Review on Natural Products Databases: Where to Find Data in 2020

Overview

Journal J Cheminform

Publisher Biomed Central

Specialty Chemistry

Date 2021 Jan 12

PMID 33431011

Citations 131

Authors

Maria Sorokina

Christoph Steinbeck

Affiliations

Soon will be listed here.

Abstract

Natural products (NPs) have been the centre of attention of the scientific community in the last decencies and the interest around them continues to grow incessantly. As a consequence, in the last 20 years, there was a rapid multiplication of various databases and collections as generalistic or thematic resources for NP information. In this review, we establish a complete overview of these resources, and the numbers are overwhelming: over 120 different NP databases and collections were published and re-used since 2000. 98 of them are still somehow accessible and only 50 are open access. The latter include not only databases but also big collections of NPs published as supplementary material in scientific publications and collections that were backed up in the ZINC database for commercially-available compounds. Some databases, even published relatively recently are already not accessible anymore, which leads to a dramatic loss of data on NPs. The data sources are presented in this manuscript, together with the comparison of the content of open ones. With this review, we also compiled the open-access natural compounds in one single dataset a COlleCtion of Open NatUral producTs (COCONUT), which is available on Zenodo and contains structures and sparse annotations for over 400,000 non-redundant NPs, which makes it the biggest open collection of NPs available to this date.

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References

Xu J, Yang Y . Traditional Chinese medicine in the Chinese health care system. Health Policy. 2008; 90(2-3):133-9. PMC: 7114631. DOI: 10.1016/j.healthpol.2008.09.003. View

Blunt J, Carroll A, Copp B, Davis R, Keyzers R, Prinsep M . Marine natural products. Nat Prod Rep. 2018; 35(1):8-53. DOI: 10.1039/c7np00052a. View

Boonen J, Bronselaer A, Nielandt J, Veryser L, De Tre G, De Spiegeleer B . Alkamid database: Chemistry, occurrence and functionality of plant N-alkylamides. J Ethnopharmacol. 2012; 142(3):563-90. DOI: 10.1016/j.jep.2012.05.038. View

Altman T, Travers M, Kothari A, Caspi R, Karp P . A systematic comparison of the MetaCyc and KEGG pathway databases. BMC Bioinformatics. 2013; 14:112. PMC: 3665663. DOI: 10.1186/1471-2105-14-112. View

Guijas C, Montenegro-Burke J, Domingo-Almenara X, Palermo A, Warth B, Hermann G . METLIN: A Technology Platform for Identifying Knowns and Unknowns. Anal Chem. 2018; 90(5):3156-3164. PMC: 5933435. DOI: 10.1021/acs.analchem.7b04424. View

Tung C, Lin Y, Chang H, Wang C, Chen I, Jheng J . TIPdb-3D: the three-dimensional structure database of phytochemicals from Taiwan indigenous plants. Database (Oxford). 2014; 2014. PMC: 4057645. DOI: 10.1093/database/bau055. View

Seiler K, Kuehn H, Pat Happ M, DeCaprio D, Clemons P . Using ChemBank to probe chemical biology. Curr Protoc Bioinformatics. 2008; Chapter 14:14.5.1-14.5.26. DOI: 10.1002/0471250953.bi1405s22. View

Potshangbam A, Polavarapu R, Rathore R, Naresh D, Prabhu N, Potshangbam N . MedPServer: A database for identification of therapeutic targets and novel leads pertaining to natural products. Chem Biol Drug Des. 2018; 93(4):438-446. DOI: 10.1111/cbdd.13430. View

Qiao X, Hou T, Zhang W, Guo S, Xu X . A 3D structure database of components from Chinese traditional medicinal herbs. J Chem Inf Comput Sci. 2002; 42(3):481-9. DOI: 10.1021/ci010113h. View

10.

Newman D, Cragg G . Natural Products as Sources of New Drugs from 1981 to 2014. J Nat Prod. 2016; 79(3):629-61. DOI: 10.1021/acs.jnatprod.5b01055. View

11.

He Q, He Q, Deng X, Yao L, Meng E, Liu Z . ATDB: a uni-database platform for animal toxins. Nucleic Acids Res. 2007; 36(Database issue):D293-7. PMC: 2238984. DOI: 10.1093/nar/gkm832. View

12.

Kang H, Tang K, Liu Q, Sun Y, Huang Q, Zhu R . HIM-herbal ingredients in-vivo metabolism database. J Cheminform. 2013; 5(1):28. PMC: 3679852. DOI: 10.1186/1758-2946-5-28. View

13.

Rothwell J, Perez-Jimenez J, Neveu V, Medina-Remon A, Mhiri N, Garcia-Lobato P . Phenol-Explorer 3.0: a major update of the Phenol-Explorer database to incorporate data on the effects of food processing on polyphenol content. Database (Oxford). 2013; 2013:bat070. PMC: 3792339. DOI: 10.1093/database/bat070. View

14.

Yue Y, Chu G, Liu X, Tang X, Wang W, Liu G . TMDB: a literature-curated database for small molecular compounds found from tea. BMC Plant Biol. 2014; 14:243. PMC: 4172869. DOI: 10.1186/s12870-014-0243-1. View

15.

Amoa Onguene P, Ntie-Kang F, Mbah J, Lifongo L, Ndom J, Sippl W . The potential of anti-malarial compounds derived from African medicinal plants, part III: an in silico evaluation of drug metabolism and pharmacokinetics profiling. Org Med Chem Lett. 2015; 4(1):6. PMC: 4970435. DOI: 10.1186/s13588-014-0006-x. View

16.

Meetei P, Singh P, Nongdam P, Prabhu N, Rathore R, Vindal V . NeMedPlant: a database of therapeutic applications and chemical constituents of medicinal plants from north-east region of India. Bioinformation. 2012; 8(4):209-11. PMC: 3302005. DOI: 10.6026/97320630008209. View

17.

Chang K, Tsai T, Chen K, Yang S, Huang H, Chang T . iSMART: an integrated cloud computing web server for traditional Chinese medicine for online virtual screening, de novo evolution and drug design. J Biomol Struct Dyn. 2011; 29(1):243-50. DOI: 10.1080/073911011010524988. View

18.

Pilon-Jimenez B, Saldivar-Gonzalez F, Diaz-Eufracio B, Medina-Franco J . BIOFACQUIM: A Mexican Compound Database of Natural Products. Biomolecules. 2019; 9(1). PMC: 6358837. DOI: 10.3390/biom9010031. View

19.

Williamson A, Ylioja P, Robertson M, Antonova-Koch Y, Avery V, Baell J . Open Source Drug Discovery: Highly Potent Antimalarial Compounds Derived from the Tres Cantos Arylpyrroles. ACS Cent Sci. 2016; 2(10):687-701. PMC: 5084075. DOI: 10.1021/acscentsci.6b00086. View

20.

Pereira F, Aires-de-Sousa J . Computational Methodologies in the Exploration of Marine Natural Product Leads. Mar Drugs. 2018; 16(7). PMC: 6070892. DOI: 10.3390/md16070236. View