PubChem as a public resource for drug discovery

By Qingliang Li, Tiejun Cheng, Yanli Wang, Stephen H. Bryant. 2010

358 citations recorded by the source corpus.

PubChem is a public repository of small molecules and their biological properties. Currently, it contains over 25 million unique chemical structures and 90 million bioactivity outcomes associated with several thousand macromolecular targets. To address the potential utility of this public resource for drug discovery, we systematically summarized the protein targets in PubChem by the function, three-dimensional (3D) structure and biological pathway. Moreover, we analyzed the potency, selectivity and promiscuity of the bioactive compounds identified for these biological targets, including the chemical probes generated by the NIH Molecular Libraries Program (MLP). As a public resource, PubChem lowers the barrier for researchers to advance the development of chemical tools for modulating biological processes and drug candidates for disease treatments.

Subfields: Computational Theory and Mathematics, Organic Chemistry, Pharmacology, Computational Chemistry & Drug Discovery

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Citations in the corpus

Molecular Docking and Structure-Based Drug Design Strategies (2015, methodology): “Database Zinc [175,176] PubChem [177,178] ChemSpider [179,180] ChEMBL [181,182] NuBBE DB [183,184] ChemBank [185,186] eMolecules [187] DrugBank [188,189] Binding DB [190,191] In a following step, the prepared database is docked into the target binding site.”
Predicting potential drug-drug interactions by integrating chemical, biological, phenotypic and network data (2017, background): “PubChem Compound data-base [12, 15] can provide drug structures.”
Discovery and resupply of pharmacologically active plant-derived natural products: A review (2015, methodology): “Besides mammalian cells, also yeasts have been employed for the establishment of whole-cell phenotypic assays with applications in drug discovery, e.g., for high throughput functional screening based on the activation of caspases and other proteases involved in cell death and inflammation (Hayashi…”
HMDB 3.0—The Human Metabolome Database in 2013 (2012, background): “In particular, we developed a custom structure-checking program that used direct structure comparison (via a Mol file) of each of HMDB’s structures against the corresponding structures in other databases (PubChem, ChEBI, ChemSpider, etc.).”
New Perspectives on How to Discover Drugs from Herbal Medicines: CAM's Outstanding Contribution to Modern Therapeutics (2013, background): “By 2010, the BioAssay database is comprised of more than 2,700 bioassays associated with more than one million compounds tested against several thousand molecular targets [139].”
TCMSP: a database of systems pharmacology for drug discovery from herbal medicines (2014, methodology): “Structure files of molecules were downloaded from PubChem [18] Compound database, ChEMBL [19] and ChemSpider [20], or produced by ISIS Draw 2.5 (MDL Information Systems, Inc.) and further optimized by Sybyl 6.9 (Tripos, Inc.) with Sybyl force field and default parameters [2,21].”
ChemMine tools: an online service for analyzing and clustering small molecules (2011, methodology): “To efficiently mine much of the chemical structure and bioactivity space available in the public domain, the ChemMine Tools service provides text and structure similarity search methods that interface with the PubChem database (15) via its SOAP-based Power User Gateway (PUG) data exchange feature.”
The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands (2015, background): “portantly, anyone else) can generate a detailed analysis of our content (14,15).”