Ecological Base-Conditioned Preparation of Dipeptides Using Unprotected α-Amino Acids Containing Hydrophilic Side Chains

Ezawa, Tetsuya; Jung, Seunghee; Kawashima, Yuya; Noguchi, Takuya; Imai, Nobuyuki

doi:10.1246/bcsj.20170035

Cited by 12 publications

(9 citation statements)

References 23 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To apply our synthesis-first approach to the discovery of new conjugated bile acids, we selected a chloroformate-mediated amide coupling for combinatorial synthesis of amino acidconjugated bile amidates 36 . Specifically, ethyl chloroformate was utilized in combination with triethylamine to activate the carboxylic acids of eight different bile acids contained in separate vessels into their reactive mixed anhydride intermediates.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

A Synthesis-Based Reverse Metabolomics Approach for the Discovery of Chemical Structures from Humans and Animals.

Dorrestein

Gentry

Collins

et al. 2021

Preprint

View full text Add to dashboard Cite

Identification of metabolites in humans remains challenging. Here, we present synthesis-based reverse metabolomics as a strategy for structure elucidation that aims to also find phenotypic associations. In this approach, MS/MS spectra are acquired from newly synthesized compounds, and searched against public metabolomics data to uncover their phenotypic associations. To demonstrate the concept, we used combinatorial amide coupling reactions to synthesize an array of amino acid conjugated bile acids. A total of 16,587 spectral matches were found for 145 amidates synthesized, representing the single largest expansion of structures in the 170+ year history of bile acids. Furthermore, some new bile acids were associated with health-related phenotypes such as inflammatory bowel diseases and obesity. Using independent human cohorts for validation revealed that some cholic and chenodeoxycholic acid conjugates were elevated in Crohn’s disease, of which some were also potent PXR agonists. Bacteria belonging to bifidobacterium, clostridium, and enterococci genera were the main producers of these new conjugated bile acids. Because searching repositories with MS/MS spectra has only recently become possible, this synthesis-based reverse metabolomics approach can now be employed as a general strategy to elucidate structures and discover other new molecules from human and animal ecosystems.

show abstract

Section: Resultsmentioning

confidence: 99%

“…Synthesis of the conjugated bile acids was adapted from a previous method by Ezawa et al 36 . Bile acid (0.25 mmol, 1 equiv) was dissolved in anhydrous THF (4.9 mL, 0.05M) and cooled to 0°C with stirring.…”

Section: Synthesis Of Pure Compounds Of the Top 12 Most Intense Ones In Ihmp2mentioning

confidence: 99%

A Synthesis-Based Reverse Metabolomics Approach for the Discovery of Chemical Structures from Humans and Animals.

Dorrestein

Gentry

Collins

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…All MCBAs were purified according to literature precedent and char acterization data are consistent with reported data 31,33,42,77,78 . Synthesis of the conjugated bile acids was adapted from a previously published method 79 . Bile acid (0.25 mmol, 1 equiv) was dissolved in anhydrous tetrahydrofuran (4.9 ml, 0.05 M) and cooled to 0 °C with stirring.…”

Section: Mcba Synthesismentioning

confidence: 99%

Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut

et al. 2023

View full text Add to dashboard Cite

Bile acids (BAs) mediate the crosstalk between human and microbial cells and influence diseases including Clostridioides difficile infection (CDI). While bile salt hydrolases (BSHs) shape the BA pool by deconjugating conjugated BAs, the basis for their substrate selectivity and impact on C. difficile remain elusive. Here we survey the diversity of BSHs in the gut commensals Lactobacillaceae, which are commonly used as probiotics, and other members of the human gut microbiome. We structurally pinpoint a loop that predicts BSH preferences for either glycine or taurine substrates. BSHs with varying specificities were shown to restrict C. difficile spore germination and growth in vitro and colonization in pre-clinical in vivo models of CDI. Furthermore, BSHs reshape the pool of microbial conjugated bile acids (MCBAs) in the murine gut, and these MCBAs can further restrict C. difficile virulence in vitro. The recognition of conjugated BAs by BSHs defines the resulting BA pool, including the expansive MCBAs. This work provides insights into the structural basis of BSH mechanisms that shape the BA landscape and promote colonization resistance against C. difficile.

show abstract

“…Annotations of two “truly novel” bile acid conjugates, phenylalanine (Phe) and tryptophan (Trp) conjugates of chenodeoxycholic acid (CDCA), were verified by comparing their fragmentation spectra and retention times with those of synthetic standards. Phe-CDCA ( 7 ) and Trp-CDCA ( 12 ) were synthesized using a procedure adapted from a previous method by Ezawa et al 81 . Chenodeoxycholic acid (98.1 mg, 0.25 mmol, 1 eq.)…”

Section: Methodsmentioning

confidence: 99%

Assigning confidence to structural annotations from mass spectra with COSMIC

Hoffmann

Nothias

Ludwig

et al. 2021

Preprint

View full text Add to dashboard Cite

Untargeted metabolomics experiments rely on spectral libraries for structure annotation, but these libraries are vastly incomplete; in silico methods search in structure databases but cannot distinguish between correct and incorrect annotations. As biological interpretation relies on accurate structure annotations, the ability to assign confidence to such annotations is a key outstanding problem. We introduce the COSMIC workflow that combines structure database generation, in silico annotation, and a confidence score consisting of kernel density p-value estimation and a Support Vector Machine with enforced directionality of features. In evaluation, COSMIC annotates a substantial number of hits at small false discovery rates, and outperforms spectral library search for this purpose. To demonstrate that COSMIC can annotate structures never reported before, we annotated twelve novel bile acid conjugates; nine structures were confirmed by manual evaluation and two structures using synthetic standards. Second, we annotated and manually evaluated 315 molecular structures in human samples currently absent from the Human Metabolome Database. Third, we applied COSMIC to 17,400 experimental runs and annotated 1,715 structures with high confidence that were absent from spectral libraries.

show abstract

Ecological Base-Conditioned Preparation of Dipeptides Using Unprotected α-Amino Acids Containing Hydrophilic Side Chains

Cited by 12 publications

References 23 publications

A Synthesis-Based Reverse Metabolomics Approach for the Discovery of Chemical Structures from Humans and Animals.

A Synthesis-Based Reverse Metabolomics Approach for the Discovery of Chemical Structures from Humans and Animals.

Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut

Assigning confidence to structural annotations from mass spectra with COSMIC

Contact Info

Product

Resources

About