Cyclodextrin knowledgebase a web-based service managing CD-ligand complexation data
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Abstract
Cyclodextrins are cyclic oligosaccharides that are able to form water-soluble inclusion complexes with small molecules. Because of their complexing ability, they are widely applied in food, pharmaceutical and chemical industries. In this paper we describe the development of a free web-service, Cyclodextrin KnowledgeBase: (http://www.cyclodextrin.net). The database contains four modules: the Publication, Interaction, Chirality and Analysis Modules. In the Publication Module, almost 50,000 publication details are collected that can be retrieved by text search. In the Interaction and Chirality Modules relevant literature data on cyclodextrin complexation and chiral recognition are collected that can be retrieved by both text and structural searches. Moreover, in the Analysis Module, the geometries of small molecule-cyclodextrin complexes can be predicted using molecular docking tools in order to explore the structures and interaction energies of the inclusion complexes. Complex geometry prediction is made possible by the built-in database of 95 cyclodextrin derivatives, where the 3D structures as well as the partial charges are calculated and stored for further utilization. The use of the database is demonstrated by several examples.
Keywords
Cyclodextrin Interaction database In silico prediction Literature database Chiral recognitionNotes
Acknowledgment
The financial supports of Jedlik Ányos grant 00180/2007, NKFP_A3-2008-0211 are acknowledged.
References
- 1.Szejtli J (1994) Med Res Rev 14(3):353CrossRefGoogle Scholar
- 2.Davis ME, Brewster ME (2004) Nat Rev Drug Discov 3(12):1023CrossRefGoogle Scholar
- 3.Del Valle EMM (2004) Process Biochem 39(9):1033CrossRefGoogle Scholar
- 4.Loftsson T, Jarho P, Masson M, Jarvinen T (2005) Expert Opin Drug Deliv 2(2):335CrossRefGoogle Scholar
- 5.Chari R, Qureshi F, Moschera J, Tarantino R, Kalonia D (2009) Pharm Res 26(1):161CrossRefGoogle Scholar
- 6.Jonsdottir SO, Jorgensen FS, Brunak S (2005) Bioinformatics 21(10):2145CrossRefGoogle Scholar
- 7.Esposito R, Ermondi G, Caron G (2009) J Comput Aided Mol Des 23(9):669CrossRefGoogle Scholar
- 8.Steinbeck C, Kuhn S (2004) Phytochemistry 65(19):2711CrossRefGoogle Scholar
- 9.Humphrey W, Dalke A, Schulten K (1996) J Mol Graph 14(1):33CrossRefGoogle Scholar
- 10.Miller MA (2002) Nat Rev Drug Discov 1(3):220CrossRefGoogle Scholar
- 11.Ermondi G, Cillis GI, Caron G (2007) J Incl Phenom Macrocycl Chem 57(1–4):355CrossRefGoogle Scholar
- 12.Garcia-Zubiri IX, Gonzalez-Gaitano G, Isasi JR (2007) J Incl Phenom Macrocycl Chem 57(1–4):265CrossRefGoogle Scholar
- 13.Zhou HW, Lai WP, Zhang ZQ, Li WK, Cheung HY (2009) J Comput Aided Mol Des 23(3):153CrossRefGoogle Scholar
- 14.Bikadi Z, Hazai E (2009) Journal of Cheminform 1(1):15CrossRefGoogle Scholar
- 15.Bikadi Z, Hazai I, Demko L, Hari P, Hazai E (2010) Lett Drug Des Discov 7(3):200CrossRefGoogle Scholar
- 16.Franco C, Schwingel L, Lula I, Sinisterra RD, Koester LS, Bassani VL (2009) Int J Pharm 369(1–2):5CrossRefGoogle Scholar