br Acknowledgments br The study

Acknowledgments
The study was funded by the European Commission FP7-project Beta-JUDO (Grant 279153), and Swedish Diabetes Association (Grant DIA 2013-043) and Family Ernfors Foundation (Grant 150430).
Free fatty PIK-III receptors (FFARs) represent a family of G-protein coupled receptors (GPCRs) that acts as fatty acid sensors and plays a crucial role in glucose homeostasis. This family includes 6 different GPCRs; FFAR1, FFAR2, FFAR3, GPR42, GPR119, and GPR120., These receptors have diverse tissue distribution. FFAR1 and GPR119 are highly expressed in β-cells of the pancreas, while GPR120 is exclusively expressed in the intestine. FFAR2 and FFAR3 have different tissue distribution., Recent studies have demonstrated that dietary fatty acids as well as synthetic agonists can stimulate glucose-dependent insulin secretion by acting on FFAR1 and GPR119. Activation of GPR120 was found to enhance the release of glucagon like peptide-1 which in turn stimulates insulin secretion., Therefore, agonists of these receptors could be useful for enhancing insulin secretion (insulin secretagogue) in patients with diabetes mellitus. It is worth noting that FFAR1 is the best characterized of this family and a vast number of studies was published within the last few years by leading pharmaceutical companies investigating the modulation of FFAR1 for the treatment of type II diabetes., , , Another interesting category of anti-diabetic agents is the thiazolidinediones (TZDs). These agents are insulin sensitizers acting mainly on the peroxisome proliferator-activated receptor-γ (PPARγ). PPARs are a group of nuclear receptors that control cellular metabolism through the modulation of gene expression. There are three distinct subtypes of these receptors: PPARα, PPARδ, and PPARγ. Activation of PPARγ has been shown to regulate glucose homeostasis, cellular differentiation, apoptosis and inflammatory responses., Upon activation, the receptor interacts with co-activator proteins in the nucleus, activating the transcription of a number of specific genes which stimulate lipid uptake and adipogenesis by fat cells (insulin sensitizer)., The two TZDs currently in use are rosiglitazone and Pioglitazone. It is widely accepted that TZDs possess some agonistic activity on FFAR1. It has been reported that TZDs activate FFAR1 expressed in human Hela cells with micromolar potency., In 2007, a research group tried to exploit TZD scaffold for the design of FFAR1 ligands by combining fatty acids substructures with the thiazolidinedione head but, again, only micromolar activity was achieved. A careful literature survey revealed an evident similarity between the ligands reported for FFAR1 and those acting on PPARγ., , , A typical FFAR1 agonist consists of an acidic head attached to an aromatic scaffold, a heteroalkyl linker, and a hydrophobic tail. Notably, TZDs have very similar pharmacophoric features and physicochemical properties. Representative examples of both FFAR1 and PPARγ agonists are shown in . Till the date of our study, the X-ray crystal structure of FFAR1 was not resolved. Furthermore, no computational studies had commented on the binding mode of TZDs into FFAR1 or the mechanism of activation of FFAR1 by this class of compounds. Some mutagenesis and molecular modeling studies had successfully revealed the key residues of FFAR1 essential for the interaction with both fatty acids and small synthetic agonists., , However, the involvement of these residues in the binding and activation of FFAR1 by TZDs remains unclear. In the present study, a homology model of the human FFAR1 was constructed based on the crystal structure of B2-adrenergic receptor (PDB: ). This model was refined using iterative energy minimizations and MD simulations. Then, the most studied FFAR1 agonist; GW9805 as well as two TZDs, rosiglitazone and Pioglitazone (), were docked into the binding site of the refined homology model. Furthermore, the final refined model, in its inactive form as well as in complex with each of the aforementioned compounds, was embedded in a DPPC/TIP3P membrane environment and subjected to a 20ns MD simulation. This protocol led to a better understanding of the mechanism of activation of FFAR1. Moreover, it gave unambiguous explanation of the binding modes of TZDs into FFAR1. To the best of our knowledge, this is the first FFAR1 model relaxed in an explicit membrane-aqueous environment and the first MD simulation study of TZDs in complex with FFAR1. Knowledge gained from this study could delineate the key pharmacophoric features required for binding to both PPARγ and FFAR1. This could help in the design of dual agonists for FFAR1 and PPARγ for the effective management of diabetes mellitus.