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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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The ligand binding site of the free fatty acid 1–3 receptors a: the binding site in the FFA1 crystal structure; b and c: the binding site in the FFA1-based homology model of FFA2 and FFA3, respectively. The side chain of the binding site residues in FFAs is shown in blue, pink and green, respectively. H-bonding, π- π and π-cation interactions are shown in black, blue and green dotted lines, respectively
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Fig6: The ligand binding site of the free fatty acid 1–3 receptors a: the binding site in the FFA1 crystal structure; b and c: the binding site in the FFA1-based homology model of FFA2 and FFA3, respectively. The side chain of the binding site residues in FFAs is shown in blue, pink and green, respectively. H-bonding, π- π and π-cation interactions are shown in black, blue and green dotted lines, respectively

Mentions: Comparison of FFA2 with FFA1 structure reveals a more intensive network of interactions within the FFA2 binding site due to extra hydrophilic and aromatic residues (Fig. 6, a and b). Thus, Y165EL2 in FFA2 (L171 in FFA1) and Y903.33 (F87 in FFA1) contribute to aromatic and H-bond networks of interactions with conserved Y943.37, R1805.39, Y2386.51 and R2557.35. Residue H2426.55 (N244 in FFA1) forms an H-bond with R2557.53 and aromatic and hydrophobic interactions with Y943.37 and Y2386.51. In addition, residues K652.60, E682.63 and E166EL2 contribute to an H-bonding network within the binding site. The major difference with the previous FFA2 homology models [10, 25] is that we didn’t observe this intensive network of hydrogen bond and aromatic interactions. The higher quality FFA2 homology model suggests that the binding site is more packed and less opened from the extracellular side.Fig. 6


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

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

The ligand binding site of the free fatty acid 1–3 receptors a: the binding site in the FFA1 crystal structure; b and c: the binding site in the FFA1-based homology model of FFA2 and FFA3, respectively. The side chain of the binding site residues in FFAs is shown in blue, pink and green, respectively. H-bonding, π- π and π-cation interactions are shown in black, blue and green dotted lines, respectively
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig6: The ligand binding site of the free fatty acid 1–3 receptors a: the binding site in the FFA1 crystal structure; b and c: the binding site in the FFA1-based homology model of FFA2 and FFA3, respectively. The side chain of the binding site residues in FFAs is shown in blue, pink and green, respectively. H-bonding, π- π and π-cation interactions are shown in black, blue and green dotted lines, respectively
Mentions: Comparison of FFA2 with FFA1 structure reveals a more intensive network of interactions within the FFA2 binding site due to extra hydrophilic and aromatic residues (Fig. 6, a and b). Thus, Y165EL2 in FFA2 (L171 in FFA1) and Y903.33 (F87 in FFA1) contribute to aromatic and H-bond networks of interactions with conserved Y943.37, R1805.39, Y2386.51 and R2557.35. Residue H2426.55 (N244 in FFA1) forms an H-bond with R2557.53 and aromatic and hydrophobic interactions with Y943.37 and Y2386.51. In addition, residues K652.60, E682.63 and E166EL2 contribute to an H-bonding network within the binding site. The major difference with the previous FFA2 homology models [10, 25] is that we didn’t observe this intensive network of hydrogen bond and aromatic interactions. The higher quality FFA2 homology model suggests that the binding site is more packed and less opened from the extracellular side.Fig. 6

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