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

Abstract

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 Y913.37 played a pivotal role in the activation process of FFAR1. The agonist could disrupt the Y913.37-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).

Mechanistic Studies on the Stereoselectivity of FFAR1 Modulators

“…By examining the trajectories from the MD simulations, we found that both ( R )-AM-8596 and ( S )-AM-8596 form salt bridge interactions with R183 5.39 and R258 7.35 (Figure A–D). Such salt bridge interactions have also been observed in the crystal structures 4PHU and 5TZR. , The computational and experimental studies on FFAR1 have shown that residues R183 5.39 and R258 7.35 are critical for the activity of agonists bound at site 1. , Compared with ( R )-AM-8596, ( S )-AM-8596 forms stronger salt bridge interactions with R183 5.39 and R258 7.35 (Figure A,B) (Table S2), which is most likely the main reason why ( S )-AM-8596 has a higher binding affinity to the FFAR1 than ( R )-AM-8596. In this work, R183 5.39 and R258 7.35 act like anchors and play a critical role in the ligand binding to FFAR1.…”

“…Such salt bridge interactions have also been observed in the crystal structures 4PHU 11 and 5TZR. 35 , 36 The computational and experimental studies on FFAR1 have shown that residues R183 5.39 and R258 7.35 are critical for the activity of agonists bound at site 1. 37 , 38 Compared with ( R )-AM-8596, ( S )-AM-8596 forms stronger salt bridge interactions with R183 5.39 and R258 7.35 ( Figure 3 A,B) ( Table S2 ), which is most likely the main reason why ( S )-AM-8596 has a higher binding affinity to the FFAR1 than ( R )-AM-8596.…”

Ensemble-based screening of natural products and FDA-approved drugs identified potent inhibitors of SARS-CoV-2 that work with two distinct mechanisms

“…Water is known to play an important role in protein-ligand interaction, protein function and molecular recognition [[ 66 ]]. The role of water in mediating the interaction of drug and protein was also investigated.…”

In Silico Searching for Alternative Lead Compounds to Treat Type 2 Diabetes through a QSAR and Molecular Dynamics Study

“…T2DM is characterized by reduced secretion of insulin from β-cells and resulting hyperglycemia associated with cardiovascular complications such as cardiac ischemia and stroke [3,4]. Current methods to control blood sugar, including controlled diet, metformin, sulfonylurea, and insulin [5], have limited efficacy and are associated with potential health problems such as hypoglycemia, weight gain, and lack of sustained efficacy [6][7][8].…”

“…The biological activity was used as the logarithm of the half-maximal effective concentration (pEC 50 ), and the best model was statistically well-validated in terms of leave-one-out cross validation. Furthermore, the X-ray crystallographic structure of the binding mode in the FFA1 was elucidated [24], and molecular dynamics simulation [8] and experimental studies [25] clarify the activation mechanism of FFA1 to treat diabetes. Strong hydrogen bond interactions with Tyr-91, Arg-183, Asn-244, and Arg-258 are linked with higher agonist potency on the activation of FFA1 [26].…”