KRAS(G12D) can be targeted by potent inhibitors via formation of salt bridge

Abstract

KRAS mutation occurs in nearly 30% of human cancers, yet the most prevalent and oncogenic KRAS(G12D) variant still lacks inhibitors. Herein, we designed a series of potent inhibitors that can form a salt bridge with KRAS’s Asp12 residue. Our ITC results show that these inhibitors have similar binding affinity with both GDP-bound and GTP-bound KRAS(G12D), and our crystallographic studies reveal the structural basis of inhibitor binding-induced switch-II pocket in KRAS(G12D), experimentally confirming the formation of a salt bridge between the piperazine moiety of the inhibitors and the Asp12 residue of the mutant protein. Among KRAS family proteins and mutants, both ITC and enzymatic assays demonstrate the selectivity of the inhibitors for KRAS(G12D); and the inhibitors disrupt the KRAS–CRAF interaction. We also observed the inhibition of cancer cell proliferation as well as MAPK signaling by a representative inhibitor (TH-Z835). However, since the inhibition was not fully dependent on KRAS mutation status, it is possible that our inhibitors may have off-target effects via targeting non-KRAS small GTPases. Experiments with mouse xenograft models of pancreatic cancer showed that TH-Z835 significantly reduced tumor volume and synergized with an anti-PD-1 antibody. Collectively, our study demonstrates proof-of-concept for a strategy based on salt-bridge and induced-fit pocket formation for KRAS(G12D) targeting, which warrants future medicinal chemistry efforts for optimal efficacy and minimized off-target effects.

Targeting a broad spectrum of KRAS-mutant cancers by hyperactivation-induced cell death

“…Therefore, targeting the SHANK3-KRAS interaction represents a new pan-KRAS-mutant compatible strategy for selective killing of KRAS-mutant cancer cells. Secondly, current efforts strive to develop KRAS inhibitors (12,(15)(16)(17)43), whereas we describe a mechanism to hyperactivate KRAS-MAPK signalling to cytotoxic levels by disrupting KRAS interaction with SHANK3.…”

“…KRAS mutations have a long history of resistance to drug therapy. However, through the accrued knowledge of the structural and biochemical characteristics of these mutants, the field has seen a recent development of mutation-specific drugs with promising preclinical and clinical efficacy (10)(11)(12)(13)(14)(15)(16)(17)(18). The most promising mutation-specific inhibitors are those targeting KRASG12C, a mutation found in ~12% of all KRASdriven tumours (11-16, 19, 20).…”

Mutant RAS and the tumor microenvironment as dual therapeutic targets for advanced colorectal cancer

“…For example, direct inhibitors binding the more common G12D variant, by formation of a salt bridge with the aspartate residue, are in development (e.g. MRTX1133) [103,104]. Furthermore, KR12, a DNA-alkylating agent that binds with high affinity to the minor groove of specific KRAS codon 12 mutants (G12D and G12V), induces inhibition of cell growth in vivo and in vitro, by causing double-strand DNA breaks, cellular senescence and subsequently apoptosis [105].…”

ROR1 plays a critical role in pancreatic tumor-initiating cells with a partial EMT signature

“…Moreover, 60% of the tumors with wild-type KRAS harbored an alternative RAS-MAPK activating pathway, which highlights the importance of the RAS pathway in PDAC. Recently, inhibitors against mutant KRAS G12D or KRAS G12C have been developed and have given hope for breakthrough therapies in malignancies with KRAS mutations, including PDAC (Wang et al , 2022; Mao et al , 2022; Canon et al , 2019). However, resistance mechanisms have become uncovered, and thus, other therapeutic strategies have also been explored (Xue et al , 2020; Awad et al , 2021).…”