Discovery of TK-642 as a highly potent, selective, orally bioavailable pyrazolopyrazine-based allosteric SHP2 inhibitor

Design, synthesis, anticancer activity evaluation and molecular dynamics study of pyrazine N-oxide-based SHP2 allosteric inhibitors

Src homology-2-containing protein tyrosine phosphatase 2 (SHP2), the first oncoprotein identified in the protein phosphatase family, has emerged as a promising anticancer target in recent years. Here, we report the discovery of a novel series of pyrazine N-oxide derivatives as potent SHP2 allosteric inhibitors and the identification of compound C5 as a highly potent and selective SHP2 allosteric inhibitor (SHP2WT IC50 = 0.023 μM, SHP2E76K IC50 = 0.119 μM). At the cellular level, C5 exerted significant antiproliferative effect on KYSE-520 and MV-411 cells (KYSE-520 IC50 = 6.97 μM, MV-411 IC50 = 0.67 μM) and induced apoptosis of MV-411 cells by downregulating the SHP2-mediated ERK cell signaling. Molecular dynamics simulations revealed that C5 could form stable hydrogen bond interactions, cation-π interactions and water bridges with key residues Glu110, Arg111, Phe113, Gly115 and Thr253, thereby effectively binding to the tunnel allosteric site of SHP2. Notably, the pyrazine N-oxide scaffold could additionally form a strong and stable hydrogen bond with Arg111. Collectively, this work uncovers a novel and potent scaffold as well as presents compound C5 as a promising lead for the development of new chemotypes of SHP2 allosteric inhibitors.

Structure-Guided Design of Pyrazolopyrimidinones as Highly Potent and Selective Allosteric SHP2 Inhibitors

Src homology-2-containing protein tyrosine phosphatase 2 (SHP2) plays crucial roles in various biological processes and has become a promising target for cancer therapy. In this work, we presented the structure-guided design of new allosteric SHP2 inhibitors, leading to the identification of the pyrazolopyrimidinone derivatives TK-684 and TK-685. Both compounds were highly potent and selective allosteric SHP2 inhibitors (TK-684: SHP2WT IC50 = 2.1 nM; Ki = 0.89 nM; TK-685: SHP2WT IC50 = 1.5 nM; Ki = 0.87 nM), likely binding to the "tunnel" allosteric site of SHP2. By targeting SHP2-mediated AKT and ERK signaling pathways, TK-684 and TK-685 suppressed cell proliferation and induced apoptosis in esophageal cancer cells. Additionally, oral administration of TK-685 demonstrated good antitumor effects in the KYSE-150 xenograft mouse model, with a T/C value of 76.8%. Collectively, the pyrazolopyrimidinone derivatives represent promising lead compounds for the treatment of esophageal cancer, where SHP2 is dysregulated.

Discovery of novel substituted pyridine carboxamide derivatives as potent allosteric SHP2 inhibitors

Src homology-2-containing protein tyrosine phosphatase 2 (SHP2), a critical regulator of proliferation pathways and immune checkpoint signaling in various cancers, is an attractive target for cancer therapy. Here, we report the discovery of a novel series of substituted pyridine carboxamide derivatives as potent allosteric SHP2 inhibitors. Among them, compound C6 showed excellent inhibitory activity against SHP2 and antiproliferative effect on MV-4-11 cell line with IC50 values of 0.13 and 3.5 nM, respectively. Importantly, orally administered C6 displayed robust in vivo antitumor efficacy in the MV-4-11 xenograft mouse model (TGI = 69.5 %, 30 mg/kg). Subsequent H&E and Ki67 staining showed that C6 significantly suppressed the proliferation of tumor cells. Notably, flow cytometry, ELISA and immunofluorescence experiments showed that C6 remarkably decreased the population of CD206+/Ly6C+ M2-like tumor-associated macrophages (TAMs), the expression level of interleukin-10 (IL-10), and the number of F4/80+/CD206+ M2-like TAMs, suggesting that C6 could effectively alleviate the activation and infiltration of M2-like TAMs. Taken together, these results illustrate that C6 is a promising SHP2 inhibitor worthy of further development.

Advances in SHP2 tunnel allosteric inhibitors and bifunctional molecules

SHP2 is a non-receptor tyrosine phosphatase encoded by PTPN11, which performs the functions of regulating cell proliferation, differentiation, apoptosis, and survival through removing tyrosine phosphorylation and modulating various signaling pathways. The overexpression of SHP2 or its mutations is related to developmental diseases and several cancers. Numerous allosteric inhibitors with striking inhibitory potency against SHP2 allosteric pockets have recently been identified, and several SHP2 tunnel allosteric inhibitors have been applied in clinical trials to treat cancers. However, based on clinical results, the efficacy of single-agent treatments has been proven to be suboptimal. Most clinical trials involving SHP2 inhibitors have adopted drug combination strategies. This review briefly discusses the research progress on SHP2 allosteric inhibitors and pathway-dependent drug combination strategies for SHP2 in cancer therapy. In addition, we summarize the current bifunctional molecules of SHP2 and elaborate on the design and structural optimization strategies of these bifunctional molecules in detail, offering further direction for the research on novel SHP2 inhibitors.