Free fatty acid receptors: Structural models and elucidation of ligand binding interactions Computational analysis

BMC Structural Biology

Volumn 15, Issue 1, 2015, Pages

  Tikhonova, Irina G ^a   Poerio, Elena ^a  

^a QUEEN'S UNIVERSITY BELFAST   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

FASIGLIFAM; FREE FATTY ACID RECEPTOR 2; FREE FATTY ACID RECEPTOR 3; G PROTEIN COUPLED RECEPTOR; G PROTEIN COUPLED RECEPTOR 40; UNCLASSIFIED DRUG; BENZOFURAN DERIVATIVE; FATTY ACID; SULFONE; TAK-875;

ARTICLE; BINDING AFFINITY; BINDING SITE; CONTROLLED STUDY; CRYSTAL STRUCTURE; HYDROPHILICITY; LIGAND BINDING; MOLECULAR DOCKING; MUTAGENESIS; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS; CHEMISTRY; GENETICS; HUMAN; METABOLISM; MOLECULAR MODEL; MUTATION; PHYLOGENY; PROTEIN SECONDARY STRUCTURE; STRUCTURE ACTIVITY RELATION;

BENZOFURANS; BINDING SITES; FATTY ACIDS, NONESTERIFIED; HUMANS; MODELS, MOLECULAR; MOLECULAR DOCKING SIMULATION; MUTATION; PHYLOGENY; PROTEIN STRUCTURE, SECONDARY; RECEPTORS, G-PROTEIN-COUPLED; STRUCTURAL HOMOLOGY, PROTEIN; STRUCTURE-ACTIVITY RELATIONSHIP; SULFONES;

EID: 84941000099     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/s12900-015-0044-2     Document Type: Article

References (51)

1. Stoddart LA, Smith NJ, Milligan G. International Union of Pharmacology. LXXI. Free fatty acid receptors FFA1, -2, and -3: pharmacology and pathophysiological functions. Pharmacol Rev. 2008;60(4):405-17.
2. Briscoe CP, Peat AJ, McKeown SC, Corbett DF, Goetz AS, Littleton TR, et al. Pharmacological regulation of insulin secretion in MIN6 cells through the fatty acid receptor GPR40: identification of agonist and antagonist small molecules. Br J Pharmacol. 2006;148(5):619-28.
3. Itoh Y, Hinuma S. GPR40, a free fatty acid receptor on pancreatic beta cells, regulates insulin secretion. Hepatol Res. 2005;33(2):171-3.
4. Brown AJ, Goldsworthy SM, Barnes AA, Eilert MM, Tcheang L, Daniels D, et al. The Orphan G protein-coupled receptors GPR41 and GPR43 are activated by propionate and other short chain carboxylic acids. J Biol Chem. 2003;278(13):11312-9.
5. Ulven T. Short-chain free fatty acid receptors FFA2/GPR43 and FFA3/GPR41 as new potential therapeutic targets. Front Endocrinol (Lausanne). 2012;3:111.
6. Dranse HJ, Kelly ME, Hudson BD. Drugs or diet? - Developing novel therapeutic strategies targeting the free fatty acid family of GPCRs. Br J Pharmacol. 2013;170(4):696-711.
7. Milligan G, Ulven T, Murdoch H, Hudson BD. G-protein-coupled receptors for free fatty acids: nutritional and therapeutic targets. Br J Nutr. 2014;111:S3-7.
8. Bindels LB, Dewulf EM, Delzenne NM. GPR43/FFA2: physiopathological relevance and therapeutic prospects. Trends Pharmacol Sci. 2013;34(4):226-32.
9. Watterson KR, Hudson BD, Ulven T, Milligan G. Treatment of type 2 diabetes by free Fatty Acid receptor agonists. Front Endocrinol (Lausanne). 2014;5:137.
10. Schmidt J, Smith NJ, Christiansen E, Tikhonova IG, Grundmann M, Hudson BD, et al. Selective orthosteric free fatty acid receptor 2 (FFA2) agonists: identification of the structural and chemical requirements for selective activation of FFA2 versus FFA3. J Biol Chem. 2011;286(12):10628-40.
11. Hoveyda H, Brantis CE, Dutheuil G, Zoute L, Schils D, Bernard J: Compounds, pharmaceutical composition and methods for use in treating metabolic disorders. June 17, 2010, International patent application WO 2010/066682.
12. Wang Y, Jiao X, Kayser F, Liu J, Wang Z, Wanska M, et al. The first synthetic agonists of FFA2: Discovery and SAR of phenylacetamides as allosteric modulators. Bioorg Med Chem Lett. 2010;20(2):493-8.
13. Tikhonova IG, Sum CS, Neumann S, Thomas CJ, Raaka BM, Costanzi S, et al. Bidirectional, iterative approach to the structural delineation of the functional "Chemoprint" in GPR40 for agonist recognition. J Med Chem. 2007;50(13):2981-9.
14. Sum CS, Tikhonova IG, Neumann S, Engel S, Raaka BM, Costanzi S, et al. Identification of residues important for agonist recognition and activation in GPR40. J Biol Chem. 2007;282:29248-55.
15. Tikhonova IG, Sum CS, Neumann S, Engel S, Raaka BM, Costanzi S, et al. Discovery of novel Agonists and antagonists of the free fatty acid receptor 1 (FFAR1) using virtual screening. J Med Chem. 2008;51(3):625-33.
16. Srivastava A, Yano J, Hirozane Y, Kefala G, Gruswitz F, Snell G, et al. High-resolution structure of the human GPR40 receptor bound to allosteric agonist TAK-875. Nature. 2014;513(7516):124-7.
17. Sum CS, Tikhonova IG, Costanzi S, Gershengorn MC. Two Arginine-Glutamate Ionic Locks Near the Extracellular Surface of FFAR1 Gate Receptor Activation. J Biol Chem. 2009;284(6):3529-36.
18. Zhang C, Srinivasan Y, Arlow DH, Fung JJ, Palmer D, Zheng Y, et al. High-resolution crystal structure of human protease-activated receptor 1. Nature. 2012;492(7429):387-92.
19. Yabuki C, Komatsu H, Tsujihata Y, Maeda R, Ito R, Matsuda-Nagasumi K, et al. A Novel Antidiabetic Drug, Fasiglifam/TAK-875, Acts as an Ago-Allosteric Modulator of FFAR1. PLoS One. 2013;8(10), e76280.
20. Schrödinger, LLC, New York, NY, USA: Glide 6.5. 2014.
21. Schrodinger, LLC, New York, NY, USA: Induced Fit Docking protocol 2014-4, Glide version 6.4, Prime version 3.7. 2014.
22. Christiansen E, Hansen SV, Urban C, Hudson BD, Wargent ET, Grundmann M, et al. Discovery of TUG-770: A Highly Potent Free Fatty Acid Receptor 1 (FFA1/GPR40) Agonist for Treatment of Type 2 Diabetes. ACS Med Chem Lett. 2013;4(5):441-5.
23. Lin DC, Guo Q, Luo J, Zhang J, Nguyen K, Chen M, et al. Identification and pharmacological characterization of multiple allosteric binding sites on the free fatty acid 1 receptor. Mol Pharmacol. 2012;82(5):843-59.
24. Luo J, Swaminath G, Brown SP, Zhang J, Guo Q, Chen M, et al. A potent class of GPR40 full agonists engages the enteroinsular axis to promote glucose control in rodents. PLoS One. 2012;7(10):e46300.
25. Hudson BD, Due-Hansen ME, Christiansen E, Hansen AM, Mackenzie AE, Murdoch H, et al. Defining the molecular basis for the first potent and selective orthosteric agonists of the FFA2 free fatty acid receptor. J Biol Chem. 2013;288(24):17296-312.
26. Stoddart LA, Smith NJ, Jenkins L, Brown AJ, Milligan G. Conserved polar residues in transmembrane domains V, VI, and VII of free fatty acid receptor 2 and free fatty acid receptor 3 are required for the binding and function of short chain fatty acids. J Biol Chem. 2008;283(47):32913-24.
27. Hudson BD, Tikhonova IG, Pandey SK, Ulven T, Milligan G. Extracellular ionic locks determine variation in constitutive activity and ligand potency between species orthologs of the free fatty acid receptors FFA2 and FFA3. J Biol Chem. 2012;287(49):41195-209.
28. Swaminath G, Jaeckel P, Guo Q, Cardozo M, Weiszmann J, Lindberg R, et al. Mutational analysis of G-protein coupled receptor - FFA2. Biochem Biophys Res Commun. 2011;405(1):122-7.
29. Lee T, Schwandner R, Swaminath G, Weiszmann J, Cardozo M, Greenberg J, et al. Identification and functional characterization of allosteric agonists for the G protein-coupled receptor FFA2. Mol Pharmacol. 2008;74(6):1599-609.
30. Hudson BD, Christiansen E, Murdoch H, Jenkins L, Hojgaard Hansen A, Madsen OB, et al. Complex Pharmacology of Novel Allosteric Free Fatty Acid 3 Receptor Ligands. Mol Pharmacol. 2014;86:200-10.
31. Smith NJ, Ward RJ, Stoddart LA, Hudson BD, Kostenis E, Ulven T, et al. Extracellular loop 2 of the free fatty acid receptor 2 mediates allosterism of a phenylacetamide ago-allosteric modulator. Mol Pharmacol. 2011;80(1):163-73.
32. Michino M, Abola E, Brooks 3rd CL, Dixon JS, Moult J, Stevens RC, et al. Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008. Nat Rev Drug Discov. 2009;8(6):455-63.
33. Kufareva I, Rueda M, Katritch V, Stevens RC, Abagyan R, GPCR Dock 2010 participants. Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure. 2011;19(8):1108-26.
34. Kufareva I, Katritch V, Stevens RC, Abagyan R, Participants of GPCR Dock 2013. Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges. Structure. 2014;22(8):1120-39.
35. Worth CL, Kleinau G, Krause G. Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models. PLoS One. 2009;4(9):e7011.
36. Bera I, Laskar A, Ghoshal N. Exploring the structure of opioid receptors with homology modeling based on single and multiple templates and subsequent docking: a comparative study. J Mol Model. 2011;17(5):1207-21.
37. Watson SJ, Brown AJ, Holliday ND. Differential signaling by splice variants of the human free fatty acid receptor GPR120. Mol Pharmacol. 2012;81(5):631-42.
38. Hudson BD, Shimpukade B, Milligan G, Ulven T. The molecular basis of ligand interaction at free fatty acid receptor 4 (FFA4/GPR120). J Biol Chem. 2014;289:20345-58.
39. Costanzi S. Homology modeling of class a G protein-coupled receptors. Methods Mol Biol. 2012;857:259-79.
40. Thompson JD, Higgins DG, Gibson TJ. Clustal-W - Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Position-Specific Gap Penalties and Weight Matrix Choice. Nucleic Acids Res. 1994;22(22):4673-80.
41. Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A. 1992;89(22):10915-9.
42. Soding J. Protein homology detection by HMM-HMM comparison. Bioinformatics. 2005;21(7):951-60.
43. Schrödinger, LLC, New York, NY, USA: Prime 3.0. 2011.
44. Schrodinger, LLC, New York, NY, USA: Maestro 9.9. 2014.
45. Sherman W, Day T, Jacobson MP, Friesner RA, Farid R. Novel procedure for modeling ligand/receptor induced fit effects. J Med Chem. 2006;49(2):534-53.
46. Sherman W, Beard HS, Farid R. Use of an induced fit receptor structure in virtual screening. Chem Biol Drug Des. 2006;67(1):83-4.
47. Humphrey W, Dalke A, Schulten K. VMD: Visual molecular dynamics. J Mol Graph. 1996;14(1):33-8.
48. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, et al. UCSF Chimera - a visualization system for exploratory research and analysis. J Comput Chem. 2004;25(13):1605-12.
49. Schrodinger, LLC, New York, NY, USA: SiteMap 3.3, 2014.
50. Schrodinger, LLC, New York, NY, USA: MacroModel 10.6. 2014.
51. Ballesteros JA, Weinstein H. Modeling transmembrane helix contacts in GPCR. Biophys J. 1995;68(2 PART 2):A446.