title: Probing binding and cellular activity of pyrrolidinone and piperidinone small molecules targeting the urokinase receptor.
abstract: 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.
authors.affiliation: Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202 (USA).
authors.forename: Timmy
authors.initials: T
authors.lastname: Mani
authors.forename: Degang
authors.initials: D
authors.lastname: Liu
authors.forename: Donghui
authors.initials: D
authors.lastname: Zhou
authors.forename: Liwei
authors.initials: L
authors.lastname: Li
authors.forename: William Eric
authors.initials: WE
authors.lastname: Knabe
authors.forename: Fang
authors.initials: F
authors.lastname: Wang
authors.forename: Kyungsoo
authors.initials: K
authors.lastname: Oh
authors.forename: Samy O
authors.initials: SO
authors.lastname: Meroueh
mesh_terms: D017209:Apoptosis / Q000187:drug effects; D001665:Binding Sites; D002448:Cell Adhesion / Q000187:drug effects; D045744:Cell Line, Tumor; D002465:Cell Movement / Q000187:drug effects; D006801:Humans; D019950:Mitogen-Activated Protein Kinase 1 / Q000378:metabolism; D048052:Mitogen-Activated Protein Kinase 3 / Q000378:metabolism; D062105:Molecular Docking Simulation; D010880:Piperidines / Q000737:chemistry* / Q000378:metabolism / Q000633:toxicity; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D011760:Pyrrolidinones / Q000737:chemistry* / Q000378:metabolism / Q000633:toxicity; D021281:Quantitative Structure-Activity Relationship; D055293:Receptors, Urokinase Plasminogen Activator / Q000037:antagonists & inhibitors* / Q000378:metabolism; D015398:Signal Transduction / Q000187:drug effects; D013816:Thermodynamics
chemical_list: D010880:Piperidines; D011760:Pyrrolidinones; D055293:Receptors, Urokinase Plasminogen Activator; D019950:Mitogen-Activated Protein Kinase 1; D048052:Mitogen-Activated Protein Kinase 3
keywords: cancer; inhibitors; invasion; metastasis; protein-protein interaction; small molecules; uPAR; urokinase; urokinase receptors