Limits...
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

Violin plots of distances between the phenolic oxygen of Tyr158 and the respective ligands.White dots depict the medians. Thick vertical lines indicate the interquartile ranges (IQR), thin lines extend to 1.5 ⋅ IQR from the third and first quartile, respectively. The shape of the violins illustrates the kernel density estimation of the respective distribution.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4440617&req=5

pone.0127009.g007: Violin plots of distances between the phenolic oxygen of Tyr158 and the respective ligands.White dots depict the medians. Thick vertical lines indicate the interquartile ranges (IQR), thin lines extend to 1.5 ⋅ IQR from the third and first quartile, respectively. The shape of the violins illustrates the kernel density estimation of the respective distribution.

Mentions: We now focus on the ligand and analyze first the hydrogen bond between Tyr158 and the A-ring phenolic oxygen, which is a highly conserved interaction between diphenyl ethers and InhA. For analysis, the distance between the Tyr158 oxygen (OH) and the phenolic oxygen of the ligands was followed over the entire trajectory (cf. Fig 7). PT70-bound monomers show by far the lowest distance with medians ranging from 2.82 Å to 2.85 Å, followed by 6PP (2.84 Å to 3.21 Å) and TCL (3.00 Å to 7.34 Å). The bimodal distributions observed for the TCL monomers 1 and 4 are caused by the transition to an alternative binding mode of TCL further described below. The shorter distances for 6PP and especially PT70 evince that the differences in the chemical structures of the ligands directly influence the formation and maintenance of the important hydrogen bond between Tyr158 and the ligands. The measured distances correlate with the relative affinity of the ligands (Fig 2), showing a stably maintained hydrogen bond for PT70, a partially maintained hydrogen bond for 6PP, and a hardly stable interaction for TCL.


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

Merget B, Sotriffer CA - PLoS ONE (2015)

Violin plots of distances between the phenolic oxygen of Tyr158 and the respective ligands.White dots depict the medians. Thick vertical lines indicate the interquartile ranges (IQR), thin lines extend to 1.5 ⋅ IQR from the third and first quartile, respectively. The shape of the violins illustrates the kernel density estimation of the respective distribution.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0127009.g007: Violin plots of distances between the phenolic oxygen of Tyr158 and the respective ligands.White dots depict the medians. Thick vertical lines indicate the interquartile ranges (IQR), thin lines extend to 1.5 ⋅ IQR from the third and first quartile, respectively. The shape of the violins illustrates the kernel density estimation of the respective distribution.
Mentions: We now focus on the ligand and analyze first the hydrogen bond between Tyr158 and the A-ring phenolic oxygen, which is a highly conserved interaction between diphenyl ethers and InhA. For analysis, the distance between the Tyr158 oxygen (OH) and the phenolic oxygen of the ligands was followed over the entire trajectory (cf. Fig 7). PT70-bound monomers show by far the lowest distance with medians ranging from 2.82 Å to 2.85 Å, followed by 6PP (2.84 Å to 3.21 Å) and TCL (3.00 Å to 7.34 Å). The bimodal distributions observed for the TCL monomers 1 and 4 are caused by the transition to an alternative binding mode of TCL further described below. The shorter distances for 6PP and especially PT70 evince that the differences in the chemical structures of the ligands directly influence the formation and maintenance of the important hydrogen bond between Tyr158 and the ligands. The measured distances correlate with the relative affinity of the ligands (Fig 2), showing a stably maintained hydrogen bond for PT70, a partially maintained hydrogen bond for 6PP, and a hardly stable interaction for TCL.

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