Systematic characterization of adenosine triphosphate response to lung cancer epidermal growth factor receptor missense mutations: A molecular insight into “generic” drug resistance mutations

Abstract

Many missense mutations in human epidermal growth factor receptor (EGFR) are clinically involved in lung cancer and may cause acquired resistance to tyrosine kinase inhibitors. Traditionally, the resistance is considered to be established by impairing inhibitor affinity due to the mutations. However, it was found that, instead of blocking inhibitor binding, the gatekeeper mutation T790M can improve the kinase affinity for its natural substrate adenosine triphosphate (ATP), which is thus regarded as a "generic" resistance mutation that will reduce the potency of any ATP-competitive reversible kinase inhibitor. In this study, we attempt to systematically investigate the binding behavior of ATP to clinically observed EGFR missense mutants in nonsmall-cell lung cancer to identify those substantial mutations that may significantly increase (or decrease) ATP affinity. Several substantial mutations are excluded because they are also involved in kinase's catalytic activity or directly influence inhibitor binding, thus largely complicating the multiple dependent relationships of kinase, ATP, and inhibitor. Two new "generic" resistance mutations, A839T and E758G, are identified, which can improve ATP affinity by forming a favor

Molecular analysis and systematic profiling of allosteric inhibitor response to clinically significant epidermal growth factor receptor missense mutations in non‐small cell lung cancer

“…The AMP is a nonhydrolyzable analog of ATP; the only difference between them is that the AMP possesses a secondary amine moiety but not an oxygen atom in ATP, which bridges between the first and second phosphates. [20] Therefore, the AMP structure in the complex template could be readily modified to ATP manually (Figure 7).…”

“…[19] Further study revealed that a number of EGFR missense mutations can considerably or moderately reshape the binding behavior of ATP to EGFR ATP site, thus indirectly influencing the inhibitory capability of ATP-completive inhibitors against EGFR kinase. [20] Here, we first attempted to investigate the molecular effect of the allosteric inhibitor-induced EGFR conformational change on ATP binding. In this procedure, the binding energy changes (ΔΔG ALT ) upon EGFR allostery induced by 11 curated allosteric inhibitors were calculated using molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method based on molecular dynamics (MD) production trajectory, which created a ΔΔG ALT profile to visualize ATP response to the binding of 11 allosteric inhibitors to EGFR.…”

“…In particular, the drugresistant T790M and A839T mutations were calculated to enhance ATP-binding potency significantly (ΔΔG MUT ranges between À1.5 and À2 kcal/mol), which were previously reported as generic resistance mutation by increasing ATP affinity. [19,20] The electrostatic effect seems to play an important role in the mutation-induced ATP binding change; those charged residue-involved mutations such as E758G, R803W, and L858R can influence ATP potency considerably. In addition, the location of mutations relative to ATP site seems to be also important in ATP binding.…”

“…[22] From the SIRTMP profile, we identified a number of representative mutation/inhibitor pairs, including six strong sensitization pairs and four strong deactivation pairs (Table 1); they distribute on four kinase residues 758, 790, 854, and 858, in which the residues 758, 854, and 858 are located in allosteric site, while the residue 790 is in ATP site. All the four mutations are biologically significant and have been frequently observed in NSCLC; the E758G and T790M increase ATP affinity and cause generic drug resistance, [19,20] and the T854A and L858R are within activation loop and can confer constitutive activity to the kinase. [23] By visually examining the wild-type and mutant kinase-inhibitor complex structures of 10 representative pairs, it is revealed as follows:…”

Noncognate HER2 sensitivity to cognate EGFR allosteric inhibitors at molecular level: New uses for old drugs in gynecological tumors

“…However, we also observed a modest or moderate activity change (up to 3.8-fold increase) of allosteric inhibitors upon the mutation. This can be explained by two aspects: (i) this mutation is located at the N-terminus of kinase activation loop and can reshape the loop conformation that is involved in the allosteric site, and (ii) the mutation has been reported to influence substrate entry, [22] which would shift the kinase activity and thus alter the kinase-inhibitor interactive behavior. Consequently, all these indirect factors of HER2 C805S mutation come together to modestly or moderately influence the inhibitory activity of allosteric inhibitors.…”