Electrospray mass spectrometry for the direct accurate mass measurement of ligands in complex with the retinoid X receptor α ligand binding domain

Accurate mass measurements are often used in the structural determination of unknown compounds of low molecular mass (i.e., below approximately 500 Da). Recently, it has been shown that accurate mass measurements also can be made on small denatured proteins (i.e., M(r), approximately 17,000) to confirm their amino acid composition and identify the presence of isoforms. In the current report, we present nondenaturing electrospray (ES) mass spectrometry data on the direct accurate mass measurement of ligands in complex with the retinoid X receptor ligand binding domain (RXR LBD; M(r) 31,370.92). Average mass errors were below 0.198 Da, 6.3 ppm (standard deviation [SD], 0.146; n = 10) for low-affinity fatty acid agonists analyzed in complex with the RXR LBD. Protein consumption was less than 15 pmol, with fatty acid ligands present at concentrations corresponding to their median effective concentration value (low micromolar, determined in transfection assays). Although determination of fatty acid mass was only sufficiently accurate to give nominal mass values, measurements were of sufficient accuracy to assign fatty acid chain length, degree of unsaturation, or cyclization. Using 17beta-estradiol as a control, the ability to observe specific ligand binding is shown for both high- and low-affinity RXRalpha agonists. In addition, binding of a novel synthetic receptor agonist XCT0315908 to the RXRalpha LBD is reported. This compound showed a high degree of complex formation, and the receptor-ligand complex could be mass measured with an average mass error of -0.024 Da, 0.8 ppm (SD, 0.092; n = 9). Thus, specific binding of both nanomolar and micromolar affinity ligands to a nuclear receptor LBD can be directly observed using nondenaturing ES mass spectrometry and accurate mass measurements additionally can be made on intact complexes in the same experiment. This methodology also is applicable when ligands are present as components of mixtures.     

Estrogen receptor microarrays: subtype-selective ligand binding

We present the first example of a nuclear hormone receptor microarray, using for illustration the ligand-binding domains of the two estrogen receptors, ERalpha-LBD and ERbeta-LBD. The proteins are printed and allowed to attach to aldehyde slides; the efficiency of attachment depends on whether the LBD is liganded with agonists (low attachment) versus liganded with antagonists or unliganded (high attachment). This suggests that attachment is orientation specific and involves principally a single lysine residue. The attached ERs retain good ligand-binding activity that can be assessed using an estradiol-fluorophore conjugate, and specific and ER subtype-selective binding of ligands can be determined conveniently in competitive binding assays. This powerful new, high-throughput technique to study ligand binding to ER-LBDs can be extended to other nuclear hormone receptors and adapted to assay the recruitment of coregulator proteins.     

Discovery of a protein-metabolite interaction between unsaturated fatty acids and the nuclear receptor Nur77 using a metabolomics approach

Neuron-derived clone 77 (Nur77) is an orphan nuclear receptor with currently no known natural ligands. Here we applied a metabolomics platform for detecting protein-metabolite interactions (PMIs) to identify lipids that bind to Nur77. Using this approach, we discovered that the Nur77 ligand-binding domain (Nur77LBD) enriches unsaturated fatty acids (UFAs) in tissue lipid mixtures. The interaction of Nur77 with arachidonic acid and docosahexaenoic acid was subsequently characterized using a number of biophysical and biochemical assays. Together these data indicate that UFAs bind to Nur77LBD to cause changes in the conformation and oligomerization of the receptor. UFAs are the only endogenous lipids reported to bind to Nur77, which highlights the use of metabolomics in the discovery of novel PMIs.     

Design and Synthesis of New Bile AcidSterol Conjugates Linked via 1,2,3‐Triazole Ring

A new steroid conjugates have been obtained from bile acids and sterol derivatives using ‘click chemistry’. Intermolecular 1,3‐dipolar cycloaddition of the propargyl ester of bile acids (lithocholic, deoxycholic, and cholic acid) and azide derivatives of sterols (ergosterol and cholesterol) gave a new bile acid? sterol conjugates linked with a 1,2,3‐triazole ring. The structures of all products were confirmed by spectroscopic (¹H‐ and ¹³C‐NMR, and FT‐IR) analyses, mass spectrometry (ESI‐MS), and in silico biological activity evaluation methods (PASS), as well as PM5 semiempirical methods.     

Differentiation of various traditional Chinese medicines derived from animal bile and gallstone: simultaneous determination of bile acids by liquid chromatography coupled with triple quadrupole mass spectrometry

Animal biles and gallstones are popularly used in traditional Chinese medicines, and bile acids are their major bioactive constituents. Some of these medicines, like cow-bezoar, are very expensive, and may be adulterated or even replaced by less expensive but similar species. Due to poor ultraviolet absorbance and structural similarity of bile acids, effective technology for species differentiation and quality control of bile-based Chinese medicines is still lacking. In this study, a rapid and reliable method was established for the simultaneous qualitative and quantitative analysis of 18 bile acids, including 6 free steroids (cholic acid, chenodeoxycholic acid, deoxycholic acid, lithocholic acid, hyodeoxycholic acid, and ursodeoxycholic acid) and their corresponding glycine conjugates and taurine conjugates, by using liquid chromatography coupled with tandem mass spectrometry (LC/MS/MS). This method was used to analyze six bile-based Chinese medicines: bear bile, cattle bile, pig bile, snake bile, cow-bezoar, and artificial cow-bezoar. Samples were separated on an Atlantis dC₁₈ column and were eluted with methanol–acetonitrile–water containing ammonium acetate. The mass spectrometer was monitored in the negative electrospray ionization mode. Total ion currents of the samples were compared for species differentiation, and the contents of bile acids were determined by monitoring specific ion pairs in a selected reaction monitoring program. All 18 bile acids showed good linearity (r² > 0.993) in a wide dynamic range of up to 2000-fold, using dehydrocholic acid as the internal standard. Different animal biles could be explicitly distinguished by their major characteristic bile acids: tauroursodeoxycholic acid and taurochenodeoxycholic acid for bear bile, glycocholic acid, cholic acid and taurocholic acid for cattle bile, glycohyodeoxycholic acid and glycochenodeoxycholic acid for pig bile, and taurocholic acid for snake bile. Furthermore, cattle bile, cow-bezoar, and artificial cow-bezoar could be differentiated by the existence of hyodeoxycholic acid and the ratio of cholic acid to deoxycholic acid. This study provided bile acid profiles of bile-based Chinese medicines for the first time, which could be used for their quality control.     

The effect of antagonists on the conformational exchange of the retinoid X receptor alpha ligand‐binding domain

The effect of retinoid X receptor (RXR) antagonists on the conformational exchange of the RXR ligand‐binding domain (LBD) remains poorly characterized. To address this question, we used nuclear magnetic resonance spectroscopy to compare the chemical shift perturbations induced by RXR antagonists and agonists on the RXRα LBD when partnered with itself as a homodimer and as the heterodimeric partner with the peroxisome proliferator‐activated receptor γ (PPARγ) LBD. Chemical shift mapping on the crystal structure showed that agonist binding abolished a line‐broadening effect caused by a conformational exchange on backbone amide signals for residues in helix H3 and other regions of either the homo‐ or hetero‐dimer, whereas binding of antagonists with similar binding affinities failed to do so. A lineshape analysis of a glucocorticoid receptor‐interacting protein 1 NR box 2 coactivator peptide showed that the antagonists enhanced peptide binding to the RXRα LBD homodimer, but to a lesser extent than that enhanced by the agonists. This was further supported by a lineshape analysis of the RXR C‐terminal residue, threonine 462 (T462) in the homodimer but not in the heterodimer. Contrary to the agonists, the antagonists failed to abolish a line‐broadening effect caused by a conformational exchange on the T462 signal corresponding to the RXRα LBD–antagonist–peptide ternary complex. These results suggest that the antagonists lack the ability of the agonists to shift the equilibrium of multiple RXRα LBD conformations in favor of a compact state, and that a PPARγ LBD‐agonist complex can prevent the antagonist from enhancing the RXRα LBD‐coactivator binding interaction. Copyright © 2009 John Wiley & Sons, Ltd.     

Bile acid alkylamide derivatives as low molecular weight organogelators: systematic gelation studies and qualitative structural analysis of the systems

A series of amino- and hydroxyalkyl amides of bile acids have been synthesized and characterized by Fourier transform infrared spectroscopy (FTIR), (1)H and (13)C nuclear magnetic resonance spectroscopy (NMR), as well as electrospray ionization mass spectrometry (ESI-MS) measurements. The ability of the synthesized molecules to promote gel formation was systematically investigated. Out of 396 combinations formed by 11 compounds and 36 different solvents, 22 gel-containing systems were obtained with 1% (w/v) gelator concentration. Apart from one exception, the gelator compounds were lithocholic acid derivatives. This challenges the general trend of bile acid-based physical gelators, according to which the gelation ability of lithocholic acid derivatives is poor. A correlation between the values of Kamlet-Taft parameters and solvent preferences for gelators was observed. The morphologies of the solid and gel structures studied with scanning electron microscopy (SEM) showed variability from fibers to spherical microscale aggregates, the latter of which are unique among bile acid-based organogels. The gels exhibited more complex behavior than was previously established with bile acid derivatives, judging by the microscale diversity present in gelating and non-gelating systems and the tendency for polymorphism. This study underlines the importance of both the molecular and colloidal scale aspects of the gelation phenomenon.     

Gas-Phase Binding of Noncovalent Complexes Between α-cyclodextrin and Amino Acids Investigated by Mass Spectrometry

Noncovalent complexes between cyclodextrins and small molecules have been extensively studied recently because of their widespread application in the pharmaceutical industry for chiral and molecular recognition. To date, gas phase noncovalent binding affinities between α-cyclodextrin and amino acids have not been widely investigated. In this study, gas-phase binding of noncovalent complexes between α-CD and amino acids was investigated by electrospray ionization mass spectrometry (ESI-MS), demonstrating the formation of 1:1 stoichiometric noncovalent complexes. The binding of the complexes were further confirmed by collision-induced dissociation by tandem mass spectrometry. Mass spectrometric titrations between α-cyclodextrin and phenylalanine, glutamic acid, and arginine were performed to provide binding constants (lgK_a) as references for competitive ESI-MS. Calibration curves for the complexes of α-cyclodextrin with phenylalanine, glutamic acid, and arginine were plotted. Through competitive ESI-MS, the lgK_a for the complexes of α-CD with aspartic acid, lysine, proline, glycine, alanine, asparagine, cystine, glutamine, histidine, leucine, isoleucine, methionine, serine, threonine, and valine were measured directly. By comparison, it is seen that the measured binding constants for the complexes of α-cyclodextrin with basic amino acids such as arginine and lysine are lower than those for most complexes of neutral amino acids. The chiral selectivity of α-cyclodextrin for L- and D-isomers of methionine, threonine, asparagine, and phenylalanine determined by ESI-MS revealed its application as a chiral selector.     

Studies on steroids. CCXXVIII Trace analysis of bile acids by gas chromatography-mass spectrometry with negative ion chemical ionization detection

A suitable derivatization method for the trace analysis of bile acids by gas chromatography (GC) in combination with negative ion chemical ionization (NICI) mass spectrometry is described. Of various derivatives for the carboxyl group, the pentafluorobenzyl (PFB) ester provided the highest value of the ratio of the negative to the positive ion current. A characteristic carboxylate anion [M - 181]- was produced as the most abundant ion by the loss of the PFB group in NICI. The PFB esters were further derivatized to the dimethylethylsilyl (DMES) ethers, whereby lithocholic acid, deoxycholic acid, chenodeoxycholic acid, ursodeoxycholic acid and cholic acid were distinctly separated by GC on a cross-linked methyl silicone fused-silica capillary column. The detection limit for the PFB-DMES derivatives of dihydroxylated bile acids was 2 fg when the fragment ion was monitored at m/z 563 in the NICI mode using isobutane as a reagent gas.     

Rapid and accurate reversed-phase high-performance liquid chromatographic determination of conjugated bile acids in human bile for routine clinical applications. Therapeutic control during gallstone dissolution therapy

This paper introduces a new method to detect the taurine and glycine conjugates of five different bile acids (cholic acid, deoxycholic acid, chenodeoxycholic acid, ursodeoxycholic acid and lithocholic acid) in human bile. Advantages of this method are sufficient separation of compounds within a short period of time and a high rate of reproducibility. Using a mobile phase gradient of acetonitrile and water, modified with tetrabutylammonium hydrogen sulphate (0.0075 mol/l), we were able to maximize the differentiation between ursodeoxycholic acid and lithocholic acid, which is of primary interest during conservative gallstone dissolution therapy. Use of this gradient reduced analysis time to less than 0.5 h. Recovery rates for this modified method ranged from 94% to 100%, and reproducibility was 98%, sufficient for routine clinical applications.     

The Effect of the Side Chain on Gelation Properties of Bile Acid Alkyl Amides

Six bile acid alkyl amide derivatives were studied with respect to their gelation properties. The derivatives were composed of three different bile acids with hexyl or cyclohexyl side chains. The gelation behaviour of all six compounds were studied for 36 solvents with varying polarities. Gelation was observed mainly in aromatic solvents, which is characteristic for bile-acid-based low molecular weight gelators. Out of 108 bile acid-solvent combinations, a total of 44 gel systems were formed, 28 of which from lithocholic acid derivatives, only two from deoxycholic acid derivatives, and 14 from cholic acid derivatives. The majority of the gel systems were formed from bile acids with hexyl side chains, contrary to the cyclohexyl group, which seems to be a poor gelation moiety. These results indicate that the spatial demand of the side chain is the key feature for the gelation properties of the bile acid amides.     

Molecular modeling study of species-selective peroxisome proliferator-activated receptor (PPAR) alpha agonist; possible mechanism(s) of human PPARalpha selectivity of an alpha-substituted phenylpropanoic acid derivative (KCL)

In order to investigate the reason why phenylpropanoic acid derivative (KCL), a potent, human peroxisome proliferator-activated receptor (PPAR) alpha-selective agonist, shows this selectivity, we analyzed the binding modes of KCL and a related compound to the ligand-binding domain of human PPARalpha and rat PPARalpha by means of computer-aided molecular modeling. We concluded that the characteristic specificity of KCL is due to a specific hydrophobic contact between the hydrophobic tail part (the 4-trifluoromethyl group) and the key amino acid Ile272 located on the helix three region of the human PPARalpha ligand binding domain. We propose a possible binding mode of KCL with the ligand-binding domain of human PPARalpha. This binding model should offer important insights for further structural design of subtype-selective PPARalpha agonists for the treatment of altered metabolic homeostasis, such as dyslipidemia, obesity, and diabetes.     

Improved method for the determination of the major neutral steroids and unconjugated bile acids in human faeces using capillary gas chromatography

An improved method has been developed for the determination of the major neutral steroids (cholesterol and 5 beta-cholestan-3 beta-ol) and unconjugated bile acids (deoxycholic acid and lithocholic acid) in human faeces, using capillary gas chromatography with flame ionization detection. The freeze-dried faecal sample was subjected to a two-stage Soxhlet extraction followed by an aqueous alkali-organic solvent partition step to separate neutral steroids from bile acids. The neutral steroids were analysed as their trimethylsilyl ether derivatives on an OV-1 capillary column. The bile acids were further purified on a Sep-Pak C18 cartridge and then fractionated on a Sep-Pak SIL cartridge. Unconjugated bile acids were analysed as their methyl ester-trimethylsilyl ether derivatives also on an OV-1 capillary column. Quantitation of neutral steroids and unconjugated bile acids was achieved by reference to appropriate internal standards, added to the faecal extract immediately after the Soxhlet extraction stage. The method is being used in a study of the effect of diet on the metabolic activity of human gut flora.     

Design and synthesis of bile acid-peptide conjugates linked via triazole moiety

A conjugation of bile acids with peptides via Cu(I)-catalyzed click chemistry has been described. Novel bile acid-peptide conjugates linked via a 1,2,3-triazole moiety based on cholic, deoxycholic and lithocholic acid derivatives were synthesized using Cu(I)-catalyzed 1,3-dipolar cycloaddition ("click" reaction). It was shown that up to three peptide fragments can be attached to a central steroid core, thus forming complex three-dimensional polyconjugate structures, which can find important applications in biochemistry, medicinal chemistry, and coordination chemistry.     

Determination of bile acids in pig liver, pig kidney and bovine liver by gas chromatography-chemical ionization tandem mass spectrometry with total ion chromatograms and extraction ion chromatograms

An effective method has been developed for quantitative determination of six bile acids including lithocholic acid (LCA), deoxycholic acid (DCA), chenodeoxycholic acid (CDCA), hydodeoxycholic acid (HDCA), cholic acid (CA) and ursodeoxycholic acid (UDCA) in biological tissues including pig liver, pig kidney and bovine liver by gas chromatography-chemical ionization/tandem mass spectrometry (GC-CI/MS/MS). Camphor-10-sulphonic acid (CSA) was proposed as effective catalyst for bile acid derivatization. Reactions were accelerated ultrasonically. The effects of different catalysts and reaction times on derivatization efficiency were evaluated and optimized. Bile acids were determined as methyl ester-trimethylsilyl ether and methyl ester-acetate derivatives. The efficiency of trimethylsilylation and acetylation was evaluated. Trimethylsilylation was done with N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA) as the trimethylsilyl donating reagent in a ultrasonic bath for 20 min. Acetylation was done in pyridine with acetic anhydride at 40-45°C for 4 h. The former reaction was faster than the latter. Thus, trimethylsilylation was employed for the quantitative analysis. Negligible interferences from sterols in biological matrices were observed when the biological samples were treated with solid phase extraction before GC-CI/MS/MS. The linearity, reproducibility, detection limit and recovery were evaluated under the optimized conditions. Satisfactory results were obtained when bile acid derivatives of LCA, CDCA, HDCA, and UDCA were determined with total ion chromatograms (TIC) while DCA and CA were determined with extracted ion chromatograms (EIC), respectively. The detection limits (S/N=3) for six bile acids in biological tissues were ranging from 0.40 to 1.6 ng/mL and the recoveries indicated that the proposed method was feasible for the determination of trace bile acids in the biological samples studied. The experimental results for the animal tissues purchased from five different markets were compared. Interestingly, all of the six bile acids were present in pig liver while only the dihydroxy bile acids, DCA, CDCA and HDCA were found in pig kidney. In addition to DCA and CDCA, trihydroxy bile acid, CA, are the major bile acids in bovine liver.     

Thin-layer chromatography/liquid secondary ion mass spectrometry in the determination of major bile salts in dog bile

Positive and negative ion liquid-state secondary-ion mass spectrometry (LSIMS) was applied to several bile acids and bile salts and their spectra were measured directly from the surface of silica gel thin-layer chromatograms. Such spectra were identical to the LSIMS spectra of the pure compound at the same concentration. Three-dimensional ion images were obtained of a model mixture of cholic, chenodeoxycholic and lithocholic acids in both the positive and negative ion modes. A sample of dog bile was prepared, and the bile acids extracted from it were separated by high-performance TLC; TLC/LSIMS spectra were obtained for sodium taurocholate and sodium taurochenodeoxycholate/taurodeoxycholate, the predominant bile salts present. Quantitative estimates of the analytes were obtained by monitoring the ion intensity for the sample spot and a standard spot that had been developed in parallel on the same TLC plate. The concentration of sodium taurocholate in the bile of this particular dog was found to be 38 mg/ml.     

Pharmacophore model for bile acids recognition by the FPR receptor

Formyl-peptide receptors (FPRs) belong to the family A of the G-protein coupled receptor superfamily and include three subtypes: FPR, FPR-like-1 and FPR-like-2. They have been involved in the control of␣many inflammatory processes promoting the recruitment and infiltration of leukocytes in regions of inflammation through the molecular recognition of chemotactic factors. A large number of structurally diverse chemotypes modulate the activity of FPRs. Newly identified antagonists include bile acids deoxycholic acid (DCA) and chenodeoxycholic acid (CDCA). The molecular recognition of these compounds at FPR receptor was computationally investigated using both ligand- and structure-based approaches. Our findings suggest that all antagonists bind at the first third of the seven helical bundles. A closer inspection of bile acid interaction reveals a number of unexploited anchor points in the binding site that may be used to aid the design of new potent and selective bile acids derivatives at FPR.     

Resolving self-assembly of bile acids at the molecular length scale

The self-assembly behavior of the naturally occurring steroidal bile compounds cholic, deoxycholic, ursodeoxycholic, and lithocholic acid was studied by combining atomic force microscopy (AFM), polarized optical microscopy (POM), Fourier-transform infrared spectroscopy (FTIR), absorption spectroscopy (UV-vis), circular dichroism (CD), and wide-angle X-ray scattering (WAXS). Molecular solutions of these mono-, di-, and trihydroxyl substituted bile acids spontaneously evolved into supramolecular aggregates upon the incremental addition of H(2)O as a poor solvent. Highly crystalline nanostructured multilayered assemblies were formed, which revealed a very rich polymorphism of micro- and macro-structures depending on the chemical structure of the bile acid and the properties of the cosolvent (EtOH or DMSO) used. In particular, AFM allowed resolving the crystalline structure to an unprecedented level. It was thus possible to establish that bile acids associate into H-bonded chiral dimer building blocks, which organize in 2D layers of nanostructured lamellar surface topologies with unique facial amphiphilicity. The detailed understanding of the hierarchical organization in bile acid assemblies may contribute to develop strategies to design bioinspired materials with tailor-made nanostructured surface topologies.     

Determination of related impurities of bile acids in bulk drugs by cyclodextrin-modified micellar electrokinetic chromatography

A cyclodextrin-modified micellar electrokinetic chromatography (CD-MEKC) method has been developed and validated for purity determination of two bile acids, ursodeoxycholic acid (UDCA) and deoxycholic acid (DCA). Quantitation of related impurities such as lithocholic acid (LCA), chenodeoxycholic acid (CDCA), cholic acid (CA), and DCA in UDCA and CA in DCA was performed. A running buffer containing 20 mM borate-phosphate, 50 mM sodium dodecyl sulfate (SDS), 2.0 mM beta-cyclodextrin, and acetonitrile was used. Modifiers were added to improve resolution and selectivity. The applied voltage was 25 kV and detection was performed at 185 nm. Validation parameters such as selectivity, linearity, repeatability, intermediate precision, limit of detection, limit of quantitation, and robustness were evaluated. The method was simple and proved to be useful for the purity testing of bile acids in bulk drugs. Good results were obtained for related impurities at concentration levels from 0.05 to 1.5% with respect to the main component, according to international requirements.