BART: A transferable liquid chromatography retention time library for bile acids

Identification of unknown bile acids, especially the distinguishment between isomers, requires retention times of a large number of reference standards, which are often not commercially available. Meanwhile, published retention information cannot be directly transferred across labs due to the differences between liquid chromatography (LC) systems, such as different extra column volume and dwell volume. To improve this situation, a transferrable retention time library for bile acids named BART was developed. BART was composed of isocratic retention models of 272 bile acids and a software tool to predict their gradient retention times on various LC systems. The isocratic retention times of bile acids were acquired on a Waters BEH C18 column with mobile phases of acidic ammonium acetate buffer and acetonitrile, and fit to the quadratic solvent strength model (QSSM). Segmented linear gradient retention times were calculated with holdup time (t0), dwell time (tD) and actual gradient profile corrected using 21 bile acid calibration standards. In addition to the reference system where the isocratic retention times were acquired, this approach has been validated on four other LC-MS systems in four labs with two gradient methods. Average root mean square errors (RMSE) between predicted and experimental retention times were 0.052 and 0.054 min for the two gradients tested, which were 9-fold more accurate than referring to a static retention time library. The library is freely available at https://bafinder.github.io/.

Integration of semi-empirical MS/MS library with characteristic features for the annotation of novel amino acid-conjugated bile acids

Recently, amino acids other than glycine and taurine were found to be conjugated with bile acids by the gut microbiome in mouse and human. As potential diagnostic markers for inflammatory bowel disease and farnesoid X receptor agonists, their physiological effects and mechanisms, however, remain to be elucidated. A tool for the rapid and comprehensive annotation of such new metabolites is required. Thus, we developed a semi-empirical MS/MS library for bile acids conjugated with 18 common amino acids, including alanine, arginine, asparagine, aspartate, glutamine, glutamate, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, and valine. To investigate their fragmentation rules, these amino acids were chemically conjugated with lithocholic acid, deoxycholic acid, and cholic acid, and their accurate-mass MS/MS spectra were acquired. The common fragmentation patterns from the amino acid moieties were combined with 10 general bile acid skeletons to generate a semi-empirical MS/MS library of 180 structures. Software named BAFinder 2.0 was developed to combine the semi-empirical library in negative mode and the characteristic fragments in positive mode for automatic unknown identification. As a proof of concept, this workflow was applied to the LC-MS/MS analysis of the feces of human, beagle dogs, and rats. In total, 171 common amino acid-conjugated bile acids were annotated and 105 of them were confirmed with the retention times of synthesized compounds. To explore other potential bile acid conjugates, user-defined small molecules were in-silico conjugated with bile acids and searched in the fecal dataset. Four novel bile acid conjugates were discovered, including D-Ala-D-Ala, Lys(iso)-Gly, L-2-aminobutyric acid, and ornithine.

Characterization of Calculus bovis by principal component analysis assisted qHNMR profiling to distinguish nefarious frauds

A new approach is developed for the reliable classification of Calculus bovis along with the identification of willfully contaminated C. bovis species and the quantification of unclaimed adulterants. Guided by a principal component analysis, NMR data mining achieved a near-holistic chemical characterization of three types of authenticated C. bovis, including natural C. bovis (NCB), in vitro cultured C. bovis (Ivt-CCB), and artificial C. bovis (ACB). In addition, species-specific markers used for quality evaluation and species classification were confirmed. That is, the content of taurine in NCB is near negligible, while choline and hyodeoxycholic acid are characteristic for identifying Ivt-CCB and ACB, respectively. Besides, the peak shapes and chemical shifts of H₂-25 of glycocholic acid could assist in the recognition of the origins of C. bovis. Based on these discoveries, a set of commercial NCB samples, macroscopically identified as problematic species, was examined with deliberately added sugars and outliers discovered. Absolute quantification of the identified sugars was realized by qHNMR using a single, nonidentical internal calibrant (IC). This study represents the first systematic study of C. bovis metabolomics via an NMR-driven methodology, which advances the toolbox for quality control of TCM and provides a more definitive reference point for future chemical and biological studies of C. bovis as a valuable materia medica.

BAFinder: A Software for Unknown Bile Acid Identification Using Accurate Mass LC-MS/MS in Positive and Negative Modes

Most LC-MS based bile acid analyses target common bile acids. The identification of unknown bile acids remains challenging in untargeted experiments. Here, a software named BAFinder was developed to improve the identification of unknown bile acids from accurate mass LC-MS/MS data in both the positive and negative ESI modes. A wide variety of bile acid structures were covered in BAFinder, including oxidized bile acids and sugar conjugates that were often ignored. The annotation of unknown bile acids was based on a thorough investigation of MS/MS fragmentation patterns of 84 bile acid reference standards in both modes. Specifically, BAFinder took the peak alignment result and MS/MS spectra, grouped candidate features in positive and negative modes, searched their representative MS/MS spectra against a MS/MS library, and used characteristic product ions and neutral losses to annotate bile acids not covered in the library. Finally, the number of hydroxyl groups and double bonds, conjugation, and isomer information of bile acids were reported with four different levels of annotation confidence. The use of BAFinder was demonstrated through successful application to the analysis of human plasma and urine samples, in which a total of 112 and 244 bile acids were annotated and 75 and 111 of them were confirmed with standards or synthesized compounds, respectively. The software is freely available at https://bafinder.github.io/.

A streamlined synthesis of the neurosteroid 3β-methoxypregnenolone assisted by a statistical experimental design and automation

The potential of integrating flow synthesizers, statistical design of experiments and automation has been exemplified to realize the streamlined etherification of pregnenolone to the neurosteroid 3β-methoxypregnenolone (MAP4343).

Discovery of 3α,7α,11β-Trihydroxy-6α-ethyl-5β-cholan-24-oic Acid (TC-100), a Novel Bile Acid as Potent and Highly Selective FXR Agonist for Enterohepatic Disorders

As a continuation of previous efforts in mapping functional hot spots on the bile acid scaffold, we here demonstrate that the introduction of a hydroxy group at the C11β position affords high selectivity for FXR. In particular, the synthesis and FXR/TGR5 activity of novel bile acids bearing different hydroxylation patterns at the C ring are reported and discussed from a structure-activity standpoint. The results obtained led us to discover the first bile acid derivative endowed with high potency and selectivity at the FXR receptor, 3α,7α,11β-trihydroxy-6α-ethyl-5β-cholan-24-oic acid (TC-100, 7) which also shows a remarkable physicochemical and pharmacological profile. Compound 7 combines the excellent physicochemical properties of hydrophilic bile acids such as ursodeoxycholic acid, with the distinct ability to specifically bind and regulate FXR activity in vivo, thus providing a bona fide novel therapeutic agent to treat enterohepatic disorders such as cholestasis, NASH, and inflammatory bowel disease.

Taurine zinc solid dispersions enhance bile-incubated L02 cell viability and improve liver function by inhibiting ERK2 and JNK phosphorylation during cholestasis

Dietary intakes of taurine and zinc are associated with decreased risk of liver disease. In this study, solid dispersions (SDs) of a taurine zinc complex on hepatic injury were examined in vitro using the immortalized human hepatocyte cell line L02 and in a rat model of bile duct ligation. Sham-operated and bile duct ligated Sprague-Dawley rats were treated with the vehicle alone or taurine zinc (40, 80, 160mg/kg) for 17days. Bile duct ligation significantly increased blood lipid levels, and promoted hepatocyte apoptosis, inflammation and compensatory biliary proliferation. In vitro, incubation with bile significantly reduced L02 cell viability; this effect was significantly attenuated by pretreatment with SP600125 (a JNK inhibitor) and enhanced when co-incubated with taurine zinc SDs. In vivo, administration of taurine zinc SDs decreased serum alanine aminotransferase and aspartate aminotransferase activities in a dose-dependent manner and attenuated the increases in serum total bilirubin, total cholesterol and low density lipoprotein cholesterol levels after bile duct ligation. Additionally, taurine zinc SDs downregulated the expression of interleukin-1β and inhibited the phosphorylation of Jun N-terminal kinase (JNK) and extracellular signal-regulated kinase2 (ERK2) in the liver after bile duct ligation. Moreover, taurine zinc SDs had more potent blood lipid regulatory and anti-apoptotic effects than the physical mixture of taurine and zinc acetate. Therefore, we speculate that taurine zinc SDs protect liver function at least in part via a mechanism linked to reduce phosphorylation of JNK and ERK2, which suppresses inflammation, apoptosis and cholangiocyte proliferation during cholestasis.

Integrating multicomponent flow synthesis and computational approaches for the generation of a tetrahydroquinoline compound based library

The combination of flow chemistry and computational tools has been successfully applied to prepare a focused library of tricyclic tetrahydroquinolines endowed with drug-like properties.

Efficient amide bond formation through a rapid and strong activation of carboxylic acids in a microflow reactor

The development of highly efficient amide bond forming methods which are devoid of side reactions, including epimerization, is important, and such a method is described herein and is based on the concept of rapid and strong activation of carboxylic acids. Various carboxylic acids are rapidly (0.5 s) converted into highly active species, derived from the inexpensive and less-toxic solid triphosgene, and then rapidly (4.3 s) reacted with various amines to afford the desired peptides in high yields (74%-quant.) without significant epimerization (≤3%). Our process can be carried out at ambient temperature, and only CO2 and HCl salts of diisopropylethyl amine are generated. In the long history of peptide synthesis, a significant number of active coupling reagents have been abandoned because the highly active electrophilic species generated are usually susceptible to side reactions such as epimerization. The concept presented herein should renew interest in the use of these reagents.

Building a sulfonamide library by eco-friendly flow synthesis

A rapid and eco-friendly synthesis of a sulfonamide library under flow conditions is described. The study illustrates an efficient, safe, and easily scalable preparation of sulfonamides by use of a meso-reactor apparatus, thus demonstrating the impact of flow technologies within drug discovery. Waste minimization, employment of green media, and nontoxic reactants are achieved by the optimization of the flow setup and experimental protocol designed to sequentially synthesize primary, secondary, and tertiary sulfonamides. Isolation of the products involves only extraction and precipitation affording pure compounds in good to high yields without further purification for biological evaluation.