Structural and Biophysical Analyses of Human MEK2 in Complex with Two Inhibitors Reveal the Determinants of Isoform-Dependent Inhibitor Binding

Selective inhibition of MEK isoforms remains a central challenge in MAPK-targeted drug discovery, largely due to the structural similarity between MEK1 and MEK2. While MEK1 has been extensively characterized, the structural basis of MEK2-specific ligand recognition is not fully understood. Here, we present crystal structures of human MEK2 in complex with the noncompetitive inhibitor U0126 and the allosteric inhibitor refametinib at resolutions of 3.15 Å and 3.30 Å, respectively. Despite a conserved kinase fold, MEK2 exhibits isoform-specific features within the N-lobe β-sheet. Additional differences are observed in the relative orientation of the helix C and activation segment, and the helix F-supported regulatory spine. Structural differences are reflected in micromolar binding affinities for U0126 (Kd = 9.8 μM) and refametinib (Kd = 7.4 μM). Notably, a single N-lobe substitution (Thr87 in MEK2 versus Phe83 in MEK1) selectively enhanced U0126 binding. The MEK2 T87F mutant exhibited an approximately twofold increase in affinity, while refametinib binding remained largely unchanged. SEC–MALS analysis demonstrated that MEK2 predominantly exists as a monomer in solution, contrasting with the reported homodimeric behavior of MEK1. Molecular dynamics simulations supported these findings by revealing isoform-specific differences in oligomeric state-dependent flexibility and inhibitor-induced dynamics. Collectively, our findings define the structural basis underlying the differential inhibitor recognition of MEK2 and MEK1, providing mechanistic insight into isoform-selective MEK-targeted drug design.