Limits...
Elucidation of Ligand-Dependent Modulation of Disorder-Order Transitions in the Oncoprotein MDM2.

Bueren-Calabuig JA, Michel J - PLoS Comput. Biol. (2015)

Bottom Line: Here clarification was sought for cases where interactions of different ligands with the same disordered protein region yield qualitatively different results.The resulting conformational ensembles for MDM2, free and bound to p53 TAD (17-29) peptide identify lid states compatible with previous NMR measurements.By contrast, Nutlin or benzodiazepinedione inhibitors, that bind with similar affinity to full lid and lid-truncated MDM2 constructs, interact additionally through their solubilizing groups with N-terminal lid residues that are more disordered in apo MDM2.

View Article: PubMed Central - PubMed

Affiliation: EaStCHEM School of Chemistry, the University of Edinburgh, Edinburgh, United Kingdom.

ABSTRACT
Numerous biomolecular interactions involve unstructured protein regions, but how to exploit such interactions to enhance the affinity of a lead molecule in the context of rational drug design remains uncertain. Here clarification was sought for cases where interactions of different ligands with the same disordered protein region yield qualitatively different results. Specifically, conformational ensembles for the disordered lid region of the N-terminal domain of the oncoprotein MDM2 in the presence of different ligands were computed by means of a novel combination of accelerated molecular dynamics, umbrella sampling, and variational free energy profile methodologies. The resulting conformational ensembles for MDM2, free and bound to p53 TAD (17-29) peptide identify lid states compatible with previous NMR measurements. Remarkably, the MDM2 lid region is shown to adopt distinct conformational states in the presence of different small-molecule ligands. Detailed analyses of small-molecule bound ensembles reveal that the ca. 25-fold affinity improvement of the piperidinone family of inhibitors for MDM2 constructs that include the full lid correlates with interactions between ligand hydrophobic groups and the C-terminal lid region that is already partially ordered in apo MDM2. By contrast, Nutlin or benzodiazepinedione inhibitors, that bind with similar affinity to full lid and lid-truncated MDM2 constructs, interact additionally through their solubilizing groups with N-terminal lid residues that are more disordered in apo MDM2.

No MeSH data available.


Ligand-dependent modulation of MDM2 lid flexibility.Left) per-lid residue average backbone RMSD. Right) Backbone RMSD over full lid (green) or core (blue) regions. From top to bottom, A) apo MDM2, B) p53-bound MDM2, C) Nutlin-3a-bound MDM2, D) Bzd-bound MDM2, E) Pip2-bound MDM2.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4457491&req=5

pcbi.1004282.g003: Ligand-dependent modulation of MDM2 lid flexibility.Left) per-lid residue average backbone RMSD. Right) Backbone RMSD over full lid (green) or core (blue) regions. From top to bottom, A) apo MDM2, B) p53-bound MDM2, C) Nutlin-3a-bound MDM2, D) Bzd-bound MDM2, E) Pip2-bound MDM2.

Mentions: Uncertainties in the computed free energy surfaces for each system were assessed by monitoring convergence over regular time-intervals (S2–S3 Figs). Equilibrium properties of the ligand-bound complexes are reasonably reproducible, with greater uncertainties observed for the most flexible lid residues in apo MDM2 (Figs 3–5). Three major low free energy regions were identified in the FES of apo MDM2 (Fig 2A). The lowest corresponds to a “closed” state (CV1 = 31 Å; CV2 = 62°), with the lid adopting a semi-extended conformation in contact with α2 helix residues. While this conformation would hinder binding of the p53 TAD as a result of steric clashes with the lid, the Phe19-Trp23-Leu26 cleft was still accessible to small molecules such as Nutlins. The second region (CV1 = 7 Å; CV2 = 119°) corresponds to an “open”, compact state of the lid. In this state, the p53-binding site is fully accessible to large and small ligands. No open, extended lid conformations were observed, thus the lid in the open state adopts collapsed structures. A third additional region (CV1 = 10 Å; CV2 = 64°) corresponds to an intermediate “semi-open” state. In this conformation, the lid approaches the core of MDM2. Although the hydrophobic pocket was still fully accessible to small ligands, binding of the larger p53 TAD would be hindered.


Elucidation of Ligand-Dependent Modulation of Disorder-Order Transitions in the Oncoprotein MDM2.

Bueren-Calabuig JA, Michel J - PLoS Comput. Biol. (2015)

Ligand-dependent modulation of MDM2 lid flexibility.Left) per-lid residue average backbone RMSD. Right) Backbone RMSD over full lid (green) or core (blue) regions. From top to bottom, A) apo MDM2, B) p53-bound MDM2, C) Nutlin-3a-bound MDM2, D) Bzd-bound MDM2, E) Pip2-bound MDM2.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4457491&req=5

pcbi.1004282.g003: Ligand-dependent modulation of MDM2 lid flexibility.Left) per-lid residue average backbone RMSD. Right) Backbone RMSD over full lid (green) or core (blue) regions. From top to bottom, A) apo MDM2, B) p53-bound MDM2, C) Nutlin-3a-bound MDM2, D) Bzd-bound MDM2, E) Pip2-bound MDM2.
Mentions: Uncertainties in the computed free energy surfaces for each system were assessed by monitoring convergence over regular time-intervals (S2–S3 Figs). Equilibrium properties of the ligand-bound complexes are reasonably reproducible, with greater uncertainties observed for the most flexible lid residues in apo MDM2 (Figs 3–5). Three major low free energy regions were identified in the FES of apo MDM2 (Fig 2A). The lowest corresponds to a “closed” state (CV1 = 31 Å; CV2 = 62°), with the lid adopting a semi-extended conformation in contact with α2 helix residues. While this conformation would hinder binding of the p53 TAD as a result of steric clashes with the lid, the Phe19-Trp23-Leu26 cleft was still accessible to small molecules such as Nutlins. The second region (CV1 = 7 Å; CV2 = 119°) corresponds to an “open”, compact state of the lid. In this state, the p53-binding site is fully accessible to large and small ligands. No open, extended lid conformations were observed, thus the lid in the open state adopts collapsed structures. A third additional region (CV1 = 10 Å; CV2 = 64°) corresponds to an intermediate “semi-open” state. In this conformation, the lid approaches the core of MDM2. Although the hydrophobic pocket was still fully accessible to small ligands, binding of the larger p53 TAD would be hindered.

Bottom Line: Here clarification was sought for cases where interactions of different ligands with the same disordered protein region yield qualitatively different results.The resulting conformational ensembles for MDM2, free and bound to p53 TAD (17-29) peptide identify lid states compatible with previous NMR measurements.By contrast, Nutlin or benzodiazepinedione inhibitors, that bind with similar affinity to full lid and lid-truncated MDM2 constructs, interact additionally through their solubilizing groups with N-terminal lid residues that are more disordered in apo MDM2.

View Article: PubMed Central - PubMed

Affiliation: EaStCHEM School of Chemistry, the University of Edinburgh, Edinburgh, United Kingdom.

ABSTRACT
Numerous biomolecular interactions involve unstructured protein regions, but how to exploit such interactions to enhance the affinity of a lead molecule in the context of rational drug design remains uncertain. Here clarification was sought for cases where interactions of different ligands with the same disordered protein region yield qualitatively different results. Specifically, conformational ensembles for the disordered lid region of the N-terminal domain of the oncoprotein MDM2 in the presence of different ligands were computed by means of a novel combination of accelerated molecular dynamics, umbrella sampling, and variational free energy profile methodologies. The resulting conformational ensembles for MDM2, free and bound to p53 TAD (17-29) peptide identify lid states compatible with previous NMR measurements. Remarkably, the MDM2 lid region is shown to adopt distinct conformational states in the presence of different small-molecule ligands. Detailed analyses of small-molecule bound ensembles reveal that the ca. 25-fold affinity improvement of the piperidinone family of inhibitors for MDM2 constructs that include the full lid correlates with interactions between ligand hydrophobic groups and the C-terminal lid region that is already partially ordered in apo MDM2. By contrast, Nutlin or benzodiazepinedione inhibitors, that bind with similar affinity to full lid and lid-truncated MDM2 constructs, interact additionally through their solubilizing groups with N-terminal lid residues that are more disordered in apo MDM2.

No MeSH data available.