Bitterdb: Taste ligands and receptors database in 2019

Nucleic Acids Research

Volumn 47, Issue D1, 2019, Pages D1179-D1185

  Dagan Wiener, Ayana ^a   Di Pizio, Antonella ^a,b   Nissim, Ido ^a   Bahia, Malkeet S ^a,c   Dubovski, Nitzan ^a   Margulis, Eitan ^a   Niv, Masha Y ^a  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^c BAR ILAN UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; AVERSIVE AGENT; G PROTEIN COUPLED RECEPTOR; TASTE RECEPTORS, TYPE 2;

ARTICLE; BIOLOGICAL MODEL; BITTER DATABASE; BITTER TASTE; CAT; CHICKEN; DATA BASE; EXPERIMENTAL STUDY; PRIORITY JOURNAL; PROTEIN EXPRESSION; QUANTITATIVE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS; TASTE ACUITY; TASTE BUD; ANIMAL; BIOLOGY; CHEMISTRY; FACTUAL DATABASE; GENETICS; HUMAN; INTERNET; METABOLISM; MOUSE; MUTATION; PROCEDURES; SPECIES DIFFERENCE; TASTE;

ANIMALS; AVERSIVE AGENTS; CATS; CHICKENS; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; HUMANS; INTERNET; LIGANDS; MICE; MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; RECEPTORS, G-PROTEIN-COUPLED; SPECIES SPECIFICITY; TASTE;

EID: 85059799078     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gky974     Document Type: Article

References (56)

1. Chandrashekar,J., Hoon,M.A., Ryba,N.J.P. and Zuker,C.S. (2006) The receptors and cells for mammalian taste. Nature, 444, 288-294.
2. Chaudhari,N. and Roper,S.D. (2010) The cell biology of taste. J. Cell Biol. 190, 285-296
3. Behrens,M., Korsching,S.I. and Meyerhof,W. (2014) Tuning properties of avian and frog bitter taste receptors dynamically fit gene repertoire sizes. Mol. Biol. Evol., 31, 3216-3227.
4. Lossow,K., Hubner,S., Roudnitzky,N., Slack,J.P., Pollastro,F., Behrens,M. and Meyerhof,W. (2016) Comprehensive analysis of mouse bitter taste receptors reveals different molecular receptive ranges for orthologous receptors in mice and humans. J. Biol. Chem., 291, 15358-15377.
5. Behrens,M. and Meyerhof,W. (2018) Vertebrate bitter taste receptors: keys for survival in changing environments. J. Agric. Food Chem. 66, 2204-2213
6. Xue,A.Y., Di Pizio,A., Levit,A., Yarnitzky,T., Penn,O., Pupko,T. and Niv,M.Y. (2018) Independent evolution of strychnine recognition by bitter taste receptor subtypes. Front. Mol. Biosci., 5, 9.
7. Jaggupilli,A., Howard,R., Upadhyaya,J.D., Bhullar,R.P. and Chelikani,P. (2016) Bitter taste receptors: novel insights into the biochemistry and pharmacology. Int. J. Biochem. Cell Biol. 77, 184-196
8. Shaik,F.A., Singh,N., Arakawa,M., Duan,K., Bhullar,R.P. and Chelikani,P. (2016) Bitter taste receptors: extraoral roles in pathophysiology. Int. J. Biochem. Cell Biol., 77, 197-204
9. Behrens,M. and Meyerhof,W. (2011) Gustatory and extragustatory functions of mammalian taste receptors. Physiol. Behav, 105, 4-13
10. Avau,B. and Depoortere,I. (2016) The bitter truth about bitter taste receptors: beyond sensing bitter in the oral cavity. Acta Physiol, 216, 407-420
11. Wiener,A., Shudler,M., Levit,A. and Niv,M.Y. (2012) BitterDB: a database of bitter compounds. Nucleic Acids Res., 40, D413-D419
12. Dagan-Wiener,A., Nissim,I., Ben Abu,N., Borgonovo,G., Bassoli,A. and Niv,M.Y. (2017) Bitter or not? BitterPredict, a tool for predicting taste from chemical structure. Sci. Rep., 7, 12074.
13. Huang,W., Shen,Q., Su,X., Ji,M., Liu,X., Chen,Y., Lu,S., Zhuang,H. and Zhang,J. (2016) BitterX: a tool for understanding bitter taste in humans. Sci. Rep., 6, 23450.
14. Zheng,S., Jiang,M., Zhao,C., Zhu,R., Hu,Z., Xu,Y. and Lin,F. (2018) e-Bitter: Bitterant prediction by the consensus voting from the machine-learning methods. Front. Chem., 6, 82.
15. Banerjee,P. and Preissner,R. (2018) BitterSweetForest: a random forest based binary classifier to predict bitterness and sweetness of chemical compounds. Front. Chem, 6, 93
16. Nissim,I., Dagan-Wiener,A. and Niv,M.Y. (2017) The taste of toxicity: a quantitative analysis of bitter and toxic molecules. IUBMB Life, 69, 938-946.
17. Mennella,J.A., Spector,A.C., Reed,D.R. and Coldwell,S.E. (2013) The bad taste of medicines: overview of basic research on bitter taste. Clin. Ther., 35, 1225-1246.
18. Mohamed-Ahmed,A.H., Soto,J., Ernest,T. and Tuleu,C. (2016) Non-human tools for the evaluation of bitter taste in the design and development of medicines: a systematic review. Drug Discov. Today, 21, 1170-1180.
19. Bahia,M.S., Nissim,I. and Niv,MY. (2018) Bitterness prediction in-silico: a step towards better drugs. Int. J. Pharm., 536, 526-529
20. Di Pizio,A., Levit,A., Slutzki,M., Behrens,M., Karaman,R. and Niv,M.Y. (2016) Comparing Class A GPCRs to bitter taste receptors: Structural motifs, ligand interactions and agonist-to-antagonist ratios. Methods Cell Biol. 132, 401-427
21. Yarnitzky,T., Levit,A. and Niv,M.Y. (2010) Homology modeling of G-protein-coupled receptors with X-ray structures on the rise. Curr. Opin. Drug Discov. Dev., 13, 317-325.
22. Di Pizio,A., Kruetzfeldt,L.M., Cheled-Shoval,S., Meyerhof,W., Behrens,M. and Niv,M.Y. (2017) Ligand binding modes from low resolution GPCR models and mutagenesis: chicken bitter taste receptor as a test-case. Sci. Rep., 7, 8223.
23. Nowak,S., Di Pizio,A., Levit,A., Niv,M.Y., Meyerhof,W. and Behrens,M. (2018) Reengineering the ligand sensitivity of the broadly tuned human bitter taste receptor TAS2R14. Biochim. Biophys. Acta, 1862, 2162-2173.
24. Roudnitzky,N., Behrens,M., Engel,A., Kohl,S., Thalmann,S., Hubner,S., Lossow,K., Wooding,S.P. and Meyerhof,W. (2015) Receptor polymorphism and genomic structure interact to shape bitter taste perception. PLoS Genet., 11, e1005530.
25. Pronin,A.N., Xu,H., Tang,H., Zhang,L., Li,Q. and Li,X. (2007) Specific alleles of bitter receptor genes influence human sensitivity to the bitterness of aloin and saccharin. Curr. Biol., 17, 1403-1408.
26. Bufe,B., Breslin,P.A., Kuhn,C., Reed,D.R., Tharp,C.D., Slack,J.P., Kim,U.K., Drayna,D. and Meyerhof,W. (2005) The molecular basis of individual differences in phenylthiocarbamide and propylthiouracil bitterness perception. Curr. Biol., 15, 322-327.
27. Hayes,J.E., Wallace,M.R., Knopik,V.S., Herbstman,D.M., Bartoshuk,L.M. and Duffy,V.B. (2011) Allelic variation in TAS2R bitter receptor genes associates with variation in sensations from and ingestive behaviors toward common bitter beverages in adults. Chem. Senses, 36, 311-319.
28. Tomasulo,P. (2002) ChemIDplus-super source for chemical and drug information. Med. Ref. Serv. Q. 21, 53-59
29. Meyerhof,W., Batram,C., Kuhn,C., Brockhoff,A., Chudoba,E., Bufe,B., Appendino,G. and Behrens,M. (2010) The molecular receptive ranges of human TAS2R bitter taste receptors. Chem. Senses, 35, 157-170.
30. Riedel,K., Sombroek,D., Fiedler,B., Siems,K. and Krohn,M. (2017) Human cell-based taste perception - a bittersweet job for industry. Nat. Prod. Rep., 34, 484-495.
31. Kim,S., Thiessen,P.A., Bolton,E.E., Chen,J., Fu,G., Gindulyte,A., Han,L., He,J., He,S., Shoemaker,B.A. et al. (2016) PubChem Substance and Compound databases. Nucleic Acids Res., 44, D1202-D1213.
32. Sterling,T. and Irwin,J.J. (2015) ZINC 15-ligand discovery for everyone. J. Chem. Inf. Model. 55, 2324-2337
33. Wishart,D.S., Feunang,Y.D., Guo,A.C., Lo,E.J., Marcu,A., Grant,J.R., Sajed,T., Johnson,D., Li,C., Sayeeda,Z. et al. (2018) DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Res., 46, D1074-D1082.
34. Harding,S.D., Sharman,J.L., Faccenda,E., Southan,C., Pawson,A.J., Ireland,S., Gray,A.J.G., Bruce,L., Alexander,S.P.H., Anderton,S. et al. (2018) The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to immunopharmacology. Nucleic Acids Res., 46, D1091-D1106.
35. Sherry,S.T., Ward,M.H., Kholodov,M., Baker,J., Phan,L., Smigielski,E.M. and Sirotkin,K. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res., 29, 308-311.
36. The UniProt, C. (2017) UniProt: the universal protein knowledgebase. Nucleic Acids Res. 45, D158-D169
37. Pandy-Szekeres,G., Munk,C., Tsonkov,T.M., Mordalski,S., Harpsoe,K., Hauser,A.S., Bojarski,A.J. and Gloriam,D.E. (2018) GPCRdb in 2018: adding GPCR structure models and ligands. Nucleic Acids Res., 46, D440-D446.
38. Kent,W.J., Sugnet,C.W., Furey,T.S., Roskin,K.M., Pringle,T.H., Zahler,A.M. and Haussler,D. (2002) The human genome browser at UCSC. Genome Res., 12, 996-1006.
39. Uhlen,M., Fagerberg,L., Hallstrom,B.M., Lindskog,C., Oksvold,P., Mardinoglu,A., Sivertsson,A., Kampf,C., Sjostedt,E., Asplund,A. et al. (2015) Proteomics. Tissue-based map of the human proteome. Science, 347, 1260419.
40. Stelzer,G., Rosen,N., Plaschkes,I., Zimmerman,S., Twik,M., Fishilevich,S., Stein,T.I., Nudel,R., Lieder,I., Mazor,Y. et al. (2016) The GeneCards Suite: From gene data mining to disease genome sequence analyses. Curr. Protoc. Bioinformatics, 54, 1.30.1-1.30.33.
41. Duffy,F.J., Verniere,M., Devocelle,M., Bernard,E., Shields,D.C. and Chubb,A.J. (2011) CycloPs: generating virtual libraries of cyclized and constrained peptides including nonnatural amino acids. J. Chem. Inf. Model., 51, 829-836.
42. Roland,W.S., van Buren,L., Gruppen,H., Driesse,M., Gouka,R.J., Smit,G. and Vincken,J.P. (2013) Bitter taste receptor activation by flavonoids and isoflavonoids: modeled structural requirements for activation of hTAS2R14 and hTAS2R39. J. Agric. Food Chem., 61, 10454-10466.
43. Stark,T. and Hofmann,T. (2005) Structures, sensory activity, and dose/response functions of 2,5-diketopiperazines in roasted cocoa nibs (Theobroma cacao). J. Agric. Food Chem. 53, 7222-7231
44. Brockhoff,A., Behrens,M., Massarotti,A., Appendino,G. and Meyerhof,W. (2007) Broad tuning of the human bitter taste receptor hTAS2R46 to various sesquiterpene lactones, clerodane and labdane diterpenoids, strychnine, and denatonium. J. Agric. Food Chem., 55, 6236-6243.
45. Dresel,M., Dunkel,A. and Hofmann,T. (2015) Sensomics analysis of key bitter compounds in the hard resin of hops (Humulus lupulus L.) and their contribution to the bitter profile of Pilsner-type beer. J. Agric. Food Chem., 63, 3402-3418.
46. Dresel,M., Vogt,C., Dunkel,A. and Hofmann,T. (2016) The bitter chemodiversity of hops (Humulus lupulus L.). J. Agric. Food Chem., 64, 7789-7799.
47. Lei,W., Ravoninjohary,A., Li,X., Margolskee,R.F., Reed,D.R., Beauchamp,G.K. and Jiang,P. (2015) Functional analyses of bitter taste receptors in domestic cats (Felis catus). PLoS One, 10, e0139670.
48. Intelmann,D., Batram,C., Kuhn,C., Haseleu,G., Meyerhof,W. and Hofmann,T. (2009) Three TAS2R bitter taste receptors mediate the psychophysical responses to bitter compounds of hops (Humulus lupulus L.) and beer. Chemosens Percept., 2, 118-132.
49. Degenhardt,A.G. and Hofmann,T. (2010) Bitter-tasting and kokumi-enhancing molecules in thermally processed avocado (Persea americana Mill.). J. Agric. Food Chem. 58, 12906-12915
50. DDimitrov,S.D., Diderich,R., Sobanski,T., Pavlov,T.S., Chankov,G.V., Chapkanov,A.S., Karakolev,Y.H., Temelkov,S.G., Vasilev,R.A., Gerova,K.D. et al. (2016) QSAR Toolbox - workflow and major functionalities. SAR QSAR Environ. Res., 27, 203-219.
51. Johnson,M., Zaretskaya,I., Raytselis,Y., Merezhuk,Y., McGinnis,S. and Madden,T.L. (2008) NCBI BLAST: a better web interface. Nucleic Acids Res., 36, W5-W9.
52. OLeary,N.A., Wright,M.W., Brister,J.R., Ciufo,S., Haddad,D., McVeigh,R., Rajput,B., Robbertse,B., Smith-White,B., Ako-Adjei,D. et al. (2016) Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res., 44, D733-D745.
53. Thawabteh,A., Lelario,F., Scrano,L., Bufo,S.A., Nowak,S., Behrens,M., Di Pizio,A., Niv,M.Y. and Karaman,R. (2018) Bitterless guaifenesin prodrugs - design, synthesis, characterization, in vitro kinetics and bitterness studies. Chem. Biol. Drug Des., doi:10.1111/cbdd.13409.
54. Pei,J., Kim,B.H. and Grishin,N.V. (2008) PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucleic Acids Res., 36, 2295-2300.
55. Rose,A.S., Bradley,A.R., Valasatava,Y., Duarte,J.M., Prlic,A. and Rose,P.W. (2018) NGL Viewer: Web-based molecular graphics for large complexes. Bioinformatics, doi:10.1093/bioinformatics/bty419.
56. Yachdav,G., Wilzbach,S., Rauscher,B., Sheridan,R., Sillitoe,I., Procter,J., Lewis,S.E., Rost,B. and Goldberg,T. (2016) MSAViewer: interactive JavaScript visualization of multiple sequence alignments. Bioinformatics, 32, 3501-3503.