Multiple LPA₃ Receptor Agonist Binding Sites Evidenced Under Docking and Functional Studies.

Area of Science:

• Biochemistry
• Molecular Biology
• Pharmacology

Background:

• Lysophosphatidic acid (LPA) receptors are critical in cellular signaling.
• Understanding ligand-receptor interactions is key to drug development.
• The LPA3 receptor's binding mechanism remains incompletely understood.

Purpose of the Study:

• To investigate the distinct binding interactions of lysophosphatidic acid (LPA) and its synthetic agonist OMPT with the LPA3 receptor.
• To identify and characterize potential multiple ligand-binding cavities within the LPA3 receptor.
• To correlate molecular modeling data with functional experimental results.

Main Methods:

• Agonist docking studies were performed on the LPA3 receptor, exploring various ligand protonation states.
• Receptor modeling was achieved using AlphaFold3, incorporating membrane and lipid environments.
• Mutagenesis of predicted binding site amino acids followed by in cellulo functional assays.

Main Results:

• Two distinct ligand-binding cavities were identified: a Lower Cavity for LPA and an Upper Cavity for OMPT.
• Docking studies and AlphaFold3 modeling predicted similar conformations, validating the binding pocket locations.
• Mutagenesis of the Lower Cavity significantly affected OMPT binding but had minimal impact on LPA binding.

Conclusions:

• The LPA3 receptor possesses distinct binding cavities for LPA and OMPT.
• These findings provide crucial insights into the molecular basis of LPA receptor activation.
• The differential binding affinities support the development of selective LPA receptor modulators.