DOI: 10.5061/dryad.np5hqc04q
title: Bespoke plant glycoconjugates for gut microbiota-mediated drug targeting

description: The gut microbiota of mammals possess unique metabolic pathways with
 untapped therapeutic potential. Using molecular insights into dietary
 fiber metabolism by the human gut microbiota, we designed a targeted drug
 delivery system based on bespoke glycoconjugates of a complex plant
 oligosaccharide called GlycoCaging. GlycoCaging of exemplar
 anti-inflammatory drugs enabled the release of active molecules triggered
 by unique glycosidases of autochthonous gut bacteria. GlycoCaging
  ensured drug efficacy was potentiated, and off-target effects
 were eliminated in murine models of inflammatory bowel disease. 
 Biochemical and metagenomic analyses of gut microbiota of individual
 humans confirmed the broad applicability of this strategy.
description: # Bespoke plant glycoconjugates for gut microbiota-mediated drug targeting
 [DOI:10.5061/dryad.np5hqc04q](https://doi.org/10.5061/dryad.np5hqc04q) ##
 Description of the data and file structure This dataset contains diverse
 data types and analyses, including from chemical synthesis, enzyme
 kinetics, murine models, pharmacokinetics, and metagenomics.  Please see
 the published article for full experimental details, final data
 presentation, and interpretations. Files are organized into compressed
 archives, first by overall analysis type, and then by corresponding figure
 in the published article. ### File: CompoundNMR.7z Contains original
 free-induction decay (FID) spectra and acquisition parameters for all one-
 and two-dimensional nuclear magnetic resonance (NMR) analyses of synthetic
 compounds. Within this archive, sub-archives contain data corresponding to
 Figures S16-S27, as indicated in the filenames:
 FigS16_FID_PerAcXXXX-OH.7z, FigS17_FID_PerAcXXXG-TCA.7z,
 FigS18_FID_PerAcXXXG-Dex.7z, FigS19-22_FID_XXXG-Dex.7z,
 FigS23-24_FID_XXXG-Bud.7z, FigS25-26_FID_XXXG5ASA.7z,
 FigS27_FID_AcXXXG-Carbonate.7z. ### File: EnzymeKinetics.zip Contains
 enzyme assay data and Michaelis-Menten analyses for GlycoCaged compounds
 corresponding to Figure 1E. Within this archive, sub-archives contain data
 for each compound and enzyme, as indicated in the filenames:
 Fig1E_XXXG-Dex.zip, Fig1E_XXXG-Pred.zip, Fig1E_XXXG-Bude.zip. Data
 processing spreadsheets (.xlsx) and graphing software files (.opj) are
 provided. ### File: TCellTransferModel.zip Contains all numerical gross
 pathology, histopathology, cytokine assay, and flow cytometry data for the
 T Cell Transfer mouse model, corresponding to Figures 2 and S8. Within
 this archive, spreadsheet files (.xlsx) are named by figure:
 Figure2_MouseData.xlsx, FigureS8_MouseData.xlsx. Within each file, data is
 organized into individual sheets by figure panel letter. ### File:
 SHIPModel.zip Contains all numerical gross pathology, histopathology, and
 cytokine assay data for the SHIP-/- mouse model, corresponding to Figures
 3, 4, and S10. Within this archive, spreadsheet files (.xlsx) are named by
 figure: Figure3_MouseGIData.xlsx, Figure4_MouseLungData.xlsx,
 FigureS10_MouseWild-TypeData.xlsx. Within each file, data is organized
 into individual sheets by figure panel letter. ### File:
 Pharmacokinetics.zip Contains pharmacokinetic data obtained by LC-MS/MS
 corresponding to Figures S9 and S11. Within this archive, sub-archives
 contain data for each administered compound and biological sample, with
 filenames indicating the corresponding figure panel: FigureS9PanelA.zip
 through FigureS9PanelD.zip, FigureS11PanelA.zip through
 FigureS11PanelBB.zip. Within sub-archives, original report files from the
 MS service facility (.pdf or .xlsx), data processing spreadsheets (.xlsx),
 and graphing software files are provided (.opj). ### File:
 DecagingBacteriaMouseGut.zip Contains fluorimetric assay data and colony
 enumeration data regarding the presence of prodrug-decaging
 (xyloglucanase-positive) bacteria in the gastrointestinal tracts of mice.
 Subfolders within this archive contain data corresponding to Figures
 S5-S7, as indicated by the folder names. Individual filenames indicate
 corresponding figure panel and data type. Data processing spreadsheets
 (.csv, .xlsx), statistical analysis results (.pdf), and graphing software
 files are provided (.jnb). ### File: DecagingBacteriaHumanGut.zip Contains
 fluorimetric assay data, enumeration data, and metagenome analyses
 regarding the presence of prodrug-decaging (xyloglucanase-positive)
 bacteria in the gastrointestinal tracts of humans. Within this archive,
 sub-archives contain data corresponding to Figures 5, and S12-13, as
 indicated in the filenames: FigS12_HealthyHumanAssay.zip,
 Fig5AB_IBD+ControlsAssay.zip, Fig5CD+S13+S14_Metagenomics.zip. An
 additional README.md file describes in detail the file structure within
 the Metagenomics archive. ## Access information Publicly available
 metagenomes and associated metadata from the Human Microbiome Project 2
 (HMP2) study were downloaded from the Human Microbiome Bioactives Resource
 data portal
 ([https://portal.microbiome-bioactives.org/](https://portal.microbiome-bioactives.org/)). ## Code/software * NMR data can be visualized with various software e.g., Bruker TopSpin, Mestrelab Mnova NMR (45-day free trial version currently available, March 2025). One-dimensional NMR data may be visualized with Mnova NMR Lite. * Spreadsheets (.xlsx) and tabular data (.tsv) can be viewed with Microsoft Excel or equivalent. * Graphical software data can be viewed with SigmaPlot (.jnb) or Origin (.opj). For Origin files, Origin Viewer is currently (March 2025) freely available. * Scripts used to analyze metagenomic data are available on Zenodo and GitHub ([DOI:10.5281/zenodo.14828870](https://doi.org/10.5281/zenodo.14828870)). Please see the Materials and Methods section of the published article for details on the analysis pipeline, including other publicly available software used.