Allele-specific inhibitors inactivate mutant KRAS G12C by a trapping mechanism

Abstract

It is thought that KRAS oncoproteins are constitutively active because their guanosine triphosphatase (GTPase) activity is disabled. Consequently, drugs targeting the inactive or guanosine 5'-diphosphate-bound conformation are not expected to be effective. We describe a mechanism that enables such drugs to inhibit KRAS(G12C) signaling and cancer cell growth. Inhibition requires intact GTPase activity and occurs because drug-bound KRAS(G12C) is insusceptible to nucleotide exchange factors and thus trapped in its inactive state. Indeed, mutants completely lacking GTPase activity and those promoting exchange reduced the potency of the drug. Suppressing nucleotide exchange activity downstream of various tyrosine kinases enhanced KRAS(G12C) inhibition, whereas its potentiation had the opposite effect. These findings reveal that KRAS(G12C) undergoes nucleotide cycling in cancer cells and provide a basis for developing effective therapies to treat KRAS(G12C)-driven cancers.

Fig. 1. Selective inhibition of KRAS^G12C signaling and cancer cell growth by ARS853

(A) KRAS^G12C mutant cells (H358) were treated with a novel (ARS853) or a previously described (cmpd 6) compound for 5 hours. The effect on the level of active, or GTP-bound, KRAS was determined by a RAS-binding domain pull-down (RBD:PD) assay and immunoblotting with a KRAS-specific antibody. The effect on ERK and AKT signaling was determined by immunoblotting with the indicated antibodies. A representative of at least two independent experiments for each compound is shown. (B) H358 cells were treated for 72 hours with increasing concentrations of the indicated inhibitors, followed by determination of viable cells by the ATP glow assay (n = 3 replicates). (C) The effect of ARS853 treatment on the inhibition of signaling intermediates in a panel of KRAS^G12C-mutant lung cancer cell lines. KRAS^WTA375 cells were used as a control. A representative of at least two independent experiments for each cell line is shown. (D and E) The cell lines were treated over time to determine the effect of ARS853 on the proliferation of G12C (D) or non-G12C (E) KRAS models (n = 3 replicates). (F) The effect of ARS853 treatment on the cleavage of apoptotic intermediates was determined by immunoblotting with the indicated antibodies. A representative of two independent experiments is shown. (G) Cell extracts from the indicated cell lines treated with ARS853 were subjected to a caspase activation assay with the Z-DEVD-AMC reporter substrate. The increase in fluorescence relative to untreated (0) is shown (n = 3 replicates). (H) Following treatment with ARS853 for 24 hours, the cells were stained with annexin V and evaluated by flow cytometry to determine the increase in annexin V–positive cells relative to untreated cells. Data in (B), (D), (E), and (G) are mean and SEM.

Fig. 2. Inhibition of active KRAS levels despite an interaction with GDP-bound KRAS^G12C

(A) KRAS^G12C-mutant lung cancer cell lines were treated with ARS853 (10 μM) over time, and cellular extracts were analyzed to determine the effect on KRAS-GTP as in Fig. 1A. (B) Recombinant KRAS^G12C was loaded with GDP or nonhydrolyzable GTPγS and then reacted with ARS853 at a 1:1 molar ratio for 1 hour, at room temperature. The samples were analyzed by differential scanning fluorimentry to determine the shift in thermal denaturation curve induced by ARS853 binding (n = 4 replicates for GDP and n = 3 replicates for GTPγS). Mean and SEM are shown.

Fig. 3. Inhibition of KRAS^G12C requires GTPase activity and is attenuated by nucleotide exchange

(A) Schematic of the mutations used to block the GTPase activity of KRAS. NTF, nucleotide free. (B) KRAS mutants, expressed and affinity purified from HEK293 cells, were subjected to a GTPase reaction. The orthophosphate product was measured by the Cytophos reagent and expressed as fold change over GTP alone (n = 3, mean and SEM). (C) HEK293 cells expressing HA-tagged KRAS constructs were treated with ARS853 for 5 hours. Cell extracts were evaluated by RBD:PD and immunoblotting with an anti-HA antibody, to determine the effect on GTP-bound mutant KRAS^G12C. A representative of three independent experiments is shown. (D) Extracts from cells expressing the KRAS constructs treated as shown were evaluated by mass spectrometry to determine the percentage of KRAS^G12C bound to the drug. KRAS^G12C-GTP levels in the same extracts were determined as in (C) and quantified by densitometry (n = 3, mean and SEM). (E) HEK293 cells expressing the constructs shown were treated with ARS853 for 5 hours. HA-tagged KRAS was immunoprecipitated (IP) and subjected to a binding assay with the catalytic domain of SOS (SOS^cat). (F) Schematic of the mutations used to biochemically increase (+) or decrease (−) the nucleotide exchange function of KRAS^G12C. (G) HEK293 cells expressing the indicated constructs were analyzed as in (C). (H) The level of active KRAS-GTP was quantified by densitometry. Each replicate is shown. A similar result was obtained in H358 cells (fig. S6F). The baseline level of KRAS^G12C/Y40A detected by the RBD:PD is low because the Y40 mutation impairs the interaction of RAS with RAF (33). See also the effects of N116H and A146V mutations, which increase nucleotide exchange without affecting RAS-RAF interaction (fig. S6G).

Fig. 4. Tyrosine kinase activation of nucleotide exchange modulates KRAS^G12C inhibition in cancer cells

(A) A schematic of the trapping mechanism by which ARS853 targets KRAS^G12C-dependent signaling and the role of RTK- or feedback-regulated nucleotide exchange in this process. Structures were adapted from Protein Data Bank accessions 4luc (inhibitor-bound KRAS^G12C-GDP), 4ldj (KRAS^G12C-GDP), and 4l9w (HRAS^G12C-GTP). (B) H358 cells were serum starved overnight followed by treatment with ARS853 (10 μM), with or without EGF (100 ng/ml) for the indicated times, to determine the effect on KRAS-GTP. A representative of two independent experiments is shown. (C) The indicated cell lines, selected because of their relative insensitivity to KRAS^G12C inhibition, were treated with inhibitors of RTK signaling, alone or in combination with ARS853 for 5 days, in order to determine the most effective combinations. The effect of treatment is shown relative to the proliferation of untreated cells. The dots indicate combination treatments resulting in significantly more pronounced inhibition, compared to either drug alone (n = 3 replicates, mean). DMSO, dimethyl sulfoxide. (D) The effect of inhibitors targeting tyrosine kinases on the antiproliferative effect of KRAS^G12C inhibition in KRAS^G12C mutant cell lines (n = 3 replicates, mean and SEM). The concentrations of the inhibitors used in (C) and (D) are noted in Materials and Methods.