8Q0T

Identification and optimisation of novel inhibitors of the Polyketide synthetase 13 thioesterase domain with antitubercular activity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Identification and Optimization of Novel Inhibitors of the Polyketide Synthase 13 Thioesterase Domain with Antitubercular Activity.

Green, S.R.Wilson, C.Eadsforth, T.C.Punekar, A.S.Tamaki, F.K.Wood, G.Caldwell, N.Forte, B.Norcross, N.R.Kiczun, M.Post, J.M.Lopez-Roman, E.M.Engelhart, C.A.Lukac, I.Zuccotto, F.Epemolu, O.Boshoff, H.I.M.Schnappinger, D.Walpole, C.Gilbert, I.H.Read, K.D.Wyatt, P.G.Baragana, B.

(2023) J Med Chem 66: 15380-15408

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01514
  • Primary Citation of Related Structures:  
    8Q0T, 8Q0U, 8Q17

  • PubMed Abstract: 

    There is an urgent need for new tuberculosis (TB) treatments, with novel modes of action, to reduce the incidence/mortality of TB and to combat resistance to current treatments. Through both chemical and genetic methodologies, polyketide synthase 13 (Pks13) has been validated as essential for mycobacterial survival and as an attractive target for Mycobacterium tuberculosis growth inhibitors. A benzofuran series of inhibitors that targeted the Pks13 thioesterase domain, failed to progress to preclinical development due to concerns over cardiotoxicity. Herein, we report the identification of a novel oxadiazole series of Pks13 inhibitors, derived from a high-throughput screening hit and structure-guided optimization. This new series binds in the Pks13 thioesterase domain, with a distinct binding mode compared to the benzofuran series. Through iterative rounds of design, assisted by structural information, lead compounds were identified with improved antitubercular potencies (MIC < 1 μM) and in vitro ADMET profiles.


  • Organizational Affiliation

    Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyketide synthase Pks13
A, B
286Mycobacterium tuberculosisMutation(s): 0 
Gene Names: pks13Rv3800c
EC: 2.3.1
UniProt
Find proteins for I6X8D2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore I6X8D2 
Go to UniProtKB:  I6X8D2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6X8D2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IJJ (Subject of Investigation/LOI)
Query on IJJ

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
3-(3,4-dimethoxyphenyl)-~{N}-[2-(3,4-dimethoxyphenyl)ethyl]-1,2,4-oxadiazole-5-carboxamide
C21 H23 N3 O6
GVKZOYXTOVFRQE-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.273α = 90
b = 110.247β = 90
c = 57.862γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom100195/Z/12/Z
Bill & Melinda Gates FoundationUnited StatesOPP1066891

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-22
    Type: Initial release
  • Version 1.1: 2023-12-06
    Changes: Database references