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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

Two proposed binding modes for the GW9508 agonist in FFA1. a: mode 1, similar to the binding of TAK-875 in the FFA1 crystal structure. b: mode 2, the alternative pose derived from flexible docking. Hydrogen bonds, π- π and π-cation interactions are in black and blue, respectively. The binding site residues, E145 and E172 of the second extracellular loop predicted to form salt bridges in the earlier models and K622.60 predicted here to form the allosteric binding site are shown
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Fig5: Two proposed binding modes for the GW9508 agonist in FFA1. a: mode 1, similar to the binding of TAK-875 in the FFA1 crystal structure. b: mode 2, the alternative pose derived from flexible docking. Hydrogen bonds, π- π and π-cation interactions are in black and blue, respectively. The binding site residues, E145 and E172 of the second extracellular loop predicted to form salt bridges in the earlier models and K622.60 predicted here to form the allosteric binding site are shown

Mentions: The ligand is docked in the similar orientation but with the higher RMSD of 3 Å, mainly for the biphenyl tail. To achieve this result, the docking protocol with van der Waals radius of protein atoms soften from 1 to 0.8 Å was used. We anticipate that mutation at position 3.34 in the crystal structure could correct the agonist position. It appears this change however is not dramatic for the TAK-875 binding affinity [16]. Linoleic acid and GW9508 were placed similar to TAK-875 in the binding site. The docking position of GW9508, as an example is shown in Fig. 5a.Fig. 5


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

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

Two proposed binding modes for the GW9508 agonist in FFA1. a: mode 1, similar to the binding of TAK-875 in the FFA1 crystal structure. b: mode 2, the alternative pose derived from flexible docking. Hydrogen bonds, π- π and π-cation interactions are in black and blue, respectively. The binding site residues, E145 and E172 of the second extracellular loop predicted to form salt bridges in the earlier models and K622.60 predicted here to form the allosteric binding site are shown
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig5: Two proposed binding modes for the GW9508 agonist in FFA1. a: mode 1, similar to the binding of TAK-875 in the FFA1 crystal structure. b: mode 2, the alternative pose derived from flexible docking. Hydrogen bonds, π- π and π-cation interactions are in black and blue, respectively. The binding site residues, E145 and E172 of the second extracellular loop predicted to form salt bridges in the earlier models and K622.60 predicted here to form the allosteric binding site are shown
Mentions: The ligand is docked in the similar orientation but with the higher RMSD of 3 Å, mainly for the biphenyl tail. To achieve this result, the docking protocol with van der Waals radius of protein atoms soften from 1 to 0.8 Å was used. We anticipate that mutation at position 3.34 in the crystal structure could correct the agonist position. It appears this change however is not dramatic for the TAK-875 binding affinity [16]. Linoleic acid and GW9508 were placed similar to TAK-875 in the binding site. The docking position of GW9508, as an example is shown in Fig. 5a.Fig. 5

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