Synergy Maps: Exploring compound combinations using network-based visualization

Journal of Cheminformatics

Volumn 7, Issue 1, 2015, Pages

  Lewis, Richard ^a   Guha, Rajarshi ^b   Korcsmaros, Tamás ^c,d   Bender, Andreas ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

^c EARLHAM INSTITUTE   (United Kingdom)

^d INSTITUTE OF FOOD RESEARCH   (United Kingdom)

Author keywords

Compound combinations; Dimensionality reduction; Mixtures; Network; Synergy; Visualization

Indexed keywords

EID: 84938598105     PISSN: None     EISSN: 17582946     Source Type: Journal    
DOI: 10.1186/s13321-015-0090-6     Document Type: Article

References (49)

1. Yuan S, Wang F, Wang J, Huang P, Chen G, Zhang H et al (2012) effective elimination of cancer stem cells by a novel drug combination strategy. Stem Cells 31:23-34
2. Hill JA, Nislow C, Ammar R, Torti D, Cowen LE (2013) Genetic and genomic architecture of the evolution of resistance to antifungal drug combinations. PLoS Genetics 9:e1003390
3. Tan X, Hu L, Luquette LJ, Gao G, Liu Y, Qu H et al (2012) Systematic identification of synergistic drug pairs targeting HIV. Nat Biotechnol 30:1125-1130
4. Katouli AA, Komarova NL (2010) Optimizing combination therapies with existing and future CML drugs. PLoS One 5:e12300
5. Berenbaum MC (1989) What is synergy? Pharmacol Rev 41:93-141
6. Krueger AS, Avery W, Heilbut AM, Johansen LM, Price ER, Rickles RJ et al (2009) Synergistic drug combinations tend to improve therapeutically relevant selectivity. Nat Biotechnol 27:659-666
7. Greco WR, Bravo G, Parsons JC (1995) The search for synergy: a critical review from a response surface perspective. Pharmacol Rev 47:331-385
8. Wang Y-Y, Xu K-J, Song J, Zhao X-M (2012) Exploring drug combinations in genetic interaction network. BMC Bioinform 13(Suppl 7):S7
9. Ryall RA, Tan AC (2015) Systems biology approaches for advancing the discovery of effective drug combinations. J Cheminform 7:7
10. Bulusu KC, Guha R, Mason DJ, Lewis RPI, Muratov EN, Motamedi YK et al (2015) Modelling of compound combination effects and applications to efficacy and toxicity: state-of-the-art, challenges and perspectives. Drug Discov Today (in press)
11. Lehár J, Zimmermann GR, Krueger AS, Molnar RA, Ledell JT, Heilbut AM et al (2007) Chemical combination effects predict connectivity in biological systems. Mol Syst Biol 3:80
12. Zhao X-M, Iskar M, Zeller G, Kuhn M, Van Noort V, Bork P (2011) Prediction of drug combinations by integrating molecular and pharmacological data. PLoS Comput Biol 7:e1002323
13. Huang H, Zhang P, Qu XA, Sanseau P, Yang L (2014) Systematic prediction of drug combinations based on clinical side-effects. Sci Rep 4:7160
14. Li P, Huang C, Fu Y, Wang J, Wu Z, Ru J et al. (2015) Large-scale exploration and analysis of drug combinations. Bioinformatics 31(12):2007-2016
15. Guimerà R, Sales-Pardo M (2013) A network inference method for large-scale unsupervised identification of novel drug-drug interactions. PLoS Comput Biol 9:e1003374
16. Yeh P, Tschumi AI, Kishony R (2006) Functional classification of drugs by properties of their pairwise interactions. Nat Genet 38:489-494
17. Guo AC, Knox C, Wishart DS, Pon A, Law V, Banco K (2010) DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs. Nucleic Acids Res 39(Database):D1035-D1041
18. Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, Tzur D et al (2007) A knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res 36(Database):D901-D906
19. Yin N, Ma W, Pei J, Ouyang Q, Tang C, Lai L (2014) Synergistic and antagonistic drug combinations depend on network topology. PLoS One 9:e3960
20. Jia J, Zhu F, Ma X, Cao Z, Cao ZW, Li Y et al (2009) Mechanisms of drug combinations: interaction and network perspectives. Nat Rev Drug Discov 8:111-128
21. Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H et al (2014) A community computational challenge to predict the activity of pairs of compounds. Nat Biotechnol 32(12):1213-1222
22. Bliss CI (1939) The toxicity of poisons applied jointly. Ann Appl Biol 26:585-615
23. Severyn B, Liehr RA, Wolicki A, Nguyen KH, Hudak EM, Ferrer M et al (2011) Parsimonious discovery of synergistic drug combinations. ACS Chem Biol 6:1391-1398
24. Yilancioglu K, Weinstein ZB, Meydan C, Akhmetov A, Toprak I, Durmaz A et al. (2014) Target-independent prediction of drug synergies using only drug lipophilicity. J Chem Inform Model 54(8):2286-2293
25. Cokol M, Chua HN, Tasan M, Mutlu B, Weinstein ZB, Suzuki Y et al (2011) Systematic exploration of synergistic drug pairs. Mol Syst Biol 7:544
26. Holbeck S, Collins JM, Doroshow JH (2012) 27 NCI-60 combination screening matrix of approved anticancer drugs. Eur J Cancer 48(Suppl 6):11
27. Tukey JW (1977) Exploratory data analysis. Addison-Wesley
28. Tornero-Velez R, Egeghy PP, Cohen Hubal EA (2011) Biogeographical analysis of chemical co-occurrence data to identify priorities for mixtures research. Risk Anal 32:224-236
29. Zimmermann GR, Keith CT, Lehár J (2007) Multi-target therapeutics: when the whole is greater than the sum of the parts. Drug Discov Today 12:34-42
30. Yeh P, Kishony R (2007) Networks from drug-drug surfaces. Mol Syst Biol 3:85
31. Stockwell BR, Giaever G, Nislow C, Lehár J (2008) Combination chemical genetics. Nat Chem Biol 4:674-681
32. Yeh PJ, Hegreness MJ, Aiden AP, Kishony R (2009) Drug interactions and the evolution of antibiotic resistance. Nat Rev Microbiol 7:460-466
33. Baur M, Brandes U (2005) Crossing Reduction in Circular Layouts. In: Graph-theoretic concepts in computer science. Springer Berlin Heidelberg, Berlin, Heidelberg, pp 332-343
34. Fruchterman TMJ, Reingold EM (1991) Graph drawing by force-directed placement. Softw Pract Exp 21:1129-1164
35. Pearson K (1901) On lines and planes of closest fit to systems of points in space. Philos Mag Ser 6(2):559-572
36. van der Maaten L, Hinton G (2008) Visualizing data using t-SNE. J Mach Learn Res 9:2579-2605
37. (2012) Visualization Prospect - Merck Molecular Activity Challenge. https://www.kaggle.com/c/MerckActivity/details/visualization-prospect. Accessed 29 July 2015
38. Guha R, Mott BT, Eastman RT, Sherlach KS, Siriwardana A, Shinn P (2015) High-throughput matrix screening identifies antimalarial drug combinations. Sci Rep (in review)
39. Griner LAM, Guha R, Shinn P, Young RM, Keller JM, Liu D et al. (2014) High-throughput combinatorial screening identifies drugs that cooperate with ibrutinib to kill activated B-celllike diffuse large B-cell lymphoma cells. Proc Natl Acad Sci 111(6):2349-2354
40. ChemAxon: Standardizer. https://www.chemaxon.com/products/standardizer/. Accessed 29 July 2015
41. Yap CW (2011) PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints. J Comput Chem 32:1466-1474
42. RDKit: Open-source cheminformatics. http://www.rdkit.org. Accessed 29 July 2015
43. Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, Hersey A et al (2011) ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res 40:D1100-D1107
44. Bender A, Jenkins JL, Glick M, Zhan D, Nettles JH, Davies JW (2006) "Bayes affinity fingerprints" Improve retrieval rates in virtual screening and define orthogonal bioactivity space: when are multitarget drugs a feasible concept? J Chem Inf Model 46:2445-2456
45. Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O et al (2011) Scikit-learn: machine learning in python. J Mach Learn Res 12:2825-2830
46. Pallavi R, Roy N, Nageshan RK, Talukdar P, Pavithra SR, Reddy R et al (2010) Heat shock protein 90 as a drug target against protozoan infections: biochemical characterization of HSP90 from Plasmodium falciparum and Trypanosoma evansi and evaluation of its inhibitor as a candidate drug. J Biol Chem 285:37964-37975
47. Hunter JD (2007) Matplotlib: a 2D graphics environment. Comput Sci Eng 9:99-104
48. Christmas R, Avila-Campillo I, Bolouri H, Schwikowski B, Anderson M, Kelley R et al (2005) Cytoscape: a software environment for integrated models of biomolecular interaction networks. AACR Educ Book 2005:12
49. Morgan HL (1965) The generation of a unique machine description for chemical structures - a technique developed at chemical abstracts service. J Chem Doc 5:107-113