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. 2018 Mar 16;13(3):647-656.
doi: 10.1021/acschembio.7b00980. Epub 2018 Jan 18.

Dual Allosteric Inhibition of SHP2 Phosphatase

Michelle Fodor  1 , Edmund Price  1 , Ping Wang  1 , Hengyu Lu  1 , Andreea Argintaru  1 , Zhouliang Chen  1 , Meir Glick  1 , Huai-Xiang Hao  1 , Mitsunori Kato  1 , Robert Koenig  1 , Jonathan R LaRochelle  2 , Gang Liu  1 , Eric McNeill  1 , Dyuti Majumdar  1 , Gisele A Nishiguchi  1 , Lawrence B Perez  1 , Gregory Paris  1 , Christopher M Quinn  1 , Timothy Ramsey  1 , Martin Sendzik  1 , Michael David Shultz  1 , Sarah L Williams  1 , Travis Stams  1 , Stephen C Blacklow  2 , Michael G Acker  1 , Matthew J LaMarche  1
Affiliations

Dual Allosteric Inhibition of SHP2 Phosphatase

Michelle Fodor et al. ACS Chem Biol. .

Abstract

SHP2 is a cytoplasmic protein tyrosine phosphatase encoded by the PTPN11 gene and is involved in cell proliferation, differentiation, and survival. Recently, we reported an allosteric mechanism of inhibition that stabilizes the auto-inhibited conformation of SHP2. SHP099 (1) was identified and characterized as a moderately potent, orally bioavailable, allosteric small molecule inhibitor, which binds to a tunnel-like pocket formed by the confluence of three domains of SHP2. In this report, we describe further screening strategies that enabled the identification of a second, distinct small molecule allosteric site. SHP244 (2) was identified as a weak inhibitor of SHP2 with modest thermal stabilization of the enzyme. X-ray crystallography revealed that 2 binds and stabilizes the inactive, closed conformation of SHP2, at a distinct, previously unexplored binding site-a cleft formed at the interface of the N-terminal SH2 and PTP domains. Derivatization of 2 using structure-based design resulted in an increase in SHP2 thermal stabilization, biochemical inhibition, and subsequent MAPK pathway modulation. Downregulation of DUSP6 mRNA, a downstream MAPK pathway marker, was observed in KYSE-520 cancer cells. Remarkably, simultaneous occupation of both allosteric sites by 1 and 2 was possible, as characterized by cooperative biochemical inhibition experiments and X-ray crystallography. Combining an allosteric site 1 inhibitor with an allosteric site 2 inhibitor led to enhanced pharmacological pathway inhibition in cells. This work illustrates a rare example of dual allosteric targeted protein inhibition, demonstrates screening methodology and tactics to identify allosteric inhibitors, and enables further interrogation of SHP2 in cancer and related pathologies.

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