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. 2013 Jan;41(Database issue):D1130-6.
doi: 10.1093/nar/gks1253. Epub 2012 Nov 28.

StreptomeDB: A Resource for Natural Compounds Isolated From Streptomyces Species

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Free PMC article

StreptomeDB: A Resource for Natural Compounds Isolated From Streptomyces Species

Xavier Lucas et al. Nucleic Acids Res. .
Free PMC article

Abstract

Bacteria from the genus Streptomyces are very important for the production of natural bioactive compounds such as antibiotic, antitumour or immunosuppressant drugs. Around two-thirds of all known natural antibiotics are produced by these bacteria. An enormous quantity of crucial data related to this genus has been generated and published, but so far no freely available and comprehensive database exists. Here, we present StreptomeDB (http://www.pharmaceutical-bioinformatics.de/streptomedb/). To the best of our knowledge, this is the largest database of natural products isolated from Streptomyces. It contains >2400 unique and diverse compounds from >1900 different Streptomyces strains and substrains. In addition to names and molecular structures of the compounds, information about source organisms, references, biological role, activities and synthesis routes (e.g. polyketide synthase derived and non-ribosomal peptides derived) is included. Data can be accessed through queries on compound names, chemical structures or organisms. Extraction from the literature was performed through automatic text mining of thousands of articles from PubMed, followed by manual curation. All annotated compound structures can be downloaded from the website and applied for in silico screenings for identifying new active molecules with undiscovered properties.

Figures

Figure 1.
Figure 1.
Examples of NPs produced by Streptomyces spp. included in StreptomeDB. (a) Enduracidin A, NRPS-derived antibiotic; (b) daunorubicin, antitumour anthracycline; (c) oxytetracycline, tetracycline antibiotic; (d) bleomycin, NRPS/PKS-derived anticancer; (e) geldanamycin, macro-cyclic Hsp90 inhibitor; (f) epothilone B, anticancer macro-cycle; (g) fredericamycin A, C-5 spirocyclic DNA-polymerase inhibitor; (h) chloramphenicol, broad-spectrum antibiotic; (i) tacrolimus, macro-cyclic immunosuppressive; (j) fosfomycin, broad-spectrum antibiotic; (k) geranylphenazinediol, acetyl-CoA inhibitor; (l) actinomycin, NRPS/PKS-derived antineoplastic agent and (m) daptomycin, NRPS-derived antibiotic.
Figure 2.
Figure 2.
MCSS panel in StreptomeDB, featuring the most common cyclic structures included in the database.
Figure 3.
Figure 3.
Workflow of a substructure search for arizidine-containing compounds in StreptomeDB.

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