Targeting Oncogenic Src Homology 2 Domain-Containing Phosphatase 2 (SHP2) by Inhibiting Its Protein-Protein Interactions.

Sara Bobone ,Elisabetta Flex ,Maja Šolman ,Valentina Tirelli ,Giulia Fasano ,Tommaso Gandini ,Giovanna Carpentieri ,Massimo Sanchez ,Giuseppe Torini ,Giada Cattani ,Alessio Bocedi ,Andrea Quercioli ,Barbara Biondi ,Antonella Lauri ,Luca Pannone ,Valerio Santucci ,Martina Venditti ,Marco Tartaglia ,Cristina Peggion ,Chiara De Faveri ,Jelmer Hoeksma ,Simone Martinelli ,Viviana Claudia Canale ,Fernando Formaggio ,Paolo Calligari ,Jeroen Den Hertog ,Gianfranco Bocchinfuso ,Lorenzo Stella

doi:10.1021/acs.jmedchem.1c01371

Abstract

We developed a new class of inhibitors of protein–protein interactions of the SHP2 phosphatase, which is pivotal in cell signaling and represents a central target in the therapy of cancer and rare diseases. Currently available SHP2 inhibitors target the catalytic site or an allosteric pocket but lack specificity or are ineffective for disease-associated SHP2 mutants. Considering that pathogenic lesions cause signaling hyperactivation due to increased levels of SHP2 association with cognate proteins, we developed peptide-based molecules with nanomolar affinity for the N-terminal Src homology domain of SHP2, good selectivity, stability to degradation, and an affinity for pathogenic variants of SHP2 that is 2–20 times higher than for the wild-type protein. The best peptide reverted the effects of a pathogenic variant (D61G) in zebrafish embryos. Our results provide a novel route for SHP2-targeted therapies and a tool for investigating the role of protein–protein interactions in the function of SHP2.

Highlights

The Src homology 2 (SH2) domain-containing phosphatase 2 (SHP2), encoded by the PTPN11 gene,[1] is ubiquitously expressed and mediates signal transduction downstream of various receptor tyrosine kinases (RTKs)
The peptide corresponding to pY1172 or pY1179 of insulin receptor substrate 1 (IRS-1) has one of the highest known binding affinities for the N-SH2 domain of SHP2.18,47 On the basis of our study of the structural determinants of a high affinity for this domain, the IRS-1 pY1172 sequence is near to optimal in several respects, because it has apolar residues at positions +1, +3, and +5, which point toward the hydrophobic groove in the N-SH2 structure, and anionic amino acids at positions +2 and +4, which can interact with a peculiar KxK motif in the BG loop.[18]
Our findings provide several insights into the interaction of phosphopeptides with SH2 domains and, in particular, with the N-SH2 domain of SHP2 and into the suitability of these recognition units as therapeutic targets

Summary

■ INTRODUCTION

The Src homology 2 (SH2) domain-containing phosphatase 2 (SHP2), encoded by the PTPN11 gene,[1] is ubiquitously expressed and mediates signal transduction downstream of various receptor tyrosine kinases (RTKs). As discussed in the Introduction, we and others have hypothesized that, in its autoinhibited state, the conformation of the NSH2 domain prevents efficient association with binding partners, while the affinity of SHP2 for phosphorylated sequences is maximized in the open, active state.[19,21−23] This model has many relevant consequences, because it implies that pathogenic mutants have a twofold effect: they increase the activity of the phosphatase and its affinity for binding partners In principle, both effects could be the origin of the hyperactivation of the signal transduction pathways involved in the pathologies caused by PTPN11 mutations. This finding indicates that the peptide could inhibit SHP2 PPIs, causing only a limited increase in catalytic activity. These results indicate that co-injection of the OP rescued the developmental defects induced by a pathogenic, basally activated Shp2a variant, while it had no effect on wild-type embryos

■ DISCUSSION

■ ACKNOWLEDGMENTS

■ REFERENCES