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Review
. 2010 Dec;15(23-24):1052-7.
doi: 10.1016/j.drudis.2010.10.003. Epub 2010 Oct 21.

PubChem as a public resource for drug discovery

Qingliang Li  1 , Tiejun Cheng, Yanli Wang, Stephen H Bryant
Affiliations
Review

PubChem as a public resource for drug discovery

Qingliang Li et al. Drug Discov Today. 2010 Dec.

Abstract

PubChem is a public repository of small molecules and their biological properties. Currently, it contains more than 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 function, 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. 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.

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Figures

Figure 1
Figure 1
Linking protein super-families and three-dimensional structures to PubChem bioassay targets. a & c represent super-family annotations; b & d indicate the availability of related 3D structures derived from homologous analysis at each sequence similarity level. a & b denote the entire set of protein targets in PubChem; c & d represent the protein targets that are involved in high-throughput screening (HTS) assays from the NIH Molecular Libraries Program (MLP).
Figure 2
Figure 2
The distribution of the potency of the bioactive compounds and protein targets in PubChem. a. blue bars show the distribution of the potency for entire bioactive compounds in PubChem in seven potency groups; red bars denote the frequency of the protein targets with most potent compounds falling in respective potency group. b. blue bars represent the distribution of potency for chemical probes indentified by the NIH Molecular Libraries Program (MLP); red bars show the frequency of the protein targets with most potent chemical probes falling in respective potency group.
Figure 3
Figure 3
An overview of the selectivity property of bioactive compounds in PubChem. a. the distribution of compounds’ across-target activity. X-axis represents the number of distinct active protein targets associated with a compound, while Y-axis represents the frequency of compounds at each across-activity level. It shows that majority compounds are associated with one or a few protein targets, and a small portion of them interact with a large amount of targets; b. the blue bars represent the distribution of the number of tested targets for selective compounds (only active to one protein target in PubChem). Compounds are divided into six selectivity groups. It suggests that the majority of the selective compounds have been tested across over 150 targets. The red bars denote the frequency of the protein targets associated with the compounds in the respective selectivity group.
Figure 4
Figure 4
The distribution of the selective compounds in PubChem. X-axis represents the potency in micromole; Y-axis represents the frequency in the scale of log10. The colour of the bars denotes the ranges of how many targets against which the selective compounds were tested. For example, the range of [100,150) means that this group of compounds were tested against 100 to 150 targets and selectively against one of them.
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