A fluorescence-based thiol quantification assay for ultra-high-throughput screening for inhibitors of coenzyme A production.

Here we report the development and miniaturization of a cell-free enzyme assay for ultra-high-throughput screening (uHTS) for inhibitors of two potential drug targets for obesity and cancer: fatty acid synthase (FAS) and acetyl-coenzyme A (CoA) carboxylase (ACC) 2. This assay detects CoA, a product of the FAS-catalyzed condensation of malonyl-CoA and acetyl-CoA. The free thiol of CoA can react with 7-diethylamino-3-(4'-maleimidylphenyl)-4-methylcoumarin (CPM), a profluorescent coumarin maleimide derivative that becomes fluorescent upon reaction with thiols. FAS produces long-chain fatty acid and CoA from the condensation of malonyl-CoA and acetyl-CoA. In our FAS assay, CoA released in the FAS reaction forms a fluorescence adduct with CPM that emits at 530 nm when excited at 405 nm. Using this detection method for CoA, we measured the activity of sequential enzymes in the fatty acid synthesis pathway to develop an ACC2/FAS-coupled assay where ACC2 produces malonyl-CoA from acetyl-CoA. We miniaturized the FAS and ACC2/FAS assays to 3,456- and 1,536-well plate format, respectively, and completed uHTSs for small molecule inhibitors of this enzyme system. This report shows the results of assay development, miniaturization, and inhibitor screening for these potential drug targets.

3-Aryl-4-hydroxyquinolin-2(1H)-one derivatives as type I fatty acid synthase inhibitors.

A series of 3-aryl-4-hydroxyquinolin-2(1H)-ones with fatty acid synthase inhibitory activity was prepared. Starting from a derivative with an IC(50) = 1.4 microM, SAR studies led to compounds with more than 70-fold increase in potency (IC(50) < 20 nM).

Expression, refolding, and purification of recombinant human phosphodiesterase 3B: definition of the N-terminus of the catalytic core.

We have developed an expression, refolding, and purification protocol for the catalytic domain of human Phosphodiesterase 3B (PDE3B). High level expression in Escherichia coli has been achieved with yields of up to 20mg/L. The catalytic domain of the enzyme was purified by affinity chromatography utilizing a novel affinity ligand. PDE3B, purified by affinity chromatography, with no single impurity #10878;1% as determined by SDS-PAGE, has a specific activity of 2210+/-442nmol/min/mg and a KM for cAMP of 44+/-4.5nM. Reducing the size of the expressed catalytic domain from residues 387-1112 to residues 654-1086 greatly reduced the aggregation phenomena observed with the affinity purified PDE3B. The definition of the N-terminus of the catalytic core was examined through the generation of several truncation mutants spanning amino acid residues 636-674. Constructs starting at E665 and M674 were fully active and devoid of activity, respectively. A construct starting at D668 had a Vmax reduced by approximately 10-fold relative to the longer constructs, yet the KM was not affected. This indicates the minimal N-terminus of the catalytic core lies between E665 and Y667. Refolding and affinity purification of the 654-1073 catalytic core of PDE3B has been employed to produce large quantities of highly pure enzyme for structural studies.

Crystal structure of human phosphodiesterase 3B: atomic basis for substrate and inhibitor specificity.

Phosphodiesterases (PDEs) are enzymes that modulate cyclic nucleotide signaling and as such are clinical targets for a range of disorders including congestive heart failure, erectile dysfunction, and inflammation. The PDE3 family comprises two highly homologous subtypes expressed in different tissues, and inhibitors of this family have been shown to increase lipolysis in adipocytes. A specific PDE3B (the lipocyte-localized subtype) inhibitor would be a very useful tool to evaluate the effects of PDE3 inhibition on lipolysis and metabolic rate and might become a novel tool for treatment of obesity. We report here the three-dimensional structures of the catalytic domain of human PDE3B in complex with a generic PDE inhibitor and a novel PDE3 selective inhibitor. These structures explain the dual cAMP/cGMP binding capabilities of PDE3, provide the molecular basis for inhibitor specificity, and can supply a valid platform for the design of improved compounds.

Crystallization and preliminary X-ray diffraction analysis of the catalytic domain of recombinant human phosphodiesterase 3B.

The catalytic domain of human phosphodiesterase 3B has been cloned, expressed in Escherichia coli and purified in the presence of the PDE3 inhibitors IBMX (3-isobutylmethylxanthine) or MERCK1 by affinity chromatography. Initial screening of crystallization conditions for these complexes in the hanging-drop vapor-diffusion mode resulted in three different crystal forms, all characterized by quite large unit-cell parameters, elevated solvent content and poor diffraction quality. Subsequent optimization of these conditions led to crystals that diffract to 2.4 A and belong to space group C2, with unit-cell parameters a = 146.7, b = 121.5, c = 126.3 A, beta = 100.6 degrees. Rotation-function analysis indicates that the asymmetric unit contains four copies of the monomeric enzyme, corresponding to a solvent content of 64%. To solve the structure of the PDE3B catalytic domain, molecular replacement as well as multiple isomorphous replacement methods are currently being utilized.

The role of tryptophan 1072 in human PDE3B inhibitor binding.

The catalytic domain of recombinant human PDE3B was expressed in Escherichia coli as inclusion bodies and refolded to form active enzyme. A mutation at tryptophan 1072 in PDE3B disrupts inhibitor binding, but has minimal effect on cAMP hydrolysis. The W1072A mutation caused a 158-fold decrease in affinity for cilostamide, a 740-fold decrease for cGMP, and a 15-fold decrease in affinity for IBMX. The corresponding tyrosine mutation had a smaller effect. However, the K(m) of cAMP for the W1072A mutation was only increased by about 7-fold. The data indicate that the inhibitor binding region is not completely coincident with the substrate binding region. The homologous residue in PDE4B is located on helix 16 within 7A of the predicted bound substrate. A model of PDE3B was constructed based on the X-ray crystal structure of PDE4B.