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

  • Nucleic Acids Res. 2018 Jan 4;46(D1):D1217-D1222. doi: 10.1093/nar/gkx1026.
Xian Zeng  1  2 ,  Peng Zhang  2 ,  Weidong He  2 ,  Chu Qin  2 ,  Shangying Chen  2 ,  Lin Tao  2  3 ,  Yali Wang  2 ,  Ying Tan  1 ,  Dan Gao  1 ,  Bohua Wang  4  5 ,  Zhe Chen  3 ,  Weiping Chen  4 ,  Yu Yang Jiang  1 ,  Yu Zong Chen  1  2
Affiliations
  • 1. Breeding Base-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen, Tsinghua University, Shenzhen Kivita Innovative Drug Discovery Institute, Shenzhen 518055, PR China.
  • 2. Bioinformatics and Drug Design group, Department of Pharmacy, National University of Singapore, Singapore 117543, Singapore.
  • 3. Zhejiang Key Laboratory of Gastro-intestinal Pathophysiology, Zhejiang Hospital of Traditional Chinese Medicine, Zhejiang Chinese Medical University, School of Medicine, Hangzhou Normal University, Hangzhou 310006, RP China.
  • 4. Key Lab of Agricultural Products Processing and Quality Control of Nanchang City, Jiangxi Agricultural University, Nanchang 330045, PR China.
  • 5. College of Life and Environmental Sciences, Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Hunan University of Arts and Science, Changde, Hunan 415000, PR China.
PMID: 29106619 DOI: 10.1093/nar/gkx1026
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.