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Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation
Published on: May 20, 2020
Molecular Dynamics Analysis of Binding of Kinase Inhibitors to WT EGFR and the T790M Mutant
Jiyong Park1, Joseph J McDonald2, Russell C Petter2
1Department of Chemistry and Biochemistry, University of California , Los Angeles, California 90095, United States.
Abstract:
Epidermal growth factor receptor (EGFR) inhibitors interrupt EGFR-dependent cellular signaling pathways that lead to accelerated tumor growth and proliferation. Mutation of a threonine in the inhibitor binding pocket, known as the "gatekeeper", to methionine (T790M) confers acquired resistance to several EGFR-selective inhibitors. We studied interactions between EGFR inhibitors and the gatekeeper residues of the target protein. Thermodynamic integration (TI) with Amber14 indicates that the binding energies of gefitinib and AEE788 to the active state of the T790M mutant EGFR is 3 kcal/mol higher than to the wild type (WT), whereas ATP binding energy to the mutant is similar to the WT. Using metadynamics MD simulations with NAMD v2.9, the conformational equilibrium between the inactive resting state and the catalytically competent activate state was determined for the WT EGFR. When combined with the results obtained by Sutto and Gervasio, our simulations showed that the T790M point mutation lowers the free energy of the active state by 5 kcal/mol relative to the inactive state of the enzyme. Relative to the WT, the T790M mutant binds gefitinib more strongly. The T790M mutation is nevertheless resistant due to its increased binding of ATP. By contrast, the binding of AEE788 to the active state causes a conformational change in the αC-helix adjacent to the inhibitor binding pocket, that results in a 2 kcal/mol energy penalty. The energy penalty explains why the binding of AEE788 to the T790M mutant is unfavorable relative to binding to WT EGFR. These results establish the role of the gatekeeper mutation on inhibitor selectivity. Additional molecular dynamics (MD) simulations, TI, and metadynamics MD simulations reveal the origins of the changes in binding energy of WT and mutants.
Insights
The T790M gatekeeper mutation in EGFR affects drug binding, conferring resistance to inhibitors like gefitinib by altering protein states. This mutation impacts ATP binding and inhibitor selectivity, explaining resistance mechanisms in cancer therapy.
Area of Science:
- Molecular Biology
- Biochemistry
- Computational Chemistry
Background:
- Epidermal growth factor receptor (EGFR) inhibitors are crucial in cancer therapy, targeting signaling pathways driving tumor growth.
- Acquired resistance to EGFR inhibitors often arises from mutations in the EGFR protein, particularly the T790M
- gatekeeper
- mutation.
- Understanding these resistance mechanisms at a molecular level is vital for developing more effective treatments.
Purpose of the Study:
- To investigate the molecular interactions between EGFR inhibitors and the gatekeeper T790M mutation.
- To elucidate the thermodynamic and conformational changes associated with inhibitor binding to wild-type (WT) and mutant EGFR.
- To explain the differential binding affinities and selectivity of EGFR inhibitors in the presence of the T790M mutation.
Main Methods:
- Molecular dynamics (MD) simulations using NAMD v2.9.
- Thermodynamic integration (TI) calculations with Amber14.
- Metadynamics simulations to determine conformational equilibria between inactive and active EGFR states.
Main Results:
- The T790M mutation increases the binding energy of gefitinib to EGFR by 3 kcal/mol compared to WT EGFR.
- ATP binding energy to the T790M mutant is similar to WT EGFR, contributing to resistance.
- The T790M mutation shifts the conformational equilibrium towards the active state, lowering its free energy by 5 kcal/mol relative to the inactive state.
- AEE788 binding to the active state of EGFR incurs a 2 kcal/mol energy penalty due to conformational changes in the αC-helix, making it unfavorable for the T790M mutant.
Conclusions:
- The T790M gatekeeper mutation plays a significant role in determining the selectivity of EGFR inhibitors.
- Differential binding of ATP and conformational changes induced by inhibitors explain the observed resistance and selectivity patterns.
- These findings provide insights into the molecular basis of acquired resistance to EGFR inhibitors and can guide the design of new therapeutic strategies.
