Computational Insights into Molecular Activation and Positive Cooperative Mechanisms of FFAR1 Modulators

Free fatty acid receptor 1 (FFAR1), a member of class A in G-protein-coupled receptors (GPCRs), is a promising antidiabetic target. The crystal structure of FFAR1 revealed that one agonist (MK-8666) binds to the extracellular vestibule of this receptor, while another (AP8) occupies the surface pocket between transmembrane (TM) helices TM4 and TM5. In this study, we performed 1 μs unbiased molecular dynamics (MD) simulation on each of five systems, to uncover why two ligands in completely different sites both serve as agonists and how they exert a positive synergistic effect together. They are two agonist-bound systems (FFAR1_MK-8666 and FFAR1_AP8), a ternary complex system FFAR1_MK-8666_AP8, an antagonist-bound system (FFAR1_15i), and an unliganded (apo) system, among which the antagonist 15i-bound and apo systems were used as controls. The results showed that Y91^3.37 played a pivotal role in the activation process of FFAR1. The agonist could disrupt the Y91^3.37-centered residue interaction network within protein, whereas the antagonist could stabilize the network. Furthermore, our simulations revealed that the hydrophobic layer amino acid residues next to the transmission switch (CWXP) formed a gate and could open only upon agonist activation, which might exert an important role in the formation of water pathway. These results would be helpful for elucidating the molecular activation mechanism of FFAR1 and provide insights into the design and discovery of novel allosteric agonists of FFAR1 for the treatment of type 2 diabetes mellitus (T2DM).