https://orcid.org/0000-0002-9413-619X
Abstract
Compound databases (DBs) are essential tools for drug discovery. The number of DBs in public domain is increasing, so it is important to analyze these DBs. In this article, the main characteristics of 64 DBs will be presented. The methodological strategy used was a literature search. To analyze the characteristics obtained in the review, the DBs were categorized into two subsections: Open Access and Commercial DBs. Open access includes generalist DBs (containing compounds of diverse origins), DBs with specific applicability, DBs exclusive to natural products and those containing compounds with specific pharmacological action. The literature review showed that there are challenges to making these repositories available, such as standardizing information curation practices and funding to maintain and sustain them.
GRAPHICAL ABSTRACT
Background
Compound databases (DBs) are crucial tools in the development of multidisciplinary research fields, such as drug discovery. The number of DBs of public domain compounds is increasing, however the process of building and curating these libraries is critical as the data must be diverse and reliable to enable safe trials. Therefore, it is of outmost importance the assembly and analysis of compound DBs regarding their structure and the legitimacy of the structures. In this article, an overview of the compound DBs is presented in order to assess and analyze their constitutional characteristics, the curation strategies and the contributions to the screening of new drugs, as well as other research areas.
Methodology
As a methodological strategy, a comprehensive bibliographic search was carried out to extract relevant DBs of compounds.
Results & discussion
34 articles containing diverse information about 64 DBs were manually selected. Most of these DBs were developed mainly in the period 2006–2010 in China, built by universities and research institutes, for the most part. These DB have various purposes, from repositories of curated 3D structures to DBs with applicability in the research and development of new drugs for specific diseases which collects potential bioactive compounds with antiviral action. Most of the DBs are open access, favoring the reach of thousands of users and the information contained in the researched DBs, were manually extracted from the literature, undergo largely curatorial processes and comprise a diversity of information related to physicochemical properties, spectral data, chemical space configuration, in silico prediction studies, in vitro assays and bioactivity. It was also found that several DBs incorporate chemoinformatics tools to query, mine and analyze the contents of the library.
Conclusion
In this article an overview of the DBs of compounds was presented in order to assess and analyze their constitutional characteristics, the curation strategies and the contributions to the screening of new drugs, as well as other research areas. This literature review has also shown that there are still challenges in making these repositories available, such as standardizing procedures for curating information and materials, and attracting funding and researchers to maintain and sustain them.
Supplemental material
Supplemental data for this article can be accessed at https://doi.org/10.1080/17568919.2024.2342203
Acknowledgments
Please refer to the Author Disclosure Form regarding inclusion of individuals in the author list, versus acknowledging their contributions in this section.
Author contributions
All the authors participated in writing and revision of the manuscript; DQ de Azevedo, BM Campioni and FA Pedroz Lima participated actively in the systematic revision process and preparing of figures and tables; JL Medina-Franco, RO Castilho and VG Maltarollo carried out the experimental design and supervision of the revision process. For more information, please see the Author Disclosure Form.
Financial disclosure
This research was funded by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq – 303757/2019-1), CAPES foundation, grant numbers 88887.595578/2020-00; 88887.684031/2022-00; 311875/2022-0; 88887.636342/2021-00 and 88887.696385/2022-00, R21AI171824, UFMG and Pró-Reitoria de Pós-Graduação da UFMG (PRPG) for intramural funding. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.
Competing interests disclosure
The authors have no competing interests or relevant affiliations with any organization or entity with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.
Writing disclosure
No writing assistance was utilized in the production of this manuscript.