A Virtual Screening Approach For Identifying Plants with Anti H5N1 Neuraminidase Activity

Ikram, Nur Kusaira Khairul; Durrant, Jacob D.; Muchtaridi, Muchtaridi; Zalaludin, Ayunni Salihah; Purwitasari, Neny; Mohamed, Norita; Rahim, Aisyah Saad Abdul; Lam, Chan Kit; Normi, Yahaya M.; Rahman, Noorsaadah Abdul; Amaro, Rommie E.; Wahab, Habibah A.

doi:10.1021/ci500405g

Cited by 50 publications

(35 citation statements)

References 65 publications

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“…The Natural Product Discovery System (NADI) [38] contains over 3000 natural compounds from more than 15,000 Malaysian plant species. Despite being developed and maintained by the University Sains Malaysia, it is not open for academic use.…”

Section: Commercial 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: Commercial Databasesmentioning

confidence: 99%

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

2020

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“…The bioinformatics data such as the protein crystal structure, either in apo-form or holoform, is freely downloadable from protein databases such as the Protein Data Bank, commonly abbreviated as PDB (accessible at www.rscb.org). The ligands could also be freely downloaded from chemical databases such as ZINC [98], Natural Product Discovery (NADI) [99] and National Cancer Institute (NCI) [100]. Alternatively, if the ligand is a new chemical entity, its molecular structure could be directly drawn based on their chemical structures shown in published articles.…”

Section: Computational Drug Modelling Targeting Hemopexin Of Mmp9mentioning

confidence: 99%

Matrix metalloproteinase9 as the protein target in anti-breast cancer drug discovery: an approach by targeting hemopexin domain

et al. 2019

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Background: The discovery and development of anticancer still remain a challenge especially regarding the problem of cancer cell selectivity. Matrix metalloproteinase (MMP) was broadly studied as one of the protein targets to stop cancer angiogenesis as well as its cell migration. Main text: The MMP degrades extracellular matrix (ECM) such as collagen and gelatin which are important to control the cell migration from one to other sites. In cancer, this cell migration is regarded with metastasis, which is essential for the formation of new blood vessels called angiogenesis. The most common target in MMP, i.e. the catalytic site, is currently reported as being the non-selective target for inhibitor compounds that inhibit all MMPs but is associated with adverse side effects. Hemopexin, especially in MMP9 (PEX9) was found to be different from other domains in the MMP family which could potentially be the next target for anticancer due to the availability of its crystal structure in the Protein Data Bank (PDB). Conclusion: The PEX9 crystal structure was resolved as a homodimer connected by a hydrophobic area between two blades along the β-propeller which its structure and function for computational drug modelling can be studied.

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“…The database offers rich and high-quality metadata on food NP activities and structures and limited free access to scientists to try the resource. The Natural Product Discovery System (NADI) [34] contains over 3000 natural compounds from more than 15000 Malaysian plant species. Despite being developed and maintained by the University Sains Malaysia, it is not open for academic use.…”

Section: Commercial 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.

show abstract

A Virtual Screening Approach For Identifying Plants with Anti H5N1 Neuraminidase Activity

Cited by 50 publications

References 65 publications

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

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

Matrix metalloproteinase9 as the protein target in anti-breast cancer drug discovery: an approach by targeting hemopexin domain

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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