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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

c-Src Dynamics, (left) difference in the Cα RMSF (Δrmsf) between the apo and ligand-bound forms of c-Src averaged over 1 μs-long MD simulations.Low (blue) values correspond to regions that are more rigid (lower RMSF) in the bound form, high (red) values correspond to regions that are more flexible in the bound form. (right) Experimentally determined order parameters S2 for the apo (blue) and bound (red) forms.
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f2: c-Src Dynamics, (left) difference in the Cα RMSF (Δrmsf) between the apo and ligand-bound forms of c-Src averaged over 1 μs-long MD simulations.Low (blue) values correspond to regions that are more rigid (lower RMSF) in the bound form, high (red) values correspond to regions that are more flexible in the bound form. (right) Experimentally determined order parameters S2 for the apo (blue) and bound (red) forms.

Mentions: The 2D 1H, 15N-TROSY NMR spectrum of the ligand-free (apo) form of c-Src is shown in SI Fig. S1. Out of 268 backbone amides, 196 signals are visible, of which 179 (91%) were assigned (BMRB entry 25756). Most of the signals corresponding to the A-loop (Figs 1 and 2), the αC helix and some of those corresponding to the αG helix are missing.


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)

c-Src Dynamics, (left) difference in the Cα RMSF (Δrmsf) between the apo and ligand-bound forms of c-Src averaged over 1 μs-long MD simulations.Low (blue) values correspond to regions that are more rigid (lower RMSF) in the bound form, high (red) values correspond to regions that are more flexible in the bound form. (right) Experimentally determined order parameters S2 for the apo (blue) and bound (red) forms.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2: c-Src Dynamics, (left) difference in the Cα RMSF (Δrmsf) between the apo and ligand-bound forms of c-Src averaged over 1 μs-long MD simulations.Low (blue) values correspond to regions that are more rigid (lower RMSF) in the bound form, high (red) values correspond to regions that are more flexible in the bound form. (right) Experimentally determined order parameters S2 for the apo (blue) and bound (red) forms.
Mentions: The 2D 1H, 15N-TROSY NMR spectrum of the ligand-free (apo) form of c-Src is shown in SI Fig. S1. Out of 268 backbone amides, 196 signals are visible, of which 179 (91%) were assigned (BMRB entry 25756). Most of the signals corresponding to the A-loop (Figs 1 and 2), the αC helix and some of those corresponding to the αG helix are missing.

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