NPASS: natural product activity and species source database for natural product research, discovery and tool development

Abstract

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.

Virtual Screening of Natural Products against Type II Transmembrane Serine Protease (TMPRSS2), the Priming Agent of Coronavirus 2 (SARS-CoV-2)

“…Natural Product Activity and Species Source (NPASS) is a freely accessible database containing 30,927 natural compounds classified into 18 different superclasses, which include alkaloids and derivatives, lipids and lipid-like molecules, benzenoids, lignans, neolignans and associated compounds, and so on [32]. These natural products are found in the kingdom or super-kingdom of bacteria (6.7%), fungi (7.9%), metazoan (9.4%), and viridiplantae (67.8%) from 6814 genera.…”

“…The binding site residues were also altered significantly in the mutant. Other top-ranked drug-like compounds, potential inhibitor of TMPRSS2 [32], were the marine natural product excavatolide M (compound 2), a briarane-type diterpene, the cembranolide durumolide K (compound 6), predicted as toxic, the dibenzylcyclooctadiene lignan schisphenin A (compound 3) from Shisandra sphenanthera, the fungal decalactone dictyosphaeric acid A, obtained from the green alga Dictyosphaeria versluyii, with antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus faecium, and Candida albicans [38]. (compound 4), the endogenous cytidine (5 )-diphosphocholine, known as citicoline, (compound 5), with beneficial effects in transient global and focal cerebral ischemia [39], 5-methoxyhydnocarpin (compound 7), a Berberis species flavonolignan similar to silymarin and reported as a strong inhibitor of the NorA pump (an endogenous efflux transporter of S. aureus in the plasma membrane [40]), compound 8 from the free-floating algae known as Sargassum, the p-terphenyl antioxidant curtisian L (compound 9) from the wild mushroom Paxillus, microcarpin (compound 10), a bianthraquinone from Asphodelus microcarpus, the green tea polyphenol (-)-epicatechin 3-O-(3 -O-methyl) gallate (EGCG3"Me) (compound 11), and the aromatase inhibitor isogemichalcone B (compound 12), mainly from Artocarpus and Broussonetia genera.…”

“…We screened the Natural Product Activity and Species Source database (NPASS, available at http://bidd2.nus.edu.sg/NPASS) which contains 30,927 compounds [32]. Pharmacophore-and molecular docking-based screening were performed, using the MOE software.…”

Review on natural products databases: where to find data in 2020

“…The Natural Product Activity and Species Source Database (NPASS) [70] contains over 30,000 NPs from plants, bacteria, fungi and animals and is developed and maintained at the National University of Singapore. This database was created to provide a reliable source for highly curated NPs with structures, experimental activity values and the organisms that synthesize them.…”

A survey of web resources and tools for the study of TCM network pharmacology

“…The NPASS (the Natural Product Activity and Species Source Database) [32] provides detailed information of species sources and biological activities of natural products. This database contains 35,032 unique natural products (compounds) isolated from 25,041 source organisms, including 16,581 plant species, 1,675 bacteria species, 2,503 metazoa species and 2,107 fungi species.…”