Abstract
Natural products play a significant role in drug discovery and development. Many topological pharmacophore patterns are common between natural products and commercial drugs. A better understanding of the specific physicochemical and structural features of natural products is important for corresponding drug development. Several encyclopedias of natural compounds have been composed, but the information remains scattered or not freely available. The first version of the Supernatural database containing ∼50 000 compounds was published in 2006 to face these challenges. Here we present a new, updated and expanded version of natural product database, Super Natural II (http://bioinformatics.charite.de/supernatural), comprising ∼326 000 molecules. It provides all corresponding 2D structures, the most important structural and physicochemical properties, the predicted toxicity class for ∼170 000 compounds and the vendor information for the vast majority of compounds. The new version allows a template-based search for similar compounds as well as a search for compound names, vendors, specific physical properties or any substructures. Super Natural II also provides information about the pathways associated with synthesis and degradation of the natural products, as well as their mechanism of action with respect to structurally similar drugs and their target proteins.
Highlights
Natural products (NPs) are classical starting points for drug discovery
A better understanding of the specific physicochemical and structural features of natural products is important for corresponding drug development
Super Natural II contains a lot of information for each compound, including NP class, predicted toxicity class, mechanism of action (MoA) and pathways information
Summary
Natural products (NPs) are classical starting points for drug discovery. All herbal-based medicines are derived from natural compounds [1]. Often macrocyclic NPs such as erythromycin, rapamycin, tacrolimus possess favorable drug-like physicochemical and pharmacokinetic properties like lipophilicity, metabolic stability, increased solubility and bioavailability [7] Such properties are important for protein–protein interaction targets [8]. Consumption of alphaamanitin, a toxic peptide produced by Amanita mushrooms [19], can lead to irreversible kidney and liver damage [20] This NP molecule is considered as one of the deadliest compounds known. Super Natural II is a freely available, web-based and easy to access database of NPs. Super Natural II contains a lot of information for each compound, including NP class, predicted toxicity class, mechanism of action (MoA) and pathways information. A comparison of Super Natural II to other NP databases is provided in Supplementary Table S1
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