CMAUP: a database of collective molecular activities of useful plants

Zeng, Xian; Zhang, Peng; Wang, Yali; Chu, Qing; Chen, Shangying; He, Weidong; Lin, Tao; Tan, Ying; Gao, Dan; Wang, Bohua; Chen, Zhe; Chen, Weiping; Jiang, Yu; Chen, Yu Zong

doi:10.1093/nar/gky965

Cited by 90 publications

(60 citation statements)

References 57 publications

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“…Collective Molecular Activities of Useful Plants (CMAUP) [79], a relatively new database, contains very extensive information on plants that are linked to human activities together with their chemical constituents, i.e. NPs.…”

Section: Natural Products By the Taxonomy Of The Synthesizing Organismmentioning

confidence: 99%

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

2020

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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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Section: Natural Products By the Taxonomy Of The Synthesizing Organismmentioning

confidence: 99%

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

2020

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“…With the advancement of information technology and bioinformatics, there is an increasing trend to build resources and databases that report herbal formulations, active components of the herb, and related information. There are several efforts like Chinese Medicine Integrated Database (TCMID) [183], Collective Molecular Activities of Useful Plants (CMAUP) [184], SymMap [185], encyclopedia of traditional Chinese medicine (ETCM) [186] etc. In addition, several researchers have developed strategies for in silico pharmacokinetic properties of molecules/drugs [187][188][189][190][191].…”

Section: Modern Trends In Traditional Medicine Informatics and Opportmentioning

confidence: 99%

Anticancer Plants: A Review of the Active Phytochemicals, Applications in Animal Models, and Regulatory Aspects

Khan

Ali

Khan³

et al. 2019

Biomolecules

263

118

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The rising burden of cancer worldwide calls for an alternative treatment solution. Herbal medicine provides a very feasible alternative to western medicine against cancer. This article reviews the selected plant species with active phytochemicals, the animal models used for these studies, and their regulatory aspects. This study is based on a meticulous literature review conducted through the search of relevant keywords in databases, Web of Science, Scopus, PubMed, and Google Scholar. Twenty plants were selected based on defined selection criteria for their potent anticancer compounds. The detailed analysis of the research studies revealed that plants play an indispensable role in fighting different cancers such as breast, stomach, oral, colon, lung, hepatic, cervical, and blood cancer cell lines. The in vitro studies showed cancer cell inhibition through DNA damage and activation of apoptosis-inducing enzymes by the secondary metabolites in the plant extracts. Studies that reported in vivo activities of these plants showed remarkable results in the inhibition of cancer in animal models. Further studies should be performed on exploring more plants, their active compounds, and the mechanism of anticancer actions for use as standard herbal medicine.

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“…To gain a better understanding of the bioactivity areas encompassed by each collection, we chose five examples related to drug molecules, metabolomes and natural product extracts. More specifically, we considered 6,505 approved and experimental drugs (REPO Hub) 11 , 8,603 endogenous human metabolites (HMDB) 12 , 6,355 metabolites found in other species beyond vertebrates (MetaboLights) 13 , 49,818 food constituents (FooDB; www.foodb.ca) and 6,502 plant chemicals (CMAUP) 14 . Figure 3b shows that, despite their variable depth of annotation ( Figure S9), these collections, for the most part, are laid out in high-α regions of the GSig space.…”

Section: Bioactivity-guided Navigation Of the Chemical Spacementioning

confidence: 99%

Bioactivity descriptors for uncharacterized compounds

Bertoni

Duran‐Frigola

Badia-i-Mompel

et al. 2020

Preprint

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Chemical descriptors encode the physicochemical and structural properties of small molecules, and they are at the core of chemoinformatics. The broad release of bioactivity data has prompted enriched representations of compounds, reaching beyond chemical structures and capturing their known biological properties. Unfortunately, ‘bioactivity descriptors’ are not available for most small molecules, which limits their applicability to a few thousand well characterized compounds. Here we present a collection of deep neural networks able to infer bioactivity signatures for any compound of interest, even when little or no experimental information is available for them. Our ‘signaturizers’ relate to bioactivities of 25 different types (including target profiles, cellular response and clinical outcomes) and can be used as drop-in replacements for chemical descriptors in day-to-day chemoinformatics tasks. Indeed, we illustrate how inferred bioactivity signatures are useful to navigate the chemical space in a biologically relevant manner, and unveil higher-order organization in drugs and natural product collections. Moreover, we implement a battery of signature-activity relationship (SigAR) models and show a substantial improvement in performance, with respect to chemistry-based classifiers, across a series of biophysics and physiology activity prediction benchmarks.

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CMAUP: a database of collective molecular activities of useful plants

Cited by 90 publications

References 57 publications

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

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

Anticancer Plants: A Review of the Active Phytochemicals, Applications in Animal Models, and Regulatory Aspects

Bioactivity descriptors for uncharacterized compounds

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