Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase

Abstract

Activating mutations in the epidermal growth factor receptor (EGFR) tyrosine kinase are frequently found in many cancers. It has been suggested that changes in the equilibrium between its active and inactive conformations are linked to its oncogenic potential. Here, we quantify the effects of some of the most common single (L858R and T790M) and double (T790M-L858R) oncogenic mutations on the conformational free-energy landscape of the EGFR kinase domain by using massive molecular dynamics simulations together with parallel tempering, metadynamics, and one of the best force-fields available. Whereas the wild-type EGFR catalytic domain monomer is mostly found in an inactive conformation, our results show a clear shift toward the active conformation for all of the mutants. The L858R mutation stabilizes the active conformation at the expense of the inactive conformation and rigidifies the αC-helix. The T790M gatekeeper mutant favors activation by stabilizing a hydrophobic cluster. Finally, T790M with L858R shows a significant positive epistasis effect. This combination not only stabilizes the active conformation, but in nontrivial ways changes the free-energy landscape lowering the transition barriers.conformational changes | resistance-causing mutations

Molecular mechanisms of asymmetric RAF dimer activation

“…On the other hand, ligand-free dimers favour juxtamembrane segment dissociation and membrane burial, and formation of inactive symmetric kinase dimers [46]. Enhanced sampling methods, such as metadynamics, were also used to elucidate and characterize active and inactive states [47]. Wild-type and mutant forms of EGFR showed conformational differences of the salt bridges between the VAIK motif, the αC-helix and the AL, affecting the stabilization of the active forms of the kinase [47].…”

An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G-Protein-Coupled Receptor Ligands

“…The metadynamics technique can be used to compute the binding free energy along physically meaningful pathways, predicting both the thermodynamics and kinetics of binding, and has established itself as the method of choice for free-energy prediction in complex molecular processes. 3,[13][14][15][16][17][18][19][20][21][22][23][24] However, metadynamics (and similar approaches) require the definition of one or more collective variables (CVs) that approximate the reaction coordinate, which must be chosen carefully. 21,25,26 The time needed to converge a free energy profile increases significantly when poorly suited or too many CVs are selected.…”

Evolution of Tyrosine Kinase Resistance in Egfr Mutated Non-Small Cell Lung Cancer

“…Наиболее тщательно этот вопрос был изучен для вторичной мутации Т790М. Если на первом этапе высокочувствительные методы позволяли выявлять Т790М в ИТК-наивных образцах, то последние исследования с применени-ем высокопродуктивных методов секвенирования следующего поколения показали крайне невысокую частоту мутаций Т790М до лечения (< 1%) [22,25,42,[51][52][53][54][55]. In vitro эксперименты с клеточными линиями показали принципиальную возможность как предсу-ществования Т790М, так и de novo появление Т790М из «drug tolerant» клеток [56].…”