Related Experiment Video

Updated: Dec 19, 2025

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
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Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

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Structure and Characterization of a Covalent Inhibitor of Src Kinase

Deepak Gurbani1, Guangyan Du2,3, Nathaniel J Henning2,3

  • 1Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX, United States.

Frontiers in Molecular Biosciences
|June 9, 2020
PubMed

Insights

New Src inhibitors show high potency and selectivity for cancer therapy. Optimization of covalent linkers is needed to improve the kinetics of covalent bond formation for better drug development.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Medicinal Chemistry

Background:

  • Unregulated Src kinase activity drives cancer progression.
  • Existing Src inhibitors face challenges due to off-target effects and toxicity.
  • Development of selective Src inhibitors is crucial for targeted cancer therapies.

Purpose of the Study:

  • To biochemically and biophysically characterize the irreversible Src inhibitor DGY-06-116.
  • To elucidate the structural basis for DGY-06-116's potency and selectivity.
  • To understand the kinetics of covalent bond formation for optimizing Src-directed therapies.

Main Methods:

  • X-ray crystallography to determine the co-crystal structure of DGY-06-116 with Src.
  • Biochemical assays to assess inhibitor potency and selectivity.
  • Kinetic analysis to evaluate the rate of covalent inactivation.

Main Results:

  • DGY-06-116 forms a covalent bond with the Src kinase p-loop and occupies the back hydrophobic pocket, explaining its high potency and selectivity.
  • A reversible analog demonstrated comparable potency, suggesting a strong reversible interaction is key.
  • The covalent inactivation rate was slow compared to other approved covalent kinase inhibitors, indicating a requirement for p-loop movement.

Conclusions:

  • The study provides structural and kinetic insights into the Src inhibitor DGY-06-116.
  • A strong reversible interaction is necessary to facilitate the covalent reaction.
  • Further optimization of the covalent linker could enhance the kinetics of covalent bond formation for improved therapeutic potential.
Keywords:
cancerdasatinibirreversible inhibitorselectivitysrc kinase

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