scholarly journals COCONUT online: Collection of Open Natural Products database

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Maria Sorokina ◽  
Peter Merseburger ◽  
Kohulan Rajan ◽  
Mehmet Aziz Yirik ◽  
Christoph Steinbeck
Keyword(s):  
Natural Products ◽  
Small Molecules ◽  
In Silico ◽  
Web Interface ◽  
Computational Screening ◽  
Online Resource ◽  
The World ◽  
Potential Applications ◽  
Living Organisms ◽  
Application Fields

AbstractNatural products (NPs) are small molecules produced by living organisms with potential applications in pharmacology and other industries as many of them are bioactive. This potential raised great interest in NP research around the world and in different application fields, therefore, over the years a multiplication of generalistic and thematic NP databases has been observed. However, there is, at this moment, no online resource regrouping all known NPs in just one place, which would greatly simplify NPs research and allow computational screening and other in silico applications. In this manuscript we present the online version of the COlleCtion of Open Natural prodUcTs (COCONUT): an aggregated dataset of elucidated and predicted NPs collected from open sources and a web interface to browse, search and easily and quickly download NPs. COCONUT web is freely available at https://coconut.naturalproducts.net.

scholarly journals Coconut Online: Collection of Open Natural Products Database

2020 ◽  
Author(s):  
Maria Sorokina ◽  
Peter Merseburger ◽  
Kohulan Rajan ◽  
Mehmet Aziz Yirik ◽  
Christoph Steinbeck
Keyword(s):  
Natural Products ◽  
Small Molecules ◽  
In Silico ◽  
Web Interface ◽  
Computational Screening ◽  
Online Resource ◽  
Potential Applications ◽  
Living Organisms

Abstract Natural products (NPs) are small molecules produced by living organisms with potential applications in pharmacology and other industries for their high bioactivities. Over the years a multiplication of thematic NP databases has been observed. However, there is no online resource regrouping all known NPs in just one place, which would greatly simplify NP research and allow computational screening and other in silico applications. Here we present the COlleCtion of Open Natural prodUcTs (COCONUT): an aggregated dataset of NPs available in different open sources and a subsequent web interface to browse, search and easily and quickly download NPs. COCONUT web is freely available at https://coconut.naturalproducts.net.

scholarly journals Too sweet: cheminformatics for deglycosylation in natural products

2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Jonas Schaub ◽  
Achim Zielesny ◽  
Christoph Steinbeck ◽  
Maria Sorokina
Keyword(s):  
Natural Products ◽  
Small Molecules ◽  
Open Source Software ◽  
In Silico ◽  
Web Application ◽  
Systematic Approach ◽  
Computational Procedure ◽  
Molecular Structures ◽  
Biological Origin ◽  
And Function

Abstract Sugar units in natural products are pharmacokinetically important but often redundant and therefore obstructing the study of the structure and function of the aglycon. Therefore, it is recommended to remove the sugars before a theoretical or experimental study of a molecule. Deglycogenases, enzymes that specialized in sugar removal from small molecules, are often used in laboratories to perform this task. However, there is no standardized computational procedure to perform this task in silico. In this work, we present a systematic approach for in silico removal of ring and linear sugars from molecular structures. Particular attention is given to molecules of biological origin and to their structural specificities. This approach is made available in two forms, through a free and open web application and as standalone open-source software.

scholarly journals Too sweet: cheminformatics for deglycosylation in natural products

2020 ◽  
Author(s):  
Jonas Schaub ◽  
Achim Zielesny ◽  
Christoph Steinbeck ◽  
Maria Sorokina
Keyword(s):  
Natural Products ◽  
Small Molecules ◽  
Open Source Software ◽  
In Silico ◽  
Web Application ◽  
Systematic Approach ◽  
Computational Procedure ◽  
Molecular Structures ◽  
Biological Origin ◽  
And Function

Abstract Sugar units in natural products are pharmacokinetically important but often redundant and therefore obstructing the study of the structure and function of the aglycon. Therefore, it is recommended to remove the sugars before a theoretical or experimental study of a molecule. Deglycogenases, enzymes that specialized in sugar removal from small molecules, are often used in laboratories to perform this task. However, there is no standardized computational procedure to perform this task in silico . In this work, we present a systematic approach for in silico removal of ring and linear sugars from molecular structures. Particular attention is given to molecules of biological origin and to their structural specificities. This approach is made available in two forms, through a free and open web application and as standalone open-source software.

scholarly journals Natural Products From Madagascar, Socio-Cultural Usage, and Potential Applications in Advanced Biomedicine: A Concise Review

2021 ◽  
Author(s):  
Camillo La Mesa ◽  
Oliarinony Ranalison ◽  
Lovasoa N. Randriantseheno ◽  
Gianfranco Risuleo
Keyword(s):  
Natural Products ◽  
Biological Activity ◽  
Primary Source ◽  
Therapeutic Agents ◽  
Botanical Origin ◽  
Disadvantaged Area ◽  
Concise Review ◽  
The World ◽  
Potential Applications ◽  
Natural Means

Natural products endowed of biological activity represent a primary source of commodities ranging from nutrition to therapeutic agents, as well as cosmetic tools, and recreational principles. These natural means have been used by mankind since centuries if not millennia. They are commonly used all over the world and socio-economical contexts but are particularly attractive in disadvantaged area or economically emerging situations all over the world. This is very likely due to the relatively easy recovery of these bioactive principles from the environment, to the low if any cost as well as ease of administration and to the general popular compliance concerning their consumption/ingestion. In this concise review, we focus on some popular bioactive principles of botanical origin which find a wide use in the Madagascan populations. But, due to space limitations only some most common and largely diffused principles in this country are considered. Finally, a possible nanotechnological administration is discussed in the case where a potential therapeutic usage is envisaged.

scholarly journals Control of Nucleophile Chemoselectivity in Cyanobactin YcaO Heterocyclases PatD and TruD

2021 ◽  
Author(s):  
Wenjia Gu ◽  
Yiwu Zheng ◽  
Taras Pogorelov ◽  
Satish K. Nair ◽  
Eric W. Schmidt
Keyword(s):  
Natural Products ◽  
Synthetic Biology ◽  
Post Translational Modifications ◽  
Pharmaceutical Development ◽  
The World ◽  
Academic Settings ◽  
Living Organisms

<div><div><div><p>YcaO proteins are ubiquitous in living organisms, where they perform crucial post-translational modifications of peptides and proteins. They are used extensively in biotechnology in companies and academic settings around the world. They also underlie some of the most important natural products in pharmaceutical development, such as thiopeptides (thiostrepton, etc.). Here, we solve one of the major outstanding mysteries behind YcaO proteins: how they exert precision selectivity of the nucleophile. The resulting findings have major implications in understanding the >30,000 YcaO proteins currently in sequencing databases and will be used widely for precision synthetic biology applications.</p></div></div></div>

scholarly journals Too sweet: cheminformatics for deglycosylation in natural products

2020 ◽  
Author(s):  
Jonas Schaub ◽  
Achim Zielesny ◽  
Christoph Steinbeck ◽  
Maria Sorokina
Keyword(s):  
Natural Products ◽  
Small Molecules ◽  
Open Source Software ◽  
In Silico ◽  
Web Application ◽  
Systematic Approach ◽  
Computational Procedure ◽  
Molecular Structures ◽  
Biological Origin ◽  
And Function

Abstract Sugar units in natural products are pharmacokinetically important but often redundant and therefore obstructing the study of the structure and function of the aglycon. Therefore, it is recommended to remove the sugars before a theoretical or experimental study of a molecule. Deglycogenases, enzymes that specialized in sugar removal from small molecules, are often used in laboratories to perform this task. However, there is no standardized computational procedure to perform this task in silico . In this work, we present a systematic approach for in silico removal of ring and linear sugars from molecular structures. Particular attention is given to molecules of biological origin and to their structural specificities. This approach is made available in two forms, through a free and open web application and as standalone open-source software.

scholarly journals Too sweet: cheminformatics for deglycosylation in natural products

2020 ◽  
Author(s):  
Jonas Schaub ◽  
Achim Zielesny ◽  
Christoph Steinbeck ◽  
Maria Sorokina
Keyword(s):  
Natural Products ◽  
Small Molecules ◽  
Open Source Software ◽  
In Silico ◽  
Web Application ◽  
Systematic Approach ◽  
Computational Procedure ◽  
Molecular Structures ◽  
Biological Origin ◽  
And Function

Abstract Sugar units in natural products are pharmacokinetically important but often redundant and therefore obstructing the study of the structure and function of the aglycon. Therefore, it is recommended to remove the sugars before a theoretical or experimental study of a molecule. Deglycogenases, enzymes that specialized in sugar removal from small molecules, are often used in laboratories to perform this task. However, there is no standardized computational procedure to perform this task in silico. In this work, we present a systematic approach for in silico removal of ring and linear sugars from molecular structures. Particular attention is given to molecules of biological origin and to their structural specificities. This approach is made available in two forms, through a free and open web application and as standalone open-source software.

Recent Advance in Natural Products with Antiviral Activities

2021 ◽  
Vol 21 ◽  
Author(s):  
Zhi-Gang Sun ◽  
Zhi-Na Li ◽  
Xiang-Wan Miao ◽  
Shuang Li ◽  
Hai-Liang Zhu
Keyword(s):  
Natural Products ◽  
Nucleic Acid ◽  
Antiviral Activity ◽  
Infectious Diseases ◽  
Living Cells ◽  
Chemical Substances ◽  
The World ◽  
Antiviral Activities ◽  
Living Organisms ◽  
Epidemic Diseases

: Virus is a type of noncellular organism, which is simple in structure, small in size and contains only one kind of nucleic acid (RNA or DNA). It must be parasitized in living cells and proliferates by replication. Viruses can infect plants or animals, which leads to many epidemic diseases, such as the current pandemic COVID-19. Viral infectious diseases have brought serious threats to the health of people around the world. Natural products are chemical substances that are usually produced by living organisms and have biological or pharmacological activity. Many of these natural products show antiviral activity. Based on the increasing importance of antiviral research, this paper focuses on the discovery and development of antiviral natural products since 2010.

scholarly journals Control of Nucleophile Chemoselectivity in Cyanobactin YcaO Heterocyclases PatD and TruD

2021 ◽  
Author(s):  
Wenjia Gu ◽  
Yiwu Zheng ◽  
Taras Pogorelov ◽  
Satish K. Nair ◽  
Eric W. Schmidt
Keyword(s):  
Natural Products ◽  
Synthetic Biology ◽  
Post Translational Modifications ◽  
Pharmaceutical Development ◽  
The World ◽  
Academic Settings ◽  
Living Organisms

<div><div><div><p>YcaO proteins are ubiquitous in living organisms, where they perform crucial post-translational modifications of peptides and proteins. They are used extensively in biotechnology in companies and academic settings around the world. They also underlie some of the most important natural products in pharmaceutical development, such as thiopeptides (thiostrepton, etc.). Here, we solve one of the major outstanding mysteries behind YcaO proteins: how they exert precision selectivity of the nucleophile. The resulting findings have major implications in understanding the >30,000 YcaO proteins currently in sequencing databases and will be used widely for precision synthetic biology applications.</p></div></div></div>

scholarly journals Natural Products from Madagascar, Socio-Cultural Usage, and Potential Applications in Advanced Biomedicine: A Concise Review

Molecules ◽  
2021 ◽  
Vol 26 (15) ◽  
pp. 4507
Author(s):  
Camillo La Mesa ◽  
Oliarinony Ranalison ◽  
Lovasoa N. Randriantseheno ◽  
Gianfranco Risuleo
Keyword(s):  
Natural Products ◽  
Biological Activity ◽  
Primary Source ◽  
Therapeutic Agents ◽  
Botanical Origin ◽  
Concise Review ◽  
The World ◽  
Potential Applications ◽  
Natural Means

Natural products endowed of biological activity represent a primary source of commodities ranging from nutrition to therapeutic agents, as well as cosmetic tools and recreational principles. These natural means have been used by mankind for centuries, if not millennia. They are commonly used all over the world in socio-economical contexts, but are particularly attractive in disadvantaged areas or economically emerging situations all over the world. This is very likely due to the relatively easy recovery of these bioactive principles from the environment, at a low if any cost, as well as ease of administration and the general popular compliance concerning their consumption/ingestion. In this concise review, we focus on some popular bioactive principles of botanical origin which find a wide use in the Madagascan populations. However, due to space limitations, only some of the most common and largely diffused principles in this country are considered. Finally, a possible nanotechnological administration is discussed in the case where a potential therapeutic usage is envisaged.

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