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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

Distances between the NAD+ nicotinamide oxygen and the phenolic oxygen of the ligand or the Ile194 backbone nitrogen.Distances are shown as a function of time in a moving-average plot with a window of 20 frames. Monomers 1 and 4 are illustrated for the TCL complex. Continuous lines indicate distances to the ligand, whereas dotted lines are used for distances to Ile194. For each illustrated ligand a stable interaction with a distance below 3 Å can be observed after the binding-mode change, while the interaction of NAD+ with Ile194 (present in the starting structure) is only slightly affected.
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pone.0127009.g009: Distances between the NAD+ nicotinamide oxygen and the phenolic oxygen of the ligand or the Ile194 backbone nitrogen.Distances are shown as a function of time in a moving-average plot with a window of 20 frames. Monomers 1 and 4 are illustrated for the TCL complex. Continuous lines indicate distances to the ligand, whereas dotted lines are used for distances to Ile194. For each illustrated ligand a stable interaction with a distance below 3 Å can be observed after the binding-mode change, while the interaction of NAD+ with Ile194 (present in the starting structure) is only slightly affected.

Mentions: The initial change of binding mode can be observed at 100 ns, resulting in the final binding mode shortly after, which stays stable until the end of the simulation (150 ns). Very similar observations were made for TCL monomer 4, but starting already at 70 ns (cf. also Fig 9).


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

Merget B, Sotriffer CA - PLoS ONE (2015)

Distances between the NAD+ nicotinamide oxygen and the phenolic oxygen of the ligand or the Ile194 backbone nitrogen.Distances are shown as a function of time in a moving-average plot with a window of 20 frames. Monomers 1 and 4 are illustrated for the TCL complex. Continuous lines indicate distances to the ligand, whereas dotted lines are used for distances to Ile194. For each illustrated ligand a stable interaction with a distance below 3 Å can be observed after the binding-mode change, while the interaction of NAD+ with Ile194 (present in the starting structure) is only slightly affected.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0127009.g009: Distances between the NAD+ nicotinamide oxygen and the phenolic oxygen of the ligand or the Ile194 backbone nitrogen.Distances are shown as a function of time in a moving-average plot with a window of 20 frames. Monomers 1 and 4 are illustrated for the TCL complex. Continuous lines indicate distances to the ligand, whereas dotted lines are used for distances to Ile194. For each illustrated ligand a stable interaction with a distance below 3 Å can be observed after the binding-mode change, while the interaction of NAD+ with Ile194 (present in the starting structure) is only slightly affected.
Mentions: The initial change of binding mode can be observed at 100 ns, resulting in the final binding mode shortly after, which stays stable until the end of the simulation (150 ns). Very similar observations were made for TCL monomer 4, but starting already at 70 ns (cf. also Fig 9).

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