Trametinib Promotes MEK Binding to the RAF-Family Pseudokinase KSR

Despite the clinical utility of MEK inhibitors such as trametinib, resistance can occur, necessitating a better understanding of how these drugs function. Khan, Real, Marsiglia, and colleagues obtained two crystal structures of trametinib-bound MEK1, one in complex with KSR1 and the other with KSR2. KSR proteins are RAF-family pseudokinases that lack the enzymatic activity of other RAF family members. In both structures, the ATP-noncompetitive inhibitor trametinib bound the canonical MEK inhibitor pocket, an allosteric site adjacent to ATP. Notably, trametinib's section C (one of three pharmacophores possessed by the drug) bound a pocket in the interface between MEK and KSR, where the drug was in contact with MEK's activation segment. MEK1′s inhibitor pocket took on a different shape and size when bound to KSR1 or KSR2, with a larger allosteric pocket than that observed when MEK1 was bound to MEK inhibitors other than trametinib; thus, KSR1/2 binding altered the conformation of MEK1 such that trametinib could inhabit the enlarged allosteric binding pocket. Previous work has demonstrated that trametinib hinders MEK–RAF binding, raising the question of why trametinib-engaged MEK could bind the RAF-family protein KSR but not RAF. Superimposing a BRAF–MEK1 crystal structure with the KSR–MEK1 crystal structures revealed a possible steric clash between the phenyl acetamide moiety of trametinib and BRAF's pre-helix αG loop, and this clash was not present with the homologous region of KSR. Mutating the loop to make KSR more BRAF-like or BRAF more KSR-like confirmed that MEK1 binding to KSR or BRAF in the presence of trametinib was hindered by the presence of a BRAF-like loop. Together, these results suggest that trametinib prevents RAF-mediated activation of MEK by promoting MEK binding to the pseudokinase KSR over binding to active RAF proteins. Using the structural data, a trametinib analogue dubbed trametiglue was designed to limit adaptive resistance. In summary, this study provides insight into the mechanism of trametinib, a drug critical for the treatment of melanoma and possibly other malignancies.

Khan ZM, Real AM, Marsiglia WM, Chow A, Duffy ME, Yerabolu JR, et al. Structural basis for the action of the drug trametinib at KSR-bound MEK. Nature 2020 Sep 14 [Epub ahead of print].

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