Discovery and Characterization of a Substrate Selective p38α Inhibitor

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Abstract
A novel inhibitor of p38 mitogen-activated protein kinase (p38), CMPD1, identified by high-throughput screening, is characterized herein. Unlike the p38 inhibitors described previously, this inhibitor is substrate selective and noncompetitive with ATP. In steady-state kinetics experiments, CMPD1 was observed to prevent the p38α-dependent phosphorylation (Kiapp = 330 nM) of the splice variant of mitogen-activated protein kinase-activated protein kinase 2 (MK2a) that contains a docking domain for p38α and p38β, but it did not prevent the phosphorylation of ATF-2 (Kiapp > 20 μM). In addition to kinetic studies, isothermal titration calorimetry and surface plasmon resonance experiments were performed to elucidate the mechanism of inhibition. While isothermal titration calorimetry analysis indicated that CMPD1 binds to p38α, CMPD1 was not observed to compete with ATP for p38α, nor was it able to interrupt the binding of p38α to MK2a observed by surface plasmon resonance. Therefore, deuterium exchange mass spectrometry (DXMS) was employed to study the p38α·CMPD1 inhibitory complex, to provide new insight into the mechanism of substrate selective inhibition. The DXMS data obtained for the p38α·CMPD1 complex were compared to the data obtained for the p38α·MK2a complex and a p38α·active site binding inhibitor complex. Alterations in the DXMS behavior of both p38α and MK2a were observed upon complex formation, including but not limited to the interaction between the carboxy-terminal docking domain of MK2a and its binding groove on p38α. Alterations in the D2O exchange of p38α produced by CMPD1 suggest that the substrate selective inhibitor binds in the vicinity of the active site of p38α, resulting in perturbations to regions containing nucleotide binding pocket residues, docking groove residues (E160 and D161), and a Mg2+ ion cofactor binding residue (D168). Although the exact mechanism of substrate selective inhibition by this novel inhibitor has not yet been disclosed, the results suggest that CMPD1 binding in the active site region of p38α induces perturbations that may result in the suboptimal positioning of substrates and cofactors in the transition state, resulting in selective inhibition of p38α activity.