Probing binding and cellular activity of pyrrolidinone and piperidinone small molecules targeting the urokinase receptor

Timmy Mani, Degang Liu, Donghui Zhou, Liwei Li, William Eric Knabe, Fang Wang, Kyungsoo Oh, Samy O. Meroueh

Research output: Contribution to journalArticlepeer-review

10 Scopus citations


The urokinase receptor (uPAR) is a cell-surface protein that is part of an intricate web of transient and tight protein interactions that promote cancer cell invasion and metastasis. Here, we evaluate the binding and biological activity of a new class of pyrrolidinone and piperidinone compounds, along with derivatives of previously-identified pyrazole and propylamine compounds. Competition assays revealed that the compounds displace a fluorescently labeled peptide (AE147-FAM) with inhibition constant (Ki) values ranging from 6 to 63 μM. Structure-based computational pharmacophore analysis followed by extensive explicit-solvent molecular dynamics (MD) simulations and free energy calculations suggested the pyrazole-based and piperidinone-based compounds adopt different binding modes, despite their similar two-dimensional structures. In cells, pyrazole-based compounds showed significant inhibition of breast adenocarcinoma (MDA-MB-231) and pancreatic ductal adenocarcinoma (PDAC) cell proliferation, but piperidinone-containing compounds exhibited no cytotoxicity even at concentrations of 100 μM. One pyrazole-based compound impaired MDA-MB-231 invasion, adhesion, and migration in a concentration-dependent manner, while the piperidinone inhibited only invasion. The pyrazole derivative inhibited matrix metalloprotease-9 (gelatinase) activity in a concentration-dependent manner, while the piperidinone showed no effect suggesting different mechanisms for inhibition of cell invasion. Signaling studies further highlighted these differences, showing that pyrazole compounds completely inhibited ERK phosphorylation and impaired HIF1α and NF-κB signaling, while pyrrolidinones and piperidinones had no effect. Annexin V staining suggested that the effect of the pyrazole-based compound on proliferation was due to cell killing through an apoptotic mechanism. The compounds identified represent valuable leads in the design of further derivatives with higher affinities and potential probes to unravel the protein-protein interactions of uPAR. Optimization through computation: Pyrazole-, propylamine-, pyrrolidinone- and piperidinone-containing compounds were designed, synthesized and evaluated as inhibitors of urokinase receptor (uPAR), a cell-surface protein known to be involved in cancer cell invasion and metastasis.

Original languageEnglish (US)
Pages (from-to)1963-1977
Number of pages15
Issue number12
StatePublished - Dec 2013


  • cancer
  • inhibitors
  • invasion
  • metastasis
  • protein-protein interaction
  • small molecules
  • uPAR
  • urokinase
  • urokinase receptors

ASJC Scopus subject areas

  • Pharmacology, Toxicology and Pharmaceutics(all)
  • Organic Chemistry
  • Molecular Medicine

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