The T790M mutation in EGFR kinase causes drug resistance by increasing the affinity for ATP

Abstract

Lung cancers caused by activating mutations in the epidermal growth factor receptor (EGFR) are initially responsive to small molecule tyrosine kinase inhibitors (TKIs), but the efficacy of these agents is often limited because of the emergence of drug resistance conferred by a second mutation, T790M. Threonine 790 is the "gatekeeper" residue, an important determinant of inhibitor specificity in the ATP binding pocket. The T790M mutation has been thought to cause resistance by sterically blocking binding of TKIs such as gefitinib and erlotinib, but this explanation is difficult to reconcile with the fact that it remains sensitive to structurally similar irreversible inhibitors. Here, we show by using a direct binding assay that T790M mutants retain low-nanomolar affinity for gefitinib. Furthermore, we show that the T790M mutation activates WT EGFR and that introduction of the T790M mutation increases the ATP affinity of the oncogenic L858R mutant by more than an order of magnitude. The increased ATP affinity is the primary mechanism by which the T790M mutation confers drug resistance. Crystallographic analysis of the T790M mutant shows how it can adapt to accommodate tight binding of diverse inhibitors, including the irreversible inhibitor HKI-272, and also suggests a structural mechanism for catalytic activation. We conclude that the T790M mutation is a "generic" resistance mutation that will reduce the potency of any ATP-competitive kinase inhibitor and that irreversible inhibitors overcome this resistance simply through covalent binding, not as a result of an alternative binding mode.

Fig. 1.

Chemical structures of selected EGFR inhibitors. All compounds are drawn in a consistent orientation and conformation that reflects their approximate binding mode in the EGFR kinase. HKI-272 and EKB-569 are examples of irreversible inhibitors. Lapatinib and HKI-272 are thought to require the inactive conformation of EGFR for binding because of their additional aniline substitutions.

Fig. 2.

Crystal structures of the EGFR T790M mutant show that inhibitors are readily accommodated in the active and inactive conformations of the kinase. (A) Superposition of EGFR T790M/AEE788 complex (yellow) and WT/AEE788 complex [light blue; drawn from PDB ID code 2J6M (8)]. Dashed lines indicate hydrogen bonds to the kinase hinge region that are preserved in both complexes. The location of the T790M mutation is indicated. (B) Superposition of EGFR T790M/AEE788 complex (yellow) and apo-T790M structure (green). Note the alternate side-chain conformation of Met-790 in the presence of the inhibitor. (C) Crystal structure of HKI-272 in complex with the T790M mutant. The kinase adopts an inactive conformation, with the C-helix displaced. A covalent bond is formed between Cys-797 and the crotonamide Michael acceptor of HKI-272. (D) The structure of the T790M mutant in complex with HKI-272 (yellow) is superimposed on the structure of the WT EGFR kinase in complex with Lapatinib [light blue; drawn from PDB ID code 1XKK (32)]. In both structures, the kinase adopts the same inactive conformation and the inhibitors bind in a similar manner, with a single hydrogen bond to the hinge (dashed lines) and with their aniline substituents extending into the enlarged hydrophobic pocket that is characteristic of the inactive conformation.

Fig. 3.

The drug resistance of T790M secondary mutation is manifested only at cellular concentrations of ATP. (A) The calculated K_i^app for the L858R single mutant and L858R/T790M double mutant are plotted versus ATP concentration, using experimentally measured values for the K_m[ATP] (Table 2) and setting K_i = K_d as measured (Table 1). Note the expected loss of potency of the double mutant (solid line) as ATP concentrations approach cellular levels (≈1 mM). (B) Inhibition of L858R mutant EGFR kinase by gefitinib in the presence of 10 μM (black squares) or 1.0 mM ATP (red circles). (C) Inhibition of the L858R/T790M double mutant EGFR by gefitinib in the presence of 10 μM (black squares) or 1.0 mM ATP (red circles). In B and C, the in vitro kinase activity of the indicated EGFR mutant was measured in the presence of the indicated concentrations of gefitinib by using an EGFR Tyr-1173 autophosphorylation site peptide (ENAEYLRVA) as substrate.