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Slow-Onset Inhibition of Mycobacterium tuberculosis InhA: Revealing Molecular Determinants of Residence Time by MD Simulations.

Merget B, Sotriffer CA - PLoS ONE (2015)

Bottom Line: Whereas the diphenyl ether inhibitors 6PP and triclosan (TCL) do not show loop ordering and thus, no slow-binding inhibition and high koff values, the slightly modified PT70 leads to an ordered loop and a residence time of 24 minutes.The individual simulations show comparable conformational features with respect to both the binding pocket and the SBL, allowing to define five recurring conformational families.The most abundant conformation besides the stable EI* state is characterized by a shift of Ile202 and Val203 toward the hydrophobic pocket of InhA.

View Article: PubMed Central - PubMed

Affiliation: Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, D-97074, Würzburg, Germany.

ABSTRACT
An important kinetic parameter for drug efficacy is the residence time of a compound at a drug target, which is related to the dissociation rate constant koff. For the essential antimycobacterial target InhA, this parameter is most likely governed by the ordering of the flexible substrate binding loop (SBL). Whereas the diphenyl ether inhibitors 6PP and triclosan (TCL) do not show loop ordering and thus, no slow-binding inhibition and high koff values, the slightly modified PT70 leads to an ordered loop and a residence time of 24 minutes. To assess the structural differences of the complexes from a dynamic point of view, molecular dynamics (MD) simulations with a total sampling time of 3.0 µs were performed for three ligand-bound and two ligand-free (perturbed) InhA systems. The individual simulations show comparable conformational features with respect to both the binding pocket and the SBL, allowing to define five recurring conformational families. Based on their different occurrence frequencies in the simulated systems, the conformational preferences could be linked to structural differences of the respective ligands to reveal important determinants of residence time. The most abundant conformation besides the stable EI* state is characterized by a shift of Ile202 and Val203 toward the hydrophobic pocket of InhA. The analyses revealed potential directions for avoiding this conformational change and, thus, hindering rapid dissociation: (1) an anchor group in 2'-position of the B-ring for scaffold stabilization, (2) proper occupation of the hydrophobic pocket, and (3) the introduction of a barricade substituent in 5'-position of the diphenyl ether B-ring.

No MeSH data available.


Related in: MedlinePlus

Collective backbone RMSD values (C, N, and Cα atoms) of InhA monomers.Each monomer of the simulated homotetrameric systems (150 ns) was fitted individually onto chain A of the 2X23 crystal structure as reference for the RMSD measurements and the data of the four monomers were combined to one box plot per system. Boxes indicate the interquartile range (first to third quartile), black lines in the boxes show the median of each distribution. The whiskers extend to values 1.5 times the interquartile range from the box. Significant differences in the medians are indicated by non-overlapping notches. Average values are marked by white triangles.
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pone.0127009.g004: Collective backbone RMSD values (C, N, and Cα atoms) of InhA monomers.Each monomer of the simulated homotetrameric systems (150 ns) was fitted individually onto chain A of the 2X23 crystal structure as reference for the RMSD measurements and the data of the four monomers were combined to one box plot per system. Boxes indicate the interquartile range (first to third quartile), black lines in the boxes show the median of each distribution. The whiskers extend to values 1.5 times the interquartile range from the box. Significant differences in the medians are indicated by non-overlapping notches. Average values are marked by white triangles.

Mentions: As the ordering of the SBL is supposed to play an important role in slow-binding inhibition of InhA [6, 7, 13], the dynamic behavior of this structural segment deserves special attention. To look first at the overall backbone dynamics of the entire systems, the RMS deviation of the backbone atoms of each monomer was calculated with respect to chain A of the 2X23 crystal structure (Fig 4). All ligand-bound systems show high stability of the overall structure throughout the entire simulation. With averages of 1.19 Å and 1.27 Å, the PT70 and 6PP complexes display slightly lower RMS deviations than the complex with TCL (1.38 Å). Not unexpectedly, the perturbed systems without ligand show a clear shift toward higher values and larger fluctuations. Nevertheless, the medians and averages remain well below 2 Å in all cases, indicating reasonable stability of the entire trajectories.


Slow-Onset Inhibition of Mycobacterium tuberculosis InhA: Revealing Molecular Determinants of Residence Time by MD Simulations.

Merget B, Sotriffer CA - PLoS ONE (2015)

Collective backbone RMSD values (C, N, and Cα atoms) of InhA monomers.Each monomer of the simulated homotetrameric systems (150 ns) was fitted individually onto chain A of the 2X23 crystal structure as reference for the RMSD measurements and the data of the four monomers were combined to one box plot per system. Boxes indicate the interquartile range (first to third quartile), black lines in the boxes show the median of each distribution. The whiskers extend to values 1.5 times the interquartile range from the box. Significant differences in the medians are indicated by non-overlapping notches. Average values are marked by white triangles.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4440617&req=5

pone.0127009.g004: Collective backbone RMSD values (C, N, and Cα atoms) of InhA monomers.Each monomer of the simulated homotetrameric systems (150 ns) was fitted individually onto chain A of the 2X23 crystal structure as reference for the RMSD measurements and the data of the four monomers were combined to one box plot per system. Boxes indicate the interquartile range (first to third quartile), black lines in the boxes show the median of each distribution. The whiskers extend to values 1.5 times the interquartile range from the box. Significant differences in the medians are indicated by non-overlapping notches. Average values are marked by white triangles.
Mentions: As the ordering of the SBL is supposed to play an important role in slow-binding inhibition of InhA [6, 7, 13], the dynamic behavior of this structural segment deserves special attention. To look first at the overall backbone dynamics of the entire systems, the RMS deviation of the backbone atoms of each monomer was calculated with respect to chain A of the 2X23 crystal structure (Fig 4). All ligand-bound systems show high stability of the overall structure throughout the entire simulation. With averages of 1.19 Å and 1.27 Å, the PT70 and 6PP complexes display slightly lower RMS deviations than the complex with TCL (1.38 Å). Not unexpectedly, the perturbed systems without ligand show a clear shift toward higher values and larger fluctuations. Nevertheless, the medians and averages remain well below 2 Å in all cases, indicating reasonable stability of the entire trajectories.

Bottom Line: Whereas the diphenyl ether inhibitors 6PP and triclosan (TCL) do not show loop ordering and thus, no slow-binding inhibition and high koff values, the slightly modified PT70 leads to an ordered loop and a residence time of 24 minutes.The individual simulations show comparable conformational features with respect to both the binding pocket and the SBL, allowing to define five recurring conformational families.The most abundant conformation besides the stable EI* state is characterized by a shift of Ile202 and Val203 toward the hydrophobic pocket of InhA.

View Article: PubMed Central - PubMed

Affiliation: Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, D-97074, Würzburg, Germany.

ABSTRACT
An important kinetic parameter for drug efficacy is the residence time of a compound at a drug target, which is related to the dissociation rate constant koff. For the essential antimycobacterial target InhA, this parameter is most likely governed by the ordering of the flexible substrate binding loop (SBL). Whereas the diphenyl ether inhibitors 6PP and triclosan (TCL) do not show loop ordering and thus, no slow-binding inhibition and high koff values, the slightly modified PT70 leads to an ordered loop and a residence time of 24 minutes. To assess the structural differences of the complexes from a dynamic point of view, molecular dynamics (MD) simulations with a total sampling time of 3.0 µs were performed for three ligand-bound and two ligand-free (perturbed) InhA systems. The individual simulations show comparable conformational features with respect to both the binding pocket and the SBL, allowing to define five recurring conformational families. Based on their different occurrence frequencies in the simulated systems, the conformational preferences could be linked to structural differences of the respective ligands to reveal important determinants of residence time. The most abundant conformation besides the stable EI* state is characterized by a shift of Ile202 and Val203 toward the hydrophobic pocket of InhA. The analyses revealed potential directions for avoiding this conformational change and, thus, hindering rapid dissociation: (1) an anchor group in 2'-position of the B-ring for scaffold stabilization, (2) proper occupation of the hydrophobic pocket, and (3) the introduction of a barricade substituent in 5'-position of the diphenyl ether B-ring.

No MeSH data available.


Related in: MedlinePlus