Design of pyrido[2,3-d]pyrimidin-7-one inhibitors of receptor interacting protein kinase-2 (RIPK2) and nucleotide-binding oligomerization domain (NOD) cell signaling

Eur J Med Chem. 2021 Apr 5:215:113252. doi: 10.1016/j.ejmech.2021.113252. Epub 2021 Feb 3.

Abstract

Receptor interacting protein kinase-2 (RIPK2) is an enzyme involved in the transduction of pro-inflammatory nucleotide-binding oligomerization domain (NOD) cell signaling, a pathway implicated in numerous chronic inflammatory conditions. Herein, a pyrido[2,3-d]pyrimidin-7-one based class of RIPK2 kinase and NOD2 cell signaling inhibitors is described. For example, 33 (e.g. UH15-15) inhibited RIPK2 kinase (IC50 = 8 ± 4 nM) and displayed > 300-fold selectivity versus structurally related activin receptor-like kinase 2 (ALK2). This molecule blocked NOD2-dependent HEKBlue NF-κB activation (IC50 = 20 ± 5 nM) and CXCL8 production (at concentrations > 10 nM). Molecular docking suggests that engagement of Ser25 in the glycine-rich loop may provide increased selectivity versus ALK2 and optimal occupancy of the region between the gatekeeper and the αC-helix may contribute to potent NOD2 cell signaling inhibition. Finally, this compound also demonstrated favorable in vitro ADME and pharmacokinetic properties (e.g. Cmax = 5.7 μM, Tmax = 15 min, t1/2 = 3.4 h and Cl = 45 mL/min/kg following single 10 mg/kg intraperitoneal administration) further supporting the use of pyrido[2,3-d]pyrimidin-7-ones as a new structure class of RIPK2 kinase and NOD cell signaling inhibitors.

Keywords: Inhibitor; Kinase; NOD; Nucleotide-binding oligomerization domain; Pyrido[2,3-d]pyrimidin-7-one; RIPK2; Receptor-interacting protein kinase 2.

MeSH terms

  • Antineoplastic Agents / chemical synthesis
  • Antineoplastic Agents / metabolism
  • Antineoplastic Agents / pharmacology*
  • Cell Line, Tumor
  • Drug Design
  • Humans
  • Molecular Docking Simulation
  • Nod2 Signaling Adaptor Protein / antagonists & inhibitors*
  • Nod2 Signaling Adaptor Protein / chemistry
  • Nod2 Signaling Adaptor Protein / metabolism
  • Protein Binding
  • Protein Domains
  • Protein Kinase Inhibitors / chemical synthesis
  • Protein Kinase Inhibitors / metabolism
  • Protein Kinase Inhibitors / pharmacology*
  • Pyridines / chemical synthesis
  • Pyridines / metabolism
  • Pyridines / pharmacology*
  • Pyrimidinones / chemical synthesis
  • Pyrimidinones / metabolism
  • Pyrimidinones / pharmacology*
  • Receptor-Interacting Protein Serine-Threonine Kinase 2 / antagonists & inhibitors*
  • Receptor-Interacting Protein Serine-Threonine Kinase 2 / chemistry
  • Receptor-Interacting Protein Serine-Threonine Kinase 2 / metabolism
  • Signal Transduction / drug effects

Substances

  • Antineoplastic Agents
  • NOD2 protein, human
  • Nod2 Signaling Adaptor Protein
  • Protein Kinase Inhibitors
  • Pyridines
  • Pyrimidinones
  • RIPK2 protein, human
  • Receptor-Interacting Protein Serine-Threonine Kinase 2