Molecular Dynamics Simulation on the Suppression Mechanism of Phosphorylation to Ser222 by Allosteric Inhibitors Targeting MEK1/2 Kinase

Allosteric inhibitors of mitogen-activated protein kinase 1 (MEK1) reveal distinct interactions with MEK1 activation loop residues. The structural analyses will determine whether, and how, distinct inhibitors suppress the phosphorylation of MEK1 and may guide future therapeutic development. In this study, we explored the suppression mechanism of the phosphorylation process in the presence of MEK allosteric inhibitors, such as selumetinib, trametinib, cobimetinib, and CH5126766, by employing molecular dynamics simulations accompanied by principal component analysis. The simulations of wildtype MEK1 show that Ser222 can come close to γ-phosphate but not Ser218. We have found the conformation where Ser222 is within 5 Å of distance, which makes Ser222 accessible for γ-phosphate. The conformation analysis from the simulations of MEK1 in the presence of allosteric inhibitors reveals that the inhibitor restricts the flexibility of Ser222 through strong interactions with the activation loop, Lys97, and water mediates interactions with amino acids in the vicinity. The results reveal that all the inhibitors act as screeners between the activation loop and Mg-ATP and restricting the flexibility of the activation loop through strong interaction causes the suppression of the phosphorylation process of MEK1. The results conclude that a strong interaction of allosteric inhibitors with the activation loop restricts the movement of Ser222 toward Mg-ATP, which could be the dominant factor for the suppression of phosphorylation in MEK1. This research will provide novel insights to design effective anticancer therapeutics for targeting MEK1 in the future.