Crystal Structure of Enoyl-[acyl-carrier-protein] reductase InhA from Mycobacterium abscessus in complex with NAD

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 

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Efficacy and Mode of Action of a Direct Inhibitor of Mycobacterium abscessus InhA.

Alcaraz, M.Roquet-Baneres, F.Leon-Icaza, S.A.Abendroth, J.Boudehen, Y.M.Cougoule, C.Edwards, T.E.Kremer, L.

(2022) ACS Infect Dis 8: 2171-2186

  • DOI: https://doi.org/10.1021/acsinfecdis.2c00314
  • Primary Citation of Related Structures:  
    7KLI, 7L6C, 7U0M

  • PubMed Abstract: 

    There is an unmet medical need for effective treatments against Mycobacterium abscessus pulmonary infections, to which cystic fibrosis (CF) patients are particularly vulnerable. Recent studies showed that the antitubercular drug isoniazid is inactive against M. abscessus due to the incapacity of the catalase-peroxidase to convert the pro-drug into a reactive metabolite that inhibits the enoyl-ACP reductase InhA. To validate InhA MAB as a druggable target in M. abscessus , we assayed the activity of NITD-916, a 4-hydroxy-2-pyridone lead candidate initially described as a direct inhibitor of InhA that bypasses KatG bioactivation in Mycobacterium tuberculosis . The compound displayed low MIC values against rough and smooth clinical isolates in vitro and significantly reduced the bacterial burden inside human macrophages. Moreover, treatment with NITD-916 reduced the number and size of intracellular mycobacterial cords, regarded as markers of the severity of the infection. Importantly, NITD-916 significantly lowered the M. abscessus burden in CF-derived lung airway organoids. From a mechanistic perspective, NITD-916 abrogated de novo synthesis of mycolic acids and NITD-916-resistant spontaneous mutants harbored point mutations in InhA MAB at residue 96. That NITD-916 targets InhA MAB directly without activation requirements was confirmed genetically and by resolving the crystal structure of the protein in complex with NADH and NITD-916. These findings collectively indicate that InhA MAB is an attractive target to be exploited for future chemotherapeutic developments against this difficult-to-treat mycobacterium and highlight the potential of NITD-916 derivatives for further evaluation in preclinical settings.

  • Organizational Affiliation

    Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Enoyl-[acyl-carrier-protein] reductase [NADH]
A, B, C, D
277Mycobacteroides abscessus ATCC 19977Mutation(s): 0 
Gene Names: MAB_2722c
Find proteins for B1MC30 (Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CCUG 20993 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543 / L948))
Explore B1MC30 
Go to UniProtKB:  B1MC30
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1MC30
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
K [auth C],
M [auth D]
C21 H27 N7 O14 P2
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
C2 H6 O2
Query on NA

Download Ideal Coordinates CCD File 
H [auth A],
J [auth B],
L [auth C],
N [auth D]
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 206.66α = 90
b = 92.63β = 118.318
c = 98.13γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHENIXmodel building
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2022-10-05
    Changes: Database references
  • Version 1.2: 2022-10-26
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description