Multiple LPA3 receptor agonist binding sites evidenced under docking and functional studies

Comparative studies using (lysophosphatidic acid) LPA and the synthetic agonist, oleoyl-methoxy glycerophosphothionate, OMPT, in cells expressing the LPA3 receptor revealed differences in the action of these agents. The possibility that more than one recognition cavity might exist for these ligands in the LPA3 receptor was considered. We performed agonist docking studies exploring the whole protein to obtain tridimensional details of the ligand-receptor interaction. Functional in-cellulo experiments using mutants were also executed. Our work includes blind docking using the unrefined and refined proteins subjected to hot spot predictions. Distinct ligand protonation (charge-1 and-2) states were evaluated. One LPA recognition cavity is located near the lower surface of the receptor close to the cytoplasm (Lower Cavity). OMPT displayed an affinity for an additional identification cavity detected in the transmembrane and extracellular regions (Upper Cavity). Docking targeted to Trp102 favored binding of both ligands in the transmembrane domain near the extracellular areas (Upper Cavity), but the associating amino acids were not identical due to close sub-cavities. In the in-cellulo studies, LPA action was much less affected by the distinct mutations than that of OMPT (which was almost abolished). Docking and functional data suggest distinct agonist binding cavities in the LPA3 receptor