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Interaction of wild type, G68R and L125M isoforms of the arylamine-N-acetyltransferase from Mycobacterium tuberculosis with isoniazid: a computational study on a new possible mechanism of resistance

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Abstract

Isoniazid (INH) is a front-line drug used in the treatment of tuberculosis (TB), a disease that remains a major cause of death worldwide. Isoniazid is a prodrug, requiring activation in the mycobacterial cell by the catalase-peroxidase (CP) enzyme. Recent studies have suggested that acetylation of INH by the arylamine-N-acetyltransferase from Mycobacterium tuberculosis (TBNAT) may be a possible cause of inactivation of the drug thus resulting in resistant strains. In this study, computational techniques were applied to investigate the binding of isoniazid to three TBNAT isoforms: wild type, G68R and L125M. Since there is no experimental structure available, molecular dynamics (MD) simulations were initially used for the refinement of TBNAT homology models. Distinct conformations of the models were selected during the production stage of MD simulations for molecular docking experiments with the drug. Finally, each mode of binding was refined by new molecular MD simulations. Essential dynamics (ED) analysis and linear interaction energy calculations (LIE) were used to evaluate the impact of amino acid substitutions on the structural and binding properties of the enzymes. The results suggest that the wild type and the G68R TBNATs have a similar pattern of affinity to INH. On the other hand, the calculated enzyme-INH dissociation constant (KD) was estimated 33 times lower for L125M isoform in comparison with wild type enzyme. This last finding is consistent with the hypothesis that isolated mutations in the tbnat gene can produce M. tuberculosis strains resistant to isoniazid.

Global structure of the complexes and binding mode of INH calculated for the last frame of MD simulations

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Abbreviations

TB:

Tuberculosis

INH:

Isoniazid

CP:

Catalase-peroxidase

NAT:

Arylamine N-acetyltransferase

TBNAT:

Arylamine-N-acetyltransferase from Mycobacterium tuberculosis

MD:

Molecular dynamics

ED:

Essential dynamics

LIE:

Linear interaction energy

SNPs:

Single nucleotide polymorphisms

K D :

Dissociation constant

NCBI:

National Center for Biotechnology Information

InChITM :

The IUPAC International Chemical Identifier

AM1:

Austin model 1

MEP:

Molecular electrostatic potential

CHELPG:

Charges from electrostatic grid based

SPC:

Simple point charge

ADT:

AutoDock tools

RMSD:

Root mean square deviation

LGA:

Lamarckian genetic algorithm

LS:

Local search

vdW:

van der Waals

el:

Electrostatic

Rg:

Radius of gyration

NHb:

Number of intramolecular hydrogen bonds

SASA:

Surface accessible solvent area

RMSF:

Root mean square fluctuation

MC:

Monte Carlo

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Authors and Affiliations

  1. Laboratório de Bioinformática Estrutural (LaBiE), Universidade Luterana do Brasil (ULBRA), Av. Farroupilha 1001, Prédio 01, Sala 122, Canoas, RS, Brazil, 92450-900

    Ricardo Martins Ramos, Janaína Menezes Perez, Luis André Baptista & Hermes Luís Neubauer de Amorim

  2. Instituto Federal do Piauí (IFPI), Praça da Liberdade 1597, Centro, Teresina, PI, Brazil, 64000-040

    Ricardo Martins Ramos

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  1. Ricardo Martins Ramos
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  2. Janaína Menezes Perez
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  3. Luis André Baptista
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  4. Hermes Luís Neubauer de Amorim
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Correspondence to Hermes Luís Neubauer de Amorim.

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Ramos, R.M., Perez, J.M., Baptista, L.A. et al. Interaction of wild type, G68R and L125M isoforms of the arylamine-N-acetyltransferase from Mycobacterium tuberculosis with isoniazid: a computational study on a new possible mechanism of resistance. J Mol Model 18, 4013–4024 (2012). https://doi.org/10.1007/s00894-012-1383-6

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  • DOI: https://doi.org/10.1007/s00894-012-1383-6

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