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Exploring the binding pattern between pepsin and deferasirox using detailed experimental and computer simulation

Ji Yang1,2, Qiaohong Du1, Na Gan1

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Deferasirox (DFX) forms a hydrogen-bonded complex with pepsin, with minimal impact on pepsin's structure. This interaction slightly enhances pepsin activity by influencing the active site.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Pharmacology

Background:

  • Deferasirox (DFX) is an iron-chelating agent.
  • Pepsin is a key digestive enzyme.
  • Understanding drug-protein interactions is crucial for drug development and efficacy.

Purpose of the Study:

  • To investigate the binding interaction between deferasirox (DFX) and pepsin.
  • To elucidate the thermodynamic and structural consequences of DFX-pepsin complex formation.
  • To determine the effect of DFX binding on pepsin enzyme activity.

Main Methods:

  • Steady-state fluorescence spectroscopy to study complex formation and binding parameters.
  • Molecular dynamics (MD) simulations to analyze the binding model and forces.
  • Synchronous fluorescence, 3D fluorescence, and circular dichroism (CD) spectroscopy to assess structural changes.
  • Pepsin enzyme activity assays.

Main Results:

  • DFX forms a ground-state complex with pepsin, characterized by a single high-affinity binding site.
  • The binding is primarily driven by hydrogen bonding, supplemented by hydrophobic interactions.
  • DFX binding minimally affects pepsin's overall structure and secondary structure, with minor alterations around specific residues (Leu48-Ala49-Cys50-Ser51-Asp52).
  • DFX binding leads to a slight enhancement of pepsin enzyme activity, likely due to proximity to the Asp-215 active site.

Conclusions:

  • Deferasirox binds to pepsin through hydrogen bonds, forming a stable complex with a single binding site.
  • The interaction has a negligible impact on pepsin's structural integrity and secondary structure.
  • DFX binding enhances pepsin activity, suggesting a potential allosteric effect or modulation of the active site environment.