CMNPD: a comprehensive marine natural products database towards facilitating drug discovery from the ocean

Abstract

Marine organisms are expected to be an important source of inspiration for drug discovery after terrestrial plants and microorganisms. Despite the remarkable progress in the field of marine natural products (MNPs) chemistry, there are only a few open access databases dedicated to MNPs research. To meet the growing demand for mining and sharing for MNPs-related data resources, we developed CMNPD, a comprehensive marine natural products database based on manually curated data. CMNPD currently contains more than 31 000 chemical entities with various physicochemical and pharmacokinetic properties, standardized biological activity data, systematic taxonomy and geographical distribution of source organisms, and detailed literature citations. It is an integrated platform for structure dereplication (assessment of novelty) of (marine) natural products, discovery of lead compounds, data mining of structure-activity relationships and investigation of chemical ecology. Access is available through a user-friendly web interface at https://www.cmnpd.org. We are committed to providing a free data sharing platform for not only professional MNPs researchers but also the broader scientific community to facilitate drug discovery from the ocean.

Figure 1.

Schematic overview of the CMNPD content. (A) Phylogenetic tree of marine organisms. Core nodes include domains, kingdoms, phyla, classes, orders and families. Internal nodes include their corresponding superior and subordinate taxonomic units, which are based on the NCBI Taxonomy database (38). The bar chart shows the number of compounds in each family. This figure was produced using the Interactive Tree Of Life (iTOL) web server (39). (B) Knowledge graph of the chemical entity.

Figure 2.

Data query in the web interface. (A) Free-text quick search. Users can retrieve a list of entities matching a selected keyword (e.g. all organisms matching ‘spongia’) or go directly to a report card page for a selected entry (e.g. organism Demospongiae: CMNPD330032). (B) Advanced search. Query conditions are combined with Boolean operators. The inner Boolean operation of the grouped conditions is executed first, and then the outer Boolean operations are performed in order from top to bottom. (C) Search result of the keyword ‘spongia’. Users can further select the entries through the interactive filters on the left.

Figure 3.

Data visualizations. (A) Sunburst chart showing different hierarchies of organism taxonomy. The classification is arranged in concentric circles, and from inside to outside are kingdoms, phyla, classes, orders, families, genera and species. Users can click a section to expand the hierarchy and the corresponding entries can be retrieved using the button below the chart. (B) Dot distribution map showing the collection sites of organisms (e.g. sponges). Users can click the dot on the map to retrieve the compounds discovered in the corresponding area. (C) Network showing the relationship between organisms, compounds and targets. Users can click any node to enter the report card page of the corresponding entry.