MedPServer: A database for identification of therapeutic targets and novel leads pertaining to natural products

Abstract

Natural products have been the source of treatment for various human diseases from time immemorial. Interests in natural product‐based scaffolds for the discovery of modern drugs have grown in recent years. However, research on exploring the traditional medicinal systems for modern therapeutics is severely limited due to our incomplete understanding of the therapeutic mechanism of action. One possible solution is to develop computational approaches, based on ligand‐ and structure‐based screening tools, for fast and plausible target identification, leading to elucidation of the therapeutic mechanism. In the present work, we present two methods based on shape‐based and pharmacophore search to predict targets of natural products and elucidate their mechanism, and to identify natural product‐based leads. These methods were tested on an in‐house developed database of medicinal plants that include information from a largely unexplored North‐East region of India, known as one of the twelve mega biodiversity regions. However, depending on the choice of the lead molecules, any existing databases can be used for screening. MedPServer is an open access resource available at http://bif.uohyd.ac.in/medserver/.

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

“…The first one, IMPPAT [104] is the manually curated database of over 10,000 phytochemicals extracted from 1700 Indian medicinal plants, their phytochemistry and their therapeutic effects. The other, MedPServer [105] contains NPs from plants from North-East India used in traditional medicine. It aims towards the understanding of the therapeutic mechanisms of action of the 1124 NPs from these plants by integrating ligand-based and structurebased approaches.…”

Translational Informatics for Natural Products as Antidepressant Agents

“…Other examples include CMNPD (Comprehensive Marine Natural Products Database) ( https://www.cmnpd.org/ ) ( Lyu et al, 2021 ) and PAMDB ( Pseudomonas Aeruginosa Metabolome Database) ( http://pseudomonas.umaryland.edu/ ) ( Huang W. et al, 2018 ) that encompass data on marine natural products and the metabolic pathway diagrams and metabolomics on Pseudomonas aeruginosa , respectively. There are some others that include, PSC-db ( http://pscdb.appsbio.utalca.cl ) ( Valdés-Jiménez et al, 2021 ), TeroKit ( http://terokit.qmclab.com ) ( Zeng et al, 2020 ), MedPServer ( http://bif.uohyd.ac.in/medserver ) ( Potshangbam et al, 2018 ), TriForC ( http://bioinformatics.psb.ugent.be/triforc ) ( Miettinen et al, 2018 ), 3DMET ( http://www.3dmet.dna.affrc.go.jp ) ( Maeda and Kondo, 2013 ), BiG-FAM ( https://bigfam.bioinformatics.nl ) ( Kautsar et al, 2021 ), DEREP-NP ( https://github.com/clzani/DE ) ( Zani and Carroll, 2017 ), TMDB ( http://pcsb.ahau.edu.cn:8080/TCDB/index.jsp ) ( Yue et al, 2014 ). In all, these databases with an enormous wealth of information on natural products and their source species (biological sources) might be instrumental in augmenting the efforts directed towards screening of anti-depression therapeutics, drug discovery, and development.…”

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

“…The first one, IMPPAT [99] is the manually curated database of over 10000 phytochemicals extracted from 1700 Indian medicinal plants, their phytochemistry and their therapeutic effects. The other, MedPServer [100] contains natural products from plants from North-East India used in traditional medicine. It aims towards the understanding of the therapeutic mechanisms of action of the 1124 NPs from these plants by integrating ligand-based and structure-based approaches.…”