Fluorescent Cascade and Direct Assays for Characterization of RAF Signaling Pathway Inhibitors

RAF kinases are part of a conserved signaling pathway that impacts cell growth, differentiation, and survival, and RAF pathway dysregulation is an attractive target for therapeutic intervention. We describe two homogeneous fluorescent formats that distinguish RAF pathway inhibitors from direct RAF kinase inhibitors, using B-RAF, B-RAF V599E, and C-RAF. A Förster-resonance energy transfer (FRET) based method was used to develop RAF and MEK cascade assays as well as a direct ERK kinase assay. This method uses a peptide substrate, that is terminally labeled with a FRET-pair of fluorophores, and that is more sensitive to proteolysis relative to the phosphorylated peptide. A second time-resolved FRET-based assay using fluorescently labeled MEK substrate was used to detect direct inhibitors of RAF kinase activity. The cascade assays detect compounds that interact with activated and unactivated kinases within the recapitulated RAF pathway, and the direct assays isolate the point of action for an inhibitor

The biosynthesis of GDP-L-colitose: C-3 deoxygenation is catalyzed by a unique coenzyme B₆-dependent enzyme

l-Colitose (1) is a 3,6-dideoxyhexose found in the O-antigen of gram-negative lipopoly-saccharides. While the biosynthesis of many deoxysugars have previously been investigated, l-colitose is distinct in that it originates from GDP-d-mannose. In contrast, other 3,6-dideoxyhexoses arise from CDP-d-glucose. Therefore, the enzymes involved in the l-colitose biosynthetic pathway must be specifically tailored to utilize such a modified substrate. The mode for deoxygenation at C-3 of colitose is of particular interest because this conversion in other naturally occurring 3,6-dideoxyhexoses requires a pair of enzymes, E₁ and E₃, acting in concert. Interestingly, no E₃ equivalent was identified in the five open reading frames of the col biosynthetic gene cluster from Yersinia pseudotuberculosis IVA. However, the gene product of colD showed moderate similarity with the E₁ gene (ddhC/ascC) of the ascarylose pathway (27% identity and 42% similarity). Because E₁ is a pyridoxamine 5′-phosphate (PMP)-dependent enzyme, it was thought that ColD might also utilize PMP. Indeed, turnover was observed during incubation of ColD with substrate in the presence of excess PMP, but not with pyridoxal 5′-phosphate (PLP). However, the rate of product formation increased by more than 40-fold when l-glutamate was included in the PLP incubation. The formation of α-ketoglutarate as a byproduct under these conditions clearly indicated that ColD functions as a transaminase, recognizing both PMP and PLP. In this paper, we propose a novel biosynthetic route for colitose, including the unprecedented C-3 deoxygenation performed solely by ColD. The utilization of PMP in a dehydration reaction is rare, but the combined deoxygenation-transamination activity makes ColD a unique enzyme. Copyright © 2003 American Chemical Society

Identification of Pregnane X Receptor Ligands Using Time-Resolved Fluorescence Resonance Energy Transfer and Quantitative High-Throughput Screening

The human pregnane X nuclear receptor (PXR) is a xenobiotic-regulated receptor that is activated by a range of diverse chemicals, including antibiotics, antifungals, glucocorticoids, and herbal extracts. PXR has been characterized as an important receptor in the metabolism of xenobiotics due to induction of cytochrome P450 isozymes and activation by a large number of prescribed medications. Developing methodologies that can efficiently detect PXR ligands will be clinically beneficial to avoid potential drug–drug interactions. To facilitate the identification of PXR ligands, a time-resolved fluorescence resonance energy transfer (TR-FRET) assay was miniaturized to a 1,536-well microtiter plate format to employ quantitative high-throughput screening (qHTS). The optimized 1,536-well TR-FRET assay showed Z′-factors of ≥0.5. Seven- to 15-point concentration–response curves (CRCs) were generated for 8,280 compounds using both terbium and fluorescein emission data, resulting in the generation of 241,664 data points. The qHTS method allowed us to retrospectively examine single concentration screening datasets to assess the sensitivity and selectivity of the PXR assay at different compound screening concentrations. Furthermore, nonspecific assay artifacts such as concentration-based quenching of the terbium signal and compound fluorescence were identified through the examination of CRCs for specific emission channels. The CRC information was also used to define chemotypes associated with PXR ligands. This study demonstrates the feasibility of profiling thousands of compounds against PXR using the TR-FRET assay in a high-throughput format

Covalent Peroxisome Proliferator-activated Receptor γ Adduction by Nitro-fatty Acids: SELECTIVE LIGAND ACTIVITY AND ANTI-DIABETIC SIGNALING ACTIONS*

The peroxisome proliferator-activated receptor-γ (PPARγ) binds diverse ligands to transcriptionally regulate metabolism and inflammation. Activators of PPARγ include lipids and anti-hyperglycemic drugs such as thiazolidinediones (TZDs). Recently, TZDs have raised concern after being linked with increased risk of peripheral edema, weight gain, and adverse cardiovascular events. Most reported endogenous PPARγ ligands are intermediates of lipid metabolism and oxidation that bind PPARγ with very low affinity. In contrast, nitro derivatives of unsaturated fatty acids (NO2-FA) are endogenous products of nitric oxide (•NO) and nitrite (NO2−)-mediated redox reactions that activate PPARγ at nanomolar concentrations. We report that NO2-FA act as partial agonists of PPARγ and covalently bind PPARγ at Cys-285 via Michael addition. NO2-FA show selective PPARγ modulator characteristics by inducing coregulator protein interactions, PPARγ-dependent expression of key target genes, and lipid accumulation is distinctively different from responses induced by the TZD rosiglitazone. Administration of this class of signaling mediators to ob/ob mice revealed that NO2-FA lower insulin and glucose levels without inducing adverse side effects such as the increased weight gain induced by TZDs