6NDL

Crystal structure of Staphylococcus aureus biotin protein ligase in complex with a sulfonamide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Sulfonamide-Based Inhibitors of Biotin Protein Ligase as New Antibiotic Leads.

Lee, K.J.Tieu, W.Blanco-Rodriguez, B.Paparella, A.S.Yu, J.Hayes, A.Feng, J.Marshall, A.C.Noll, B.Milne, R.Cini, D.Wilce, M.C.J.Booker, G.W.Bruning, J.B.Polyak, S.W.Abell, A.D.

(2019) ACS Chem Biol 14: 1990-1997

  • DOI: https://doi.org/10.1021/acschembio.9b00463
  • Primary Citation of Related Structures:  
    6NDL

  • PubMed Abstract: 

    Here, we report the design, synthesis, and evaluation of a series of inhibitors of Staphylococcus aureus BPL ( Sa BPL), where the central acyl phosphate of the natural intermediate biotinyl-5'-AMP ( 1 ) is replaced by a sulfonamide isostere. Acylsulfamide ( 6 ) and amino sulfonylurea ( 7 ) showed potent in vitro inhibitory activity ( K i = 0.007 ± 0.003 and 0.065 ± 0.03 μM, respectively) and antibacterial activity against S. aureus ATCC49775 with minimum inhibitory concentrations of 0.25 and 4 μg/mL, respectively. Additionally, the bimolecular interactions between the BPL and inhibitors 6 and 7 were defined by X-ray crystallography and molecular dynamics simulations. The high acidity of the sulfonamide linkers of 6 and 7 likely contributes to the enhanced in vitro inhibitory activities by promoting interaction with Sa BPL Lys187. Analogues with alkylsulfamide ( 8 ), β-ketosulfonamide ( 9 ), and β-hydroxysulfonamide ( 10 ) isosteres were devoid of significant activity. Binding free energy estimation using computational methods suggests deprotonated 6 and 7 to be the best binders, which is consistent with enzyme assay results. Compound 6 was unstable in whole blood, leading to poor pharmacokinetics. Importantly, 7 has a vastly improved pharmacokinetic profile compared to that of 6 presumably due to the enhanced metabolic stability of the sulfonamide linker moiety.


  • Organizational Affiliation

    Department of Chemistry, School of Physical Sciences , University of Adelaide , Adelaide , South Australia 5005 , Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Biotin Protein Ligase330Staphylococcus aureusMutation(s): 0 
EC: 6.3.4.15
UniProt
Find proteins for Q2G258 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2G258 
Go to UniProtKB:  Q2G258
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2G258
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.031α = 90
b = 94.031β = 90
c = 130.977γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Source and taxonomy
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description