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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

Free energies for local unfolding.The values are derived from the kintr and kexch parameters obtained from H/D exchange NMR measurements. Red circles indicate αD and αG, the regions with increased exposure to the solvent in the bound structure.
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f5: Free energies for local unfolding.The values are derived from the kintr and kexch parameters obtained from H/D exchange NMR measurements. Red circles indicate αD and αG, the regions with increased exposure to the solvent in the bound structure.

Mentions: To investigate the dynamics on longer time scales and, possibly, further confirm that a cracking-like mechanism is involved, we performed H/D exchange NMR experiments and determined the protection factors and free energies for local unfolding45 (Fig. 5, SI Methods and SI Fig. S7). The values are directly related to the ease of exchange of amide protons with the solvent and give a good estimate of the energy needed to locally unfold the structure. Lower values correspond to regions that are (at least transiently) solvent exposed and unfolded.


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)

Free energies for local unfolding.The values are derived from the kintr and kexch parameters obtained from H/D exchange NMR measurements. Red circles indicate αD and αG, the regions with increased exposure to the solvent in the bound structure.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f5: Free energies for local unfolding.The values are derived from the kintr and kexch parameters obtained from H/D exchange NMR measurements. Red circles indicate αD and αG, the regions with increased exposure to the solvent in the bound structure.
Mentions: To investigate the dynamics on longer time scales and, possibly, further confirm that a cracking-like mechanism is involved, we performed H/D exchange NMR experiments and determined the protection factors and free energies for local unfolding45 (Fig. 5, SI Methods and SI Fig. S7). The values are directly related to the ease of exchange of amide protons with the solvent and give a good estimate of the energy needed to locally unfold the structure. Lower values correspond to regions that are (at least transiently) solvent exposed and unfolded.

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