Molecular determinants of thapsigargin binding by SERCA Ca2+-ATPase: a computational docking study

Area of Science:

• Biochemistry and Molecular Biology
• Structural Biology
• Pharmacology

Background:

• Thapsigargin (TG) is a widely used inhibitor of sarco/endoplasmic reticulum Ca2+-ATPases (SERCA).
• Understanding TG's binding mechanism is crucial for its application and for designing new SERCA inhibitors.
• Recent crystal structures of SERCA1a in E1 and E2 conformations provide a basis for molecular modeling.

Purpose of the Study:

• To computationally characterize the molecular interactions governing thapsigargin (TG) binding to SERCA.
• To elucidate the role of enzyme conformation in TG binding affinity and inhibitory mechanism.
• To assess the binding modes and affinities of TG analogs and SERCA mutants.

Main Methods:

• Computational docking studies using GOLD and ChemScore.
• Docking of TG into E1 and E2 conformations of SERCA1a.
• Docking of TG analogs and modeled SERCA1a Phe256 mutants.

Main Results:

• Docking revealed a consensus binding mode for TG, driven primarily by hydrophobic interactions.
• TG binding affinity is significantly reduced during the E2 to E1 conformational transition.
• Docking predictions correlated well with experimental data for TG analogs and Phe256 mutants.

Conclusions:

• TG inhibits SERCA by binding tightly to the E2 conformation, preventing the functional E1 transition.
• Hydrophobic interactions are key determinants of TG binding to SERCA.
• Computational docking accurately predicts the effects of structural modifications on TG binding and potency.