iMDLab Logo

POLYPHARMA: A Polypharmacology Database
Search Database Instructions Citation Application Feedback
If you are interested in this database, please refer the following papers for further references.

1. Tan Z, Chen L, Zhang S. Comprehensive Modeling and Discovery of Mebendazole as a Novel TRAF2- and NCK-interacting Kinase Inhibitor. Sci Rep. . Sep 21;6:33534.(2016).

1. Tan Z, Zhang S. Polypharmacology in Drug Development: A Minireview of Current Technologies. ChemMedChem . Jun 20;11(12)(2016).

1. Reddy AS, Tan Z, Zhang S. Curation and analysis of multitargeting agents for polypharmacological modeling. J Chem Inf Model . 54 (9) (2014).

1. Reddy AS, Zhang S. Polypharmacology: drug discovery for the future. Expert Rev Clin Pharmacol. 6(1), 41-47 (2013).

2. Phatak SS, Zhang S. A novel multi-modal drug repurposing approach for identification of potent ack1 inhibitors. Pac Symp Biocomput. 29-40 (2013).

3. Morrow JK, Tian L, Zhang S. Molecular networks in drug discovery. Crit Rev Biomed Eng. 38, 143-156 (2010).

4. Yook Sh, Oltvai Zn, Barabasi Al. Functional and topological characterization of protein interaction networks. Proteomics 4(4), 928-942 (2004).

5. Lipinski C, Hopkins A. Navigating chemical space for biology and medicine. Nature 432(7019), 855-861 (2004).

6. Hopkins Al. Network pharmacology: the next paradigm in drug discovery. Nature Chemical Biology 4(11), 682-690 (2008).

7. Hopkins Al. Drug discovery: Predicting promiscuity. Nature 462(7270), 167-168 (2009).

8. Apsel B, Blair Ja, Gonzalez B et al. Targeted polypharmacology: discovery of dual inhibitors of tyrosine and phosphoinositide kinases. Nature Chemical Biology 4(11), 691-699 (2008).

9. Simon Z, Peragovics A, Vigh-Smeller M et al. Drug effect prediction by polypharmacology-based interaction profiling. J Chem Inf Model 52(1), 134-145 (2012).

10.  Brianso F, Carrascosa Mc, Oprea Ti, Mestres J. Cross-Pharmacology Analysis of G Protein-Coupled Receptors. Curr Top Med Chem (2011).

11.  Paolini Gv, Shapland Rh, Van Hoorn Wp, Mason Js, Hopkins Al. Global mapping of pharmacological space. Nat Biotechnol 24(7), 805-815 (2006).

12.  Yildirim Ma, Goh Ki, Cusick Me, Barabasi Al, Vidal M. Drug-target network. Nat Biotechnol 25(10), 1119-1126 (2007).

13.  Durrant Jd, Amaro Re, Xie L et al. A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology. PLoS Comput Biol 6(1), e1000648 (2010 ).

14.  Oprea Ti, Mestres J. Drug Repurposing: Far Beyond New Targets for Old Drugs. Aaps J (2012).

15.  Boran Adw, Iyengar R. Systems approaches to polypharmacology and drug discovery. Current Opinion in Drug Discovery & Development 13(3), 297-309 (2010).

16.  Boran Adw, Iyengar R. Systems Pharmacology. Mount Sinai Journal of Medicine 77(4), 333-344 (2010).

17.  Xie L, Xie L, Kinnings Sl, Bourne Pe. Novel Computational Approaches to Polypharmacology as a Means to Define Responses to Individual Drugs. Annual Review of Pharmacology and Toxicology, Vol 52 52, 361 (2012).

18.  Hopkins Al. Network pharmacology. Nature Biotechnology 25(10), 1110-1111 (2007).

19.  Oprea Ti, Nielsen Sk, Ursu O et al. Associating Drugs, Targets and Clinical Outcomes into an Integrated Network Affords a New Platform for Computer-Aided Drug Repurposing. Mol Inform 30(2-3), 100-111 (2011).

20.  Achenbach J, Tiikkainen P, Franke L, Proschak E. Computational tools for polypharmacology and repurposing. Future Medicinal Chemistry 3(8), 961-968 (2011).

21.  Yamanishi Y, Araki M, Gutteridge A, Honda W, Kanehisa M. Prediction of drug-target interaction networks from the integration of chemical and genomic spaces. Bioinformatics 24(13), i232-240 (2008).

22.  Dar Ac, Das Tk, Shokat Km, Cagan Rl. Chemical genetic discovery of targets and anti-targets for cancer polypharmacology. Nature 486(7401), 80-84 (2012).

23.  Baumann Kh, Du Bois A, Meier W et al. A phase II trial (AGO 2.11) in platinum-resistant ovarian cancer: a randomized multicenter trial with sunitinib (SU11248) to evaluate dosage, schedule, tolerability, toxicity and effectiveness of a multitargeted receptor tyrosine kinase inhibitor monotherapy. Annals of Oncology 23(9), 2265-2271 (2012).

24.  Winum Jy, Maresca A, Carta F, Scozzafava A, Supuran Ct. Polypharmacology of sulfonamides: pazopanib, a multitargeted receptor tyrosine kinase inhibitor in clinical use, potently inhibits several mammalian carbonic anhydrases. Chemical Communications 48(66), 8177-8179 (2012).

25.  Schmid A, Blank Lm. Hypothesis-driven omics integration. Nature Chemical Biology 6(7), 485-487 (2010).

26.  Joyce Ar, Palsson Bo. The model organism as a system: integrating 'omics' data sets. Nature Reviews Molecular Cell Biology 7(3), 198-210 (2006).

27.  Zhao S, Iyengar R. Systems Pharmacology: Network Analysis to Identify Multiscale Mechanisms of Drug Action. Annual Review of Pharmacology and Toxicology, Vol 52 52, 505-521 (2012).

28.  Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 40(Database issue), D109-114 (2012).

29.  Kuhn M, Von Mering C, Campillos M, Jensen Lj, Bork P. STITCH: interaction networks of chemicals and proteins. Nucleic Acids Res 36(Database issue), D684-688 (2008).

30.  Hecker N, Ahmed J, Von Eichborn J et al. SuperTarget goes quantitative: update on drug-target interactions. Nucleic Acids Res 40(Database issue), D1113-1117 (2012).

31.  Sharman Jl, Mpamhanga Cp, Spedding M et al. IUPHAR-DB: new receptors and tools for easy searching and visualization of pharmacological data. Nucleic Acids Res 39(Database issue), D534-538 (2011).

32.  Olah M, Mracec M, Ostopovici L et al. WOMBAT: World of molecular bioactivity. In: Chemoinformatics in Drug Discovery. Oprea Ti (Ed. Wiley-VCH, New York 223-239 (2004).

33.  Keiser Mj, Roth Bl, Armbruster Bn, Ernsberger P, Irwin Jj, Shoichet Bk. Relating protein pharmacology by ligand chemistry. Nat Biotechnol 25(2), 197-206 (2007).

34.  Lounkine E, Keiser Mj, Whitebread S et al. Large-scale prediction and testing of drug activity on side-effect targets. Nature 486(7403), 361-367 (2012).

35.  Barabasi Al, Oltvai Zn. Network biology: understanding the cell's functional organization. Nat Rev Genet 5(2), 101-113 (2004).

36.  Zhang Ah, Sun H, Yang B, Wang Xj. Predicting new molecular targets for rhein using network pharmacology. Bmc Systems Biology 6(2012).

37.  Cheng F, Zhou Y, Li W, Liu G, Tang Y. Prediction of chemical-protein interactions network with weighted network-based inference method. PLoS One 7(7), e41064 (2012).

38.  Campillos M, Kuhn M, Gavin Ac, Jensen Lj, Bork P. Drug target identification using side-effect similarity. Science 321(5886), 263-266 (2008).

39.  Grinter Sz, Liang Y, Huang Sy, Hyder Sm, Zou X. An inverse docking approach for identifying new potential anti-cancer targets. J Mol Graph Model 29(6), 795-799 (2011).

40.  Hui-Fang L, Qing S, Jian Z, Wei F. Evaluation of various inverse docking schemes in multiple targets identification. J Mol Graph Model 29(3), 326-330 (2010).

41.  Chen Yz, Zhi Dg. Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule. Proteins 43(2), 217-226 (2001).

42.  Abdulhameed Mdm, Chaudhury S, Singh N, Sun H, Wallqvist A, Tawa Gj. Exploring Polypharmacology Using a ROCS-Based Target Fishing Approach. Journal of Chemical Information and Modeling 52(2), 492-505 (2012).

43.  Davis Ap, Murphy Cg, Rosenstein Mc, Wiegers Tc, Mattingly Cj. The Comparative Toxicogenomics Database facilitates identification and understanding of chemical-gene-disease associations: arsenic as a case study. BMC Med Genomics 1, 48 (2008).

44.  Hirschman L, Burns Ga, Krallinger M et al. Text mining for the biocuration workflow. Database (Oxford) 2012, bas020 (2012).

45.  Krallinger M, Leitner F, Vazquez M et al. How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience. Database (Oxford) 2012, bas017 (2012).

46.  Dowell Kg, Mcandrews-Hill Ms, Hill Dp, Drabkin Hj, Blake Ja. Integrating text mining into the MGI biocuration workflow. Database (Oxford) 2009, bap019 (2009).

47.  Wiegers Tc, Davis Ap, Cohen Kb, Hirschman L, Mattingly Cj. Text mining and manual curation of chemical-gene-disease networks for the comparative toxicogenomics database (CTD). BMC Bioinformatics 10, 326 (2009).

48.  Kolb P, Ferreira Rs, Irwin Jj, Shoichet Bk. Docking and chemoinformatic screens for new ligands and targets. Curr Opin Biotechnol 20(4), 429-436 (2009).

49.  Adams Jc, Keiser Mj, Basuino L et al. A mapping of drug space from the viewpoint of small molecule metabolism. PLoS Comput Biol 5(8), e1000474 (2009).

50.  Wren Jd, Bekeredjian R, Stewart Ja, Shohet Rv, Garner Hr. Knowledge discovery by automated identification and ranking of implicit relationships. Bioinformatics 20(3), 389-398 (2004).

51.  Cheng T, Li Q, Zhou Z, Wang Y, Bryant Sh. Structure-based virtual screening for drug discovery: a problem-centric review. Aaps J 14(1), 133-141 (2012).

52.  Nidhi, Glick M, Davies Jw, Jenkins Jl. Prediction of biological targets for compounds using multiple-category Bayesian models trained on chemogenomics databases. J Chem Inf Model 46(3), 1124-1133 (2006).

53.  Ravot E, Lisziewicz J, Lori F. New uses for old drugs in HIV infection: the role of hydroxyurea, cyclosporin and thalidomide. Drugs 58(6), 953-963 (1999).

54.  Chong Cr, Sullivan Dj, Jr. New uses for old drugs. Nature 448(7154), 645-646 (2007).

55.  Chen D, Dou Qp. New uses for old copper-binding drugs: converting the pro-angiogenic copper to a specific cancer cell death inducer. Expert Opin Ther Targets 12(6), 739-748 (2008).

56.  Sannella Ar, Casini A, Gabbiani C et al. New uses for old drugs. Auranofin, a clinically established antiarthritic metallodrug, exhibits potent antimalarial effects in vitro: Mechanistic and pharmacological implications. FEBS Lett 582(6), 844-847 (2008).

57.  Vazquez-Martin A, Lopez-Bonetc E, Cufi S et al. Repositioning chloroquine and metformin to eliminate cancer stem cell traits in pre-malignant lesions. Drug Resist Updat 14(4-5), 212-223 (2010).

58.  Allison M. NCATS launches drug repurposing program. Nat Biotechnol 30(7), 571-572 (2012).


© 2024 iMDLab