Super Natural II—a database of natural products

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.

High-Resolution Liquid Chromatography Tandem Mass Spectrometry Enables Large Scale Molecular Characterization of Dissolved Organic Matter

“…In order to loosely categorize "likely" and "unlikely" H/C and O/C ratios in DOM, we also mapped out the distributions of previously characterized metabolite formulas in Van Krevelen space using structures <500 Da from the Supernatural database (Banerjee et al, 2015). (Banerjee et al, 2015), which includes molecular formulas from more than 230,000 natural products.…”

“…(Banerjee et al, 2015), which includes molecular formulas from more than 230,000 natural products. The Supernatural Van Krevelen plot and density plots of H/C and O/C ratios are shown in Figures 3C,D.…”

“…The generated formulas were filtered by the following rules: N rule, O/C ratio ≤ 1, H/C ratio ≤ 4 and >0, element counts: C ≤ 100, H ≤ 200, O ≤ 80, N ≤ 10, S ≤ 2 modified from (Cortés-Francisco et al, 2014) and our inspection of ∼233.000 molecular formulas obtained from the supernatural structure database (Banerjee et al, 2015), and maximal mass error of 5 ppm. Resulting molecular formulas were scored by the method described by (Böcker et al, 2009) and the top1 hit was used for downstream statistical analysis.…”

Molecular similarity-based predictions of the Tox21 screening outcome

“…Although several molecular fingerprints, such as extended-connectivity, substructure-based or path-based fingerprints are standards in the chemoinformatics field and have been successfully applied to prediction tasks, the results are dependent on the data and none of the methods is able to clearly outperform the others (Duan et al, 2010). To avoid the choice of the wrong descriptor, the combination of (independent) fingerprints has been suggested (Duan et al, 2010) and several studies have successfully applied combinations of path-and substructure-based fingerprints (Drwal et al, 2014;Banerjee et al, 2015). As we report here, the combination of different fingerprint types has also been of advantage for the prediction of estrogen receptor ligands.…”

From covalent bonds to eco-physiological pharmacology of secondary plant metabolites

“…Supernatural [77] and other databases now lists approximately 326,000 naturally occurring bioactive molecules and their known metabolites [77,78] and have led to the concept of "Epimutation Computer-aided Drug Design" [79] and to a better understanding of the protein-protein interactions involved in diverse biological processes [80].…”