic residue at position +4 increases selectivity for C-SH2 over N-SH2.
- N-terminal residues form transient interactions not seen in crystal structures, affecting binding.

## Abstract

SH2 domain-containing
tyrosine phosphatase 2 (SHP2), encoded by PTPN11,
plays a crucial role in multiple cellular processes,
including proliferation and differentiation. Mutations in PTPN11 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.