Database Commons

a catalog of worldwide biological databases

Bioactive natural products (NPs) are valuable sources for biomedical and various applications. Comprehensive information on their species sources and quantitative properties (including compositions, bioactivities, and toxicities) is of great utility to the research community. Here, we introduced NPASS 3.0 with major updates to significantly expand the previous version and add new data derived from emerging technologies. Firstly, we manually curated new records from 1822 publications to provide: (i) an additional 87 507 quantitative composition records for 4873 NPs in 1030 species and (ii) 878 NPs produced by 341 symbiont organisms and 164 elicitor-responsive organisms, together with an additional 109 engineered organisms and 43 co-culture organisms. Secondly, 34 975 new quantitative toxicity records for 3662 NPs and 9713 quantitative ADME records for 744 NPs. Thirdly, this update substantially increased the records of NPASS, with 9.37%-206.30% data expansion over NPASS 2.0. Currently, NPASS includes 204 023 NPs, 48 940 organisms, 8764 targets, 1 048 756 experimental activity records, 34 975 toxicity records, 9713 quantitative ADME records, 208 415 NP composition records, and 1 117 269 organism-NP pairs. Furthermore, bioactivities were grouped into three classes for better serving pharmaceutical research. We also updated the NPASS web interface, which includes an enhanced search option and a submission page for crowdsourcing curation. NPASS 3.0 is accessible at https://bidd.group/NPASS/index.php.

There has been renewed interests in the exploration of natural products (NPs) for drug discovery, and continuous investigations of the therapeutic claims and mechanisms of traditional and herbal medicines. In-silico methods have been employed for facilitating these studies. These studies and the optimization of in-silico algorithms for NP applications can be facilitated by the quantitative activity and species source data of the NPs. A number of databases collectively provide the structural and other information of ?470 000 NPs, including qualitative activity information for many NPs, but only ?4000 NPs are with the experimental activity values. There is a need for the activity and species source data of more NPs. We therefore developed a new database, NPASS (Natural Product Activity and Species Source) to complement other databases by providing the experimental activity values and species sources of 35 032 NPs from 25 041 species targeting 5863 targets (2946 proteins, 1352 microbial species and 1227 cell-lines). NPASS contains 446 552 quantitative activity records (e.g. IC50, Ki, EC50, GI50 or MIC mainly in units of nM) of 222 092 NP-target pairs and 288 002 NP-species pairs. NPASS, http://bidd2.nus.edu.sg/NPASS/, is freely accessible with its contents searchable by keywords, physicochemical property range, structural similarity, species and target search facilities.