Background: Understanding the function of FFA2 has been slowed by a lack of selective orthosteric ligands.Results: Residues within FFA2 that dictate the recognition and function of potent and selective orthosteric agonists are described.Conclusion: Key aspects of ligand interaction with the orthosteric binding pocket of FFA2 are defined.Significance: This work will be invaluable in future drug development at the FFA2 receptor.

Background: Differences in ligand potency and selectivity are observed between human and mouse FFA2 and FFA3 orthologs.Results: Potency differences result from differential constitutive activity between species.Conclusion: An “ionic lock” between extracellular loop 2 and the ligand binding pocket regulates constitutive activity.Significance: Understanding species differences in FFA2 and FFA3 function is critical to future studies with these receptors.

Medium chain fatty acids can activate the pro-inflammatory receptor GPR84 but so also can molecules related to 3,3′-diindolylmethane. 3,3′-Diindolylmethane and decanoic acid acted as strong positive allosteric modulators of the function of each other and analysis showed the affinity of 3,3′-diindolylmethane to be at least 100 fold higher. Methyl decanoate was not an agonist at GPR84. This implies a key role in binding for the carboxylic acid of the fatty acid. Via homology modelling we predicted and confirmed an integral role of arginine172, located in the 2nd extracellular loop, in the action of decanoic acid but not of 3,3′-diindolylmethane. Exemplars from a patented series of GPR84 antagonists were able to block agonist actions of both decanoic acid and 3,3′-diindolylmethane at GPR84. However, although a radiolabelled form of a related antagonist, [3H]G9543, was able to bind with high affinity to GPR84, this was not competed for by increasing concentrations of either decanoic acid or 3,3′-diindolylmethane and was not affected adversely by mutation of arginine172. These studies identify three separable ligand binding sites within GPR84 and suggest that if medium chain fatty acids are true endogenous regulators then co-binding with a positive allosteric modulator would greatly enhance their function in physiological settings.

GPR40 was formerly an orphan G protein-coupled receptor whose endogenous ligands have recently been identified as free fatty acids (FFAs). The receptor, now named FFA receptor 1, has been implicated in the pathophysiology of type 2 diabetes and is a drug target because of its role in FFA-mediated enhancement of glucose-stimulated insulin release. Guided by molecular modeling, we investigated the molecular determinants contributing to binding of linoleic acid, a C18 polyunsaturated FFA, and GW9508, a synthetic small molecule agonist. Twelve residues within the putative GPR40-binding pocket including hydrophilic/positively charged, aromatic, and hydrophobic residues were identified and were subjected to site-directed mutagenesis. GPR40 was discovered a decade ago, along with its closely related family members GPR41 and 43, in a screen for GPCR 2 homologous sequences that cluster in chromosomal locus 19q13.1 (1). This family of receptors shares an overall sequence homology of 30 -50% (2, 3) and a higher homology within their putative transmembrane domains (3, 4). Nevertheless, their ligands were not known until recently when this family of orphans was found to be activated by free fatty acids of different chain lengths with varying degrees of specificity. GPR40 prefers fatty acids of medium to long chain length (5, 6) and has also been called FFA receptor 1. GPR41 and 43 prefer chain lengths between two to five (7) and are now called FFA receptors 3 and 2, respectively. GPR40 couples to G q (8, 9), which results in activation of phospholipase C (10, 11) and subsequent increases in cytoplasmic free calcium (5, 6). GPR40 has also been reported to inhibit the activity of potassium channels via a cAMP-dependent pathway (12).GPR40 mRNA is expressed primarily in the pancreas, brain, and monocytes (5), and its biology has generated excitement in the field of pancreas and diabetes research. It was generally understood that fatty acids enhance glucose-stimulated insulin secretion through the malonyl-CoA pathway upon intracellular metabolism (reviewed in Refs. 13 and 14), but a number of in vitro and in vivo studies have now demonstrated that fatty acids could potentiate glucose-stimulated insulin secretion by acting on GPR40 (6,9,10,12,15,16). It remains controversial whether GPR40 offers a protective role in glucose metabolism under certain circumstances; however, in one study, GPR40Ϫ/Ϫ knock-out mice were protected from high fat diet-induced hepatic steatosis and impaired glucose homeostasis (16). Together these studies point to a dual role for GPR40 in the regulation of glucose homeostasis in diet-related type II diabetes.Despite their important physiological implications, little is known about the mechanism underlying the interaction of fatty acids with their receptors. Moreover, functional studies of GPR40 have been limited by lack of ligands of high specificity and potency. The potencies of medium to long chain fatty acid range from 2 to 17 M (5). Screening of compound libraries followed by chemical modifications has ...

GPR40, free fatty acid receptor 1 (FFAR1), is a member of the GPCR superfamily and a possible target for the treatment of type 2 diabetes. In this work, we conducted a bidirectional iterative investigation, including computational modeling and site-directed mutagenesis, aimed at delineating amino acid residues forming the functional "chemoprint" of GPR40 for agonist recognition. The computational and experimental studies revolved around the recognition of the potent synthetic agonist GW9508. Our experimentally supported model suggested that H137(4.56), R183(5.39), N244(6.55), and R258(7.35) are directly involved in interactions with the ligand. We have proposed a polarized NH-pi interaction between H137(4.56) and GW9508 as one of the contributing forces leading to the high potency of GW9508. The modeling approach presented in this work provides a general strategy for the exploration of receptor-ligand interactions in G-protein coupled receptors beginning prior to acquisition of experimental data.

The G-protein-coupled receptor free fatty acid receptor 1 (FFAR1), previously named GPR40, is a possible novel target for the treatment of type 2 diabetes. In an attempt to identify new ligands for this receptor, we performed virtual screening (VS) based on two-dimensional (2D) similarity, three-dimensional (3D) pharmacophore searches, and docking studies by using the structure of known agonists and our model of the ligand binding site, which was validated by mutagenesis. VS of a database of 2.6 million compounds followed by extraction of structural neighbors of functionally confirmed hits resulted in identification of 15 compounds active at FFAR1 either as full agonists, partial agonists, or pure antagonists. Site-directed mutagenesis and docking studies revealed different patterns of ligand-receptor interactions and provided important information on the role of specific amino acids in binding and activation of FFAR1.

Allosteric agonists are powerful tools for exploring the pharmacology of closely related G protein-coupled receptors that have nonselective endogenous ligands, such as the short chain fatty acids at free fatty acid receptors 2 and 3 (FFA2/GPR43 and FFA3/GPR41, respectively). We explored the molecular mechanisms mediating the activity of 4-chloro-␣-(1-methylethyl)-N-2-thiazolylbenzeneacetamide (4-CMTB), a recently described phenylacetamide allosteric agonist and allosteric modulator of endogenous ligand function at human FFA2, by combining our previous knowledge of the orthosteric binding site with targeted examination of 4-CMTB structure-activity relationships and mutagenesis and chimeric receptor generation. Here we show that 4-CMTB is a selective agonist for FFA2 that binds to a site distinct from the orthosteric site of the receptor. Ligand structure-activity relationship studies indicated that the N-thiazolyl amide is likely to provide hydrogen bond donor/acceptor interactions with the receptor. Substitution at Leu 173 or the exchange of the entire extracellular loop 2 of FFA2 with that of FFA3 was sufficient to reduce or ablate, respectively, allosteric communication between the endogenous and allosteric agonists. Thus, we conclude that extracellular loop 2 of human FFA2 is required for transduction of cooperative signaling between the orthosteric and an as-yet-undefined allosteric binding site of the FFA2 receptor that is occupied by 4-CMTB.

Free fatty acid receptor 2 (FFA2; GPR43) is a G protein-coupled seven-transmembrane receptor for short-chain fatty acids (SCFAs) that is implicated in inflammatory and metabolic disorders. The SCFA propionate has close to optimal ligand efficiency for FFA2 and can hence be considered as highly potent given its size. Propionate, however, does not discriminate between FFA2 and the closely related receptor FFA3 (GPR41). To identify FFA2-selective ligands and understand the molecular basis for FFA2 selectivity, a targeted library of small carboxylic acids was examined using holistic, label-free dynamic mass redistribution technology for primary screening and the receptor-proximal G protein [35S]guanosine 5′-(3-O-thio)triphosphate activation, inositol phosphate, and cAMP accumulation assays for hit confirmation. Structure-activity relationship analysis allowed formulation of a general rule to predict selectivity for small carboxylic acids at the orthosteric binding site where ligands with substituted sp3-hybridized α-carbons preferentially activate FFA3, whereas ligands with sp2- or sp-hybridized α-carbons prefer FFA2. The orthosteric binding mode was verified by site-directed mutagenesis: replacement of orthosteric site arginine residues by alanine in FFA2 prevented ligand binding, and molecular modeling predicted the detailed mode of binding. Based on this, selective mutation of three residues to their non-conserved counterparts in FFA3 was sufficient to transfer FFA3 selectivity to FFA2. Thus, selective activation of FFA2 via the orthosteric site is achievable with rather small ligands, a finding with significant implications for the rational design of therapeutic compounds selectively targeting the SCFA receptors.