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Free fatty acid receptors: structural models and elucidation of ligand binding interactions.

Tikhonova IG, Poerio E - BMC Struct. Biol. (2015)

Bottom Line: This binding mode can explain mutagenesis results for residues at positions 4.56 and 5.42.The novel structural models of FFAs provide information on specific modes of ligand binding at FFA subtypes and new suggestions for mutagenesis and ligand modification, guiding the development of novel orthosteric and allosteric chemical probes to validate the importance of FFAs in metabolic and inflammatory conditions.Using our FFA homology modelling experience, a strategy to model a GPCR, which is phylogenetically distant from GPCRs with the available crystal structures, is discussed.

View Article: PubMed Central - PubMed

Affiliation: Molecular Therapeutics, School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland, UK. i.tikhonova@qub.ac.uk.

ABSTRACT

Background: The free fatty acid receptors (FFAs), including FFA1 (orphan name: GPR40), FFA2 (GPR43) and FFA3 (GPR41) are G protein-coupled receptors (GPCRs) involved in energy and metabolic homeostasis. Understanding the structural basis of ligand binding at FFAs is an essential step toward designing potent and selective small molecule modulators.

Results: We analyse earlier homology models of FFAs in light of the newly published FFA1 crystal structure co-crystallized with TAK-875, an ago-allosteric ligand, focusing on the architecture of the extracellular binding cavity and agonist-receptor interactions. The previous low-resolution homology models of FFAs were helpful in highlighting the location of the ligand binding site and the key residues for ligand anchoring. However, homology models were not accurate in establishing the nature of all ligand-receptor contacts and the precise ligand-binding mode. From analysis of structural models and mutagenesis, it appears that the position of helices 3, 4 and 5 is crucial in ligand docking. The FFA1-based homology models of FFA2 and FFA3 were constructed and used to compare the FFA subtypes. From docking studies we propose an alternative binding mode for orthosteric agonists at FFA1 and FFA2, involving the interhelical space between helices 4 and 5. This binding mode can explain mutagenesis results for residues at positions 4.56 and 5.42. The novel FFAs structural models highlight higher aromaticity of the FFA2 binding cavity and higher hydrophilicity of the FFA3 binding cavity. The role of the residues at the second extracellular loop used in mutagenesis is reanalysed. The third positively-charged residue in the binding cavity of FFAs, located in helix 2, is identified and predicted to coordinate allosteric modulators.

Conclusions: The novel structural models of FFAs provide information on specific modes of ligand binding at FFA subtypes and new suggestions for mutagenesis and ligand modification, guiding the development of novel orthosteric and allosteric chemical probes to validate the importance of FFAs in metabolic and inflammatory conditions. Using our FFA homology modelling experience, a strategy to model a GPCR, which is phylogenetically distant from GPCRs with the available crystal structures, is discussed.

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Related in: MedlinePlus

Agonists of the free fatty acid 1–3 receptors. The potency of compounds was taken from ref. 5, 9 and 13
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Fig1: Agonists of the free fatty acid 1–3 receptors. The potency of compounds was taken from ref. 5, 9 and 13

Mentions: Several FFA1 agonists including GW9508, TAK-875/fasiglifam, AMG-837, AM1638, AM8182 (Fig. 1), LY2881835, JTT-851 and P11187 were developed by industry using high-throughput screening and subsequent medicinal chemistry. Some of these agonists were tested in clinical trials but removed due to toxicity [9]. Small selective FFA2/FFA3 carboxylic acids derived from the endogenous fatty acids (Fig. 1) have been developed as FFA2/FFA3 agonists by academia, though with poor potency [10]. A series of synthetic agonists has been patented by Euroscreen with potency up to 13nM [11]. AMG7703, also referred to as 4-CMTB, is a FFA2 selective allosteric agonist (Fig. 1) that was discovered by Amgen to inhibit lipolysis [12], yet, unfavourable pharmacokinetic properties of AMG7703 prevented this compound from progressing to clinical trials [12]. No highly potent orthosteric agonists have been developed at FFA3 to date. A series of FFA3 selective molecules, for example 2 (Fig. 1) was reported by Arena Pharmaceuticals to act as positive or negative allosteric modulators [9]. It is evident that a few available ligands of FFAs have various limitations for clinical tests and the development of novel FFA ligands presenting drug-like properties is an emerging challenge to validate the role of FFAs modulation in the therapy of metabolic and immune disorders.Fig. 1


Free fatty acid receptors: structural models and elucidation of ligand binding interactions.

Tikhonova IG, Poerio E - BMC Struct. Biol. (2015)

Agonists of the free fatty acid 1–3 receptors. The potency of compounds was taken from ref. 5, 9 and 13
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4561419&req=5

Fig1: Agonists of the free fatty acid 1–3 receptors. The potency of compounds was taken from ref. 5, 9 and 13
Mentions: Several FFA1 agonists including GW9508, TAK-875/fasiglifam, AMG-837, AM1638, AM8182 (Fig. 1), LY2881835, JTT-851 and P11187 were developed by industry using high-throughput screening and subsequent medicinal chemistry. Some of these agonists were tested in clinical trials but removed due to toxicity [9]. Small selective FFA2/FFA3 carboxylic acids derived from the endogenous fatty acids (Fig. 1) have been developed as FFA2/FFA3 agonists by academia, though with poor potency [10]. A series of synthetic agonists has been patented by Euroscreen with potency up to 13nM [11]. AMG7703, also referred to as 4-CMTB, is a FFA2 selective allosteric agonist (Fig. 1) that was discovered by Amgen to inhibit lipolysis [12], yet, unfavourable pharmacokinetic properties of AMG7703 prevented this compound from progressing to clinical trials [12]. No highly potent orthosteric agonists have been developed at FFA3 to date. A series of FFA3 selective molecules, for example 2 (Fig. 1) was reported by Arena Pharmaceuticals to act as positive or negative allosteric modulators [9]. It is evident that a few available ligands of FFAs have various limitations for clinical tests and the development of novel FFA ligands presenting drug-like properties is an emerging challenge to validate the role of FFAs modulation in the therapy of metabolic and immune disorders.Fig. 1

Bottom Line: This binding mode can explain mutagenesis results for residues at positions 4.56 and 5.42.The novel structural models of FFAs provide information on specific modes of ligand binding at FFA subtypes and new suggestions for mutagenesis and ligand modification, guiding the development of novel orthosteric and allosteric chemical probes to validate the importance of FFAs in metabolic and inflammatory conditions.Using our FFA homology modelling experience, a strategy to model a GPCR, which is phylogenetically distant from GPCRs with the available crystal structures, is discussed.

View Article: PubMed Central - PubMed

Affiliation: Molecular Therapeutics, School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland, UK. i.tikhonova@qub.ac.uk.

ABSTRACT

Background: The free fatty acid receptors (FFAs), including FFA1 (orphan name: GPR40), FFA2 (GPR43) and FFA3 (GPR41) are G protein-coupled receptors (GPCRs) involved in energy and metabolic homeostasis. Understanding the structural basis of ligand binding at FFAs is an essential step toward designing potent and selective small molecule modulators.

Results: We analyse earlier homology models of FFAs in light of the newly published FFA1 crystal structure co-crystallized with TAK-875, an ago-allosteric ligand, focusing on the architecture of the extracellular binding cavity and agonist-receptor interactions. The previous low-resolution homology models of FFAs were helpful in highlighting the location of the ligand binding site and the key residues for ligand anchoring. However, homology models were not accurate in establishing the nature of all ligand-receptor contacts and the precise ligand-binding mode. From analysis of structural models and mutagenesis, it appears that the position of helices 3, 4 and 5 is crucial in ligand docking. The FFA1-based homology models of FFA2 and FFA3 were constructed and used to compare the FFA subtypes. From docking studies we propose an alternative binding mode for orthosteric agonists at FFA1 and FFA2, involving the interhelical space between helices 4 and 5. This binding mode can explain mutagenesis results for residues at positions 4.56 and 5.42. The novel FFAs structural models highlight higher aromaticity of the FFA2 binding cavity and higher hydrophilicity of the FFA3 binding cavity. The role of the residues at the second extracellular loop used in mutagenesis is reanalysed. The third positively-charged residue in the binding cavity of FFAs, located in helix 2, is identified and predicted to coordinate allosteric modulators.

Conclusions: The novel structural models of FFAs provide information on specific modes of ligand binding at FFA subtypes and new suggestions for mutagenesis and ligand modification, guiding the development of novel orthosteric and allosteric chemical probes to validate the importance of FFAs in metabolic and inflammatory conditions. Using our FFA homology modelling experience, a strategy to model a GPCR, which is phylogenetically distant from GPCRs with the available crystal structures, is discussed.

Show MeSH
Related in: MedlinePlus