9CJ3

Dual phosphorylated human p38 alpha bound to pexmetinib

This is a non-PDB format compatible entry.

Summary for 9CJ3

• Entry DOI: 10.2210/pdb9cj3/pdb
• Descriptor: Mitogen-activated protein kinase 14, SULFATE ION, 1,2-ETHANEDIOL, ... (8 entities in total)
• Functional Keywords: mapk14, kinase, inhibitor, phosphorylated, transferase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 1
• Total formula weight: 42728.58

Authors

Stadnicki, E.J.,Ludewig, H.,Prem Kumar, R.,Kern, D.,Bradshaw, N. (deposition date: 2024-07-05, release date: 2024-11-13)

Primary citation

Stadnicki, E.J.,Ludewig, H.,Kumar, R.P.,Wang, X.,Qiao, Y.,Kern, D.,Bradshaw, N.
Dual-Action Kinase Inhibitors Influence p38 alpha MAP Kinase Dephosphorylation.
Biorxiv, 2024

PubMed Abstract: Reversible protein phosphorylation directs essential cellular processes including cell division, cell growth, cell death, inflammation, and differentiation. Because protein phosphorylation drives diverse diseases, kinases and phosphatases have been targets for drug discovery, with some achieving remarkable clinical success. Most protein kinases are activated by phosphorylation of their activation loops, which shifts the conformational equilibrium of the kinase towards the active state. To turn off the kinase, protein phosphatases dephosphorylate these sites, but how the conformation of the dynamic activation loop contributes to dephosphorylation was not known. To answer this, we modulated the activation loop conformational equilibrium of human p38α ΜΑP kinase with existing kinase inhibitors that bind and stabilize specific inactive activation loop conformations. From this, we discovered three inhibitors that increase the rate of dephosphorylation of the activation loop phospho-threonine by the PPM serine/threonine phosphatase WIP1. Hence, these compounds are "dual-action" inhibitors that simultaneously block the active site and stimulate p38α dephosphorylation. Our X-ray crystal structures of phosphorylated p38α bound to the dual-action inhibitors reveal a shared flipped conformation of the activation loop with a fully accessible phospho-threonine. In contrast, our X-ray crystal structure of phosphorylated apo human p38α reveals a different activation loop conformation with an inaccessible phospho-threonine, thereby explaining the increased rate of dephosphorylation upon inhibitor binding. These findings reveal a conformational preference of phosphatases for their targets and suggest a new approach to achieving improved potency and specificity for therapeutic kinase inhibitors.

PubMed: 39149408
DOI: 10.1101/2024.05.15.594272

Experimental method

X-RAY DIFFRACTION (1.95 Å)