Abstract
Access to suitable databases is essential for the rapid dereplication (assessment of novelty) of crude extracts in natural product research. The efficiency of this dereplication process relies heavily on the interpretation of molecular mass, molecular formula, UV, and NMR spectral data. In this chapter, the availability and the suitability of the available databases for dereplication is critically examined. The chapter concludes with examples of dereplication strategy based on available natural product databases.
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Buckingham J (ed) (2011) Dictionary of natural products on DVD. Chapman & Hall/CRC, Boca Raton
CAS, www.cas.org. Accessed 18 Nov 2011
Reaxys, https://www.reaxys.com/info/. Accessed 18 Nov 2011
CAS Registry, www.cas.org/expertise/cascontent/registry/index.html. Accessed 18 Nov 2011
STN, http://www.stn-international.de/index.php?id=123. Accessed 18 Nov 2011
SciFinder, http://www.cas.org/products/scifindr/. Accessed 18 Nov 2011
ChemNetBase, http://www.chemnetbase.com/. Accessed 18 Nov 2011
Blunt JW, Munro MHG (eds) (2008) Dictionary of marine natural products. Chapman & Hall/CRC, Boca Raton
Jaspars M (2008) Underwater chemistry. Chem World 5(Jan). http://www.rsc.org/chemistryworld/Issues/2008/January/Reviews.asp. Accessed 18 Nov 2011
AntiBase, http://www.wiley-vch.de/publish/dt/books/forthcomingTitles/LS00/3-527-32827-0/?sID=fdd57124490d0f87cfd550f72e2684d5. Accessed 18 Nov 2011
SpecInfo, http://cds.dl.ac.uk/cds/datasets/spec/specinfo/specinfo.html. Accessed 18 Nov 2011
MarinLit, http://www.chem.canterbury.ac.nz/marinlit/marinlit.shtml. Accessed 18 Nov 2011
ACD/Labs, http://www.acdlabs.com. Accessed 18 Nov 2011
AntiMarin: a combination database formed from AntiBase and MarinLit. http://www.wiley-vch.de/publish/dt/books/forthcomingTitles/LS00/3-527-32827-0/?sID=fdd57124490d0f87cfd550f72e2684d5 and http://www.chem.canterbury.ac.nz/marinlit/marinlit.shtml. Accessed 18 Nov 2011
http://depth-first.com/articles/2011/10/12/sixty-four-free-chemistry-databases/. Accessed 18 Nov 2011
Williams AJ (2008) Public chemical compound databases. Current Opin Drug Discov Develop 11:393–404
PubChem, http://pubchem.ncbi.nlm.nih.gov/. Accessed 18 Nov 2011
CSLS, http://cactus.nci.nih.gov/lookup/. Accessed 18 Nov 2011
ChemSpider, http://www.chemspider.com/. Accessed 18 Nov 2011
NaprAlert, http://www.napralert.org/. Accessed 18 Nov 2011
Perry NB, Ettouati L, Litaudon M et al (1994) Alkaloids from the Antarctic sponge Kirkpatrickia varialosa Part 1: Variolin B, a new antitumor and antiviral compound. Tetrahedron 50:3987–3892
Nielsen KF, Smedsgaard J (2003) Fungal metabolite screening: database of 474 mycotoxins and fungal metabolites for dereplication by standardized liquid chromatography-UV-mass spectrometry methodology. J Chrom A 1002:111–136
Dumdei EJ, Blunt JW, Munro MHG et al (1997) Isolation of the calyculins, calyculinamides and swinholide H from the New Zealand deep water sponge Lamellomorpha strongylata. J Org Chem 62:2636–2639
The Marine Group, University of Canterbury’s UV data was acquired on a Dionex HPLC using Chromeleon software. The library of known compounds is available on application to murray.munro@canterbury.ac.nz or john.blunt@canterbury.ac.nz
NMR Shift DB, http://nmrshiftdb.nmr.uni-koeln.de/. Accessed 18 Nov 2011
Naproc-13, http://c13.usal.es/c13/usuario/views/inicio.jsp?lang=en&country=EN. Accessed 18 Nov 2011
SuperNatural, http://bioinformatics.charite.de/supernatural/. Accessed 18 Nov 2011
SDBS (Spectral Database for Organic Compounds), http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_index.cgi?lang=eng. Accessed 18 Nov 2011
Wellington KD, Cambie RC, Rutledge PS et al (2000) Chemistry of sponges 19. Novel bioactive metabolites from Hamigera taragensis. J Nat Prod 63:79–85
Davis RA, Aalbersberg W, Meo S et al (2002) The isolation and synthesis of polyandrocarpamines A and B. Two new 2-aminoimidazolone compounds from the Fijian ascidian, Polyandrocarpa sp. Tetrahedron 58:3263–3269
MacLean WJ (2005) Unpublished results. PhD thesis. University of Canterbury, Christchurch
Suzuki K, Kuwahara A, Nishikiori T et al (1997) NF00659A1, A2, A3, B1 and B2, novel antitumor antibiotics produced by Aspergillus sp. NF 00659. II. Structural elucidation. J Antibiot 50:318–324
Sun Lin (2009) Unpublished work. PhD thesis. University of Canterbury, Christchurch
Wright AD, Goclik E, Konig GM (2003) Oxygenated analogues of gorgosterol and ergosterol from the soft coral Capnella lacertiliensis. J Nat Prod 66:157–160
See for example http://www.bruker-biospin.com/cryoprobes.html, or http://www.varianinc.com/cgi-bin/nav?products/nmr/probes/liquids/cold_probes/index&cid=LNMJOLHKFI. Accessed 18 Nov 2011
http://www.protasis.com/OMNMR/index.htm. Accessed 18 Nov 2011
Lang G, Mayhudin NA, Mitova MI et al (2008) Evolving trends in the dereplication of natural product extracts: new methodology for rapid, small-scale investigation of natural product extracts. J Nat Prod 71:1595–1599
Mitova MI, Murphy AC, Lang G et al (2008) Evolving trends in the dereplication of natural product extracts. 2. The isolation of chrysaibol, an antibiotic peptaibol from a New Zealand sample of the mycoparasitic fungus Sepedonium chrysospermum. J Nat Prod 71:1600–1603
Coreley DG, Durley RC (1994) Strategies for database dereplication of natural products. J Nat Prod 57:1484–1490
GVK Biosciences Natural Product DB, http://www.gvkbio.com/db_products.html. Accessed 18 Nov 2011
Lei J, Zhou J (2002) A marine natural product database. J Chem Info Comput Sci 42:742–748
Bitzer J, Kopcke B, Stadler M et al (2007) Accelerated dereplication of natural products, supported by reference libraries. Chimia 61:332–338
Moss S, Bovermann G, Denay R et al (2007) Efficient structure elucidation of natural products in the pharmaceutical industry. Chimia 61:346–349
The National Centre for Plant and Microbial Metabolomics, http://www.metabolomics.bbsrc.ac.uk/currentactivities.htm. Accessed 18 Nov 2011
CH-NMR-NP, http://www.las.jp/english/software/chnmrnp.html. Accessed 18 Nov 2011
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Blunt, J., Munro, M., Upjohn, M. (2012). The Role of Databases in Marine Natural Products Research. In: Fattorusso, E., Gerwick, W., Taglialatela-Scafati, O. (eds) Handbook of Marine Natural Products. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-3834-0_6
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DOI: https://doi.org/10.1007/978-90-481-3834-0_6
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