Implementing the “Best Template Searching-tool into Adenosiland platform
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- 作者：Matteo Floris (1)
Davide Sabbadin (2)
Antonella Ciancetta (2)
Ricardo Medda (1)
Alberto Cuzzolin (2)
Stefano Moro (2) - 关键词：G protein ; coupled receptors ; Adenosine receptors ; Receptor modelling ; Bioinformatics platform ; Adenosiland
- 刊名：In Silico Pharmacology
- 出版年：2013
- 出版时间：December 2013
- 年：2013
- 卷：1
- 期：1
- 全文大小：211 KB
- 参考文献：1. Ballester PJ, Richards WG: Ultrafast shape recognition to search compound databases for similar molecular shapes. / J Comput Chem 2007, 28:1711-723. CrossRef
2. Congreve M, Andrews SP, Doré AS, Hollenstein K, Hurrell E, Langmead CJ, Mason JS, Ng IW, Tehan B, Zhukov A, Weir M, Marshall FH: Discovery of 1,2,4-triazine derivatives as adenosine A 2A antagonists using structure based drug design. / J Med Chem 2012, 55:1898-903. CrossRef
3. Doré AS, Robertson N, Errey JC, Ng I, Hollenstein K, Tehan B, Hurrell E, Bennett K, Congreve M, Magnani F, Tate CG, Weir M, Marshall FH: Structure of the adenosine A 2A receptor in complex with ZM241385 and the xanthines XAC and caffeine. / Structure 2011, 19:1283-293. CrossRef
4. Floris M, Masciocchi J, Fanton M, Moro S: Swimming into peptidomimetic chemical space using pepMMsMIMIC. / Nucleic Acids Res 2011, 39:W261-W269. CrossRef
5. Floris M, Sabbadin D, Medda R, Bulfone A, Moro S: Adenosiland: walking through adenosine receptors landscape. / Eur J Med Chem 2013, 58:248-57. CrossRef
6. Fredholm BB, IJzerman AP, Jacobson KA, Klotz KN, Linden J: International Union of Pharmacology. XXV. Nomenclature and classification of adenosine receptors. / Pharmacol Rev 2001, 53:527-52.
7. Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, Hersey A, Light Y, McGlinchey S, Michalovich D, Al-Lazikani B, Overington JP: ChEMBL: a large-scale bioactivity database for drug discovery. / Nucleic Acids Res 2011, 40:D1100-D1107. CrossRef
8. Hino T, Arakawa T, Iwanari H, Yurugi-Kobayashi T, Ikeda-Suno C, Nakada-Nakura Y, Kusano-Arai O, Weyand S, Shimamura T, Nomura N, Cameron AD, Kobayashi T, Hamakubo T, Iwata S, Murata T: G-protein-coupled receptor inactivation by an allosteric inverse-agonist antibody. / Nature 2012, 482:237-40.
9. Inamdar GS, Pandya AN, Thakar HM, Sudarsanam V, Kachler S, Sabbadin D, Moro S, Klotz K-N, Vasu KK: New insight into adenosine receptors selectivity derived from a novel series of [5-substituted-4-phenyl-1,3-thiazol-2-yl] benzamides and furamides. / Eur J Med Chem 2013, 63:924-34. CrossRef
10. Jaakola VP, Griffith MT, Hanson MA, Cherezov V, Chien EYT, Lane JR, Ijzerman AP, Stevens RC: The 2.6 angstrom crystal structure of a human A 2A adenosine receptor bound to antagonist. / Science 2008, 322:1211-217. CrossRef
11. Lebon G, Warne T, Edwards PC, Bennett K, Langmead CJ, Leslie AGW, Tate CG: Agonist-bound adenosine A 2A receptor structures reveal common features of GPCR activation. / Nature 2011, 474:521-25. CrossRef
12. Liu W, Chun E, Thompson AA, Chubukov P, Xu F, Katritch V, Han GW, Roth CB, Heitman LH, IJzerman AP, Cherezov V, Stevens RC: Structural basis for allosteric regulation of GPCRs by sodium ions. / Science 2012, 337:232-36. CrossRef
13. Steinbeck C, Han Y, Kuhn S, Horlacher O, Luttmann E, Willighagen E: The chemistry development kit (CDK): an open-source Java library for chemo- and bioinformatics. / J Chem Inf Comput Sci 2003, 43:493-00. CrossRef
14. Steinbeck C, Hoppe C, Kuhn S, Floris M, Guha R, Willighagen EL: Recent developments of the chemistry development kit (CDK) an open-source java library for chemo- and bioinformatics. / Curr Pharm Des 2006, 12:2111-120. CrossRef
15. Taminau J, Thijs G, De Winter H: Pharao: pharmacophore alignment and Optimization. / J Mol Graph Model 2008, 27:161-69. CrossRef
16. Xu F, Wu H, Katritch V, Han GW, Jacobson KA, Gao Z-G, Cherezov V, Stevens RC: Structure of an agonist-bound human A 2A adenosine receptor. / Science 2011, 332:322-27. CrossRef - 作者单位：Matteo Floris (1)
Davide Sabbadin (2)
Antonella Ciancetta (2)
Ricardo Medda (1)
Alberto Cuzzolin (2)
Stefano Moro (2)
1. CRS4, Parco Polaris, 09010, Pula, CA, Italy
2. Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, I-35131, Padova, Italy - ISSN：2193-9616
文摘
Background Adenosine receptors (ARs) belong to the G protein-coupled receptors (GCPRs) family. The recent release of X-ray structures of the human A2A AR (h A2A AR ) in complex with agonists and antagonists has increased the application of structure-based drug design approaches to this class of receptors. Among them, homology modeling represents the method of choice to gather structural information on the other receptor subtypes, namely A1, A2B, and A3 ARs. With the aim of helping users in the selection of either a template to build its own models or ARs homology models publicly available on our platform, we implemented our web-resource dedicated to ARs, Adenosiland, with the -em class="a-plus-plus">Best Template Searching-facility. This tool is freely accessible at the following web address: http://mms.dsfarm.unipd.it/Adenosiland/ligand.php. Findings The template suggestions and homology models provided by the -em class="a-plus-plus">Best Template Searching-tool are guided by the similarity of a query structure (putative or known ARs ligand) with all ligands co-crystallized with hA2A AR subtype. The tool computes several similarity indexes and sort the outcoming results according to the index selected by the user. Conclusions We have implemented our web-resource dedicated to ARs Adenosiland with the -em class="a-plus-plus">Best Template Searching-facility, a tool to guide template and models selection for hARs modelling. The underlying idea of our new facility, that is the selection of a template (or models built upon a template) whose co-crystallized ligand shares the highest similarity with the query structure, can be easily extended to other GPCRs.