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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

Structure of the kinase domain of c-Src with a detailed view of the DFG motif in the DFG-in apo conformation (DFG represented as green sticks; PDB ID: 2SRC).The inset shows the DFG-out Imatinib-bound form (the DFG and Imatinib are shown as green and blue sticks, respectively; PDB ID: 2OIQ).
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f1: Structure of the kinase domain of c-Src with a detailed view of the DFG motif in the DFG-in apo conformation (DFG represented as green sticks; PDB ID: 2SRC).The inset shows the DFG-out Imatinib-bound form (the DFG and Imatinib are shown as green and blue sticks, respectively; PDB ID: 2OIQ).

Mentions: An interesting case, which has recently attracted much attention, is that of the powerful anti-leukemic drug Imatinib (also know as Gleevec), that revolutionized cancer treatment since its discovery in 20016. The drug has a 2300-fold lower inhibitory power towards the c-Src tyrosine kinase (TK)7 relative to its specific target, the c-Abl tyrosine kinase89, despite the high sequence identity (47%). Both conformational selection and induced fit effects have been invoked to justify such a dramatic difference. Imatinib binds to an inactive conformation, where the aspartate (Asp404 in c-Src) of the conserved Asp-Phe-Gly motif (DFG), located at the N-terminal end of the long activation loop (A-loop), points outwards from the ATP cavity10 (Fig. 1). Thus, at first, the selectivity of Imatinib towards c-Abl has been attributed to the inability of c-Src of assuming this peculiar “DFG-out” conformation1112. However, subsequent X-ray structures of Imatinib co-crystallized with c-Src revealed a DFG-out conformation and an extremely similar binding mode13. A DFG-out conformation has since been observed in many PKs14 and a functional role for the in-to-out flip has been proposed10.


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)

Structure of the kinase domain of c-Src with a detailed view of the DFG motif in the DFG-in apo conformation (DFG represented as green sticks; PDB ID: 2SRC).The inset shows the DFG-out Imatinib-bound form (the DFG and Imatinib are shown as green and blue sticks, respectively; PDB ID: 2OIQ).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: Structure of the kinase domain of c-Src with a detailed view of the DFG motif in the DFG-in apo conformation (DFG represented as green sticks; PDB ID: 2SRC).The inset shows the DFG-out Imatinib-bound form (the DFG and Imatinib are shown as green and blue sticks, respectively; PDB ID: 2OIQ).
Mentions: An interesting case, which has recently attracted much attention, is that of the powerful anti-leukemic drug Imatinib (also know as Gleevec), that revolutionized cancer treatment since its discovery in 20016. The drug has a 2300-fold lower inhibitory power towards the c-Src tyrosine kinase (TK)7 relative to its specific target, the c-Abl tyrosine kinase89, despite the high sequence identity (47%). Both conformational selection and induced fit effects have been invoked to justify such a dramatic difference. Imatinib binds to an inactive conformation, where the aspartate (Asp404 in c-Src) of the conserved Asp-Phe-Gly motif (DFG), located at the N-terminal end of the long activation loop (A-loop), points outwards from the ATP cavity10 (Fig. 1). Thus, at first, the selectivity of Imatinib towards c-Abl has been attributed to the inability of c-Src of assuming this peculiar “DFG-out” conformation1112. However, subsequent X-ray structures of Imatinib co-crystallized with c-Src revealed a DFG-out conformation and an extremely similar binding mode13. A DFG-out conformation has since been observed in many PKs14 and a functional role for the in-to-out flip has been proposed10.

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