ABSTRACT
Bacterial histidine kinases have been proposed as targets for the discovery of new antibiotics, yet few specific inhibitors of bacterial histidine kinases have been reported. We report here a novel thienopyridine (TEP) compound that inhibits bacterial histidine kinases competitively with respect to ATP but does not comparably inhibit mammalian serine/threonine kinases. Although it partitions into membranes and does not inhibit the growth of bacterial or mammalian cells, TEP could serve as a starting compound for a new class of histidine kinase inhibitors with antibacterial activity.
Subject(s)
Bacterial Proteins/drug effects , Enzyme Inhibitors/pharmacology , Protein Kinases/drug effects , Pyridines/pharmacology , Bacterial Proteins/metabolism , Dose-Response Relationship, Drug , Enzyme Inhibitors/chemistry , Histidine Kinase , Protein Kinases/metabolism , Pyridines/chemistryABSTRACT
We have integrated two complementary methods, high-throughput virtual screening with a "high-content" wet screening technique based on frontal affinity chromatography with mass spectrometry detection (FAC-MS), for identification of hits against the erythropoietin-producing hepatocellular B2 (EphB2) receptor tyrosine kinase domain. Both an EphB2-directed virtual screen combining docking and scoring and a kinase-directed pharmacophore search strategy were used to identify a compound set enriched in bioactive compounds against EphB2. The coupling of virtual screening methodologies with FAC-MS is a unique hybrid approach that can be used to increase the efficacy of both hit discovery and optimization efforts in drug discovery and has successfully identified hits, in particular 19a (36% shift, IC(50) = 5.2 microM, K(d) = 3.3 microM), as inhibitors for EphB2, a potential cancer target.
Subject(s)
Antineoplastic Agents/chemistry , Receptor, EphB2/antagonists & inhibitors , Receptor, EphB2/chemistry , Antineoplastic Agents/pharmacology , Binding Sites , Cell Line, Tumor , Chromatography, Affinity , Databases, Factual , Enzyme-Linked Immunosorbent Assay , Heterocyclic Compounds/chemistry , Heterocyclic Compounds/pharmacology , Humans , Mass Spectrometry , Models, Molecular , Molecular Weight , Naphthoquinones/chemistry , Naphthoquinones/pharmacology , Phosphorylation , Protein Structure, Tertiary , Quantitative Structure-Activity Relationship , Receptor, EphB2/metabolism , Sulfides/chemistry , Sulfides/pharmacologyABSTRACT
Utilizing frontal affinity chromatography with mass spectrometry detection (FAC-MS), we have identified novel applications in the discovery of small-molecule hits to protein targets that are difficult if not impossible to accomplish using traditional assays. We demonstrate for the first time an ability to distinguish between competitive ligands for the ATP and substrate sites of protein kinase C independently in the same experiment and show that ATP competitive ligands using a functionally inactive receptor tyrosine kinase can be identified. This ability of FAC-MS to simultaneously monitor binding at the ATP and substrate binding sites, as well as measure ligand binding to both active and inactive kinases, suggests that FAC-MS can be used as a "global kinase binding assay".
Subject(s)
Chromatography, Affinity/methods , Drug Evaluation, Preclinical/methods , Mass Spectrometry/methods , Protein Kinase Inhibitors/chemistry , Protein Kinases/chemistry , Alkaloids/chemistry , Alkaloids/metabolism , Animals , Benzophenanthridines/chemistry , Benzophenanthridines/metabolism , Binding Sites , Binding, Competitive , Catalytic Domain , Humans , Imidazoles/chemistry , Imidazoles/metabolism , Mice , Molecular Structure , Peptides/chemistry , Peptides/metabolism , Phosphorylation , Protein Binding , Protein Kinase C-alpha/antagonists & inhibitors , Protein Kinase C-alpha/chemistry , Protein Kinase C-alpha/metabolism , Protein Kinase Inhibitors/metabolism , Protein Kinase Inhibitors/pharmacology , Protein Kinases/metabolism , Pyridines/chemistry , Pyridines/metabolism , Quinazolines/chemistry , Quinazolines/metabolism , Receptor, EphB2/antagonists & inhibitors , Receptor, EphB2/chemistry , Receptor, EphB2/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/metabolismABSTRACT
FAC-MS offers a convenient method for measuring the relative binding strengths of ligands in a mixture and enables a rapid ranking and identification of ligands in the mixture as potential hits against immobilized targets. Using immobilized EphB2 receptor tyrosine kinase as the target and known kinase inhibitors, the results of FAC-MS screening (% shift) have been shown to correlate with the binding constant, K(d), and with IC(50) results from the more traditional ELISA assay. Therefore, since FAC-MS can accommodate a wide variety of target proteins, its applications could play a broad role in drug discovery not only at the hit discovery stage but also during the subsequent more rigorous screening at the hit-to-lead and lead optimization stages.
Subject(s)
Enzyme Inhibitors/chemistry , Receptor, EphB2/chemistry , Chromatography, Affinity/methods , Enzyme-Linked Immunosorbent Assay , Ligands , Mass Spectrometry , Models, Molecular , Receptor, EphB2/antagonists & inhibitorsABSTRACT
Two-component signal transduction systems (TCSs) play fundamental roles in bacterial survival and pathogenesis and have been proposed as targets for the development of novel classes of antibiotics. A new coupled assay was developed and applied to analyse the kinetic mechanisms of three new kinds of inhibitors of TCS function. The assay exploits the biochemical properties of the cognate HpkA-DrrA histidine kinase-response regulator pair from Thermotoga maritima and allows multiple turnovers of HpkA, linear formation of phosphorylated DrrA, and Michaelis-Menten analysis of inhibitors. The assay was validated in several ways, including confirmation of competitive inhibition by adenosine 5'-beta,gamma-imidotriphosphate (AMP-PNP). The coupled assay, autophosphorylation and chemical cross-linking were used to determine the mechanisms by which several compounds inhibit TCS function. A cyanoacetoacetamide showed non-competitive inhibition with respect to ATP concentration in the coupled assay. The cyanoacetoacetamide also inhibited autophosphorylation of histidine kinases from other bacteria, indicating that the coupled assay could detect general inhibitors of histidine kinase function. Inhibition of HpkA autophosphorylation by this compound was probably caused by aggregation of HpkA, consistent with a previous model for other hydrophobic compounds. In contrast, ethodin was a potent inhibitor of the combined assay, did not inhibit HpkA autophosphorylation, but still led to aggregation of HpkA. These data suggest that ethodin bound to the HpkA kinase and inhibited transfer of the phosphoryl group to DrrA. A peptide corresponding to the phosphorylation site of DrrA appeared to inhibit TCS function by a mechanism similar to that of ethodin, except that autophosphorylation was inhibited at high peptide concentrations. The latter mechanism of inhibition of TCS function is unusual and its analysis demonstrates the utility of these approaches to the kinetic analyses of additional new classes of inhibitors of TCS function.
