Selective targeting of the αC and DFG-out pocket in p38 MAPK

Eur J Med Chem. 2020 Dec 15;208:112721. doi: 10.1016/j.ejmech.2020.112721. Epub 2020 Aug 20.

Abstract

The p38 MAPK cascade is a key signaling pathway linked to a multitude of physiological functions and of central importance in inflammatory and autoimmune diseases. Although studied extensively, little is known about how conformation-specific inhibitors alter signaling outcomes. Here, we have explored the highly dynamic back pocket of p38 MAPK with allosteric urea fragments. However, screening against known off-targets showed that these fragments maintained the selectivity issues of their parent compound BIRB-796, while combination with the hinge-binding motif of VPC-00628 greatly enhanced inhibitor selectivity. Further efforts focused therefore on the exploration of the αC-out pocket of p38 MAPK, yielding compound 137 as a highly selective type-II inhibitor. Even though 137 is structurally related to a recent p38 type-II chemical probe, SR-318, the data presented here provide valuable insights into back-pocket interactions that are not addressed in SR-318 and it provides an alternative chemical tool with good cellular activity targeting also the p38 back pocket.

Keywords: Allosteric BIRB fragments; Differential scanning fluorimetry (DSF); Folded P-loop; NanoBRET(TM) assay; Selective type-II p38 MAPK inhibitor.

MeSH terms

  • Allosteric Regulation
  • Allosteric Site
  • Animals
  • Cell Line, Tumor
  • Fluorometry
  • HEK293 Cells
  • Humans
  • Mice
  • Microsomes, Liver / metabolism
  • Phenylurea Compounds / chemical synthesis
  • Phenylurea Compounds / metabolism
  • Phenylurea Compounds / pharmacology*
  • Protein Binding
  • Protein Kinase Inhibitors / chemical synthesis
  • Protein Kinase Inhibitors / metabolism
  • Protein Kinase Inhibitors / pharmacology*
  • p38 Mitogen-Activated Protein Kinases / antagonists & inhibitors*
  • p38 Mitogen-Activated Protein Kinases / chemistry
  • p38 Mitogen-Activated Protein Kinases / metabolism

Substances

  • Phenylurea Compounds
  • Protein Kinase Inhibitors
  • p38 Mitogen-Activated Protein Kinases