3PN1

Novel Bacterial NAD+-dependent DNA Ligase Inhibitors with Broad Spectrum Potency and Antibacterial Efficacy In Vivo


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Novel Bacterial NAD+-Dependent DNA Ligase Inhibitors with Broad-Spectrum Activity and Antibacterial Efficacy In Vivo.

Mills, S.D.Eakin, A.E.Buurman, E.T.Newman, J.V.Gao, N.Huynh, H.Johnson, K.D.Lahiri, S.Shapiro, A.B.Walkup, G.K.Yang, W.Stokes, S.S.

(2011) Antimicrob.Agents Chemother. 55: 1088-1096

  • DOI: 10.1128/AAC.01181-10

  • PubMed Abstract: 
  • DNA ligases are indispensable enzymes playing a critical role in DNA replication, recombination, and repair in all living organisms. Bacterial NAD+-dependent DNA ligase (LigA) was evaluated for its potential as a broad-spectrum antibacterial target. ...

    DNA ligases are indispensable enzymes playing a critical role in DNA replication, recombination, and repair in all living organisms. Bacterial NAD+-dependent DNA ligase (LigA) was evaluated for its potential as a broad-spectrum antibacterial target. A novel class of substituted adenosine analogs was discovered by target-based high-throughput screening (HTS), and these compounds were optimized to render them more effective and selective inhibitors of LigA. The adenosine analogs inhibited the LigA activities of Escherichia coli, Haemophilus influenzae, Mycoplasma pneumoniae, Streptococcus pneumoniae, and Staphylococcus aureus, with inhibitory activities in the nanomolar range. They were selective for bacterial NAD+-dependent DNA ligases, showing no inhibitory activity against ATP-dependent human DNA ligase 1 or bacteriophage T4 ligase. Enzyme kinetic measurements demonstrated that the compounds bind competitively with NAD+. X-ray crystallography demonstrated that the adenosine analogs bind in the AMP-binding pocket of the LigA adenylation domain. Antibacterial activity was observed against pathogenic Gram-positive and atypical bacteria, such as S. aureus, S. pneumoniae, Streptococcus pyogenes, and M. pneumoniae, as well as against Gram-negative pathogens, such as H. influenzae and Moraxella catarrhalis. The mode of action was verified using recombinant strains with altered LigA expression, an Okazaki fragment accumulation assay, and the isolation of resistant strains with ligA mutations. In vivo efficacy was demonstrated in a murine S. aureus thigh infection model and a murine S. pneumoniae lung infection model. Treatment with the adenosine analogs reduced the bacterial burden (expressed in CFU) in the corresponding infected organ tissue as much as 1,000-fold, thus validating LigA as a target for antibacterial therapy.


    Organizational Affiliation

    AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA. Scott.Mills@astrazeneca.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA ligase
A
318Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)Mutation(s): 0 
Gene Names: ligA (lig, ligN)
EC: 6.5.1.2
Find proteins for P43813 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Go to UniProtKB:  P43813
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IWH
Query on IWH

Download SDF File 
Download CCD File 
A
1-(2,4-dimethylbenzyl)-6-oxo-1,6-dihydropyridine-3-carboxamide
C15 H16 N2 O2
TUJVPUNUHQIBSM-UHFFFAOYSA-N
 Ligand Interaction
IVH
Query on IVH

Download SDF File 
Download CCD File 
A
2-(butylsulfanyl)adenosine
C14 H21 N5 O4 S
JUZWTKSKLZRPBL-QYVSTXNMSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IVHIC50: 507 nM BINDINGMOAD
IVHKi: 110 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.201 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 137.806α = 90.00
b = 137.806β = 90.00
c = 56.023γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
DENZOdata reduction
AMoREphasing
CrystalCleardata collection
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-02-22
    Type: Structure summary
  • Version 1.3: 2017-11-08
    Type: Refinement description