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Conformational Selection and Induced Fit Mechanisms in the Binding of an Anticancer Drug to the c-Src Kinase.

Morando MA, Saladino G, D'Amelio N, Pucheta-Martinez E, Lovera S, Lelli M, López-Méndez B, Marenchino M, Campos-Olivas R, Gervasio FL - Sci Rep (2016)

Bottom Line: The conserved three amino-acid DFG motif undergoes an "in to out" movement resulting in a particular inactive conformation to which "type II" kinase inhibitors, such as the anti-cancer drug Imatinib, bind.Here we combine various NMR experiments and surface plasmon resonance with enhanced sampling molecular dynamics simulations to shed light into the conformational dynamics associated with the binding of Imatinib to the proto-oncogene c-Src.Moreover, an external binding pose and local unfolding (cracking) of the aG helix are observed.

View Article: PubMed Central - PubMed

Affiliation: Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), c/Melchor Fernandez Almagro 3, 28029, Madrid, Spain.

ABSTRACT
Understanding the conformational changes associated with the binding of small ligands to their biological targets is a fascinating and meaningful question in chemistry, biology and drug discovery. One of the most studied and important is the so-called "DFG-flip" of tyrosine kinases. The conserved three amino-acid DFG motif undergoes an "in to out" movement resulting in a particular inactive conformation to which "type II" kinase inhibitors, such as the anti-cancer drug Imatinib, bind. Despite many studies, the details of this prototypical conformational change are still debated. Here we combine various NMR experiments and surface plasmon resonance with enhanced sampling molecular dynamics simulations to shed light into the conformational dynamics associated with the binding of Imatinib to the proto-oncogene c-Src. We find that both conformational selection and induced fit play a role in the binding mechanism, reconciling opposing views held in the literature. Moreover, an external binding pose and local unfolding (cracking) of the aG helix are observed.

No MeSH data available.


Related in: MedlinePlus

Imatinib binding free energy profile along the Spath variable, which defines an optimal association coordinate.The most relevant minima and the transition state are labelled and discussed in the text. The area of the transition state is represented as a dashed line due to a larger uncertainty. The two profiles in the region  to  (secondary pocket to the unbound state) correspond to the conformational selection mechanism (red line, “flip-bind”) and to an induced fit mechanism (yellow line, “bind-flip”). The 2D FES in the inset shows the dependence of the free energy from the DFG-flip coordinate.
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f4: Imatinib binding free energy profile along the Spath variable, which defines an optimal association coordinate.The most relevant minima and the transition state are labelled and discussed in the text. The area of the transition state is represented as a dashed line due to a larger uncertainty. The two profiles in the region to (secondary pocket to the unbound state) correspond to the conformational selection mechanism (red line, “flip-bind”) and to an induced fit mechanism (yellow line, “bind-flip”). The 2D FES in the inset shows the dependence of the free energy from the DFG-flip coordinate.

Mentions: The free energy profile associated to the (un)-binding of Imatinib from c-Src obtained by extensive Parallel Tempering Metadynamics (PT-MetaD)38 simulations is shown in Fig. 4.


Conformational Selection and Induced Fit Mechanisms in the Binding of an Anticancer Drug to the c-Src Kinase.

Morando MA, Saladino G, D'Amelio N, Pucheta-Martinez E, Lovera S, Lelli M, López-Méndez B, Marenchino M, Campos-Olivas R, Gervasio FL - Sci Rep (2016)

Imatinib binding free energy profile along the Spath variable, which defines an optimal association coordinate.The most relevant minima and the transition state are labelled and discussed in the text. The area of the transition state is represented as a dashed line due to a larger uncertainty. The two profiles in the region  to  (secondary pocket to the unbound state) correspond to the conformational selection mechanism (red line, “flip-bind”) and to an induced fit mechanism (yellow line, “bind-flip”). The 2D FES in the inset shows the dependence of the free energy from the DFG-flip coordinate.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4834493&req=5

f4: Imatinib binding free energy profile along the Spath variable, which defines an optimal association coordinate.The most relevant minima and the transition state are labelled and discussed in the text. The area of the transition state is represented as a dashed line due to a larger uncertainty. The two profiles in the region to (secondary pocket to the unbound state) correspond to the conformational selection mechanism (red line, “flip-bind”) and to an induced fit mechanism (yellow line, “bind-flip”). The 2D FES in the inset shows the dependence of the free energy from the DFG-flip coordinate.
Mentions: The free energy profile associated to the (un)-binding of Imatinib from c-Src obtained by extensive Parallel Tempering Metadynamics (PT-MetaD)38 simulations is shown in Fig. 4.

Bottom Line: The conserved three amino-acid DFG motif undergoes an "in to out" movement resulting in a particular inactive conformation to which "type II" kinase inhibitors, such as the anti-cancer drug Imatinib, bind.Here we combine various NMR experiments and surface plasmon resonance with enhanced sampling molecular dynamics simulations to shed light into the conformational dynamics associated with the binding of Imatinib to the proto-oncogene c-Src.Moreover, an external binding pose and local unfolding (cracking) of the aG helix are observed.

View Article: PubMed Central - PubMed

Affiliation: Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), c/Melchor Fernandez Almagro 3, 28029, Madrid, Spain.

ABSTRACT
Understanding the conformational changes associated with the binding of small ligands to their biological targets is a fascinating and meaningful question in chemistry, biology and drug discovery. One of the most studied and important is the so-called "DFG-flip" of tyrosine kinases. The conserved three amino-acid DFG motif undergoes an "in to out" movement resulting in a particular inactive conformation to which "type II" kinase inhibitors, such as the anti-cancer drug Imatinib, bind. Despite many studies, the details of this prototypical conformational change are still debated. Here we combine various NMR experiments and surface plasmon resonance with enhanced sampling molecular dynamics simulations to shed light into the conformational dynamics associated with the binding of Imatinib to the proto-oncogene c-Src. We find that both conformational selection and induced fit play a role in the binding mechanism, reconciling opposing views held in the literature. Moreover, an external binding pose and local unfolding (cracking) of the aG helix are observed.

No MeSH data available.


Related in: MedlinePlus