4UFZ

Synthesis of Novel NAD Dependant DNA Ligase Inhibitors via Negishi Cross-Coupling: Development of SAR and Resistance Studies


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Negishi Cross-Coupling Enabled Synthesis of Novel Nad(+)-Dependent DNA Ligase Inhibitors and Sar Development.

Murphy-Benenato, K.E.Gingipalli, L.Boriack-Sjodin, P.A.Martinez-Botella, G.Carcanague, D.Eyermann, C.J.Gowravaram, M.Harang, J.Hale, M.R.Ioannidis, G.Jahic, H.Johnstone, M.Kutschke, A.Laganas, V.A.Loch, J.T.Miller, M.D.Oguto, H.Patel, S.J.

(2015) Bioorg.Med.Chem.Lett. 25: 5172

  • DOI: 10.1016/j.bmcl.2015.09.075

  • PubMed Abstract: 
  • Two novel compounds, pyridopyrimidines (1) and naphthyridines (2) were identified as potent inhibitors of bacterial NAD(+)-dependent DNA ligase (Lig) A in a fragment screening. SAR was guided by molecular modeling and X-ray crystallography. It was ob ...

    Two novel compounds, pyridopyrimidines (1) and naphthyridines (2) were identified as potent inhibitors of bacterial NAD(+)-dependent DNA ligase (Lig) A in a fragment screening. SAR was guided by molecular modeling and X-ray crystallography. It was observed that the diaminonitrile pharmacophore made a key interaction with the ligase enzyme, specifically residues Glu114, Lys291, and Leu117. Synthetic challenges limited opportunities for diversification of the naphthyridine core, therefore most of the SAR was focused on a pyridopyrimidine scaffold. The initial diversification at R(1) improved both enzyme and cell potency. Further SAR developed at the R(2) position using the Negishi cross-coupling reaction provided several compounds, among these compounds 22g showed good enzyme potency and cellular potency.


    Organizational Affiliation

    Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA LIGASE
A
324Haemophilus 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
IA7
Query on IA7

Download SDF File 
Download CCD File 
A
5,7-bis(azanyl)-2-tert-butyl-4-(1,3-thiazol-2-yl)pyrido[2,3-d]pyrimidine-6-carbonitrile
C15 H15 N7 S
VDKRFQKJPXSMOG-UHFFFAOYSA-N
 Ligand Interaction
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.221 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 138.814α = 90.00
b = 138.814β = 90.00
c = 56.165γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata reduction
AMoREphasing
DTSCALEdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2015-10-28
    Type: Initial release
  • Version 1.1: 2015-11-11
    Type: Database references
  • Version 1.2: 2018-04-04
    Type: Data collection