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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

Open and closed conformations of InhA observed in the MD simulations.Figure (a) shows the closed state represented by the medoid of conformational Family 1, figure (b) illustrates the open state represented by the medoid of cluster 4 (belonging to conformational Family 3). The same view of the binding pocket as in Fig 3 of Li et al. [17] is used for better comparison. In this view, the portal-forming elements are located left (helix α6) and right (strand-4) of the binding site. The distances highlighted as yellow dashed lines were measured between Ala198/Ile202 on helix α6 and Phe97 on strand-4. For comparison, in the crystal structure of the PT70 complex (PDB 2X23) respresenting the closed state, a distance of 4 Å is found between Ile202 and Phe97, whereas the open state is characterized by a distance of about 10 Å between Ala198 and Phe97 in chain B of the PT155-complex crystal structure (PDB 4OXN) [17].
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pone.0127009.g011: Open and closed conformations of InhA observed in the MD simulations.Figure (a) shows the closed state represented by the medoid of conformational Family 1, figure (b) illustrates the open state represented by the medoid of cluster 4 (belonging to conformational Family 3). The same view of the binding pocket as in Fig 3 of Li et al. [17] is used for better comparison. In this view, the portal-forming elements are located left (helix α6) and right (strand-4) of the binding site. The distances highlighted as yellow dashed lines were measured between Ala198/Ile202 on helix α6 and Phe97 on strand-4. For comparison, in the crystal structure of the PT70 complex (PDB 2X23) respresenting the closed state, a distance of 4 Å is found between Ile202 and Phe97, whereas the open state is characterized by a distance of about 10 Å between Ala198 and Phe97 in chain B of the PT155-complex crystal structure (PDB 4OXN) [17].

Mentions: A comparison of this PT155-structure with the conformational families suggests that Family 3 indeed captures the characteristics of the EI state: Ile202 is positioned above the ligand, Val203 is moved to the back, and helix α6 adopts a very open conformation. Fig 11b highlights this open state for a Family 3 representative: it shows a distance between helix α6 and strand-4 (used by Li et al. [17] to measure the degree of opening) of 11 Å, whereas only 5 Å are measured for Family 1 (Fig 11).


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

Merget B, Sotriffer CA - PLoS ONE (2015)

Open and closed conformations of InhA observed in the MD simulations.Figure (a) shows the closed state represented by the medoid of conformational Family 1, figure (b) illustrates the open state represented by the medoid of cluster 4 (belonging to conformational Family 3). The same view of the binding pocket as in Fig 3 of Li et al. [17] is used for better comparison. In this view, the portal-forming elements are located left (helix α6) and right (strand-4) of the binding site. The distances highlighted as yellow dashed lines were measured between Ala198/Ile202 on helix α6 and Phe97 on strand-4. For comparison, in the crystal structure of the PT70 complex (PDB 2X23) respresenting the closed state, a distance of 4 Å is found between Ile202 and Phe97, whereas the open state is characterized by a distance of about 10 Å between Ala198 and Phe97 in chain B of the PT155-complex crystal structure (PDB 4OXN) [17].
© Copyright Policy
Related In: Results  -  Collection

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

pone.0127009.g011: Open and closed conformations of InhA observed in the MD simulations.Figure (a) shows the closed state represented by the medoid of conformational Family 1, figure (b) illustrates the open state represented by the medoid of cluster 4 (belonging to conformational Family 3). The same view of the binding pocket as in Fig 3 of Li et al. [17] is used for better comparison. In this view, the portal-forming elements are located left (helix α6) and right (strand-4) of the binding site. The distances highlighted as yellow dashed lines were measured between Ala198/Ile202 on helix α6 and Phe97 on strand-4. For comparison, in the crystal structure of the PT70 complex (PDB 2X23) respresenting the closed state, a distance of 4 Å is found between Ile202 and Phe97, whereas the open state is characterized by a distance of about 10 Å between Ala198 and Phe97 in chain B of the PT155-complex crystal structure (PDB 4OXN) [17].
Mentions: A comparison of this PT155-structure with the conformational families suggests that Family 3 indeed captures the characteristics of the EI state: Ile202 is positioned above the ligand, Val203 is moved to the back, and helix α6 adopts a very open conformation. Fig 11b highlights this open state for a Family 3 representative: it shows a distance between helix α6 and strand-4 (used by Li et al. [17] to measure the degree of opening) of 11 Å, whereas only 5 Å are measured for Family 1 (Fig 11).

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