Application of GPCR Structures for Modelling of Free Fatty Acid Receptors

Abstract

Five G protein-coupled receptors (GPCRs) have been identified to be activated by free fatty acids (FFA). Among them, FFA1 (GPR40) and FFA4 (GPR120) bind long-chain fatty acids, FFA2 (GPR43) and FFA3 (GPR41) bind short-chain fatty acids and GPR84 binds medium-chain fatty acids. Free fatty acid receptors have now emerged as potential targets for the treatment of diabetes, obesity and immune diseases. The recent progress in crystallography of GPCRs has now enabled the elucidation of the structure of FFA1 and provided reliable templates for homology modelling of other FFA receptors. Analysis of the crystal structure and improved homology models, along with mutagenesis data and structure activity, highlighted an unusual arginine charge pairing interaction in FFA1-3 for receptor modulation, distinct structural features for ligand binding to FFA1 and FFA4 and an arginine of the second extracellular loop as a possible anchoring point for FFA at GPR84. Structural data will be helpful for searching novel small molecule modulators at the FFA receptors.

Three classes of ligands each bind to distinct sites on the orphan G protein-coupled receptor GPR84

“…These studies, however, did not identify a potential charge partner for the carboxylate of the fatty acid near the extracellular surface and, indeed, concluded that the carboxylate of C10 was pointing downwards, deep into the cleft of the seven transmembrane domain core of the receptor and interacting with an asparagine located at position 104 in the primary amino acid sequence 3 . As we have highlighted recently 9 GPR84 and the β 2 -adrenoceptor are only distantly related whilst, of the currently available atomic level GPCR structures, the orexin OX 1 receptor 34 has highest overall sequence identity (31%) with GPR84. We, therefore, generated and employed a new homology model of GPR84 based on the transmembrane domain architecture of the OX 1 receptor (Fig.…”

“…To try to identify how a MCFA might interact with GPR84 we turned to homology modelling studies. Although GPR84 is not closely related to the other GPCRs that respond to either short chain (FFA2, FFA3) or long chain (FFA1, FFA4) fatty acids 8 , 9 , in each of the other cases the carboxylate of the fatty acid is co-ordinated by one or more arginine residues located at or near the extracellular surface 12 – 14 . A previous effort to model the structure of GPR84 and to predict the mode and orientation of binding of C10 developed a receptor homology model based on the atomic level, active-state structure of the β 2 -adrenoceptor 3 .…”

“…GPR84 is not closely related to either of the groups of previously defined free fatty acid-responsive GPCRs, FFA1-3 and FFA4. However, a feature shared by FFA1-4 is that each possesses at least one arginine residue located close to the extracellular face of the receptor that acts as the charge partner for the carboxylate moiety of fatty acid ligands 8 , 9 . Earlier studies showed that wild type GPR84 failed to respond to decylamine 3 and herein we confirm the importance of the carboxylate of C10 to activation of the receptor because methyl decanoate was also unable to act as an agonist at GPR84.…”

“…In recent times the expansion of available atomic level structures of different GPCRs means that potentially better starting points for homology modelling can be selected from receptors that have higher levels of sequence similarity. Of the currently available structures, the orexin OX 1 receptor 34 is most closely related to GPR84, and using this as a template to model the transmembrane domain architecture, in concert with recognition that the sequence of ECL2 of GPR84 is highly homologous to that of rhodopsin, for which atomic level structures are known, allowed us to build a novel homology model 9 that predicted that Arg 172 , within ECL2, might provide a charge partner for the fatty acid carboxylate. Indeed, this prediction was supported.…”

“…1 ) and undecanoic acid (C11). Lack of full acceptance of MCFAs as the key endogenous activators of GPR84 may reflect that the mode of interaction of the MCFAs with GPR84 is poorly defined 3 , 8 , 9 and that the reported potency of these ligands at GPR84, particularly in cells natively expressing this receptor, is very modest 2 .

Figure 1 Structures of GPR84 ligands used in the studies.

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