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.

Figure 1.

Super Natural II database search options. The compound search (blue arrow) enable search via compound name, supplier, molecular weight, logP, hydrogen-bond donor and acceptor, classifications, toxicity class as well as compounds that are purchasable. Template search (green arrow) allows searching via a pre-defined template. MoA search (purple arrow) can be performed for a molecule structure or a target name; clusters (orange arrow) can be searched via name, SNID (unique identifier for the Super Natural II database), IUPAC name or SMILES. All search results contain information about physicochemical properties, toxicity class, vendor and pathway. Cluster results are displayed using heat maps and related similarity values for compounds of the cluster. Pathway information (red arrow) can be obtained for specific species and pathway. Additionally, the molecule structure is shown.