Endophytes: The Unmapped Repository for Natural Products

Sarethy, Indira P.; Pan, Sharadwata

doi:10.1007/978-981-13-7154-7_2

Cited by 6 publications

(3 citation statements)

References 115 publications

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“…In order to avoid biological provenance confusion, it needs to be noted that in some cases, NPs isolated from plants and animals can actually be synthesized by microorganisms that live on or in the host [76]. This is particularly the case of endophytes, bacteria living inside plant cells and very difficult to differentiate from the latter during preparation for metabolomics experiments [77]. Although the confusion is rare due to the improvement of identification methods and genetic approaches, it can create a bias in reproducibility of the NP isolation and needs, therefore, to be taken into account.…”

Section: Thematic Databasesmentioning

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: Thematic Databasesmentioning

confidence: 99%

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

2020

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“…Endophytes have been reported to produce many bioactive secondary metabolites with antimicrobial activity against a wide range of pathogenic microorganisms. These compounds show great structural diversity and complexity, representing a variety of different chemical classes, such as aliphatic compounds, alkaloids and other nitrogenous compounds, peptides, phenolics, polyketides and terpenoids [ 82 , 83 ]. In the following section, several examples of previously unknown compounds with antimicrobial activity that were first discovered as endophyte metabolites are described according to their broad chemical classification, along with their reported activities.…”

Section: Antimicrobial Potential Of Endophytic Fungimentioning

confidence: 99%

Exploring the Promise of Endophytic Fungi: A Review of Novel Antimicrobial Compounds

et al. 2022

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Over the last few decades, many of the existing drugs used to treat infectious diseases have become increasingly ineffective due to the global emergence of antimicrobial resistance (AMR). As such, there is a constant demand to find new, effective compounds that could help to alleviate some of this pressure. Endophytic fungi have captured the attention of many researchers in this field, as they have displayed a vast ability to produce novel bioactive compounds, many of which possess wide-ranging antimicrobial activities. However, while highly promising, research in this area is still in its infancy. Endophytes inhabit the healthy tissues of plants asymptomatically, resulting in a mutualistic symbiosis in which the endophytes produce a plethora of bioactive compounds that support the fitness of the host plant. These compounds display great chemical diversity, representing structural groups, such as aliphatic compounds, alkaloids, peptides, phenolics, polyketides and terpenoids. In this review, the significant antimicrobial potential of endophytic fungi is detailed, highlighting their ability to produce novel and diverse antimicrobial compounds active against human, plant and marine pathogens. In doing so, it also highlights the significant contributions that endophytic fungi can make in our battle against AMR, thus providing the motivation to increase efforts in the search for new and effective antimicrobial drugs.

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“…In order to avoid biological provenance confusion, it needs to be noted that in some cases, NPs isolated from plants and animals can actually be synthesized by microorganisms that live on or in the host [71] . This is particularly the case of endophytes, bacteria living inside plant cells and very difficult to differentiate from the latter during preparation for metabolomics experiments [72] . Although the confusion is rare due to the improvement of identification methods and genetic approaches, it can create a bias in reproducibility of the NP isolation and needs, therefore, to be taken into account.…”

Section: Thematic Databasesmentioning

confidence: 99%

On the Redundancy of Natural Products Public Databases and Where to Find Data in 2020 - A Review on Natural Products Databases

Sorokina¹,

Steinbeck²

2019

Preprint

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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 400000 non-redundant NPs, which makes it the biggest open collection of NPs available to this date.

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Endophytes: The Unmapped Repository for Natural Products

Cited by 6 publications

References 115 publications

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

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

Exploring the Promise of Endophytic Fungi: A Review of Novel Antimicrobial Compounds

On the Redundancy of Natural Products Public Databases and Where to Find Data in 2020 - A Review on Natural Products Databases

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