7U0O

Crystal structure of an enoyl-[acyl-carrier-protein] reductase InhA from Mycobacterium fortuitum bound to NAD and NITD-916


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

In Vitro and In Vivo Efficacy of NITD-916 against Mycobacterium fortuitum.

Roquet-Baneres, F.Alcaraz, M.Hamela, C.Abendroth, J.Edwards, T.E.Kremer, L.

(2023) Antimicrob Agents Chemother 67: e0160722-e0160722

  • DOI: https://doi.org/10.1128/aac.01607-22
  • Primary Citation of Related Structures:  
    7K73, 7U0O

  • PubMed Abstract: 

    Mycobacterium fortuitum represents one of the most clinically relevant rapid-growing mycobacterial species. Treatments are complex due to antibiotic resistance and to severe side effects of effective drugs, prolonged time of treatment, and co-infection with other pathogens. Herein, we explored the activity of NITD-916, a direct inhibitor of the enoyl-ACP reductase InhA of the type II fatty acid synthase in Mycobacterium tuberculosis. We found that this compound displayed very low MIC values against a panel of M. fortuitum clinical strains and exerted potent antimicrobial activity against M. fortuitum in macrophages. Remarkably, the compound was also highly efficacious in a zebrafish model of infection. Short duration treatments were sufficient to significantly protect the infected larvae from M. fortuitum-induced killing, which correlated with reduced bacterial burdens and abscesses. Biochemical analyses demonstrated an inhibition of de novo synthesis of mycolic acids. Resolving the crystal structure of the InhA MFO in complex with NAD and NITD-916 confirmed that NITD-916 is a direct inhibitor of InhA MFO . Importantly, single nucleotide polymorphism leading to a G96S substitution in InhA MFO conferred high resistance levels to NITD-916, thus resolving its target in M. fortuitum. Overall, these findings indicate that NITD-916 is highly active against M. fortuitum both in vitro and in vivo and should be considered in future preclinical evaluations for the treatment of M. fortuitum pulmonary diseases.


  • Organizational Affiliation

    Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Enoyl-[acyl-carrier-protein] reductase [NADH]
A, B
277Mycolicibacterium fortuitumMutation(s): 0 
Gene Names: fabIinhAA5637_21995A5751_12770FKW78_11710NCTC1542_01491XA26_29600
EC: 1.3.1.9
UniProt
Find proteins for A0A0N9XSE6 (Mycolicibacterium fortuitum)
Explore A0A0N9XSE6 
Go to UniProtKB:  A0A0N9XSE6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0N9XSE6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
3KY (Subject of Investigation/LOI)
Query on 3KY

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
6-[(4,4-dimethylcyclohexyl)methyl]-4-hydroxy-3-phenylpyridin-2(1H)-one
C20 H25 N O2
WKDRRKVUJLNFSR-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.3α = 90
b = 101.54β = 114.36
c = 76.48γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2023-03-01
    Changes: Database references
  • Version 1.2: 2023-03-29
    Changes: Database references
  • Version 1.3: 2023-05-03
    Changes: Database references
  • Version 1.4: 2023-10-25
    Changes: Data collection, Refinement description