8USM

FmlH Lectin Domain UTI89 - AM4085


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.202 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of Orally Bioavailable FmlH Lectin Antagonists as Treatment for Urinary Tract Infections.

Maddirala, A.R.Tamadonfar, K.Pinkner, J.S.Sanick, D.Hultgren, S.J.Janetka, J.W.

(2024) J Med Chem 67: 3668-3678

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c02128
  • Primary Citation of Related Structures:  
    8USM

  • PubMed Abstract: 

    FmlH, a bacterial adhesin of uropathogenic Escherichia coli (UPEC), has been shown to provide a fitness advantage in colonizing the bladder during chronic urinary tract infections (UTIs). Previously reported ortho -biphenyl glycosides based on βGal and βGalNAc have excellent binding affinity to FmlH and potently block binding to its natural carbohydrate receptor, but they lack oral bioavailability. In this paper, we outline studies where we have optimized compounds for improved pharmacokinetics, leading to the discovery of novel analogues with good oral bioavailability. We synthesized galactosides with the anomeric O-linker replaced with more stable S- and C-linked linkers. We also investigated modifications to the GalNAc sugar and modifications to the biphenyl aglycone. We identified GalNAc 69 with an IC 50 of 0.19 μM against FmlH and 53% oral bioavailability in mice. We also obtained a FimlH-bound X-ray structure of lead compound 69 (AM4085) which has potential as a new antivirulence therapeutic for UTIs.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fimbrial protein (Fragment)
A, B
166Escherichia coliMutation(s): 0 
Gene Names: G3W53_27805
UniProt
Find proteins for A0A8T6QH46 (Escherichia coli)
Explore A0A8T6QH46 
Go to UniProtKB:  A0A8T6QH46
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8T6QH46
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XC8 (Subject of Investigation/LOI)
Query on XC8

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
4'-fluoro-6-(trifluoromethyl)[1,1'-biphenyl]-2-yl 2-acetamido-2-deoxy-beta-D-galactopyranoside
C21 H21 F4 N O6
HRLDWJXNEKTIOQ-XIKSMUEASA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.245α = 90
b = 116.45β = 90
c = 50.955γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01DK10884

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-14
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Database references