Journal:SistematX, an online web-based cheminformatics tool for data management of secondary metabolites

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Full article title SistematX, an online web-based cheminformatics tool for data management of secondary metabolites
Journal Molecules
Author(s) Scotti, Marcus T.; Herrera-Acevedo, Chonny; Oliveira, Tiago B.; Costa, Renan P.O.; de Oliveira Santos, Silas Y.K.;
Rodrigues, Ricardo P.; Scotti, Luciana; Da-Costa, Fernando B.
Author affiliation(s) Federal University of Paraíba, Federal University of Sergipe, University of São Paulo
Primary contact Phone: +55-83-99869-0415
Year published 2018
Volume and issue 23(1)
Page(s) 103
DOI 10.3390/molecules23010103
ISSN 1420-3049
Distribution license Creative Commons Attribution 4.0 International
Download (PDF)


The traditional work of a natural products researcher consists in large part of time-consuming experimental work, collecting biota to prepare, extracts to analyze, and innovative metabolites to identify. However, along this long scientific path, much information is lost or restricted to a specific niche. The large amounts of data already produced and the science of metabolomics reveal new questions: Are these compounds known or new? How fast can this information be obtained? To answer these and other relevant questions, an appropriate procedure to correctly store information on the data retrieved from the discovered metabolites is necessary. The SistematX ( interface is implemented considering the following aspects: (a) the ability to search by structure, SMILES (Simplified Molecular-Input Line-Entry System) code, compound name, and species; (b) the ability to save chemical structures found by searching; (c) the ability to display compound data results, including important characteristics for natural products chemistry; and (d) the user's ability to find specific information for taxonomic rank (from family to species) of the plant from which the compound was isolated, the searched-for molecule, and the bibliographic reference and Global Positioning System (GPS) coordinates. The SistematX homepage allows the user to log into the data management area using a login name and password and gain access to administration pages. In this article, we introduce a modern and innovative web interface for the management of a secondary metabolite database. With its multi-platform design, it is able to be properly consulted via the internet and managed from any accredited computer. The interface provided by SistematX contains a wealth of useful information for the scientific community about natural products, highlighting the locations of species from which compounds are isolated.

Keywords: SistematX, secondary metabolites, data management, online web-based tool


The traditional work of a natural products researcher can be summarized as the collection of biological samples, preparation of extracts for biological screening or bioassay-guided fractionation, and isolation and purification of (bioactive or not) compounds. However, the first question that may arise is the following: are these compounds known or new? In addition, metabolomics studies have introduced a new question: how fast can this information be obtained?[1]

The stage of dereplication, a process known as the rapid characterization of previously known compounds in mixtures without their prior purification, has become a strategically important area for natural products research involved in screening programs in several commercial and non-commercial databases.[2][3][4] These databases can be searched with minimal information, such as structural chemical and biological data from compounds; however, dereplication now requires additional information, such as biogeographical and taxonomic information, or the presence of a certain compound (new or known) in other individuals of the same species, genus, subfamily, and family. This information can also help to reduce the number of hits during chemical identification by dereplication.

Large structure-based data collections, such as ChemSpider[5], PubChem[6], ChEBI[7], and ZINC[8] can be used for this purpose.[9][10] However, these databases are not specialized in secondary metabolite information that is valuable to the natural products researchers, for example, botanical occurrence and geographical localization. For this reason, a number of specialized natural products databases were developed that are commercially or freely available and only contain restricted information, for example, the Dictionary of Natural Products (DNP)[11], NAPRALERT[12], Marinlit for marine natural products[13], and Antibase for microorganisms and higher fungi materials. Nevertheless, none of these provide structural collections in a format that can be rapidly integrated into software such as ACD/Structure Elucidator and others.[9]

Other natural products databases provide natural products extracted from various resources and contain various associated information such as toxicity prediction, but so far, little or nothing is known about these resources, for example, SUPER NATURAL II.[14] Natural products databases exhibit a huge range of structural complexity and thus are expected to contribute to the ability of such databases to provide positive hits.[2][15] These structures are available in regional databases, for example, NUBBEdb [16], SANCDB [17], TM-CM [18], TCM-Database@Taiwan [19], NANPDB [20], and TCMID [21]. Many have been used in virtual screening research studies. In addition to the database information described above that uses two-dimensional (2D) structures, several databases have selected methods and tools for generating three-dimensional (3D) structures of small organic molecules, often for use in structure-based drug design.


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This presentation is faithful to the original, with only a few minor changes to presentation. In some cases important information was missing from the references, and that information was added.