PSC-db: A Structured and Searchable 3D-Database for Plant Secondary Compounds

Abstract

Plants synthesize a large number of natural products, many of which are bioactive and have practical values as well as commercial potential. To explore this vast structural diversity, we present PSC-db, a unique plant metabolite database aimed to categorize the diverse phytochemical space by providing 3D-structural information along with physicochemical and pharmaceutical properties of the most relevant natural products. PSC-db may be utilized, for example, in qualitative estimation of biological activities (Quantitative Structure-Activity Relationship, QSAR) or massive docking campaigns to identify new bioactive compounds, as well as potential binding sites in target proteins. PSC-db has been implemented using the open-source PostgreSQL database platform where all compounds with their complementary and calculated information (classification, redundant names, unique IDs, physicochemical properties, etc.) were hierarchically organized. The source organism for each compound, as well as its biological activities against protein targets, cell lines and different organism were also included. PSC-db is freely available for public use and is hosted at the Universidad de Talca.

Keywords: 3D-structures; chemical and structural properties; database; natural products; physicochemical and pharmaceutical descriptors; plant secondary metabolites.

Figure 1

PSC-db search function. Users can search by the phytochemical compounds’ classification (A), by structural similarity (B), and by the following filters: compound ID, name, molecular formula, molecular weight range, source organism (species) and biological target (C).

Figure 2

Selection of multiple compounds using two different searching tools (red arrows). For each phytochemical compound the PSC-db ID is given, as well as the names, chemical formula, molecular weight, and CAS number (right panel). More detailed information is available through the “eye” and “list” buttons (blue arrows).

Figure 3

PSC statistics based on the calculated physicochemical and pharmaceutical properties. Statistics for the molecular weight (A) and the correlation between the molecular weight and the lipophilicity (B) of 716 selected alkaloids are shown.