In non-small-cell lung cancer, the efficacies of tyrosine-kinase inhibitors (TKIs) are known to be decreased by mutations in target proteins such as ALK and RET, and in some cases there are no effective therapeutic strategies to overcome drug resistance. Here, we approach molecular mechanisms to acquire the resistance by combining molecular dynamics (MD) simulations on the nano- to micro-seconds timescales and our developed alchemical free energy perturbation method to compute the protein-drug binding affinity. In cases of drug resistance mutations in ALK, most of which occur near the drug binding site (&lt; 10 angstroms), decreases in the efficacy tend to be successfully quantified by the binding free energy computation based on short MD simulations (~50ns), characterizing conformational differences in the drug binding site between wild-type and mutant proteins. Recently, a RET mutation (S904F) has been reported to confer resistance to a TKI, vandetanib, and interestingly this residue is located in the activation loop and away from the drug binding site (~26 angstroms). Microsecond MD simulations show that the mutation causes not only decreasing the flexibility of the activation loop but also a significant geometrical distortion of the hydrogen-bond network connecting this loop, alpha-C helix, and glycine-rich loop. Furthermore, the free energy simulation based on these trajectories characterizes a mutant-specific transient conformer incompatible with binding of the drug, supporting experimentally-measured thermal instability of the RET mutant complexed with vandetanib. This finding suggests the significance of a mutation-triggered allosteric conformational change on drug resistance. Structure information on protein-drug interactions, captured by these simulations, is expected to be useful for drug design to overcome the resistance.

Drug resistance acquired by local and allosteric conformational changes in oncogenic tyrosine kinases

2019 Spring National Meeting

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