PubChem applications in drug discovery: A bibliometric analysis

Drug Discovery Today

Volumn 19, Issue 11, 2014, Pages 1751-1756

  Cheng, Tiejun ^a   Pan, Yongmei ^a   Hao, Ming ^a   Wang, Yanli ^a   Bryant, Stephen H ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIBLIOMETRICS; BIOLOGICAL ACTIVITY; DATA BASE; DRUG DEVELOPMENT; DRUG TARGETING; HEALTH CARE UTILIZATION; INFORMATION PROCESSING; INFORMATION RETRIEVAL; INFORMATION SCIENCE; INFORMATION SERVICE; MEDICINAL CHEMISTRY; POLYPHARMACOLOGY; PROCESS OPTIMIZATION; REVIEW; STRUCTURE ACTIVITY RELATION; CHEMICAL DATABASE; FACTUAL DATABASE;

BIBLIOMETRICS; DATABASES, CHEMICAL; DATABASES, FACTUAL; DRUG DISCOVERY; INFORMATICS;

EID: 84910652816     PISSN: 13596446     EISSN: 18785832     Source Type: Journal    
DOI: 10.1016/j.drudis.2014.08.008     Document Type: Review

References (59)

1. Y. Wang PubChem BioAssay: 2014 update Nucleic Acids Res. 42 2014 D1075 D1082
2. Y. Wang PubChem: a public information system for analyzing bioactivities of small molecules Nucleic Acids Res. 37 2009 W623 W633
3. Y. Wang An overview of the PubChem BioAssay resource Nucleic Acids Res. 38 2009 D255 D266
4. E.E. Bolton PubChem: integrated platform of small molecules and biological activities A.W. Ralph, C.S. David, Annual Reports in Computational Chemistry vol. 4 2008 Elsevier 217 241
5. Q. Li PubChem as a public resource for drug discovery Drug Discov. Today 15 2010 1052 1057
6. A. Dander [COMMODE] a large-scale database of molecular descriptors using compounds from PubChem Source Code Biol. Med. 8 2013 22
7. S.G. Rohrer, and K. Baumann Maximum unbiased validation (MUV) data sets for virtual screening based on PubChem bioactivity data J. Chem. Inf. Model. 49 2009 169 184
8. S. Preissner SuperCYP: a comprehensive database on cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions Nucleic Acids Res. 38 2010 D237 D243
9. J. Hur, and D.J. Wild PubChemSR: a search and retrieval tool for PubChem Chem. Cent. J. 2 2008 11
10. M.R. Southern, and P.R. Griffin A Java API for working with PubChem datasets Bioinformatics 27 2011 741 742
11. M.D. Hanwell Avogadro: an advanced semantic chemical editor, visualization, and analysis platform J. Cheminform. 4 2012 17
12. T.W. Backman ChemMine tools: an online service for analyzing and clustering small molecules Nucleic Acids Res. 39 2011 W486 W491
13. U. Visser BioAssay ontology (BAO): a semantic description of bioassays and high-throughput screening results BMC Bioinformatics 12 2011 257
14. R. van Deursen Visualisation of the chemical space of fragments, lead-like and drug-like molecules in PubChem J. Comput. Aided Mol. Des. 25 2011 649 662
15. N. Singh Chemoinformatic analysis of combinatorial libraries, drugs, natural products, and molecular libraries small molecule repository J. Chem. Inf. Model. 49 2009 1010 1024
16. M.P. Krein, and N. Sukumar Exploration of the topology of chemical spaces with network measures J. Phys. Chem. A 115 2011 12905 12918
17. E. Lounkine Activity-aware clustering of high throughput screening data and elucidation of orthogonal structure-activity relationships J. Chem. Inf. Model. 51 2011 3158 3168
18. D.G. Covell Integrating constitutive gene expression and chemoactivity: mining the NCI60 anticancer screen PLoS ONE 7 2012 e44631
19. B. Chen PubChem as a source of polypharmacology J. Chem. Inf. Model. 49 2009 2044 2055
20. Y. Hu, and J. Bajorath What is the likelihood of an active compound to be promiscuous? Systematic assessment of compound promiscuity on the basis of PubChem confirmatory bioassay data AAPS J. 15 2013 808 815
21. V. Periwal Computational models for in-vitro anti-tubercular activity of molecules based on high-throughput chemical biology screening datasets BMC Pharmacol. 12 2012 1
22. Y. Pouliot Predicting adverse drug reactions using publicly available PubChem BioAssay data Clin. Pharmacol. Ther. 90 2011 90 99
23. N. Nagamine Integrating statistical predictions and experimental verifications for enhancing protein-chemical interaction predictions in virtual screening PLoS Comput. Biol. 5 2009 e1000397
24. B. Wendt Toluidinesulfonamide hypoxia-induced factor 1 inhibitors: alleviating drug-drug interactions through use of PubChem data and comparative molecular field analysis guided synthesis J. Med. Chem. 54 2011 3982 3986
25. T.F. Chou Structure-activity relationship study reveals ML240 and ML241 as potent and selective inhibitors of p97 ATPase ChemMedChem 8 2013 297 312
26. H.J. Feldman CO: a chemical ontology for identification of functional groups and semantic comparison of small molecules FEBS Lett. 579 2005 4685 4691
27. M.K. Matlock Scaffold network generator: a tool for mining molecular structures Bioinformatics 29 2013 2655 2656
28. M. Butkiewicz Benchmarking ligand-based virtual high-throughput screening with the PubChem database Molecules 18 2013 735 756
29. X.Q. Xie, and J.Z. Chen Data mining a small molecule drug screening representative subset from NIH PubChem J. Chem. Inf. Model. 48 2008 465 475
30. H. Chen Prediction of molecular targets of cancer preventing flavonoid compounds using computational methods PLoS ONE 7 2012 e38261
31. J.R. Fernández Identification of small molecule compounds with higher binding affinity to guanine deaminase (cypin) than guanine Bioorg. Med. Chem. 18 2010 6748 6755
32. N. Mast In silico and intuitive predictions of CYP46A1 inhibition by marketed drugs with subsequent enzyme crystallization in complex with fluvoxamine Mol. Pharmacol. 82 2012 824 834
33. J.W. Huang Fragment-based design of small molecule X-linked inhibitor of apoptosis protein inhibitors J. Med. Chem. 51 2008 7111 7118
34. J.-X. Ren Discovery of novel Pim-1 kinase inhibitors by a hierarchical multistage virtual screening approach based on SVM model, pharmacophore, and molecular docking J. Chem. Inf. Model. 51 2011 1364 1375
35. A. Srinivasan Identification and characterization of human apurinic/apyrimidinic endonuclease-1 inhibitors Biochemistry 51 2012 6246 6259
36. F.Y. Lin Dual dehydrosqualene/squalene synthase inhibitors: leads for innate immune system-based therapeutics ChemMedChem 7 2012 561 564
37. D.A. O'Leary Identification of small molecule and genetic modulators of AON-induced dystrophin exon skipping by high-throughput screening PLoS ONE 4 2009 e8348
38. J.Y. Ho Ovatodiolide targets beta-catenin signaling in suppressing tumorigenesis and overcoming drug resistance in renal cell carcinoma Evid. Based Complement. Alternat. Med. 2013 2013 161628
39. G. Tiwari, and D. Mohanty An in silico analysis of the binding modes and binding affinities of small molecule modulators of PDZ-peptide interactions PLoS ONE 8 2013 e71340
40. A. Alam Novel anti-inflammatory activity of epoxyazadiradione against macrophage migration inhibitory factor: inhibition of tautomerase and proinflammatory activities of macrophage migration inhibitory factor J. Biol. Chem. 287 2012 24844 24861
41. S. Saraswati Tylophorine, a phenanthraindolizidine alkaloid isolated from tylophora indica exerts antiangiogenic and antitumor activity by targeting vascular endothelial growth factor receptor 2-mediated angiogenesis Mol. Cancer 12 2013 82
42. F. Tholander, and B.M. Sjoberg Discovery of antimicrobial ribonucleotide reductase inhibitors by screening in microwell format Proc. Natl. Acad. Sci. U. S. A. 109 2012 9798 9803
43. M.E. Mattmann Identification of (R)-N-(4-(4-methoxyphenyl)thiazol-2-yl)-1-tosylpiperidine-2-carboxamide, ML277, as a novel, potent and selective k(v)7.1 (KCNQ1) potassium channel activator Bioorg. Med. Chem. Lett. 22 2012 5936 5941
44. S.M. Firestine Identification of inhibitors of N5-carboxyaminoimidazole ribonucleotide synthetase by high-throughput screening Bioorg. Med. Chem. 17 2009 3317 3323
45. A. Crowe Identification of aminothienopyridazine inhibitors of tau assembly by quantitative high-throughput screening Biochemistry 48 2009 7732 7745
46. T. Vang LYP inhibits T-cell activation when dissociated from CSK Nat. Chem. Biol. 8 2012 437 446
47. D.J. Rickard Identification of benzimidazole diamides as selective inhibitors of the nucleotide-binding oligomerization domain 2 (NOD2) signaling pathway PLoS ONE 8 2013 e69619
48. A. Kumar Chemical correction of pre-mRNA splicing defects associated with sequestration of muscleblind-like 1 protein by expanded r(CAG)-containing transcripts ACS Chem. Biol. 7 2012 496 505
49. Q. Cheng, and F.P. Guengerich Identification of endogenous substrates of orphan cytochrome P450 enzymes through the use of untargeted metabolomics approaches Methods Mol. Biol. 987 2013 71 77
50. D.K. Derewacz Antimicrobial drug resistance affects broad changes in metabolomic phenotype in addition to secondary metabolism Proc. Natl. Acad. Sci. U. S. A. 110 2013 2336 2341
51. 50 and retention index models for nontargeted metabolomics: identification of 1,3-dicyclohexylurea in human serum by HPLC/mass spectrometry J. Chem. Inf. Model. 52 2012 1222 1237
52. M. Wang Calcium-deficiency assessment and biomarker identification by an integrated urinary metabonomics analysis BMC Med. 11 2013 86
53. D.W. Hill Mass spectral metabonomics beyond elemental formula: chemical database querying by matching experimental with computational fragmentation spectra Anal. Chem. 80 2008 5574 5582
54. S.A. Hasson High-content genome-wide RNAi screens identify regulators of parkin upstream of mitophagy Nature 504 2013 291 295
55. Z. Yin A screen for morphological complexity identifies regulators of switch-like transitions between discrete cell shapes Nat. Cell Biol. 15 2013 860 871
56. S. Dakshanamurthy Predicting new indications for approved drugs using a proteochemometric method J. Med. Chem. 55 2012 6832 6848
57. M. Hao An efficient algorithm coupled with synthetic minority over-sampling technique to classify imbalanced PubChem BioAssay data Anal. Chim. Acta 806 2014 117 127
58. B.T. Calhoun Automatically detecting workflows in PubChem J. Biomol. Screen. 17 2012 1071 1079
59. K. Schorpp Identification of small-molecule frequent hitters from AlphaScreen high-throughput screens J. Biomol. Screen. 19 2013 715 726