Current status and prospects of computational resources for natural product dereplication: a review

Mohamed, Ahmed; Nguyen, Canh Hao; Mamitsuka, Hiroshi

doi:10.1093/bib/bbv042

Cited by 43 publications

(49 citation statements)

References 150 publications

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“…In order to isolate novel products from MT, particularly those with potential bioactivity, it is important to firstly perform a dereplication process ( 54 ), distinguishing the novel compounds from previously reported compounds. Techniques capable of quickly and accurately identifying previously isolated compounds are therefore of great value.…”

Section: Isolation and Structural Characterization Of Compounds From mentioning

confidence: 99%

The Antitumor Activities of Marsdenia tenacissima

et al. 2018

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Marsdenia tenacissima (MT), a traditional Chinese herbal medicine, has long been used for thousands of years to treat asthma, tracheitis, rheumatism, etc. An increasing number of recent studies have focused on the antitumor effects of MT. The effects of MT on cancer are the result of various activated signaling pathways and inhibiting factors and the high expression levels of regulatory proteins. MT can inhibit different cancer types including non-small cell lung cancer (NSCLC), malignant tumors, hepatic carcinoma, and so on. This article mainly focuses on the activities and mechanisms of MT. In addition, the efficacy and toxicity of MT are also discussed. Further studies of MT are required for improved medicinal utilization.

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Section: Isolation and Structural Characterization Of Compounds From mentioning

confidence: 99%

The Antitumor Activities of Marsdenia tenacissima

et al. 2018

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“…This decision might have been premature, not only because restocking our antibiotic supplies is a public health priority, but also because modern advances in genome sequencing technologies and the development of bioinformatics have reinvigorated antibiotic discovery. The abundance of bacterial genome sequences now available enables genome-mining approaches for finding new bioactive small molecules, while simultaneously facilitating cheminformatic dereplication methods (Gaudêncio and Pereira 2015;Mohamed, Nguyen and Mamitsuka 2016).…”

Section: Introductionmentioning

confidence: 99%

Antibiotic dialogues: induction of silent biosynthetic gene clusters by exogenous small molecules

Okada¹,

Seyedsayamdost²

2016

FEMS Microbiology Reviews

170

150

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One sentence summary: Microbial secondary metabolites represent a significant source of potential drug leads; however, the majority of the corresponding biosynthetic genes are not expressed under normal laboratory conditions. In this review, we assess the capacity of exogenous small molecules, especially antibiotics, to activate these silent gene clusters. Editor: Aimee Shen ABSTRACTNatural products have traditionally served as a dominant source of therapeutic agents. They are produced by dedicated biosynthetic gene clusters that assemble complex, bioactive molecules from simple precursors. Recent genome sequencing efforts coupled with advances in bioinformatics indicate that the majority of biosynthetic gene clusters are not expressed under normal laboratory conditions. Termed 'silent' or 'cryptic', these gene clusters represent a treasure trove for discovery of novel small molecules, their regulatory circuits and their biosynthetic pathways. In this review, we assess the capacity of exogenous small molecules in activating silent secondary metabolite gene clusters. Several approaches that have been developed are presented, including coculture techniques, ribosome engineering, chromatin remodeling and high-throughput elicitor screens. The rationale, applications and mechanisms attendant to each are discussed. Some general conclusions can be drawn from our analysis: exogenous small molecules comprise a productive avenue for the discovery of cryptic metabolites. Specifically, growth-inhibitory molecules, in some cases clinically used antibiotics, serve as effective inducers of silent biosynthetic gene clusters, suggesting that old antibiotics may be used to find new ones. The involvement of natural antibiotics in modulating secondary metabolism at subinhibitory concentrations suggests that they represent part of the microbial vocabulary through which inter-and intraspecies interactions are mediated.

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“…After the collection of UV/VIS absorption spectra, molecular mass, and further structure data, the gained information needs to be compared with database entries. Over the decades, many different databases covering a wide range of compounds have been established (Mohamed et al 2016;Guijas et al 2018 is an open-access knowledge base that aims to let NP chemists work together and share their raw, processed, or identified MS/MS spectrometry data. We believe that crowdsourced curation of freely available reference MS libraries as well as a fast-growing database of MS/MS spectra will rapidly accelerate the annotation and thus the search of prior unknown compounds (Wang et al 2016;Kind et al 2017;Quinn et al 2017).…”

Section: Algae 21%mentioning

confidence: 99%

Secondary Metabolites of Marine Microbes: From Natural Products Chemistry to Chemical Ecology

Petersen

Kellermann

Schupp

2019

YOUMARES 9 - The Oceans: Our Research, Our Future

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Marine natural products (MNPs) exhibit a wide range of pharmaceutically relevant bioactivities, including antibiotic, antiviral, anticancer, or anti-inflammatory properties. Besides marine macroorganisms such as sponges, algae, or corals, specifically marine bacteria and fungi have shown to produce novel secondary metabolites (SMs) with unique and diverse chemical structures that may hold the key for the development of novel drugs or drug leads. Apart from highlighting their potential benefit to humankind, this review is focusing on the manifold functions of SMs in the marine ecosystem. For example, potent MNPs have the ability to exile predators and competing organisms, act as attractants for mating purposes, or serve as dye for the expulsion or attraction of other organisms. A large compilation of literature on the role of MNPs in marine ecology is available, and several reviews evaluated the function of MNPs for the aforementioned topics. Therefore, we focused the second part of this review on the importance of bioactive compounds from crustose coralline algae (CCA) and their role during coral settlement, a topic that has received less attention. It has been shown that certain SMs derived from CCA and their associated bacteria are able to induce attachment and/or metamorphosis of many benthic invertebrate larvae, including globally threatened reef-building scleractinian corals. This review provides an overview on bioactivities of MNPs from marine microbes and their potential use in medicine as well as on the latest findings of the chemical ecology and settlement process of scleractinian corals and other invertebrate larvae.

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Current status and prospects of computational resources for natural product dereplication: a review

Cited by 43 publications

References 150 publications

The Antitumor Activities of Marsdenia tenacissima

The Antitumor Activities of Marsdenia tenacissima

Antibiotic dialogues: induction of silent biosynthetic gene clusters by exogenous small molecules

Secondary Metabolites of Marine Microbes: From Natural Products Chemistry to Chemical Ecology

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