6TPR

PqsR (MvfR) bound to inhibitory compound 40


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.207 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Hit Identification of New Potent PqsR Antagonists as Inhibitors of Quorum Sensing in Planktonic and Biofilm GrownPseudomonas aeruginosa.

Soukarieh, F.Liu, R.Romero, M.Roberston, S.N.Richardson, W.Lucanto, S.Oton, E.V.Qudus, N.R.Mashabi, A.Grossman, S.Ali, S.Sou, T.Kukavica-Ibrulj, I.Levesque, R.C.Bergstrom, C.A.S.Halliday, N.Mistry, S.N.Emsley, J.Heeb, S.Williams, P.Camara, M.Stocks, M.J.

(2020) Front Chem 8: 204-204

  • DOI: https://doi.org/10.3389/fchem.2020.00204
  • Primary Citation of Related Structures:  
    6TPR

  • PubMed Abstract: 

    Current treatments for Pseudomonas aeruginosa infections are becoming less effective because of the increasing rates of multi-antibiotic resistance. Pharmacological targeting of virulence through inhibition of quorum sensing (QS) dependent virulence gene regulation has considerable therapeutic potential. In P. aeruginosa , the pqs QS system regulates the production of multiple virulence factors as well as biofilm maturation and is a promising approach for developing antimicrobial adjuvants for combatting drug resistance. In this work, we report the hit optimisation for a series of potent novel inhibitors of PqsR, a key regulator of the pqs system, bearing a 2-((5-methyl-5 H -[1,2,4]triazino[5,6- b ]indol-3-yl)thio) acetamide scaffold. The initial hit compound 7 (PAO1-L IC 50 0.98 ± 0.02 μM, PA14 inactive at 10 μM) was obtained through a virtual screening campaign performed on the PqsR ligand binding domain using the University of Nottingham Managed Chemical Compound Collection. Hit optimisation gave compounds with enhanced potency against strains PAO1-L and PA14, evaluated using P. aeruginosa pqs -based QS bioreporter assays. Compound 40 (PAO1-L IC 50 0.25 ± 0.12 μM, PA14 IC 50 0.34 ± 0.03 μM) is one of the most potent PqsR antagonists reported showing significant inhibition of P. aeruginosa pyocyanin production and pqs system signaling in both planktonic cultures and biofilms. The co-crystal structure of 40 with the PqsR ligand binding domain revealed the specific binding interactions occurring between inhibitor and this key regulatory protein.


  • Organizational Affiliation

    School of Life Sciences, University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulator MvfR239Pseudomonas aeruginosa UCBPP-PA14Mutation(s): 0 
Gene Names: mvfRPA14_51340
UniProt
Find proteins for A0A0H2Z7A6 (Pseudomonas aeruginosa (strain UCBPP-PA14))
Explore A0A0H2Z7A6 
Go to UniProtKB:  A0A0H2Z7A6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2Z7A6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NV5 (Subject of Investigation/LOI)
Query on NV5

Download Ideal Coordinates CCD File 
B [auth A]2-[(5-methyl-[1,2,4]triazino[5,6-b]indol-3-yl)sulfanyl]-~{N}-(4-pyridin-2-yloxyphenyl)ethanamide
C23 H18 N6 O2 S
ZQQZWZKGMACADA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.207 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.754α = 90
b = 118.754β = 90
c = 115.242γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release
  • Version 2.0: 2020-05-20
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Polymer sequence, Structure summary
  • Version 2.1: 2020-05-27
    Changes: Database references
  • Version 2.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description