Exploring Natural Products from the Biodiversity of Pakistan for Computational Drug Discovery Studies: Collection, Optimization, Design and Development of A Chemical Database (ChemDP)
Shaher Bano Mirza,
Muhammad Qaiser Fatmi.
Pakistan possesses a rich and vast source of natural products (NPs). Some of these
secondary metabolites have been identified as potent therapeutic agents. However, the medicinal usage
of most of these compounds has not yet been fully explored. The discoveries for new scaffolds of NPs
as inhibitors of certain enzymes or receptors using advanced computational drug discovery approaches
are also limited due to the unavailability of accurate 3D structures of NPs. An organized database
incorporating all relevant information, therefore, can facilitate to explore the medicinal importance of
the metabolites from Pakistani Biodiversity. The Chemical Database of Pakistan (ChemDP; release
01) is a fully-referenced, evolving, web-based, virtual database which has been designed and developed to introduce
natural products (NPs) and their derivatives from the biodiversity of Pakistan to Global scientific communities. The prime
aim is to provide quality structures of compounds with relevant information for computer-aided drug discovery studies.
For this purpose, over 1000 NPs have been identified from more than 400 published articles, for which 2D and 3D
molecular structures have been generated with a special focus on their stereochemistry, where applicable. The PM7 semiempirical
quantum chemistry method has been used to energy optimize the 3D structure of NPs. The 2D and 3D structures
can be downloaded as .sdf, .mol, .sybyl, .mol2, and .pdb files – readable formats by many chemoinformatics/bioinformatics
software packages. Each entry in ChemDP contains over 100 data fields representing various molecular, biological,
physico-chemical and pharmacological properties, which have been properly documented in the database for end users.
These pieces of information have been either manually extracted from the literatures or computationally calculated using
various computational tools. Cross referencing to a major data repository i.e. ChemSpider has been made available for
overlapping compounds. An android application of ChemDP is available at its website. The ChemDP is freely accessible
Keywords: ChemDP, chemical database, chemspider, computer-aided drug designing, molecular docking and virtual
screening, natural products of Pakistan, physico-chemical properties, semi-empirical quantum chemistry calculations.
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