First comprehensive structural and biophysical analysis of MAPK13 inhibitors targeting DFG-in and DFG-out binding modes

Zeynep Yurtsever, Dhara A. Patel, Daniel L. Kober, Alvin Su, Chantel A. Miller, Arthur G. Romero, Michael J. Holtzman, Tom J. Brett

Research output: Contribution to journalArticlepeer-review

11 Scopus citations


Background P38 MAP kinases are centrally involved in mediating extracellular signaling in various diseases. While much attention has previously been focused on the ubiquitously expressed family member MAPK14 (p38α), recent studies indicate that family members such as MAPK13 (p38δ) display a more selective cellular and tissue expression and might therefore represent a specific kinase to target in certain diseases. Methods To facilitate the design of potent and specific inhibitors, we present here the structural, biophysical, and functional characterization of two new MAPK13-inhibitor complexes, as well as the first comprehensive structural, biophysical, and functional analysis of MAPK13 complexes with four different inhibitor compounds of greatly varying potency. Results These inhibitors display IC50 values either in the nanomolar range or micromolar range (> 800-fold range). The nanomolar inhibitors exhibit much longer ligand-enzyme complex half-lives compared to the micromolar inhibitors as measured by biolayer interferometry. Crystal structures of the MAPK13 inhibitor complexes reveal that the nanomolar inhibitors engage MAPK13 in the DFG-out binding mode, while the micromolar inhibitors are in the DFG-in mode. Detailed structural and computational docking analyses suggest that this difference in binding mode engagement is driven by conformational restraints imposed by the chemical structure of the inhibitors, and may be fortified by an additional hydrogen bond to MAPK13 in the nanomolar inhibitors. Conclusions These studies provide a structural basis for understanding the differences in potency exhibited by these inhibitors. General significance They also provide the groundwork for future studies to improve specificity, potency, pharmacodynamics, and pharmacokinetic properties.

Original languageEnglish (US)
Pages (from-to)2335-2344
Number of pages10
JournalBiochimica et Biophysica Acta - General Subjects
Issue number11
StatePublished - Nov 1 2016
Externally publishedYes


  • Chronic inflammatory lung disease
  • Differential scanning fluorimetry
  • Inhibitor half-lives
  • Kinase inhibitor
  • p38 kinase
  • Structure-based drug design

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Molecular Biology


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