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Crystal structure of the FLT3 kinase domain bound to the inhibitor Quizartinib (AC220).

Zorn JA, Wang Q, Fujimura E, Barros T, Kuriyan J - PLoS ONE (2015)

Bottom Line: This conformation is similar to that observed for the uncomplexed intracellular domain of FLT3 as well as for related receptor tyrosine kinases, except for a localized induced fit in the activation loop.The co-crystal structure reveals the interactions between quizartinib and the active site of FLT3 that are key for achieving its high potency against both wild-type FLT3 as well as a FLT3 variant observed in many AML patients.This co-complex further provides a structural rationale for quizartinib-resistance mutations.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America; California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America.

ABSTRACT
More than 30% of acute myeloid leukemia (AML) patients possess activating mutations in the receptor tyrosine kinase FMS-like tyrosine kinase 3 or FLT3. A small-molecule inhibitor of FLT3 (known as quizartinib or AC220) that is currently in clinical trials appears promising for the treatment of AML. Here, we report the co-crystal structure of the kinase domain of FLT3 in complex with quizartinib. FLT3 with quizartinib bound adopts an "Abl-like" inactive conformation with the activation loop stabilized in the "DFG-out" orientation and folded back onto the kinase domain. This conformation is similar to that observed for the uncomplexed intracellular domain of FLT3 as well as for related receptor tyrosine kinases, except for a localized induced fit in the activation loop. The co-crystal structure reveals the interactions between quizartinib and the active site of FLT3 that are key for achieving its high potency against both wild-type FLT3 as well as a FLT3 variant observed in many AML patients. This co-complex further provides a structural rationale for quizartinib-resistance mutations.

No MeSH data available.


Related in: MedlinePlus

Interactions between FLT3 and quizartinib.(A) Chemical structure of quizartinib (AC220). (B) An unbiased electron density map (2mFO-DFC) of quizartinib (yellow) contoured at 1.0 σ (light blue). A simulated annealing refinement in Phenix on FLT3 with quizartinib deleted resulted in a model that was used to calculate the electron density for quizartinib. The simulated annealing was performed with an initial temperature of 5000 K to a final temperature of 300 K over 50 steps. A superposition of quizartinib with this unbiased electron density map for the compound is shown for clarity. (C) The structure of the FLT3 kinase domain bound to quizartinib (left) with a zoomed-in view of the active site (right). (D) A detailed view of the interactions between FLT3 and quizartinib.
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pone.0121177.g004: Interactions between FLT3 and quizartinib.(A) Chemical structure of quizartinib (AC220). (B) An unbiased electron density map (2mFO-DFC) of quizartinib (yellow) contoured at 1.0 σ (light blue). A simulated annealing refinement in Phenix on FLT3 with quizartinib deleted resulted in a model that was used to calculate the electron density for quizartinib. The simulated annealing was performed with an initial temperature of 5000 K to a final temperature of 300 K over 50 steps. A superposition of quizartinib with this unbiased electron density map for the compound is shown for clarity. (C) The structure of the FLT3 kinase domain bound to quizartinib (left) with a zoomed-in view of the active site (right). (D) A detailed view of the interactions between FLT3 and quizartinib.

Mentions: Our previous report utilizing molecular docking suggest that the top-ranked binding pose of quizartinib in the active site of FLT3 is rotated 180° relative to the structure determined here (Fig 3A) [19]. However, the second-ranked pose in the docking calculation is consistent with the quizartinib-FLT3 co-crystal structure (Fig 3B). An unbiased electron density map of the compound in the active site of FLT3, which was generated by performing a simulated annealing refinement on the FLT3 structure with the compound deleted, clearly reveals the orientation of quizartinib (Fig 4A and 4B).


Crystal structure of the FLT3 kinase domain bound to the inhibitor Quizartinib (AC220).

Zorn JA, Wang Q, Fujimura E, Barros T, Kuriyan J - PLoS ONE (2015)

Interactions between FLT3 and quizartinib.(A) Chemical structure of quizartinib (AC220). (B) An unbiased electron density map (2mFO-DFC) of quizartinib (yellow) contoured at 1.0 σ (light blue). A simulated annealing refinement in Phenix on FLT3 with quizartinib deleted resulted in a model that was used to calculate the electron density for quizartinib. The simulated annealing was performed with an initial temperature of 5000 K to a final temperature of 300 K over 50 steps. A superposition of quizartinib with this unbiased electron density map for the compound is shown for clarity. (C) The structure of the FLT3 kinase domain bound to quizartinib (left) with a zoomed-in view of the active site (right). (D) A detailed view of the interactions between FLT3 and quizartinib.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383440&req=5

pone.0121177.g004: Interactions between FLT3 and quizartinib.(A) Chemical structure of quizartinib (AC220). (B) An unbiased electron density map (2mFO-DFC) of quizartinib (yellow) contoured at 1.0 σ (light blue). A simulated annealing refinement in Phenix on FLT3 with quizartinib deleted resulted in a model that was used to calculate the electron density for quizartinib. The simulated annealing was performed with an initial temperature of 5000 K to a final temperature of 300 K over 50 steps. A superposition of quizartinib with this unbiased electron density map for the compound is shown for clarity. (C) The structure of the FLT3 kinase domain bound to quizartinib (left) with a zoomed-in view of the active site (right). (D) A detailed view of the interactions between FLT3 and quizartinib.
Mentions: Our previous report utilizing molecular docking suggest that the top-ranked binding pose of quizartinib in the active site of FLT3 is rotated 180° relative to the structure determined here (Fig 3A) [19]. However, the second-ranked pose in the docking calculation is consistent with the quizartinib-FLT3 co-crystal structure (Fig 3B). An unbiased electron density map of the compound in the active site of FLT3, which was generated by performing a simulated annealing refinement on the FLT3 structure with the compound deleted, clearly reveals the orientation of quizartinib (Fig 4A and 4B).

Bottom Line: This conformation is similar to that observed for the uncomplexed intracellular domain of FLT3 as well as for related receptor tyrosine kinases, except for a localized induced fit in the activation loop.The co-crystal structure reveals the interactions between quizartinib and the active site of FLT3 that are key for achieving its high potency against both wild-type FLT3 as well as a FLT3 variant observed in many AML patients.This co-complex further provides a structural rationale for quizartinib-resistance mutations.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America; California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America.

ABSTRACT
More than 30% of acute myeloid leukemia (AML) patients possess activating mutations in the receptor tyrosine kinase FMS-like tyrosine kinase 3 or FLT3. A small-molecule inhibitor of FLT3 (known as quizartinib or AC220) that is currently in clinical trials appears promising for the treatment of AML. Here, we report the co-crystal structure of the kinase domain of FLT3 in complex with quizartinib. FLT3 with quizartinib bound adopts an "Abl-like" inactive conformation with the activation loop stabilized in the "DFG-out" orientation and folded back onto the kinase domain. This conformation is similar to that observed for the uncomplexed intracellular domain of FLT3 as well as for related receptor tyrosine kinases, except for a localized induced fit in the activation loop. The co-crystal structure reveals the interactions between quizartinib and the active site of FLT3 that are key for achieving its high potency against both wild-type FLT3 as well as a FLT3 variant observed in many AML patients. This co-complex further provides a structural rationale for quizartinib-resistance mutations.

No MeSH data available.


Related in: MedlinePlus