4BAE

Optimisation of pyrroleamides as mycobacterial GyrB ATPase inhibitors: Structure Activity Relationship and in vivo efficacy in the mouse model of tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Optimization of Pyrrolamides as Mycobacterial Gyrb ATPase Inhibitors: Structure Activity Relationship and in Vivo Efficacy in the Mouse Model of Tuberculosis.

Hameed, S.P.Solapure, S.Mukherjee, K.Nandi, V.Waterson, D.Shandil, R.Balganesh, M.Sambandamurthy, V.K.Raichurkar, A.K.Deshpande, A.Ghosh, A.Awasthy, D.Shanbhag, G.Sheikh, G.Mcmiken, H.Puttur, J.Reddy, J.Werngren, J.Read, J.Kumar, M.Manjunatha, R.Chinnapattu, M.Madhavapeddi, P.Manjrekar, P.Basu, R.Gaonkar, S.Sharma, S.Hoffner, S.Humnabadkar, V.Subbulakshmi, V.Panduga, V.

(2014) Antimicrob.Agents Chemother. 58: 61

  • DOI: 10.1128/AAC.01751-13

  • PubMed Abstract: 
  • Moxifloxacin has shown excellent activity against drug-sensitive as well as drug-resistant tuberculosis (TB), thus confirming DNA gyrase as a clinically validated target for discovering novel anti-TB agents. We have identified novel inhibitors in the ...

    Moxifloxacin has shown excellent activity against drug-sensitive as well as drug-resistant tuberculosis (TB), thus confirming DNA gyrase as a clinically validated target for discovering novel anti-TB agents. We have identified novel inhibitors in the pyrrolamide class which kill Mycobacterium tuberculosis through inhibition of ATPase activity catalyzed by the GyrB domain of DNA gyrase. A homology model of the M. tuberculosis H37Rv GyrB domain was used for deciphering the structure-activity relationship and binding interactions of inhibitors with mycobacterial GyrB enzyme. Proposed binding interactions were later confirmed through cocrystal structure studies with the Mycobacterium smegmatis GyrB ATPase domain. The most potent compound in this series inhibited supercoiling activity of DNA gyrase with a 50% inhibitory concentration (IC50) of <5 nM, an MIC of 0.03 μg/ml against M. tuberculosis H37Rv, and an MIC90 of <0.25 μg/ml against 99 drug-resistant clinical isolates of M. tuberculosis. The frequency of isolating spontaneous resistant mutants was ∼10(-6) to 10(-8), and the point mutation mapped to the M. tuberculosis GyrB domain (Ser208 Ala), thus confirming its mode of action. The best compound tested for in vivo efficacy in the mouse model showed a 1.1-log reduction in lung CFU in the acute model and a 0.7-log reduction in the chronic model. This class of GyrB inhibitors could be developed as novel anti-TB agents.


    Organizational Affiliation

    AstraZeneca India Pvt Ltd., Hebbal, Bangalore, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA GYRASE SUBUNIT B
A, B, C, D
205Mycobacterium smegmatisMutation(s): 1 
Gene Names: gyrB
EC: 5.6.2.3
Find proteins for P0C559 (Mycobacterium smegmatis)
Go to UniProtKB:  P0C559
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
RWX
Query on RWX

Download SDF File 
Download CCD File 
A, B, C, D
2-[(3S,4R)-4-[(3-bromanyl-4-chloranyl-5-methyl-1H-pyrrol-2-yl)carbonylamino]-3-methoxy-piperidin-1-yl]-4-(2-methyl-1,2,4-triazol-3-yl)-1,3-thiazole-5-carboxylic acid
C19 H21 Br Cl N7 O4 S
IXOKPDRRYHAGRW-ZJUUUORDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RWXIC50: 3 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.191α = 90.00
b = 78.249β = 90.01
c = 89.750γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-30
    Type: Initial release
  • Version 1.1: 2014-01-15
    Type: Database references
  • Version 1.2: 2016-12-14
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Source and taxonomy