Structural and energetic basis for novel epicatechin derivatives acting as GPER agonists through the MMGBSA method

(-)-Epicatechin (Epi) has been demonstrated to activate pathways involved in GPER-stimulated nitric oxide (NO) production via endothelial NO synthase, known as the eNOS/NO pathway. Previous studies combining synthesis of four Epi derivatives demonstrated that Epi and Epi-prop, Epi-4-prop and Epi-5-prop were able to bind GPER by acting as GPER agonists, whereas docking studies allowed observation of structural details of the binding of these derivatives at the GPER binding site. However, due to the nature of past studies, the theoretical methods employed did not allow observation of structural and energetic details linked to ligand binding at the GPER binding site. In this contribution, we explore the structural and energetic changes coupling the binding of Epi and its four derivatives to GPER. To this end, MD simulations on the microsecond scale (1 μs) with an MMGBSA approach were used for each GPER-ligand complex. Energetic analysis demonstrated that incorporation of several aliphatic chains to Epi contributed to increasing the affinity towards the GPER binding site, thus helping to explain the experimental evidence. Structural analysis demonstrated that Epi, Epi-4-prop and Epi-5-prop share more similar interactions at GPER binding sites with similar conformational behavior than with Epi-prop and Epi-Ms. However, Epi-prop had additional residues that could explain its different but related biological effects.